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  1. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/__pycache__/__config__.cpython-311.pyc +0 -0
  2. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/__pycache__/__init__.cpython-311.pyc +0 -0
  3. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/__pycache__/_distributor_init.cpython-311.pyc +0 -0
  4. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/__pycache__/conftest.cpython-311.pyc +0 -0
  5. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/__pycache__/version.cpython-311.pyc +0 -0
  6. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/datasets/__init__.py +90 -0
  7. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/datasets/_download_all.py +74 -0
  8. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/datasets/_fetchers.py +229 -0
  9. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/datasets/_registry.py +26 -0
  10. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/datasets/_utils.py +84 -0
  11. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/differentiate/__init__.py +27 -0
  12. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/differentiate/_differentiate.py +1140 -0
  13. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/__init__.py +103 -0
  14. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/_basic.py +428 -0
  15. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/_helper.py +115 -0
  16. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/_pseudo_diffs.py +554 -0
  17. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/_realtransforms.py +598 -0
  18. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/basic.py +20 -0
  19. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/helper.py +19 -0
  20. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/pseudo_diffs.py +22 -0
  21. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/realtransforms.py +19 -0
  22. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_bsplines.py +2614 -0
  23. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_cubic.py +1029 -0
  24. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_fitpack.cpython-311-x86_64-linux-gnu.so +0 -0
  25. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_ndbspline.py +518 -0
  26. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_ndgriddata.py +330 -0
  27. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_pade.py +67 -0
  28. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_polyint.py +1029 -0
  29. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_rbf.py +292 -0
  30. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_rbfinterp_common.py +32 -0
  31. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_rbfinterp_xp.py +266 -0
  32. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_rgi.py +812 -0
  33. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/dfitpack.py +24 -0
  34. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/fitpack.py +31 -0
  35. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/fitpack2.py +29 -0
  36. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/interpnd.py +21 -0
  37. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/ndgriddata.py +23 -0
  38. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/polyint.py +24 -0
  39. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/__init__.py +121 -0
  40. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/_fortran.py +354 -0
  41. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/_idl.py +917 -0
  42. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/_mmio.py +968 -0
  43. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/_netcdf.py +1104 -0
  44. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/harwell_boeing.py +17 -0
  45. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/idl.py +17 -0
  46. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/mmio.py +17 -0
  47. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/netcdf.py +17 -0
  48. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/wavfile.py +944 -0
  49. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/linalg/__init__.pxd +1 -0
  50. data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/linalg/__init__.py +234 -0
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data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/datasets/__init__.py ADDED
@@ -0,0 +1,90 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """
2
+ ================================
3
+ Datasets (:mod:`scipy.datasets`)
4
+ ================================
5
+
6
+ .. currentmodule:: scipy.datasets
7
+
8
+ Dataset Methods
9
+ ===============
10
+
11
+ .. autosummary::
12
+ :toctree: generated/
13
+
14
+ ascent
15
+ face
16
+ electrocardiogram
17
+
18
+ Utility Methods
19
+ ===============
20
+
21
+ .. autosummary::
22
+ :toctree: generated/
23
+
24
+ download_all -- Download all the dataset files to specified path.
25
+ clear_cache -- Clear cached dataset directory.
26
+
27
+
28
+ Usage of Datasets
29
+ =================
30
+
31
+ SciPy dataset methods can be simply called as follows: ``'<dataset-name>()'``
32
+ This downloads the dataset files over the network once, and saves the cache,
33
+ before returning a `numpy.ndarray` object representing the dataset.
34
+
35
+ Note that the return data structure and data type might be different for
36
+ different dataset methods. For a more detailed example on usage, please look
37
+ into the particular dataset method documentation above.
38
+
39
+
40
+ How dataset retrieval and storage works
41
+ =======================================
42
+
43
+ SciPy dataset files are stored within individual GitHub repositories under the
44
+ SciPy GitHub organization, following a naming convention as
45
+ ``'dataset-<name>'``, for example `scipy.datasets.face` files live at
46
+ https://github.com/scipy/dataset-face. The `scipy.datasets` submodule utilizes
47
+ and depends on `Pooch <https://www.fatiando.org/pooch/latest/>`_, a Python
48
+ package built to simplify fetching data files. Pooch uses these repos to
49
+ retrieve the respective dataset files when calling the dataset function.
50
+
51
+ A registry of all the datasets, essentially a mapping of filenames with their
52
+ SHA256 hash and repo urls are maintained, which Pooch uses to handle and verify
53
+ the downloads on function call. After downloading the dataset once, the files
54
+ are saved in the system cache directory under ``'scipy-data'``.
55
+
56
+ Dataset cache locations may vary on different platforms.
57
+
58
+ For macOS::
59
+
60
+ '~/Library/Caches/scipy-data'
61
+
62
+ For Linux and other Unix-like platforms::
63
+
64
+ '~/.cache/scipy-data' # or the value of the XDG_CACHE_HOME env var, if defined
65
+
66
+ For Windows::
67
+
68
+ 'C:\\Users\\<user>\\AppData\\Local\\<AppAuthor>\\scipy-data\\Cache'
69
+
70
+
71
+ In environments with constrained network connectivity for various security
72
+ reasons or on systems without continuous internet connections, one may manually
73
+ load the cache of the datasets by placing the contents of the dataset repo in
74
+ the above mentioned cache directory to avoid fetching dataset errors without
75
+ the internet connectivity.
76
+
77
+ """
78
+
79
+
80
+ from ._fetchers import face, ascent, electrocardiogram
81
+ from ._download_all import download_all
82
+ from ._utils import clear_cache
83
+
84
+ __all__ = ['ascent', 'electrocardiogram', 'face',
85
+ 'download_all', 'clear_cache']
86
+
87
+
88
+ from scipy._lib._testutils import PytestTester
89
+ test = PytestTester(__name__)
90
+ del PytestTester
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/datasets/_download_all.py ADDED
@@ -0,0 +1,74 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """
2
+ Platform independent script to download all the
3
+ `scipy.datasets` module data files.
4
+ This doesn't require a full scipy build.
5
+
6
+ Run: python _download_all.py <download_dir>
7
+ """
8
+
9
+ from scipy._lib._array_api import xp_capabilities
10
+
11
+ import argparse
12
+ try:
13
+ import pooch
14
+ except ImportError:
15
+ pooch = None
16
+
17
+
18
+ if __package__ is None or __package__ == '':
19
+ # Running as python script, use absolute import
20
+ import _registry # type: ignore
21
+ else:
22
+ # Running as python module, use relative import
23
+ from . import _registry
24
+
25
+
26
+ @xp_capabilities(out_of_scope=True)
27
+ def download_all(path=None):
28
+ """
29
+ Utility method to download all the dataset files
30
+ for `scipy.datasets` module.
31
+
32
+ Parameters
33
+ ----------
34
+ path : str, optional
35
+ Directory path to download all the dataset files.
36
+ If None, default to the system cache_dir detected by pooch.
37
+
38
+ Examples
39
+ --------
40
+ Download the datasets to the default cache location:
41
+
42
+ >>> from scipy import datasets
43
+ >>> datasets.download_all()
44
+
45
+ Download the datasets to the current directory:
46
+
47
+ >>> datasets.download_all(".")
48
+
49
+ """
50
+ if pooch is None:
51
+ raise ImportError("Missing optional dependency 'pooch' required "
52
+ "for scipy.datasets module. Please use pip or "
53
+ "conda to install 'pooch'.")
54
+ if path is None:
55
+ path = pooch.os_cache('scipy-data')
56
+ # https://github.com/scipy/scipy/issues/21879
57
+ downloader = pooch.HTTPDownloader(headers={"User-Agent": "SciPy"})
58
+ for dataset_name, dataset_hash in _registry.registry.items():
59
+ pooch.retrieve(url=_registry.registry_urls[dataset_name],
60
+ known_hash=dataset_hash,
61
+ fname=dataset_name, path=path, downloader=downloader)
62
+
63
+
64
+ def main():
65
+ parser = argparse.ArgumentParser(description='Download SciPy data files.')
66
+ parser.add_argument("path", nargs='?', type=str,
67
+ default=pooch.os_cache('scipy-data'),
68
+ help="Directory path to download all the data files.")
69
+ args = parser.parse_args()
70
+ download_all(args.path)
71
+
72
+
73
+ if __name__ == "__main__":
74
+ main()
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/datasets/_fetchers.py ADDED
@@ -0,0 +1,229 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ import sys
2
+
3
+ from numpy import array, frombuffer, load
4
+ from ._registry import registry, registry_urls
5
+
6
+ from scipy._lib._array_api import xp_capabilities
7
+
8
+ try:
9
+ import pooch
10
+ except ImportError:
11
+ pooch = None
12
+ data_fetcher = None
13
+ else:
14
+ data_fetcher = pooch.create(
15
+ # Use the default cache folder for the operating system
16
+ # Pooch uses appdirs (https://github.com/ActiveState/appdirs) to
17
+ # select an appropriate directory for the cache on each platform.
18
+ path=pooch.os_cache("scipy-data"),
19
+
20
+ # The remote data is on Github
21
+ # base_url is a required param, even though we override this
22
+ # using individual urls in the registry.
23
+ base_url="https://github.com/scipy/",
24
+ registry=registry,
25
+ urls=registry_urls
26
+ )
27
+
28
+
29
+ def fetch_data(dataset_name, data_fetcher=data_fetcher):
30
+ if data_fetcher is None:
31
+ raise ImportError("Missing optional dependency 'pooch' required "
32
+ "for scipy.datasets module. Please use pip or "
33
+ "conda to install 'pooch'.")
34
+ # https://github.com/scipy/scipy/issues/21879
35
+ downloader = pooch.HTTPDownloader(
36
+ headers={"User-Agent": f"SciPy {sys.modules['scipy'].__version__}"}
37
+ )
38
+ # The "fetch" method returns the full path to the downloaded data file.
39
+ return data_fetcher.fetch(dataset_name, downloader=downloader)
40
+
41
+
42
+ @xp_capabilities(out_of_scope=True)
43
+ def ascent():
44
+ """
45
+ Get an 8-bit grayscale bit-depth, 512 x 512 derived image for easy
46
+ use in demos.
47
+
48
+ The image is derived from
49
+ https://pixnio.com/people/accent-to-the-top
50
+
51
+ Parameters
52
+ ----------
53
+ None
54
+
55
+ Returns
56
+ -------
57
+ ascent : ndarray
58
+ convenient image to use for testing and demonstration
59
+
60
+ Examples
61
+ --------
62
+ >>> import scipy.datasets
63
+ >>> ascent = scipy.datasets.ascent()
64
+ >>> ascent.shape
65
+ (512, 512)
66
+ >>> ascent.max()
67
+ np.uint8(255)
68
+
69
+ >>> import matplotlib.pyplot as plt
70
+ >>> plt.gray()
71
+ >>> plt.imshow(ascent)
72
+ >>> plt.show()
73
+
74
+ """
75
+ import pickle
76
+
77
+ # The file will be downloaded automatically the first time this is run,
78
+ # returning the path to the downloaded file. Afterwards, Pooch finds
79
+ # it in the local cache and doesn't repeat the download.
80
+ fname = fetch_data("ascent.dat")
81
+ # Now we just need to load it with our standard Python tools.
82
+ with open(fname, 'rb') as f:
83
+ ascent = array(pickle.load(f))
84
+ return ascent
85
+
86
+
87
+ @xp_capabilities(out_of_scope=True)
88
+ def electrocardiogram():
89
+ """
90
+ Load an electrocardiogram as an example for a 1-D signal.
91
+
92
+ The returned signal is a 5 minute long electrocardiogram (ECG), a medical
93
+ recording of the heart's electrical activity, sampled at 360 Hz.
94
+
95
+ Returns
96
+ -------
97
+ ecg : ndarray
98
+ The electrocardiogram in millivolt (mV) sampled at 360 Hz.
99
+
100
+ Notes
101
+ -----
102
+ The provided signal is an excerpt (19:35 to 24:35) from the `record 208`_
103
+ (lead MLII) provided by the MIT-BIH Arrhythmia Database [1]_ on
104
+ PhysioNet [2]_. The excerpt includes noise induced artifacts, typical
105
+ heartbeats as well as pathological changes.
106
+
107
+ .. _record 208: https://physionet.org/physiobank/database/html/mitdbdir/records.htm#208
108
+
109
+ .. versionadded:: 1.1.0
110
+
111
+ References
112
+ ----------
113
+ .. [1] Moody GB, Mark RG. The impact of the MIT-BIH Arrhythmia Database.
114
+ IEEE Eng in Med and Biol 20(3):45-50 (May-June 2001).
115
+ (PMID: 11446209); :doi:`10.13026/C2F305`
116
+ .. [2] Goldberger AL, Amaral LAN, Glass L, Hausdorff JM, Ivanov PCh,
117
+ Mark RG, Mietus JE, Moody GB, Peng C-K, Stanley HE. PhysioBank,
118
+ PhysioToolkit, and PhysioNet: Components of a New Research Resource
119
+ for Complex Physiologic Signals. Circulation 101(23):e215-e220;
120
+ :doi:`10.1161/01.CIR.101.23.e215`
121
+
122
+ Examples
123
+ --------
124
+ >>> from scipy.datasets import electrocardiogram
125
+ >>> ecg = electrocardiogram()
126
+ >>> ecg
127
+ array([-0.245, -0.215, -0.185, ..., -0.405, -0.395, -0.385], shape=(108000,))
128
+ >>> ecg.shape, ecg.mean(), ecg.std()
129
+ ((108000,), -0.16510875, 0.5992473991177294)
130
+
131
+ As stated the signal features several areas with a different morphology.
132
+ E.g., the first few seconds show the electrical activity of a heart in
133
+ normal sinus rhythm as seen below.
134
+
135
+ >>> import numpy as np
136
+ >>> import matplotlib.pyplot as plt
137
+ >>> fs = 360
138
+ >>> time = np.arange(ecg.size) / fs
139
+ >>> plt.plot(time, ecg)
140
+ >>> plt.xlabel("time in s")
141
+ >>> plt.ylabel("ECG in mV")
142
+ >>> plt.xlim(9, 10.2)
143
+ >>> plt.ylim(-1, 1.5)
144
+ >>> plt.show()
145
+
146
+ After second 16, however, the first premature ventricular contractions,
147
+ also called extrasystoles, appear. These have a different morphology
148
+ compared to typical heartbeats. The difference can easily be observed
149
+ in the following plot.
150
+
151
+ >>> plt.plot(time, ecg)
152
+ >>> plt.xlabel("time in s")
153
+ >>> plt.ylabel("ECG in mV")
154
+ >>> plt.xlim(46.5, 50)
155
+ >>> plt.ylim(-2, 1.5)
156
+ >>> plt.show()
157
+
158
+ At several points large artifacts disturb the recording, e.g.:
159
+
160
+ >>> plt.plot(time, ecg)
161
+ >>> plt.xlabel("time in s")
162
+ >>> plt.ylabel("ECG in mV")
163
+ >>> plt.xlim(207, 215)
164
+ >>> plt.ylim(-2, 3.5)
165
+ >>> plt.show()
166
+
167
+ Finally, examining the power spectrum reveals that most of the biosignal is
168
+ made up of lower frequencies. At 60 Hz the noise induced by the mains
169
+ electricity can be clearly observed.
170
+
171
+ >>> from scipy.signal import welch
172
+ >>> f, Pxx = welch(ecg, fs=fs, nperseg=2048, scaling="spectrum")
173
+ >>> plt.semilogy(f, Pxx)
174
+ >>> plt.xlabel("Frequency in Hz")
175
+ >>> plt.ylabel("Power spectrum of the ECG in mV**2")
176
+ >>> plt.xlim(f[[0, -1]])
177
+ >>> plt.show()
178
+ """
179
+ fname = fetch_data("ecg.dat")
180
+ with load(fname) as file:
181
+ ecg = file["ecg"].astype(int) # np.uint16 -> int
182
+ # Convert raw output of ADC to mV: (ecg - adc_zero) / adc_gain
183
+ ecg = (ecg - 1024) / 200.0
184
+ return ecg
185
+
186
+
187
+ @xp_capabilities(out_of_scope=True)
188
+ def face(gray=False):
189
+ """
190
+ Get a 1024 x 768, color image of a raccoon face.
191
+
192
+ The image is derived from
193
+ https://pixnio.com/fauna-animals/raccoons/raccoon-procyon-lotor
194
+
195
+ Parameters
196
+ ----------
197
+ gray : bool, optional
198
+ If True return 8-bit grey-scale image, otherwise return a color image
199
+
200
+ Returns
201
+ -------
202
+ face : ndarray
203
+ image of a raccoon face
204
+
205
+ Examples
206
+ --------
207
+ >>> import scipy.datasets
208
+ >>> face = scipy.datasets.face()
209
+ >>> face.shape
210
+ (768, 1024, 3)
211
+ >>> face.max()
212
+ np.uint8(255)
213
+
214
+ >>> import matplotlib.pyplot as plt
215
+ >>> plt.gray()
216
+ >>> plt.imshow(face)
217
+ >>> plt.show()
218
+
219
+ """
220
+ import bz2
221
+ fname = fetch_data("face.dat")
222
+ with open(fname, 'rb') as f:
223
+ rawdata = f.read()
224
+ face_data = bz2.decompress(rawdata)
225
+ face = frombuffer(face_data, dtype='uint8').reshape((768, 1024, 3))
226
+ if gray is True:
227
+ face = (0.21 * face[:, :, 0] + 0.71 * face[:, :, 1] +
228
+ 0.07 * face[:, :, 2]).astype('uint8')
229
+ return face
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/datasets/_registry.py ADDED
@@ -0,0 +1,26 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ##########################################################################
2
+ # This file serves as the dataset registry for SciPy Datasets SubModule.
3
+ ##########################################################################
4
+
5
+
6
+ # To generate the SHA256 hash, use the command
7
+ # openssl sha256 <filename>
8
+ registry = {
9
+ "ascent.dat": "03ce124c1afc880f87b55f6b061110e2e1e939679184f5614e38dacc6c1957e2",
10
+ "ecg.dat": "f20ad3365fb9b7f845d0e5c48b6fe67081377ee466c3a220b7f69f35c8958baf",
11
+ "face.dat": "9d8b0b4d081313e2b485748c770472e5a95ed1738146883d84c7030493e82886"
12
+ }
13
+
14
+ registry_urls = {
15
+ "ascent.dat": "https://raw.githubusercontent.com/scipy/dataset-ascent/main/ascent.dat",
16
+ "ecg.dat": "https://raw.githubusercontent.com/scipy/dataset-ecg/main/ecg.dat",
17
+ "face.dat": "https://raw.githubusercontent.com/scipy/dataset-face/main/face.dat"
18
+ }
19
+
20
+ # dataset method mapping with their associated filenames
21
+ # <method_name> : ["filename1", "filename2", ...]
22
+ method_files_map = {
23
+ "ascent": ["ascent.dat"],
24
+ "electrocardiogram": ["ecg.dat"],
25
+ "face": ["face.dat"]
26
+ }
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/datasets/_utils.py ADDED
@@ -0,0 +1,84 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ import os
2
+ import shutil
3
+ from ._registry import method_files_map
4
+
5
+ from scipy._lib._array_api import xp_capabilities
6
+
7
+ try:
8
+ import platformdirs
9
+ except ImportError:
10
+ platformdirs = None # type: ignore[assignment]
11
+
12
+
13
+ def _clear_cache(datasets, cache_dir=None, method_map=None):
14
+ if method_map is None:
15
+ # Use SciPy Datasets method map
16
+ method_map = method_files_map
17
+ if cache_dir is None:
18
+ # Use default cache_dir path
19
+ if platformdirs is None:
20
+ # platformdirs is pooch dependency
21
+ raise ImportError("Missing optional dependency 'pooch' required "
22
+ "for scipy.datasets module. Please use pip or "
23
+ "conda to install 'pooch'.")
24
+ cache_dir = platformdirs.user_cache_dir("scipy-data")
25
+
26
+ if not os.path.exists(cache_dir):
27
+ print(f"Cache Directory {cache_dir} doesn't exist. Nothing to clear.")
28
+ return
29
+
30
+ if datasets is None:
31
+ print(f"Cleaning the cache directory {cache_dir}!")
32
+ shutil.rmtree(cache_dir)
33
+ else:
34
+ if not isinstance(datasets, list | tuple):
35
+ # single dataset method passed should be converted to list
36
+ datasets = [datasets, ]
37
+ for dataset in datasets:
38
+ assert callable(dataset)
39
+ dataset_name = dataset.__name__ # Name of the dataset method
40
+ if dataset_name not in method_map:
41
+ raise ValueError(f"Dataset method {dataset_name} doesn't "
42
+ "exist. Please check if the passed dataset "
43
+ "is a subset of the following dataset "
44
+ f"methods: {list(method_map.keys())}")
45
+
46
+ data_files = method_map[dataset_name]
47
+ data_filepaths = [os.path.join(cache_dir, file)
48
+ for file in data_files]
49
+ for data_filepath in data_filepaths:
50
+ if os.path.exists(data_filepath):
51
+ print("Cleaning the file "
52
+ f"{os.path.split(data_filepath)[1]} "
53
+ f"for dataset {dataset_name}")
54
+ os.remove(data_filepath)
55
+ else:
56
+ print(f"Path {data_filepath} doesn't exist. "
57
+ "Nothing to clear.")
58
+
59
+
60
+ @xp_capabilities(out_of_scope=True)
61
+ def clear_cache(datasets=None):
62
+ """
63
+ Cleans the scipy datasets cache directory.
64
+
65
+ If a scipy.datasets method or a list/tuple of the same is
66
+ provided, then clear_cache removes all the data files
67
+ associated to the passed dataset method callable(s).
68
+
69
+ By default, it removes all the cached data files.
70
+
71
+ Parameters
72
+ ----------
73
+ datasets : callable or list/tuple of callable or None
74
+
75
+ Examples
76
+ --------
77
+ >>> from scipy import datasets
78
+ >>> ascent_array = datasets.ascent()
79
+ >>> ascent_array.shape
80
+ (512, 512)
81
+ >>> datasets.clear_cache([datasets.ascent])
82
+ Cleaning the file ascent.dat for dataset ascent
83
+ """
84
+ _clear_cache(datasets)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/differentiate/__init__.py ADDED
@@ -0,0 +1,27 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """
2
+ ==============================================================
3
+ Finite Difference Differentiation (:mod:`scipy.differentiate`)
4
+ ==============================================================
5
+
6
+ .. currentmodule:: scipy.differentiate
7
+
8
+ SciPy ``differentiate`` provides functions for performing finite difference
9
+ numerical differentiation of black-box functions.
10
+
11
+ .. autosummary::
12
+ :toctree: generated/
13
+
14
+ derivative
15
+ jacobian
16
+ hessian
17
+
18
+ """
19
+
20
+
21
+ from ._differentiate import *
22
+
23
+ __all__ = ['derivative', 'jacobian', 'hessian']
24
+
25
+ from scipy._lib._testutils import PytestTester
26
+ test = PytestTester(__name__)
27
+ del PytestTester
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/differentiate/_differentiate.py ADDED
@@ -0,0 +1,1140 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # mypy: disable-error-code="attr-defined"
2
+ import warnings
3
+ import numpy as np
4
+ import scipy._lib._elementwise_iterative_method as eim
5
+ from scipy._lib._util import _RichResult
6
+ from scipy._lib._array_api import array_namespace, xp_copy, xp_promote, xp_capabilities
7
+ import scipy._lib.array_api_extra as xpx
8
+
9
+ _EERRORINCREASE = -1 # used in derivative
10
+
11
+ def _derivative_iv(f, x, args, tolerances, maxiter, order, initial_step,
12
+ step_factor, step_direction, preserve_shape, callback):
13
+ # Input validation for `derivative`
14
+ xp = array_namespace(x)
15
+
16
+ if not callable(f):
17
+ raise ValueError('`f` must be callable.')
18
+
19
+ if not np.iterable(args):
20
+ args = (args,)
21
+
22
+ tolerances = {} if tolerances is None else tolerances
23
+ atol = tolerances.get('atol', None)
24
+ rtol = tolerances.get('rtol', None)
25
+
26
+ # tolerances are floats, not arrays; OK to use NumPy
27
+ message = 'Tolerances and step parameters must be non-negative scalars.'
28
+ tols = np.asarray([atol if atol is not None else 1,
29
+ rtol if rtol is not None else 1,
30
+ step_factor])
31
+ if (not np.issubdtype(tols.dtype, np.number) or np.any(tols < 0)
32
+ or np.any(np.isnan(tols)) or tols.shape != (3,)):
33
+ raise ValueError(message)
34
+ step_factor = float(tols[2])
35
+
36
+ maxiter_int = int(maxiter)
37
+ if maxiter != maxiter_int or maxiter <= 0:
38
+ raise ValueError('`maxiter` must be a positive integer.')
39
+
40
+ order_int = int(order)
41
+ if order_int != order or order <= 0:
42
+ raise ValueError('`order` must be a positive integer.')
43
+
44
+ step_direction = xp.asarray(step_direction)
45
+ initial_step = xp.asarray(initial_step)
46
+ temp = xp.broadcast_arrays(x, step_direction, initial_step)
47
+ x, step_direction, initial_step = temp
48
+
49
+ message = '`preserve_shape` must be True or False.'
50
+ if preserve_shape not in {True, False}:
51
+ raise ValueError(message)
52
+
53
+ if callback is not None and not callable(callback):
54
+ raise ValueError('`callback` must be callable.')
55
+
56
+ return (f, x, args, atol, rtol, maxiter_int, order_int, initial_step,
57
+ step_factor, step_direction, preserve_shape, callback)
58
+
59
+
60
+
61
+ _array_api_strict_skip_reason = 'Array API does not support fancy indexing assignment.'
62
+ _dask_reason = 'boolean indexing assignment'
63
+
64
+
65
+ @xp_capabilities(skip_backends=[('array_api_strict', _array_api_strict_skip_reason),
66
+ ('dask.array', _dask_reason)], jax_jit=False)
67
+ def derivative(f, x, *, args=(), tolerances=None, maxiter=10,
68
+ order=8, initial_step=0.5, step_factor=2.0,
69
+ step_direction=0, preserve_shape=False, callback=None):
70
+ """Evaluate the derivative of an elementwise, real scalar function numerically.
71
+
72
+ For each element of the output of `f`, `derivative` approximates the first
73
+ derivative of `f` at the corresponding element of `x` using finite difference
74
+ differentiation.
75
+
76
+ This function works elementwise when `x`, `step_direction`, and `args` contain
77
+ (broadcastable) arrays.
78
+
79
+ Parameters
80
+ ----------
81
+ f : callable
82
+ The function whose derivative is desired. The signature must be::
83
+
84
+ f(xi: ndarray, *argsi) -> ndarray
85
+
86
+ where each element of ``xi`` is a finite real number and ``argsi`` is a tuple,
87
+ which may contain an arbitrary number of arrays that are broadcastable with
88
+ ``xi``. `f` must be an elementwise function: each scalar element ``f(xi)[j]``
89
+ must equal ``f(xi[j])`` for valid indices ``j``. It must not mutate the array
90
+ ``xi`` or the arrays in ``argsi``.
91
+ x : float array_like
92
+ Abscissae at which to evaluate the derivative. Must be broadcastable with
93
+ `args` and `step_direction`.
94
+ args : tuple of array_like, optional
95
+ Additional positional array arguments to be passed to `f`. Arrays
96
+ must be broadcastable with one another and the arrays of `init`.
97
+ If the callable for which the root is desired requires arguments that are
98
+ not broadcastable with `x`, wrap that callable with `f` such that `f`
99
+ accepts only `x` and broadcastable ``*args``.
100
+ tolerances : dictionary of floats, optional
101
+ Absolute and relative tolerances. Valid keys of the dictionary are:
102
+
103
+ - ``atol`` - absolute tolerance on the derivative
104
+ - ``rtol`` - relative tolerance on the derivative
105
+
106
+ Iteration will stop when ``res.error < atol + rtol * abs(res.df)``. The default
107
+ `atol` is the smallest normal number of the appropriate dtype, and
108
+ the default `rtol` is the square root of the precision of the
109
+ appropriate dtype.
110
+ order : int, default: 8
111
+ The (positive integer) order of the finite difference formula to be
112
+ used. Odd integers will be rounded up to the next even integer.
113
+ initial_step : float array_like, default: 0.5
114
+ The (absolute) initial step size for the finite difference derivative
115
+ approximation.
116
+ step_factor : float, default: 2.0
117
+ The factor by which the step size is *reduced* in each iteration; i.e.
118
+ the step size in iteration 1 is ``initial_step/step_factor``. If
119
+ ``step_factor < 1``, subsequent steps will be greater than the initial
120
+ step; this may be useful if steps smaller than some threshold are
121
+ undesirable (e.g. due to subtractive cancellation error).
122
+ maxiter : int, default: 10
123
+ The maximum number of iterations of the algorithm to perform. See
124
+ Notes.
125
+ step_direction : integer array_like
126
+ An array representing the direction of the finite difference steps (for
127
+ use when `x` lies near to the boundary of the domain of the function.)
128
+ Must be broadcastable with `x` and all `args`.
129
+ Where 0 (default), central differences are used; where negative (e.g.
130
+ -1), steps are non-positive; and where positive (e.g. 1), all steps are
131
+ non-negative.
132
+ preserve_shape : bool, default: False
133
+ In the following, "arguments of `f`" refers to the array ``xi`` and
134
+ any arrays within ``argsi``. Let ``shape`` be the broadcasted shape
135
+ of `x` and all elements of `args` (which is conceptually
136
+ distinct from ``xi` and ``argsi`` passed into `f`).
137
+
138
+ - When ``preserve_shape=False`` (default), `f` must accept arguments
139
+ of *any* broadcastable shapes.
140
+
141
+ - When ``preserve_shape=True``, `f` must accept arguments of shape
142
+ ``shape`` *or* ``shape + (n,)``, where ``(n,)`` is the number of
143
+ abscissae at which the function is being evaluated.
144
+
145
+ In either case, for each scalar element ``xi[j]`` within ``xi``, the array
146
+ returned by `f` must include the scalar ``f(xi[j])`` at the same index.
147
+ Consequently, the shape of the output is always the shape of the input
148
+ ``xi``.
149
+
150
+ See Examples.
151
+ callback : callable, optional
152
+ An optional user-supplied function to be called before the first
153
+ iteration and after each iteration.
154
+ Called as ``callback(res)``, where ``res`` is a ``_RichResult``
155
+ similar to that returned by `derivative` (but containing the current
156
+ iterate's values of all variables). If `callback` raises a
157
+ ``StopIteration``, the algorithm will terminate immediately and
158
+ `derivative` will return a result. `callback` must not mutate
159
+ `res` or its attributes.
160
+
161
+ Returns
162
+ -------
163
+ res : _RichResult
164
+ An object similar to an instance of `scipy.optimize.OptimizeResult` with the
165
+ following attributes. The descriptions are written as though the values will
166
+ be scalars; however, if `f` returns an array, the outputs will be
167
+ arrays of the same shape.
168
+
169
+ success : bool array
170
+ ``True`` where the algorithm terminated successfully (status ``0``);
171
+ ``False`` otherwise.
172
+ status : int array
173
+ An integer representing the exit status of the algorithm.
174
+
175
+ - ``0`` : The algorithm converged to the specified tolerances.
176
+ - ``-1`` : The error estimate increased, so iteration was terminated.
177
+ - ``-2`` : The maximum number of iterations was reached.
178
+ - ``-3`` : A non-finite value was encountered.
179
+ - ``-4`` : Iteration was terminated by `callback`.
180
+ - ``1`` : The algorithm is proceeding normally (in `callback` only).
181
+
182
+ df : float array
183
+ The derivative of `f` at `x`, if the algorithm terminated
184
+ successfully.
185
+ error : float array
186
+ An estimate of the error: the magnitude of the difference between
187
+ the current estimate of the derivative and the estimate in the
188
+ previous iteration.
189
+ nit : int array
190
+ The number of iterations of the algorithm that were performed.
191
+ nfev : int array
192
+ The number of points at which `f` was evaluated.
193
+ x : float array
194
+ The value at which the derivative of `f` was evaluated
195
+ (after broadcasting with `args` and `step_direction`).
196
+
197
+ See Also
198
+ --------
199
+ jacobian, hessian
200
+
201
+ Notes
202
+ -----
203
+ The implementation was inspired by jacobi [1]_, numdifftools [2]_, and
204
+ DERIVEST [3]_, but the implementation follows the theory of Taylor series
205
+ more straightforwardly (and arguably naively so).
206
+ In the first iteration, the derivative is estimated using a finite
207
+ difference formula of order `order` with maximum step size `initial_step`.
208
+ Each subsequent iteration, the maximum step size is reduced by
209
+ `step_factor`, and the derivative is estimated again until a termination
210
+ condition is reached. The error estimate is the magnitude of the difference
211
+ between the current derivative approximation and that of the previous
212
+ iteration.
213
+
214
+ The stencils of the finite difference formulae are designed such that
215
+ abscissae are "nested": after `f` is evaluated at ``order + 1``
216
+ points in the first iteration, `f` is evaluated at only two new points
217
+ in each subsequent iteration; ``order - 1`` previously evaluated function
218
+ values required by the finite difference formula are reused, and two
219
+ function values (evaluations at the points furthest from `x`) are unused.
220
+
221
+ Step sizes are absolute. When the step size is small relative to the
222
+ magnitude of `x`, precision is lost; for example, if `x` is ``1e20``, the
223
+ default initial step size of ``0.5`` cannot be resolved. Accordingly,
224
+ consider using larger initial step sizes for large magnitudes of `x`.
225
+
226
+ The default tolerances are challenging to satisfy at points where the
227
+ true derivative is exactly zero. If the derivative may be exactly zero,
228
+ consider specifying an absolute tolerance (e.g. ``atol=1e-12``) to
229
+ improve convergence.
230
+
231
+ References
232
+ ----------
233
+ .. [1] Hans Dembinski (@HDembinski). jacobi.
234
+ https://github.com/HDembinski/jacobi
235
+ .. [2] Per A. Brodtkorb and John D'Errico. numdifftools.
236
+ https://numdifftools.readthedocs.io/en/latest/
237
+ .. [3] John D'Errico. DERIVEST: Adaptive Robust Numerical Differentiation.
238
+ https://www.mathworks.com/matlabcentral/fileexchange/13490-adaptive-robust-numerical-differentiation
239
+ .. [4] Numerical Differentition. Wikipedia.
240
+ https://en.wikipedia.org/wiki/Numerical_differentiation
241
+
242
+ Examples
243
+ --------
244
+ Evaluate the derivative of ``np.exp`` at several points ``x``.
245
+
246
+ >>> import numpy as np
247
+ >>> from scipy.differentiate import derivative
248
+ >>> f = np.exp
249
+ >>> df = np.exp # true derivative
250
+ >>> x = np.linspace(1, 2, 5)
251
+ >>> res = derivative(f, x)
252
+ >>> res.df # approximation of the derivative
253
+ array([2.71828183, 3.49034296, 4.48168907, 5.75460268, 7.3890561 ])
254
+ >>> res.error # estimate of the error
255
+ array([7.13740178e-12, 9.16600129e-12, 1.17594823e-11, 1.51061386e-11,
256
+ 1.94262384e-11])
257
+ >>> abs(res.df - df(x)) # true error
258
+ array([2.53130850e-14, 3.55271368e-14, 5.77315973e-14, 5.59552404e-14,
259
+ 6.92779167e-14])
260
+
261
+ Show the convergence of the approximation as the step size is reduced.
262
+ Each iteration, the step size is reduced by `step_factor`, so for
263
+ sufficiently small initial step, each iteration reduces the error by a
264
+ factor of ``1/step_factor**order`` until finite precision arithmetic
265
+ inhibits further improvement.
266
+
267
+ >>> import matplotlib.pyplot as plt
268
+ >>> iter = list(range(1, 12)) # maximum iterations
269
+ >>> hfac = 2 # step size reduction per iteration
270
+ >>> hdir = [-1, 0, 1] # compare left-, central-, and right- steps
271
+ >>> order = 4 # order of differentiation formula
272
+ >>> x = 1
273
+ >>> ref = df(x)
274
+ >>> errors = [] # true error
275
+ >>> for i in iter:
276
+ ... res = derivative(f, x, maxiter=i, step_factor=hfac,
277
+ ... step_direction=hdir, order=order,
278
+ ... # prevent early termination
279
+ ... tolerances=dict(atol=0, rtol=0))
280
+ ... errors.append(abs(res.df - ref))
281
+ >>> errors = np.array(errors)
282
+ >>> plt.semilogy(iter, errors[:, 0], label='left differences')
283
+ >>> plt.semilogy(iter, errors[:, 1], label='central differences')
284
+ >>> plt.semilogy(iter, errors[:, 2], label='right differences')
285
+ >>> plt.xlabel('iteration')
286
+ >>> plt.ylabel('error')
287
+ >>> plt.legend()
288
+ >>> plt.show()
289
+ >>> (errors[1, 1] / errors[0, 1], 1 / hfac**order)
290
+ (0.06215223140159822, 0.0625)
291
+
292
+ The implementation is vectorized over `x`, `step_direction`, and `args`.
293
+ The function is evaluated once before the first iteration to perform input
294
+ validation and standardization, and once per iteration thereafter.
295
+
296
+ >>> def f(x, p):
297
+ ... f.nit += 1
298
+ ... return x**p
299
+ >>> f.nit = 0
300
+ >>> def df(x, p):
301
+ ... return p*x**(p-1)
302
+ >>> x = np.arange(1, 5)
303
+ >>> p = np.arange(1, 6).reshape((-1, 1))
304
+ >>> hdir = np.arange(-1, 2).reshape((-1, 1, 1))
305
+ >>> res = derivative(f, x, args=(p,), step_direction=hdir, maxiter=1)
306
+ >>> np.allclose(res.df, df(x, p))
307
+ True
308
+ >>> res.df.shape
309
+ (3, 5, 4)
310
+ >>> f.nit
311
+ 2
312
+
313
+ By default, `preserve_shape` is False, and therefore the callable
314
+ `f` may be called with arrays of any broadcastable shapes.
315
+ For example:
316
+
317
+ >>> shapes = []
318
+ >>> def f(x, c):
319
+ ... shape = np.broadcast_shapes(x.shape, c.shape)
320
+ ... shapes.append(shape)
321
+ ... return np.sin(c*x)
322
+ >>>
323
+ >>> c = [1, 5, 10, 20]
324
+ >>> res = derivative(f, 0, args=(c,))
325
+ >>> shapes
326
+ [(4,), (4, 8), (4, 2), (3, 2), (2, 2), (1, 2)]
327
+
328
+ To understand where these shapes are coming from - and to better
329
+ understand how `derivative` computes accurate results - note that
330
+ higher values of ``c`` correspond with higher frequency sinusoids.
331
+ The higher frequency sinusoids make the function's derivative change
332
+ faster, so more function evaluations are required to achieve the target
333
+ accuracy:
334
+
335
+ >>> res.nfev
336
+ array([11, 13, 15, 17], dtype=int32)
337
+
338
+ The initial ``shape``, ``(4,)``, corresponds with evaluating the
339
+ function at a single abscissa and all four frequencies; this is used
340
+ for input validation and to determine the size and dtype of the arrays
341
+ that store results. The next shape corresponds with evaluating the
342
+ function at an initial grid of abscissae and all four frequencies.
343
+ Successive calls to the function evaluate the function at two more
344
+ abscissae, increasing the effective order of the approximation by two.
345
+ However, in later function evaluations, the function is evaluated at
346
+ fewer frequencies because the corresponding derivative has already
347
+ converged to the required tolerance. This saves function evaluations to
348
+ improve performance, but it requires the function to accept arguments of
349
+ any shape.
350
+
351
+ "Vector-valued" functions are unlikely to satisfy this requirement.
352
+ For example, consider
353
+
354
+ >>> def f(x):
355
+ ... return [x, np.sin(3*x), x+np.sin(10*x), np.sin(20*x)*(x-1)**2]
356
+
357
+ This integrand is not compatible with `derivative` as written; for instance,
358
+ the shape of the output will not be the same as the shape of ``x``. Such a
359
+ function *could* be converted to a compatible form with the introduction of
360
+ additional parameters, but this would be inconvenient. In such cases,
361
+ a simpler solution would be to use `preserve_shape`.
362
+
363
+ >>> shapes = []
364
+ >>> def f(x):
365
+ ... shapes.append(x.shape)
366
+ ... x0, x1, x2, x3 = x
367
+ ... return [x0, np.sin(3*x1), x2+np.sin(10*x2), np.sin(20*x3)*(x3-1)**2]
368
+ >>>
369
+ >>> x = np.zeros(4)
370
+ >>> res = derivative(f, x, preserve_shape=True)
371
+ >>> shapes
372
+ [(4,), (4, 8), (4, 2), (4, 2), (4, 2), (4, 2)]
373
+
374
+ Here, the shape of ``x`` is ``(4,)``. With ``preserve_shape=True``, the
375
+ function may be called with argument ``x`` of shape ``(4,)`` or ``(4, n)``,
376
+ and this is what we observe.
377
+
378
+ """
379
+ # TODO (followup):
380
+ # - investigate behavior at saddle points
381
+ # - multivariate functions?
382
+ # - relative steps?
383
+ # - show example of `np.vectorize`
384
+
385
+ res = _derivative_iv(f, x, args, tolerances, maxiter, order, initial_step,
386
+ step_factor, step_direction, preserve_shape, callback)
387
+ (func, x, args, atol, rtol, maxiter, order,
388
+ h0, fac, hdir, preserve_shape, callback) = res
389
+
390
+ # Initialization
391
+ # Since f(x) (no step) is not needed for central differences, it may be
392
+ # possible to eliminate this function evaluation. However, it's useful for
393
+ # input validation and standardization, and everything else is designed to
394
+ # reduce function calls, so let's keep it simple.
395
+ temp = eim._initialize(func, (x,), args, preserve_shape=preserve_shape)
396
+ func, xs, fs, args, shape, dtype, xp = temp
397
+
398
+ finfo = xp.finfo(dtype)
399
+ atol = finfo.smallest_normal if atol is None else atol
400
+ rtol = finfo.eps**0.5 if rtol is None else rtol # keep same as `hessian`
401
+
402
+ x, f = xs[0], fs[0]
403
+ df = xp.full_like(f, xp.nan)
404
+
405
+ # Ideally we'd broadcast the shape of `hdir` in `_elementwise_algo_init`, but
406
+ # it's simpler to do it here than to generalize `_elementwise_algo_init` further.
407
+ # `hdir` and `x` are already broadcasted in `_derivative_iv`, so we know
408
+ # that `hdir` can be broadcasted to the final shape. Same with `h0`.
409
+ hdir = xp.broadcast_to(hdir, shape)
410
+ hdir = xp.reshape(hdir, (-1,))
411
+ hdir = xp.astype(xp.sign(hdir), dtype)
412
+ h0 = xp.broadcast_to(h0, shape)
413
+ h0 = xp.reshape(h0, (-1,))
414
+ h0 = xp.astype(h0, dtype)
415
+ h0 = xpx.at(h0)[h0 <= 0].set(xp.nan)
416
+
417
+ status = xp.full_like(x, eim._EINPROGRESS, dtype=xp.int32) # in progress
418
+ nit, nfev = 0, 1 # one function evaluations performed above
419
+ # Boolean indices of left, central, right, and (all) one-sided steps
420
+ il = hdir < 0
421
+ ic = hdir == 0
422
+ ir = hdir > 0
423
+ io = il | ir
424
+
425
+ # Most of these attributes are reasonably obvious, but:
426
+ # - `fs` holds all the function values of all active `x`. The zeroth
427
+ # axis corresponds with active points `x`, the first axis corresponds
428
+ # with the different steps (in the order described in
429
+ # `_derivative_weights`).
430
+ # - `terms` (which could probably use a better name) is half the `order`,
431
+ # which is always even.
432
+ work = _RichResult(x=x, df=df, fs=f[:, xp.newaxis], error=xp.nan, h=h0,
433
+ df_last=xp.nan, error_last=xp.nan, fac=fac,
434
+ atol=atol, rtol=rtol, nit=nit, nfev=nfev,
435
+ status=status, dtype=dtype, terms=(order+1)//2,
436
+ hdir=hdir, il=il, ic=ic, ir=ir, io=io,
437
+ # Store the weights in an object so they can't get compressed
438
+ # Using RichResult to allow dot notation, but a dict would work
439
+ diff_state=_RichResult(central=[], right=[], fac=None))
440
+
441
+ # This is the correspondence between terms in the `work` object and the
442
+ # final result. In this case, the mapping is trivial. Note that `success`
443
+ # is prepended automatically.
444
+ res_work_pairs = [('status', 'status'), ('df', 'df'), ('error', 'error'),
445
+ ('nit', 'nit'), ('nfev', 'nfev'), ('x', 'x')]
446
+
447
+ def pre_func_eval(work):
448
+ """Determine the abscissae at which the function needs to be evaluated.
449
+
450
+ See `_derivative_weights` for a description of the stencil (pattern
451
+ of the abscissae).
452
+
453
+ In the first iteration, there is only one stored function value in
454
+ `work.fs`, `f(x)`, so we need to evaluate at `order` new points. In
455
+ subsequent iterations, we evaluate at two new points. Note that
456
+ `work.x` is always flattened into a 1D array after broadcasting with
457
+ all `args`, so we add a new axis at the end and evaluate all point
458
+ in one call to the function.
459
+
460
+ For improvement:
461
+ - Consider measuring the step size actually taken, since ``(x + h) - x``
462
+ is not identically equal to `h` with floating point arithmetic.
463
+ - Adjust the step size automatically if `x` is too big to resolve the
464
+ step.
465
+ - We could probably save some work if there are no central difference
466
+ steps or no one-sided steps.
467
+ """
468
+ n = work.terms # half the order
469
+ h = work.h[:, xp.newaxis] # step size
470
+ c = work.fac # step reduction factor
471
+ d = c**0.5 # square root of step reduction factor (one-sided stencil)
472
+ # Note - no need to be careful about dtypes until we allocate `x_eval`
473
+
474
+ if work.nit == 0:
475
+ hc = h / c**xp.arange(n, dtype=work.dtype)
476
+ hc = xp.concat((-xp.flip(hc, axis=-1), hc), axis=-1)
477
+ else:
478
+ hc = xp.concat((-h, h), axis=-1) / c**(n-1)
479
+
480
+ if work.nit == 0:
481
+ hr = h / d**xp.arange(2*n, dtype=work.dtype)
482
+ else:
483
+ hr = xp.concat((h, h/d), axis=-1) / c**(n-1)
484
+
485
+ n_new = 2*n if work.nit == 0 else 2 # number of new abscissae
486
+ x_eval = xp.zeros((work.hdir.shape[0], n_new), dtype=work.dtype)
487
+ il, ic, ir = work.il, work.ic, work.ir
488
+ x_eval = xpx.at(x_eval)[ir].set(work.x[ir][:, xp.newaxis] + hr[ir])
489
+ x_eval = xpx.at(x_eval)[ic].set(work.x[ic][:, xp.newaxis] + hc[ic])
490
+ x_eval = xpx.at(x_eval)[il].set(work.x[il][:, xp.newaxis] - hr[il])
491
+ return x_eval
492
+
493
+ def post_func_eval(x, f, work):
494
+ """ Estimate the derivative and error from the function evaluations
495
+
496
+ As in `pre_func_eval`: in the first iteration, there is only one stored
497
+ function value in `work.fs`, `f(x)`, so we need to add the `order` new
498
+ points. In subsequent iterations, we add two new points. The tricky
499
+ part is getting the order to match that of the weights, which is
500
+ described in `_derivative_weights`.
501
+
502
+ For improvement:
503
+ - Change the order of the weights (and steps in `pre_func_eval`) to
504
+ simplify `work_fc` concatenation and eliminate `fc` concatenation.
505
+ - It would be simple to do one-step Richardson extrapolation with `df`
506
+ and `df_last` to increase the order of the estimate and/or improve
507
+ the error estimate.
508
+ - Process the function evaluations in a more numerically favorable
509
+ way. For instance, combining the pairs of central difference evals
510
+ into a second-order approximation and using Richardson extrapolation
511
+ to produce a higher order approximation seemed to retain accuracy up
512
+ to very high order.
513
+ - Alternatively, we could use `polyfit` like Jacobi. An advantage of
514
+ fitting polynomial to more points than necessary is improved noise
515
+ tolerance.
516
+ """
517
+ n = work.terms
518
+ n_new = n if work.nit == 0 else 1
519
+ il, ic, io = work.il, work.ic, work.io
520
+
521
+ # Central difference
522
+ # `work_fc` is *all* the points at which the function has been evaluated
523
+ # `fc` is the points we're using *this iteration* to produce the estimate
524
+ work_fc = (f[ic][:, :n_new], work.fs[ic], f[ic][:, -n_new:])
525
+ work_fc = xp.concat(work_fc, axis=-1)
526
+ if work.nit == 0:
527
+ fc = work_fc
528
+ else:
529
+ fc = (work_fc[:, :n], work_fc[:, n:n+1], work_fc[:, -n:])
530
+ fc = xp.concat(fc, axis=-1)
531
+
532
+ # One-sided difference
533
+ work_fo = xp.concat((work.fs[io], f[io]), axis=-1)
534
+ if work.nit == 0:
535
+ fo = work_fo
536
+ else:
537
+ fo = xp.concat((work_fo[:, 0:1], work_fo[:, -2*n:]), axis=-1)
538
+
539
+ work.fs = xp.zeros((ic.shape[0], work.fs.shape[-1] + 2*n_new), dtype=work.dtype)
540
+ work.fs = xpx.at(work.fs)[ic].set(work_fc)
541
+ work.fs = xpx.at(work.fs)[io].set(work_fo)
542
+
543
+ wc, wo = _derivative_weights(work, n, xp)
544
+ work.df_last = xp.asarray(work.df, copy=True)
545
+ work.df = xpx.at(work.df)[ic].set(fc @ wc / work.h[ic])
546
+ work.df = xpx.at(work.df)[io].set(fo @ wo / work.h[io])
547
+ work.df = xpx.at(work.df)[il].multiply(-1)
548
+
549
+ work.h /= work.fac
550
+ work.error_last = work.error
551
+ # Simple error estimate - the difference in derivative estimates between
552
+ # this iteration and the last. This is typically conservative because if
553
+ # convergence has begin, the true error is much closer to the difference
554
+ # between the current estimate and the *next* error estimate. However,
555
+ # we could use Richarson extrapolation to produce an error estimate that
556
+ # is one order higher, and take the difference between that and
557
+ # `work.df` (which would just be constant factor that depends on `fac`.)
558
+ work.error = xp.abs(work.df - work.df_last)
559
+
560
+ def check_termination(work):
561
+ """Terminate due to convergence, non-finite values, or error increase"""
562
+ stop = xp.astype(xp.zeros_like(work.df), xp.bool)
563
+
564
+ i = work.error < work.atol + work.rtol*abs(work.df)
565
+ work.status = xpx.at(work.status)[i].set(eim._ECONVERGED)
566
+ stop = xpx.at(stop)[i].set(True)
567
+
568
+ if work.nit > 0:
569
+ i = ~((xp.isfinite(work.x) & xp.isfinite(work.df)) | stop)
570
+ work.df = xpx.at(work.df)[i].set(xp.nan)
571
+ work.status = xpx.at(work.status)[i].set(eim._EVALUEERR)
572
+ stop = xpx.at(stop)[i].set(True)
573
+
574
+ # With infinite precision, there is a step size below which
575
+ # all smaller step sizes will reduce the error. But in floating point
576
+ # arithmetic, catastrophic cancellation will begin to cause the error
577
+ # to increase again. This heuristic tries to avoid step sizes that are
578
+ # too small. There may be more theoretically sound approaches for
579
+ # detecting a step size that minimizes the total error, but this
580
+ # heuristic seems simple and effective.
581
+ i = (work.error > work.error_last*10) & ~stop
582
+ work.status = xpx.at(work.status)[i].set(_EERRORINCREASE)
583
+ stop = xpx.at(stop)[i].set(True)
584
+
585
+ return stop
586
+
587
+ def post_termination_check(work):
588
+ return
589
+
590
+ def customize_result(res, shape):
591
+ return shape
592
+
593
+ return eim._loop(work, callback, shape, maxiter, func, args, dtype,
594
+ pre_func_eval, post_func_eval, check_termination,
595
+ post_termination_check, customize_result, res_work_pairs,
596
+ xp, preserve_shape)
597
+
598
+
599
+ def _derivative_weights(work, n, xp):
600
+ # This produces the weights of the finite difference formula for a given
601
+ # stencil. In experiments, use of a second-order central difference formula
602
+ # with Richardson extrapolation was more accurate numerically, but it was
603
+ # more complicated, and it would have become even more complicated when
604
+ # adding support for one-sided differences. However, now that all the
605
+ # function evaluation values are stored, they can be processed in whatever
606
+ # way is desired to produce the derivative estimate. We leave alternative
607
+ # approaches to future work. To be more self-contained, here is the theory
608
+ # for deriving the weights below.
609
+ #
610
+ # Recall that the Taylor expansion of a univariate, scalar-values function
611
+ # about a point `x` may be expressed as:
612
+ # f(x + h) = f(x) + f'(x)*h + f''(x)/2!*h**2 + O(h**3)
613
+ # Suppose we evaluate f(x), f(x+h), and f(x-h). We have:
614
+ # f(x) = f(x)
615
+ # f(x + h) = f(x) + f'(x)*h + f''(x)/2!*h**2 + O(h**3)
616
+ # f(x - h) = f(x) - f'(x)*h + f''(x)/2!*h**2 + O(h**3)
617
+ # We can solve for weights `wi` such that:
618
+ # w1*f(x) = w1*(f(x))
619
+ # + w2*f(x + h) = w2*(f(x) + f'(x)*h + f''(x)/2!*h**2) + O(h**3)
620
+ # + w3*f(x - h) = w3*(f(x) - f'(x)*h + f''(x)/2!*h**2) + O(h**3)
621
+ # = 0 + f'(x)*h + 0 + O(h**3)
622
+ # Then
623
+ # f'(x) ~ (w1*f(x) + w2*f(x+h) + w3*f(x-h))/h
624
+ # is a finite difference derivative approximation with error O(h**2),
625
+ # and so it is said to be a "second-order" approximation. Under certain
626
+ # conditions (e.g. well-behaved function, `h` sufficiently small), the
627
+ # error in the approximation will decrease with h**2; that is, if `h` is
628
+ # reduced by a factor of 2, the error is reduced by a factor of 4.
629
+ #
630
+ # By default, we use eighth-order formulae. Our central-difference formula
631
+ # uses abscissae:
632
+ # x-h/c**3, x-h/c**2, x-h/c, x-h, x, x+h, x+h/c, x+h/c**2, x+h/c**3
633
+ # where `c` is the step factor. (Typically, the step factor is greater than
634
+ # one, so the outermost points - as written above - are actually closest to
635
+ # `x`.) This "stencil" is chosen so that each iteration, the step can be
636
+ # reduced by the factor `c`, and most of the function evaluations can be
637
+ # reused with the new step size. For example, in the next iteration, we
638
+ # will have:
639
+ # x-h/c**4, x-h/c**3, x-h/c**2, x-h/c, x, x+h/c, x+h/c**2, x+h/c**3, x+h/c**4
640
+ # We do not reuse `x-h` and `x+h` for the new derivative estimate.
641
+ # While this would increase the order of the formula and thus the
642
+ # theoretical convergence rate, it is also less stable numerically.
643
+ # (As noted above, there are other ways of processing the values that are
644
+ # more stable. Thus, even now we store `f(x-h)` and `f(x+h)` in `work.fs`
645
+ # to simplify future development of this sort of improvement.)
646
+ #
647
+ # The (right) one-sided formula is produced similarly using abscissae
648
+ # x, x+h, x+h/d, x+h/d**2, ..., x+h/d**6, x+h/d**7, x+h/d**7
649
+ # where `d` is the square root of `c`. (The left one-sided formula simply
650
+ # uses -h.) When the step size is reduced by factor `c = d**2`, we have
651
+ # abscissae:
652
+ # x, x+h/d**2, x+h/d**3..., x+h/d**8, x+h/d**9, x+h/d**9
653
+ # `d` is chosen as the square root of `c` so that the rate of the step-size
654
+ # reduction is the same per iteration as in the central difference case.
655
+ # Note that because the central difference formulas are inherently of even
656
+ # order, for simplicity, we use only even-order formulas for one-sided
657
+ # differences, too.
658
+
659
+ # It's possible for the user to specify `fac` in, say, double precision but
660
+ # `x` and `args` in single precision. `fac` gets converted to single
661
+ # precision, but we should always use double precision for the intermediate
662
+ # calculations here to avoid additional error in the weights.
663
+ fac = float(work.fac)
664
+
665
+ # Note that if the user switches back to floating point precision with
666
+ # `x` and `args`, then `fac` will not necessarily equal the (lower
667
+ # precision) cached `_derivative_weights.fac`, and the weights will
668
+ # need to be recalculated. This could be fixed, but it's late, and of
669
+ # low consequence.
670
+
671
+ diff_state = work.diff_state
672
+ if fac != diff_state.fac:
673
+ diff_state.central = []
674
+ diff_state.right = []
675
+ diff_state.fac = fac
676
+
677
+ if len(diff_state.central) != 2*n + 1:
678
+ # Central difference weights. Consider refactoring this; it could
679
+ # probably be more compact.
680
+ # Note: Using NumPy here is OK; we convert to xp-type at the end
681
+ i = np.arange(-n, n + 1)
682
+ p = np.abs(i) - 1. # center point has power `p` -1, but sign `s` is 0
683
+ s = np.sign(i)
684
+
685
+ h = s / fac ** p
686
+ A = np.vander(h, increasing=True).T
687
+ b = np.zeros(2*n + 1)
688
+ b[1] = 1
689
+ weights = np.linalg.solve(A, b)
690
+
691
+ # Enforce identities to improve accuracy
692
+ weights[n] = 0
693
+ for i in range(n):
694
+ weights[-i-1] = -weights[i]
695
+
696
+ # Cache the weights. We only need to calculate them once unless
697
+ # the step factor changes.
698
+ diff_state.central = weights
699
+
700
+ # One-sided difference weights. The left one-sided weights (with
701
+ # negative steps) are simply the negative of the right one-sided
702
+ # weights, so no need to compute them separately.
703
+ i = np.arange(2*n + 1)
704
+ p = i - 1.
705
+ s = np.sign(i)
706
+
707
+ h = s / np.sqrt(fac) ** p
708
+ A = np.vander(h, increasing=True).T
709
+ b = np.zeros(2 * n + 1)
710
+ b[1] = 1
711
+ weights = np.linalg.solve(A, b)
712
+
713
+ diff_state.right = weights
714
+
715
+ return (xp.asarray(diff_state.central, dtype=work.dtype),
716
+ xp.asarray(diff_state.right, dtype=work.dtype))
717
+
718
+
719
+ @xp_capabilities(skip_backends=[('array_api_strict', _array_api_strict_skip_reason),
720
+ ('dask.array', _dask_reason)], jax_jit=False)
721
+ def jacobian(f, x, *, tolerances=None, maxiter=10, order=8, initial_step=0.5,
722
+ step_factor=2.0, step_direction=0):
723
+ r"""Evaluate the Jacobian of a function numerically.
724
+
725
+ Parameters
726
+ ----------
727
+ f : callable
728
+ The function whose Jacobian is desired. The signature must be::
729
+
730
+ f(xi: ndarray) -> ndarray
731
+
732
+ where each element of ``xi`` is a finite real. If the function to be
733
+ differentiated accepts additional arguments, wrap it (e.g. using
734
+ `functools.partial` or ``lambda``) and pass the wrapped callable
735
+ into `jacobian`. `f` must not mutate the array ``xi``. See Notes
736
+ regarding vectorization and the dimensionality of the input and output.
737
+ x : float array_like
738
+ Points at which to evaluate the Jacobian. Must have at least one dimension.
739
+ See Notes regarding the dimensionality and vectorization.
740
+ tolerances : dictionary of floats, optional
741
+ Absolute and relative tolerances. Valid keys of the dictionary are:
742
+
743
+ - ``atol`` - absolute tolerance on the derivative
744
+ - ``rtol`` - relative tolerance on the derivative
745
+
746
+ Iteration will stop when ``res.error < atol + rtol * abs(res.df)``. The default
747
+ `atol` is the smallest normal number of the appropriate dtype, and
748
+ the default `rtol` is the square root of the precision of the
749
+ appropriate dtype.
750
+ maxiter : int, default: 10
751
+ The maximum number of iterations of the algorithm to perform. See
752
+ Notes.
753
+ order : int, default: 8
754
+ The (positive integer) order of the finite difference formula to be
755
+ used. Odd integers will be rounded up to the next even integer.
756
+ initial_step : float array_like, default: 0.5
757
+ The (absolute) initial step size for the finite difference derivative
758
+ approximation. Must be broadcastable with `x` and `step_direction`.
759
+ step_factor : float, default: 2.0
760
+ The factor by which the step size is *reduced* in each iteration; i.e.
761
+ the step size in iteration 1 is ``initial_step/step_factor``. If
762
+ ``step_factor < 1``, subsequent steps will be greater than the initial
763
+ step; this may be useful if steps smaller than some threshold are
764
+ undesirable (e.g. due to subtractive cancellation error).
765
+ step_direction : integer array_like
766
+ An array representing the direction of the finite difference steps (e.g.
767
+ for use when `x` lies near to the boundary of the domain of the function.)
768
+ Must be broadcastable with `x` and `initial_step`.
769
+ Where 0 (default), central differences are used; where negative (e.g.
770
+ -1), steps are non-positive; and where positive (e.g. 1), all steps are
771
+ non-negative.
772
+
773
+ Returns
774
+ -------
775
+ res : _RichResult
776
+ An object similar to an instance of `scipy.optimize.OptimizeResult` with the
777
+ following attributes. The descriptions are written as though the values will
778
+ be scalars; however, if `f` returns an array, the outputs will be
779
+ arrays of the same shape.
780
+
781
+ success : bool array
782
+ ``True`` where the algorithm terminated successfully (status ``0``);
783
+ ``False`` otherwise.
784
+ status : int array
785
+ An integer representing the exit status of the algorithm.
786
+
787
+ - ``0`` : The algorithm converged to the specified tolerances.
788
+ - ``-1`` : The error estimate increased, so iteration was terminated.
789
+ - ``-2`` : The maximum number of iterations was reached.
790
+ - ``-3`` : A non-finite value was encountered.
791
+
792
+ df : float array
793
+ The Jacobian of `f` at `x`, if the algorithm terminated
794
+ successfully.
795
+ error : float array
796
+ An estimate of the error: the magnitude of the difference between
797
+ the current estimate of the Jacobian and the estimate in the
798
+ previous iteration.
799
+ nit : int array
800
+ The number of iterations of the algorithm that were performed.
801
+ nfev : int array
802
+ The number of points at which `f` was evaluated.
803
+
804
+ Each element of an attribute is associated with the corresponding
805
+ element of `df`. For instance, element ``i`` of `nfev` is the
806
+ number of points at which `f` was evaluated for the sake of
807
+ computing element ``i`` of `df`.
808
+
809
+ See Also
810
+ --------
811
+ derivative, hessian
812
+
813
+ Notes
814
+ -----
815
+ Suppose we wish to evaluate the Jacobian of a function
816
+ :math:`f: \mathbf{R}^m \rightarrow \mathbf{R}^n`. Assign to variables
817
+ ``m`` and ``n`` the positive integer values of :math:`m` and :math:`n`,
818
+ respectively, and let ``...`` represent an arbitrary tuple of integers.
819
+ If we wish to evaluate the Jacobian at a single point, then:
820
+
821
+ - argument `x` must be an array of shape ``(m,)``
822
+ - argument `f` must be vectorized to accept an array of shape ``(m, ...)``.
823
+ The first axis represents the :math:`m` inputs of :math:`f`; the remainder
824
+ are for evaluating the function at multiple points in a single call.
825
+ - argument `f` must return an array of shape ``(n, ...)``. The first
826
+ axis represents the :math:`n` outputs of :math:`f`; the remainder
827
+ are for the result of evaluating the function at multiple points.
828
+ - attribute ``df`` of the result object will be an array of shape ``(n, m)``,
829
+ the Jacobian.
830
+
831
+ This function is also vectorized in the sense that the Jacobian can be
832
+ evaluated at ``k`` points in a single call. In this case, `x` would be an
833
+ array of shape ``(m, k)``, `f` would accept an array of shape
834
+ ``(m, k, ...)`` and return an array of shape ``(n, k, ...)``, and the ``df``
835
+ attribute of the result would have shape ``(n, m, k)``.
836
+
837
+ Suppose the desired callable ``f_not_vectorized`` is not vectorized; it can
838
+ only accept an array of shape ``(m,)``. A simple solution to satisfy the required
839
+ interface is to wrap ``f_not_vectorized`` as follows::
840
+
841
+ def f(x):
842
+ return np.apply_along_axis(f_not_vectorized, axis=0, arr=x)
843
+
844
+ Alternatively, suppose the desired callable ``f_vec_q`` is vectorized, but
845
+ only for 2-D arrays of shape ``(m, q)``. To satisfy the required interface,
846
+ consider::
847
+
848
+ def f(x):
849
+ m, batch = x.shape[0], x.shape[1:] # x.shape is (m, ...)
850
+ x = np.reshape(x, (m, -1)) # `-1` is short for q = prod(batch)
851
+ res = f_vec_q(x) # pass shape (m, q) to function
852
+ n = res.shape[0]
853
+ return np.reshape(res, (n,) + batch) # return shape (n, ...)
854
+
855
+ Then pass the wrapped callable ``f`` as the first argument of `jacobian`.
856
+
857
+ References
858
+ ----------
859
+ .. [1] Jacobian matrix and determinant, *Wikipedia*,
860
+ https://en.wikipedia.org/wiki/Jacobian_matrix_and_determinant
861
+
862
+ Examples
863
+ --------
864
+ The Rosenbrock function maps from :math:`\mathbf{R}^m \rightarrow \mathbf{R}`;
865
+ the SciPy implementation `scipy.optimize.rosen` is vectorized to accept an
866
+ array of shape ``(m, p)`` and return an array of shape ``p``. Suppose we wish
867
+ to evaluate the Jacobian (AKA the gradient because the function returns a scalar)
868
+ at ``[0.5, 0.5, 0.5]``.
869
+
870
+ >>> import numpy as np
871
+ >>> from scipy.differentiate import jacobian
872
+ >>> from scipy.optimize import rosen, rosen_der
873
+ >>> m = 3
874
+ >>> x = np.full(m, 0.5)
875
+ >>> res = jacobian(rosen, x)
876
+ >>> ref = rosen_der(x) # reference value of the gradient
877
+ >>> res.df, ref
878
+ (array([-51., -1., 50.]), array([-51., -1., 50.]))
879
+
880
+ As an example of a function with multiple outputs, consider Example 4
881
+ from [1]_.
882
+
883
+ >>> def f(x):
884
+ ... x1, x2, x3 = x
885
+ ... return [x1, 5*x3, 4*x2**2 - 2*x3, x3*np.sin(x1)]
886
+
887
+ The true Jacobian is given by:
888
+
889
+ >>> def df(x):
890
+ ... x1, x2, x3 = x
891
+ ... one = np.ones_like(x1)
892
+ ... return [[one, 0*one, 0*one],
893
+ ... [0*one, 0*one, 5*one],
894
+ ... [0*one, 8*x2, -2*one],
895
+ ... [x3*np.cos(x1), 0*one, np.sin(x1)]]
896
+
897
+ Evaluate the Jacobian at an arbitrary point.
898
+
899
+ >>> rng = np.random.default_rng(389252938452)
900
+ >>> x = rng.random(size=3)
901
+ >>> res = jacobian(f, x)
902
+ >>> ref = df(x)
903
+ >>> res.df.shape == (4, 3)
904
+ True
905
+ >>> np.allclose(res.df, ref)
906
+ True
907
+
908
+ Evaluate the Jacobian at 10 arbitrary points in a single call.
909
+
910
+ >>> x = rng.random(size=(3, 10))
911
+ >>> res = jacobian(f, x)
912
+ >>> ref = df(x)
913
+ >>> res.df.shape == (4, 3, 10)
914
+ True
915
+ >>> np.allclose(res.df, ref)
916
+ True
917
+
918
+ """
919
+ xp = array_namespace(x)
920
+ x0 = xp_promote(x, force_floating=True, xp=xp)
921
+
922
+ if x0.ndim < 1:
923
+ message = "Argument `x` must be at least 1-D."
924
+ raise ValueError(message)
925
+
926
+ m = x0.shape[0]
927
+ i = xp.arange(m)
928
+
929
+ def wrapped(x):
930
+ p = () if x.ndim == x0.ndim else (x.shape[-1],) # number of abscissae
931
+
932
+ new_shape = (m, m) + x0.shape[1:] + p
933
+ xph = xp.expand_dims(x0, axis=1)
934
+ if x.ndim != x0.ndim:
935
+ xph = xp.expand_dims(xph, axis=-1)
936
+ xph = xp_copy(xp.broadcast_to(xph, new_shape), xp=xp)
937
+ xph = xpx.at(xph)[i, i].set(x)
938
+ return f(xph)
939
+
940
+ res = derivative(wrapped, x, tolerances=tolerances,
941
+ maxiter=maxiter, order=order, initial_step=initial_step,
942
+ step_factor=step_factor, preserve_shape=True,
943
+ step_direction=step_direction)
944
+
945
+ del res.x # the user knows `x`, and the way it gets broadcasted is meaningless here
946
+ return res
947
+
948
+
949
+ @xp_capabilities(skip_backends=[('array_api_strict', _array_api_strict_skip_reason),
950
+ ('dask.array', _dask_reason)], jax_jit=False)
951
+ def hessian(f, x, *, tolerances=None, maxiter=10,
952
+ order=8, initial_step=0.5, step_factor=2.0):
953
+ r"""Evaluate the Hessian of a function numerically.
954
+
955
+ Parameters
956
+ ----------
957
+ f : callable
958
+ The function whose Hessian is desired. The signature must be::
959
+
960
+ f(xi: ndarray) -> ndarray
961
+
962
+ where each element of ``xi`` is a finite real. If the function to be
963
+ differentiated accepts additional arguments, wrap it (e.g. using
964
+ `functools.partial` or ``lambda``) and pass the wrapped callable
965
+ into `hessian`. `f` must not mutate the array ``xi``. See Notes
966
+ regarding vectorization and the dimensionality of the input and output.
967
+ x : float array_like
968
+ Points at which to evaluate the Hessian. Must have at least one dimension.
969
+ See Notes regarding the dimensionality and vectorization.
970
+ tolerances : dictionary of floats, optional
971
+ Absolute and relative tolerances. Valid keys of the dictionary are:
972
+
973
+ - ``atol`` - absolute tolerance on the derivative
974
+ - ``rtol`` - relative tolerance on the derivative
975
+
976
+ Iteration will stop when ``res.error < atol + rtol * abs(res.df)``. The default
977
+ `atol` is the smallest normal number of the appropriate dtype, and
978
+ the default `rtol` is the square root of the precision of the
979
+ appropriate dtype.
980
+ order : int, default: 8
981
+ The (positive integer) order of the finite difference formula to be
982
+ used. Odd integers will be rounded up to the next even integer.
983
+ initial_step : float, default: 0.5
984
+ The (absolute) initial step size for the finite difference derivative
985
+ approximation.
986
+ step_factor : float, default: 2.0
987
+ The factor by which the step size is *reduced* in each iteration; i.e.
988
+ the step size in iteration 1 is ``initial_step/step_factor``. If
989
+ ``step_factor < 1``, subsequent steps will be greater than the initial
990
+ step; this may be useful if steps smaller than some threshold are
991
+ undesirable (e.g. due to subtractive cancellation error).
992
+ maxiter : int, default: 10
993
+ The maximum number of iterations of the algorithm to perform. See
994
+ Notes.
995
+
996
+ Returns
997
+ -------
998
+ res : _RichResult
999
+ An object similar to an instance of `scipy.optimize.OptimizeResult` with the
1000
+ following attributes. The descriptions are written as though the values will
1001
+ be scalars; however, if `f` returns an array, the outputs will be
1002
+ arrays of the same shape.
1003
+
1004
+ success : bool array
1005
+ ``True`` where the algorithm terminated successfully (status ``0``);
1006
+ ``False`` otherwise.
1007
+ status : int array
1008
+ An integer representing the exit status of the algorithm.
1009
+
1010
+ - ``0`` : The algorithm converged to the specified tolerances.
1011
+ - ``-1`` : The error estimate increased, so iteration was terminated.
1012
+ - ``-2`` : The maximum number of iterations was reached.
1013
+ - ``-3`` : A non-finite value was encountered.
1014
+
1015
+ ddf : float array
1016
+ The Hessian of `f` at `x`, if the algorithm terminated
1017
+ successfully.
1018
+ error : float array
1019
+ An estimate of the error: the magnitude of the difference between
1020
+ the current estimate of the Hessian and the estimate in the
1021
+ previous iteration.
1022
+ nfev : int array
1023
+ The number of points at which `f` was evaluated.
1024
+
1025
+ Each element of an attribute is associated with the corresponding
1026
+ element of `ddf`. For instance, element ``[i, j]`` of `nfev` is the
1027
+ number of points at which `f` was evaluated for the sake of
1028
+ computing element ``[i, j]`` of `ddf`.
1029
+
1030
+ See Also
1031
+ --------
1032
+ derivative, jacobian
1033
+
1034
+ Notes
1035
+ -----
1036
+ Suppose we wish to evaluate the Hessian of a function
1037
+ :math:`f: \mathbf{R}^m \rightarrow \mathbf{R}`, and we assign to variable
1038
+ ``m`` the positive integer value of :math:`m`. If we wish to evaluate
1039
+ the Hessian at a single point, then:
1040
+
1041
+ - argument `x` must be an array of shape ``(m,)``
1042
+ - argument `f` must be vectorized to accept an array of shape
1043
+ ``(m, ...)``. The first axis represents the :math:`m` inputs of
1044
+ :math:`f`; the remaining axes indicated by ellipses are for evaluating
1045
+ the function at several abscissae in a single call.
1046
+ - argument `f` must return an array of shape ``(...)``.
1047
+ - attribute ``dff`` of the result object will be an array of shape ``(m, m)``,
1048
+ the Hessian.
1049
+
1050
+ This function is also vectorized in the sense that the Hessian can be
1051
+ evaluated at ``k`` points in a single call. In this case, `x` would be an
1052
+ array of shape ``(m, k)``, `f` would accept an array of shape
1053
+ ``(m, ...)`` and return an array of shape ``(...)``, and the ``ddf``
1054
+ attribute of the result would have shape ``(m, m, k)``. Note that the
1055
+ axis associated with the ``k`` points is included within the axes
1056
+ denoted by ``(...)``.
1057
+
1058
+ Currently, `hessian` is implemented by nesting calls to `jacobian`.
1059
+ All options passed to `hessian` are used for both the inner and outer
1060
+ calls with one exception: the `rtol` used in the inner `jacobian` call
1061
+ is tightened by a factor of 100 with the expectation that the inner
1062
+ error can be ignored. A consequence is that `rtol` should not be set
1063
+ less than 100 times the precision of the dtype of `x`; a warning is
1064
+ emitted otherwise.
1065
+
1066
+ References
1067
+ ----------
1068
+ .. [1] Hessian matrix, *Wikipedia*,
1069
+ https://en.wikipedia.org/wiki/Hessian_matrix
1070
+
1071
+ Examples
1072
+ --------
1073
+ The Rosenbrock function maps from :math:`\mathbf{R}^m \rightarrow \mathbf{R}`;
1074
+ the SciPy implementation `scipy.optimize.rosen` is vectorized to accept an
1075
+ array of shape ``(m, ...)`` and return an array of shape ``...``. Suppose we
1076
+ wish to evaluate the Hessian at ``[0.5, 0.5, 0.5]``.
1077
+
1078
+ >>> import numpy as np
1079
+ >>> from scipy.differentiate import hessian
1080
+ >>> from scipy.optimize import rosen, rosen_hess
1081
+ >>> m = 3
1082
+ >>> x = np.full(m, 0.5)
1083
+ >>> res = hessian(rosen, x)
1084
+ >>> ref = rosen_hess(x) # reference value of the Hessian
1085
+ >>> np.allclose(res.ddf, ref)
1086
+ True
1087
+
1088
+ `hessian` is vectorized to evaluate the Hessian at multiple points
1089
+ in a single call.
1090
+
1091
+ >>> rng = np.random.default_rng(4589245925010)
1092
+ >>> x = rng.random((m, 10))
1093
+ >>> res = hessian(rosen, x)
1094
+ >>> ref = [rosen_hess(xi) for xi in x.T]
1095
+ >>> ref = np.moveaxis(ref, 0, -1)
1096
+ >>> np.allclose(res.ddf, ref)
1097
+ True
1098
+
1099
+ """
1100
+ # todo:
1101
+ # - add ability to vectorize over additional parameters (*args?)
1102
+ # - error estimate stack with inner jacobian (or use legit 2D stencil)
1103
+
1104
+ kwargs = dict(maxiter=maxiter, order=order, initial_step=initial_step,
1105
+ step_factor=step_factor)
1106
+ tolerances = {} if tolerances is None else tolerances
1107
+ atol = tolerances.get('atol', None)
1108
+ rtol = tolerances.get('rtol', None)
1109
+
1110
+ xp = array_namespace(x)
1111
+ x0 = xp_promote(x, force_floating=True, xp=xp)
1112
+
1113
+ finfo = xp.finfo(x0.dtype)
1114
+ rtol = finfo.eps**0.5 if rtol is None else rtol # keep same as `derivative`
1115
+
1116
+ # tighten the inner tolerance to make the inner error negligible
1117
+ rtol_min = finfo.eps * 100
1118
+ message = (f"The specified `{rtol=}`, but error estimates are likely to be "
1119
+ f"unreliable when `rtol < {rtol_min}`.")
1120
+ if 0 < rtol < rtol_min: # rtol <= 0 is an error
1121
+ warnings.warn(message, RuntimeWarning, stacklevel=2)
1122
+ rtol = rtol_min
1123
+
1124
+ def df(x):
1125
+ tolerances = dict(rtol=rtol/100, atol=atol)
1126
+ temp = jacobian(f, x, tolerances=tolerances, **kwargs)
1127
+ nfev.append(temp.nfev if len(nfev) == 0 else temp.nfev.sum(axis=-1))
1128
+ return temp.df
1129
+
1130
+ nfev = [] # track inner function evaluations
1131
+ res = jacobian(df, x, tolerances=tolerances, **kwargs) # jacobian of jacobian
1132
+
1133
+ nfev = xp.cumulative_sum(xp.stack(nfev), axis=0)
1134
+ res_nit = xp.astype(res.nit[xp.newaxis, ...], xp.int64) # appease torch
1135
+ res.nfev = xp.take_along_axis(nfev, res_nit, axis=0)[0]
1136
+ res.ddf = res.df
1137
+ del res.df # this is renamed to ddf
1138
+ del res.nit # this is only the outer-jacobian nit
1139
+
1140
+ return res
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/__init__.py ADDED
@@ -0,0 +1,103 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """
2
+ =========================================================
3
+ Legacy discrete Fourier transforms (:mod:`scipy.fftpack`)
4
+ =========================================================
5
+
6
+ .. legacy::
7
+
8
+ New code should use :mod:`scipy.fft`.
9
+
10
+ Fast Fourier Transforms (FFTs)
11
+ ==============================
12
+
13
+ .. autosummary::
14
+ :toctree: generated/
15
+
16
+ fft - Fast (discrete) Fourier Transform (FFT)
17
+ ifft - Inverse FFT
18
+ fft2 - 2-D FFT
19
+ ifft2 - 2-D inverse FFT
20
+ fftn - N-D FFT
21
+ ifftn - N-D inverse FFT
22
+ rfft - FFT of strictly real-valued sequence
23
+ irfft - Inverse of rfft
24
+ dct - Discrete cosine transform
25
+ idct - Inverse discrete cosine transform
26
+ dctn - N-D Discrete cosine transform
27
+ idctn - N-D Inverse discrete cosine transform
28
+ dst - Discrete sine transform
29
+ idst - Inverse discrete sine transform
30
+ dstn - N-D Discrete sine transform
31
+ idstn - N-D Inverse discrete sine transform
32
+
33
+ Differential and pseudo-differential operators
34
+ ==============================================
35
+
36
+ .. autosummary::
37
+ :toctree: generated/
38
+
39
+ diff - Differentiation and integration of periodic sequences
40
+ tilbert - Tilbert transform: cs_diff(x,h,h)
41
+ itilbert - Inverse Tilbert transform: sc_diff(x,h,h)
42
+ hilbert - Hilbert transform: cs_diff(x,inf,inf)
43
+ ihilbert - Inverse Hilbert transform: sc_diff(x,inf,inf)
44
+ cs_diff - cosh/sinh pseudo-derivative of periodic sequences
45
+ sc_diff - sinh/cosh pseudo-derivative of periodic sequences
46
+ ss_diff - sinh/sinh pseudo-derivative of periodic sequences
47
+ cc_diff - cosh/cosh pseudo-derivative of periodic sequences
48
+ shift - Shift periodic sequences
49
+
50
+ Helper functions
51
+ ================
52
+
53
+ .. autosummary::
54
+ :toctree: generated/
55
+
56
+ fftshift - Shift the zero-frequency component to the center of the spectrum
57
+ ifftshift - The inverse of `fftshift`
58
+ fftfreq - Return the Discrete Fourier Transform sample frequencies
59
+ rfftfreq - DFT sample frequencies (for usage with rfft, irfft)
60
+ next_fast_len - Find the optimal length to zero-pad an FFT for speed
61
+
62
+ Note that ``fftshift``, ``ifftshift`` and ``fftfreq`` are numpy functions
63
+ exposed by ``fftpack``; importing them from ``numpy`` should be preferred.
64
+
65
+ Convolutions (:mod:`scipy.fftpack.convolve`)
66
+ ============================================
67
+
68
+ .. module:: scipy.fftpack.convolve
69
+
70
+ .. autosummary::
71
+ :toctree: generated/
72
+
73
+ convolve
74
+ convolve_z
75
+ init_convolution_kernel
76
+ destroy_convolve_cache
77
+
78
+ """
79
+
80
+
81
+ __all__ = ['fft','ifft','fftn','ifftn','rfft','irfft',
82
+ 'fft2','ifft2',
83
+ 'diff',
84
+ 'tilbert','itilbert','hilbert','ihilbert',
85
+ 'sc_diff','cs_diff','cc_diff','ss_diff',
86
+ 'shift',
87
+ 'fftfreq', 'rfftfreq',
88
+ 'fftshift', 'ifftshift',
89
+ 'next_fast_len',
90
+ 'dct', 'idct', 'dst', 'idst', 'dctn', 'idctn', 'dstn', 'idstn'
91
+ ]
92
+
93
+ from ._basic import *
94
+ from ._pseudo_diffs import *
95
+ from ._helper import *
96
+ from ._realtransforms import *
97
+
98
+ # Deprecated namespaces, to be removed in v2.0.0
99
+ from . import basic, helper, pseudo_diffs, realtransforms
100
+
101
+ from scipy._lib._testutils import PytestTester
102
+ test = PytestTester(__name__)
103
+ del PytestTester
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/_basic.py ADDED
@@ -0,0 +1,428 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """
2
+ Discrete Fourier Transforms - _basic.py
3
+ """
4
+ # Created by Pearu Peterson, August,September 2002
5
+ __all__ = ['fft','ifft','fftn','ifftn','rfft','irfft',
6
+ 'fft2','ifft2']
7
+
8
+ from scipy.fft import _pocketfft
9
+ from ._helper import _good_shape
10
+
11
+
12
+ def fft(x, n=None, axis=-1, overwrite_x=False):
13
+ """
14
+ Return discrete Fourier transform of real or complex sequence.
15
+
16
+ The returned complex array contains ``y(0), y(1),..., y(n-1)``, where
17
+
18
+ ``y(j) = (x * exp(-2*pi*sqrt(-1)*j*np.arange(n)/n)).sum()``.
19
+
20
+ Parameters
21
+ ----------
22
+ x : array_like
23
+ Array to Fourier transform.
24
+ n : int, optional
25
+ Length of the Fourier transform. If ``n < x.shape[axis]``, `x` is
26
+ truncated. If ``n > x.shape[axis]``, `x` is zero-padded. The
27
+ default results in ``n = x.shape[axis]``.
28
+ axis : int, optional
29
+ Axis along which the fft's are computed; the default is over the
30
+ last axis (i.e., ``axis=-1``).
31
+ overwrite_x : bool, optional
32
+ If True, the contents of `x` can be destroyed; the default is False.
33
+
34
+ Returns
35
+ -------
36
+ z : complex ndarray
37
+ with the elements::
38
+
39
+ [y(0),y(1),..,y(n/2),y(1-n/2),...,y(-1)] if n is even
40
+ [y(0),y(1),..,y((n-1)/2),y(-(n-1)/2),...,y(-1)] if n is odd
41
+
42
+ where::
43
+
44
+ y(j) = sum[k=0..n-1] x[k] * exp(-sqrt(-1)*j*k* 2*pi/n), j = 0..n-1
45
+
46
+ See Also
47
+ --------
48
+ ifft : Inverse FFT
49
+ rfft : FFT of a real sequence
50
+
51
+ Notes
52
+ -----
53
+ The packing of the result is "standard": If ``A = fft(a, n)``, then
54
+ ``A[0]`` contains the zero-frequency term, ``A[1:n/2]`` contains the
55
+ positive-frequency terms, and ``A[n/2:]`` contains the negative-frequency
56
+ terms, in order of decreasingly negative frequency. So ,for an 8-point
57
+ transform, the frequencies of the result are [0, 1, 2, 3, -4, -3, -2, -1].
58
+ To rearrange the fft output so that the zero-frequency component is
59
+ centered, like [-4, -3, -2, -1, 0, 1, 2, 3], use `fftshift`.
60
+
61
+ Both single and double precision routines are implemented. Half precision
62
+ inputs will be converted to single precision. Non-floating-point inputs
63
+ will be converted to double precision. Long-double precision inputs are
64
+ not supported.
65
+
66
+ This function is most efficient when `n` is a power of two, and least
67
+ efficient when `n` is prime.
68
+
69
+ Note that if ``x`` is real-valued, then ``A[j] == A[n-j].conjugate()``.
70
+ If ``x`` is real-valued and ``n`` is even, then ``A[n/2]`` is real.
71
+
72
+ If the data type of `x` is real, a "real FFT" algorithm is automatically
73
+ used, which roughly halves the computation time. To increase efficiency
74
+ a little further, use `rfft`, which does the same calculation, but only
75
+ outputs half of the symmetrical spectrum. If the data is both real and
76
+ symmetrical, the `dct` can again double the efficiency by generating
77
+ half of the spectrum from half of the signal.
78
+
79
+ Examples
80
+ --------
81
+ >>> import numpy as np
82
+ >>> from scipy.fftpack import fft, ifft
83
+ >>> x = np.arange(5)
84
+ >>> np.allclose(fft(ifft(x)), x, atol=1e-15) # within numerical accuracy.
85
+ True
86
+
87
+ """
88
+ return _pocketfft.fft(x, n, axis, None, overwrite_x)
89
+
90
+
91
+ def ifft(x, n=None, axis=-1, overwrite_x=False):
92
+ """
93
+ Return discrete inverse Fourier transform of real or complex sequence.
94
+
95
+ The returned complex array contains ``y(0), y(1),..., y(n-1)``, where
96
+
97
+ ``y(j) = (x * exp(2*pi*sqrt(-1)*j*np.arange(n)/n)).mean()``.
98
+
99
+ Parameters
100
+ ----------
101
+ x : array_like
102
+ Transformed data to invert.
103
+ n : int, optional
104
+ Length of the inverse Fourier transform. If ``n < x.shape[axis]``,
105
+ `x` is truncated. If ``n > x.shape[axis]``, `x` is zero-padded.
106
+ The default results in ``n = x.shape[axis]``.
107
+ axis : int, optional
108
+ Axis along which the ifft's are computed; the default is over the
109
+ last axis (i.e., ``axis=-1``).
110
+ overwrite_x : bool, optional
111
+ If True, the contents of `x` can be destroyed; the default is False.
112
+
113
+ Returns
114
+ -------
115
+ ifft : ndarray of floats
116
+ The inverse discrete Fourier transform.
117
+
118
+ See Also
119
+ --------
120
+ fft : Forward FFT
121
+
122
+ Notes
123
+ -----
124
+ Both single and double precision routines are implemented. Half precision
125
+ inputs will be converted to single precision. Non-floating-point inputs
126
+ will be converted to double precision. Long-double precision inputs are
127
+ not supported.
128
+
129
+ This function is most efficient when `n` is a power of two, and least
130
+ efficient when `n` is prime.
131
+
132
+ If the data type of `x` is real, a "real IFFT" algorithm is automatically
133
+ used, which roughly halves the computation time.
134
+
135
+ Examples
136
+ --------
137
+ >>> from scipy.fftpack import fft, ifft
138
+ >>> import numpy as np
139
+ >>> x = np.arange(5)
140
+ >>> np.allclose(ifft(fft(x)), x, atol=1e-15) # within numerical accuracy.
141
+ True
142
+
143
+ """
144
+ return _pocketfft.ifft(x, n, axis, None, overwrite_x)
145
+
146
+
147
+ def rfft(x, n=None, axis=-1, overwrite_x=False):
148
+ """
149
+ Discrete Fourier transform of a real sequence.
150
+
151
+ Parameters
152
+ ----------
153
+ x : array_like, real-valued
154
+ The data to transform.
155
+ n : int, optional
156
+ Defines the length of the Fourier transform. If `n` is not specified
157
+ (the default) then ``n = x.shape[axis]``. If ``n < x.shape[axis]``,
158
+ `x` is truncated, if ``n > x.shape[axis]``, `x` is zero-padded.
159
+ axis : int, optional
160
+ The axis along which the transform is applied. The default is the
161
+ last axis.
162
+ overwrite_x : bool, optional
163
+ If set to true, the contents of `x` can be overwritten. Default is
164
+ False.
165
+
166
+ Returns
167
+ -------
168
+ z : real ndarray
169
+ The returned real array contains::
170
+
171
+ [y(0),Re(y(1)),Im(y(1)),...,Re(y(n/2))] if n is even
172
+ [y(0),Re(y(1)),Im(y(1)),...,Re(y(n/2)),Im(y(n/2))] if n is odd
173
+
174
+ where::
175
+
176
+ y(j) = sum[k=0..n-1] x[k] * exp(-sqrt(-1)*j*k*2*pi/n)
177
+ j = 0..n-1
178
+
179
+ See Also
180
+ --------
181
+ fft, irfft, scipy.fft.rfft
182
+
183
+ Notes
184
+ -----
185
+ Within numerical accuracy, ``y == rfft(irfft(y))``.
186
+
187
+ Both single and double precision routines are implemented. Half precision
188
+ inputs will be converted to single precision. Non-floating-point inputs
189
+ will be converted to double precision. Long-double precision inputs are
190
+ not supported.
191
+
192
+ To get an output with a complex datatype, consider using the newer
193
+ function `scipy.fft.rfft`.
194
+
195
+ Examples
196
+ --------
197
+ >>> from scipy.fftpack import fft, rfft
198
+ >>> a = [9, -9, 1, 3]
199
+ >>> fft(a)
200
+ array([ 4. +0.j, 8.+12.j, 16. +0.j, 8.-12.j])
201
+ >>> rfft(a)
202
+ array([ 4., 8., 12., 16.])
203
+
204
+ """
205
+ return _pocketfft.rfft_fftpack(x, n, axis, None, overwrite_x)
206
+
207
+
208
+ def irfft(x, n=None, axis=-1, overwrite_x=False):
209
+ """
210
+ Return inverse discrete Fourier transform of real sequence x.
211
+
212
+ The contents of `x` are interpreted as the output of the `rfft`
213
+ function.
214
+
215
+ Parameters
216
+ ----------
217
+ x : array_like
218
+ Transformed data to invert.
219
+ n : int, optional
220
+ Length of the inverse Fourier transform.
221
+ If n < x.shape[axis], x is truncated.
222
+ If n > x.shape[axis], x is zero-padded.
223
+ The default results in n = x.shape[axis].
224
+ axis : int, optional
225
+ Axis along which the ifft's are computed; the default is over
226
+ the last axis (i.e., axis=-1).
227
+ overwrite_x : bool, optional
228
+ If True, the contents of `x` can be destroyed; the default is False.
229
+
230
+ Returns
231
+ -------
232
+ irfft : ndarray of floats
233
+ The inverse discrete Fourier transform.
234
+
235
+ See Also
236
+ --------
237
+ rfft, ifft, scipy.fft.irfft
238
+
239
+ Notes
240
+ -----
241
+ The returned real array contains::
242
+
243
+ [y(0),y(1),...,y(n-1)]
244
+
245
+ where for n is even::
246
+
247
+ y(j) = 1/n (sum[k=1..n/2-1] (x[2*k-1]+sqrt(-1)*x[2*k])
248
+ * exp(sqrt(-1)*j*k* 2*pi/n)
249
+ + c.c. + x[0] + (-1)**(j) x[n-1])
250
+
251
+ and for n is odd::
252
+
253
+ y(j) = 1/n (sum[k=1..(n-1)/2] (x[2*k-1]+sqrt(-1)*x[2*k])
254
+ * exp(sqrt(-1)*j*k* 2*pi/n)
255
+ + c.c. + x[0])
256
+
257
+ c.c. denotes complex conjugate of preceding expression.
258
+
259
+ For details on input parameters, see `rfft`.
260
+
261
+ To process (conjugate-symmetric) frequency-domain data with a complex
262
+ datatype, consider using the newer function `scipy.fft.irfft`.
263
+
264
+ Examples
265
+ --------
266
+ >>> from scipy.fftpack import rfft, irfft
267
+ >>> a = [1.0, 2.0, 3.0, 4.0, 5.0]
268
+ >>> irfft(a)
269
+ array([ 2.6 , -3.16405192, 1.24398433, -1.14955713, 1.46962473])
270
+ >>> irfft(rfft(a))
271
+ array([1., 2., 3., 4., 5.])
272
+
273
+ """
274
+ return _pocketfft.irfft_fftpack(x, n, axis, None, overwrite_x)
275
+
276
+
277
+ def fftn(x, shape=None, axes=None, overwrite_x=False):
278
+ """
279
+ Return multidimensional discrete Fourier transform.
280
+
281
+ The returned array contains::
282
+
283
+ y[j_1,..,j_d] = sum[k_1=0..n_1-1, ..., k_d=0..n_d-1]
284
+ x[k_1,..,k_d] * prod[i=1..d] exp(-sqrt(-1)*2*pi/n_i * j_i * k_i)
285
+
286
+ where d = len(x.shape) and n = x.shape.
287
+
288
+ Parameters
289
+ ----------
290
+ x : array_like
291
+ The (N-D) array to transform.
292
+ shape : int or array_like of ints or None, optional
293
+ The shape of the result. If both `shape` and `axes` (see below) are
294
+ None, `shape` is ``x.shape``; if `shape` is None but `axes` is
295
+ not None, then `shape` is ``numpy.take(x.shape, axes, axis=0)``.
296
+ If ``shape[i] > x.shape[i]``, the ith dimension is padded with zeros.
297
+ If ``shape[i] < x.shape[i]``, the ith dimension is truncated to
298
+ length ``shape[i]``.
299
+ If any element of `shape` is -1, the size of the corresponding
300
+ dimension of `x` is used.
301
+ axes : int or array_like of ints or None, optional
302
+ The axes of `x` (`y` if `shape` is not None) along which the
303
+ transform is applied.
304
+ The default is over all axes.
305
+ overwrite_x : bool, optional
306
+ If True, the contents of `x` can be destroyed. Default is False.
307
+
308
+ Returns
309
+ -------
310
+ y : complex-valued N-D NumPy array
311
+ The (N-D) DFT of the input array.
312
+
313
+ See Also
314
+ --------
315
+ ifftn
316
+
317
+ Notes
318
+ -----
319
+ If ``x`` is real-valued, then
320
+ ``y[..., j_i, ...] == y[..., n_i-j_i, ...].conjugate()``.
321
+
322
+ Both single and double precision routines are implemented. Half precision
323
+ inputs will be converted to single precision. Non-floating-point inputs
324
+ will be converted to double precision. Long-double precision inputs are
325
+ not supported.
326
+
327
+ Examples
328
+ --------
329
+ >>> import numpy as np
330
+ >>> from scipy.fftpack import fftn, ifftn
331
+ >>> y = (-np.arange(16), 8 - np.arange(16), np.arange(16))
332
+ >>> np.allclose(y, fftn(ifftn(y)))
333
+ True
334
+
335
+ """
336
+ shape = _good_shape(x, shape, axes)
337
+ return _pocketfft.fftn(x, shape, axes, None, overwrite_x)
338
+
339
+
340
+ def ifftn(x, shape=None, axes=None, overwrite_x=False):
341
+ """
342
+ Return inverse multidimensional discrete Fourier transform.
343
+
344
+ The sequence can be of an arbitrary type.
345
+
346
+ The returned array contains::
347
+
348
+ y[j_1,..,j_d] = 1/p * sum[k_1=0..n_1-1, ..., k_d=0..n_d-1]
349
+ x[k_1,..,k_d] * prod[i=1..d] exp(sqrt(-1)*2*pi/n_i * j_i * k_i)
350
+
351
+ where ``d = len(x.shape)``, ``n = x.shape``, and ``p = prod[i=1..d] n_i``.
352
+
353
+ For description of parameters see `fftn`.
354
+
355
+ See Also
356
+ --------
357
+ fftn : for detailed information.
358
+
359
+ Examples
360
+ --------
361
+ >>> from scipy.fftpack import fftn, ifftn
362
+ >>> import numpy as np
363
+ >>> y = (-np.arange(16), 8 - np.arange(16), np.arange(16))
364
+ >>> np.allclose(y, ifftn(fftn(y)))
365
+ True
366
+
367
+ """
368
+ shape = _good_shape(x, shape, axes)
369
+ return _pocketfft.ifftn(x, shape, axes, None, overwrite_x)
370
+
371
+
372
+ def fft2(x, shape=None, axes=(-2,-1), overwrite_x=False):
373
+ """
374
+ 2-D discrete Fourier transform.
375
+
376
+ Return the 2-D discrete Fourier transform of the 2-D argument
377
+ `x`.
378
+
379
+ See Also
380
+ --------
381
+ fftn : for detailed information.
382
+
383
+ Examples
384
+ --------
385
+ >>> import numpy as np
386
+ >>> from scipy.fftpack import fft2, ifft2
387
+ >>> y = np.mgrid[:5, :5][0]
388
+ >>> y
389
+ array([[0, 0, 0, 0, 0],
390
+ [1, 1, 1, 1, 1],
391
+ [2, 2, 2, 2, 2],
392
+ [3, 3, 3, 3, 3],
393
+ [4, 4, 4, 4, 4]])
394
+ >>> np.allclose(y, ifft2(fft2(y)))
395
+ True
396
+ """
397
+ return fftn(x,shape,axes,overwrite_x)
398
+
399
+
400
+ def ifft2(x, shape=None, axes=(-2,-1), overwrite_x=False):
401
+ """
402
+ 2-D discrete inverse Fourier transform of real or complex sequence.
403
+
404
+ Return inverse 2-D discrete Fourier transform of
405
+ arbitrary type sequence x.
406
+
407
+ See `ifft` for more information.
408
+
409
+ See Also
410
+ --------
411
+ fft2, ifft
412
+
413
+ Examples
414
+ --------
415
+ >>> import numpy as np
416
+ >>> from scipy.fftpack import fft2, ifft2
417
+ >>> y = np.mgrid[:5, :5][0]
418
+ >>> y
419
+ array([[0, 0, 0, 0, 0],
420
+ [1, 1, 1, 1, 1],
421
+ [2, 2, 2, 2, 2],
422
+ [3, 3, 3, 3, 3],
423
+ [4, 4, 4, 4, 4]])
424
+ >>> np.allclose(y, fft2(ifft2(y)))
425
+ True
426
+
427
+ """
428
+ return ifftn(x,shape,axes,overwrite_x)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/_helper.py ADDED
@@ -0,0 +1,115 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ import operator
2
+
3
+ import numpy as np
4
+ from numpy.fft import fftshift, ifftshift, fftfreq
5
+
6
+ import scipy.fft._pocketfft.helper as _helper
7
+
8
+ __all__ = ['fftshift', 'ifftshift', 'fftfreq', 'rfftfreq', 'next_fast_len']
9
+
10
+
11
+ def rfftfreq(n, d=1.0):
12
+ """DFT sample frequencies (for usage with rfft, irfft).
13
+
14
+ The returned float array contains the frequency bins in
15
+ cycles/unit (with zero at the start) given a window length `n` and a
16
+ sample spacing `d`::
17
+
18
+ f = [0,1,1,2,2,...,n/2-1,n/2-1,n/2]/(d*n) if n is even
19
+ f = [0,1,1,2,2,...,n/2-1,n/2-1,n/2,n/2]/(d*n) if n is odd
20
+
21
+ Parameters
22
+ ----------
23
+ n : int
24
+ Window length.
25
+ d : scalar, optional
26
+ Sample spacing. Default is 1.
27
+
28
+ Returns
29
+ -------
30
+ out : ndarray
31
+ The array of length `n`, containing the sample frequencies.
32
+
33
+ Examples
34
+ --------
35
+ >>> import numpy as np
36
+ >>> from scipy import fftpack
37
+ >>> sig = np.array([-2, 8, 6, 4, 1, 0, 3, 5], dtype=float)
38
+ >>> sig_fft = fftpack.rfft(sig)
39
+ >>> n = sig_fft.size
40
+ >>> timestep = 0.1
41
+ >>> freq = fftpack.rfftfreq(n, d=timestep)
42
+ >>> freq
43
+ array([ 0. , 1.25, 1.25, 2.5 , 2.5 , 3.75, 3.75, 5. ])
44
+
45
+ """
46
+ n = operator.index(n)
47
+ if n < 0:
48
+ raise ValueError(f"n = {n} is not valid. "
49
+ "n must be a nonnegative integer.")
50
+
51
+ return (np.arange(1, n + 1, dtype=int) // 2) / float(n * d)
52
+
53
+
54
+ def next_fast_len(target):
55
+ """
56
+ Find the next fast size of input data to `fft`, for zero-padding, etc.
57
+
58
+ SciPy's FFTPACK has efficient functions for radix {2, 3, 4, 5}, so this
59
+ returns the next composite of the prime factors 2, 3, and 5 which is
60
+ greater than or equal to `target`. (These are also known as 5-smooth
61
+ numbers, regular numbers, or Hamming numbers.)
62
+
63
+ Parameters
64
+ ----------
65
+ target : int
66
+ Length to start searching from. Must be a positive integer.
67
+
68
+ Returns
69
+ -------
70
+ out : int
71
+ The first 5-smooth number greater than or equal to `target`.
72
+
73
+ Notes
74
+ -----
75
+ .. versionadded:: 0.18.0
76
+
77
+ Examples
78
+ --------
79
+ On a particular machine, an FFT of prime length takes 133 ms:
80
+
81
+ >>> from scipy import fftpack
82
+ >>> import numpy as np
83
+ >>> rng = np.random.default_rng()
84
+ >>> min_len = 10007 # prime length is worst case for speed
85
+ >>> a = rng.standard_normal(min_len)
86
+ >>> b = fftpack.fft(a)
87
+
88
+ Zero-padding to the next 5-smooth length reduces computation time to
89
+ 211 us, a speedup of 630 times:
90
+
91
+ >>> fftpack.next_fast_len(min_len)
92
+ 10125
93
+ >>> b = fftpack.fft(a, 10125)
94
+
95
+ Rounding up to the next power of 2 is not optimal, taking 367 us to
96
+ compute, 1.7 times as long as the 5-smooth size:
97
+
98
+ >>> b = fftpack.fft(a, 16384)
99
+
100
+ """
101
+ # Real transforms use regular sizes so this is backwards compatible
102
+ return _helper.good_size(target, True)
103
+
104
+
105
+ def _good_shape(x, shape, axes):
106
+ """Ensure that shape argument is valid for scipy.fftpack
107
+
108
+ scipy.fftpack does not support len(shape) < x.ndim when axes is not given.
109
+ """
110
+ if shape is not None and axes is None:
111
+ shape = _helper._iterable_of_int(shape, 'shape')
112
+ if len(shape) != np.ndim(x):
113
+ raise ValueError("when given, axes and shape arguments"
114
+ " have to be of the same length")
115
+ return shape
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/_pseudo_diffs.py ADDED
@@ -0,0 +1,554 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """
2
+ Differential and pseudo-differential operators.
3
+ """
4
+ # Created by Pearu Peterson, September 2002
5
+
6
+ __all__ = ['diff',
7
+ 'tilbert','itilbert','hilbert','ihilbert',
8
+ 'cs_diff','cc_diff','sc_diff','ss_diff',
9
+ 'shift']
10
+
11
+ import threading
12
+
13
+ from numpy import pi, asarray, sin, cos, sinh, cosh, tanh, iscomplexobj
14
+ from . import convolve
15
+
16
+ from scipy.fft._pocketfft.helper import _datacopied
17
+
18
+
19
+ _cache = threading.local()
20
+
21
+
22
+ def diff(x,order=1,period=None, _cache=_cache):
23
+ """
24
+ Return kth derivative (or integral) of a periodic sequence x.
25
+
26
+ If x_j and y_j are Fourier coefficients of periodic functions x
27
+ and y, respectively, then::
28
+
29
+ y_j = pow(sqrt(-1)*j*2*pi/period, order) * x_j
30
+ y_0 = 0 if order is not 0.
31
+
32
+ Parameters
33
+ ----------
34
+ x : array_like
35
+ Input array.
36
+ order : int, optional
37
+ The order of differentiation. Default order is 1. If order is
38
+ negative, then integration is carried out under the assumption
39
+ that ``x_0 == 0``.
40
+ period : float, optional
41
+ The assumed period of the sequence. Default is ``2*pi``.
42
+
43
+ Notes
44
+ -----
45
+ If ``sum(x, axis=0) = 0`` then ``diff(diff(x, k), -k) == x`` (within
46
+ numerical accuracy).
47
+
48
+ For odd order and even ``len(x)``, the Nyquist mode is taken zero.
49
+
50
+ """
51
+ if isinstance(_cache, threading.local):
52
+ if not hasattr(_cache, 'diff_cache'):
53
+ _cache.diff_cache = {}
54
+ _cache = _cache.diff_cache
55
+
56
+ tmp = asarray(x)
57
+ if order == 0:
58
+ return tmp
59
+ if iscomplexobj(tmp):
60
+ return diff(tmp.real, order, period, _cache)+1j*diff(
61
+ tmp.imag, order, period, _cache)
62
+ if period is not None:
63
+ c = 2*pi/period
64
+ else:
65
+ c = 1.0
66
+ n = len(x)
67
+ omega = _cache.get((n,order,c))
68
+ if omega is None:
69
+ if len(_cache) > 20:
70
+ while _cache:
71
+ _cache.popitem()
72
+
73
+ def kernel(k,order=order,c=c):
74
+ if k:
75
+ return pow(c*k,order)
76
+ return 0
77
+ omega = convolve.init_convolution_kernel(n,kernel,d=order,
78
+ zero_nyquist=1)
79
+ _cache[(n,order,c)] = omega
80
+ overwrite_x = _datacopied(tmp, x)
81
+ return convolve.convolve(tmp,omega,swap_real_imag=order % 2,
82
+ overwrite_x=overwrite_x)
83
+
84
+
85
+ def tilbert(x, h, period=None, _cache=_cache):
86
+ """
87
+ Return h-Tilbert transform of a periodic sequence x.
88
+
89
+ If x_j and y_j are Fourier coefficients of periodic functions x
90
+ and y, respectively, then::
91
+
92
+ y_j = sqrt(-1)*coth(j*h*2*pi/period) * x_j
93
+ y_0 = 0
94
+
95
+ Parameters
96
+ ----------
97
+ x : array_like
98
+ The input array to transform.
99
+ h : float
100
+ Defines the parameter of the Tilbert transform.
101
+ period : float, optional
102
+ The assumed period of the sequence. Default period is ``2*pi``.
103
+
104
+ Returns
105
+ -------
106
+ tilbert : ndarray
107
+ The result of the transform.
108
+
109
+ Notes
110
+ -----
111
+ If ``sum(x, axis=0) == 0`` and ``n = len(x)`` is odd, then
112
+ ``tilbert(itilbert(x)) == x``.
113
+
114
+ If ``2 * pi * h / period`` is approximately 10 or larger, then
115
+ numerically ``tilbert == hilbert``
116
+ (theoretically oo-Tilbert == Hilbert).
117
+
118
+ For even ``len(x)``, the Nyquist mode of ``x`` is taken zero.
119
+
120
+ """
121
+ if isinstance(_cache, threading.local):
122
+ if not hasattr(_cache, 'tilbert_cache'):
123
+ _cache.tilbert_cache = {}
124
+ _cache = _cache.tilbert_cache
125
+
126
+ tmp = asarray(x)
127
+ if iscomplexobj(tmp):
128
+ return tilbert(tmp.real, h, period, _cache) + \
129
+ 1j * tilbert(tmp.imag, h, period, _cache)
130
+
131
+ if period is not None:
132
+ h = h * 2 * pi / period
133
+
134
+ n = len(x)
135
+ omega = _cache.get((n, h))
136
+ if omega is None:
137
+ if len(_cache) > 20:
138
+ while _cache:
139
+ _cache.popitem()
140
+
141
+ def kernel(k, h=h):
142
+ if k:
143
+ return 1.0/tanh(h*k)
144
+
145
+ return 0
146
+
147
+ omega = convolve.init_convolution_kernel(n, kernel, d=1)
148
+ _cache[(n,h)] = omega
149
+
150
+ overwrite_x = _datacopied(tmp, x)
151
+ return convolve.convolve(tmp,omega,swap_real_imag=1,overwrite_x=overwrite_x)
152
+
153
+
154
+ def itilbert(x,h,period=None, _cache=_cache):
155
+ """
156
+ Return inverse h-Tilbert transform of a periodic sequence x.
157
+
158
+ If ``x_j`` and ``y_j`` are Fourier coefficients of periodic functions x
159
+ and y, respectively, then::
160
+
161
+ y_j = -sqrt(-1)*tanh(j*h*2*pi/period) * x_j
162
+ y_0 = 0
163
+
164
+ For more details, see `tilbert`.
165
+
166
+ """
167
+ if isinstance(_cache, threading.local):
168
+ if not hasattr(_cache, 'itilbert_cache'):
169
+ _cache.itilbert_cache = {}
170
+ _cache = _cache.itilbert_cache
171
+
172
+ tmp = asarray(x)
173
+ if iscomplexobj(tmp):
174
+ return itilbert(tmp.real, h, period, _cache) + \
175
+ 1j*itilbert(tmp.imag, h, period, _cache)
176
+ if period is not None:
177
+ h = h*2*pi/period
178
+ n = len(x)
179
+ omega = _cache.get((n,h))
180
+ if omega is None:
181
+ if len(_cache) > 20:
182
+ while _cache:
183
+ _cache.popitem()
184
+
185
+ def kernel(k,h=h):
186
+ if k:
187
+ return -tanh(h*k)
188
+ return 0
189
+ omega = convolve.init_convolution_kernel(n,kernel,d=1)
190
+ _cache[(n,h)] = omega
191
+ overwrite_x = _datacopied(tmp, x)
192
+ return convolve.convolve(tmp,omega,swap_real_imag=1,overwrite_x=overwrite_x)
193
+
194
+
195
+ def hilbert(x, _cache=_cache):
196
+ """
197
+ Return Hilbert transform of a periodic sequence x.
198
+
199
+ If x_j and y_j are Fourier coefficients of periodic functions x
200
+ and y, respectively, then::
201
+
202
+ y_j = sqrt(-1)*sign(j) * x_j
203
+ y_0 = 0
204
+
205
+ Parameters
206
+ ----------
207
+ x : array_like
208
+ The input array, should be periodic.
209
+ _cache : dict, optional
210
+ Dictionary that contains the kernel used to do a convolution with.
211
+
212
+ Returns
213
+ -------
214
+ y : ndarray
215
+ The transformed input.
216
+
217
+ See Also
218
+ --------
219
+ scipy.signal.hilbert : Compute the analytic signal, using the Hilbert
220
+ transform.
221
+
222
+ Notes
223
+ -----
224
+ If ``sum(x, axis=0) == 0`` then ``hilbert(ihilbert(x)) == x``.
225
+
226
+ For even len(x), the Nyquist mode of x is taken zero.
227
+
228
+ The sign of the returned transform does not have a factor -1 that is more
229
+ often than not found in the definition of the Hilbert transform. Note also
230
+ that `scipy.signal.hilbert` does have an extra -1 factor compared to this
231
+ function.
232
+
233
+ """
234
+ if isinstance(_cache, threading.local):
235
+ if not hasattr(_cache, 'hilbert_cache'):
236
+ _cache.hilbert_cache = {}
237
+ _cache = _cache.hilbert_cache
238
+
239
+ tmp = asarray(x)
240
+ if iscomplexobj(tmp):
241
+ return hilbert(tmp.real, _cache) + 1j * hilbert(tmp.imag, _cache)
242
+ n = len(x)
243
+ omega = _cache.get(n)
244
+ if omega is None:
245
+ if len(_cache) > 20:
246
+ while _cache:
247
+ _cache.popitem()
248
+
249
+ def kernel(k):
250
+ if k > 0:
251
+ return 1.0
252
+ elif k < 0:
253
+ return -1.0
254
+ return 0.0
255
+ omega = convolve.init_convolution_kernel(n,kernel,d=1)
256
+ _cache[n] = omega
257
+ overwrite_x = _datacopied(tmp, x)
258
+ return convolve.convolve(tmp,omega,swap_real_imag=1,overwrite_x=overwrite_x)
259
+
260
+
261
+ def ihilbert(x, _cache=_cache):
262
+ """
263
+ Return inverse Hilbert transform of a periodic sequence x.
264
+
265
+ If ``x_j`` and ``y_j`` are Fourier coefficients of periodic functions x
266
+ and y, respectively, then::
267
+
268
+ y_j = -sqrt(-1)*sign(j) * x_j
269
+ y_0 = 0
270
+
271
+ """
272
+ if isinstance(_cache, threading.local):
273
+ if not hasattr(_cache, 'ihilbert_cache'):
274
+ _cache.ihilbert_cache = {}
275
+ _cache = _cache.ihilbert_cache
276
+ return -hilbert(x, _cache)
277
+
278
+
279
+ def cs_diff(x, a, b, period=None, _cache=_cache):
280
+ """
281
+ Return (a,b)-cosh/sinh pseudo-derivative of a periodic sequence.
282
+
283
+ If ``x_j`` and ``y_j`` are Fourier coefficients of periodic functions x
284
+ and y, respectively, then::
285
+
286
+ y_j = -sqrt(-1)*cosh(j*a*2*pi/period)/sinh(j*b*2*pi/period) * x_j
287
+ y_0 = 0
288
+
289
+ Parameters
290
+ ----------
291
+ x : array_like
292
+ The array to take the pseudo-derivative from.
293
+ a, b : float
294
+ Defines the parameters of the cosh/sinh pseudo-differential
295
+ operator.
296
+ period : float, optional
297
+ The period of the sequence. Default period is ``2*pi``.
298
+
299
+ Returns
300
+ -------
301
+ cs_diff : ndarray
302
+ Pseudo-derivative of periodic sequence `x`.
303
+
304
+ Notes
305
+ -----
306
+ For even len(`x`), the Nyquist mode of `x` is taken as zero.
307
+
308
+ """
309
+ if isinstance(_cache, threading.local):
310
+ if not hasattr(_cache, 'cs_diff_cache'):
311
+ _cache.cs_diff_cache = {}
312
+ _cache = _cache.cs_diff_cache
313
+
314
+ tmp = asarray(x)
315
+ if iscomplexobj(tmp):
316
+ return cs_diff(tmp.real, a, b, period, _cache) + \
317
+ 1j*cs_diff(tmp.imag, a, b, period, _cache)
318
+ if period is not None:
319
+ a = a*2*pi/period
320
+ b = b*2*pi/period
321
+ n = len(x)
322
+ omega = _cache.get((n,a,b))
323
+ if omega is None:
324
+ if len(_cache) > 20:
325
+ while _cache:
326
+ _cache.popitem()
327
+
328
+ def kernel(k,a=a,b=b):
329
+ if k:
330
+ return -cosh(a*k)/sinh(b*k)
331
+ return 0
332
+ omega = convolve.init_convolution_kernel(n,kernel,d=1)
333
+ _cache[(n,a,b)] = omega
334
+ overwrite_x = _datacopied(tmp, x)
335
+ return convolve.convolve(tmp,omega,swap_real_imag=1,overwrite_x=overwrite_x)
336
+
337
+
338
+ def sc_diff(x, a, b, period=None, _cache=_cache):
339
+ """
340
+ Return (a,b)-sinh/cosh pseudo-derivative of a periodic sequence x.
341
+
342
+ If x_j and y_j are Fourier coefficients of periodic functions x
343
+ and y, respectively, then::
344
+
345
+ y_j = sqrt(-1)*sinh(j*a*2*pi/period)/cosh(j*b*2*pi/period) * x_j
346
+ y_0 = 0
347
+
348
+ Parameters
349
+ ----------
350
+ x : array_like
351
+ Input array.
352
+ a,b : float
353
+ Defines the parameters of the sinh/cosh pseudo-differential
354
+ operator.
355
+ period : float, optional
356
+ The period of the sequence x. Default is 2*pi.
357
+
358
+ Notes
359
+ -----
360
+ ``sc_diff(cs_diff(x,a,b),b,a) == x``
361
+ For even ``len(x)``, the Nyquist mode of x is taken as zero.
362
+
363
+ """
364
+ if isinstance(_cache, threading.local):
365
+ if not hasattr(_cache, 'sc_diff_cache'):
366
+ _cache.sc_diff_cache = {}
367
+ _cache = _cache.sc_diff_cache
368
+
369
+ tmp = asarray(x)
370
+ if iscomplexobj(tmp):
371
+ return sc_diff(tmp.real, a, b, period, _cache) + \
372
+ 1j * sc_diff(tmp.imag, a, b, period, _cache)
373
+ if period is not None:
374
+ a = a*2*pi/period
375
+ b = b*2*pi/period
376
+ n = len(x)
377
+ omega = _cache.get((n,a,b))
378
+ if omega is None:
379
+ if len(_cache) > 20:
380
+ while _cache:
381
+ _cache.popitem()
382
+
383
+ def kernel(k,a=a,b=b):
384
+ if k:
385
+ return sinh(a*k)/cosh(b*k)
386
+ return 0
387
+ omega = convolve.init_convolution_kernel(n,kernel,d=1)
388
+ _cache[(n,a,b)] = omega
389
+ overwrite_x = _datacopied(tmp, x)
390
+ return convolve.convolve(tmp,omega,swap_real_imag=1,overwrite_x=overwrite_x)
391
+
392
+
393
+ def ss_diff(x, a, b, period=None, _cache=_cache):
394
+ """
395
+ Return (a,b)-sinh/sinh pseudo-derivative of a periodic sequence x.
396
+
397
+ If x_j and y_j are Fourier coefficients of periodic functions x
398
+ and y, respectively, then::
399
+
400
+ y_j = sinh(j*a*2*pi/period)/sinh(j*b*2*pi/period) * x_j
401
+ y_0 = a/b * x_0
402
+
403
+ Parameters
404
+ ----------
405
+ x : array_like
406
+ The array to take the pseudo-derivative from.
407
+ a,b
408
+ Defines the parameters of the sinh/sinh pseudo-differential
409
+ operator.
410
+ period : float, optional
411
+ The period of the sequence x. Default is ``2*pi``.
412
+
413
+ Notes
414
+ -----
415
+ ``ss_diff(ss_diff(x,a,b),b,a) == x``
416
+
417
+ """
418
+ if isinstance(_cache, threading.local):
419
+ if not hasattr(_cache, 'ss_diff_cache'):
420
+ _cache.ss_diff_cache = {}
421
+ _cache = _cache.ss_diff_cache
422
+
423
+ tmp = asarray(x)
424
+ if iscomplexobj(tmp):
425
+ return ss_diff(tmp.real, a, b, period, _cache) + \
426
+ 1j*ss_diff(tmp.imag, a, b, period, _cache)
427
+ if period is not None:
428
+ a = a*2*pi/period
429
+ b = b*2*pi/period
430
+ n = len(x)
431
+ omega = _cache.get((n,a,b))
432
+ if omega is None:
433
+ if len(_cache) > 20:
434
+ while _cache:
435
+ _cache.popitem()
436
+
437
+ def kernel(k,a=a,b=b):
438
+ if k:
439
+ return sinh(a*k)/sinh(b*k)
440
+ return float(a)/b
441
+ omega = convolve.init_convolution_kernel(n,kernel)
442
+ _cache[(n,a,b)] = omega
443
+ overwrite_x = _datacopied(tmp, x)
444
+ return convolve.convolve(tmp,omega,overwrite_x=overwrite_x)
445
+
446
+
447
+ def cc_diff(x, a, b, period=None, _cache=_cache):
448
+ """
449
+ Return (a,b)-cosh/cosh pseudo-derivative of a periodic sequence.
450
+
451
+ If x_j and y_j are Fourier coefficients of periodic functions x
452
+ and y, respectively, then::
453
+
454
+ y_j = cosh(j*a*2*pi/period)/cosh(j*b*2*pi/period) * x_j
455
+
456
+ Parameters
457
+ ----------
458
+ x : array_like
459
+ The array to take the pseudo-derivative from.
460
+ a,b : float
461
+ Defines the parameters of the sinh/sinh pseudo-differential
462
+ operator.
463
+ period : float, optional
464
+ The period of the sequence x. Default is ``2*pi``.
465
+
466
+ Returns
467
+ -------
468
+ cc_diff : ndarray
469
+ Pseudo-derivative of periodic sequence `x`.
470
+
471
+ Notes
472
+ -----
473
+ ``cc_diff(cc_diff(x,a,b),b,a) == x``
474
+
475
+ """
476
+ if isinstance(_cache, threading.local):
477
+ if not hasattr(_cache, 'cc_diff_cache'):
478
+ _cache.cc_diff_cache = {}
479
+ _cache = _cache.cc_diff_cache
480
+
481
+ tmp = asarray(x)
482
+ if iscomplexobj(tmp):
483
+ return cc_diff(tmp.real, a, b, period, _cache) + \
484
+ 1j * cc_diff(tmp.imag, a, b, period, _cache)
485
+ if period is not None:
486
+ a = a*2*pi/period
487
+ b = b*2*pi/period
488
+ n = len(x)
489
+ omega = _cache.get((n,a,b))
490
+ if omega is None:
491
+ if len(_cache) > 20:
492
+ while _cache:
493
+ _cache.popitem()
494
+
495
+ def kernel(k,a=a,b=b):
496
+ return cosh(a*k)/cosh(b*k)
497
+ omega = convolve.init_convolution_kernel(n,kernel)
498
+ _cache[(n,a,b)] = omega
499
+ overwrite_x = _datacopied(tmp, x)
500
+ return convolve.convolve(tmp,omega,overwrite_x=overwrite_x)
501
+
502
+
503
+ def shift(x, a, period=None, _cache=_cache):
504
+ """
505
+ Shift periodic sequence x by a: y(u) = x(u+a).
506
+
507
+ If x_j and y_j are Fourier coefficients of periodic functions x
508
+ and y, respectively, then::
509
+
510
+ y_j = exp(j*a*2*pi/period*sqrt(-1)) * x_f
511
+
512
+ Parameters
513
+ ----------
514
+ x : array_like
515
+ The array to take the pseudo-derivative from.
516
+ a : float
517
+ Defines the parameters of the sinh/sinh pseudo-differential
518
+ period : float, optional
519
+ The period of the sequences x and y. Default period is ``2*pi``.
520
+ """
521
+ if isinstance(_cache, threading.local):
522
+ if not hasattr(_cache, 'shift_cache'):
523
+ _cache.shift_cache = {}
524
+ _cache = _cache.shift_cache
525
+
526
+ tmp = asarray(x)
527
+ if iscomplexobj(tmp):
528
+ return shift(tmp.real, a, period, _cache) + 1j * shift(
529
+ tmp.imag, a, period, _cache)
530
+ if period is not None:
531
+ a = a*2*pi/period
532
+ n = len(x)
533
+ omega = _cache.get((n,a))
534
+ if omega is None:
535
+ if len(_cache) > 20:
536
+ while _cache:
537
+ _cache.popitem()
538
+
539
+ def kernel_real(k,a=a):
540
+ return cos(a*k)
541
+
542
+ def kernel_imag(k,a=a):
543
+ return sin(a*k)
544
+ omega_real = convolve.init_convolution_kernel(n,kernel_real,d=0,
545
+ zero_nyquist=0)
546
+ omega_imag = convolve.init_convolution_kernel(n,kernel_imag,d=1,
547
+ zero_nyquist=0)
548
+ _cache[(n,a)] = omega_real,omega_imag
549
+ else:
550
+ omega_real,omega_imag = omega
551
+ overwrite_x = _datacopied(tmp, x)
552
+ return convolve.convolve_z(tmp,omega_real,omega_imag,
553
+ overwrite_x=overwrite_x)
554
+
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/_realtransforms.py ADDED
@@ -0,0 +1,598 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """
2
+ Real spectrum transforms (DCT, DST, MDCT)
3
+ """
4
+
5
+ __all__ = ['dct', 'idct', 'dst', 'idst', 'dctn', 'idctn', 'dstn', 'idstn']
6
+
7
+ from scipy.fft import _pocketfft
8
+ from ._helper import _good_shape
9
+
10
+ _inverse_typemap = {1: 1, 2: 3, 3: 2, 4: 4}
11
+
12
+
13
+ def dctn(x, type=2, shape=None, axes=None, norm=None, overwrite_x=False):
14
+ """
15
+ Return multidimensional Discrete Cosine Transform along the specified axes.
16
+
17
+ Parameters
18
+ ----------
19
+ x : array_like
20
+ The input array.
21
+ type : {1, 2, 3, 4}, optional
22
+ Type of the DCT (see Notes). Default type is 2.
23
+ shape : int or array_like of ints or None, optional
24
+ The shape of the result. If both `shape` and `axes` (see below) are
25
+ None, `shape` is ``x.shape``; if `shape` is None but `axes` is
26
+ not None, then `shape` is ``numpy.take(x.shape, axes, axis=0)``.
27
+ If ``shape[i] > x.shape[i]``, the ith dimension is padded with zeros.
28
+ If ``shape[i] < x.shape[i]``, the ith dimension is truncated to
29
+ length ``shape[i]``.
30
+ If any element of `shape` is -1, the size of the corresponding
31
+ dimension of `x` is used.
32
+ axes : int or array_like of ints or None, optional
33
+ Axes along which the DCT is computed.
34
+ The default is over all axes.
35
+ norm : {None, 'ortho'}, optional
36
+ Normalization mode (see Notes). Default is None.
37
+ overwrite_x : bool, optional
38
+ If True, the contents of `x` can be destroyed; the default is False.
39
+
40
+ Returns
41
+ -------
42
+ y : ndarray of real
43
+ The transformed input array.
44
+
45
+ See Also
46
+ --------
47
+ idctn : Inverse multidimensional DCT
48
+
49
+ Notes
50
+ -----
51
+ For full details of the DCT types and normalization modes, as well as
52
+ references, see `dct`.
53
+
54
+ Examples
55
+ --------
56
+ >>> import numpy as np
57
+ >>> from scipy.fftpack import dctn, idctn
58
+ >>> rng = np.random.default_rng()
59
+ >>> y = rng.standard_normal((16, 16))
60
+ >>> np.allclose(y, idctn(dctn(y, norm='ortho'), norm='ortho'))
61
+ True
62
+
63
+ """
64
+ shape = _good_shape(x, shape, axes)
65
+ return _pocketfft.dctn(x, type, shape, axes, norm, overwrite_x)
66
+
67
+
68
+ def idctn(x, type=2, shape=None, axes=None, norm=None, overwrite_x=False):
69
+ """
70
+ Return multidimensional Discrete Cosine Transform along the specified axes.
71
+
72
+ Parameters
73
+ ----------
74
+ x : array_like
75
+ The input array.
76
+ type : {1, 2, 3, 4}, optional
77
+ Type of the DCT (see Notes). Default type is 2.
78
+ shape : int or array_like of ints or None, optional
79
+ The shape of the result. If both `shape` and `axes` (see below) are
80
+ None, `shape` is ``x.shape``; if `shape` is None but `axes` is
81
+ not None, then `shape` is ``numpy.take(x.shape, axes, axis=0)``.
82
+ If ``shape[i] > x.shape[i]``, the ith dimension is padded with zeros.
83
+ If ``shape[i] < x.shape[i]``, the ith dimension is truncated to
84
+ length ``shape[i]``.
85
+ If any element of `shape` is -1, the size of the corresponding
86
+ dimension of `x` is used.
87
+ axes : int or array_like of ints or None, optional
88
+ Axes along which the IDCT is computed.
89
+ The default is over all axes.
90
+ norm : {None, 'ortho'}, optional
91
+ Normalization mode (see Notes). Default is None.
92
+ overwrite_x : bool, optional
93
+ If True, the contents of `x` can be destroyed; the default is False.
94
+
95
+ Returns
96
+ -------
97
+ y : ndarray of real
98
+ The transformed input array.
99
+
100
+ See Also
101
+ --------
102
+ dctn : multidimensional DCT
103
+
104
+ Notes
105
+ -----
106
+ For full details of the IDCT types and normalization modes, as well as
107
+ references, see `idct`.
108
+
109
+ Examples
110
+ --------
111
+ >>> import numpy as np
112
+ >>> from scipy.fftpack import dctn, idctn
113
+ >>> rng = np.random.default_rng()
114
+ >>> y = rng.standard_normal((16, 16))
115
+ >>> np.allclose(y, idctn(dctn(y, norm='ortho'), norm='ortho'))
116
+ True
117
+
118
+ """
119
+ type = _inverse_typemap[type]
120
+ shape = _good_shape(x, shape, axes)
121
+ return _pocketfft.dctn(x, type, shape, axes, norm, overwrite_x)
122
+
123
+
124
+ def dstn(x, type=2, shape=None, axes=None, norm=None, overwrite_x=False):
125
+ """
126
+ Return multidimensional Discrete Sine Transform along the specified axes.
127
+
128
+ Parameters
129
+ ----------
130
+ x : array_like
131
+ The input array.
132
+ type : {1, 2, 3, 4}, optional
133
+ Type of the DST (see Notes). Default type is 2.
134
+ shape : int or array_like of ints or None, optional
135
+ The shape of the result. If both `shape` and `axes` (see below) are
136
+ None, `shape` is ``x.shape``; if `shape` is None but `axes` is
137
+ not None, then `shape` is ``numpy.take(x.shape, axes, axis=0)``.
138
+ If ``shape[i] > x.shape[i]``, the ith dimension is padded with zeros.
139
+ If ``shape[i] < x.shape[i]``, the ith dimension is truncated to
140
+ length ``shape[i]``.
141
+ If any element of `shape` is -1, the size of the corresponding
142
+ dimension of `x` is used.
143
+ axes : int or array_like of ints or None, optional
144
+ Axes along which the DCT is computed.
145
+ The default is over all axes.
146
+ norm : {None, 'ortho'}, optional
147
+ Normalization mode (see Notes). Default is None.
148
+ overwrite_x : bool, optional
149
+ If True, the contents of `x` can be destroyed; the default is False.
150
+
151
+ Returns
152
+ -------
153
+ y : ndarray of real
154
+ The transformed input array.
155
+
156
+ See Also
157
+ --------
158
+ idstn : Inverse multidimensional DST
159
+
160
+ Notes
161
+ -----
162
+ For full details of the DST types and normalization modes, as well as
163
+ references, see `dst`.
164
+
165
+ Examples
166
+ --------
167
+ >>> import numpy as np
168
+ >>> from scipy.fftpack import dstn, idstn
169
+ >>> rng = np.random.default_rng()
170
+ >>> y = rng.standard_normal((16, 16))
171
+ >>> np.allclose(y, idstn(dstn(y, norm='ortho'), norm='ortho'))
172
+ True
173
+
174
+ """
175
+ shape = _good_shape(x, shape, axes)
176
+ return _pocketfft.dstn(x, type, shape, axes, norm, overwrite_x)
177
+
178
+
179
+ def idstn(x, type=2, shape=None, axes=None, norm=None, overwrite_x=False):
180
+ """
181
+ Return multidimensional Discrete Sine Transform along the specified axes.
182
+
183
+ Parameters
184
+ ----------
185
+ x : array_like
186
+ The input array.
187
+ type : {1, 2, 3, 4}, optional
188
+ Type of the DST (see Notes). Default type is 2.
189
+ shape : int or array_like of ints or None, optional
190
+ The shape of the result. If both `shape` and `axes` (see below) are
191
+ None, `shape` is ``x.shape``; if `shape` is None but `axes` is
192
+ not None, then `shape` is ``numpy.take(x.shape, axes, axis=0)``.
193
+ If ``shape[i] > x.shape[i]``, the ith dimension is padded with zeros.
194
+ If ``shape[i] < x.shape[i]``, the ith dimension is truncated to
195
+ length ``shape[i]``.
196
+ If any element of `shape` is -1, the size of the corresponding
197
+ dimension of `x` is used.
198
+ axes : int or array_like of ints or None, optional
199
+ Axes along which the IDST is computed.
200
+ The default is over all axes.
201
+ norm : {None, 'ortho'}, optional
202
+ Normalization mode (see Notes). Default is None.
203
+ overwrite_x : bool, optional
204
+ If True, the contents of `x` can be destroyed; the default is False.
205
+
206
+ Returns
207
+ -------
208
+ y : ndarray of real
209
+ The transformed input array.
210
+
211
+ See Also
212
+ --------
213
+ dstn : multidimensional DST
214
+
215
+ Notes
216
+ -----
217
+ For full details of the IDST types and normalization modes, as well as
218
+ references, see `idst`.
219
+
220
+ Examples
221
+ --------
222
+ >>> import numpy as np
223
+ >>> from scipy.fftpack import dstn, idstn
224
+ >>> rng = np.random.default_rng()
225
+ >>> y = rng.standard_normal((16, 16))
226
+ >>> np.allclose(y, idstn(dstn(y, norm='ortho'), norm='ortho'))
227
+ True
228
+
229
+ """
230
+ type = _inverse_typemap[type]
231
+ shape = _good_shape(x, shape, axes)
232
+ return _pocketfft.dstn(x, type, shape, axes, norm, overwrite_x)
233
+
234
+
235
+ def dct(x, type=2, n=None, axis=-1, norm=None, overwrite_x=False):
236
+ r"""
237
+ Return the Discrete Cosine Transform of arbitrary type sequence x.
238
+
239
+ Parameters
240
+ ----------
241
+ x : array_like
242
+ The input array.
243
+ type : {1, 2, 3, 4}, optional
244
+ Type of the DCT (see Notes). Default type is 2.
245
+ n : int, optional
246
+ Length of the transform. If ``n < x.shape[axis]``, `x` is
247
+ truncated. If ``n > x.shape[axis]``, `x` is zero-padded. The
248
+ default results in ``n = x.shape[axis]``.
249
+ axis : int, optional
250
+ Axis along which the dct is computed; the default is over the
251
+ last axis (i.e., ``axis=-1``).
252
+ norm : {None, 'ortho'}, optional
253
+ Normalization mode (see Notes). Default is None.
254
+ overwrite_x : bool, optional
255
+ If True, the contents of `x` can be destroyed; the default is False.
256
+
257
+ Returns
258
+ -------
259
+ y : ndarray of real
260
+ The transformed input array.
261
+
262
+ See Also
263
+ --------
264
+ idct : Inverse DCT
265
+
266
+ Notes
267
+ -----
268
+ For a single dimension array ``x``, ``dct(x, norm='ortho')`` is equal to
269
+ MATLAB ``dct(x)``.
270
+
271
+ There are, theoretically, 8 types of the DCT, only the first 4 types are
272
+ implemented in scipy. 'The' DCT generally refers to DCT type 2, and 'the'
273
+ Inverse DCT generally refers to DCT type 3.
274
+
275
+ **Type I**
276
+
277
+ There are several definitions of the DCT-I; we use the following
278
+ (for ``norm=None``)
279
+
280
+ .. math::
281
+
282
+ y_k = x_0 + (-1)^k x_{N-1} + 2 \sum_{n=1}^{N-2} x_n \cos\left(
283
+ \frac{\pi k n}{N-1} \right)
284
+
285
+ If ``norm='ortho'``, ``x[0]`` and ``x[N-1]`` are multiplied by a scaling
286
+ factor of :math:`\sqrt{2}`, and ``y[k]`` is multiplied by a scaling factor
287
+ ``f``
288
+
289
+ .. math::
290
+
291
+ f = \begin{cases}
292
+ \frac{1}{2}\sqrt{\frac{1}{N-1}} & \text{if }k=0\text{ or }N-1, \\
293
+ \frac{1}{2}\sqrt{\frac{2}{N-1}} & \text{otherwise} \end{cases}
294
+
295
+ .. versionadded:: 1.2.0
296
+ Orthonormalization in DCT-I.
297
+
298
+ .. note::
299
+ The DCT-I is only supported for input size > 1.
300
+
301
+ **Type II**
302
+
303
+ There are several definitions of the DCT-II; we use the following
304
+ (for ``norm=None``)
305
+
306
+ .. math::
307
+
308
+ y_k = 2 \sum_{n=0}^{N-1} x_n \cos\left(\frac{\pi k(2n+1)}{2N} \right)
309
+
310
+ If ``norm='ortho'``, ``y[k]`` is multiplied by a scaling factor ``f``
311
+
312
+ .. math::
313
+ f = \begin{cases}
314
+ \sqrt{\frac{1}{4N}} & \text{if }k=0, \\
315
+ \sqrt{\frac{1}{2N}} & \text{otherwise} \end{cases}
316
+
317
+ which makes the corresponding matrix of coefficients orthonormal
318
+ (``O @ O.T = np.eye(N)``).
319
+
320
+ **Type III**
321
+
322
+ There are several definitions, we use the following (for ``norm=None``)
323
+
324
+ .. math::
325
+
326
+ y_k = x_0 + 2 \sum_{n=1}^{N-1} x_n \cos\left(\frac{\pi(2k+1)n}{2N}\right)
327
+
328
+ or, for ``norm='ortho'``
329
+
330
+ .. math::
331
+
332
+ y_k = \frac{x_0}{\sqrt{N}} + \sqrt{\frac{2}{N}} \sum_{n=1}^{N-1} x_n
333
+ \cos\left(\frac{\pi(2k+1)n}{2N}\right)
334
+
335
+ The (unnormalized) DCT-III is the inverse of the (unnormalized) DCT-II, up
336
+ to a factor ``2N``. The orthonormalized DCT-III is exactly the inverse of
337
+ the orthonormalized DCT-II.
338
+
339
+ **Type IV**
340
+
341
+ There are several definitions of the DCT-IV; we use the following
342
+ (for ``norm=None``)
343
+
344
+ .. math::
345
+
346
+ y_k = 2 \sum_{n=0}^{N-1} x_n \cos\left(\frac{\pi(2k+1)(2n+1)}{4N} \right)
347
+
348
+ If ``norm='ortho'``, ``y[k]`` is multiplied by a scaling factor ``f``
349
+
350
+ .. math::
351
+
352
+ f = \frac{1}{\sqrt{2N}}
353
+
354
+ .. versionadded:: 1.2.0
355
+ Support for DCT-IV.
356
+
357
+ References
358
+ ----------
359
+ .. [1] 'A Fast Cosine Transform in One and Two Dimensions', by J.
360
+ Makhoul, `IEEE Transactions on acoustics, speech and signal
361
+ processing` vol. 28(1), pp. 27-34,
362
+ :doi:`10.1109/TASSP.1980.1163351` (1980).
363
+ .. [2] Wikipedia, "Discrete cosine transform",
364
+ https://en.wikipedia.org/wiki/Discrete_cosine_transform
365
+
366
+ Examples
367
+ --------
368
+ The Type 1 DCT is equivalent to the FFT (though faster) for real,
369
+ even-symmetrical inputs. The output is also real and even-symmetrical.
370
+ Half of the FFT input is used to generate half of the FFT output:
371
+
372
+ >>> from scipy.fftpack import fft, dct
373
+ >>> import numpy as np
374
+ >>> fft(np.array([4., 3., 5., 10., 5., 3.])).real
375
+ array([ 30., -8., 6., -2., 6., -8.])
376
+ >>> dct(np.array([4., 3., 5., 10.]), 1)
377
+ array([ 30., -8., 6., -2.])
378
+
379
+ """
380
+ return _pocketfft.dct(x, type, n, axis, norm, overwrite_x)
381
+
382
+
383
+ def idct(x, type=2, n=None, axis=-1, norm=None, overwrite_x=False):
384
+ """
385
+ Return the Inverse Discrete Cosine Transform of an arbitrary type sequence.
386
+
387
+ Parameters
388
+ ----------
389
+ x : array_like
390
+ The input array.
391
+ type : {1, 2, 3, 4}, optional
392
+ Type of the DCT (see Notes). Default type is 2.
393
+ n : int, optional
394
+ Length of the transform. If ``n < x.shape[axis]``, `x` is
395
+ truncated. If ``n > x.shape[axis]``, `x` is zero-padded. The
396
+ default results in ``n = x.shape[axis]``.
397
+ axis : int, optional
398
+ Axis along which the idct is computed; the default is over the
399
+ last axis (i.e., ``axis=-1``).
400
+ norm : {None, 'ortho'}, optional
401
+ Normalization mode (see Notes). Default is None.
402
+ overwrite_x : bool, optional
403
+ If True, the contents of `x` can be destroyed; the default is False.
404
+
405
+ Returns
406
+ -------
407
+ idct : ndarray of real
408
+ The transformed input array.
409
+
410
+ See Also
411
+ --------
412
+ dct : Forward DCT
413
+
414
+ Notes
415
+ -----
416
+ For a single dimension array `x`, ``idct(x, norm='ortho')`` is equal to
417
+ MATLAB ``idct(x)``.
418
+
419
+ 'The' IDCT is the IDCT of type 2, which is the same as DCT of type 3.
420
+
421
+ IDCT of type 1 is the DCT of type 1, IDCT of type 2 is the DCT of type
422
+ 3, and IDCT of type 3 is the DCT of type 2. IDCT of type 4 is the DCT
423
+ of type 4. For the definition of these types, see `dct`.
424
+
425
+ Examples
426
+ --------
427
+ The Type 1 DCT is equivalent to the DFT for real, even-symmetrical
428
+ inputs. The output is also real and even-symmetrical. Half of the IFFT
429
+ input is used to generate half of the IFFT output:
430
+
431
+ >>> from scipy.fftpack import ifft, idct
432
+ >>> import numpy as np
433
+ >>> ifft(np.array([ 30., -8., 6., -2., 6., -8.])).real
434
+ array([ 4., 3., 5., 10., 5., 3.])
435
+ >>> idct(np.array([ 30., -8., 6., -2.]), 1) / 6
436
+ array([ 4., 3., 5., 10.])
437
+
438
+ """
439
+ type = _inverse_typemap[type]
440
+ return _pocketfft.dct(x, type, n, axis, norm, overwrite_x)
441
+
442
+
443
+ def dst(x, type=2, n=None, axis=-1, norm=None, overwrite_x=False):
444
+ r"""
445
+ Return the Discrete Sine Transform of arbitrary type sequence x.
446
+
447
+ Parameters
448
+ ----------
449
+ x : array_like
450
+ The input array.
451
+ type : {1, 2, 3, 4}, optional
452
+ Type of the DST (see Notes). Default type is 2.
453
+ n : int, optional
454
+ Length of the transform. If ``n < x.shape[axis]``, `x` is
455
+ truncated. If ``n > x.shape[axis]``, `x` is zero-padded. The
456
+ default results in ``n = x.shape[axis]``.
457
+ axis : int, optional
458
+ Axis along which the dst is computed; the default is over the
459
+ last axis (i.e., ``axis=-1``).
460
+ norm : {None, 'ortho'}, optional
461
+ Normalization mode (see Notes). Default is None.
462
+ overwrite_x : bool, optional
463
+ If True, the contents of `x` can be destroyed; the default is False.
464
+
465
+ Returns
466
+ -------
467
+ dst : ndarray of reals
468
+ The transformed input array.
469
+
470
+ See Also
471
+ --------
472
+ idst : Inverse DST
473
+
474
+ Notes
475
+ -----
476
+ For a single dimension array ``x``.
477
+
478
+ There are, theoretically, 8 types of the DST for different combinations of
479
+ even/odd boundary conditions and boundary off sets [1]_, only the first
480
+ 4 types are implemented in scipy.
481
+
482
+ **Type I**
483
+
484
+ There are several definitions of the DST-I; we use the following
485
+ for ``norm=None``. DST-I assumes the input is odd around `n=-1` and `n=N`.
486
+
487
+ .. math::
488
+
489
+ y_k = 2 \sum_{n=0}^{N-1} x_n \sin\left(\frac{\pi(k+1)(n+1)}{N+1}\right)
490
+
491
+ Note that the DST-I is only supported for input size > 1.
492
+ The (unnormalized) DST-I is its own inverse, up to a factor ``2(N+1)``.
493
+ The orthonormalized DST-I is exactly its own inverse.
494
+
495
+ **Type II**
496
+
497
+ There are several definitions of the DST-II; we use the following for
498
+ ``norm=None``. DST-II assumes the input is odd around `n=-1/2` and
499
+ `n=N-1/2`; the output is odd around :math:`k=-1` and even around `k=N-1`
500
+
501
+ .. math::
502
+
503
+ y_k = 2 \sum_{n=0}^{N-1} x_n \sin\left(\frac{\pi(k+1)(2n+1)}{2N}\right)
504
+
505
+ if ``norm='ortho'``, ``y[k]`` is multiplied by a scaling factor ``f``
506
+
507
+ .. math::
508
+
509
+ f = \begin{cases}
510
+ \sqrt{\frac{1}{4N}} & \text{if }k = 0, \\
511
+ \sqrt{\frac{1}{2N}} & \text{otherwise} \end{cases}
512
+
513
+ **Type III**
514
+
515
+ There are several definitions of the DST-III, we use the following (for
516
+ ``norm=None``). DST-III assumes the input is odd around `n=-1` and even
517
+ around `n=N-1`
518
+
519
+ .. math::
520
+
521
+ y_k = (-1)^k x_{N-1} + 2 \sum_{n=0}^{N-2} x_n \sin\left(
522
+ \frac{\pi(2k+1)(n+1)}{2N}\right)
523
+
524
+ The (unnormalized) DST-III is the inverse of the (unnormalized) DST-II, up
525
+ to a factor ``2N``. The orthonormalized DST-III is exactly the inverse of the
526
+ orthonormalized DST-II.
527
+
528
+ .. versionadded:: 0.11.0
529
+
530
+ **Type IV**
531
+
532
+ There are several definitions of the DST-IV, we use the following (for
533
+ ``norm=None``). DST-IV assumes the input is odd around `n=-0.5` and even
534
+ around `n=N-0.5`
535
+
536
+ .. math::
537
+
538
+ y_k = 2 \sum_{n=0}^{N-1} x_n \sin\left(\frac{\pi(2k+1)(2n+1)}{4N}\right)
539
+
540
+ The (unnormalized) DST-IV is its own inverse, up to a factor ``2N``. The
541
+ orthonormalized DST-IV is exactly its own inverse.
542
+
543
+ .. versionadded:: 1.2.0
544
+ Support for DST-IV.
545
+
546
+ References
547
+ ----------
548
+ .. [1] Wikipedia, "Discrete sine transform",
549
+ https://en.wikipedia.org/wiki/Discrete_sine_transform
550
+
551
+ """
552
+ return _pocketfft.dst(x, type, n, axis, norm, overwrite_x)
553
+
554
+
555
+ def idst(x, type=2, n=None, axis=-1, norm=None, overwrite_x=False):
556
+ """
557
+ Return the Inverse Discrete Sine Transform of an arbitrary type sequence.
558
+
559
+ Parameters
560
+ ----------
561
+ x : array_like
562
+ The input array.
563
+ type : {1, 2, 3, 4}, optional
564
+ Type of the DST (see Notes). Default type is 2.
565
+ n : int, optional
566
+ Length of the transform. If ``n < x.shape[axis]``, `x` is
567
+ truncated. If ``n > x.shape[axis]``, `x` is zero-padded. The
568
+ default results in ``n = x.shape[axis]``.
569
+ axis : int, optional
570
+ Axis along which the idst is computed; the default is over the
571
+ last axis (i.e., ``axis=-1``).
572
+ norm : {None, 'ortho'}, optional
573
+ Normalization mode (see Notes). Default is None.
574
+ overwrite_x : bool, optional
575
+ If True, the contents of `x` can be destroyed; the default is False.
576
+
577
+ Returns
578
+ -------
579
+ idst : ndarray of real
580
+ The transformed input array.
581
+
582
+ See Also
583
+ --------
584
+ dst : Forward DST
585
+
586
+ Notes
587
+ -----
588
+ 'The' IDST is the IDST of type 2, which is the same as DST of type 3.
589
+
590
+ IDST of type 1 is the DST of type 1, IDST of type 2 is the DST of type
591
+ 3, and IDST of type 3 is the DST of type 2. For the definition of these
592
+ types, see `dst`.
593
+
594
+ .. versionadded:: 0.11.0
595
+
596
+ """
597
+ type = _inverse_typemap[type]
598
+ return _pocketfft.dst(x, type, n, axis, norm, overwrite_x)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/basic.py ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file is not meant for public use and will be removed in SciPy v2.0.0.
2
+ # Use the `scipy.fftpack` namespace for importing the functions
3
+ # included below.
4
+
5
+ from scipy._lib.deprecation import _sub_module_deprecation
6
+
7
+ __all__ = [ # noqa: F822
8
+ 'fft','ifft','fftn','ifftn','rfft','irfft',
9
+ 'fft2','ifft2'
10
+ ]
11
+
12
+
13
+ def __dir__():
14
+ return __all__
15
+
16
+
17
+ def __getattr__(name):
18
+ return _sub_module_deprecation(sub_package="fftpack", module="basic",
19
+ private_modules=["_basic"], all=__all__,
20
+ attribute=name)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/helper.py ADDED
@@ -0,0 +1,19 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file is not meant for public use and will be removed in SciPy v2.0.0.
2
+ # Use the `scipy.fftpack` namespace for importing the functions
3
+ # included below.
4
+
5
+ from scipy._lib.deprecation import _sub_module_deprecation
6
+
7
+ __all__ = [ # noqa: F822
8
+ 'fftshift', 'ifftshift', 'fftfreq', 'rfftfreq', 'next_fast_len'
9
+ ]
10
+
11
+
12
+ def __dir__():
13
+ return __all__
14
+
15
+
16
+ def __getattr__(name):
17
+ return _sub_module_deprecation(sub_package="fftpack", module="helper",
18
+ private_modules=["_helper"], all=__all__,
19
+ attribute=name)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/pseudo_diffs.py ADDED
@@ -0,0 +1,22 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file is not meant for public use and will be removed in SciPy v2.0.0.
2
+ # Use the `scipy.fftpack` namespace for importing the functions
3
+ # included below.
4
+
5
+ from scipy._lib.deprecation import _sub_module_deprecation
6
+
7
+ __all__ = [ # noqa: F822
8
+ 'diff',
9
+ 'tilbert', 'itilbert', 'hilbert', 'ihilbert',
10
+ 'cs_diff', 'cc_diff', 'sc_diff', 'ss_diff',
11
+ 'shift', 'convolve'
12
+ ]
13
+
14
+
15
+ def __dir__():
16
+ return __all__
17
+
18
+
19
+ def __getattr__(name):
20
+ return _sub_module_deprecation(sub_package="fftpack", module="pseudo_diffs",
21
+ private_modules=["_pseudo_diffs"], all=__all__,
22
+ attribute=name)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/fftpack/realtransforms.py ADDED
@@ -0,0 +1,19 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file is not meant for public use and will be removed in SciPy v2.0.0.
2
+ # Use the `scipy.fftpack` namespace for importing the functions
3
+ # included below.
4
+
5
+ from scipy._lib.deprecation import _sub_module_deprecation
6
+
7
+ __all__ = [ # noqa: F822
8
+ 'dct', 'idct', 'dst', 'idst', 'dctn', 'idctn', 'dstn', 'idstn'
9
+ ]
10
+
11
+
12
+ def __dir__():
13
+ return __all__
14
+
15
+
16
+ def __getattr__(name):
17
+ return _sub_module_deprecation(sub_package="fftpack", module="realtransforms",
18
+ private_modules=["_realtransforms"], all=__all__,
19
+ attribute=name)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_bsplines.py ADDED
@@ -0,0 +1,2614 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ import operator
2
+ from math import prod
3
+ from types import GenericAlias
4
+
5
+ import numpy as np
6
+ from scipy._lib._util import normalize_axis_index
7
+ from scipy.linalg import (get_lapack_funcs, LinAlgError,
8
+ cholesky_banded, cho_solve_banded,
9
+ solve, solve_banded)
10
+ from scipy.optimize import minimize_scalar
11
+ from . import _dierckx
12
+ from . import _fitpack_impl
13
+ from scipy.sparse import csr_array
14
+ from scipy.special import poch
15
+ from itertools import combinations
16
+
17
+ from scipy._lib._array_api import array_namespace, concat_1d, xp_capabilities
18
+
19
+ __all__ = ["BSpline", "make_interp_spline", "make_lsq_spline",
20
+ "make_smoothing_spline"]
21
+
22
+
23
+ def _get_dtype(dtype):
24
+ """Return np.complex128 for complex dtypes, np.float64 otherwise."""
25
+ if np.issubdtype(dtype, np.complexfloating):
26
+ return np.complex128
27
+ else:
28
+ return np.float64
29
+
30
+
31
+ def _as_float_array(x, check_finite=False):
32
+ """Convert the input into a C contiguous float array.
33
+
34
+ NB: Upcasts half- and single-precision floats to double precision.
35
+ """
36
+ x = np.ascontiguousarray(x)
37
+ dtyp = _get_dtype(x.dtype)
38
+ x = x.astype(dtyp, copy=False)
39
+ if check_finite and not np.isfinite(x).all():
40
+ raise ValueError("Array must not contain infs or nans.")
41
+ return x
42
+
43
+
44
+ def _dual_poly(j, k, t, y):
45
+ """
46
+ Dual polynomial of the B-spline B_{j,k,t} -
47
+ polynomial which is associated with B_{j,k,t}:
48
+ $p_{j,k}(y) = (y - t_{j+1})(y - t_{j+2})...(y - t_{j+k})$
49
+ """
50
+ if k == 0:
51
+ return 1
52
+ return np.prod([(y - t[j + i]) for i in range(1, k + 1)])
53
+
54
+
55
+ def _diff_dual_poly(j, k, y, d, t):
56
+ """
57
+ d-th derivative of the dual polynomial $p_{j,k}(y)$
58
+ """
59
+ if d == 0:
60
+ return _dual_poly(j, k, t, y)
61
+ if d == k:
62
+ return poch(1, k)
63
+ comb = list(combinations(range(j + 1, j + k + 1), d))
64
+ res = 0
65
+ for i in range(len(comb) * len(comb[0])):
66
+ res += np.prod([(y - t[j + p]) for p in range(1, k + 1)
67
+ if (j + p) not in comb[i//d]])
68
+ return res
69
+
70
+ @xp_capabilities(
71
+ cpu_only=True, jax_jit=False,
72
+ skip_backends=[
73
+ ("dask.array",
74
+ "https://github.com/data-apis/array-api-extra/issues/488")
75
+ ]
76
+ )
77
+ class BSpline:
78
+ r"""Univariate spline in the B-spline basis.
79
+
80
+ .. math::
81
+
82
+ S(x) = \sum_{j=0}^{n-1} c_j B_{j, k; t}(x)
83
+
84
+ where :math:`B_{j, k; t}` are B-spline basis functions of degree `k`
85
+ and knots `t`.
86
+
87
+ Parameters
88
+ ----------
89
+ t : ndarray, shape (n+k+1,)
90
+ knots
91
+ c : ndarray, shape (>=n, ...)
92
+ spline coefficients
93
+ k : int
94
+ B-spline degree
95
+ extrapolate : bool or 'periodic', optional
96
+ whether to extrapolate beyond the base interval, ``t[k] .. t[n]``,
97
+ or to return nans.
98
+ If True, extrapolates the first and last polynomial pieces of b-spline
99
+ functions active on the base interval.
100
+ If 'periodic', periodic extrapolation is used.
101
+ Default is True.
102
+ axis : int, optional
103
+ Interpolation axis. Default is zero.
104
+
105
+ Attributes
106
+ ----------
107
+ t : ndarray
108
+ knot vector
109
+ c : ndarray
110
+ spline coefficients
111
+ k : int
112
+ spline degree
113
+ extrapolate : bool
114
+ If True, extrapolates the first and last polynomial pieces of b-spline
115
+ functions active on the base interval.
116
+ axis : int
117
+ Interpolation axis.
118
+ tck : tuple
119
+ A read-only equivalent of ``(self.t, self.c, self.k)``
120
+
121
+ Methods
122
+ -------
123
+ __call__
124
+ basis_element
125
+ derivative
126
+ antiderivative
127
+ integrate
128
+ insert_knot
129
+ construct_fast
130
+ design_matrix
131
+ from_power_basis
132
+
133
+ Notes
134
+ -----
135
+ B-spline basis elements are defined via
136
+
137
+ .. math::
138
+
139
+ B_{i, 0}(x) = 1, \textrm{if $t_i \le x < t_{i+1}$, otherwise $0$,}
140
+
141
+ B_{i, k}(x) = \frac{x - t_i}{t_{i+k} - t_i} B_{i, k-1}(x)
142
+ + \frac{t_{i+k+1} - x}{t_{i+k+1} - t_{i+1}} B_{i+1, k-1}(x)
143
+
144
+ **Implementation details**
145
+
146
+ - At least ``k+1`` coefficients are required for a spline of degree `k`,
147
+ so that ``n >= k+1``. Additional coefficients, ``c[j]`` with
148
+ ``j > n``, are ignored.
149
+
150
+ - B-spline basis elements of degree `k` form a partition of unity on the
151
+ *base interval*, ``t[k] <= x <= t[n]``.
152
+
153
+
154
+ Examples
155
+ --------
156
+ Translating the recursive definition of B-splines into Python code, we have:
157
+
158
+ >>> def B(x, k, i, t):
159
+ ... if k == 0:
160
+ ... return 1.0 if t[i] <= x < t[i+1] else 0.0
161
+ ... if t[i+k] == t[i]:
162
+ ... c1 = 0.0
163
+ ... else:
164
+ ... c1 = (x - t[i])/(t[i+k] - t[i]) * B(x, k-1, i, t)
165
+ ... if t[i+k+1] == t[i+1]:
166
+ ... c2 = 0.0
167
+ ... else:
168
+ ... c2 = (t[i+k+1] - x)/(t[i+k+1] - t[i+1]) * B(x, k-1, i+1, t)
169
+ ... return c1 + c2
170
+
171
+ >>> def bspline(x, t, c, k):
172
+ ... n = len(t) - k - 1
173
+ ... assert (n >= k+1) and (len(c) >= n)
174
+ ... return sum(c[i] * B(x, k, i, t) for i in range(n))
175
+
176
+ Note that this is an inefficient (if straightforward) way to
177
+ evaluate B-splines --- this spline class does it in an equivalent,
178
+ but much more efficient way.
179
+
180
+ Here we construct a quadratic spline function on the base interval
181
+ ``2 <= x <= 4`` and compare with the naive way of evaluating the spline:
182
+
183
+ >>> from scipy.interpolate import BSpline
184
+ >>> k = 2
185
+ >>> t = [0, 1, 2, 3, 4, 5, 6]
186
+ >>> c = [-1, 2, 0, -1]
187
+ >>> spl = BSpline(t, c, k)
188
+ >>> spl(2.5)
189
+ array(1.375)
190
+ >>> bspline(2.5, t, c, k)
191
+ 1.375
192
+
193
+ Note that outside of the base interval results differ. This is because
194
+ `BSpline` extrapolates the first and last polynomial pieces of B-spline
195
+ functions active on the base interval.
196
+
197
+ >>> import matplotlib.pyplot as plt
198
+ >>> import numpy as np
199
+ >>> fig, ax = plt.subplots()
200
+ >>> xx = np.linspace(1.5, 4.5, 50)
201
+ >>> ax.plot(xx, [bspline(x, t, c ,k) for x in xx], 'r-', lw=3, label='naive')
202
+ >>> ax.plot(xx, spl(xx), 'b-', lw=4, alpha=0.7, label='BSpline')
203
+ >>> ax.grid(True)
204
+ >>> ax.legend(loc='best')
205
+ >>> plt.show()
206
+
207
+
208
+ References
209
+ ----------
210
+ .. [1] Tom Lyche and Knut Morken, Spline methods,
211
+ http://www.uio.no/studier/emner/matnat/ifi/INF-MAT5340/v05/undervisningsmateriale/
212
+ .. [2] Carl de Boor, A practical guide to splines, Springer, 2001.
213
+
214
+ """
215
+
216
+ # generic type compatibility with scipy-stubs
217
+ __class_getitem__ = classmethod(GenericAlias)
218
+
219
+
220
+ def __init__(self, t, c, k, extrapolate=True, axis=0):
221
+ super().__init__()
222
+
223
+ self._asarray = array_namespace(c, t).asarray
224
+
225
+ self.k = operator.index(k)
226
+ self._c = np.asarray(c)
227
+ self._t = np.ascontiguousarray(t, dtype=np.float64)
228
+
229
+ if extrapolate == 'periodic':
230
+ self.extrapolate = extrapolate
231
+ else:
232
+ self.extrapolate = bool(extrapolate)
233
+
234
+ n = self._t.shape[0] - self.k - 1
235
+
236
+ axis = normalize_axis_index(axis, self._c.ndim)
237
+
238
+ # Note that the normalized axis is stored in the object.
239
+ self.axis = axis
240
+ if axis != 0:
241
+ # roll the interpolation axis to be the first one in self.c
242
+ # More specifically, the target shape for self.c is (n, ...),
243
+ # and axis !=0 means that we have c.shape (..., n, ...)
244
+ # ^
245
+ # axis
246
+ self._c = np.moveaxis(self._c, axis, 0)
247
+
248
+ if k < 0:
249
+ raise ValueError("Spline order cannot be negative.")
250
+ if self._t.ndim != 1:
251
+ raise ValueError("Knot vector must be one-dimensional.")
252
+ if n < self.k + 1:
253
+ raise ValueError(f"Need at least {2*k + 2} knots for degree {k}")
254
+ if (np.diff(self._t) < 0).any():
255
+ raise ValueError("Knots must be in a non-decreasing order.")
256
+ if len(np.unique(self._t[k:n+1])) < 2:
257
+ raise ValueError("Need at least two internal knots.")
258
+ if not np.isfinite(self._t).all():
259
+ raise ValueError("Knots should not have nans or infs.")
260
+ if self._c.ndim < 1:
261
+ raise ValueError("Coefficients must be at least 1-dimensional.")
262
+ if self._c.shape[0] < n:
263
+ raise ValueError("Knots, coefficients and degree are inconsistent.")
264
+
265
+ dt = _get_dtype(self._c.dtype)
266
+
267
+ self._c = np.ascontiguousarray(self._c, dtype=dt)
268
+
269
+ @classmethod
270
+ def construct_fast(cls, t, c, k, extrapolate=True, axis=0):
271
+ """Construct a spline without making checks.
272
+
273
+ Accepts same parameters as the regular constructor. Input arrays
274
+ `t` and `c` must of correct shape and dtype.
275
+ """
276
+ self = object.__new__(cls)
277
+ self._t, self._c, self.k = np.asarray(t), np.asarray(c), k
278
+ self.extrapolate = extrapolate
279
+ self.axis = axis
280
+ self._asarray = array_namespace(t, c).asarray
281
+ return self
282
+
283
+ @property
284
+ def tck(self):
285
+ """Equivalent to ``(self.t, self.c, self.k)`` (read-only).
286
+ """
287
+ return self.t, self.c, self.k
288
+
289
+ # Under the hood, self._c and self._t are always saved as numpy array
290
+ # because they are used in a C extension expecting numpy arrays.
291
+ @property
292
+ def t(self):
293
+ return self._asarray(self._t)
294
+
295
+ @t.setter
296
+ def t(self, t):
297
+ self._t = np.asarray(t)
298
+
299
+ @property
300
+ def c(self):
301
+ return self._asarray(self._c)
302
+
303
+ @c.setter
304
+ def c(self, c):
305
+ self._c = np.asarray(c)
306
+
307
+ @classmethod
308
+ def basis_element(cls, t, extrapolate=True):
309
+ """Return a B-spline basis element ``B(x | t[0], ..., t[k+1])``.
310
+
311
+ Parameters
312
+ ----------
313
+ t : ndarray, shape (k+2,)
314
+ internal knots
315
+ extrapolate : bool or 'periodic', optional
316
+ whether to extrapolate beyond the base interval, ``t[0] .. t[k+1]``,
317
+ or to return nans.
318
+ If 'periodic', periodic extrapolation is used.
319
+ Default is True.
320
+
321
+ Returns
322
+ -------
323
+ basis_element : callable
324
+ A callable representing a B-spline basis element for the knot
325
+ vector `t`.
326
+
327
+ Notes
328
+ -----
329
+ The degree of the B-spline, `k`, is inferred from the length of `t` as
330
+ ``len(t)-2``. The knot vector is constructed by appending and prepending
331
+ ``k+1`` elements to internal knots `t`.
332
+
333
+ Examples
334
+ --------
335
+ Construct a cubic B-spline:
336
+
337
+ >>> import numpy as np
338
+ >>> from scipy.interpolate import BSpline
339
+ >>> b = BSpline.basis_element([0, 1, 2, 3, 4])
340
+ >>> k = b.k
341
+ >>> b.t[k:-k]
342
+ array([ 0., 1., 2., 3., 4.])
343
+ >>> k
344
+ 3
345
+
346
+ Construct a quadratic B-spline on ``[0, 1, 1, 2]``, and compare
347
+ to its explicit form:
348
+
349
+ >>> t = [0, 1, 1, 2]
350
+ >>> b = BSpline.basis_element(t)
351
+ >>> def f(x):
352
+ ... return np.where(x < 1, x*x, (2. - x)**2)
353
+
354
+ >>> import matplotlib.pyplot as plt
355
+ >>> fig, ax = plt.subplots()
356
+ >>> x = np.linspace(0, 2, 51)
357
+ >>> ax.plot(x, b(x), 'g', lw=3)
358
+ >>> ax.plot(x, f(x), 'r', lw=8, alpha=0.4)
359
+ >>> ax.grid(True)
360
+ >>> plt.show()
361
+
362
+ """
363
+ xp = array_namespace(t)
364
+ t = np.asarray(t)
365
+ k = t.shape[0] - 2
366
+ t = _as_float_array(t) # TODO: use concat_1d instead of np.r_
367
+ t = np.r_[(t[0]-1,) * k, t, (t[-1]+1,) * k]
368
+ c = np.zeros_like(t)
369
+ c[k] = 1.
370
+
371
+ t, c = xp.asarray(t), xp.asarray(c)
372
+ return cls.construct_fast(t, c, k, extrapolate)
373
+
374
+ @classmethod
375
+ def design_matrix(cls, x, t, k, extrapolate=False):
376
+ """
377
+ Returns a design matrix as a CSR format sparse array.
378
+
379
+ Parameters
380
+ ----------
381
+ x : array_like, shape (n,)
382
+ Points to evaluate the spline at.
383
+ t : array_like, shape (nt,)
384
+ Sorted 1D array of knots.
385
+ k : int
386
+ B-spline degree.
387
+ extrapolate : bool or 'periodic', optional
388
+ Whether to extrapolate based on the first and last intervals
389
+ or raise an error. If 'periodic', periodic extrapolation is used.
390
+ Default is False.
391
+
392
+ .. versionadded:: 1.10.0
393
+
394
+ Returns
395
+ -------
396
+ design_matrix : `csr_array` object
397
+ Sparse matrix in CSR format where each row contains all the basis
398
+ elements of the input row (first row = basis elements of x[0],
399
+ ..., last row = basis elements x[-1]).
400
+
401
+ Examples
402
+ --------
403
+ Construct a design matrix for a B-spline
404
+
405
+ >>> from scipy.interpolate import make_interp_spline, BSpline
406
+ >>> import numpy as np
407
+ >>> x = np.linspace(0, np.pi * 2, 4)
408
+ >>> y = np.sin(x)
409
+ >>> k = 3
410
+ >>> bspl = make_interp_spline(x, y, k=k)
411
+ >>> design_matrix = bspl.design_matrix(x, bspl.t, k)
412
+ >>> design_matrix.toarray()
413
+ [[1. , 0. , 0. , 0. ],
414
+ [0.2962963 , 0.44444444, 0.22222222, 0.03703704],
415
+ [0.03703704, 0.22222222, 0.44444444, 0.2962963 ],
416
+ [0. , 0. , 0. , 1. ]]
417
+
418
+ Construct a design matrix for some vector of knots
419
+
420
+ >>> k = 2
421
+ >>> t = [-1, 0, 1, 2, 3, 4, 5, 6]
422
+ >>> x = [1, 2, 3, 4]
423
+ >>> design_matrix = BSpline.design_matrix(x, t, k).toarray()
424
+ >>> design_matrix
425
+ [[0.5, 0.5, 0. , 0. , 0. ],
426
+ [0. , 0.5, 0.5, 0. , 0. ],
427
+ [0. , 0. , 0.5, 0.5, 0. ],
428
+ [0. , 0. , 0. , 0.5, 0.5]]
429
+
430
+ This result is equivalent to the one created in the sparse format
431
+
432
+ >>> c = np.eye(len(t) - k - 1)
433
+ >>> design_matrix_gh = BSpline(t, c, k)(x)
434
+ >>> np.allclose(design_matrix, design_matrix_gh, atol=1e-14)
435
+ True
436
+
437
+ Notes
438
+ -----
439
+ .. versionadded:: 1.8.0
440
+
441
+ In each row of the design matrix all the basis elements are evaluated
442
+ at the certain point (first row - x[0], ..., last row - x[-1]).
443
+
444
+ `nt` is a length of the vector of knots: as far as there are
445
+ `nt - k - 1` basis elements, `nt` should be not less than `2 * k + 2`
446
+ to have at least `k + 1` basis element.
447
+
448
+ Out of bounds `x` raises a ValueError.
449
+ """
450
+ x = _as_float_array(x, True)
451
+ t = _as_float_array(t, True)
452
+
453
+ if extrapolate != 'periodic':
454
+ extrapolate = bool(extrapolate)
455
+
456
+ if k < 0:
457
+ raise ValueError("Spline order cannot be negative.")
458
+ if t.ndim != 1 or np.any(t[1:] < t[:-1]):
459
+ raise ValueError(f"Expect t to be a 1-D sorted array_like, but "
460
+ f"got t={t}.")
461
+ # There are `nt - k - 1` basis elements in a BSpline built on the
462
+ # vector of knots with length `nt`, so to have at least `k + 1` basis
463
+ # elements we need to have at least `2 * k + 2` elements in the vector
464
+ # of knots.
465
+ if len(t) < 2 * k + 2:
466
+ raise ValueError(f"Length t is not enough for k={k}.")
467
+
468
+ if extrapolate == 'periodic':
469
+ # With periodic extrapolation we map x to the segment
470
+ # [t[k], t[n]].
471
+ n = t.size - k - 1
472
+ x = t[k] + (x - t[k]) % (t[n] - t[k])
473
+ extrapolate = False
474
+ elif not extrapolate and (
475
+ (min(x) < t[k]) or (max(x) > t[t.shape[0] - k - 1])
476
+ ):
477
+ # Checks from `find_interval` function
478
+ raise ValueError(f'Out of bounds w/ x = {x}.')
479
+
480
+ # Compute number of non-zeros of final CSR array in order to determine
481
+ # the dtype of indices and indptr of the CSR array.
482
+ n = x.shape[0]
483
+ nnz = n * (k + 1)
484
+ if nnz < np.iinfo(np.int32).max:
485
+ int_dtype = np.int32
486
+ else:
487
+ int_dtype = np.int64
488
+
489
+ # Get the non-zero elements of the design matrix and per-row `offsets`:
490
+ # In row `i`, k+1 nonzero elements are consecutive, and start from `offset[i]`
491
+ data, offsets, _ = _dierckx.data_matrix(x, t, k, np.ones_like(x), extrapolate)
492
+ data = data.ravel()
493
+
494
+ if offsets.dtype != int_dtype:
495
+ offsets = offsets.astype(int_dtype)
496
+
497
+ # Convert from per-row offsets to the CSR indices/indptr format
498
+ indices = np.repeat(offsets, k+1).reshape(-1, k+1)
499
+ indices = indices + np.arange(k+1, dtype=int_dtype)
500
+ indices = indices.ravel()
501
+
502
+ indptr = np.arange(0, (n + 1) * (k + 1), k + 1, dtype=int_dtype)
503
+
504
+ return csr_array(
505
+ (data, indices, indptr),
506
+ shape=(x.shape[0], t.shape[0] - k - 1)
507
+ )
508
+
509
+ def __call__(self, x, nu=0, extrapolate=None):
510
+ """
511
+ Evaluate a spline function.
512
+
513
+ Parameters
514
+ ----------
515
+ x : array_like
516
+ points to evaluate the spline at.
517
+ nu : int, optional
518
+ derivative to evaluate (default is 0).
519
+ extrapolate : bool or 'periodic', optional
520
+ whether to extrapolate based on the first and last intervals
521
+ or return nans. If 'periodic', periodic extrapolation is used.
522
+ Default is `self.extrapolate`.
523
+
524
+ Returns
525
+ -------
526
+ y : array_like
527
+ Shape is determined by replacing the interpolation axis
528
+ in the coefficient array with the shape of `x`.
529
+
530
+ """
531
+ if extrapolate is None:
532
+ extrapolate = self.extrapolate
533
+ x = np.asarray(x)
534
+ x_shape, x_ndim = x.shape, x.ndim
535
+ x = np.ascontiguousarray(x.ravel(), dtype=np.float64)
536
+
537
+ # With periodic extrapolation we map x to the segment
538
+ # [self.t[k], self.t[n]].
539
+ if extrapolate == 'periodic':
540
+ n = self._t.size - self.k - 1
541
+ x = self._t[self.k] + (x - self._t[self.k]) % (self._t[n] - self._t[self.k])
542
+ extrapolate = False
543
+
544
+ self._ensure_c_contiguous()
545
+
546
+ # if self.c is complex: the C code in _dierckxmodule.cc expects
547
+ # floats, so make a view---this expands the last axis, and
548
+ # the view is C contiguous if the original is.
549
+ # if c.dtype is complex of shape (n,), c.view(float).shape == (2*n,)
550
+ # if c.dtype is complex of shape (n, m), c.view(float).shape == (n, 2*m)
551
+
552
+ is_complex = self._c.dtype.kind == 'c'
553
+ if is_complex:
554
+ cc = self._c.view(float)
555
+ if self._c.ndim == 1:
556
+ cc = cc.reshape(self._c.shape[0], 2)
557
+ else:
558
+ cc = self._c
559
+
560
+ # flatten the trailing dims
561
+ cc = cc.reshape(cc.shape[0], -1)
562
+
563
+ # heavy lifting: actually perform the evaluations
564
+ out = _dierckx.evaluate_spline(self._t, cc, self.k, x, nu, extrapolate)
565
+
566
+ if is_complex:
567
+ out = out.view(complex)
568
+
569
+ out = out.reshape(x_shape + self._c.shape[1:])
570
+ if self.axis != 0:
571
+ # transpose to move the calculated values to the interpolation axis
572
+ l = list(range(out.ndim))
573
+ l = l[x_ndim:x_ndim+self.axis] + l[:x_ndim] + l[x_ndim+self.axis:]
574
+ out = out.transpose(l)
575
+ return self._asarray(out)
576
+
577
+ def _ensure_c_contiguous(self):
578
+ """
579
+ c and t may be modified by the user. The Cython code expects
580
+ that they are C contiguous.
581
+
582
+ """
583
+ if not self._t.flags.c_contiguous:
584
+ self._t = self._t.copy()
585
+ if not self._c.flags.c_contiguous:
586
+ self._c = self._c.copy()
587
+
588
+ def derivative(self, nu=1):
589
+ """Return a B-spline representing the derivative.
590
+
591
+ Parameters
592
+ ----------
593
+ nu : int, optional
594
+ Derivative order.
595
+ Default is 1.
596
+
597
+ Returns
598
+ -------
599
+ b : `BSpline` object
600
+ A new instance representing the derivative.
601
+
602
+ See Also
603
+ --------
604
+ splder, splantider
605
+
606
+ """
607
+ c = self._asarray(self.c, copy=True)
608
+ t = self.t
609
+ xp = array_namespace(t, c)
610
+
611
+ # pad the c array if needed
612
+ ct = t.shape[0] - c.shape[0]
613
+ if ct > 0:
614
+ c = concat_1d(xp, c, xp.zeros((ct,) + c.shape[1:]))
615
+ tck = _fitpack_impl.splder((t, c, self.k), nu)
616
+ return self.construct_fast(*tck, extrapolate=self.extrapolate,
617
+ axis=self.axis)
618
+
619
+ def antiderivative(self, nu=1):
620
+ """Return a B-spline representing the antiderivative.
621
+
622
+ Parameters
623
+ ----------
624
+ nu : int, optional
625
+ Antiderivative order. Default is 1.
626
+
627
+ Returns
628
+ -------
629
+ b : `BSpline` object
630
+ A new instance representing the antiderivative.
631
+
632
+ Notes
633
+ -----
634
+ If antiderivative is computed and ``self.extrapolate='periodic'``,
635
+ it will be set to False for the returned instance. This is done because
636
+ the antiderivative is no longer periodic and its correct evaluation
637
+ outside of the initially given x interval is difficult.
638
+
639
+ See Also
640
+ --------
641
+ splder, splantider
642
+
643
+ """
644
+ c = self._asarray(self.c, copy=True)
645
+ t = self.t
646
+ xp = array_namespace(t, c)
647
+
648
+ # pad the c array if needed
649
+ ct = t.shape[0] - c.shape[0]
650
+ if ct > 0:
651
+ c = concat_1d(xp, c, xp.zeros((ct,) + c.shape[1:]))
652
+ tck = _fitpack_impl.splantider((t, c, self.k), nu)
653
+
654
+ if self.extrapolate == 'periodic':
655
+ extrapolate = False
656
+ else:
657
+ extrapolate = self.extrapolate
658
+
659
+ return self.construct_fast(*tck, extrapolate=extrapolate,
660
+ axis=self.axis)
661
+
662
+ def integrate(self, a, b, extrapolate=None):
663
+ """Compute a definite integral of the spline.
664
+
665
+ Parameters
666
+ ----------
667
+ a : float
668
+ Lower limit of integration.
669
+ b : float
670
+ Upper limit of integration.
671
+ extrapolate : bool or 'periodic', optional
672
+ whether to extrapolate beyond the base interval,
673
+ ``t[k] .. t[-k-1]``, or take the spline to be zero outside of the
674
+ base interval. If 'periodic', periodic extrapolation is used.
675
+ If None (default), use `self.extrapolate`.
676
+
677
+ Returns
678
+ -------
679
+ I : array_like
680
+ Definite integral of the spline over the interval ``[a, b]``.
681
+
682
+ Examples
683
+ --------
684
+ Construct the linear spline ``x if x < 1 else 2 - x`` on the base
685
+ interval :math:`[0, 2]`, and integrate it
686
+
687
+ >>> from scipy.interpolate import BSpline
688
+ >>> b = BSpline.basis_element([0, 1, 2])
689
+ >>> b.integrate(0, 1)
690
+ array(0.5)
691
+
692
+ If the integration limits are outside of the base interval, the result
693
+ is controlled by the `extrapolate` parameter
694
+
695
+ >>> b.integrate(-1, 1)
696
+ array(0.0)
697
+ >>> b.integrate(-1, 1, extrapolate=False)
698
+ array(0.5)
699
+
700
+ >>> import matplotlib.pyplot as plt
701
+ >>> fig, ax = plt.subplots()
702
+ >>> ax.grid(True)
703
+ >>> ax.axvline(0, c='r', lw=5, alpha=0.5) # base interval
704
+ >>> ax.axvline(2, c='r', lw=5, alpha=0.5)
705
+ >>> xx = [-1, 1, 2]
706
+ >>> ax.plot(xx, b(xx))
707
+ >>> plt.show()
708
+
709
+ """
710
+ if extrapolate is None:
711
+ extrapolate = self.extrapolate
712
+
713
+ # Prepare self.t and self.c.
714
+ self._ensure_c_contiguous()
715
+
716
+ # Swap integration bounds if needed.
717
+ sign = 1
718
+ if b < a:
719
+ a, b = b, a
720
+ sign = -1
721
+ n = self._t.size - self.k - 1
722
+
723
+ if extrapolate != "periodic" and not extrapolate:
724
+ # Shrink the integration interval, if needed.
725
+ a = max(a, self._t[self.k])
726
+ b = min(b, self._t[n])
727
+
728
+ if self._c.ndim == 1:
729
+ # Fast path: use FITPACK's routine
730
+ # (cf _fitpack_impl.splint).
731
+ integral = _fitpack_impl.splint(a, b, (self._t, self._c, self.k))
732
+ return self._asarray(integral * sign)
733
+
734
+ # Compute the antiderivative.
735
+ c = self._c
736
+ ct = len(self._t) - len(c)
737
+ if ct > 0:
738
+ c = np.r_[c, np.zeros((ct,) + c.shape[1:])]
739
+ ta, ca, ka = _fitpack_impl.splantider((self._t, c, self.k), 1)
740
+
741
+ if extrapolate == 'periodic':
742
+ # Split the integral into the part over period (can be several
743
+ # of them) and the remaining part.
744
+
745
+ ts, te = self._t[self.k], self._t[n]
746
+ period = te - ts
747
+ interval = b - a
748
+ n_periods, left = divmod(interval, period)
749
+
750
+ if n_periods > 0:
751
+ # Evaluate the difference of antiderivatives.
752
+ x = np.asarray([ts, te], dtype=np.float64)
753
+ out = _dierckx.evaluate_spline(ta, ca.reshape(ca.shape[0], -1),
754
+ ka, x, 0, False)
755
+ integral = out[1] - out[0]
756
+ integral *= n_periods
757
+ else:
758
+ integral = np.zeros((1, prod(self._c.shape[1:])),
759
+ dtype=self._c.dtype)
760
+
761
+ # Map a to [ts, te], b is always a + left.
762
+ a = ts + (a - ts) % period
763
+ b = a + left
764
+
765
+ # If b <= te then we need to integrate over [a, b], otherwise
766
+ # over [a, te] and from xs to what is remained.
767
+ if b <= te:
768
+ x = np.asarray([a, b], dtype=np.float64)
769
+ out = _dierckx.evaluate_spline(ta, ca.reshape(ca.shape[0], -1),
770
+ ka, x, 0, False)
771
+ integral += out[1] - out[0]
772
+ else:
773
+ x = np.asarray([a, te], dtype=np.float64)
774
+ out = _dierckx.evaluate_spline(ta, ca.reshape(ca.shape[0], -1),
775
+ ka, x, 0, False)
776
+ integral += out[1] - out[0]
777
+
778
+ x = np.asarray([ts, ts + b - te], dtype=np.float64)
779
+ out = _dierckx.evaluate_spline(ta, ca.reshape(ca.shape[0], -1),
780
+ ka, x, 0, False)
781
+ integral += out[1] - out[0]
782
+ else:
783
+ # Evaluate the difference of antiderivatives.
784
+ x = np.asarray([a, b], dtype=np.float64)
785
+ out = _dierckx.evaluate_spline(ta, ca.reshape(ca.shape[0], -1),
786
+ ka, x, 0, extrapolate)
787
+ integral = out[1] - out[0]
788
+
789
+ integral *= sign
790
+ return self._asarray(integral.reshape(ca.shape[1:]))
791
+
792
+ @classmethod
793
+ def from_power_basis(cls, pp, bc_type='not-a-knot'):
794
+ r"""
795
+ Construct a polynomial in the B-spline basis
796
+ from a piecewise polynomial in the power basis.
797
+
798
+ For now, accepts ``CubicSpline`` instances only.
799
+
800
+ Parameters
801
+ ----------
802
+ pp : CubicSpline
803
+ A piecewise polynomial in the power basis, as created
804
+ by ``CubicSpline``
805
+ bc_type : string, optional
806
+ Boundary condition type as in ``CubicSpline``: one of the
807
+ ``not-a-knot``, ``natural``, ``clamped``, or ``periodic``.
808
+ Necessary for construction an instance of ``BSpline`` class.
809
+ Default is ``not-a-knot``.
810
+
811
+ Returns
812
+ -------
813
+ b : `BSpline` object
814
+ A new instance representing the initial polynomial
815
+ in the B-spline basis.
816
+
817
+ Notes
818
+ -----
819
+ .. versionadded:: 1.8.0
820
+
821
+ Accepts only ``CubicSpline`` instances for now.
822
+
823
+ The algorithm follows from differentiation
824
+ the Marsden's identity [1]: each of coefficients of spline
825
+ interpolation function in the B-spline basis is computed as follows:
826
+
827
+ .. math::
828
+
829
+ c_j = \sum_{m=0}^{k} \frac{(k-m)!}{k!}
830
+ c_{m,i} (-1)^{k-m} D^m p_{j,k}(x_i)
831
+
832
+ :math:`c_{m, i}` - a coefficient of CubicSpline,
833
+ :math:`D^m p_{j, k}(x_i)` - an m-th defivative of a dual polynomial
834
+ in :math:`x_i`.
835
+
836
+ ``k`` always equals 3 for now.
837
+
838
+ First ``n - 2`` coefficients are computed in :math:`x_i = x_j`, e.g.
839
+
840
+ .. math::
841
+
842
+ c_1 = \sum_{m=0}^{k} \frac{(k-1)!}{k!} c_{m,1} D^m p_{j,3}(x_1)
843
+
844
+ Last ``nod + 2`` coefficients are computed in ``x[-2]``,
845
+ ``nod`` - number of derivatives at the ends.
846
+
847
+ For example, consider :math:`x = [0, 1, 2, 3, 4]`,
848
+ :math:`y = [1, 1, 1, 1, 1]` and bc_type = ``natural``
849
+
850
+ The coefficients of CubicSpline in the power basis:
851
+
852
+ :math:`[[0, 0, 0, 0, 0], [0, 0, 0, 0, 0],
853
+ [0, 0, 0, 0, 0], [1, 1, 1, 1, 1]]`
854
+
855
+ The knot vector: :math:`t = [0, 0, 0, 0, 1, 2, 3, 4, 4, 4, 4]`
856
+
857
+ In this case
858
+
859
+ .. math::
860
+
861
+ c_j = \frac{0!}{k!} c_{3, i} k! = c_{3, i} = 1,~j = 0, ..., 6
862
+
863
+ References
864
+ ----------
865
+ .. [1] Tom Lyche and Knut Morken, Spline Methods, 2005, Section 3.1.2
866
+
867
+ """
868
+ from ._cubic import CubicSpline
869
+ if not isinstance(pp, CubicSpline):
870
+ raise NotImplementedError(f"Only CubicSpline objects are accepted "
871
+ f"for now. Got {type(pp)} instead.")
872
+ x = pp.x
873
+ coef = pp.c
874
+ k = pp.c.shape[0] - 1
875
+ n = x.shape[0]
876
+
877
+ if bc_type == 'not-a-knot':
878
+ t = _not_a_knot(x, k)
879
+ elif bc_type == 'natural' or bc_type == 'clamped':
880
+ t = _augknt(x, k)
881
+ elif bc_type == 'periodic':
882
+ t = _periodic_knots(x, k)
883
+ else:
884
+ raise TypeError(f'Unknown boundary condition: {bc_type}')
885
+
886
+ nod = t.shape[0] - (n + k + 1) # number of derivatives at the ends
887
+ c = np.zeros(n + nod, dtype=pp.c.dtype)
888
+ for m in range(k + 1):
889
+ for i in range(n - 2):
890
+ c[i] += poch(k + 1, -m) * coef[m, i]\
891
+ * np.power(-1, k - m)\
892
+ * _diff_dual_poly(i, k, x[i], m, t)
893
+ for j in range(n - 2, n + nod):
894
+ c[j] += poch(k + 1, -m) * coef[m, n - 2]\
895
+ * np.power(-1, k - m)\
896
+ * _diff_dual_poly(j, k, x[n - 2], m, t)
897
+ return cls.construct_fast(t, c, k, pp.extrapolate, pp.axis)
898
+
899
+ def insert_knot(self, x, m=1):
900
+ """Insert a new knot at `x` of multiplicity `m`.
901
+
902
+ Given the knots and coefficients of a B-spline representation, create a
903
+ new B-spline with a knot inserted `m` times at point `x`.
904
+
905
+ Parameters
906
+ ----------
907
+ x : float
908
+ The position of the new knot
909
+ m : int, optional
910
+ The number of times to insert the given knot (its multiplicity).
911
+ Default is 1.
912
+
913
+ Returns
914
+ -------
915
+ spl : `BSpline` object
916
+ A new `BSpline` object with the new knot inserted.
917
+
918
+ Notes
919
+ -----
920
+ Based on algorithms from [1]_ and [2]_.
921
+
922
+ In case of a periodic spline (``self.extrapolate == "periodic"``)
923
+ there must be either at least k interior knots t(j) satisfying
924
+ ``t(k+1)<t(j)<=x`` or at least k interior knots t(j) satisfying
925
+ ``x<=t(j)<t(n-k)``.
926
+
927
+ This routine is functionally equivalent to `scipy.interpolate.insert`.
928
+
929
+ .. versionadded:: 1.13
930
+
931
+ References
932
+ ----------
933
+ .. [1] W. Boehm, "Inserting new knots into b-spline curves.",
934
+ Computer Aided Design, 12, p.199-201, 1980.
935
+ :doi:`10.1016/0010-4485(80)90154-2`.
936
+ .. [2] P. Dierckx, "Curve and surface fitting with splines, Monographs on
937
+ Numerical Analysis", Oxford University Press, 1993.
938
+
939
+ See Also
940
+ --------
941
+ scipy.interpolate.insert
942
+
943
+ Examples
944
+ --------
945
+ You can insert knots into a B-spline:
946
+
947
+ >>> import numpy as np
948
+ >>> from scipy.interpolate import BSpline, make_interp_spline
949
+ >>> x = np.linspace(0, 10, 5)
950
+ >>> y = np.sin(x)
951
+ >>> spl = make_interp_spline(x, y, k=3)
952
+ >>> spl.t
953
+ array([ 0., 0., 0., 0., 5., 10., 10., 10., 10.])
954
+
955
+ Insert a single knot
956
+
957
+ >>> spl_1 = spl.insert_knot(3)
958
+ >>> spl_1.t
959
+ array([ 0., 0., 0., 0., 3., 5., 10., 10., 10., 10.])
960
+
961
+ Insert a multiple knot
962
+
963
+ >>> spl_2 = spl.insert_knot(8, m=3)
964
+ >>> spl_2.t
965
+ array([ 0., 0., 0., 0., 5., 8., 8., 8., 10., 10., 10., 10.])
966
+
967
+ """
968
+ x = float(x)
969
+
970
+ if x < self._t[self.k] or x > self._t[-self.k-1]:
971
+ raise ValueError(f"Cannot insert a knot at {x}.")
972
+ if m <= 0:
973
+ raise ValueError(f"`m` must be positive, got {m = }.")
974
+
975
+ tt = self._t.copy()
976
+ cc = self._c.copy()
977
+
978
+ for _ in range(m):
979
+ tt, cc = _insert(x, tt, cc, self.k, self.extrapolate == "periodic")
980
+ tt, cc = self._asarray(tt), self._asarray(cc)
981
+ return self.construct_fast(tt, cc, self.k, self.extrapolate, self.axis)
982
+
983
+
984
+ def _insert(xval, t, c, k, periodic=False):
985
+ """Insert a single knot at `xval`."""
986
+ #
987
+ # This is a port of the FORTRAN `insert` routine by P. Dierckx,
988
+ # https://github.com/scipy/scipy/blob/maintenance/1.11.x/scipy/interpolate/fitpack/insert.f
989
+ # which carries the following comment:
990
+ #
991
+ # subroutine insert inserts a new knot x into a spline function s(x)
992
+ # of degree k and calculates the b-spline representation of s(x) with
993
+ # respect to the new set of knots. in addition, if iopt.ne.0, s(x)
994
+ # will be considered as a periodic spline with period per=t(n-k)-t(k+1)
995
+ # satisfying the boundary constraints
996
+ # t(i+n-2*k-1) = t(i)+per ,i=1,2,...,2*k+1
997
+ # c(i+n-2*k-1) = c(i) ,i=1,2,...,k
998
+ # in that case, the knots and b-spline coefficients returned will also
999
+ # satisfy these boundary constraints, i.e.
1000
+ # tt(i+nn-2*k-1) = tt(i)+per ,i=1,2,...,2*k+1
1001
+ # cc(i+nn-2*k-1) = cc(i) ,i=1,2,...,k
1002
+ interval = _dierckx.find_interval(t, k, float(xval), k, False)
1003
+ if interval < 0:
1004
+ # extrapolated values are guarded for in BSpline.insert_knot
1005
+ raise ValueError(f"Cannot insert the knot at {xval}.")
1006
+
1007
+ # super edge case: a knot with multiplicity > k+1
1008
+ # see https://github.com/scipy/scipy/commit/037204c3e91
1009
+ if t[interval] == t[interval + k + 1]:
1010
+ interval -= 1
1011
+
1012
+ if periodic:
1013
+ if (interval + 1 <= 2*k) and (interval + 1 >= t.shape[0] - 2*k):
1014
+ # in case of a periodic spline (iopt.ne.0) there must be
1015
+ # either at least k interior knots t(j) satisfying t(k+1)<t(j)<=x
1016
+ # or at least k interior knots t(j) satisfying x<=t(j)<t(n-k)
1017
+ raise ValueError("Not enough internal knots.")
1018
+
1019
+ # knots
1020
+ tt = np.r_[t[:interval+1], xval, t[interval+1:]]
1021
+
1022
+ newshape = (c.shape[0] + 1,) + c.shape[1:]
1023
+ cc = np.zeros(newshape, dtype=c.dtype)
1024
+
1025
+ # coefficients
1026
+ cc[interval+1:, ...] = c[interval:, ...]
1027
+
1028
+ for i in range(interval, interval-k, -1):
1029
+ fac = (xval - tt[i]) / (tt[i+k+1] - tt[i])
1030
+ cc[i, ...] = fac*c[i, ...] + (1. - fac)*c[i-1, ...]
1031
+
1032
+ cc[:interval - k+1, ...] = c[:interval - k+1, ...]
1033
+
1034
+ if periodic:
1035
+ # c incorporate the boundary conditions for a periodic spline.
1036
+ n = tt.shape[0]
1037
+ nk = n - k - 1
1038
+ n2k = n - 2*k - 1
1039
+ T = tt[nk] - tt[k] # period
1040
+
1041
+ if interval >= nk - k:
1042
+ # adjust the left-hand boundary knots & coefs
1043
+ tt[:k] = tt[nk - k:nk] - T
1044
+ cc[:k, ...] = cc[n2k:n2k + k, ...]
1045
+
1046
+ if interval <= 2*k-1:
1047
+ # adjust the right-hand boundary knots & coefs
1048
+ tt[n-k:] = tt[k+1:k+1+k] + T
1049
+ cc[n2k:n2k + k, ...] = cc[:k, ...]
1050
+
1051
+ return tt, cc
1052
+
1053
+
1054
+ #################################
1055
+ # Interpolating spline helpers #
1056
+ #################################
1057
+
1058
+ def _not_a_knot(x, k):
1059
+ """Given data x, construct the knot vector w/ not-a-knot BC.
1060
+ cf de Boor, XIII(12).
1061
+
1062
+ For even k, it's a bit ad hoc: Greville sites + omit 2nd and 2nd-to-last
1063
+ data points, a la not-a-knot.
1064
+ This seems to match what Dierckx does, too:
1065
+ https://github.com/scipy/scipy/blob/maintenance/1.11.x/scipy/interpolate/fitpack/fpcurf.f#L63-L80
1066
+ """
1067
+ x = np.asarray(x)
1068
+ if k % 2 == 1:
1069
+ k2 = (k + 1) // 2
1070
+ t = x.copy()
1071
+ else:
1072
+ k2 = k // 2
1073
+ t = (x[1:] + x[:-1]) / 2
1074
+
1075
+ t = t[k2:-k2]
1076
+ t = np.r_[(x[0],)*(k+1), t, (x[-1],)*(k+1)]
1077
+ return t
1078
+
1079
+
1080
+ def _augknt(x, k):
1081
+ """Construct a knot vector appropriate for the order-k interpolation."""
1082
+ return np.r_[(x[0],)*k, x, (x[-1],)*k]
1083
+
1084
+
1085
+ def _convert_string_aliases(deriv, target_shape):
1086
+ if isinstance(deriv, str):
1087
+ if deriv == "clamped":
1088
+ deriv = [(1, np.zeros(target_shape))]
1089
+ elif deriv == "natural":
1090
+ deriv = [(2, np.zeros(target_shape))]
1091
+ else:
1092
+ raise ValueError(f"Unknown boundary condition : {deriv}")
1093
+ return deriv
1094
+
1095
+
1096
+ def _process_deriv_spec(deriv):
1097
+ if deriv is not None:
1098
+ try:
1099
+ ords, vals = zip(*deriv)
1100
+ except TypeError as e:
1101
+ msg = ("Derivatives, `bc_type`, should be specified as a pair of "
1102
+ "iterables of pairs of (order, value).")
1103
+ raise ValueError(msg) from e
1104
+ else:
1105
+ ords, vals = [], []
1106
+ return np.atleast_1d(ords, vals)
1107
+
1108
+
1109
+ def _woodbury_algorithm(A, ur, ll, b, k):
1110
+ '''
1111
+ Solve a cyclic banded linear system with upper right
1112
+ and lower blocks of size ``(k-1) / 2`` using
1113
+ the Woodbury formula
1114
+
1115
+ Parameters
1116
+ ----------
1117
+ A : 2-D array, shape(k, n)
1118
+ Matrix of diagonals of original matrix (see
1119
+ ``solve_banded`` documentation).
1120
+ ur : 2-D array, shape(bs, bs)
1121
+ Upper right block matrix.
1122
+ ll : 2-D array, shape(bs, bs)
1123
+ Lower left block matrix.
1124
+ b : 1-D array, shape(n,)
1125
+ Vector of constant terms of the system of linear equations.
1126
+ k : int
1127
+ B-spline degree.
1128
+
1129
+ Returns
1130
+ -------
1131
+ c : 1-D array, shape(n,)
1132
+ Solution of the original system of linear equations.
1133
+
1134
+ Notes
1135
+ -----
1136
+ This algorithm works only for systems with banded matrix A plus
1137
+ a correction term U @ V.T, where the matrix U @ V.T gives upper right
1138
+ and lower left block of A
1139
+ The system is solved with the following steps:
1140
+ 1. New systems of linear equations are constructed:
1141
+ A @ z_i = u_i,
1142
+ u_i - column vector of U,
1143
+ i = 1, ..., k - 1
1144
+ 2. Matrix Z is formed from vectors z_i:
1145
+ Z = [ z_1 | z_2 | ... | z_{k - 1} ]
1146
+ 3. Matrix H = (1 + V.T @ Z)^{-1}
1147
+ 4. The system A' @ y = b is solved
1148
+ 5. x = y - Z @ (H @ V.T @ y)
1149
+ Also, ``n`` should be greater than ``k``, otherwise corner block
1150
+ elements will intersect with diagonals.
1151
+
1152
+ Examples
1153
+ --------
1154
+ Consider the case of n = 8, k = 5 (size of blocks - 2 x 2).
1155
+ The matrix of a system: U: V:
1156
+ x x x * * a b a b 0 0 0 0 1 0
1157
+ x x x x * * c 0 c 0 0 0 0 0 1
1158
+ x x x x x * * 0 0 0 0 0 0 0 0
1159
+ * x x x x x * 0 0 0 0 0 0 0 0
1160
+ * * x x x x x 0 0 0 0 0 0 0 0
1161
+ d * * x x x x 0 0 d 0 1 0 0 0
1162
+ e f * * x x x 0 0 e f 0 1 0 0
1163
+
1164
+ References
1165
+ ----------
1166
+ .. [1] William H. Press, Saul A. Teukolsky, William T. Vetterling
1167
+ and Brian P. Flannery, Numerical Recipes, 2007, Section 2.7.3
1168
+
1169
+ '''
1170
+ k_mod = k - k % 2
1171
+ bs = int((k - 1) / 2) + (k + 1) % 2
1172
+
1173
+ n = A.shape[1] + 1
1174
+ U = np.zeros((n - 1, k_mod))
1175
+ VT = np.zeros((k_mod, n - 1)) # V transpose
1176
+
1177
+ # upper right block
1178
+ U[:bs, :bs] = ur
1179
+ VT[np.arange(bs), np.arange(bs) - bs] = 1
1180
+
1181
+ # lower left block
1182
+ U[-bs:, -bs:] = ll
1183
+ VT[np.arange(bs) - bs, np.arange(bs)] = 1
1184
+
1185
+ Z = solve_banded((bs, bs), A, U)
1186
+
1187
+ H = solve(np.identity(k_mod) + VT @ Z, np.identity(k_mod))
1188
+
1189
+ y = solve_banded((bs, bs), A, b)
1190
+ c = y - Z @ (H @ (VT @ y))
1191
+
1192
+ return c
1193
+
1194
+
1195
+ def _periodic_knots(x, k):
1196
+ '''
1197
+ returns vector of nodes on circle
1198
+ '''
1199
+ xc = np.copy(x)
1200
+ n = len(xc)
1201
+ if k % 2 == 0:
1202
+ dx = np.diff(xc)
1203
+ xc[1: -1] -= dx[:-1] / 2
1204
+ dx = np.diff(xc)
1205
+ t = np.zeros(n + 2 * k)
1206
+ t[k: -k] = xc
1207
+ for i in range(0, k):
1208
+ # filling first `k` elements in descending order
1209
+ t[k - i - 1] = t[k - i] - dx[-(i % (n - 1)) - 1]
1210
+ # filling last `k` elements in ascending order
1211
+ t[-k + i] = t[-k + i - 1] + dx[i % (n - 1)]
1212
+ return t
1213
+
1214
+
1215
+ def _make_interp_per_full_matr(x, y, t, k):
1216
+ '''
1217
+ Returns a solution of a system for B-spline interpolation with periodic
1218
+ boundary conditions. First ``k - 1`` rows of matrix are conditions of
1219
+ periodicity (continuity of ``k - 1`` derivatives at the boundary points).
1220
+ Last ``n`` rows are interpolation conditions.
1221
+ RHS is ``k - 1`` zeros and ``n`` ordinates in this case.
1222
+
1223
+ Parameters
1224
+ ----------
1225
+ x : 1-D array, shape (n,)
1226
+ Values of x - coordinate of a given set of points.
1227
+ y : 1-D array, shape (n,)
1228
+ Values of y - coordinate of a given set of points.
1229
+ t : 1-D array, shape(n+2*k,)
1230
+ Vector of knots.
1231
+ k : int
1232
+ The maximum degree of spline
1233
+
1234
+ Returns
1235
+ -------
1236
+ c : 1-D array, shape (n+k-1,)
1237
+ B-spline coefficients
1238
+
1239
+ Notes
1240
+ -----
1241
+ ``t`` is supposed to be taken on circle.
1242
+
1243
+ '''
1244
+
1245
+ x, y, t = map(np.asarray, (x, y, t))
1246
+
1247
+ n = x.size
1248
+ # LHS: the colocation matrix + derivatives at edges
1249
+ matr = np.zeros((n + k - 1, n + k - 1))
1250
+
1251
+ # derivatives at x[0] and x[-1]:
1252
+ for i in range(k - 1):
1253
+ bb = _dierckx.evaluate_all_bspl(t, k, x[0], k, i + 1)
1254
+ matr[i, : k + 1] += bb
1255
+ bb = _dierckx.evaluate_all_bspl(t, k, x[-1], n + k - 1, i + 1)[:-1]
1256
+ matr[i, -k:] -= bb
1257
+
1258
+ # colocation matrix
1259
+ for i in range(n):
1260
+ xval = x[i]
1261
+ # find interval
1262
+ if xval == t[k]:
1263
+ left = k
1264
+ else:
1265
+ left = np.searchsorted(t, xval) - 1
1266
+
1267
+ # fill a row
1268
+ bb = _dierckx.evaluate_all_bspl(t, k, xval, left)
1269
+ matr[i + k - 1, left-k:left+1] = bb
1270
+
1271
+ # RHS
1272
+ b = np.r_[[0] * (k - 1), y]
1273
+
1274
+ c = solve(matr, b)
1275
+ return c
1276
+
1277
+
1278
+ def _handle_lhs_derivatives(t, k, xval, ab, kl, ku, deriv_ords, offset=0):
1279
+ """ Fill in the entries of the colocation matrix corresponding to known
1280
+ derivatives at `xval`.
1281
+
1282
+ The colocation matrix is in the banded storage, as prepared by _coloc.
1283
+ No error checking.
1284
+
1285
+ Parameters
1286
+ ----------
1287
+ t : ndarray, shape (nt + k + 1,)
1288
+ knots
1289
+ k : integer
1290
+ B-spline order
1291
+ xval : float
1292
+ The value at which to evaluate the derivatives at.
1293
+ ab : ndarray, shape(2*kl + ku + 1, nt), Fortran order
1294
+ B-spline colocation matrix.
1295
+ This argument is modified *in-place*.
1296
+ kl : integer
1297
+ Number of lower diagonals of ab.
1298
+ ku : integer
1299
+ Number of upper diagonals of ab.
1300
+ deriv_ords : 1D ndarray
1301
+ Orders of derivatives known at xval
1302
+ offset : integer, optional
1303
+ Skip this many rows of the matrix ab.
1304
+
1305
+ """
1306
+ # find where `xval` is in the knot vector, `t`
1307
+ left = _dierckx.find_interval(t, k, float(xval), k, False)
1308
+
1309
+ # compute and fill in the derivatives @ xval
1310
+ for row in range(deriv_ords.shape[0]):
1311
+ nu = deriv_ords[row]
1312
+ wrk = _dierckx.evaluate_all_bspl(t, k, xval, left, nu)
1313
+
1314
+ # if A were a full matrix, it would be just
1315
+ # ``A[row + offset, left-k:left+1] = bb``.
1316
+ for a in range(k+1):
1317
+ clmn = left - k + a
1318
+ ab[kl + ku + offset + row - clmn, clmn] = wrk[a]
1319
+
1320
+
1321
+ def _make_periodic_spline(x, y, t, k, axis, *, xp):
1322
+ '''
1323
+ Compute the (coefficients of) interpolating B-spline with periodic
1324
+ boundary conditions.
1325
+
1326
+ Parameters
1327
+ ----------
1328
+ x : array_like, shape (n,)
1329
+ Abscissas.
1330
+ y : array_like, shape (n,)
1331
+ Ordinates.
1332
+ k : int
1333
+ B-spline degree.
1334
+ t : array_like, shape (n + 2 * k,).
1335
+ Knots taken on a circle, ``k`` on the left and ``k`` on the right
1336
+ of the vector ``x``.
1337
+
1338
+ Returns
1339
+ -------
1340
+ b : `BSpline` object
1341
+ A `BSpline` object of the degree ``k`` and with knots ``t``.
1342
+
1343
+ Notes
1344
+ -----
1345
+ The original system is formed by ``n + k - 1`` equations where the first
1346
+ ``k - 1`` of them stand for the ``k - 1`` derivatives continuity on the
1347
+ edges while the other equations correspond to an interpolating case
1348
+ (matching all the input points). Due to a special form of knot vector, it
1349
+ can be proved that in the original system the first and last ``k``
1350
+ coefficients of a spline function are the same, respectively. It follows
1351
+ from the fact that all ``k - 1`` derivatives are equal term by term at ends
1352
+ and that the matrix of the original system of linear equations is
1353
+ non-degenerate. So, we can reduce the number of equations to ``n - 1``
1354
+ (first ``k - 1`` equations could be reduced). Another trick of this
1355
+ implementation is cyclic shift of values of B-splines due to equality of
1356
+ ``k`` unknown coefficients. With this we can receive matrix of the system
1357
+ with upper right and lower left blocks, and ``k`` diagonals. It allows
1358
+ to use Woodbury formula to optimize the computations.
1359
+
1360
+ '''
1361
+ n = y.shape[0]
1362
+
1363
+ extradim = prod(y.shape[1:])
1364
+ y_new = y.reshape(n, extradim)
1365
+ c = np.zeros((n + k - 1, extradim))
1366
+
1367
+ # n <= k case is solved with full matrix
1368
+ if n <= k:
1369
+ for i in range(extradim):
1370
+ c[:, i] = _make_interp_per_full_matr(x, y_new[:, i], t, k)
1371
+ c = np.ascontiguousarray(c.reshape((n + k - 1,) + y.shape[1:]))
1372
+ t, c = xp.asarray(t), xp.asarray(c)
1373
+ return BSpline.construct_fast(t, c, k, extrapolate='periodic', axis=axis)
1374
+
1375
+ nt = len(t) - k - 1
1376
+
1377
+ # size of block elements
1378
+ kul = int(k / 2)
1379
+
1380
+ # kl = ku = k
1381
+ ab = np.zeros((3 * k + 1, nt), dtype=np.float64, order='F')
1382
+
1383
+ # upper right and lower left blocks
1384
+ ur = np.zeros((kul, kul))
1385
+ ll = np.zeros_like(ur)
1386
+
1387
+ # `offset` is made to shift all the non-zero elements to the end of the
1388
+ # matrix
1389
+ # NB: 1. drop the last element of `x` because `x[0] = x[-1] + T` & `y[0] == y[-1]`
1390
+ # 2. pass ab.T to _coloc to make it C-ordered; below it'll be fed to banded
1391
+ # LAPACK, which needs F-ordered arrays
1392
+ _dierckx._coloc(x[:-1], t, k, ab.T, k)
1393
+
1394
+ # remove zeros before the matrix
1395
+ ab = ab[-k - (k + 1) % 2:, :]
1396
+
1397
+ # The least elements in rows (except repetitions) are diagonals
1398
+ # of block matrices. Upper right matrix is an upper triangular
1399
+ # matrix while lower left is a lower triangular one.
1400
+ for i in range(kul):
1401
+ ur += np.diag(ab[-i - 1, i: kul], k=i)
1402
+ ll += np.diag(ab[i, -kul - (k % 2): n - 1 + 2 * kul - i], k=-i)
1403
+
1404
+ # remove elements that occur in the last point
1405
+ # (first and last points are equivalent)
1406
+ A = ab[:, kul: -k + kul]
1407
+
1408
+ for i in range(extradim):
1409
+ cc = _woodbury_algorithm(A, ur, ll, y_new[:, i][:-1], k)
1410
+ c[:, i] = np.concatenate((cc[-kul:], cc, cc[:kul + k % 2]))
1411
+ c = np.ascontiguousarray(c.reshape((n + k - 1,) + y.shape[1:]))
1412
+ t, c = xp.asarray(t), xp.asarray(c)
1413
+ return BSpline.construct_fast(t, c, k, extrapolate='periodic', axis=axis)
1414
+
1415
+
1416
+ @xp_capabilities(cpu_only=True, jax_jit=False, allow_dask_compute=True)
1417
+ def make_interp_spline(x, y, k=3, t=None, bc_type=None, axis=0,
1418
+ check_finite=True):
1419
+ """Create an interpolating B-spline with specified degree and boundary conditions.
1420
+
1421
+ Parameters
1422
+ ----------
1423
+ x : array_like, shape (n,)
1424
+ Abscissas.
1425
+ y : array_like, shape (n, ...)
1426
+ Ordinates.
1427
+ k : int, optional
1428
+ B-spline degree. Default is cubic, ``k = 3``.
1429
+ t : array_like, shape (nt + k + 1,), optional.
1430
+ Knots.
1431
+ The number of knots needs to agree with the number of data points and
1432
+ the number of derivatives at the edges. Specifically, ``nt - n`` must
1433
+ equal ``len(deriv_l) + len(deriv_r)``.
1434
+ bc_type : 2-tuple or None
1435
+ Boundary conditions.
1436
+ Default is None, which means choosing the boundary conditions
1437
+ automatically. Otherwise, it must be a length-two tuple where the first
1438
+ element (``deriv_l``) sets the boundary conditions at ``x[0]`` and
1439
+ the second element (``deriv_r``) sets the boundary conditions at
1440
+ ``x[-1]``. Each of these must be an iterable of pairs
1441
+ ``(order, value)`` which gives the values of derivatives of specified
1442
+ orders at the given edge of the interpolation interval.
1443
+ Alternatively, the following string aliases are recognized:
1444
+
1445
+ * ``"clamped"``: The first derivatives at the ends are zero. This is
1446
+ equivalent to ``bc_type=([(1, 0.0)], [(1, 0.0)])``.
1447
+ * ``"natural"``: The second derivatives at ends are zero. This is
1448
+ equivalent to ``bc_type=([(2, 0.0)], [(2, 0.0)])``.
1449
+ * ``"not-a-knot"`` (default): The first and second segments are the
1450
+ same polynomial. This is equivalent to having ``bc_type=None``.
1451
+ * ``"periodic"``: The values and the first ``k-1`` derivatives at the
1452
+ ends are equivalent.
1453
+
1454
+ axis : int, optional
1455
+ Interpolation axis. Default is 0.
1456
+ check_finite : bool, optional
1457
+ Whether to check that the input arrays contain only finite numbers.
1458
+ Disabling may give a performance gain, but may result in problems
1459
+ (crashes, non-termination) if the inputs do contain infinities or NaNs.
1460
+ Default is True.
1461
+
1462
+ Returns
1463
+ -------
1464
+ b : `BSpline` object
1465
+ A `BSpline` object of the degree ``k`` and with knots ``t``.
1466
+
1467
+ See Also
1468
+ --------
1469
+ BSpline : base class representing the B-spline objects
1470
+ CubicSpline : a cubic spline in the polynomial basis
1471
+ make_lsq_spline : a similar factory function for spline fitting
1472
+ UnivariateSpline : a wrapper over FITPACK spline fitting routines
1473
+ splrep : a wrapper over FITPACK spline fitting routines
1474
+
1475
+ Examples
1476
+ --------
1477
+ Use cubic interpolation on Chebyshev nodes:
1478
+
1479
+ >>> import numpy as np
1480
+ >>> import matplotlib.pyplot as plt
1481
+ >>> def cheb_nodes(N):
1482
+ ... jj = 2.*np.arange(N) + 1
1483
+ ... x = np.cos(np.pi * jj / 2 / N)[::-1]
1484
+ ... return x
1485
+
1486
+ >>> x = cheb_nodes(20)
1487
+ >>> y = np.sqrt(1 - x**2)
1488
+
1489
+ >>> from scipy.interpolate import BSpline, make_interp_spline
1490
+ >>> b = make_interp_spline(x, y)
1491
+ >>> np.allclose(b(x), y)
1492
+ True
1493
+
1494
+ Note that the default is a cubic spline with a not-a-knot boundary condition
1495
+
1496
+ >>> b.k
1497
+ 3
1498
+
1499
+ Here we use a 'natural' spline, with zero 2nd derivatives at edges:
1500
+
1501
+ >>> l, r = [(2, 0.0)], [(2, 0.0)]
1502
+ >>> b_n = make_interp_spline(x, y, bc_type=(l, r)) # or, bc_type="natural"
1503
+ >>> np.allclose(b_n(x), y)
1504
+ True
1505
+ >>> x0, x1 = x[0], x[-1]
1506
+ >>> np.allclose([b_n(x0, 2), b_n(x1, 2)], [0, 0])
1507
+ True
1508
+
1509
+ Interpolation of parametric curves is also supported. As an example, we
1510
+ compute a discretization of a snail curve in polar coordinates
1511
+
1512
+ >>> phi = np.linspace(0, 2.*np.pi, 40)
1513
+ >>> r = 0.3 + np.cos(phi)
1514
+ >>> x, y = r*np.cos(phi), r*np.sin(phi) # convert to Cartesian coordinates
1515
+
1516
+ Build an interpolating curve, parameterizing it by the angle
1517
+
1518
+ >>> spl = make_interp_spline(phi, np.c_[x, y])
1519
+
1520
+ Evaluate the interpolant on a finer grid (note that we transpose the result
1521
+ to unpack it into a pair of x- and y-arrays)
1522
+
1523
+ >>> phi_new = np.linspace(0, 2.*np.pi, 100)
1524
+ >>> x_new, y_new = spl(phi_new).T
1525
+
1526
+ Plot the result
1527
+
1528
+ >>> plt.plot(x, y, 'o')
1529
+ >>> plt.plot(x_new, y_new, '-')
1530
+ >>> plt.show()
1531
+
1532
+ Build a B-spline curve with 2 dimensional y
1533
+
1534
+ >>> x = np.linspace(0, 2*np.pi, 10)
1535
+ >>> y = np.array([np.sin(x), np.cos(x)])
1536
+
1537
+ Periodic condition is satisfied because y coordinates of points on the ends
1538
+ are equivalent
1539
+
1540
+ >>> ax = plt.axes(projection='3d')
1541
+ >>> xx = np.linspace(0, 2*np.pi, 100)
1542
+ >>> bspl = make_interp_spline(x, y, k=5, bc_type='periodic', axis=1)
1543
+ >>> ax.plot3D(xx, *bspl(xx))
1544
+ >>> ax.scatter3D(x, *y, color='red')
1545
+ >>> plt.show()
1546
+
1547
+ """
1548
+ # convert string aliases for the boundary conditions
1549
+ if bc_type is None or bc_type == 'not-a-knot' or bc_type == 'periodic':
1550
+ deriv_l, deriv_r = None, None
1551
+ elif isinstance(bc_type, str):
1552
+ deriv_l, deriv_r = bc_type, bc_type
1553
+ else:
1554
+ try:
1555
+ deriv_l, deriv_r = bc_type
1556
+ except TypeError as e:
1557
+ raise ValueError(f"Unknown boundary condition: {bc_type}") from e
1558
+
1559
+ xp = array_namespace(x, y, t)
1560
+ x = _as_float_array(x, check_finite)
1561
+ y = _as_float_array(y, check_finite)
1562
+
1563
+ axis = normalize_axis_index(axis, y.ndim)
1564
+ y = np.moveaxis(y, axis, 0) # now internally interp axis is zero
1565
+
1566
+ # sanity check the input
1567
+ if bc_type == 'periodic' and not np.allclose(y[0], y[-1], atol=1e-15):
1568
+ raise ValueError("First and last points does not match while "
1569
+ "periodic case expected")
1570
+ if x.size != y.shape[0]:
1571
+ raise ValueError(f'Shapes of x {x.shape} and y {y.shape} are incompatible')
1572
+ if np.any(x[1:] == x[:-1]):
1573
+ raise ValueError("Expect x to not have duplicates")
1574
+ if x.ndim != 1 or np.any(x[1:] < x[:-1]):
1575
+ raise ValueError("Expect x to be a 1D strictly increasing sequence.")
1576
+
1577
+ # special-case k=0 right away
1578
+ if k == 0:
1579
+ if any(_ is not None for _ in (t, deriv_l, deriv_r)):
1580
+ raise ValueError("Too much info for k=0: t and bc_type can only "
1581
+ "be None.")
1582
+ t = np.r_[x, x[-1]]
1583
+ c = np.asarray(y)
1584
+ c = np.ascontiguousarray(c, dtype=_get_dtype(c.dtype))
1585
+ t, c = xp.asarray(t), xp.asarray(c)
1586
+ return BSpline.construct_fast(t, c, k, axis=axis)
1587
+
1588
+ # special-case k=1 (e.g., Lyche and Morken, Eq.(2.16))
1589
+ if k == 1 and t is None:
1590
+ if not (deriv_l is None and deriv_r is None):
1591
+ raise ValueError("Too much info for k=1: bc_type can only be None.")
1592
+ t = np.r_[x[0], x, x[-1]]
1593
+ c = np.asarray(y)
1594
+ c = np.ascontiguousarray(c, dtype=_get_dtype(c.dtype))
1595
+ t, c = xp.asarray(t), xp.asarray(c)
1596
+ return BSpline.construct_fast(t, c, k, axis=axis)
1597
+
1598
+ k = operator.index(k)
1599
+
1600
+ if bc_type == 'periodic' and t is not None:
1601
+ raise NotImplementedError("For periodic case t is constructed "
1602
+ "automatically and can not be passed "
1603
+ "manually")
1604
+
1605
+ # come up with a sensible knot vector, if needed
1606
+ if t is None:
1607
+ if deriv_l is None and deriv_r is None:
1608
+ if bc_type == 'periodic':
1609
+ t = _periodic_knots(x, k)
1610
+ else:
1611
+ t = _not_a_knot(x, k)
1612
+ else:
1613
+ t = _augknt(x, k)
1614
+
1615
+ t = _as_float_array(t, check_finite)
1616
+
1617
+ if k < 0:
1618
+ raise ValueError("Expect non-negative k.")
1619
+ if t.ndim != 1 or np.any(t[1:] < t[:-1]):
1620
+ raise ValueError("Expect t to be a 1-D sorted array_like.")
1621
+ if t.size < x.size + k + 1:
1622
+ raise ValueError(f"Got {t.size} knots, need at least {x.size + k + 1}.")
1623
+ if (x[0] < t[k]) or (x[-1] > t[-k]):
1624
+ raise ValueError(f'Out of bounds w/ x = {x}.')
1625
+
1626
+ if bc_type == 'periodic':
1627
+ return _make_periodic_spline(x, y, t, k, axis, xp=xp)
1628
+
1629
+ # Here : deriv_l, r = [(nu, value), ...]
1630
+ deriv_l = _convert_string_aliases(deriv_l, y.shape[1:])
1631
+ deriv_l_ords, deriv_l_vals = _process_deriv_spec(deriv_l)
1632
+ nleft = deriv_l_ords.shape[0]
1633
+
1634
+ deriv_r = _convert_string_aliases(deriv_r, y.shape[1:])
1635
+ deriv_r_ords, deriv_r_vals = _process_deriv_spec(deriv_r)
1636
+ nright = deriv_r_ords.shape[0]
1637
+
1638
+ if not all(0 <= i <= k for i in deriv_l_ords):
1639
+ raise ValueError(f"Bad boundary conditions at {x[0]}.")
1640
+
1641
+ if not all(0 <= i <= k for i in deriv_r_ords):
1642
+ raise ValueError(f"Bad boundary conditions at {x[-1]}.")
1643
+
1644
+ # have `n` conditions for `nt` coefficients; need nt-n derivatives
1645
+ n = x.size
1646
+ nt = t.size - k - 1
1647
+
1648
+ if nt - n != nleft + nright:
1649
+ raise ValueError("The number of derivatives at boundaries does not "
1650
+ f"match: expected {nt-n}, got {nleft}+{nright}")
1651
+
1652
+ # bail out if the `y` array is zero-sized
1653
+ if y.size == 0:
1654
+ c = np.zeros((nt,) + y.shape[1:], dtype=float)
1655
+ return BSpline.construct_fast(t, c, k, axis=axis)
1656
+
1657
+ # set up the LHS: the colocation matrix + derivatives at boundaries
1658
+ # NB: ab is in F order for banded LAPACK; _coloc needs C-ordered arrays,
1659
+ # this pass ab.T into _coloc
1660
+ kl = ku = k
1661
+ ab = np.zeros((2*kl + ku + 1, nt), dtype=np.float64, order='F')
1662
+ _dierckx._coloc(x, t, k, ab.T, nleft)
1663
+ if nleft > 0:
1664
+ _handle_lhs_derivatives(t, k, x[0], ab, kl, ku, deriv_l_ords)
1665
+ if nright > 0:
1666
+ _handle_lhs_derivatives(t, k, x[-1], ab, kl, ku, deriv_r_ords,
1667
+ offset=nt-nright)
1668
+
1669
+ # set up the RHS: values to interpolate (+ derivative values, if any)
1670
+ extradim = prod(y.shape[1:])
1671
+ rhs = np.empty((nt, extradim), dtype=y.dtype)
1672
+ if nleft > 0:
1673
+ rhs[:nleft] = deriv_l_vals.reshape(-1, extradim)
1674
+ rhs[nleft:nt - nright] = y.reshape(-1, extradim)
1675
+ if nright > 0:
1676
+ rhs[nt - nright:] = deriv_r_vals.reshape(-1, extradim)
1677
+
1678
+ # solve Ab @ x = rhs; this is the relevant part of linalg.solve_banded
1679
+ if check_finite:
1680
+ ab, rhs = map(np.asarray_chkfinite, (ab, rhs))
1681
+ gbsv, = get_lapack_funcs(('gbsv',), (ab, rhs))
1682
+ lu, piv, c, info = gbsv(kl, ku, ab, rhs,
1683
+ overwrite_ab=True, overwrite_b=True)
1684
+
1685
+ if info > 0:
1686
+ raise LinAlgError("Colocation matrix is singular.")
1687
+ elif info < 0:
1688
+ raise ValueError(f'illegal value in {-info}-th argument of internal gbsv')
1689
+ c = np.ascontiguousarray(c.reshape((nt,) + y.shape[1:]))
1690
+ t, c = xp.asarray(t), xp.asarray(c)
1691
+ return BSpline.construct_fast(t, c, k, axis=axis)
1692
+
1693
+
1694
+ @xp_capabilities(cpu_only=True, jax_jit=False, allow_dask_compute=True)
1695
+ def make_lsq_spline(x, y, t, k=3, w=None, axis=0, check_finite=True, *, method="qr"):
1696
+ r"""Create a smoothing B-spline satisfying the Least SQuares (LSQ) criterion.
1697
+
1698
+ The result is a linear combination
1699
+
1700
+ .. math::
1701
+
1702
+ S(x) = \sum_j c_j B_j(x; t)
1703
+
1704
+ of the B-spline basis elements, :math:`B_j(x; t)`, which minimizes
1705
+
1706
+ .. math::
1707
+
1708
+ \sum_{j} \left( w_j \times (S(x_j) - y_j) \right)^2
1709
+
1710
+ Parameters
1711
+ ----------
1712
+ x : array_like, shape (m,)
1713
+ Abscissas.
1714
+ y : array_like, shape (m, ...)
1715
+ Ordinates.
1716
+ t : array_like, shape (n + k + 1,).
1717
+ Knots.
1718
+ Knots and data points must satisfy Schoenberg-Whitney conditions.
1719
+ k : int, optional
1720
+ B-spline degree. Default is cubic, ``k = 3``.
1721
+ w : array_like, shape (m,), optional
1722
+ Weights for spline fitting. Must be positive. If ``None``,
1723
+ then weights are all equal.
1724
+ Default is ``None``.
1725
+ axis : int, optional
1726
+ Interpolation axis. Default is zero.
1727
+ check_finite : bool, optional
1728
+ Whether to check that the input arrays contain only finite numbers.
1729
+ Disabling may give a performance gain, but may result in problems
1730
+ (crashes, non-termination) if the inputs do contain infinities or NaNs.
1731
+ Default is True.
1732
+ method : str, optional
1733
+ Method for solving the linear LSQ problem. Allowed values are "norm-eq"
1734
+ (Explicitly construct and solve the normal system of equations), and
1735
+ "qr" (Use the QR factorization of the design matrix).
1736
+ Default is "qr".
1737
+
1738
+ Returns
1739
+ -------
1740
+ b : `BSpline` object
1741
+ A `BSpline` object of the degree ``k`` with knots ``t``.
1742
+
1743
+ See Also
1744
+ --------
1745
+ BSpline : base class representing the B-spline objects
1746
+ make_interp_spline : a similar factory function for interpolating splines
1747
+ LSQUnivariateSpline : a FITPACK-based spline fitting routine
1748
+ splrep : a FITPACK-based fitting routine
1749
+
1750
+ Notes
1751
+ -----
1752
+ The number of data points must be larger than the spline degree ``k``.
1753
+
1754
+ Knots ``t`` must satisfy the Schoenberg-Whitney conditions,
1755
+ i.e., there must be a subset of data points ``x[j]`` such that
1756
+ ``t[j] < x[j] < t[j+k+1]``, for ``j=0, 1,...,n-k-2``.
1757
+
1758
+ Examples
1759
+ --------
1760
+ Generate some noisy data:
1761
+
1762
+ >>> import numpy as np
1763
+ >>> import matplotlib.pyplot as plt
1764
+ >>> rng = np.random.default_rng()
1765
+ >>> x = np.linspace(-3, 3, 50)
1766
+ >>> y = np.exp(-x**2) + 0.1 * rng.standard_normal(50)
1767
+
1768
+ Now fit a smoothing cubic spline with a pre-defined internal knots.
1769
+ Here we make the knot vector (k+1)-regular by adding boundary knots:
1770
+
1771
+ >>> from scipy.interpolate import make_lsq_spline, BSpline
1772
+ >>> t = [-1, 0, 1]
1773
+ >>> k = 3
1774
+ >>> t = np.r_[(x[0],)*(k+1),
1775
+ ... t,
1776
+ ... (x[-1],)*(k+1)]
1777
+ >>> spl = make_lsq_spline(x, y, t, k)
1778
+
1779
+ For comparison, we also construct an interpolating spline for the same
1780
+ set of data:
1781
+
1782
+ >>> from scipy.interpolate import make_interp_spline
1783
+ >>> spl_i = make_interp_spline(x, y)
1784
+
1785
+ Plot both:
1786
+
1787
+ >>> xs = np.linspace(-3, 3, 100)
1788
+ >>> plt.plot(x, y, 'ro', ms=5)
1789
+ >>> plt.plot(xs, spl(xs), 'g-', lw=3, label='LSQ spline')
1790
+ >>> plt.plot(xs, spl_i(xs), 'b-', lw=3, alpha=0.7, label='interp spline')
1791
+ >>> plt.legend(loc='best')
1792
+ >>> plt.show()
1793
+
1794
+ **NaN handling**: If the input arrays contain ``nan`` values, the result is
1795
+ not useful since the underlying spline fitting routines cannot deal with
1796
+ ``nan``. A workaround is to use zero weights for not-a-number data points:
1797
+
1798
+ >>> y[8] = np.nan
1799
+ >>> w = np.isnan(y)
1800
+ >>> y[w] = 0.
1801
+ >>> tck = make_lsq_spline(x, y, t, w=~w)
1802
+
1803
+ Notice the need to replace a ``nan`` by a numerical value (precise value
1804
+ does not matter as long as the corresponding weight is zero.)
1805
+
1806
+ """
1807
+ xp = array_namespace(x, y, t, w)
1808
+
1809
+ x = _as_float_array(x, check_finite)
1810
+ y = _as_float_array(y, check_finite)
1811
+ t = _as_float_array(t, check_finite)
1812
+ if w is not None:
1813
+ w = _as_float_array(w, check_finite)
1814
+ else:
1815
+ w = np.ones_like(x)
1816
+ k = operator.index(k)
1817
+
1818
+ axis = normalize_axis_index(axis, y.ndim)
1819
+
1820
+ y = np.moveaxis(y, axis, 0) # now internally interp axis is zero
1821
+ if not y.flags.c_contiguous:
1822
+ # C routines in _dierckx currently require C contiguity
1823
+ y = y.copy(order='C')
1824
+
1825
+ if x.ndim != 1:
1826
+ raise ValueError("Expect x to be a 1-D sequence.")
1827
+ if x.shape[0] < k+1:
1828
+ raise ValueError("Need more x points.")
1829
+ if k < 0:
1830
+ raise ValueError("Expect non-negative k.")
1831
+ if t.ndim != 1 or np.any(t[1:] - t[:-1] < 0):
1832
+ raise ValueError("Expect t to be a 1D strictly increasing sequence.")
1833
+ if x.size != y.shape[0]:
1834
+ raise ValueError(f'Shapes of x {x.shape} and y {y.shape} are incompatible')
1835
+ if k > 0 and np.any((x < t[k]) | (x > t[-k])):
1836
+ raise ValueError(f'Out of bounds w/ x = {x}.')
1837
+ if x.size != w.size:
1838
+ raise ValueError(f'Shapes of x {x.shape} and w {w.shape} are incompatible')
1839
+ if method == "norm-eq" and np.any(x[1:] - x[:-1] <= 0):
1840
+ raise ValueError("Expect x to be a 1D strictly increasing sequence.")
1841
+ if method == "qr" and any(x[1:] - x[:-1] < 0):
1842
+ raise ValueError("Expect x to be a 1D non-decreasing sequence.")
1843
+
1844
+ # number of coefficients
1845
+ n = t.size - k - 1
1846
+
1847
+ # complex y: view as float, preserve the length
1848
+ was_complex = y.dtype.kind == 'c'
1849
+ yy = y.view(float)
1850
+ if was_complex and y.ndim == 1:
1851
+ yy = yy.reshape(y.shape[0], 2)
1852
+
1853
+ # multiple r.h.s
1854
+ extradim = prod(yy.shape[1:])
1855
+ yy = yy.reshape(-1, extradim)
1856
+
1857
+ # complex y: view as float, preserve the length
1858
+ was_complex = y.dtype.kind == 'c'
1859
+ yy = y.view(float)
1860
+ if was_complex and y.ndim == 1:
1861
+ yy = yy.reshape(y.shape[0], 2)
1862
+
1863
+ # multiple r.h.s
1864
+ extradim = prod(yy.shape[1:])
1865
+ yy = yy.reshape(-1, extradim)
1866
+
1867
+ if method == "norm-eq":
1868
+ # construct A.T @ A and rhs with A the colocation matrix, and
1869
+ # rhs = A.T @ y for solving the LSQ problem ``A.T @ A @ c = A.T @ y``
1870
+ lower = True
1871
+ ab = np.zeros((k+1, n), dtype=np.float64, order='F')
1872
+ rhs = np.zeros((n, extradim), dtype=np.float64)
1873
+ _dierckx._norm_eq_lsq(x, t, k,
1874
+ yy,
1875
+ w,
1876
+ ab.T, rhs)
1877
+
1878
+ # undo complex -> float and flattening the trailing dims
1879
+ if was_complex:
1880
+ rhs = rhs.view(complex)
1881
+
1882
+ rhs = rhs.reshape((n,) + y.shape[1:])
1883
+
1884
+ # have observation matrix & rhs, can solve the LSQ problem
1885
+ cho_decomp = cholesky_banded(ab, overwrite_ab=True, lower=lower,
1886
+ check_finite=check_finite)
1887
+ m = rhs.shape[0]
1888
+ c = cho_solve_banded((cho_decomp, lower), rhs.reshape(m, -1), overwrite_b=True,
1889
+ check_finite=check_finite).reshape(rhs.shape)
1890
+ elif method == "qr":
1891
+ _, _, c, _, _ = _lsq_solve_qr(x, yy, t, k, w)
1892
+
1893
+ if was_complex:
1894
+ c = c.view(complex)
1895
+
1896
+ else:
1897
+ raise ValueError(f"Unknown {method =}.")
1898
+
1899
+
1900
+ # restore the shape of `c` for both single and multiple r.h.s.
1901
+ c = c.reshape((n,) + y.shape[1:])
1902
+ c = np.ascontiguousarray(c)
1903
+ t, c = xp.asarray(t), xp.asarray(c)
1904
+ return BSpline.construct_fast(t, c, k, axis=axis)
1905
+
1906
+
1907
+ ######################
1908
+ # LSQ spline helpers #
1909
+ ######################
1910
+
1911
+ def _lsq_solve_qr_for_root_rati_periodic(x, y, t, k, w):
1912
+ """Solve for the LSQ spline coeffs given x, y and knots.
1913
+
1914
+ `y` is always 2D: for 1D data, the shape is ``(m, 1)``.
1915
+ `w` is always 1D: one weight value per `x` value.
1916
+
1917
+ """
1918
+ y_w = y * w[:, None]
1919
+ # Ref: https://github.com/scipy/scipy/blob/maintenance/1.16.x/scipy/interpolate/fitpack/fpperi.f#L221-L238
1920
+ R, H1, H2, offset, nc = _dierckx.data_matrix_periodic(x, t, k, w, False)
1921
+ # Ref: https://github.com/scipy/scipy/blob/maintenance/1.16.x/scipy/interpolate/fitpack/fpperi.f#L239-L314
1922
+ A1, A2, Z, p, _ = _dierckx.qr_reduce_periodic(
1923
+ R, H1, H2, offset, nc, y_w, k,
1924
+ len(t), True
1925
+ ) # modifies arguments in-place
1926
+ # Ref: https://github.com/scipy/scipy/blob/main/scipy/interpolate/fitpack/fpbacp.f
1927
+ c, residuals, _ = _dierckx.fpbacp(A1, A2, Z, k, k, x, y, t, w)
1928
+ return R, A1, A2, Z, y_w, c, p, residuals
1929
+
1930
+
1931
+ def _lsq_solve_qr(x, y, t, k, w, periodic=False):
1932
+ """Solve for the LSQ spline coeffs given x, y and knots.
1933
+
1934
+ `y` is always 2D: for 1D data, the shape is ``(m, 1)``.
1935
+ `w` is always 1D: one weight value per `x` value.
1936
+
1937
+ """
1938
+ y_w = y * w[:, None]
1939
+ if not periodic:
1940
+ A, offset, nc = _dierckx.data_matrix(x, t, k, w)
1941
+ _dierckx.qr_reduce(A, offset, nc, y_w) # modifies arguments in-place
1942
+ c, residuals, fp = _dierckx.fpback(A, nc, x, y, t, k, w, y_w)
1943
+ return A, y_w, c, fp, residuals
1944
+ else:
1945
+ # Ref: https://github.com/scipy/scipy/blob/maintenance/1.16.x/scipy/interpolate/fitpack/fpperi.f#L221-L238
1946
+ R, H1, H2, offset, nc = _dierckx.data_matrix_periodic(x, t, k, w, False)
1947
+ # Ref: https://github.com/scipy/scipy/blob/maintenance/1.16.x/scipy/interpolate/fitpack/fpperi.f#L239-L314
1948
+ A1, A2, Z, fp = _dierckx.qr_reduce_periodic(
1949
+ R, H1, H2, offset, nc, y_w, k,
1950
+ len(t), False) # modifies arguments in-place
1951
+ # Ref: https://github.com/scipy/scipy/blob/main/scipy/interpolate/fitpack/fpbacp.f
1952
+ c, residuals, _ = _dierckx.fpbacp(A1, A2, Z, k, k, x, y, t, w)
1953
+ return R, y_w, c, fp, residuals
1954
+
1955
+
1956
+
1957
+
1958
+ #############################
1959
+ # Smoothing spline helpers #
1960
+ #############################
1961
+
1962
+ def _compute_optimal_gcv_parameter(X, wE, y, w):
1963
+ """
1964
+ Returns an optimal regularization parameter from the GCV criteria [1].
1965
+
1966
+ Parameters
1967
+ ----------
1968
+ X : array, shape (5, n)
1969
+ 5 bands of the design matrix ``X`` stored in LAPACK banded storage.
1970
+ wE : array, shape (5, n)
1971
+ 5 bands of the penalty matrix :math:`W^{-1} E` stored in LAPACK banded
1972
+ storage.
1973
+ y : array, shape (n,)
1974
+ Ordinates.
1975
+ w : array, shape (n,)
1976
+ Vector of weights.
1977
+
1978
+ Returns
1979
+ -------
1980
+ lam : float
1981
+ An optimal from the GCV criteria point of view regularization
1982
+ parameter.
1983
+
1984
+ Notes
1985
+ -----
1986
+ No checks are performed.
1987
+
1988
+ References
1989
+ ----------
1990
+ .. [1] G. Wahba, "Estimating the smoothing parameter" in Spline models
1991
+ for observational data, Philadelphia, Pennsylvania: Society for
1992
+ Industrial and Applied Mathematics, 1990, pp. 45-65.
1993
+ :doi:`10.1137/1.9781611970128`
1994
+
1995
+ """
1996
+
1997
+ def compute_banded_symmetric_XT_W_Y(X, w, Y):
1998
+ """
1999
+ Assuming that the product :math:`X^T W Y` is symmetric and both ``X``
2000
+ and ``Y`` are 5-banded, compute the unique bands of the product.
2001
+
2002
+ Parameters
2003
+ ----------
2004
+ X : array, shape (5, n)
2005
+ 5 bands of the matrix ``X`` stored in LAPACK banded storage.
2006
+ w : array, shape (n,)
2007
+ Array of weights
2008
+ Y : array, shape (5, n)
2009
+ 5 bands of the matrix ``Y`` stored in LAPACK banded storage.
2010
+
2011
+ Returns
2012
+ -------
2013
+ res : array, shape (4, n)
2014
+ The result of the product :math:`X^T Y` stored in the banded way.
2015
+
2016
+ Notes
2017
+ -----
2018
+ As far as the matrices ``X`` and ``Y`` are 5-banded, their product
2019
+ :math:`X^T W Y` is 7-banded. It is also symmetric, so we can store only
2020
+ unique diagonals.
2021
+
2022
+ """
2023
+ # compute W Y
2024
+ W_Y = np.copy(Y)
2025
+
2026
+ W_Y[2] *= w
2027
+ for i in range(2):
2028
+ W_Y[i, 2 - i:] *= w[:-2 + i]
2029
+ W_Y[3 + i, :-1 - i] *= w[1 + i:]
2030
+
2031
+ n = X.shape[1]
2032
+ res = np.zeros((4, n))
2033
+ for i in range(n):
2034
+ for j in range(min(n-i, 4)):
2035
+ res[-j-1, i + j] = sum(X[j:, i] * W_Y[:5-j, i + j])
2036
+ return res
2037
+
2038
+ def compute_b_inv(A):
2039
+ """
2040
+ Inverse 3 central bands of matrix :math:`A=U^T D^{-1} U` assuming that
2041
+ ``U`` is a unit upper triangular banded matrix using an algorithm
2042
+ proposed in [1].
2043
+
2044
+ Parameters
2045
+ ----------
2046
+ A : array, shape (4, n)
2047
+ Matrix to inverse, stored in LAPACK banded storage.
2048
+
2049
+ Returns
2050
+ -------
2051
+ B : array, shape (4, n)
2052
+ 3 unique bands of the symmetric matrix that is an inverse to ``A``.
2053
+ The first row is filled with zeros.
2054
+
2055
+ Notes
2056
+ -----
2057
+ The algorithm is based on the cholesky decomposition and, therefore,
2058
+ in case matrix ``A`` is close to not positive defined, the function
2059
+ raises LinalgError.
2060
+
2061
+ Both matrices ``A`` and ``B`` are stored in LAPACK banded storage.
2062
+
2063
+ References
2064
+ ----------
2065
+ .. [1] M. F. Hutchinson and F. R. de Hoog, "Smoothing noisy data with
2066
+ spline functions," Numerische Mathematik, vol. 47, no. 1,
2067
+ pp. 99-106, 1985.
2068
+ :doi:`10.1007/BF01389878`
2069
+
2070
+ """
2071
+
2072
+ def find_b_inv_elem(i, j, U, D, B):
2073
+ rng = min(3, n - i - 1)
2074
+ rng_sum = 0.
2075
+ if j == 0:
2076
+ # use 2-nd formula from [1]
2077
+ for k in range(1, rng + 1):
2078
+ rng_sum -= U[-k - 1, i + k] * B[-k - 1, i + k]
2079
+ rng_sum += D[i]
2080
+ B[-1, i] = rng_sum
2081
+ else:
2082
+ # use 1-st formula from [1]
2083
+ for k in range(1, rng + 1):
2084
+ diag = abs(k - j)
2085
+ ind = i + min(k, j)
2086
+ rng_sum -= U[-k - 1, i + k] * B[-diag - 1, ind + diag]
2087
+ B[-j - 1, i + j] = rng_sum
2088
+
2089
+ U = cholesky_banded(A)
2090
+ for i in range(2, 5):
2091
+ U[-i, i-1:] /= U[-1, :-i+1]
2092
+ D = 1. / (U[-1])**2
2093
+ U[-1] /= U[-1]
2094
+
2095
+ n = U.shape[1]
2096
+
2097
+ B = np.zeros(shape=(4, n))
2098
+ for i in range(n - 1, -1, -1):
2099
+ for j in range(min(3, n - i - 1), -1, -1):
2100
+ find_b_inv_elem(i, j, U, D, B)
2101
+ # the first row contains garbage and should be removed
2102
+ B[0] = [0.] * n
2103
+ return B
2104
+
2105
+ def _gcv(lam, X, XtWX, wE, XtE, y):
2106
+ r"""
2107
+ Computes the generalized cross-validation criteria [1].
2108
+
2109
+ Parameters
2110
+ ----------
2111
+ lam : float, (:math:`\lambda \geq 0`)
2112
+ Regularization parameter.
2113
+ X : array, shape (5, n)
2114
+ Matrix is stored in LAPACK banded storage.
2115
+ XtWX : array, shape (4, n)
2116
+ Product :math:`X^T W X` stored in LAPACK banded storage.
2117
+ wE : array, shape (5, n)
2118
+ Matrix :math:`W^{-1} E` stored in LAPACK banded storage.
2119
+ XtE : array, shape (4, n)
2120
+ Product :math:`X^T E` stored in LAPACK banded storage.
2121
+
2122
+ Returns
2123
+ -------
2124
+ res : float
2125
+ Value of the GCV criteria with the regularization parameter
2126
+ :math:`\lambda`.
2127
+
2128
+ Notes
2129
+ -----
2130
+ Criteria is computed from the formula (1.3.2) [3]:
2131
+
2132
+ .. math:
2133
+
2134
+ GCV(\lambda) = \dfrac{1}{n} \sum\limits_{k = 1}^{n} \dfrac{ \left(
2135
+ y_k - f_{\lambda}(x_k) \right)^2}{\left( 1 - \Tr{A}/n\right)^2}$.
2136
+ The criteria is discussed in section 1.3 [3].
2137
+
2138
+ The numerator is computed using (2.2.4) [3] and the denominator is
2139
+ computed using an algorithm from [2] (see in the ``compute_b_inv``
2140
+ function).
2141
+
2142
+ References
2143
+ ----------
2144
+ .. [1] G. Wahba, "Estimating the smoothing parameter" in Spline models
2145
+ for observational data, Philadelphia, Pennsylvania: Society for
2146
+ Industrial and Applied Mathematics, 1990, pp. 45-65.
2147
+ :doi:`10.1137/1.9781611970128`
2148
+ .. [2] M. F. Hutchinson and F. R. de Hoog, "Smoothing noisy data with
2149
+ spline functions," Numerische Mathematik, vol. 47, no. 1,
2150
+ pp. 99-106, 1985.
2151
+ :doi:`10.1007/BF01389878`
2152
+ .. [3] E. Zemlyanoy, "Generalized cross-validation smoothing splines",
2153
+ BSc thesis, 2022. Might be available (in Russian)
2154
+ `here <https://www.hse.ru/ba/am/students/diplomas/620910604>`_
2155
+
2156
+ """
2157
+ # Compute the numerator from (2.2.4) [3]
2158
+ n = X.shape[1]
2159
+ c = solve_banded((2, 2), X + lam * wE, y)
2160
+ res = np.zeros(n)
2161
+ # compute ``W^{-1} E c`` with respect to banded-storage of ``E``
2162
+ tmp = wE * c
2163
+ for i in range(n):
2164
+ for j in range(max(0, i - n + 3), min(5, i + 3)):
2165
+ res[i] += tmp[j, i + 2 - j]
2166
+ numer = np.linalg.norm(lam * res)**2 / n
2167
+
2168
+ # compute the denominator
2169
+ lhs = XtWX + lam * XtE
2170
+ try:
2171
+ b_banded = compute_b_inv(lhs)
2172
+ # compute the trace of the product b_banded @ XtX
2173
+ tr = b_banded * XtWX
2174
+ tr[:-1] *= 2
2175
+ # find the denominator
2176
+ denom = (1 - sum(sum(tr)) / n)**2
2177
+ except LinAlgError:
2178
+ # cholesky decomposition cannot be performed
2179
+ raise ValueError('Seems like the problem is ill-posed')
2180
+
2181
+ res = numer / denom
2182
+
2183
+ return res
2184
+
2185
+ n = X.shape[1]
2186
+
2187
+ XtWX = compute_banded_symmetric_XT_W_Y(X, w, X)
2188
+ XtE = compute_banded_symmetric_XT_W_Y(X, w, wE)
2189
+
2190
+ if y.ndim == 1:
2191
+ gcv_est = minimize_scalar(
2192
+ _gcv, bounds=(0, n), method='Bounded', args=(X, XtWX, wE, XtE, y)
2193
+ )
2194
+ if gcv_est.success:
2195
+ return gcv_est.x
2196
+ raise ValueError(f"Unable to find minimum of the GCV "
2197
+ f"function: {gcv_est.message}")
2198
+ elif y.ndim == 2:
2199
+ gcv_est = np.empty(y.shape[1])
2200
+ for i in range(y.shape[1]):
2201
+ est = minimize_scalar(
2202
+ _gcv, bounds=(0, n), method='Bounded', args=(X, XtWX, wE, XtE, y[:, i])
2203
+ )
2204
+ if est.success:
2205
+ gcv_est[i] = est.x
2206
+ else:
2207
+ raise ValueError(f"Unable to find minimum of the GCV "
2208
+ f"function: {gcv_est.message}")
2209
+ return gcv_est
2210
+ else:
2211
+ # trailing dims must have been flattened already.
2212
+ raise RuntimeError("Internal error. Please report it to scipy developers.")
2213
+
2214
+
2215
+ def _coeff_of_divided_diff(x):
2216
+ """
2217
+ Returns the coefficients of the divided difference.
2218
+
2219
+ Parameters
2220
+ ----------
2221
+ x : array, shape (n,)
2222
+ Array which is used for the computation of divided difference.
2223
+
2224
+ Returns
2225
+ -------
2226
+ res : array_like, shape (n,)
2227
+ Coefficients of the divided difference.
2228
+
2229
+ Notes
2230
+ -----
2231
+ Vector ``x`` should have unique elements, otherwise an error division by
2232
+ zero might be raised.
2233
+
2234
+ No checks are performed.
2235
+
2236
+ """
2237
+ n = x.shape[0]
2238
+ res = np.zeros(n)
2239
+ for i in range(n):
2240
+ pp = 1.
2241
+ for k in range(n):
2242
+ if k != i:
2243
+ pp *= (x[i] - x[k])
2244
+ res[i] = 1. / pp
2245
+ return res
2246
+
2247
+
2248
+ @xp_capabilities(cpu_only=True, jax_jit=False, allow_dask_compute=True)
2249
+ def make_smoothing_spline(x, y, w=None, lam=None, *, axis=0):
2250
+ r"""
2251
+ Create a smoothing B-spline satisfying the Generalized Cross Validation (GCV) criterion.
2252
+
2253
+ Compute the (coefficients of) smoothing cubic spline function using
2254
+ ``lam`` to control the tradeoff between the amount of smoothness of the
2255
+ curve and its proximity to the data. In case ``lam`` is None, using the
2256
+ GCV criteria [1] to find it.
2257
+
2258
+ A smoothing spline is found as a solution to the regularized weighted
2259
+ linear regression problem:
2260
+
2261
+ .. math::
2262
+
2263
+ \sum\limits_{i=1}^n w_i\lvert y_i - f(x_i) \rvert^2 +
2264
+ \lambda\int\limits_{x_1}^{x_n} (f^{(2)}(u))^2 d u
2265
+
2266
+ where :math:`f` is a spline function, :math:`w` is a vector of weights and
2267
+ :math:`\lambda` is a regularization parameter.
2268
+
2269
+ If ``lam`` is None, we use the GCV criteria to find an optimal
2270
+ regularization parameter, otherwise we solve the regularized weighted
2271
+ linear regression problem with given parameter. The parameter controls
2272
+ the tradeoff in the following way: the larger the parameter becomes, the
2273
+ smoother the function gets.
2274
+
2275
+ Parameters
2276
+ ----------
2277
+ x : array_like, shape (n,)
2278
+ Abscissas. `n` must be at least 5.
2279
+ y : array_like, shape (n, ...)
2280
+ Ordinates. `n` must be at least 5.
2281
+ w : array_like, shape (n,), optional
2282
+ Vector of weights. Default is ``np.ones_like(x)``.
2283
+ lam : float, (:math:`\lambda \geq 0`), optional
2284
+ Regularization parameter. If ``lam`` is None, then it is found from
2285
+ the GCV criteria. Default is None.
2286
+ axis : int, optional
2287
+ The data axis. Default is zero.
2288
+ The assumption is that ``y.shape[axis] == n``, and all other axes of ``y``
2289
+ are batching axes.
2290
+
2291
+ Returns
2292
+ -------
2293
+ func : `BSpline` object
2294
+ An object representing a spline in the B-spline basis
2295
+ as a solution of the problem of smoothing splines using
2296
+ the GCV criteria [1] in case ``lam`` is None, otherwise using the
2297
+ given parameter ``lam``.
2298
+
2299
+ Notes
2300
+ -----
2301
+ This algorithm is a clean room reimplementation of the algorithm
2302
+ introduced by Woltring in FORTRAN [2]. The original version cannot be used
2303
+ in SciPy source code because of the license issues. The details of the
2304
+ reimplementation are discussed here (available only in Russian) [4].
2305
+
2306
+ If the vector of weights ``w`` is None, we assume that all the points are
2307
+ equal in terms of weights, and vector of weights is vector of ones.
2308
+
2309
+ Note that in weighted residual sum of squares, weights are not squared:
2310
+ :math:`\sum\limits_{i=1}^n w_i\lvert y_i - f(x_i) \rvert^2` while in
2311
+ ``splrep`` the sum is built from the squared weights.
2312
+
2313
+ In cases when the initial problem is ill-posed (for example, the product
2314
+ :math:`X^T W X` where :math:`X` is a design matrix is not a positive
2315
+ defined matrix) a ValueError is raised.
2316
+
2317
+ References
2318
+ ----------
2319
+ .. [1] G. Wahba, "Estimating the smoothing parameter" in Spline models for
2320
+ observational data, Philadelphia, Pennsylvania: Society for Industrial
2321
+ and Applied Mathematics, 1990, pp. 45-65.
2322
+ :doi:`10.1137/1.9781611970128`
2323
+ .. [2] H. J. Woltring, A Fortran package for generalized, cross-validatory
2324
+ spline smoothing and differentiation, Advances in Engineering
2325
+ Software, vol. 8, no. 2, pp. 104-113, 1986.
2326
+ :doi:`10.1016/0141-1195(86)90098-7`
2327
+ .. [3] T. Hastie, J. Friedman, and R. Tisbshirani, "Smoothing Splines" in
2328
+ The elements of Statistical Learning: Data Mining, Inference, and
2329
+ prediction, New York: Springer, 2017, pp. 241-249.
2330
+ :doi:`10.1007/978-0-387-84858-7`
2331
+ .. [4] E. Zemlyanoy, "Generalized cross-validation smoothing splines",
2332
+ BSc thesis, 2022.
2333
+ `<https://www.hse.ru/ba/am/students/diplomas/620910604>`_ (in
2334
+ Russian)
2335
+
2336
+ Examples
2337
+ --------
2338
+ Generate some noisy data
2339
+
2340
+ >>> import numpy as np
2341
+ >>> np.random.seed(1234)
2342
+ >>> n = 200
2343
+ >>> def func(x):
2344
+ ... return x**3 + x**2 * np.sin(4 * x)
2345
+ >>> x = np.sort(np.random.random_sample(n) * 4 - 2)
2346
+ >>> y = func(x) + np.random.normal(scale=1.5, size=n)
2347
+
2348
+ Make a smoothing spline function
2349
+
2350
+ >>> from scipy.interpolate import make_smoothing_spline
2351
+ >>> spl = make_smoothing_spline(x, y)
2352
+
2353
+ Plot both
2354
+
2355
+ >>> import matplotlib.pyplot as plt
2356
+ >>> grid = np.linspace(x[0], x[-1], 400)
2357
+ >>> plt.plot(x, y, '.')
2358
+ >>> plt.plot(grid, spl(grid), label='Spline')
2359
+ >>> plt.plot(grid, func(grid), label='Original function')
2360
+ >>> plt.legend(loc='best')
2361
+ >>> plt.show()
2362
+
2363
+ """ # noqa:E501
2364
+ xp = array_namespace(x, y)
2365
+
2366
+ x = np.ascontiguousarray(x, dtype=float)
2367
+ y = np.ascontiguousarray(y, dtype=float)
2368
+
2369
+ if any(x[1:] - x[:-1] <= 0):
2370
+ raise ValueError('``x`` should be an ascending array')
2371
+
2372
+ if x.ndim != 1 or x.shape[0] != y.shape[axis]:
2373
+ raise ValueError(f'``x`` should be 1D and {x.shape = } == {y.shape = }')
2374
+
2375
+ if w is None:
2376
+ w = np.ones(len(x))
2377
+ else:
2378
+ w = np.ascontiguousarray(w)
2379
+ if any(w <= 0):
2380
+ raise ValueError('Invalid vector of weights')
2381
+
2382
+ t = np.r_[[x[0]] * 3, x, [x[-1]] * 3]
2383
+ n = x.shape[0]
2384
+
2385
+ if n <= 4:
2386
+ raise ValueError('``x`` and ``y`` length must be at least 5')
2387
+
2388
+ # Internals assume that the data axis is the zero-th axis
2389
+ axis = normalize_axis_index(axis, y.ndim)
2390
+ y = np.moveaxis(y, axis, 0)
2391
+
2392
+ # flatten the trailing axes of y to simplify further manipulations
2393
+ y_shape1 = y.shape[1:]
2394
+ if y_shape1 != ():
2395
+ y = y.reshape((n, -1))
2396
+
2397
+ # It is known that the solution to the stated minimization problem exists
2398
+ # and is a natural cubic spline with vector of knots equal to the unique
2399
+ # elements of ``x`` [3], so we will solve the problem in the basis of
2400
+ # natural splines.
2401
+
2402
+ # create design matrix in the B-spline basis
2403
+ X_bspl = BSpline.design_matrix(x, t, 3)
2404
+ # move from B-spline basis to the basis of natural splines using equations
2405
+ # (2.1.7) [4]
2406
+ # central elements
2407
+ X = np.zeros((5, n))
2408
+ for i in range(1, 4):
2409
+ X[i, 2: -2] = X_bspl[i: i - 4, 3: -3][np.diag_indices(n - 4)]
2410
+
2411
+ # first elements
2412
+ X[1, 1] = X_bspl[0, 0]
2413
+ X[2, :2] = ((x[2] + x[1] - 2 * x[0]) * X_bspl[0, 0],
2414
+ X_bspl[1, 1] + X_bspl[1, 2])
2415
+ X[3, :2] = ((x[2] - x[0]) * X_bspl[1, 1], X_bspl[2, 2])
2416
+
2417
+ # last elements
2418
+ X[1, -2:] = (X_bspl[-3, -3], (x[-1] - x[-3]) * X_bspl[-2, -2])
2419
+ X[2, -2:] = (X_bspl[-2, -3] + X_bspl[-2, -2],
2420
+ (2 * x[-1] - x[-2] - x[-3]) * X_bspl[-1, -1])
2421
+ X[3, -2] = X_bspl[-1, -1]
2422
+
2423
+ # create penalty matrix and divide it by vector of weights: W^{-1} E
2424
+ wE = np.zeros((5, n))
2425
+ wE[2:, 0] = _coeff_of_divided_diff(x[:3]) / w[:3]
2426
+ wE[1:, 1] = _coeff_of_divided_diff(x[:4]) / w[:4]
2427
+ for j in range(2, n - 2):
2428
+ wE[:, j] = (x[j+2] - x[j-2]) * _coeff_of_divided_diff(x[j-2:j+3])\
2429
+ / w[j-2: j+3]
2430
+
2431
+ wE[:-1, -2] = -_coeff_of_divided_diff(x[-4:]) / w[-4:]
2432
+ wE[:-2, -1] = _coeff_of_divided_diff(x[-3:]) / w[-3:]
2433
+ wE *= 6
2434
+
2435
+ if lam is None:
2436
+ lam = _compute_optimal_gcv_parameter(X, wE, y, w)
2437
+ elif lam < 0.:
2438
+ raise ValueError('Regularization parameter should be non-negative')
2439
+
2440
+ # solve the initial problem in the basis of natural splines
2441
+ if np.ndim(lam) == 0:
2442
+ c = solve_banded((2, 2), X + lam * wE, y)
2443
+ elif np.ndim(lam) == 1:
2444
+ # XXX: solve_banded does not suppport batched `ab` matrices; loop manually
2445
+ c = np.empty((n, lam.shape[0]))
2446
+ for i in range(lam.shape[0]):
2447
+ c[:, i] = solve_banded((2, 2), X + lam[i] * wE, y[:, i])
2448
+ else:
2449
+ # this should not happen, ever
2450
+ raise RuntimeError("Internal error, please report it to SciPy developers.")
2451
+ c = c.reshape((c.shape[0], *y_shape1))
2452
+
2453
+ # hack: these are c[0], c[1] etc, shape-compatible with np.r_ below
2454
+ c0, c1 = c[0:1, ...], c[1:2, ...] # c[0], c[1]
2455
+ cm0, cm1 = c[-1:-2:-1, ...], c[-2:-3:-1, ...] # c[-1], c[-2]
2456
+
2457
+ # move back to B-spline basis using equations (2.2.10) [4]
2458
+ c_ = np.r_[c0 * (t[5] + t[4] - 2 * t[3]) + c1,
2459
+ c0 * (t[5] - t[3]) + c1,
2460
+ c[1: -1, ...],
2461
+ cm0 * (t[-4] - t[-6]) + cm1,
2462
+ cm0 * (2 * t[-4] - t[-5] - t[-6]) + cm1]
2463
+
2464
+ t, c_ = xp.asarray(t), xp.asarray(c_)
2465
+ return BSpline.construct_fast(t, c_, 3, axis=axis)
2466
+
2467
+
2468
+ ########################
2469
+ # FITPACK look-alikes #
2470
+ ########################
2471
+
2472
+ def fpcheck(x, t, k, periodic=False):
2473
+ """Check consistency of data vector `x` and knot vector `t`.
2474
+
2475
+ Parameters
2476
+ ----------
2477
+ x : array_like, shape (m,)
2478
+ 1D sorted array of data points.
2479
+ t : array_like, shape (n,)
2480
+ 1D non-decreasing knot vector.
2481
+ k : int
2482
+ Degree of the spline.
2483
+ periodic : bool, optional
2484
+ Whether the spline is periodic. Default is False.
2485
+
2486
+ Raises
2487
+ ------
2488
+ ValueError
2489
+ If the configuration of `x`, `t`, and `k` violates any required condition.
2490
+ """
2491
+ # This routine is a unified clone of the FITPACK Fortran routines `fpchec.f`
2492
+ # and `fpchep.f`:
2493
+ # - https://github.com/scipy/scipy/blob/main/scipy/interpolate/fitpack/fpchec.f
2494
+ # - https://github.com/scipy/scipy/blob/main/scipy/interpolate/fitpack/fpchep.f
2495
+ #
2496
+ # These routines verify the number and position of the knots t(j), j=1,...,n,
2497
+ # of a spline of degree k, relative to the number and distribution of data points
2498
+ # x(i), i=1,...,m. If all of the following conditions are fulfilled,
2499
+ # validation passes.
2500
+ #
2501
+ # For non-periodic splines:
2502
+ # 1) k+1 <= n-k-1 <= m
2503
+ # 2) t(1) <= t(2) <= ... <= t(k+1)
2504
+ # t(n-k) <= t(n-k+1) <= ... <= t(n)
2505
+ # 3) t(k+1) < t(k+2) < ... < t(n-k)
2506
+ # 4) t(k+1) <= x(i) <= t(n-k)
2507
+ # 5) Schoenberg-Whitney conditions hold: there exists a subset y(j) such that
2508
+ # t(j) < y(j) < t(j+k+1), for j = 1, ..., n-k-1
2509
+ #
2510
+ # For periodic splines:
2511
+ # 1) k+1 <= n-k-1 <= m + k - 1
2512
+ # 2) Same boundary knot monotonicity as above
2513
+ # 3) Same strict interior knot increase as above
2514
+ # 4) t(k+1) <= x(i) <= t(n-k)
2515
+ # 5) Schoenberg-Whitney conditions must hold for *some periodic shift*
2516
+ # of the data sequence; i.e. wrapped data points x(i) must satisfy
2517
+ # t(j) < y(j) < t(j+k+1), j = k+1, ..., n-k-1
2518
+ x = np.asarray(x)
2519
+ t = np.asarray(t)
2520
+
2521
+ if x.ndim != 1 or t.ndim != 1:
2522
+ raise ValueError(f"Expect `x` and `t` be 1D sequences. Got {x = } and {t = }")
2523
+
2524
+ m = x.shape[0]
2525
+ n = t.shape[0]
2526
+ nk1 = n - k - 1
2527
+
2528
+ # check condition no 1
2529
+ if periodic:
2530
+ # c 1) k+1 <= nk1 <= m+k-1
2531
+ if not (k + 1 <= nk1 <= m + k - 1):
2532
+ raise ValueError(f"Need k+1 <= n-k-1 <= m+k-1. Got {m = }, {n = }, {k = }")
2533
+ else:
2534
+ # c 1) k+1 <= n-k-1 <= m
2535
+ if not (k + 1 <= nk1 <= m):
2536
+ raise ValueError(f"Need k+1 <= n-k-1 <= m. Got {m = }, {n = } and {k = }.")
2537
+
2538
+ # check condition no 2
2539
+ # c 2) t(1) <= t(2) <= ... <= t(k+1)
2540
+ # c t(n-k) <= t(n-k+1) <= ... <= t(n)
2541
+ if (t[:k+1] > t[1:k+2]).any():
2542
+ raise ValueError(f"First k knots must be ordered; got {t = }.")
2543
+
2544
+ if (t[nk1:] < t[nk1-1:-1]).any():
2545
+ raise ValueError(f"Last k knots must be ordered; got {t = }.")
2546
+
2547
+ # c check condition no 3
2548
+ # c 3) t(k+1) < t(k+2) < ... < t(n-k)
2549
+ if (t[k+1:n-k] <= t[k:n-k-1]).any():
2550
+ raise ValueError(f"Internal knots must be distinct. Got {t = }.")
2551
+
2552
+ # c check condition no 4
2553
+ # c 4) t(k+1) <= x(i) <= t(n-k)
2554
+ # NB: FITPACK's fpchec only checks x[0] & x[-1], so we follow.
2555
+ if (x[0] < t[k]) or (x[-1] > t[n-k-1]):
2556
+ raise ValueError(f"Out of bounds: {x = } and {t = }.")
2557
+
2558
+ # c check condition no 5
2559
+ # c 5) the conditions specified by Schoenberg and Whitney must hold
2560
+ # c for at least one subset of data points y(j) such that
2561
+ # c t(j) < y(j) < t(j+k+1)
2562
+ # c
2563
+ # c For non-periodic splines:
2564
+ # c j = 1, 2, ..., n-k-1 (i.e., j in [1, n-k-1])
2565
+ # c The data points must lie strictly inside some B-spline supports.
2566
+ # c
2567
+ # c For periodic splines:
2568
+ # c j = k+1, ..., n-k-1
2569
+ # c The condition must hold for a wrapped subset of the data points,
2570
+ # c i.e., there exists a cyclic shift of the data such that
2571
+ # c t(j) < x(i) < t(j+k+1)
2572
+ # c holds for all j in that range. The test must account for the
2573
+ # c periodic domain length: per = t(n-k) - t(k+1), and wrap around x(i)
2574
+ # c as x(i) + per if needed.
2575
+ mesg = f"Schoenberg-Whitney condition is violated with {t = } and {x =}."
2576
+
2577
+ if periodic:
2578
+ per = t[n - k - 1] - t[k]
2579
+ m1 = m - 1
2580
+ for shift in range(1, m):
2581
+ for j in range(k, nk1):
2582
+ tj = t[j]
2583
+ tl = t[j + k + 1]
2584
+ found = False
2585
+ for i in range(shift, shift + m1 + 1):
2586
+ idx = i if i < m else i - m
2587
+ xi = x[idx] + (0 if i < m else per)
2588
+ if tj < xi < tl:
2589
+ found = True
2590
+ break
2591
+ if not found:
2592
+ break
2593
+ else:
2594
+ return
2595
+ raise ValueError(mesg)
2596
+ else:
2597
+ if (x[0] >= t[k+1]) or (x[-1] <= t[n-k-2]):
2598
+ raise ValueError(mesg)
2599
+
2600
+ m = x.shape[0]
2601
+ l = k+1
2602
+ nk3 = n - k - 3
2603
+ if nk3 < 2:
2604
+ return
2605
+ for j in range(1, nk3+1):
2606
+ tj = t[j]
2607
+ l += 1
2608
+ tl = t[l]
2609
+ i = np.argmax(x > tj)
2610
+ if i >= m-1:
2611
+ raise ValueError(mesg)
2612
+ if x[i] >= tl:
2613
+ raise ValueError(mesg)
2614
+ return
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_cubic.py ADDED
@@ -0,0 +1,1029 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """Interpolation algorithms using piecewise cubic polynomials."""
2
+
3
+ from typing import Literal
4
+
5
+ import numpy as np
6
+
7
+ from scipy.linalg import solve, solve_banded
8
+ from scipy._lib._array_api import array_namespace, xp_size, xp_capabilities
9
+ from scipy._lib.array_api_compat import numpy as np_compat
10
+
11
+ from . import PPoly
12
+ from ._polyint import _isscalar
13
+
14
+ __all__ = ["CubicHermiteSpline", "PchipInterpolator", "pchip_interpolate",
15
+ "Akima1DInterpolator", "CubicSpline"]
16
+
17
+
18
+ def prepare_input(x, y, axis, dydx=None, xp=None):
19
+ """Prepare input for cubic spline interpolators.
20
+
21
+ All data are converted to numpy arrays and checked for correctness.
22
+ Axes equal to `axis` of arrays `y` and `dydx` are moved to be the 0th
23
+ axis. The value of `axis` is converted to lie in
24
+ [0, number of dimensions of `y`).
25
+ """
26
+
27
+ x, y = map(xp.asarray, (x, y))
28
+ if xp.isdtype(x.dtype, "complex floating"):
29
+ raise ValueError("`x` must contain real values.")
30
+ x = xp.astype(x, xp.float64)
31
+
32
+ if xp.isdtype(y.dtype, "complex floating"):
33
+ dtype = xp.complex128
34
+ else:
35
+ dtype = xp.float64
36
+
37
+ if dydx is not None:
38
+ dydx = xp.asarray(dydx)
39
+ if y.shape != dydx.shape:
40
+ raise ValueError("The shapes of `y` and `dydx` must be identical.")
41
+ if xp.isdtype(dydx.dtype, "complex floating"):
42
+ dtype = xp.complex128
43
+ dydx = xp.astype(dydx, dtype, copy=False)
44
+
45
+ y = xp.astype(y, dtype, copy=False)
46
+ axis = axis % y.ndim
47
+ if x.ndim != 1:
48
+ raise ValueError("`x` must be 1-dimensional.")
49
+ if x.shape[0] < 2:
50
+ raise ValueError("`x` must contain at least 2 elements.")
51
+ if x.shape[0] != y.shape[axis]:
52
+ raise ValueError(f"The length of `y` along `axis`={axis} doesn't "
53
+ "match the length of `x`")
54
+
55
+ if not xp.all(xp.isfinite(x)):
56
+ raise ValueError("`x` must contain only finite values.")
57
+ if not xp.all(xp.isfinite(y)):
58
+ raise ValueError("`y` must contain only finite values.")
59
+
60
+ if dydx is not None and not xp.all(xp.isfinite(dydx)):
61
+ raise ValueError("`dydx` must contain only finite values.")
62
+
63
+ dx = xp.diff(x)
64
+ if xp.any(dx <= 0):
65
+ raise ValueError("`x` must be strictly increasing sequence.")
66
+
67
+ y = xp.moveaxis(y, axis, 0)
68
+ if dydx is not None:
69
+ dydx = xp.moveaxis(dydx, axis, 0)
70
+
71
+ return x, dx, y, axis, dydx
72
+
73
+
74
+ @xp_capabilities(
75
+ cpu_only=True, jax_jit=False,
76
+ skip_backends=[
77
+ ("dask.array",
78
+ "https://github.com/data-apis/array-api-extra/issues/488")
79
+ ]
80
+ )
81
+ class CubicHermiteSpline(PPoly):
82
+ """Piecewise cubic interpolator to fit values and first derivatives (C1 smooth).
83
+
84
+ The result is represented as a `PPoly` instance.
85
+
86
+ Parameters
87
+ ----------
88
+ x : array_like, shape (n,)
89
+ 1-D array containing values of the independent variable.
90
+ Values must be real, finite and in strictly increasing order.
91
+ y : array_like
92
+ Array containing values of the dependent variable. It can have
93
+ arbitrary number of dimensions, but the length along ``axis``
94
+ (see below) must match the length of ``x``. Values must be finite.
95
+ dydx : array_like
96
+ Array containing derivatives of the dependent variable. It can have
97
+ arbitrary number of dimensions, but the length along ``axis``
98
+ (see below) must match the length of ``x``. Values must be finite.
99
+ axis : int, optional
100
+ Axis along which `y` is assumed to be varying. Meaning that for
101
+ ``x[i]`` the corresponding values are ``np.take(y, i, axis=axis)``.
102
+ Default is 0.
103
+ extrapolate : {bool, 'periodic', None}, optional
104
+ If bool, determines whether to extrapolate to out-of-bounds points
105
+ based on first and last intervals, or to return NaNs. If 'periodic',
106
+ periodic extrapolation is used. If None (default), it is set to True.
107
+
108
+ Attributes
109
+ ----------
110
+ x : ndarray, shape (n,)
111
+ Breakpoints. The same ``x`` which was passed to the constructor.
112
+ c : ndarray, shape (4, n-1, ...)
113
+ Coefficients of the polynomials on each segment. The trailing
114
+ dimensions match the dimensions of `y`, excluding ``axis``.
115
+ For example, if `y` is 1-D, then ``c[k, i]`` is a coefficient for
116
+ ``(x-x[i])**(3-k)`` on the segment between ``x[i]`` and ``x[i+1]``.
117
+ axis : int
118
+ Interpolation axis. The same axis which was passed to the
119
+ constructor.
120
+
121
+ Methods
122
+ -------
123
+ __call__
124
+ derivative
125
+ antiderivative
126
+ integrate
127
+ solve
128
+ roots
129
+
130
+ See Also
131
+ --------
132
+ Akima1DInterpolator : Akima 1D interpolator.
133
+ PchipInterpolator : PCHIP 1-D monotonic cubic interpolator.
134
+ CubicSpline : Cubic spline data interpolator.
135
+ PPoly : Piecewise polynomial in terms of coefficients and breakpoints
136
+
137
+ Notes
138
+ -----
139
+ If you want to create a higher-order spline matching higher-order
140
+ derivatives, use `BPoly.from_derivatives`.
141
+
142
+ References
143
+ ----------
144
+ .. [1] `Cubic Hermite spline
145
+ <https://en.wikipedia.org/wiki/Cubic_Hermite_spline>`_
146
+ on Wikipedia.
147
+ """
148
+
149
+ def __init__(self, x, y, dydx, axis=0, extrapolate=None):
150
+ xp = array_namespace(x, y, dydx)
151
+
152
+ if extrapolate is None:
153
+ extrapolate = True
154
+
155
+ x, dx, y, axis, dydx = prepare_input(x, y, axis, dydx, xp=xp)
156
+
157
+ dxr = xp.reshape(dx, (dx.shape[0], ) + (1, ) * (y.ndim - 1))
158
+ slope = xp.diff(y, axis=0) / dxr
159
+ t = (dydx[:-1, ...] + dydx[1:, ...] - 2 * slope) / dxr
160
+
161
+ c = xp.stack((
162
+ t / dxr,
163
+ (slope - dydx[:-1, ...]) / dxr - t,
164
+ dydx[:-1, ...],
165
+ y[:-1, ...]
166
+ ))
167
+
168
+ super().__init__(c, x, extrapolate=extrapolate)
169
+ self.axis = axis
170
+
171
+
172
+ @xp_capabilities(
173
+ cpu_only=True, jax_jit=False,
174
+ skip_backends=[
175
+ ("dask.array",
176
+ "https://github.com/data-apis/array-api-extra/issues/488")
177
+ ]
178
+ )
179
+ class PchipInterpolator(CubicHermiteSpline):
180
+ r"""PCHIP shape-preserving interpolator (C1 smooth).
181
+
182
+ ``x`` and ``y`` are arrays of values used to approximate some function f,
183
+ with ``y = f(x)``. The interpolant uses monotonic cubic splines
184
+ to find the value of new points. (PCHIP stands for Piecewise Cubic
185
+ Hermite Interpolating Polynomial).
186
+
187
+ Parameters
188
+ ----------
189
+ x : ndarray, shape (npoints, )
190
+ A 1-D array of monotonically increasing real values. ``x`` cannot
191
+ include duplicate values (otherwise f is overspecified)
192
+ y : ndarray, shape (..., npoints, ...)
193
+ An N-D array of real values. ``y``'s length along the interpolation
194
+ axis must be equal to the length of ``x``. Use the ``axis``
195
+ parameter to select the interpolation axis.
196
+ axis : int, optional
197
+ Axis in the ``y`` array corresponding to the x-coordinate values. Defaults
198
+ to ``axis=0``.
199
+ extrapolate : bool, optional
200
+ Whether to extrapolate to out-of-bounds points based on first
201
+ and last intervals, or to return NaNs.
202
+
203
+ Methods
204
+ -------
205
+ __call__
206
+ derivative
207
+ antiderivative
208
+ integrate
209
+ solve
210
+ roots
211
+
212
+
213
+ See Also
214
+ --------
215
+ CubicHermiteSpline : Piecewise-cubic interpolator.
216
+ Akima1DInterpolator : Akima 1D interpolator.
217
+ CubicSpline : Cubic spline data interpolator.
218
+ PPoly : Piecewise polynomial in terms of coefficients and breakpoints.
219
+
220
+ Notes
221
+ -----
222
+ The interpolator preserves monotonicity in the interpolation data and does
223
+ not overshoot if the data is not smooth.
224
+
225
+ The first derivatives are guaranteed to be continuous, but the second
226
+ derivatives may jump at :math:`x_k`.
227
+
228
+ Determines the derivatives at the points :math:`x_k`, :math:`f'_k`,
229
+ by using PCHIP algorithm [1]_.
230
+
231
+ Let :math:`h_k = x_{k+1} - x_k`, and :math:`d_k = (y_{k+1} - y_k) / h_k`
232
+ are the slopes at internal points :math:`x_k`.
233
+ If the signs of :math:`d_k` and :math:`d_{k-1}` are different or either of
234
+ them equals zero, then :math:`f'_k = 0`. Otherwise, it is given by the
235
+ weighted harmonic mean
236
+
237
+ .. math::
238
+
239
+ \frac{w_1 + w_2}{f'_k} = \frac{w_1}{d_{k-1}} + \frac{w_2}{d_k}
240
+
241
+ where :math:`w_1 = 2 h_k + h_{k-1}` and :math:`w_2 = h_k + 2 h_{k-1}`.
242
+
243
+ The end slopes are set using a one-sided scheme [2]_.
244
+
245
+
246
+ References
247
+ ----------
248
+ .. [1] F. N. Fritsch and J. Butland,
249
+ A method for constructing local
250
+ monotone piecewise cubic interpolants,
251
+ SIAM J. Sci. Comput., 5(2), 300-304 (1984).
252
+ :doi:`10.1137/0905021`.
253
+ .. [2] C. Moler, Numerical Computing with Matlab, 2004.
254
+ :doi:`10.1137/1.9780898717952`
255
+
256
+ """
257
+
258
+ # PchipInterpolator is not generic in scipy-stubs
259
+ __class_getitem__ = None
260
+
261
+ def __init__(self, x, y, axis=0, extrapolate=None):
262
+ xp = array_namespace(x, y)
263
+ x, _, y, axis, _ = prepare_input(x, y, axis, xp=xp)
264
+ if xp.isdtype(y.dtype, "complex floating"):
265
+ msg = ("`PchipInterpolator` only works with real values for `y`. "
266
+ "If you are trying to use the real components of the passed array, "
267
+ "use `np.real` on the array before passing to `PchipInterpolator`.")
268
+ raise ValueError(msg)
269
+ xv = xp.reshape(x, (x.shape[0],) + (1,)*(y.ndim-1))
270
+ dk = self._find_derivatives(xv, y, xp=xp)
271
+ super().__init__(x, y, dk, axis=0, extrapolate=extrapolate)
272
+ self.axis = axis
273
+
274
+ @staticmethod
275
+ def _edge_case(h0, h1, m0, m1, xp):
276
+ # one-sided three-point estimate for the derivative
277
+ d = ((2*h0 + h1)*m0 - h0*m1) / (h0 + h1)
278
+
279
+ # try to preserve shape
280
+ mask = xp.sign(d) != xp.sign(m0)
281
+ mask2 = (xp.sign(m0) != xp.sign(m1)) & (xp.abs(d) > 3.*xp.abs(m0))
282
+ mmm = (~mask) & mask2
283
+
284
+ d[mask] = 0.
285
+ d[mmm] = 3.*m0[mmm]
286
+
287
+ return d
288
+
289
+ @staticmethod
290
+ def _find_derivatives(x, y, xp):
291
+ # Determine the derivatives at the points y_k, d_k, by using
292
+ # PCHIP algorithm is:
293
+ # We choose the derivatives at the point x_k by
294
+ # Let m_k be the slope of the kth segment (between k and k+1)
295
+ # If m_k=0 or m_{k-1}=0 or sgn(m_k) != sgn(m_{k-1}) then d_k == 0
296
+ # else use weighted harmonic mean:
297
+ # w_1 = 2h_k + h_{k-1}, w_2 = h_k + 2h_{k-1}
298
+ # 1/d_k = 1/(w_1 + w_2)*(w_1 / m_k + w_2 / m_{k-1})
299
+ # where h_k is the spacing between x_k and x_{k+1}
300
+ y_shape = y.shape
301
+ if y.ndim == 1:
302
+ # So that _edge_case doesn't end up assigning to scalars
303
+ x = x[:, None]
304
+ y = y[:, None]
305
+
306
+ hk = x[1:] - x[:-1]
307
+ mk = (y[1:] - y[:-1]) / hk
308
+
309
+ if y.shape[0] == 2:
310
+ # edge case: only have two points, use linear interpolation
311
+ dk = xp.zeros_like(y)
312
+ dk[0] = mk
313
+ dk[1] = mk
314
+ return xp.reshape(dk, y_shape)
315
+
316
+ smk = xp.sign(mk)
317
+ condition = (smk[1:] != smk[:-1]) | (mk[1:] == 0) | (mk[:-1] == 0)
318
+
319
+ w1 = 2*hk[1:] + hk[:-1]
320
+ w2 = hk[1:] + 2*hk[:-1]
321
+
322
+ # values where division by zero occurs will be excluded
323
+ # by 'condition' afterwards
324
+ with np.errstate(divide='ignore', invalid='ignore'):
325
+ whmean = (w1/mk[:-1] + w2/mk[1:]) / (w1 + w2)
326
+
327
+ dk = np.zeros_like(y)
328
+ dk[1:-1][condition] = 0.0
329
+ dk[1:-1][~condition] = 1.0 / whmean[~condition]
330
+
331
+ # special case endpoints, as suggested in
332
+ # Cleve Moler, Numerical Computing with MATLAB, Chap 3.6 (pchiptx.m)
333
+ dk[0] = PchipInterpolator._edge_case(hk[0], hk[1], mk[0], mk[1], xp=xp)
334
+ dk[-1] = PchipInterpolator._edge_case(hk[-1], hk[-2], mk[-1], mk[-2], xp=xp)
335
+
336
+ return xp.reshape(dk, y_shape)
337
+
338
+
339
+ def pchip_interpolate(xi, yi, x, der=0, axis=0):
340
+ """
341
+ Convenience function for pchip interpolation.
342
+
343
+ xi and yi are arrays of values used to approximate some function f,
344
+ with ``yi = f(xi)``. The interpolant uses monotonic cubic splines
345
+ to find the value of new points x and the derivatives there.
346
+
347
+ See `scipy.interpolate.PchipInterpolator` for details.
348
+
349
+ Parameters
350
+ ----------
351
+ xi : array_like
352
+ A sorted list of x-coordinates, of length N.
353
+ yi : array_like
354
+ A 1-D array of real values. `yi`'s length along the interpolation
355
+ axis must be equal to the length of `xi`. If N-D array, use axis
356
+ parameter to select correct axis.
357
+ x : scalar or array_like
358
+ Of length M.
359
+ der : int or list, optional
360
+ Derivatives to extract. The 0th derivative can be included to
361
+ return the function value.
362
+ axis : int, optional
363
+ Axis in the yi array corresponding to the x-coordinate values.
364
+
365
+ Returns
366
+ -------
367
+ y : scalar or array_like
368
+ The result, of length R or length M or M by R.
369
+
370
+ See Also
371
+ --------
372
+ PchipInterpolator : PCHIP 1-D monotonic cubic interpolator.
373
+
374
+ Examples
375
+ --------
376
+ We can interpolate 2D observed data using pchip interpolation:
377
+
378
+ >>> import numpy as np
379
+ >>> import matplotlib.pyplot as plt
380
+ >>> from scipy.interpolate import pchip_interpolate
381
+ >>> x_observed = np.linspace(0.0, 10.0, 11)
382
+ >>> y_observed = np.sin(x_observed)
383
+ >>> x = np.linspace(min(x_observed), max(x_observed), num=100)
384
+ >>> y = pchip_interpolate(x_observed, y_observed, x)
385
+ >>> plt.plot(x_observed, y_observed, "o", label="observation")
386
+ >>> plt.plot(x, y, label="pchip interpolation")
387
+ >>> plt.legend()
388
+ >>> plt.show()
389
+
390
+ """
391
+ P = PchipInterpolator(xi, yi, axis=axis)
392
+
393
+ if der == 0:
394
+ return P(x)
395
+ elif _isscalar(der):
396
+ return P.derivative(der)(x)
397
+ else:
398
+ return [P.derivative(nu)(x) for nu in der]
399
+
400
+
401
+ @xp_capabilities(cpu_only=True, xfail_backends=[
402
+ ("dask.array", "lacks nd fancy indexing"),
403
+ ("jax.numpy", "immutable arrays"),
404
+ ("array_api_strict", "fancy indexing __setitem__"),
405
+ ])
406
+ class Akima1DInterpolator(CubicHermiteSpline):
407
+ r"""Akima "visually pleasing" interpolator (C1 smooth).
408
+
409
+ Fit piecewise cubic polynomials, given vectors x and y. The interpolation
410
+ method by Akima uses a continuously differentiable sub-spline built from
411
+ piecewise cubic polynomials. The resultant curve passes through the given
412
+ data points and will appear smooth and natural.
413
+
414
+ Parameters
415
+ ----------
416
+ x : ndarray, shape (npoints, )
417
+ 1-D array of monotonically increasing real values.
418
+ y : ndarray, shape (..., npoints, ...)
419
+ N-D array of real values. The length of ``y`` along the interpolation axis
420
+ must be equal to the length of ``x``. Use the ``axis`` parameter to
421
+ select the interpolation axis.
422
+ axis : int, optional
423
+ Axis in the ``y`` array corresponding to the x-coordinate values. Defaults
424
+ to ``axis=0``.
425
+ method : {'akima', 'makima'}, optional
426
+ If ``"makima"``, use the modified Akima interpolation [2]_.
427
+ Defaults to ``"akima"``, use the Akima interpolation [1]_.
428
+
429
+ .. versionadded:: 1.13.0
430
+
431
+ extrapolate : {bool, None}, optional
432
+ If bool, determines whether to extrapolate to out-of-bounds points
433
+ based on first and last intervals, or to return NaNs. If None,
434
+ ``extrapolate`` is set to False.
435
+
436
+ Methods
437
+ -------
438
+ __call__
439
+ derivative
440
+ antiderivative
441
+ integrate
442
+ solve
443
+ roots
444
+
445
+ See Also
446
+ --------
447
+ PchipInterpolator : PCHIP 1-D monotonic cubic interpolator.
448
+ CubicSpline : Cubic spline data interpolator.
449
+ PPoly : Piecewise polynomial in terms of coefficients and breakpoints
450
+
451
+ Notes
452
+ -----
453
+ .. versionadded:: 0.14
454
+
455
+ Use only for precise data, as the fitted curve passes through the given
456
+ points exactly. This routine is useful for plotting a pleasingly smooth
457
+ curve through a few given points for purposes of plotting.
458
+
459
+ Let :math:`\delta_i = (y_{i+1} - y_i) / (x_{i+1} - x_i)` be the slopes of
460
+ the interval :math:`\left[x_i, x_{i+1}\right)`. Akima's derivative at
461
+ :math:`x_i` is defined as:
462
+
463
+ .. math::
464
+
465
+ d_i = \frac{w_1}{w_1 + w_2}\delta_{i-1} + \frac{w_2}{w_1 + w_2}\delta_i
466
+
467
+ In the Akima interpolation [1]_ (``method="akima"``), the weights are:
468
+
469
+ .. math::
470
+
471
+ \begin{aligned}
472
+ w_1 &= |\delta_{i+1} - \delta_i| \\
473
+ w_2 &= |\delta_{i-1} - \delta_{i-2}|
474
+ \end{aligned}
475
+
476
+ In the modified Akima interpolation [2]_ (``method="makima"``),
477
+ to eliminate overshoot and avoid edge cases of both numerator and
478
+ denominator being equal to 0, the weights are modified as follows:
479
+
480
+ .. math::
481
+
482
+ \begin{align*}
483
+ w_1 &= |\delta_{i+1} - \delta_i| + |\delta_{i+1} + \delta_i| / 2 \\
484
+ w_2 &= |\delta_{i-1} - \delta_{i-2}| + |\delta_{i-1} + \delta_{i-2}| / 2
485
+ \end{align*}
486
+
487
+ Examples
488
+ --------
489
+ Comparison of ``method="akima"`` and ``method="makima"``:
490
+
491
+ >>> import numpy as np
492
+ >>> from scipy.interpolate import Akima1DInterpolator
493
+ >>> import matplotlib.pyplot as plt
494
+ >>> x = np.linspace(1, 7, 7)
495
+ >>> y = np.array([-1, -1, -1, 0, 1, 1, 1])
496
+ >>> xs = np.linspace(min(x), max(x), num=100)
497
+ >>> y_akima = Akima1DInterpolator(x, y, method="akima")(xs)
498
+ >>> y_makima = Akima1DInterpolator(x, y, method="makima")(xs)
499
+
500
+ >>> fig, ax = plt.subplots()
501
+ >>> ax.plot(x, y, "o", label="data")
502
+ >>> ax.plot(xs, y_akima, label="akima")
503
+ >>> ax.plot(xs, y_makima, label="makima")
504
+ >>> ax.legend()
505
+ >>> fig.show()
506
+
507
+ The overshoot that occurred in ``"akima"`` has been avoided in ``"makima"``.
508
+
509
+ References
510
+ ----------
511
+ .. [1] A new method of interpolation and smooth curve fitting based
512
+ on local procedures. Hiroshi Akima, J. ACM, October 1970, 17(4),
513
+ 589-602. :doi:`10.1145/321607.321609`
514
+ .. [2] Makima Piecewise Cubic Interpolation. Cleve Moler and Cosmin Ionita, 2019.
515
+ https://blogs.mathworks.com/cleve/2019/04/29/makima-piecewise-cubic-interpolation/
516
+
517
+ """
518
+
519
+ # PchipInterpolator is not generic in scipy-stubs
520
+ __class_getitem__ = None
521
+
522
+ def __init__(self, x, y, axis=0, *, method: Literal["akima", "makima"]="akima",
523
+ extrapolate:bool | None = None):
524
+ if method not in {"akima", "makima"}:
525
+ raise NotImplementedError(f"`method`={method} is unsupported.")
526
+ # Original implementation in MATLAB by N. Shamsundar (BSD licensed), see
527
+ # https://www.mathworks.com/matlabcentral/fileexchange/1814-akima-interpolation
528
+
529
+ xp = array_namespace(x, y)
530
+ x, dx, y, axis, _ = prepare_input(x, y, axis, xp=xp)
531
+
532
+ if xp.isdtype(y.dtype, "complex floating"):
533
+ msg = ("`Akima1DInterpolator` only works with real values for `y`. "
534
+ "If you are trying to use the real components of the passed array, "
535
+ "use `np.real` on the array before passing to "
536
+ "`Akima1DInterpolator`.")
537
+ raise ValueError(msg)
538
+
539
+ # Akima extrapolation historically False; parent class defaults to True.
540
+ extrapolate = False if extrapolate is None else extrapolate
541
+
542
+ if y.shape[0] == 2:
543
+ # edge case: only have two points, use linear interpolation
544
+ xv = xp.reshape(x, (x.shape[0],) + (1,)*(y.ndim-1))
545
+ hk = xv[1:, ...] - xv[:-1, ...]
546
+ mk = (y[1:, ...] - y[:-1, ...]) / hk
547
+ t = xp.zeros_like(y)
548
+ t[...] = mk
549
+ else:
550
+ # determine slopes between breakpoints
551
+ m = xp.empty((x.shape[0] + 3, ) + y.shape[1:])
552
+ dx = dx[(slice(None), ) + (None, ) * (y.ndim - 1)]
553
+ m[2:-2, ...] = xp.diff(y, axis=0) / dx
554
+
555
+ # add two additional points on the left ...
556
+ m[1, ...] = 2. * m[2, ...] - m[3, ...]
557
+ m[0, ...] = 2. * m[1, ...] - m[2, ...]
558
+ # ... and on the right
559
+ m[-2, ...] = 2. * m[-3, ...] - m[-4, ...]
560
+ m[-1, ...] = 2. * m[-2, ...] - m[-3, ...]
561
+
562
+ # if m1 == m2 != m3 == m4, the slope at the breakpoint is not
563
+ # defined. This is the fill value:
564
+ t = .5 * (m[3:, ...] + m[:-3, ...])
565
+ # get the denominator of the slope t
566
+ dm = xp.abs(xp.diff(m, axis=0))
567
+ if method == "makima":
568
+ pm = xp.abs(m[1:, ...] + m[:-1, ...])
569
+ f1 = dm[2:, ...] + 0.5 * pm[2:, ...]
570
+ f2 = dm[:-2, ...] + 0.5 * pm[:-2, ...]
571
+ else:
572
+ f1 = dm[2:, ...]
573
+ f2 = dm[:-2, ...]
574
+
575
+ # makima is more numerically stable for small f12,
576
+ # so a finite cutoff should not improve any behavior
577
+ # however, akima has a qualitative discontinuity near f12=0
578
+ # a finite cutoff moves it, but cannot remove it.
579
+ # the cutoff break_mult could be made a keyword argument
580
+ # method='akima' also benefits from a check for m2=m3
581
+ break_mult = 1.e-9
582
+
583
+ f12 = f1 + f2
584
+
585
+ # These are the mask of where the slope at breakpoint is defined:
586
+ mmax = xp.max(f12) if xp_size(f12) > 0 else -xp.inf
587
+ ind = xp.nonzero(f12 > break_mult * mmax)
588
+
589
+ x_ind, y_ind = ind[0], ind[1:]
590
+ # Set the slope at breakpoint
591
+ t[ind] = m[(x_ind + 1,) + y_ind] + (
592
+ (f2[ind] / f12[ind])
593
+ * (m[(x_ind + 2,) + y_ind] - m[(x_ind + 1,) + y_ind])
594
+ )
595
+
596
+ super().__init__(x, y, t, axis=0, extrapolate=extrapolate)
597
+ self.axis = axis
598
+
599
+ def extend(self, c, x, right=True):
600
+ raise NotImplementedError("Extending a 1-D Akima interpolator is not "
601
+ "yet implemented")
602
+
603
+ # These are inherited from PPoly, but they do not produce an Akima
604
+ # interpolator. Hence stub them out.
605
+ @classmethod
606
+ def from_spline(cls, tck, extrapolate=None):
607
+ raise NotImplementedError("This method does not make sense for "
608
+ "an Akima interpolator.")
609
+
610
+ @classmethod
611
+ def from_bernstein_basis(cls, bp, extrapolate=None):
612
+ raise NotImplementedError("This method does not make sense for "
613
+ "an Akima interpolator.")
614
+
615
+
616
+ @xp_capabilities(
617
+ cpu_only=True, jax_jit=False,
618
+ skip_backends=[
619
+ ("dask.array",
620
+ "https://github.com/data-apis/array-api-extra/issues/488")
621
+ ]
622
+ )
623
+ class CubicSpline(CubicHermiteSpline):
624
+ """Piecewise cubic interpolator to fit values (C2 smooth).
625
+
626
+ Interpolate data with a piecewise cubic polynomial which is twice
627
+ continuously differentiable [1]_. The result is represented as a `PPoly`
628
+ instance with breakpoints matching the given data.
629
+
630
+ Parameters
631
+ ----------
632
+ x : array_like, shape (n,)
633
+ 1-D array containing values of the independent variable.
634
+ Values must be real, finite and in strictly increasing order.
635
+ y : array_like
636
+ Array containing values of the dependent variable. It can have
637
+ arbitrary number of dimensions, but the length along ``axis``
638
+ (see below) must match the length of ``x``. Values must be finite.
639
+ axis : int, optional
640
+ Axis along which `y` is assumed to be varying. Meaning that for
641
+ ``x[i]`` the corresponding values are ``np.take(y, i, axis=axis)``.
642
+ Default is 0.
643
+ bc_type : string or 2-tuple, optional
644
+ Boundary condition type. Two additional equations, given by the
645
+ boundary conditions, are required to determine all coefficients of
646
+ polynomials on each segment [2]_.
647
+
648
+ If `bc_type` is a string, then the specified condition will be applied
649
+ at both ends of a spline. Available conditions are:
650
+
651
+ * 'not-a-knot' (default): The first and second segment at a curve end
652
+ are the same polynomial. It is a good default when there is no
653
+ information on boundary conditions.
654
+ * 'periodic': The interpolated functions is assumed to be periodic
655
+ of period ``x[-1] - x[0]``. The first and last value of `y` must be
656
+ identical: ``y[0] == y[-1]``. This boundary condition will result in
657
+ ``y'[0] == y'[-1]`` and ``y''[0] == y''[-1]``.
658
+ * 'clamped': The first derivative at curves ends are zero. Assuming
659
+ a 1D `y`, ``bc_type=((1, 0.0), (1, 0.0))`` is the same condition.
660
+ * 'natural': The second derivative at curve ends are zero. Assuming
661
+ a 1D `y`, ``bc_type=((2, 0.0), (2, 0.0))`` is the same condition.
662
+
663
+ If `bc_type` is a 2-tuple, the first and the second value will be
664
+ applied at the curve start and end respectively. The tuple values can
665
+ be one of the previously mentioned strings (except 'periodic') or a
666
+ tuple ``(order, deriv_values)`` allowing to specify arbitrary
667
+ derivatives at curve ends:
668
+
669
+ * `order`: the derivative order, 1 or 2.
670
+ * `deriv_value`: array_like containing derivative values, shape must
671
+ be the same as `y`, excluding ``axis`` dimension. For example, if
672
+ `y` is 1-D, then `deriv_value` must be a scalar. If `y` is 3-D with
673
+ the shape (n0, n1, n2) and axis=2, then `deriv_value` must be 2-D
674
+ and have the shape (n0, n1).
675
+ extrapolate : {bool, 'periodic', None}, optional
676
+ If bool, determines whether to extrapolate to out-of-bounds points
677
+ based on first and last intervals, or to return NaNs. If 'periodic',
678
+ periodic extrapolation is used. If None (default), ``extrapolate`` is
679
+ set to 'periodic' for ``bc_type='periodic'`` and to True otherwise.
680
+
681
+ Attributes
682
+ ----------
683
+ x : ndarray, shape (n,)
684
+ Breakpoints. The same ``x`` which was passed to the constructor.
685
+ c : ndarray, shape (4, n-1, ...)
686
+ Coefficients of the polynomials on each segment. The trailing
687
+ dimensions match the dimensions of `y`, excluding ``axis``.
688
+ For example, if `y` is 1-d, then ``c[k, i]`` is a coefficient for
689
+ ``(x-x[i])**(3-k)`` on the segment between ``x[i]`` and ``x[i+1]``.
690
+ axis : int
691
+ Interpolation axis. The same axis which was passed to the
692
+ constructor.
693
+
694
+ Methods
695
+ -------
696
+ __call__
697
+ derivative
698
+ antiderivative
699
+ integrate
700
+ solve
701
+ roots
702
+
703
+ See Also
704
+ --------
705
+ Akima1DInterpolator : Akima 1D interpolator.
706
+ PchipInterpolator : PCHIP 1-D monotonic cubic interpolator.
707
+ PPoly : Piecewise polynomial in terms of coefficients and breakpoints.
708
+
709
+ Notes
710
+ -----
711
+ Parameters `bc_type` and ``extrapolate`` work independently, i.e. the
712
+ former controls only construction of a spline, and the latter only
713
+ evaluation.
714
+
715
+ When a boundary condition is 'not-a-knot' and n = 2, it is replaced by
716
+ a condition that the first derivative is equal to the linear interpolant
717
+ slope. When both boundary conditions are 'not-a-knot' and n = 3, the
718
+ solution is sought as a parabola passing through given points.
719
+
720
+ When 'not-a-knot' boundary conditions is applied to both ends, the
721
+ resulting spline will be the same as returned by `splrep` (with ``s=0``)
722
+ and `InterpolatedUnivariateSpline`, but these two methods use a
723
+ representation in B-spline basis.
724
+
725
+ .. versionadded:: 0.18.0
726
+
727
+ Examples
728
+ --------
729
+ In this example the cubic spline is used to interpolate a sampled sinusoid.
730
+ You can see that the spline continuity property holds for the first and
731
+ second derivatives and violates only for the third derivative.
732
+
733
+ >>> import numpy as np
734
+ >>> from scipy.interpolate import CubicSpline
735
+ >>> import matplotlib.pyplot as plt
736
+ >>> x = np.arange(10)
737
+ >>> y = np.sin(x)
738
+ >>> cs = CubicSpline(x, y)
739
+ >>> xs = np.arange(-0.5, 9.6, 0.1)
740
+ >>> fig, ax = plt.subplots(figsize=(6.5, 4))
741
+ >>> ax.plot(x, y, 'o', label='data')
742
+ >>> ax.plot(xs, np.sin(xs), label='true')
743
+ >>> ax.plot(xs, cs(xs), label="S")
744
+ >>> ax.plot(xs, cs(xs, 1), label="S'")
745
+ >>> ax.plot(xs, cs(xs, 2), label="S''")
746
+ >>> ax.plot(xs, cs(xs, 3), label="S'''")
747
+ >>> ax.set_xlim(-0.5, 9.5)
748
+ >>> ax.legend(loc='lower left', ncol=2)
749
+ >>> plt.show()
750
+
751
+ In the second example, the unit circle is interpolated with a spline. A
752
+ periodic boundary condition is used. You can see that the first derivative
753
+ values, ds/dx=0, ds/dy=1 at the periodic point (1, 0) are correctly
754
+ computed. Note that a circle cannot be exactly represented by a cubic
755
+ spline. To increase precision, more breakpoints would be required.
756
+
757
+ >>> theta = 2 * np.pi * np.linspace(0, 1, 5)
758
+ >>> y = np.c_[np.cos(theta), np.sin(theta)]
759
+ >>> cs = CubicSpline(theta, y, bc_type='periodic')
760
+ >>> print("ds/dx={:.1f} ds/dy={:.1f}".format(cs(0, 1)[0], cs(0, 1)[1]))
761
+ ds/dx=0.0 ds/dy=1.0
762
+ >>> xs = 2 * np.pi * np.linspace(0, 1, 100)
763
+ >>> fig, ax = plt.subplots(figsize=(6.5, 4))
764
+ >>> ax.plot(y[:, 0], y[:, 1], 'o', label='data')
765
+ >>> ax.plot(np.cos(xs), np.sin(xs), label='true')
766
+ >>> ax.plot(cs(xs)[:, 0], cs(xs)[:, 1], label='spline')
767
+ >>> ax.axes.set_aspect('equal')
768
+ >>> ax.legend(loc='center')
769
+ >>> plt.show()
770
+
771
+ The third example is the interpolation of a polynomial y = x**3 on the
772
+ interval 0 <= x<= 1. A cubic spline can represent this function exactly.
773
+ To achieve that we need to specify values and first derivatives at
774
+ endpoints of the interval. Note that y' = 3 * x**2 and thus y'(0) = 0 and
775
+ y'(1) = 3.
776
+
777
+ >>> cs = CubicSpline([0, 1], [0, 1], bc_type=((1, 0), (1, 3)))
778
+ >>> x = np.linspace(0, 1)
779
+ >>> np.allclose(x**3, cs(x))
780
+ True
781
+
782
+ References
783
+ ----------
784
+ .. [1] `Cubic Spline Interpolation
785
+ <https://en.wikiversity.org/wiki/Cubic_Spline_Interpolation>`_
786
+ on Wikiversity.
787
+ .. [2] Carl de Boor, "A Practical Guide to Splines", Springer-Verlag, 1978.
788
+ """
789
+
790
+ def __init__(self, x, y, axis=0, bc_type='not-a-knot', extrapolate=None):
791
+ xp = array_namespace(x, y)
792
+ x, dx, y, axis, _ = prepare_input(x, y, axis, xp=np_compat)
793
+ n = len(x)
794
+
795
+ bc, y = self._validate_bc(bc_type, y, y.shape[1:], axis)
796
+
797
+ if extrapolate is None:
798
+ if bc[0] == 'periodic':
799
+ extrapolate = 'periodic'
800
+ else:
801
+ extrapolate = True
802
+
803
+ if y.size == 0:
804
+ # bail out early for zero-sized arrays
805
+ s = np.zeros_like(y)
806
+ else:
807
+ dxr = dx.reshape([dx.shape[0]] + [1] * (y.ndim - 1))
808
+ slope = np.diff(y, axis=0) / dxr
809
+
810
+ # If bc is 'not-a-knot' this change is just a convention.
811
+ # If bc is 'periodic' then we already checked that y[0] == y[-1],
812
+ # and the spline is just a constant, we handle this case in the
813
+ # same way by setting the first derivatives to slope, which is 0.
814
+ if n == 2:
815
+ if bc[0] in ['not-a-knot', 'periodic']:
816
+ bc[0] = (1, slope[0])
817
+ if bc[1] in ['not-a-knot', 'periodic']:
818
+ bc[1] = (1, slope[0])
819
+
820
+ # This is a special case, when both conditions are 'not-a-knot'
821
+ # and n == 3. In this case 'not-a-knot' can't be handled regularly
822
+ # as the both conditions are identical. We handle this case by
823
+ # constructing a parabola passing through given points.
824
+ if n == 3 and bc[0] == 'not-a-knot' and bc[1] == 'not-a-knot':
825
+ A = np.zeros((3, 3)) # This is a standard matrix.
826
+ b = np.empty((3,) + y.shape[1:], dtype=y.dtype)
827
+
828
+ A[0, 0] = 1
829
+ A[0, 1] = 1
830
+ A[1, 0] = dx[1]
831
+ A[1, 1] = 2 * (dx[0] + dx[1])
832
+ A[1, 2] = dx[0]
833
+ A[2, 1] = 1
834
+ A[2, 2] = 1
835
+
836
+ b[0] = 2 * slope[0]
837
+ b[1] = 3 * (dxr[0] * slope[1] + dxr[1] * slope[0])
838
+ b[2] = 2 * slope[1]
839
+
840
+ m = b.shape[0]
841
+ s = solve(A, b.reshape(m, -1), overwrite_a=True, overwrite_b=True,
842
+ check_finite=False).reshape(b.shape)
843
+ elif n == 3 and bc[0] == 'periodic':
844
+ # In case when number of points is 3 we compute the derivatives
845
+ # manually
846
+ t = (slope / dxr).sum(0) / (1. / dxr).sum(0)
847
+ s = np.broadcast_to(t, (n,) + y.shape[1:])
848
+ else:
849
+ # Find derivative values at each x[i] by solving a tridiagonal
850
+ # system.
851
+ A = np.zeros((3, n)) # This is a banded matrix representation.
852
+ b = np.empty((n,) + y.shape[1:], dtype=y.dtype)
853
+
854
+ # Filling the system for i=1..n-2
855
+ # (x[i-1] - x[i]) * s[i-1] +\
856
+ # 2 * ((x[i] - x[i-1]) + (x[i+1] - x[i])) * s[i] +\
857
+ # (x[i] - x[i-1]) * s[i+1] =\
858
+ # 3 * ((x[i+1] - x[i])*(y[i] - y[i-1])/(x[i] - x[i-1]) +\
859
+ # (x[i] - x[i-1])*(y[i+1] - y[i])/(x[i+1] - x[i]))
860
+
861
+ A[1, 1:-1] = 2 * (dx[:-1] + dx[1:]) # The diagonal
862
+ A[0, 2:] = dx[:-1] # The upper diagonal
863
+ A[-1, :-2] = dx[1:] # The lower diagonal
864
+
865
+ b[1:-1] = 3 * (dxr[1:] * slope[:-1] + dxr[:-1] * slope[1:])
866
+
867
+ bc_start, bc_end = bc
868
+
869
+ if bc_start == 'periodic':
870
+ # Due to the periodicity, and because y[-1] = y[0], the
871
+ # linear system has (n-1) unknowns/equations instead of n:
872
+ A = A[:, 0:-1]
873
+ A[1, 0] = 2 * (dx[-1] + dx[0])
874
+ A[0, 1] = dx[-1]
875
+
876
+ b = b[:-1]
877
+
878
+ # Also, due to the periodicity, the system is not tri-diagonal.
879
+ # We need to compute a "condensed" matrix of shape (n-2, n-2).
880
+ # See https://web.archive.org/web/20151220180652/http://www.cfm.brown.edu/people/gk/chap6/node14.html
881
+ # for more explanations.
882
+ # The condensed matrix is obtained by removing the last column
883
+ # and last row of the (n-1, n-1) system matrix. The removed
884
+ # values are saved in scalar variables with the (n-1, n-1)
885
+ # system matrix indices forming their names:
886
+ a_m1_0 = dx[-2] # lower left corner value: A[-1, 0]
887
+ a_m1_m2 = dx[-1]
888
+ a_m1_m1 = 2 * (dx[-1] + dx[-2])
889
+ a_m2_m1 = dx[-3]
890
+ a_0_m1 = dx[0]
891
+
892
+ b[0] = 3 * (dxr[0] * slope[-1] + dxr[-1] * slope[0])
893
+ b[-1] = 3 * (dxr[-1] * slope[-2] + dxr[-2] * slope[-1])
894
+
895
+ Ac = A[:, :-1]
896
+ b1 = b[:-1]
897
+ b2 = np.zeros_like(b1)
898
+ b2[0] = -a_0_m1
899
+ b2[-1] = -a_m2_m1
900
+
901
+ # s1 and s2 are the solutions of (n-2, n-2) system
902
+ m = b1.shape[0]
903
+ s1 = solve_banded((1, 1), Ac, b1.reshape(m, -1), overwrite_ab=False,
904
+ overwrite_b=False, check_finite=False)
905
+ s1 = s1.reshape(b1.shape)
906
+
907
+ m = b2.shape[0]
908
+ s2 = solve_banded((1, 1), Ac, b2.reshape(m, -1), overwrite_ab=False,
909
+ overwrite_b=False, check_finite=False)
910
+ s2 = s2.reshape(b2.shape)
911
+
912
+ # computing the s[n-2] solution:
913
+ s_m1 = ((b[-1] - a_m1_0 * s1[0] - a_m1_m2 * s1[-1]) /
914
+ (a_m1_m1 + a_m1_0 * s2[0] + a_m1_m2 * s2[-1]))
915
+
916
+ # s is the solution of the (n, n) system:
917
+ s = np.empty((n,) + y.shape[1:], dtype=y.dtype)
918
+ s[:-2] = s1 + s_m1 * s2
919
+ s[-2] = s_m1
920
+ s[-1] = s[0]
921
+ else:
922
+ if bc_start == 'not-a-knot':
923
+ A[1, 0] = dx[1]
924
+ A[0, 1] = x[2] - x[0]
925
+ d = x[2] - x[0]
926
+ b[0] = ((dxr[0] + 2*d) * dxr[1] * slope[0] +
927
+ dxr[0]**2 * slope[1]) / d
928
+ elif bc_start[0] == 1:
929
+ A[1, 0] = 1
930
+ A[0, 1] = 0
931
+ b[0] = bc_start[1]
932
+ elif bc_start[0] == 2:
933
+ A[1, 0] = 2 * dx[0]
934
+ A[0, 1] = dx[0]
935
+ b[0] = -0.5 * bc_start[1] * dx[0]**2 + 3 * (y[1] - y[0])
936
+
937
+ if bc_end == 'not-a-knot':
938
+ A[1, -1] = dx[-2]
939
+ A[-1, -2] = x[-1] - x[-3]
940
+ d = x[-1] - x[-3]
941
+ b[-1] = ((dxr[-1]**2*slope[-2] +
942
+ (2*d + dxr[-1])*dxr[-2]*slope[-1]) / d)
943
+ elif bc_end[0] == 1:
944
+ A[1, -1] = 1
945
+ A[-1, -2] = 0
946
+ b[-1] = bc_end[1]
947
+ elif bc_end[0] == 2:
948
+ A[1, -1] = 2 * dx[-1]
949
+ A[-1, -2] = dx[-1]
950
+ b[-1] = 0.5 * bc_end[1] * dx[-1]**2 + 3 * (y[-1] - y[-2])
951
+
952
+ m = b.shape[0]
953
+ s = solve_banded((1, 1), A, b.reshape(m, -1), overwrite_ab=True,
954
+ overwrite_b=True, check_finite=False)
955
+ s = s.reshape(b.shape)
956
+
957
+ x, y, s = map(xp.asarray, (x, y, s))
958
+ super().__init__(x, y, s, axis=0, extrapolate=extrapolate)
959
+ self.axis = axis
960
+
961
+ @staticmethod
962
+ def _validate_bc(bc_type, y, expected_deriv_shape, axis):
963
+ """Validate and prepare boundary conditions.
964
+
965
+ Returns
966
+ -------
967
+ validated_bc : 2-tuple
968
+ Boundary conditions for a curve start and end.
969
+ y : ndarray
970
+ y casted to complex dtype if one of the boundary conditions has
971
+ complex dtype.
972
+ """
973
+ if isinstance(bc_type, str):
974
+ if bc_type == 'periodic':
975
+ if not np.allclose(y[0], y[-1], rtol=1e-15, atol=1e-15):
976
+ raise ValueError(
977
+ f"The first and last `y` point along axis {axis} must "
978
+ "be identical (within machine precision) when "
979
+ "bc_type='periodic'.")
980
+
981
+ bc_type = (bc_type, bc_type)
982
+
983
+ else:
984
+ if len(bc_type) != 2:
985
+ raise ValueError("`bc_type` must contain 2 elements to "
986
+ "specify start and end conditions.")
987
+
988
+ if 'periodic' in bc_type:
989
+ raise ValueError("'periodic' `bc_type` is defined for both "
990
+ "curve ends and cannot be used with other "
991
+ "boundary conditions.")
992
+
993
+ validated_bc = []
994
+ for bc in bc_type:
995
+ if isinstance(bc, str):
996
+ if bc == 'clamped':
997
+ validated_bc.append((1, np.zeros(expected_deriv_shape)))
998
+ elif bc == 'natural':
999
+ validated_bc.append((2, np.zeros(expected_deriv_shape)))
1000
+ elif bc in ['not-a-knot', 'periodic']:
1001
+ validated_bc.append(bc)
1002
+ else:
1003
+ raise ValueError(f"bc_type={bc} is not allowed.")
1004
+ else:
1005
+ try:
1006
+ deriv_order, deriv_value = bc
1007
+ except Exception as e:
1008
+ raise ValueError(
1009
+ "A specified derivative value must be "
1010
+ "given in the form (order, value)."
1011
+ ) from e
1012
+
1013
+ if deriv_order not in [1, 2]:
1014
+ raise ValueError("The specified derivative order must "
1015
+ "be 1 or 2.")
1016
+
1017
+ deriv_value = np.asarray(deriv_value)
1018
+ if deriv_value.shape != expected_deriv_shape:
1019
+ raise ValueError(
1020
+ f"`deriv_value` shape {deriv_value.shape} is not "
1021
+ f"the expected one {expected_deriv_shape}."
1022
+ )
1023
+
1024
+ if np.issubdtype(deriv_value.dtype, np.complexfloating):
1025
+ y = y.astype(complex, copy=False)
1026
+
1027
+ validated_bc.append((deriv_order, deriv_value))
1028
+
1029
+ return validated_bc, y
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_fitpack.cpython-311-x86_64-linux-gnu.so ADDED
Binary file (95.6 kB). View file
 
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_ndbspline.py ADDED
@@ -0,0 +1,518 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ import itertools
2
+ import functools
3
+ import operator
4
+ import numpy as np
5
+
6
+ from math import prod
7
+ from types import GenericAlias
8
+
9
+ from . import _dierckx # type: ignore[attr-defined]
10
+
11
+ import scipy.sparse.linalg as ssl
12
+ from scipy.sparse import csr_array
13
+ from scipy._lib._array_api import array_namespace, xp_capabilities
14
+
15
+ from ._bsplines import _not_a_knot, BSpline
16
+
17
+ __all__ = ["NdBSpline"]
18
+
19
+
20
+ def _get_dtype(dtype):
21
+ """Return np.complex128 for complex dtypes, np.float64 otherwise."""
22
+ if np.issubdtype(dtype, np.complexfloating):
23
+ return np.complex128
24
+ else:
25
+ return np.float64
26
+
27
+
28
+ @xp_capabilities(
29
+ cpu_only=True, jax_jit=False,
30
+ skip_backends=[
31
+ ("dask.array",
32
+ "https://github.com/data-apis/array-api-extra/issues/488")
33
+ ]
34
+ )
35
+ class NdBSpline:
36
+ """Tensor product spline object.
37
+
38
+ The value at point ``xp = (x1, x2, ..., xN)`` is evaluated as a linear
39
+ combination of products of one-dimensional b-splines in each of the ``N``
40
+ dimensions::
41
+
42
+ c[i1, i2, ..., iN] * B(x1; i1, t1) * B(x2; i2, t2) * ... * B(xN; iN, tN)
43
+
44
+
45
+ Here ``B(x; i, t)`` is the ``i``-th b-spline defined by the knot vector
46
+ ``t`` evaluated at ``x``.
47
+
48
+ Parameters
49
+ ----------
50
+ t : tuple of 1D ndarrays
51
+ knot vectors in directions 1, 2, ... N,
52
+ ``len(t[i]) == n[i] + k + 1``
53
+ c : ndarray, shape (n1, n2, ..., nN, ...)
54
+ b-spline coefficients
55
+ k : int or length-d tuple of integers
56
+ spline degrees.
57
+ A single integer is interpreted as having this degree for
58
+ all dimensions.
59
+ extrapolate : bool, optional
60
+ Whether to extrapolate out-of-bounds inputs, or return `nan`.
61
+ Default is to extrapolate.
62
+
63
+ Attributes
64
+ ----------
65
+ t : tuple of ndarrays
66
+ Knots vectors.
67
+ c : ndarray
68
+ Coefficients of the tensor-product spline.
69
+ k : tuple of integers
70
+ Degrees for each dimension.
71
+ extrapolate : bool, optional
72
+ Whether to extrapolate or return nans for out-of-bounds inputs.
73
+ Defaults to true.
74
+
75
+ Methods
76
+ -------
77
+ __call__
78
+ derivative
79
+ design_matrix
80
+
81
+ See Also
82
+ --------
83
+ BSpline : a one-dimensional B-spline object
84
+ NdPPoly : an N-dimensional piecewise tensor product polynomial
85
+
86
+ """
87
+
88
+ # generic type compatibility with scipy-stubs
89
+ __class_getitem__ = classmethod(GenericAlias)
90
+
91
+ def __init__(self, t, c, k, *, extrapolate=None):
92
+ self._k, self._indices_k1d, (self._t, self._len_t) = _preprocess_inputs(k, t)
93
+
94
+ self._asarray = array_namespace(c, *t).asarray
95
+
96
+ if extrapolate is None:
97
+ extrapolate = True
98
+ self.extrapolate = bool(extrapolate)
99
+
100
+ self._c = np.asarray(c)
101
+
102
+ ndim = self._t.shape[0] # == len(self.t)
103
+ if self._c.ndim < ndim:
104
+ raise ValueError(f"Coefficients must be at least {ndim}-dimensional.")
105
+
106
+ for d in range(ndim):
107
+ td = self.t[d]
108
+ kd = self.k[d]
109
+ n = td.shape[0] - kd - 1
110
+
111
+ if self._c.shape[d] != n:
112
+ raise ValueError(f"Knots, coefficients and degree in dimension"
113
+ f" {d} are inconsistent:"
114
+ f" got {self._c.shape[d]} coefficients for"
115
+ f" {len(td)} knots, need at least {n} for"
116
+ f" k={k}.")
117
+
118
+ dt = _get_dtype(self._c.dtype)
119
+ self._c = np.ascontiguousarray(self._c, dtype=dt)
120
+
121
+ @property
122
+ def k(self):
123
+ return tuple(self._k)
124
+
125
+ @property
126
+ def t(self):
127
+ # repack the knots into a tuple
128
+ return tuple(
129
+ self._asarray(self._t[d, :self._len_t[d]]) for d in range(self._t.shape[0])
130
+ )
131
+
132
+ @property
133
+ def c(self):
134
+ return self._asarray(self._c)
135
+
136
+ def __call__(self, xi, *, nu=None, extrapolate=None):
137
+ """Evaluate the tensor product b-spline at ``xi``.
138
+
139
+ Parameters
140
+ ----------
141
+ xi : array_like, shape(..., ndim)
142
+ The coordinates to evaluate the interpolator at.
143
+ This can be a list or tuple of ndim-dimensional points
144
+ or an array with the shape (num_points, ndim).
145
+ nu : sequence of length ``ndim``, optional
146
+ Orders of derivatives to evaluate. Each must be non-negative.
147
+ Defaults to the zeroth derivivative.
148
+ extrapolate : bool, optional
149
+ Whether to exrapolate based on first and last intervals in each
150
+ dimension, or return `nan`. Default is to ``self.extrapolate``.
151
+
152
+ Returns
153
+ -------
154
+ values : ndarray, shape ``xi.shape[:-1] + self.c.shape[ndim:]``
155
+ Interpolated values at ``xi``
156
+ """
157
+ ndim = self._t.shape[0] # == len(self.t)
158
+
159
+ if extrapolate is None:
160
+ extrapolate = self.extrapolate
161
+ extrapolate = bool(extrapolate)
162
+
163
+ if nu is None:
164
+ nu = np.zeros((ndim,), dtype=np.int64)
165
+ else:
166
+ nu = np.asarray(nu, dtype=np.int64)
167
+ if nu.ndim != 1 or nu.shape[0] != ndim:
168
+ raise ValueError(
169
+ f"invalid number of derivative orders {nu = } for "
170
+ f"ndim = {len(self.t)}.")
171
+ if any(nu < 0):
172
+ raise ValueError(f"derivatives must be positive, got {nu = }")
173
+
174
+ # prepare xi : shape (..., m1, ..., md) -> (1, m1, ..., md)
175
+ xi = np.asarray(xi, dtype=float)
176
+ xi_shape = xi.shape
177
+ xi = xi.reshape(-1, xi_shape[-1])
178
+ xi = np.ascontiguousarray(xi)
179
+
180
+ if xi_shape[-1] != ndim:
181
+ raise ValueError(f"Shapes: xi.shape={xi_shape} and ndim={ndim}")
182
+
183
+ # complex -> double
184
+ was_complex = self._c.dtype.kind == 'c'
185
+ cc = self._c
186
+ if was_complex and self._c.ndim == ndim:
187
+ # make sure that core dimensions are intact, and complex->float
188
+ # size doubling only adds a trailing dimension
189
+ cc = self._c[..., None]
190
+ cc = cc.view(float)
191
+
192
+ # prepare the coefficients: flatten the trailing dimensions
193
+ c1 = cc.reshape(cc.shape[:ndim] + (-1,))
194
+ c1r = c1.ravel()
195
+
196
+ # replacement for np.ravel_multi_index for indexing of `c1`:
197
+ _strides_c1 = np.asarray([s // c1.dtype.itemsize
198
+ for s in c1.strides], dtype=np.int64)
199
+
200
+ num_c_tr = c1.shape[-1] # # of trailing coefficients
201
+ out = _dierckx.evaluate_ndbspline(xi,
202
+ self._t,
203
+ self._len_t,
204
+ self._k,
205
+ nu,
206
+ extrapolate,
207
+ c1r,
208
+ num_c_tr,
209
+ _strides_c1,
210
+ self._indices_k1d,
211
+ )
212
+ out = out.view(self._c.dtype)
213
+ out = out.reshape(xi_shape[:-1] + self._c.shape[ndim:])
214
+ return self._asarray(out)
215
+
216
+ @classmethod
217
+ def design_matrix(cls, xvals, t, k, extrapolate=True):
218
+ """Construct the design matrix as a CSR format sparse array.
219
+
220
+ Parameters
221
+ ----------
222
+ xvals : ndarray, shape(npts, ndim)
223
+ Data points. ``xvals[j, :]`` gives the ``j``-th data point as an
224
+ ``ndim``-dimensional array.
225
+ t : tuple of 1D ndarrays, length-ndim
226
+ Knot vectors in directions 1, 2, ... ndim,
227
+ k : int
228
+ B-spline degree.
229
+ extrapolate : bool, optional
230
+ Whether to extrapolate out-of-bounds values of raise a `ValueError`
231
+
232
+ Returns
233
+ -------
234
+ design_matrix : a CSR array
235
+ Each row of the design matrix corresponds to a value in `xvals` and
236
+ contains values of b-spline basis elements which are non-zero
237
+ at this value.
238
+
239
+ """
240
+ xvals = np.asarray(xvals, dtype=float)
241
+ ndim = xvals.shape[-1]
242
+ if len(t) != ndim:
243
+ raise ValueError(
244
+ f"Data and knots are inconsistent: len(t) = {len(t)} for "
245
+ f" {ndim = }."
246
+ )
247
+
248
+ # tabulate the flat indices for iterating over the (k+1)**ndim subarray
249
+ k, _indices_k1d, (_t, len_t) = _preprocess_inputs(k, t)
250
+
251
+ # Precompute the shape and strides of the 'coefficients array'.
252
+ # This would have been the NdBSpline coefficients; in the present context
253
+ # this is a helper to compute the indices into the colocation matrix.
254
+ c_shape = tuple(len_t[d] - k[d] - 1 for d in range(ndim))
255
+
256
+ # The strides of the coeffs array: the computation is equivalent to
257
+ # >>> cstrides = [s // 8 for s in np.empty(c_shape).strides]
258
+ cs = c_shape[1:] + (1,)
259
+ cstrides = np.cumprod(cs[::-1], dtype=np.int64)[::-1].copy()
260
+
261
+ # heavy lifting happens here
262
+ data, indices, indptr = _dierckx._coloc_nd(xvals,
263
+ _t, len_t, k, _indices_k1d, cstrides)
264
+
265
+ return csr_array((data, indices, indptr))
266
+
267
+ def _bspline_derivative_along_axis(self, c, t, k, axis, nu=1):
268
+ # Move the selected axis to front
269
+ c = np.moveaxis(c, axis, 0)
270
+ n = c.shape[0]
271
+ trailing_shape = c.shape[1:]
272
+ c_flat = c.reshape(n, -1)
273
+
274
+ new_c_list = []
275
+ new_t = None
276
+
277
+ for i in range(c_flat.shape[1]):
278
+ if k >= nu:
279
+ b = BSpline.construct_fast(t, c_flat[:, i], k)
280
+ db = b.derivative(nu)
281
+ # truncate coefficients to match new knot/degree size
282
+ db.c = db.c[:len(db.t) - db.k - 1]
283
+ else:
284
+ db = BSpline.construct_fast(t, np.zeros(len(t) - 1), 0)
285
+
286
+ if new_t is None:
287
+ new_t = db.t
288
+
289
+ new_c_list.append(db.c)
290
+
291
+ new_c = np.stack(new_c_list, axis=1).reshape(
292
+ (len(new_c_list[0]),) + trailing_shape)
293
+ new_c = np.moveaxis(new_c, 0, axis)
294
+
295
+ return new_c, new_t
296
+
297
+ def derivative(self, nu):
298
+ """
299
+ Construct a new NdBSpline representing the partial derivative.
300
+
301
+ Parameters
302
+ ----------
303
+ nu : array_like of shape (ndim,)
304
+ Orders of the partial derivatives to compute along each dimension.
305
+
306
+ Returns
307
+ -------
308
+ NdBSpline
309
+ A new NdBSpline representing the partial derivative of the original spline.
310
+
311
+ """
312
+ nu_arr = np.asarray(nu, dtype=np.int64)
313
+ ndim = len(self.t)
314
+
315
+ if nu_arr.ndim != 1 or nu_arr.shape[0] != ndim:
316
+ raise ValueError(
317
+ f"invalid number of derivative orders {nu = } for "
318
+ f"ndim = {len(self.t)}.")
319
+
320
+ if any(nu_arr < 0):
321
+ raise ValueError(f"derivative orders must be positive, got {nu = }")
322
+
323
+ # extract t and c as numpy arrays
324
+ t_new = [self._t[d, :self._len_t[d]] for d in range(self._t.shape[0])]
325
+ k_new = list(self.k)
326
+ c_new = self._c.copy()
327
+
328
+ for axis, n in enumerate(nu_arr):
329
+ if n == 0:
330
+ continue
331
+
332
+ c_new, t_new[axis] = self._bspline_derivative_along_axis(
333
+ c_new, t_new[axis], k_new[axis], axis, nu=n
334
+ )
335
+ k_new[axis] = max(k_new[axis] - n, 0)
336
+
337
+ return NdBSpline(tuple(self._asarray(t) for t in t_new),
338
+ self._asarray(c_new),
339
+ tuple(k_new),
340
+ extrapolate=self.extrapolate
341
+ )
342
+
343
+ def _preprocess_inputs(k, t_tpl):
344
+ """Helpers: validate and preprocess NdBSpline inputs.
345
+
346
+ Parameters
347
+ ----------
348
+ k : int or tuple
349
+ Spline orders
350
+ t_tpl : tuple or array-likes
351
+ Knots.
352
+ """
353
+ # 1. Make sure t_tpl is a tuple
354
+ if not isinstance(t_tpl, tuple):
355
+ raise ValueError(f"Expect `t` to be a tuple of array-likes. "
356
+ f"Got {t_tpl} instead."
357
+ )
358
+
359
+ # 2. Make ``k`` a tuple of integers
360
+ ndim = len(t_tpl)
361
+ try:
362
+ len(k)
363
+ except TypeError:
364
+ # make k a tuple
365
+ k = (k,)*ndim
366
+
367
+ k = np.asarray([operator.index(ki) for ki in k], dtype=np.int64)
368
+
369
+ if len(k) != ndim:
370
+ raise ValueError(f"len(t) = {len(t_tpl)} != {len(k) = }.")
371
+
372
+ # 3. Validate inputs
373
+ ndim = len(t_tpl)
374
+ for d in range(ndim):
375
+ td = np.asarray(t_tpl[d])
376
+ kd = k[d]
377
+ n = td.shape[0] - kd - 1
378
+ if kd < 0:
379
+ raise ValueError(f"Spline degree in dimension {d} cannot be"
380
+ f" negative.")
381
+ if td.ndim != 1:
382
+ raise ValueError(f"Knot vector in dimension {d} must be"
383
+ f" one-dimensional.")
384
+ if n < kd + 1:
385
+ raise ValueError(f"Need at least {2*kd + 2} knots for degree"
386
+ f" {kd} in dimension {d}.")
387
+ if (np.diff(td) < 0).any():
388
+ raise ValueError(f"Knots in dimension {d} must be in a"
389
+ f" non-decreasing order.")
390
+ if len(np.unique(td[kd:n + 1])) < 2:
391
+ raise ValueError(f"Need at least two internal knots in"
392
+ f" dimension {d}.")
393
+ if not np.isfinite(td).all():
394
+ raise ValueError(f"Knots in dimension {d} should not have"
395
+ f" nans or infs.")
396
+
397
+ # 4. tabulate the flat indices for iterating over the (k+1)**ndim subarray
398
+ # non-zero b-spline elements
399
+ shape = tuple(kd + 1 for kd in k)
400
+ indices = np.unravel_index(np.arange(prod(shape)), shape)
401
+ _indices_k1d = np.asarray(indices, dtype=np.int64).T.copy()
402
+
403
+ # 5. pack the knots into a single array:
404
+ # ([1, 2, 3, 4], [5, 6], (7, 8, 9)) -->
405
+ # array([[1, 2, 3, 4],
406
+ # [5, 6, nan, nan],
407
+ # [7, 8, 9, nan]])
408
+ t_tpl = [np.asarray(t) for t in t_tpl]
409
+ ndim = len(t_tpl)
410
+ len_t = [len(ti) for ti in t_tpl]
411
+ _t = np.empty((ndim, max(len_t)), dtype=float)
412
+ _t.fill(np.nan)
413
+ for d in range(ndim):
414
+ _t[d, :len(t_tpl[d])] = t_tpl[d]
415
+ len_t = np.asarray(len_t, dtype=np.int64)
416
+
417
+ return k, _indices_k1d, (_t, len_t)
418
+
419
+
420
+ def _iter_solve(a, b, solver=ssl.gcrotmk, **solver_args):
421
+ # work around iterative solvers not accepting multiple r.h.s.
422
+
423
+ # also work around a.dtype == float64 and b.dtype == complex128
424
+ # cf https://github.com/scipy/scipy/issues/19644
425
+ if np.issubdtype(b.dtype, np.complexfloating):
426
+ real = _iter_solve(a, b.real, solver, **solver_args)
427
+ imag = _iter_solve(a, b.imag, solver, **solver_args)
428
+ return real + 1j*imag
429
+
430
+ if b.ndim == 2 and b.shape[1] !=1:
431
+ res = np.empty_like(b)
432
+ for j in range(b.shape[1]):
433
+ res[:, j], info = solver(a, b[:, j], **solver_args)
434
+ if info != 0:
435
+ raise ValueError(f"{solver = } returns {info =} for column {j}.")
436
+ return res
437
+ else:
438
+ res, info = solver(a, b, **solver_args)
439
+ if info != 0:
440
+ raise ValueError(f"{solver = } returns {info = }.")
441
+ return res
442
+
443
+
444
+ def make_ndbspl(points, values, k=3, *, solver=ssl.gcrotmk, **solver_args):
445
+ """Construct an interpolating NdBspline.
446
+
447
+ Parameters
448
+ ----------
449
+ points : tuple of ndarrays of float, with shapes (m1,), ... (mN,)
450
+ The points defining the regular grid in N dimensions. The points in
451
+ each dimension (i.e. every element of the `points` tuple) must be
452
+ strictly ascending or descending.
453
+ values : ndarray of float, shape (m1, ..., mN, ...)
454
+ The data on the regular grid in n dimensions.
455
+ k : int, optional
456
+ The spline degree. Must be odd. Default is cubic, k=3
457
+ solver : a `scipy.sparse.linalg` solver (iterative or direct), optional.
458
+ An iterative solver from `scipy.sparse.linalg` or a direct one,
459
+ `sparse.sparse.linalg.spsolve`.
460
+ Used to solve the sparse linear system
461
+ ``design_matrix @ coefficients = rhs`` for the coefficients.
462
+ Default is `scipy.sparse.linalg.gcrotmk`
463
+ solver_args : dict, optional
464
+ Additional arguments for the solver. The call signature is
465
+ ``solver(csr_array, rhs_vector, **solver_args)``
466
+
467
+ Returns
468
+ -------
469
+ spl : NdBSpline object
470
+
471
+ Notes
472
+ -----
473
+ Boundary conditions are not-a-knot in all dimensions.
474
+ """
475
+ ndim = len(points)
476
+ xi_shape = tuple(len(x) for x in points)
477
+
478
+ try:
479
+ len(k)
480
+ except TypeError:
481
+ # make k a tuple
482
+ k = (k,)*ndim
483
+
484
+ for d, point in enumerate(points):
485
+ numpts = len(np.atleast_1d(point))
486
+ if numpts <= k[d]:
487
+ raise ValueError(f"There are {numpts} points in dimension {d},"
488
+ f" but order {k[d]} requires at least "
489
+ f" {k[d]+1} points per dimension.")
490
+
491
+ t = tuple(_not_a_knot(np.asarray(points[d], dtype=float), k[d])
492
+ for d in range(ndim))
493
+ xvals = np.asarray([xv for xv in itertools.product(*points)], dtype=float)
494
+
495
+ # construct the colocation matrix
496
+ matr = NdBSpline.design_matrix(xvals, t, k)
497
+
498
+ # Remove zeros from the sparse matrix
499
+ # If k=1, then solve() doesn't take long enough for this to help
500
+ if k[0] >= 3:
501
+ matr.eliminate_zeros()
502
+
503
+ # Solve for the coefficients given `values`.
504
+ # Trailing dimensions: first ndim dimensions are data, the rest are batch
505
+ # dimensions, so stack `values` into a 2D array for `spsolve` to undestand.
506
+ v_shape = values.shape
507
+ vals_shape = (prod(v_shape[:ndim]), prod(v_shape[ndim:]))
508
+ vals = values.reshape(vals_shape)
509
+
510
+ if solver != ssl.spsolve:
511
+ solver = functools.partial(_iter_solve, solver=solver)
512
+ if "atol" not in solver_args:
513
+ # avoid a DeprecationWarning, grumble grumble
514
+ solver_args["atol"] = 1e-6
515
+
516
+ coef = solver(matr, vals, **solver_args)
517
+ coef = coef.reshape(xi_shape + v_shape[ndim:])
518
+ return NdBSpline(t, coef, k)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_ndgriddata.py ADDED
@@ -0,0 +1,330 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """
2
+ Convenience interface to N-D interpolation
3
+
4
+ .. versionadded:: 0.9
5
+
6
+ """
7
+ import numpy as np
8
+ from ._interpnd import (LinearNDInterpolator, NDInterpolatorBase,
9
+ CloughTocher2DInterpolator, _ndim_coords_from_arrays)
10
+ from scipy.spatial import cKDTree
11
+
12
+ __all__ = ['griddata', 'NearestNDInterpolator', 'LinearNDInterpolator',
13
+ 'CloughTocher2DInterpolator']
14
+
15
+ #------------------------------------------------------------------------------
16
+ # Nearest-neighbor interpolation
17
+ #------------------------------------------------------------------------------
18
+
19
+
20
+ class NearestNDInterpolator(NDInterpolatorBase):
21
+ """Nearest-neighbor interpolator in N > 1 dimensions.
22
+
23
+ Methods
24
+ -------
25
+ __call__
26
+
27
+ Parameters
28
+ ----------
29
+ x : (npoints, ndims) 2-D ndarray of floats
30
+ Data point coordinates.
31
+ y : (npoints, ...) N-D ndarray of float or complex
32
+ Data values. The length of `y` along the first axis must be equal to
33
+ the length of `x`.
34
+ rescale : boolean, optional
35
+ Rescale points to unit cube before performing interpolation.
36
+ This is useful if some of the input dimensions have
37
+ incommensurable units and differ by many orders of magnitude.
38
+
39
+ .. versionadded:: 0.14.0
40
+ tree_options : dict, optional
41
+ Options passed to the underlying ``cKDTree``.
42
+
43
+ .. versionadded:: 0.17.0
44
+
45
+ See Also
46
+ --------
47
+ griddata :
48
+ Interpolate unstructured D-D data.
49
+ LinearNDInterpolator :
50
+ Piecewise linear interpolator in N dimensions.
51
+ CloughTocher2DInterpolator :
52
+ Piecewise cubic, C1 smooth, curvature-minimizing interpolator in 2D.
53
+ interpn : Interpolation on a regular grid or rectilinear grid.
54
+ RegularGridInterpolator : Interpolator on a regular or rectilinear grid
55
+ in arbitrary dimensions (`interpn` wraps this
56
+ class).
57
+
58
+ Notes
59
+ -----
60
+ Uses ``scipy.spatial.cKDTree``
61
+
62
+ .. note:: For data on a regular grid use `interpn` instead.
63
+
64
+ Examples
65
+ --------
66
+ We can interpolate values on a 2D plane:
67
+
68
+ >>> from scipy.interpolate import NearestNDInterpolator
69
+ >>> import numpy as np
70
+ >>> import matplotlib.pyplot as plt
71
+ >>> rng = np.random.default_rng()
72
+ >>> x = rng.random(10) - 0.5
73
+ >>> y = rng.random(10) - 0.5
74
+ >>> z = np.hypot(x, y)
75
+ >>> X = np.linspace(min(x), max(x))
76
+ >>> Y = np.linspace(min(y), max(y))
77
+ >>> X, Y = np.meshgrid(X, Y) # 2D grid for interpolation
78
+ >>> interp = NearestNDInterpolator(list(zip(x, y)), z)
79
+ >>> Z = interp(X, Y)
80
+ >>> plt.pcolormesh(X, Y, Z, shading='auto')
81
+ >>> plt.plot(x, y, "ok", label="input point")
82
+ >>> plt.legend()
83
+ >>> plt.colorbar()
84
+ >>> plt.axis("equal")
85
+ >>> plt.show()
86
+
87
+ """
88
+
89
+ def __init__(self, x, y, rescale=False, tree_options=None):
90
+ NDInterpolatorBase.__init__(self, x, y, rescale=rescale,
91
+ need_contiguous=False,
92
+ need_values=False)
93
+ if tree_options is None:
94
+ tree_options = dict()
95
+ self.tree = cKDTree(self.points, **tree_options)
96
+ self.values = np.asarray(y)
97
+
98
+ def __call__(self, *args, **query_options):
99
+ """
100
+ Evaluate interpolator at given points.
101
+
102
+ Parameters
103
+ ----------
104
+ x1, x2, ... xn : array-like of float
105
+ Points where to interpolate data at.
106
+ x1, x2, ... xn can be array-like of float with broadcastable shape.
107
+ or x1 can be array-like of float with shape ``(..., ndim)``
108
+ **query_options
109
+ This allows ``eps``, ``p``, ``distance_upper_bound``, and ``workers``
110
+ being passed to the cKDTree's query function to be explicitly set.
111
+ See `scipy.spatial.cKDTree.query` for an overview of the different options.
112
+
113
+ .. versionadded:: 1.12.0
114
+
115
+ """
116
+ # For the sake of enabling subclassing, NDInterpolatorBase._set_xi performs
117
+ # some operations which are not required by NearestNDInterpolator.__call__,
118
+ # hence here we operate on xi directly, without calling a parent class function.
119
+ xi = _ndim_coords_from_arrays(args, ndim=self.points.shape[1])
120
+ xi = self._check_call_shape(xi)
121
+ xi = self._scale_x(xi)
122
+
123
+ # We need to handle two important cases:
124
+ # (1) the case where xi has trailing dimensions (..., ndim), and
125
+ # (2) the case where y has trailing dimensions
126
+ # We will first flatten xi to deal with case (1),
127
+ # do the computation in flattened array while retaining y's dimensionality,
128
+ # and then reshape the interpolated values back to match xi's shape.
129
+
130
+ # Flatten xi for the query
131
+ xi_flat = xi.reshape(-1, xi.shape[-1])
132
+ original_shape = xi.shape
133
+ flattened_shape = xi_flat.shape
134
+
135
+ # if distance_upper_bound is set to not be infinite,
136
+ # then we need to consider the case where cKDtree
137
+ # does not find any points within distance_upper_bound to return.
138
+ # It marks those points as having infinte distance, which is what will be used
139
+ # below to mask the array and return only the points that were deemed
140
+ # to have a close enough neighbor to return something useful.
141
+ dist, i = self.tree.query(xi_flat, **query_options)
142
+ valid_mask = np.isfinite(dist)
143
+
144
+ # create a holder interp_values array and fill with nans.
145
+ if self.values.ndim > 1:
146
+ interp_shape = flattened_shape[:-1] + self.values.shape[1:]
147
+ else:
148
+ interp_shape = flattened_shape[:-1]
149
+
150
+ if np.issubdtype(self.values.dtype, np.complexfloating):
151
+ interp_values = np.full(interp_shape, np.nan, dtype=self.values.dtype)
152
+ else:
153
+ interp_values = np.full(interp_shape, np.nan)
154
+
155
+ interp_values[valid_mask] = self.values[i[valid_mask], ...]
156
+
157
+ if self.values.ndim > 1:
158
+ new_shape = original_shape[:-1] + self.values.shape[1:]
159
+ else:
160
+ new_shape = original_shape[:-1]
161
+ interp_values = interp_values.reshape(new_shape)
162
+
163
+ return interp_values
164
+
165
+
166
+ #------------------------------------------------------------------------------
167
+ # Convenience interface function
168
+ #------------------------------------------------------------------------------
169
+
170
+
171
+ def griddata(points, values, xi, method='linear', fill_value=np.nan,
172
+ rescale=False):
173
+ """
174
+ Convenience function for interpolating unstructured data in multiple dimensions.
175
+
176
+ Parameters
177
+ ----------
178
+ points : 2-D ndarray of floats with shape (n, D), or length D tuple of 1-D ndarrays with shape (n,).
179
+ Data point coordinates.
180
+ values : ndarray of float or complex, shape (n,)
181
+ Data values.
182
+ xi : 2-D ndarray of floats with shape (m, D), or length D tuple of ndarrays broadcastable to the same shape.
183
+ Points at which to interpolate data.
184
+ method : {'linear', 'nearest', 'cubic'}, optional
185
+ Method of interpolation. One of
186
+
187
+ ``nearest``
188
+ return the value at the data point closest to
189
+ the point of interpolation. See `NearestNDInterpolator` for
190
+ more details.
191
+
192
+ ``linear``
193
+ tessellate the input point set to N-D
194
+ simplices, and interpolate linearly on each simplex. See
195
+ `LinearNDInterpolator` for more details.
196
+
197
+ ``cubic`` (1-D)
198
+ return the value determined from a cubic
199
+ spline.
200
+
201
+ ``cubic`` (2-D)
202
+ return the value determined from a
203
+ piecewise cubic, continuously differentiable (C1), and
204
+ approximately curvature-minimizing polynomial surface. See
205
+ `CloughTocher2DInterpolator` for more details.
206
+ fill_value : float, optional
207
+ Value used to fill in for requested points outside of the
208
+ convex hull of the input points. If not provided, then the
209
+ default is ``nan``. This option has no effect for the
210
+ 'nearest' method.
211
+ rescale : bool, optional
212
+ Rescale points to unit cube before performing interpolation.
213
+ This is useful if some of the input dimensions have
214
+ incommensurable units and differ by many orders of magnitude.
215
+
216
+ .. versionadded:: 0.14.0
217
+
218
+ Returns
219
+ -------
220
+ ndarray
221
+ Array of interpolated values.
222
+
223
+ See Also
224
+ --------
225
+ LinearNDInterpolator :
226
+ Piecewise linear interpolator in N dimensions.
227
+ NearestNDInterpolator :
228
+ Nearest-neighbor interpolator in N dimensions.
229
+ CloughTocher2DInterpolator :
230
+ Piecewise cubic, C1 smooth, curvature-minimizing interpolator in 2D.
231
+ interpn : Interpolation on a regular grid or rectilinear grid.
232
+ RegularGridInterpolator : Interpolator on a regular or rectilinear grid
233
+ in arbitrary dimensions (`interpn` wraps this
234
+ class).
235
+
236
+ Notes
237
+ -----
238
+
239
+ .. versionadded:: 0.9
240
+
241
+ .. note:: For data on a regular grid use `interpn` instead.
242
+
243
+ Examples
244
+ --------
245
+
246
+ Suppose we want to interpolate the 2-D function
247
+
248
+ >>> import numpy as np
249
+ >>> def func(x, y):
250
+ ... return x*(1-x)*np.cos(4*np.pi*x) * np.sin(4*np.pi*y**2)**2
251
+
252
+ on a grid in [0, 1]x[0, 1]
253
+
254
+ >>> grid_x, grid_y = np.mgrid[0:1:100j, 0:1:200j]
255
+
256
+ but we only know its values at 1000 data points:
257
+
258
+ >>> rng = np.random.default_rng()
259
+ >>> points = rng.random((1000, 2))
260
+ >>> values = func(points[:,0], points[:,1])
261
+
262
+ This can be done with `griddata` -- below we try out all of the
263
+ interpolation methods:
264
+
265
+ >>> from scipy.interpolate import griddata
266
+ >>> grid_z0 = griddata(points, values, (grid_x, grid_y), method='nearest')
267
+ >>> grid_z1 = griddata(points, values, (grid_x, grid_y), method='linear')
268
+ >>> grid_z2 = griddata(points, values, (grid_x, grid_y), method='cubic')
269
+
270
+ One can see that the exact result is reproduced by all of the
271
+ methods to some degree, but for this smooth function the piecewise
272
+ cubic interpolant gives the best results:
273
+
274
+ >>> import matplotlib.pyplot as plt
275
+ >>> plt.subplot(221)
276
+ >>> plt.imshow(func(grid_x, grid_y).T, extent=(0,1,0,1), origin='lower')
277
+ >>> plt.plot(points[:,0], points[:,1], 'k.', ms=1)
278
+ >>> plt.title('Original')
279
+ >>> plt.subplot(222)
280
+ >>> plt.imshow(grid_z0.T, extent=(0,1,0,1), origin='lower')
281
+ >>> plt.title('Nearest')
282
+ >>> plt.subplot(223)
283
+ >>> plt.imshow(grid_z1.T, extent=(0,1,0,1), origin='lower')
284
+ >>> plt.title('Linear')
285
+ >>> plt.subplot(224)
286
+ >>> plt.imshow(grid_z2.T, extent=(0,1,0,1), origin='lower')
287
+ >>> plt.title('Cubic')
288
+ >>> plt.gcf().set_size_inches(6, 6)
289
+ >>> plt.show()
290
+
291
+ """ # numpy/numpydoc#87 # noqa: E501
292
+
293
+ points = _ndim_coords_from_arrays(points)
294
+
295
+ if points.ndim < 2:
296
+ ndim = points.ndim
297
+ else:
298
+ ndim = points.shape[-1]
299
+
300
+ if ndim == 1 and method in ('nearest', 'linear', 'cubic'):
301
+ from ._interpolate import interp1d
302
+ points = points.ravel()
303
+ if isinstance(xi, tuple):
304
+ if len(xi) != 1:
305
+ raise ValueError("invalid number of dimensions in xi")
306
+ xi, = xi
307
+ # Sort points/values together, necessary as input for interp1d
308
+ idx = np.argsort(points)
309
+ points = points[idx]
310
+ values = values[idx]
311
+ if method == 'nearest':
312
+ fill_value = 'extrapolate'
313
+ ip = interp1d(points, values, kind=method, axis=0, bounds_error=False,
314
+ fill_value=fill_value)
315
+ return ip(xi)
316
+ elif method == 'nearest':
317
+ ip = NearestNDInterpolator(points, values, rescale=rescale)
318
+ return ip(xi)
319
+ elif method == 'linear':
320
+ ip = LinearNDInterpolator(points, values, fill_value=fill_value,
321
+ rescale=rescale)
322
+ return ip(xi)
323
+ elif method == 'cubic' and ndim == 2:
324
+ ip = CloughTocher2DInterpolator(points, values, fill_value=fill_value,
325
+ rescale=rescale)
326
+ return ip(xi)
327
+ else:
328
+ raise ValueError(
329
+ f"Unknown interpolation method {method!r} for {ndim} dimensional data"
330
+ )
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_pade.py ADDED
@@ -0,0 +1,67 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ from numpy import zeros, asarray, eye, poly1d, hstack, r_
2
+ from scipy import linalg
3
+
4
+ __all__ = ["pade"]
5
+
6
+ def pade(an, m, n=None):
7
+ """
8
+ Return Pade approximation to a polynomial as the ratio of two polynomials.
9
+
10
+ Parameters
11
+ ----------
12
+ an : (N,) array_like
13
+ Taylor series coefficients.
14
+ m : int
15
+ The order of the returned approximating polynomial `q`.
16
+ n : int, optional
17
+ The order of the returned approximating polynomial `p`. By default,
18
+ the order is ``len(an)-1-m``.
19
+
20
+ Returns
21
+ -------
22
+ p, q : Polynomial class
23
+ The Pade approximation of the polynomial defined by `an` is
24
+ ``p(x)/q(x)``.
25
+
26
+ Examples
27
+ --------
28
+ >>> import numpy as np
29
+ >>> from scipy.interpolate import pade
30
+ >>> e_exp = [1.0, 1.0, 1.0/2.0, 1.0/6.0, 1.0/24.0, 1.0/120.0]
31
+ >>> p, q = pade(e_exp, 2)
32
+
33
+ >>> e_exp.reverse()
34
+ >>> e_poly = np.poly1d(e_exp)
35
+
36
+ Compare ``e_poly(x)`` and the Pade approximation ``p(x)/q(x)``
37
+
38
+ >>> e_poly(1)
39
+ 2.7166666666666668
40
+
41
+ >>> p(1)/q(1)
42
+ 2.7179487179487181
43
+
44
+ """
45
+ an = asarray(an)
46
+ if n is None:
47
+ n = len(an) - 1 - m
48
+ if n < 0:
49
+ raise ValueError("Order of q <m> must be smaller than len(an)-1.")
50
+ if n < 0:
51
+ raise ValueError("Order of p <n> must be greater than 0.")
52
+ N = m + n
53
+ if N > len(an)-1:
54
+ raise ValueError("Order of q+p <m+n> must be smaller than len(an).")
55
+ an = an[:N+1]
56
+ Akj = eye(N+1, n+1, dtype=an.dtype)
57
+ Bkj = zeros((N+1, m), dtype=an.dtype)
58
+ for row in range(1, m+1):
59
+ Bkj[row,:row] = -(an[:row])[::-1]
60
+ for row in range(m+1, N+1):
61
+ Bkj[row,:] = -(an[row-m:row])[::-1]
62
+ C = hstack((Akj, Bkj))
63
+ pq = linalg.solve(C, an)
64
+ p = pq[:n+1]
65
+ q = r_[1.0, pq[n+1:]]
66
+ return poly1d(p[::-1]), poly1d(q[::-1])
67
+
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_polyint.py ADDED
@@ -0,0 +1,1029 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ import warnings
2
+ from types import GenericAlias
3
+
4
+ import numpy as np
5
+ from scipy.special import factorial
6
+ from scipy._lib._util import (_asarray_validated, float_factorial, check_random_state,
7
+ _transition_to_rng)
8
+
9
+
10
+ __all__ = ["KroghInterpolator", "krogh_interpolate",
11
+ "BarycentricInterpolator", "barycentric_interpolate",
12
+ "approximate_taylor_polynomial"]
13
+
14
+
15
+ def _isscalar(x):
16
+ """Check whether x is if a scalar type, or 0-dim"""
17
+ return np.isscalar(x) or hasattr(x, 'shape') and x.shape == ()
18
+
19
+
20
+ class _Interpolator1D:
21
+ """
22
+ Common features in univariate interpolation
23
+
24
+ Deal with input data type and interpolation axis rolling. The
25
+ actual interpolator can assume the y-data is of shape (n, r) where
26
+ `n` is the number of x-points, and `r` the number of variables,
27
+ and use self.dtype as the y-data type.
28
+
29
+ Attributes
30
+ ----------
31
+ _y_axis
32
+ Axis along which the interpolation goes in the original array
33
+ _y_extra_shape
34
+ Additional trailing shape of the input arrays, excluding
35
+ the interpolation axis.
36
+ dtype
37
+ Dtype of the y-data arrays. Can be set via _set_dtype, which
38
+ forces it to be float or complex.
39
+
40
+ Methods
41
+ -------
42
+ __call__
43
+ _prepare_x
44
+ _finish_y
45
+ _reshape_yi
46
+ _set_yi
47
+ _set_dtype
48
+ _evaluate
49
+
50
+ """
51
+
52
+ __slots__ = ('_y_axis', '_y_extra_shape', 'dtype')
53
+
54
+ # generic type compatibility with scipy-stubs
55
+ __class_getitem__ = classmethod(GenericAlias)
56
+
57
+ def __init__(self, xi=None, yi=None, axis=None):
58
+ self._y_axis = axis
59
+ self._y_extra_shape = None
60
+ self.dtype = None
61
+ if yi is not None:
62
+ self._set_yi(yi, xi=xi, axis=axis)
63
+
64
+ def __call__(self, x):
65
+ """
66
+ Evaluate the interpolant
67
+
68
+ Parameters
69
+ ----------
70
+ x : array_like
71
+ Point or points at which to evaluate the interpolant.
72
+
73
+ Returns
74
+ -------
75
+ y : array_like
76
+ Interpolated values. Shape is determined by replacing
77
+ the interpolation axis in the original array with the shape of `x`.
78
+
79
+ Notes
80
+ -----
81
+ Input values `x` must be convertible to `float` values like `int`
82
+ or `float`.
83
+
84
+ """
85
+ x, x_shape = self._prepare_x(x)
86
+ y = self._evaluate(x)
87
+ return self._finish_y(y, x_shape)
88
+
89
+ def _evaluate(self, x):
90
+ """
91
+ Actually evaluate the value of the interpolator.
92
+ """
93
+ raise NotImplementedError()
94
+
95
+ def _prepare_x(self, x):
96
+ """Reshape input x array to 1-D"""
97
+ x = _asarray_validated(x, check_finite=False, as_inexact=True)
98
+ x_shape = x.shape
99
+ return x.ravel(), x_shape
100
+
101
+ def _finish_y(self, y, x_shape):
102
+ """Reshape interpolated y back to an N-D array similar to initial y"""
103
+ y = y.reshape(x_shape + self._y_extra_shape)
104
+ if self._y_axis != 0 and x_shape != ():
105
+ nx = len(x_shape)
106
+ ny = len(self._y_extra_shape)
107
+ s = (list(range(nx, nx + self._y_axis))
108
+ + list(range(nx)) + list(range(nx+self._y_axis, nx+ny)))
109
+ y = y.transpose(s)
110
+ return y
111
+
112
+ def _reshape_yi(self, yi, check=False):
113
+ yi = np.moveaxis(np.asarray(yi), self._y_axis, 0)
114
+ if check and yi.shape[1:] != self._y_extra_shape:
115
+ ok_shape = (f"{self._y_extra_shape[-self._y_axis:]!r} + (N,) + "
116
+ f"{self._y_extra_shape[:-self._y_axis]!r}")
117
+ raise ValueError(f"Data must be of shape {ok_shape}")
118
+ return yi.reshape((yi.shape[0], -1))
119
+
120
+ def _set_yi(self, yi, xi=None, axis=None):
121
+ if axis is None:
122
+ axis = self._y_axis
123
+ if axis is None:
124
+ raise ValueError("no interpolation axis specified")
125
+
126
+ yi = np.asarray(yi)
127
+
128
+ shape = yi.shape
129
+ if shape == ():
130
+ shape = (1,)
131
+ if xi is not None and shape[axis] != len(xi):
132
+ raise ValueError("x and y arrays must be equal in length along "
133
+ "interpolation axis.")
134
+
135
+ self._y_axis = (axis % yi.ndim)
136
+ self._y_extra_shape = yi.shape[:self._y_axis] + yi.shape[self._y_axis+1:]
137
+ self.dtype = None
138
+ self._set_dtype(yi.dtype)
139
+
140
+ def _set_dtype(self, dtype, union=False):
141
+ if np.issubdtype(dtype, np.complexfloating) \
142
+ or np.issubdtype(self.dtype, np.complexfloating):
143
+ self.dtype = np.complex128
144
+ else:
145
+ if not union or self.dtype != np.complex128:
146
+ self.dtype = np.float64
147
+
148
+
149
+ class _Interpolator1DWithDerivatives(_Interpolator1D):
150
+ def derivatives(self, x, der=None):
151
+ """
152
+ Evaluate several derivatives of the polynomial at the point `x`
153
+
154
+ Produce an array of derivatives evaluated at the point `x`.
155
+
156
+ Parameters
157
+ ----------
158
+ x : array_like
159
+ Point or points at which to evaluate the derivatives
160
+ der : int or list or None, optional
161
+ How many derivatives to evaluate, or None for all potentially
162
+ nonzero derivatives (that is, a number equal to the number
163
+ of points), or a list of derivatives to evaluate. This number
164
+ includes the function value as the '0th' derivative.
165
+
166
+ Returns
167
+ -------
168
+ d : ndarray
169
+ Array with derivatives; ``d[j]`` contains the jth derivative.
170
+ Shape of ``d[j]`` is determined by replacing the interpolation
171
+ axis in the original array with the shape of `x`.
172
+
173
+ Examples
174
+ --------
175
+ >>> from scipy.interpolate import KroghInterpolator
176
+ >>> KroghInterpolator([0,0,0],[1,2,3]).derivatives(0)
177
+ array([1.0,2.0,3.0])
178
+ >>> KroghInterpolator([0,0,0],[1,2,3]).derivatives([0,0])
179
+ array([[1.0,1.0],
180
+ [2.0,2.0],
181
+ [3.0,3.0]])
182
+
183
+ """
184
+ x, x_shape = self._prepare_x(x)
185
+ y = self._evaluate_derivatives(x, der)
186
+
187
+ y = y.reshape((y.shape[0],) + x_shape + self._y_extra_shape)
188
+ if self._y_axis != 0 and x_shape != ():
189
+ nx = len(x_shape)
190
+ ny = len(self._y_extra_shape)
191
+ s = ([0] + list(range(nx+1, nx + self._y_axis+1))
192
+ + list(range(1, nx+1)) +
193
+ list(range(nx+1+self._y_axis, nx+ny+1)))
194
+ y = y.transpose(s)
195
+ return y
196
+
197
+ def derivative(self, x, der=1):
198
+ """
199
+ Evaluate a single derivative of the polynomial at the point `x`.
200
+
201
+ Parameters
202
+ ----------
203
+ x : array_like
204
+ Point or points at which to evaluate the derivatives
205
+
206
+ der : integer, optional
207
+ Which derivative to evaluate (default: first derivative).
208
+ This number includes the function value as 0th derivative.
209
+
210
+ Returns
211
+ -------
212
+ d : ndarray
213
+ Derivative interpolated at the x-points. Shape of `d` is
214
+ determined by replacing the interpolation axis in the
215
+ original array with the shape of `x`.
216
+
217
+ Notes
218
+ -----
219
+ This may be computed by evaluating all derivatives up to the desired
220
+ one (using self.derivatives()) and then discarding the rest.
221
+
222
+ """
223
+ x, x_shape = self._prepare_x(x)
224
+ y = self._evaluate_derivatives(x, der+1)
225
+ return self._finish_y(y[der], x_shape)
226
+
227
+ def _evaluate_derivatives(self, x, der=None):
228
+ """
229
+ Actually evaluate the derivatives.
230
+
231
+ Parameters
232
+ ----------
233
+ x : array_like
234
+ 1D array of points at which to evaluate the derivatives
235
+ der : integer, optional
236
+ The number of derivatives to evaluate, from 'order 0' (der=1)
237
+ to order der-1. If omitted, return all possibly-non-zero
238
+ derivatives, ie 0 to order n-1.
239
+
240
+ Returns
241
+ -------
242
+ d : ndarray
243
+ Array of shape ``(der, x.size, self.yi.shape[1])`` containing
244
+ the derivatives from 0 to der-1
245
+ """
246
+ raise NotImplementedError()
247
+
248
+
249
+ class KroghInterpolator(_Interpolator1DWithDerivatives):
250
+ """Krogh interpolator (C∞ smooth).
251
+
252
+ The polynomial passes through all the pairs ``(xi, yi)``. One may
253
+ additionally specify a number of derivatives at each point `xi`;
254
+ this is done by repeating the value `xi` and specifying the
255
+ derivatives as successive `yi` values.
256
+
257
+ Allows evaluation of the polynomial and all its derivatives.
258
+ For reasons of numerical stability, this function does not compute
259
+ the coefficients of the polynomial, although they can be obtained
260
+ by evaluating all the derivatives.
261
+
262
+ Parameters
263
+ ----------
264
+ xi : array_like, shape (npoints, )
265
+ Known x-coordinates. Must be sorted in increasing order.
266
+ yi : array_like, shape (..., npoints, ...)
267
+ Known y-coordinates. When an xi occurs two or more times in
268
+ a row, the corresponding yi's represent derivative values. The length of `yi`
269
+ along the interpolation axis must be equal to the length of `xi`. Use the
270
+ `axis` parameter to select the correct axis.
271
+ axis : int, optional
272
+ Axis in the `yi` array corresponding to the x-coordinate values. Defaults to
273
+ ``axis=0``.
274
+
275
+ Notes
276
+ -----
277
+ Be aware that the algorithms implemented here are not necessarily
278
+ the most numerically stable known. Moreover, even in a world of
279
+ exact computation, unless the x coordinates are chosen very
280
+ carefully - Chebyshev zeros (e.g., cos(i*pi/n)) are a good choice -
281
+ polynomial interpolation itself is a very ill-conditioned process
282
+ due to the Runge phenomenon. In general, even with well-chosen
283
+ x values, degrees higher than about thirty cause problems with
284
+ numerical instability in this code.
285
+
286
+ Based on [1]_.
287
+
288
+ References
289
+ ----------
290
+ .. [1] Krogh, "Efficient Algorithms for Polynomial Interpolation
291
+ and Numerical Differentiation", 1970.
292
+
293
+ Examples
294
+ --------
295
+ To produce a polynomial that is zero at 0 and 1 and has
296
+ derivative 2 at 0, call
297
+
298
+ >>> from scipy.interpolate import KroghInterpolator
299
+ >>> KroghInterpolator([0,0,1],[0,2,0])
300
+
301
+ This constructs the quadratic :math:`2x^2-2x`. The derivative condition
302
+ is indicated by the repeated zero in the `xi` array; the corresponding
303
+ yi values are 0, the function value, and 2, the derivative value.
304
+
305
+ For another example, given `xi`, `yi`, and a derivative `ypi` for each
306
+ point, appropriate arrays can be constructed as:
307
+
308
+ >>> import numpy as np
309
+ >>> rng = np.random.default_rng()
310
+ >>> xi = np.linspace(0, 1, 5)
311
+ >>> yi, ypi = rng.random((2, 5))
312
+ >>> xi_k, yi_k = np.repeat(xi, 2), np.ravel(np.dstack((yi,ypi)))
313
+ >>> KroghInterpolator(xi_k, yi_k)
314
+
315
+ To produce a vector-valued polynomial, supply a higher-dimensional
316
+ array for `yi`:
317
+
318
+ >>> KroghInterpolator([0,1],[[2,3],[4,5]])
319
+
320
+ This constructs a linear polynomial giving (2,3) at 0 and (4,5) at 1.
321
+
322
+ """
323
+
324
+ def __init__(self, xi, yi, axis=0):
325
+ super().__init__(xi, yi, axis)
326
+
327
+ self.xi = np.asarray(xi)
328
+ self.yi = self._reshape_yi(yi)
329
+ self.n, self.r = self.yi.shape
330
+
331
+ if (deg := self.xi.size) > 30:
332
+ warnings.warn(f"{deg} degrees provided, degrees higher than about"
333
+ " thirty cause problems with numerical instability "
334
+ "with 'KroghInterpolator'", stacklevel=2)
335
+
336
+ c = np.zeros((self.n+1, self.r), dtype=self.dtype)
337
+ c[0] = self.yi[0]
338
+ Vk = np.zeros((self.n, self.r), dtype=self.dtype)
339
+ for k in range(1, self.n):
340
+ s = 0
341
+ while s <= k and xi[k-s] == xi[k]:
342
+ s += 1
343
+ s -= 1
344
+ Vk[0] = self.yi[k]/float_factorial(s)
345
+ for i in range(k-s):
346
+ if xi[i] == xi[k]:
347
+ raise ValueError("Elements of `xi` can't be equal.")
348
+ if s == 0:
349
+ Vk[i+1] = (c[i]-Vk[i])/(xi[i]-xi[k])
350
+ else:
351
+ Vk[i+1] = (Vk[i+1]-Vk[i])/(xi[i]-xi[k])
352
+ c[k] = Vk[k-s]
353
+ self.c = c
354
+
355
+ def _evaluate(self, x):
356
+ pi = 1
357
+ p = np.zeros((len(x), self.r), dtype=self.dtype)
358
+ p += self.c[0,np.newaxis,:]
359
+ for k in range(1, self.n):
360
+ w = x - self.xi[k-1]
361
+ pi = w*pi
362
+ p += pi[:,np.newaxis] * self.c[k]
363
+ return p
364
+
365
+ def _evaluate_derivatives(self, x, der=None):
366
+ n = self.n
367
+ r = self.r
368
+
369
+ if der is None:
370
+ der = self.n
371
+
372
+ pi = np.zeros((n, len(x)))
373
+ w = np.zeros((n, len(x)))
374
+ pi[0] = 1
375
+ p = np.zeros((len(x), self.r), dtype=self.dtype)
376
+ p += self.c[0, np.newaxis, :]
377
+
378
+ for k in range(1, n):
379
+ w[k-1] = x - self.xi[k-1]
380
+ pi[k] = w[k-1] * pi[k-1]
381
+ p += pi[k, :, np.newaxis] * self.c[k]
382
+
383
+ cn = np.zeros((max(der, n+1), len(x), r), dtype=self.dtype)
384
+ cn[:n+1, :, :] += self.c[:n+1, np.newaxis, :]
385
+ cn[0] = p
386
+ for k in range(1, n):
387
+ for i in range(1, n-k+1):
388
+ pi[i] = w[k+i-1]*pi[i-1] + pi[i]
389
+ cn[k] = cn[k] + pi[i, :, np.newaxis]*cn[k+i]
390
+ cn[k] *= float_factorial(k)
391
+
392
+ cn[n, :, :] = 0
393
+ return cn[:der]
394
+
395
+
396
+ def krogh_interpolate(xi, yi, x, der=0, axis=0):
397
+ """Convenience function for Krogh interpolation.
398
+
399
+ See `KroghInterpolator` for more details.
400
+
401
+ Parameters
402
+ ----------
403
+ xi : array_like
404
+ Interpolation points (known x-coordinates).
405
+ yi : array_like
406
+ Known y-coordinates, of shape ``(xi.size, R)``. Interpreted as
407
+ vectors of length R, or scalars if R=1.
408
+ x : array_like
409
+ Point or points at which to evaluate the derivatives.
410
+ der : int or list or None, optional
411
+ How many derivatives to evaluate, or None for all potentially
412
+ nonzero derivatives (that is, a number equal to the number
413
+ of points), or a list of derivatives to evaluate. This number
414
+ includes the function value as the '0th' derivative.
415
+ axis : int, optional
416
+ Axis in the `yi` array corresponding to the x-coordinate values.
417
+
418
+ Returns
419
+ -------
420
+ d : ndarray
421
+ If the interpolator's values are R-D then the
422
+ returned array will be the number of derivatives by N by R.
423
+ If `x` is a scalar, the middle dimension will be dropped; if
424
+ the `yi` are scalars then the last dimension will be dropped.
425
+
426
+ See Also
427
+ --------
428
+ KroghInterpolator : Krogh interpolator
429
+
430
+ Notes
431
+ -----
432
+ Construction of the interpolating polynomial is a relatively expensive
433
+ process. If you want to evaluate it repeatedly consider using the class
434
+ KroghInterpolator (which is what this function uses).
435
+
436
+ Examples
437
+ --------
438
+ We can interpolate 2D observed data using Krogh interpolation:
439
+
440
+ >>> import numpy as np
441
+ >>> import matplotlib.pyplot as plt
442
+ >>> from scipy.interpolate import krogh_interpolate
443
+ >>> x_observed = np.linspace(0.0, 10.0, 11)
444
+ >>> y_observed = np.sin(x_observed)
445
+ >>> x = np.linspace(min(x_observed), max(x_observed), num=100)
446
+ >>> y = krogh_interpolate(x_observed, y_observed, x)
447
+ >>> plt.plot(x_observed, y_observed, "o", label="observation")
448
+ >>> plt.plot(x, y, label="krogh interpolation")
449
+ >>> plt.legend()
450
+ >>> plt.show()
451
+ """
452
+
453
+ P = KroghInterpolator(xi, yi, axis=axis)
454
+ if der == 0:
455
+ return P(x)
456
+ elif _isscalar(der):
457
+ return P.derivative(x, der=der)
458
+ else:
459
+ return P.derivatives(x, der=np.amax(der)+1)[der]
460
+
461
+
462
+ def approximate_taylor_polynomial(f,x,degree,scale,order=None):
463
+ """
464
+ Estimate the Taylor polynomial of f at x by polynomial fitting.
465
+
466
+ Parameters
467
+ ----------
468
+ f : callable
469
+ The function whose Taylor polynomial is sought. Should accept
470
+ a vector of `x` values.
471
+ x : scalar
472
+ The point at which the polynomial is to be evaluated.
473
+ degree : int
474
+ The degree of the Taylor polynomial
475
+ scale : scalar
476
+ The width of the interval to use to evaluate the Taylor polynomial.
477
+ Function values spread over a range this wide are used to fit the
478
+ polynomial. Must be chosen carefully.
479
+ order : int or None, optional
480
+ The order of the polynomial to be used in the fitting; `f` will be
481
+ evaluated ``order+1`` times. If None, use `degree`.
482
+
483
+ Returns
484
+ -------
485
+ p : poly1d instance
486
+ The Taylor polynomial (translated to the origin, so that
487
+ for example p(0)=f(x)).
488
+
489
+ Notes
490
+ -----
491
+ The appropriate choice of "scale" is a trade-off; too large and the
492
+ function differs from its Taylor polynomial too much to get a good
493
+ answer, too small and round-off errors overwhelm the higher-order terms.
494
+ The algorithm used becomes numerically unstable around order 30 even
495
+ under ideal circumstances.
496
+
497
+ Choosing order somewhat larger than degree may improve the higher-order
498
+ terms.
499
+
500
+ Examples
501
+ --------
502
+ We can calculate Taylor approximation polynomials of sin function with
503
+ various degrees:
504
+
505
+ >>> import numpy as np
506
+ >>> import matplotlib.pyplot as plt
507
+ >>> from scipy.interpolate import approximate_taylor_polynomial
508
+ >>> x = np.linspace(-10.0, 10.0, num=100)
509
+ >>> plt.plot(x, np.sin(x), label="sin curve")
510
+ >>> for degree in np.arange(1, 15, step=2):
511
+ ... sin_taylor = approximate_taylor_polynomial(np.sin, 0, degree, 1,
512
+ ... order=degree + 2)
513
+ ... plt.plot(x, sin_taylor(x), label=f"degree={degree}")
514
+ >>> plt.legend(bbox_to_anchor=(1.05, 1), loc='upper left',
515
+ ... borderaxespad=0.0, shadow=True)
516
+ >>> plt.tight_layout()
517
+ >>> plt.axis([-10, 10, -10, 10])
518
+ >>> plt.show()
519
+
520
+ """
521
+ if order is None:
522
+ order = degree
523
+
524
+ n = order+1
525
+ # Choose n points that cluster near the endpoints of the interval in
526
+ # a way that avoids the Runge phenomenon. Ensure, by including the
527
+ # endpoint or not as appropriate, that one point always falls at x
528
+ # exactly.
529
+ xs = scale*np.cos(np.linspace(0,np.pi,n,endpoint=n % 1)) + x
530
+
531
+ P = KroghInterpolator(xs, f(xs))
532
+ d = P.derivatives(x,der=degree+1)
533
+
534
+ return np.poly1d((d/factorial(np.arange(degree+1)))[::-1])
535
+
536
+
537
+ class BarycentricInterpolator(_Interpolator1DWithDerivatives):
538
+ r"""Barycentric (Lagrange with improved stability) interpolator (C∞ smooth).
539
+
540
+ Constructs a polynomial that passes through a given set of points.
541
+ Allows evaluation of the polynomial and all its derivatives,
542
+ efficient changing of the y-values to be interpolated,
543
+ and updating by adding more x- and y-values. For numerical stability, a barycentric
544
+ representation is used rather than computing the coefficients of the polynomial
545
+ directly.
546
+
547
+
548
+ Parameters
549
+ ----------
550
+ xi : array_like, shape (npoints, )
551
+ 1-D array of x-coordinates of the points the polynomial
552
+ should pass through
553
+ yi : array_like, shape (..., npoints, ...), optional
554
+ N-D array of y-coordinates of the points the polynomial should pass through.
555
+ If None, the y values will be supplied later via the `set_y` method.
556
+ The length of `yi` along the interpolation axis must be equal to the length
557
+ of `xi`. Use the ``axis`` parameter to select correct axis.
558
+ axis : int, optional
559
+ Axis in the yi array corresponding to the x-coordinate values. Defaults
560
+ to ``axis=0``.
561
+ wi : array_like, optional
562
+ The barycentric weights for the chosen interpolation points `xi`.
563
+ If absent or None, the weights will be computed from `xi` (default).
564
+ This allows for the reuse of the weights `wi` if several interpolants
565
+ are being calculated using the same nodes `xi`, without re-computation. This
566
+ also allows for computing the weights explicitly for some choices of
567
+ `xi` (see notes).
568
+ rng : {None, int, `numpy.random.Generator`}, optional
569
+ If `rng` is passed by keyword, types other than `numpy.random.Generator` are
570
+ passed to `numpy.random.default_rng` to instantiate a ``Generator``.
571
+ If `rng` is already a ``Generator`` instance, then the provided instance is
572
+ used. Specify `rng` for repeatable interpolation.
573
+
574
+ If this argument `random_state` is passed by keyword,
575
+ legacy behavior for the argument `random_state` applies:
576
+
577
+ - If `random_state` is None (or `numpy.random`), the `numpy.random.RandomState`
578
+ singleton is used.
579
+ - If `random_state` is an int, a new ``RandomState`` instance is used,
580
+ seeded with `random_state`.
581
+ - If `random_state` is already a ``Generator`` or ``RandomState`` instance then
582
+ that instance is used.
583
+
584
+ .. versionchanged:: 1.15.0
585
+ As part of the `SPEC-007 <https://scientific-python.org/specs/spec-0007/>`_
586
+ transition from use of `numpy.random.RandomState` to
587
+ `numpy.random.Generator` this keyword was changed from `random_state` to `rng`.
588
+ For an interim period, both keywords will continue to work (only specify
589
+ one of them). After the interim period using the `random_state` keyword will emit
590
+ warnings. The behavior of the `random_state` and `rng` keywords is outlined above.
591
+
592
+ Notes
593
+ -----
594
+ This method is a variant of Lagrange polynomial interpolation [1]_ based on [2]_.
595
+ Instead of using Lagrange's or Newton's formula, the polynomial is represented by
596
+ the barycentric formula
597
+
598
+ .. math::
599
+
600
+ p(x) =
601
+ \frac{\sum_{i=1}^m\ w_i y_i / (x - x_i)}{\sum_{i=1}^m w_i / (x - x_i)},
602
+
603
+ where :math:`w_i` are the barycentric weights computed with the general formula
604
+
605
+ .. math::
606
+
607
+ w_i = \left( \prod_{k \neq i} x_i - x_k \right)^{-1}.
608
+
609
+ This is the same barycentric form used by `AAA` and `FloaterHormannInterpolator`.
610
+ However, in contrast, the weights :math:`w_i` are defined such that
611
+ :math:`p(x)` is a polynomial rather than a rational function.
612
+
613
+ The barycentric representation avoids many of the problems associated with
614
+ polynomial interpolation caused by floating-point arithmetic. However, it does not
615
+ avoid issues that are intrinsic to polynomial interpolation. Namely, if the
616
+ x-coordinates are equally spaced, then the weights can be computed explicitly using
617
+ the formula from [2]_
618
+
619
+ .. math::
620
+
621
+ w_i = (-1)^i {n \choose i},
622
+
623
+ where :math:`n` is the number of x-coordinates. As noted in [2]_, this means that
624
+ for large :math:`n` the weights vary by exponentially large factors, leading to the
625
+ Runge phenomenon.
626
+
627
+ To avoid this ill-conditioning, the x-coordinates should be clustered at the
628
+ endpoints of the interval. An excellent choice of points on the interval
629
+ :math:`[a,b]` are Chebyshev points of the second kind
630
+
631
+ .. math::
632
+
633
+ x_i = \frac{a + b}{2} + \frac{a - b}{2}\cos(i\pi/n).
634
+
635
+ in which case the weights can be computed explicitly as
636
+
637
+ .. math::
638
+
639
+ w_i = \begin{cases}
640
+ (-1)^i/2 & i = 0,n \\
641
+ (-1)^i & \text{otherwise}
642
+ \end{cases}.
643
+
644
+ See [2]_ for more infomation. Note that for large :math:`n`, computing the weights
645
+ explicitly (see examples) will be faster than the generic formula.
646
+
647
+ References
648
+ ----------
649
+ .. [1] https://en.wikipedia.org/wiki/Lagrange_polynomial
650
+ .. [2] Jean-Paul Berrut and Lloyd N. Trefethen, "Barycentric Lagrange
651
+ Interpolation", SIAM Review 2004 46:3, 501-517
652
+ :doi:`10.1137/S0036144502417715`
653
+
654
+ Examples
655
+ --------
656
+ To produce a quintic barycentric interpolant approximating the function
657
+ :math:`\sin x`, and its first four derivatives, using six randomly-spaced
658
+ nodes in :math:`(0, \pi/2)`:
659
+
660
+ >>> import numpy as np
661
+ >>> import matplotlib.pyplot as plt
662
+ >>> from scipy.interpolate import BarycentricInterpolator
663
+ >>> rng = np.random.default_rng()
664
+ >>> xi = rng.random(6) * np.pi/2
665
+ >>> f, f_d1, f_d2, f_d3, f_d4 = np.sin, np.cos, lambda x: -np.sin(x), lambda x: -np.cos(x), np.sin
666
+ >>> P = BarycentricInterpolator(xi, f(xi), random_state=rng)
667
+ >>> fig, axs = plt.subplots(5, 1, sharex=True, layout='constrained', figsize=(7,10))
668
+ >>> x = np.linspace(0, np.pi, 100)
669
+ >>> axs[0].plot(x, P(x), 'r:', x, f(x), 'k--', xi, f(xi), 'xk')
670
+ >>> axs[1].plot(x, P.derivative(x), 'r:', x, f_d1(x), 'k--', xi, f_d1(xi), 'xk')
671
+ >>> axs[2].plot(x, P.derivative(x, 2), 'r:', x, f_d2(x), 'k--', xi, f_d2(xi), 'xk')
672
+ >>> axs[3].plot(x, P.derivative(x, 3), 'r:', x, f_d3(x), 'k--', xi, f_d3(xi), 'xk')
673
+ >>> axs[4].plot(x, P.derivative(x, 4), 'r:', x, f_d4(x), 'k--', xi, f_d4(xi), 'xk')
674
+ >>> axs[0].set_xlim(0, np.pi)
675
+ >>> axs[4].set_xlabel(r"$x$")
676
+ >>> axs[4].set_xticks([i * np.pi / 4 for i in range(5)],
677
+ ... ["0", r"$\frac{\pi}{4}$", r"$\frac{\pi}{2}$", r"$\frac{3\pi}{4}$", r"$\pi$"])
678
+ >>> for ax, label in zip(axs, ("$f(x)$", "$f'(x)$", "$f''(x)$", "$f^{(3)}(x)$", "$f^{(4)}(x)$")):
679
+ ... ax.set_ylabel(label)
680
+ >>> labels = ['Interpolation nodes', 'True function $f$', 'Barycentric interpolation']
681
+ >>> axs[0].legend(axs[0].get_lines()[::-1], labels, bbox_to_anchor=(0., 1.02, 1., .102),
682
+ ... loc='lower left', ncols=3, mode="expand", borderaxespad=0., frameon=False)
683
+ >>> plt.show()
684
+
685
+ Next, we show how using Chebyshev points of the second kind avoids the
686
+ Runge phenomenon. In this example, we also compute the weights explicitly.
687
+
688
+ >>> n = 20
689
+ >>> def f(x): return np.abs(x) + 0.5*x - x**2
690
+ >>> i = np.arange(n)
691
+ >>> x_cheb = np.cos(i*np.pi/(n - 1)) # Chebyshev points on [-1, 1]
692
+ >>> w_i_cheb = (-1.)**i # Explicit formula for weights of Chebyshev points
693
+ >>> w_i_cheb[[0, -1]] /= 2
694
+ >>> p_cheb = BarycentricInterpolator(x_cheb, f(x_cheb), wi=w_i_cheb)
695
+ >>> x_equi = np.linspace(-1, 1, n)
696
+ >>> p_equi = BarycentricInterpolator(x_equi, f(x_equi))
697
+ >>> xx = np.linspace(-1, 1, 1000)
698
+ >>> fig, ax = plt.subplots()
699
+ >>> ax.plot(xx, f(xx), label="Original Function")
700
+ >>> ax.plot(xx, p_cheb(xx), "--", label="Chebshev Points")
701
+ >>> ax.plot(xx, p_equi(xx), "--", label="Equally Spaced Points")
702
+ >>> ax.set(xlabel="$x$", ylabel="$f(x)$", xlim=[-1, 1])
703
+ >>> ax.legend()
704
+ >>> plt.show()
705
+
706
+ """ # numpy/numpydoc#87 # noqa: E501
707
+
708
+ @_transition_to_rng("random_state", replace_doc=False)
709
+ def __init__(self, xi, yi=None, axis=0, *, wi=None, rng=None):
710
+ super().__init__(xi, yi, axis)
711
+
712
+ rng = check_random_state(rng)
713
+
714
+ self.xi = np.asarray(xi, dtype=np.float64)
715
+ self.set_yi(yi)
716
+ self.n = len(self.xi)
717
+
718
+ # cache derivative object to avoid re-computing the weights with every call.
719
+ self._diff_cij = None
720
+
721
+ if wi is not None:
722
+ self.wi = wi
723
+ else:
724
+ # See page 510 of Berrut and Trefethen 2004 for an explanation of the
725
+ # capacity scaling and the suggestion of using a random permutation of
726
+ # the input factors.
727
+ # At the moment, the permutation is not performed for xi that are
728
+ # appended later through the add_xi interface. It's not clear to me how
729
+ # to implement that and it seems that most situations that require
730
+ # these numerical stability improvements will be able to provide all
731
+ # the points to the constructor.
732
+ self._inv_capacity = 4.0 / (np.max(self.xi) - np.min(self.xi))
733
+ permute = rng.permutation(self.n, )
734
+ inv_permute = np.zeros(self.n, dtype=np.int32)
735
+ inv_permute[permute] = np.arange(self.n)
736
+ self.wi = np.zeros(self.n)
737
+
738
+ for i in range(self.n):
739
+ dist = self._inv_capacity * (self.xi[i] - self.xi[permute])
740
+ dist[inv_permute[i]] = 1.0
741
+ prod = np.prod(dist)
742
+ if prod == 0.0:
743
+ raise ValueError("Interpolation points xi must be"
744
+ " distinct.")
745
+ self.wi[i] = 1.0 / prod
746
+
747
+ def set_yi(self, yi, axis=None):
748
+ """
749
+ Update the y values to be interpolated
750
+
751
+ The barycentric interpolation algorithm requires the calculation
752
+ of weights, but these depend only on the `xi`. The `yi` can be changed
753
+ at any time.
754
+
755
+ Parameters
756
+ ----------
757
+ yi : array_like
758
+ The y-coordinates of the points the polynomial will pass through.
759
+ If None, the y values must be supplied later.
760
+ axis : int, optional
761
+ Axis in the `yi` array corresponding to the x-coordinate values.
762
+
763
+ """
764
+ if yi is None:
765
+ self.yi = None
766
+ return
767
+ self._set_yi(yi, xi=self.xi, axis=axis)
768
+ self.yi = self._reshape_yi(yi)
769
+ self.n, self.r = self.yi.shape
770
+ self._diff_baryint = None
771
+
772
+ def add_xi(self, xi, yi=None):
773
+ """
774
+ Add more x values to the set to be interpolated
775
+
776
+ The barycentric interpolation algorithm allows easy updating by
777
+ adding more points for the polynomial to pass through.
778
+
779
+ Parameters
780
+ ----------
781
+ xi : array_like
782
+ The x coordinates of the points that the polynomial should pass
783
+ through.
784
+ yi : array_like, optional
785
+ The y coordinates of the points the polynomial should pass through.
786
+ Should have shape ``(xi.size, R)``; if R > 1 then the polynomial is
787
+ vector-valued.
788
+ If `yi` is not given, the y values will be supplied later. `yi`
789
+ should be given if and only if the interpolator has y values
790
+ specified.
791
+
792
+ Notes
793
+ -----
794
+ The new points added by `add_xi` are not randomly permuted
795
+ so there is potential for numerical instability,
796
+ especially for a large number of points. If this
797
+ happens, please reconstruct interpolation from scratch instead.
798
+ """
799
+ if yi is not None:
800
+ if self.yi is None:
801
+ raise ValueError("No previous yi value to update!")
802
+ yi = self._reshape_yi(yi, check=True)
803
+ self.yi = np.vstack((self.yi,yi))
804
+ else:
805
+ if self.yi is not None:
806
+ raise ValueError("No update to yi provided!")
807
+ old_n = self.n
808
+ self.xi = np.concatenate((self.xi,xi))
809
+ self.n = len(self.xi)
810
+ self.wi **= -1
811
+ old_wi = self.wi
812
+ self.wi = np.zeros(self.n)
813
+ self.wi[:old_n] = old_wi
814
+ for j in range(old_n, self.n):
815
+ self.wi[:j] *= self._inv_capacity * (self.xi[j]-self.xi[:j])
816
+ self.wi[j] = np.multiply.reduce(
817
+ self._inv_capacity * (self.xi[:j]-self.xi[j])
818
+ )
819
+ self.wi **= -1
820
+ self._diff_cij = None
821
+ self._diff_baryint = None
822
+
823
+ def __call__(self, x):
824
+ """Evaluate the interpolating polynomial at the points x
825
+
826
+ Parameters
827
+ ----------
828
+ x : array_like
829
+ Point or points at which to evaluate the interpolant.
830
+
831
+ Returns
832
+ -------
833
+ y : array_like
834
+ Interpolated values. Shape is determined by replacing
835
+ the interpolation axis in the original array with the shape of `x`.
836
+
837
+ Notes
838
+ -----
839
+ Currently the code computes an outer product between `x` and the
840
+ weights, that is, it constructs an intermediate array of size
841
+ ``(N, len(x))``, where N is the degree of the polynomial.
842
+ """
843
+ return _Interpolator1D.__call__(self, x)
844
+
845
+ def _evaluate(self, x):
846
+ if x.size == 0:
847
+ p = np.zeros((0, self.r), dtype=self.dtype)
848
+ else:
849
+ c = x[..., np.newaxis] - self.xi
850
+ z = c == 0
851
+ c[z] = 1
852
+ c = self.wi / c
853
+ with np.errstate(divide='ignore'):
854
+ p = np.dot(c, self.yi) / np.sum(c, axis=-1)[..., np.newaxis]
855
+ # Now fix where x==some xi
856
+ r = np.nonzero(z)
857
+ if len(r) == 1: # evaluation at a scalar
858
+ if len(r[0]) > 0: # equals one of the points
859
+ p = self.yi[r[0][0]]
860
+ else:
861
+ p[r[:-1]] = self.yi[r[-1]]
862
+ return p
863
+
864
+ def derivative(self, x, der=1):
865
+ """
866
+ Evaluate a single derivative of the polynomial at the point x.
867
+
868
+ Parameters
869
+ ----------
870
+ x : array_like
871
+ Point or points at which to evaluate the derivatives
872
+ der : integer, optional
873
+ Which derivative to evaluate (default: first derivative).
874
+ This number includes the function value as 0th derivative.
875
+
876
+ Returns
877
+ -------
878
+ d : ndarray
879
+ Derivative interpolated at the x-points. Shape of `d` is
880
+ determined by replacing the interpolation axis in the
881
+ original array with the shape of `x`.
882
+ """
883
+ x, x_shape = self._prepare_x(x)
884
+ y = self._evaluate_derivatives(x, der+1, all_lower=False)
885
+ return self._finish_y(y, x_shape)
886
+
887
+ def _evaluate_derivatives(self, x, der=None, all_lower=True):
888
+ # NB: der here is not the order of the highest derivative;
889
+ # instead, it is the size of the derivatives matrix that
890
+ # would be returned with all_lower=True, including the
891
+ # '0th' derivative (the undifferentiated function).
892
+ # E.g. to evaluate the 5th derivative alone, call
893
+ # _evaluate_derivatives(x, der=6, all_lower=False).
894
+
895
+ if (not all_lower) and (x.size == 0 or self.r == 0):
896
+ return np.zeros((0, self.r), dtype=self.dtype)
897
+
898
+ if (not all_lower) and der == 1:
899
+ return self._evaluate(x)
900
+
901
+ if (not all_lower) and (der > self.n):
902
+ return np.zeros((len(x), self.r), dtype=self.dtype)
903
+
904
+ if der is None:
905
+ der = self.n
906
+
907
+ if all_lower and (x.size == 0 or self.r == 0):
908
+ return np.zeros((der, len(x), self.r), dtype=self.dtype)
909
+
910
+ if self._diff_cij is None:
911
+ # c[i,j] = xi[i] - xi[j]
912
+ c = self.xi[:, np.newaxis] - self.xi
913
+
914
+ # avoid division by 0 (diagonal entries are so far zero by construction)
915
+ np.fill_diagonal(c, 1)
916
+
917
+ # c[i,j] = (w[j] / w[i]) / (xi[i] - xi[j]) (equation 9.4)
918
+ c = self.wi/ (c * self.wi[..., np.newaxis])
919
+
920
+ # fill in correct diagonal entries: each column sums to 0
921
+ np.fill_diagonal(c, 0)
922
+
923
+ # calculate diagonal
924
+ # c[j,j] = -sum_{i != j} c[i,j] (equation 9.5)
925
+ d = -c.sum(axis=1)
926
+ # c[i,j] = l_j(x_i)
927
+ np.fill_diagonal(c, d)
928
+
929
+ self._diff_cij = c
930
+
931
+ if self._diff_baryint is None:
932
+ # initialise and cache derivative interpolator and cijs;
933
+ # reuse weights wi (which depend only on interpolation points xi),
934
+ # to avoid unnecessary re-computation
935
+ self._diff_baryint = BarycentricInterpolator(xi=self.xi,
936
+ yi=self._diff_cij @ self.yi,
937
+ wi=self.wi)
938
+ self._diff_baryint._diff_cij = self._diff_cij
939
+
940
+ if all_lower:
941
+ # assemble matrix of derivatives from order 0 to order der-1,
942
+ # in the format required by _Interpolator1DWithDerivatives.
943
+ cn = np.zeros((der, len(x), self.r), dtype=self.dtype)
944
+ for d in range(der):
945
+ cn[d, :, :] = self._evaluate_derivatives(x, d+1, all_lower=False)
946
+ return cn
947
+
948
+ # recursively evaluate only the derivative requested
949
+ return self._diff_baryint._evaluate_derivatives(x, der-1, all_lower=False)
950
+
951
+
952
+ def barycentric_interpolate(xi, yi, x, axis=0, *, der=0, rng=None):
953
+ """Convenience function for barycentric interpolation.
954
+
955
+ Constructs a polynomial that passes through a given set of points,
956
+ then evaluates the polynomial. For reasons of numerical stability,
957
+ this function does not compute the coefficients of the polynomial.
958
+
959
+ This function uses a "barycentric interpolation" method that treats
960
+ the problem as a special case of rational function interpolation.
961
+ This algorithm is quite stable, numerically, but even in a world of
962
+ exact computation, unless the `x` coordinates are chosen very
963
+ carefully - Chebyshev zeros (e.g., cos(i*pi/n)) are a good choice -
964
+ polynomial interpolation itself is a very ill-conditioned process
965
+ due to the Runge phenomenon.
966
+
967
+ Parameters
968
+ ----------
969
+ xi : array_like
970
+ 1-D array of x coordinates of the points the polynomial should
971
+ pass through
972
+ yi : array_like
973
+ The y coordinates of the points the polynomial should pass through.
974
+ x : scalar or array_like
975
+ Point or points at which to evaluate the interpolant.
976
+ axis : int, optional
977
+ Axis in the `yi` array corresponding to the x-coordinate values.
978
+ der : int or list or None, optional
979
+ How many derivatives to evaluate, or None for all potentially
980
+ nonzero derivatives (that is, a number equal to the number
981
+ of points), or a list of derivatives to evaluate. This number
982
+ includes the function value as the '0th' derivative.
983
+ rng : `numpy.random.Generator`, optional
984
+ Pseudorandom number generator state. When `rng` is None, a new
985
+ `numpy.random.Generator` is created using entropy from the
986
+ operating system. Types other than `numpy.random.Generator` are
987
+ passed to `numpy.random.default_rng` to instantiate a ``Generator``.
988
+
989
+ Returns
990
+ -------
991
+ y : scalar or array_like
992
+ Interpolated values. Shape is determined by replacing
993
+ the interpolation axis in the original array with the shape of `x`.
994
+
995
+ See Also
996
+ --------
997
+ BarycentricInterpolator : Barycentric interpolator
998
+
999
+ Notes
1000
+ -----
1001
+ Construction of the interpolation weights is a relatively slow process.
1002
+ If you want to call this many times with the same xi (but possibly
1003
+ varying yi or x) you should use the class `BarycentricInterpolator`.
1004
+ This is what this function uses internally.
1005
+
1006
+ Examples
1007
+ --------
1008
+ We can interpolate 2D observed data using barycentric interpolation:
1009
+
1010
+ >>> import numpy as np
1011
+ >>> import matplotlib.pyplot as plt
1012
+ >>> from scipy.interpolate import barycentric_interpolate
1013
+ >>> x_observed = np.linspace(0.0, 10.0, 11)
1014
+ >>> y_observed = np.sin(x_observed)
1015
+ >>> x = np.linspace(min(x_observed), max(x_observed), num=100)
1016
+ >>> y = barycentric_interpolate(x_observed, y_observed, x)
1017
+ >>> plt.plot(x_observed, y_observed, "o", label="observation")
1018
+ >>> plt.plot(x, y, label="barycentric interpolation")
1019
+ >>> plt.legend()
1020
+ >>> plt.show()
1021
+
1022
+ """
1023
+ P = BarycentricInterpolator(xi, yi, axis=axis, rng=rng)
1024
+ if der == 0:
1025
+ return P(x)
1026
+ elif _isscalar(der):
1027
+ return P.derivative(x, der=der)
1028
+ else:
1029
+ return P.derivatives(x, der=np.amax(der)+1)[der]
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_rbf.py ADDED
@@ -0,0 +1,292 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """rbf - Radial basis functions for interpolation/smoothing scattered N-D data.
2
+
3
+ Written by John Travers <jtravs@gmail.com>, February 2007
4
+ Based closely on Matlab code by Alex Chirokov
5
+ Additional, large, improvements by Robert Hetland
6
+ Some additional alterations by Travis Oliphant
7
+ Interpolation with multi-dimensional target domain by Josua Sassen
8
+
9
+ Permission to use, modify, and distribute this software is given under the
10
+ terms of the SciPy (BSD style) license. See LICENSE.txt that came with
11
+ this distribution for specifics.
12
+
13
+ NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR OWN RISK.
14
+
15
+ Copyright (c) 2006-2007, Robert Hetland <hetland@tamu.edu>
16
+ Copyright (c) 2007, John Travers <jtravs@gmail.com>
17
+
18
+ Redistribution and use in source and binary forms, with or without
19
+ modification, are permitted provided that the following conditions are
20
+ met:
21
+
22
+ * Redistributions of source code must retain the above copyright
23
+ notice, this list of conditions and the following disclaimer.
24
+
25
+ * Redistributions in binary form must reproduce the above
26
+ copyright notice, this list of conditions and the following
27
+ disclaimer in the documentation and/or other materials provided
28
+ with the distribution.
29
+
30
+ * Neither the name of Robert Hetland nor the names of any
31
+ contributors may be used to endorse or promote products derived
32
+ from this software without specific prior written permission.
33
+
34
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
35
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
36
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
37
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
38
+ OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
39
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
40
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
41
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
42
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
43
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
44
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
45
+ """
46
+ import numpy as np
47
+
48
+ from scipy import linalg
49
+ from scipy.special import xlogy
50
+ from scipy.spatial.distance import cdist, pdist, squareform
51
+ from scipy._lib._array_api import xp_capabilities
52
+
53
+ __all__ = ['Rbf']
54
+
55
+
56
+ @xp_capabilities(out_of_scope=True)
57
+ class Rbf:
58
+ """
59
+ Rbf(*args, **kwargs)
60
+
61
+ Class for radial basis function interpolation of functions from
62
+ N-D scattered data to an M-D domain (legacy).
63
+
64
+ .. legacy:: class
65
+
66
+ `Rbf` is legacy code, for new usage please use `RBFInterpolator`
67
+ instead.
68
+
69
+ Parameters
70
+ ----------
71
+ *args : arrays
72
+ x, y, z, ..., d, where x, y, z, ... are the coordinates of the nodes
73
+ and d is the array of values at the nodes
74
+ function : str or callable, optional
75
+ The radial basis function, based on the radius, r, given by the norm
76
+ (default is Euclidean distance); the default is 'multiquadric'::
77
+
78
+ 'multiquadric': sqrt((r/self.epsilon)**2 + 1)
79
+ 'inverse': 1.0/sqrt((r/self.epsilon)**2 + 1)
80
+ 'gaussian': exp(-(r/self.epsilon)**2)
81
+ 'linear': r
82
+ 'cubic': r**3
83
+ 'quintic': r**5
84
+ 'thin_plate': r**2 * log(r)
85
+
86
+ If callable, then it must take 2 arguments (self, r). The epsilon
87
+ parameter will be available as self.epsilon. Other keyword
88
+ arguments passed in will be available as well.
89
+
90
+ epsilon : float, optional
91
+ Adjustable constant for gaussian or multiquadrics functions
92
+ - defaults to approximate average distance between nodes (which is
93
+ a good start).
94
+ smooth : float, optional
95
+ Values greater than zero increase the smoothness of the
96
+ approximation. 0 is for interpolation (default), the function will
97
+ always go through the nodal points in this case.
98
+ norm : str, callable, optional
99
+ A function that returns the 'distance' between two points, with
100
+ inputs as arrays of positions (x, y, z, ...), and an output as an
101
+ array of distance. E.g., the default: 'euclidean', such that the result
102
+ is a matrix of the distances from each point in ``x1`` to each point in
103
+ ``x2``. For more options, see documentation of
104
+ `scipy.spatial.distances.cdist`.
105
+ mode : str, optional
106
+ Mode of the interpolation, can be '1-D' (default) or 'N-D'. When it is
107
+ '1-D' the data `d` will be considered as 1-D and flattened
108
+ internally. When it is 'N-D' the data `d` is assumed to be an array of
109
+ shape (n_samples, m), where m is the dimension of the target domain.
110
+
111
+
112
+ Attributes
113
+ ----------
114
+ N : int
115
+ The number of data points (as determined by the input arrays).
116
+ di : ndarray
117
+ The 1-D array of data values at each of the data coordinates `xi`.
118
+ xi : ndarray
119
+ The 2-D array of data coordinates.
120
+ function : str or callable
121
+ The radial basis function. See description under Parameters.
122
+ epsilon : float
123
+ Parameter used by gaussian or multiquadrics functions. See Parameters.
124
+ smooth : float
125
+ Smoothing parameter. See description under Parameters.
126
+ norm : str or callable
127
+ The distance function. See description under Parameters.
128
+ mode : str
129
+ Mode of the interpolation. See description under Parameters.
130
+ nodes : ndarray
131
+ A 1-D array of node values for the interpolation.
132
+ A : internal property, do not use
133
+
134
+ See Also
135
+ --------
136
+ RBFInterpolator
137
+
138
+ Examples
139
+ --------
140
+ >>> import numpy as np
141
+ >>> from scipy.interpolate import Rbf
142
+ >>> rng = np.random.default_rng()
143
+ >>> x, y, z, d = rng.random((4, 50))
144
+ >>> rbfi = Rbf(x, y, z, d) # radial basis function interpolator instance
145
+ >>> xi = yi = zi = np.linspace(0, 1, 20)
146
+ >>> di = rbfi(xi, yi, zi) # interpolated values
147
+ >>> di.shape
148
+ (20,)
149
+
150
+ """
151
+ # Available radial basis functions that can be selected as strings;
152
+ # they all start with _h_ (self._init_function relies on that)
153
+ def _h_multiquadric(self, r):
154
+ return np.sqrt((1.0/self.epsilon*r)**2 + 1)
155
+
156
+ def _h_inverse_multiquadric(self, r):
157
+ return 1.0/np.sqrt((1.0/self.epsilon*r)**2 + 1)
158
+
159
+ def _h_gaussian(self, r):
160
+ return np.exp(-(1.0/self.epsilon*r)**2)
161
+
162
+ def _h_linear(self, r):
163
+ return r
164
+
165
+ def _h_cubic(self, r):
166
+ return r**3
167
+
168
+ def _h_quintic(self, r):
169
+ return r**5
170
+
171
+ def _h_thin_plate(self, r):
172
+ return xlogy(r**2, r)
173
+
174
+ # Setup self._function and do smoke test on initial r
175
+ def _init_function(self, r):
176
+ if isinstance(self.function, str):
177
+ self.function = self.function.lower()
178
+ _mapped = {'inverse': 'inverse_multiquadric',
179
+ 'inverse multiquadric': 'inverse_multiquadric',
180
+ 'thin-plate': 'thin_plate'}
181
+ if self.function in _mapped:
182
+ self.function = _mapped[self.function]
183
+
184
+ func_name = "_h_" + self.function
185
+ if hasattr(self, func_name):
186
+ self._function = getattr(self, func_name)
187
+ else:
188
+ functionlist = [x[3:] for x in dir(self)
189
+ if x.startswith('_h_')]
190
+ raise ValueError("function must be a callable or one of " +
191
+ ", ".join(functionlist))
192
+ self._function = getattr(self, "_h_"+self.function)
193
+ elif callable(self.function):
194
+ allow_one = False
195
+ if hasattr(self.function, 'func_code') or \
196
+ hasattr(self.function, '__code__'):
197
+ val = self.function
198
+ allow_one = True
199
+ elif hasattr(self.function, "__call__"):
200
+ val = self.function.__call__.__func__
201
+ else:
202
+ raise ValueError("Cannot determine number of arguments to "
203
+ "function")
204
+
205
+ argcount = val.__code__.co_argcount
206
+ if allow_one and argcount == 1:
207
+ self._function = self.function
208
+ elif argcount == 2:
209
+ self._function = self.function.__get__(self, Rbf)
210
+ else:
211
+ raise ValueError("Function argument must take 1 or 2 "
212
+ "arguments.")
213
+
214
+ a0 = self._function(r)
215
+ if a0.shape != r.shape:
216
+ raise ValueError("Callable must take array and return array of "
217
+ "the same shape")
218
+ return a0
219
+
220
+ def __init__(self, *args, **kwargs):
221
+ # `args` can be a variable number of arrays; we flatten them and store
222
+ # them as a single 2-D array `xi` of shape (n_args-1, array_size),
223
+ # plus a 1-D array `di` for the values.
224
+ # All arrays must have the same number of elements
225
+ self.xi = np.asarray([np.asarray(a, dtype=np.float64).flatten()
226
+ for a in args[:-1]])
227
+ self.N = self.xi.shape[-1]
228
+
229
+ self.mode = kwargs.pop('mode', '1-D')
230
+
231
+ if self.mode == '1-D':
232
+ self.di = np.asarray(args[-1]).flatten()
233
+ self._target_dim = 1
234
+ elif self.mode == 'N-D':
235
+ self.di = np.asarray(args[-1])
236
+ self._target_dim = self.di.shape[-1]
237
+ else:
238
+ raise ValueError("Mode has to be 1-D or N-D.")
239
+
240
+ if not all([x.size == self.di.shape[0] for x in self.xi]):
241
+ raise ValueError("All arrays must be equal length.")
242
+
243
+ self.norm = kwargs.pop('norm', 'euclidean')
244
+ self.epsilon = kwargs.pop('epsilon', None)
245
+ if self.epsilon is None:
246
+ # default epsilon is the "the average distance between nodes" based
247
+ # on a bounding hypercube
248
+ ximax = np.amax(self.xi, axis=1)
249
+ ximin = np.amin(self.xi, axis=1)
250
+ edges = ximax - ximin
251
+ edges = edges[np.nonzero(edges)]
252
+ self.epsilon = np.power(np.prod(edges)/self.N, 1.0/edges.size)
253
+
254
+ self.smooth = kwargs.pop('smooth', 0.0)
255
+ self.function = kwargs.pop('function', 'multiquadric')
256
+
257
+ # attach anything left in kwargs to self for use by any user-callable
258
+ # function or to save on the object returned.
259
+ for item, value in kwargs.items():
260
+ setattr(self, item, value)
261
+
262
+ # Compute weights
263
+ if self._target_dim > 1: # If we have more than one target dimension,
264
+ # we first factorize the matrix
265
+ self.nodes = np.zeros((self.N, self._target_dim), dtype=self.di.dtype)
266
+ lu, piv = linalg.lu_factor(self.A)
267
+ for i in range(self._target_dim):
268
+ self.nodes[:, i] = linalg.lu_solve((lu, piv), self.di[:, i])
269
+ else:
270
+ self.nodes = linalg.solve(self.A, self.di)
271
+
272
+ @property
273
+ def A(self):
274
+ # this only exists for backwards compatibility: self.A was available
275
+ # and, at least technically, public.
276
+ r = squareform(pdist(self.xi.T, self.norm)) # Pairwise norm
277
+ return self._init_function(r) - np.eye(self.N)*self.smooth
278
+
279
+ def _call_norm(self, x1, x2):
280
+ return cdist(x1.T, x2.T, self.norm)
281
+
282
+ def __call__(self, *args):
283
+ args = [np.asarray(x) for x in args]
284
+ if not all([x.shape == y.shape for x in args for y in args]):
285
+ raise ValueError("Array lengths must be equal")
286
+ if self._target_dim > 1:
287
+ shp = args[0].shape + (self._target_dim,)
288
+ else:
289
+ shp = args[0].shape
290
+ xa = np.asarray([a.flatten() for a in args], dtype=np.float64)
291
+ r = self._call_norm(xa, self.xi)
292
+ return np.dot(self._function(r), self.nodes).reshape(shp)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_rbfinterp_common.py ADDED
@@ -0,0 +1,32 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # Impl routines common for all backends
2
+ from itertools import combinations_with_replacement
3
+ from math import comb
4
+
5
+ def _monomial_powers_impl(ndim, degree):
6
+ """Return the powers for each monomial in a polynomial.
7
+
8
+ Parameters
9
+ ----------
10
+ ndim : int
11
+ Number of variables in the polynomial.
12
+ degree : int
13
+ Degree of the polynomial.
14
+
15
+ Returns
16
+ -------
17
+ (nmonos, ndim) int ndarray
18
+ Array where each row contains the powers for each variable in a
19
+ monomial.
20
+
21
+ """
22
+ nmonos = comb(degree + ndim, ndim)
23
+ out = [[0]*ndim for _ in range(nmonos)]
24
+ count = 0
25
+ for deg in range(degree + 1):
26
+ for mono in combinations_with_replacement(range(ndim), deg):
27
+ # `mono` is a tuple of variables in the current monomial with
28
+ # multiplicity indicating power (e.g., (0, 1, 1) represents x*y**2)
29
+ for var in mono:
30
+ out[count][var] += 1
31
+ count += 1
32
+ return out
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_rbfinterp_xp.py ADDED
@@ -0,0 +1,266 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """
2
+ 'Generic' Array API backend for RBF interpolation.
3
+
4
+ The general logic is this: `_rbfinterp.py` implements the user API and calls
5
+ into either `_rbfinterp_np` (the "numpy backend"), or `_rbfinterp_xp` (the
6
+ "generic backend".
7
+
8
+ The numpy backend offloads performance-critical computations to the
9
+ pythran-compiled `_rbfinterp_pythran` extension. This way, the call chain is
10
+
11
+ _rbfinterp.py <-- _rbfinterp_np.py <-- _rbfinterp_pythran.py
12
+
13
+ The "generic" backend here is a drop-in replacement of the API of
14
+ `_rbfinterp_np.py` for use in `_rbfinterp.py` with non-numpy arrays.
15
+
16
+ The implementation closely follows `_rbfinterp_np + _rbfinterp_pythran`, with
17
+ the following differences:
18
+
19
+ - We used vectorized code not explicit loops in `_build_system` and
20
+ `_build_evaluation_coefficients`; this is more torch/jax friendly;
21
+ - RBF kernels are also "vectorized" and not scalar: they receive an
22
+ array of norms not a single norm;
23
+ - RBF kernels accept an extra xp= argument;
24
+
25
+ In general, we would prefer less code duplication. The main blocker ATM is
26
+ that pythran cannot compile functions with an xp= argument where xp is numpy.
27
+ """
28
+ from numpy.linalg import LinAlgError
29
+ from ._rbfinterp_common import _monomial_powers_impl
30
+
31
+
32
+ def _monomial_powers(ndim, degree, xp):
33
+ out = _monomial_powers_impl(ndim, degree)
34
+ out = xp.asarray(out)
35
+ if out.shape[0] == 0:
36
+ out = xp.reshape(out, (0, ndim))
37
+ return out
38
+
39
+
40
+ def _build_and_solve_system(y, d, smoothing, kernel, epsilon, powers, xp):
41
+ """Build and solve the RBF interpolation system of equations.
42
+
43
+ Parameters
44
+ ----------
45
+ y : (P, N) float ndarray
46
+ Data point coordinates.
47
+ d : (P, S) float ndarray
48
+ Data values at `y`.
49
+ smoothing : (P,) float ndarray
50
+ Smoothing parameter for each data point.
51
+ kernel : str
52
+ Name of the RBF.
53
+ epsilon : float
54
+ Shape parameter.
55
+ powers : (R, N) int ndarray
56
+ The exponents for each monomial in the polynomial.
57
+
58
+ Returns
59
+ -------
60
+ coeffs : (P + R, S) float ndarray
61
+ Coefficients for each RBF and monomial.
62
+ shift : (N,) float ndarray
63
+ Domain shift used to create the polynomial matrix.
64
+ scale : (N,) float ndarray
65
+ Domain scaling used to create the polynomial matrix.
66
+
67
+ """
68
+ lhs, rhs, shift, scale = _build_system(
69
+ y, d, smoothing, kernel, epsilon, powers, xp
70
+ )
71
+ try:
72
+ coeffs = xp.linalg.solve(lhs, rhs)
73
+ except Exception:
74
+ # Best-effort attempt to emit a helpful message.
75
+ # `_rbfinterp_np` backend gives better diagnostics; it is hard to
76
+ # match it in a backend-agnostic way: e.g. jax emits no error at all,
77
+ # and instead returns an array of nans for a singular `lhs`.
78
+ msg = "Singular matrix"
79
+ nmonos = powers.shape[0]
80
+ if nmonos > 0:
81
+ pmat = polynomial_matrix((y - shift)/scale, powers, xp=xp)
82
+ rank = xp.linalg.matrix_rank(pmat)
83
+ if rank < nmonos:
84
+ msg = (
85
+ "Singular matrix. The matrix of monomials evaluated at "
86
+ "the data point coordinates does not have full column "
87
+ f"rank ({rank}/{nmonos})."
88
+ )
89
+ raise LinAlgError(msg)
90
+
91
+ return shift, scale, coeffs
92
+
93
+
94
+ def linear(r, xp):
95
+ return -r
96
+
97
+
98
+ def thin_plate_spline(r, xp):
99
+ # NB: changed w.r.t. pythran, vectorized
100
+ return xp.where(r == 0, 0, r**2 * xp.log(r))
101
+
102
+
103
+ def cubic(r, xp):
104
+ return r**3
105
+
106
+
107
+ def quintic(r, xp):
108
+ return -r**5
109
+
110
+
111
+ def multiquadric(r, xp):
112
+ return -xp.sqrt(r**2 + 1)
113
+
114
+
115
+ def inverse_multiquadric(r, xp):
116
+ return 1.0 / xp.sqrt(r**2 + 1.0)
117
+
118
+
119
+ def inverse_quadratic(r, xp):
120
+ return 1.0 / (r**2 + 1.0)
121
+
122
+
123
+ def gaussian(r, xp):
124
+ return xp.exp(-r**2)
125
+
126
+
127
+ NAME_TO_FUNC = {
128
+ "linear": linear,
129
+ "thin_plate_spline": thin_plate_spline,
130
+ "cubic": cubic,
131
+ "quintic": quintic,
132
+ "multiquadric": multiquadric,
133
+ "inverse_multiquadric": inverse_multiquadric,
134
+ "inverse_quadratic": inverse_quadratic,
135
+ "gaussian": gaussian
136
+ }
137
+
138
+
139
+ def kernel_matrix(x, kernel_func, xp):
140
+ """Evaluate RBFs, with centers at `x`, at `x`."""
141
+ return kernel_func(
142
+ xp.linalg.vector_norm(x[None, :, :] - x[:, None, :], axis=-1), xp
143
+ )
144
+
145
+
146
+ def polynomial_matrix(x, powers, xp):
147
+ """Evaluate monomials, with exponents from `powers`, at `x`."""
148
+ return xp.prod(x[:, None, :] ** powers, axis=-1)
149
+
150
+
151
+ def _build_system(y, d, smoothing, kernel, epsilon, powers, xp):
152
+ """Build the system used to solve for the RBF interpolant coefficients.
153
+
154
+ Parameters
155
+ ----------
156
+ y : (P, N) float ndarray
157
+ Data point coordinates.
158
+ d : (P, S) float ndarray
159
+ Data values at `y`.
160
+ smoothing : (P,) float ndarray
161
+ Smoothing parameter for each data point.
162
+ kernel : str
163
+ Name of the RBF.
164
+ epsilon : float
165
+ Shape parameter.
166
+ powers : (R, N) int ndarray
167
+ The exponents for each monomial in the polynomial.
168
+
169
+ Returns
170
+ -------
171
+ lhs : (P + R, P + R) float ndarray
172
+ Left-hand side matrix.
173
+ rhs : (P + R, S) float ndarray
174
+ Right-hand side matrix.
175
+ shift : (N,) float ndarray
176
+ Domain shift used to create the polynomial matrix.
177
+ scale : (N,) float ndarray
178
+ Domain scaling used to create the polynomial matrix.
179
+
180
+ """
181
+ s = d.shape[1]
182
+ r = powers.shape[0]
183
+ kernel_func = NAME_TO_FUNC[kernel]
184
+
185
+ # Shift and scale the polynomial domain to be between -1 and 1
186
+ mins = xp.min(y, axis=0)
187
+ maxs = xp.max(y, axis=0)
188
+ shift = (maxs + mins)/2
189
+ scale = (maxs - mins)/2
190
+ # The scale may be zero if there is a single point or all the points have
191
+ # the same value for some dimension. Avoid division by zero by replacing
192
+ # zeros with ones.
193
+ scale = xp.where(scale == 0.0, 1.0, scale)
194
+
195
+ yeps = y*epsilon
196
+ yhat = (y - shift)/scale
197
+
198
+ out_kernels = kernel_matrix(yeps, kernel_func, xp)
199
+ out_poly = polynomial_matrix(yhat, powers, xp)
200
+
201
+ lhs = xp.concat(
202
+ [
203
+ xp.concat((out_kernels, out_poly), axis=1),
204
+ xp.concat((out_poly.T, xp.zeros((r, r))), axis=1)
205
+ ]
206
+ , axis=0) + xp.diag(xp.concat([smoothing, xp.zeros(r)]))
207
+
208
+ rhs = xp.concat([d, xp.zeros((r, s))], axis=0)
209
+
210
+ return lhs, rhs, shift, scale
211
+
212
+
213
+ def _build_evaluation_coefficients(
214
+ x, y, kernel, epsilon, powers, shift, scale, xp
215
+ ):
216
+ """Construct the coefficients needed to evaluate
217
+ the RBF.
218
+
219
+ Parameters
220
+ ----------
221
+ x : (Q, N) float ndarray
222
+ Evaluation point coordinates.
223
+ y : (P, N) float ndarray
224
+ Data point coordinates.
225
+ kernel : str
226
+ Name of the RBF.
227
+ epsilon : float
228
+ Shape parameter.
229
+ powers : (R, N) int ndarray
230
+ The exponents for each monomial in the polynomial.
231
+ shift : (N,) float ndarray
232
+ Shifts the polynomial domain for numerical stability.
233
+ scale : (N,) float ndarray
234
+ Scales the polynomial domain for numerical stability.
235
+
236
+ Returns
237
+ -------
238
+ (Q, P + R) float ndarray
239
+
240
+ """
241
+ kernel_func = NAME_TO_FUNC[kernel]
242
+
243
+ yeps = y*epsilon
244
+ xeps = x*epsilon
245
+ xhat = (x - shift)/scale
246
+
247
+ # NB: changed w.r.t. pythran
248
+ vec = xp.concat(
249
+ [
250
+ kernel_func(
251
+ xp.linalg.vector_norm(
252
+ xeps[:, None, :] - yeps[None, :, :], axis=-1
253
+ ), xp
254
+ ),
255
+ xp.prod(xhat[:, None, :] ** powers, axis=-1)
256
+ ], axis=-1
257
+ )
258
+
259
+ return vec
260
+
261
+
262
+ def compute_interpolation(x, y, kernel, epsilon, powers, shift, scale, coeffs, xp):
263
+ vec = _build_evaluation_coefficients(
264
+ x, y, kernel, epsilon, powers, shift, scale, xp
265
+ )
266
+ return vec @ coeffs
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/_rgi.py ADDED
@@ -0,0 +1,812 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ __all__ = ['RegularGridInterpolator', 'interpn']
2
+
3
+ import itertools
4
+ from types import GenericAlias
5
+
6
+ import numpy as np
7
+
8
+ import scipy.sparse.linalg as ssl
9
+ from scipy._lib._array_api import array_namespace, xp_capabilities
10
+ from scipy._lib.array_api_compat import is_array_api_obj
11
+
12
+ from ._interpnd import _ndim_coords_from_arrays
13
+ from ._cubic import PchipInterpolator
14
+ from ._rgi_cython import evaluate_linear_2d, find_indices
15
+ from ._bsplines import make_interp_spline
16
+ from ._fitpack2 import RectBivariateSpline
17
+ from ._ndbspline import make_ndbspl
18
+
19
+
20
+ def _check_points(points):
21
+ descending_dimensions = []
22
+ grid = []
23
+ for i, p in enumerate(points):
24
+ # early make points float
25
+ # see https://github.com/scipy/scipy/pull/17230
26
+ p = np.asarray(p, dtype=float)
27
+ if not np.all(p[1:] > p[:-1]):
28
+ if np.all(p[1:] < p[:-1]):
29
+ # input is descending, so make it ascending
30
+ descending_dimensions.append(i)
31
+ p = np.flip(p)
32
+ else:
33
+ raise ValueError(
34
+ f"The points in dimension {i} must be strictly ascending or "
35
+ f"descending"
36
+ )
37
+ # see https://github.com/scipy/scipy/issues/17716
38
+ p = np.ascontiguousarray(p)
39
+ grid.append(p)
40
+ return tuple(grid), tuple(descending_dimensions)
41
+
42
+
43
+ def _check_dimensionality(points, values):
44
+ if len(points) > values.ndim:
45
+ raise ValueError(
46
+ f"There are {len(points)} point arrays, but values has "
47
+ f"{values.ndim} dimensions"
48
+ )
49
+ for i, p in enumerate(points):
50
+ if not np.asarray(p).ndim == 1:
51
+ raise ValueError(f"The points in dimension {i} must be 1-dimensional")
52
+ if not values.shape[i] == len(p):
53
+ raise ValueError(
54
+ f"There are {len(p)} points and {values.shape[i]} values in "
55
+ f"dimension {i}"
56
+ )
57
+
58
+
59
+ @xp_capabilities(
60
+ cpu_only=True, jax_jit=False,
61
+ skip_backends=[
62
+ ("dask.array",
63
+ "https://github.com/data-apis/array-api-extra/issues/488")
64
+ ]
65
+ )
66
+ class RegularGridInterpolator:
67
+ """Interpolator of specified order on a rectilinear grid in N ≥ 1 dimensions.
68
+
69
+ The data must be defined on a rectilinear grid; that is, a rectangular
70
+ grid with even or uneven spacing. Linear, nearest-neighbor, spline
71
+ interpolations are supported. After setting up the interpolator object,
72
+ the interpolation method may be chosen at each evaluation.
73
+
74
+ Parameters
75
+ ----------
76
+ points : tuple of ndarray of float, with shapes (m1, ), ..., (mn, )
77
+ The points defining the regular grid in n dimensions. The points in
78
+ each dimension (i.e. every elements of the points tuple) must be
79
+ strictly ascending or descending.
80
+
81
+ values : array_like, shape (m1, ..., mn, ...)
82
+ The data on the regular grid in n dimensions. Complex data is
83
+ accepted.
84
+
85
+ method : str, optional
86
+ The method of interpolation to perform. Supported are "linear",
87
+ "nearest", "slinear", "cubic", "quintic" and "pchip". This
88
+ parameter will become the default for the object's ``__call__``
89
+ method. Default is "linear".
90
+
91
+ bounds_error : bool, optional
92
+ If True, when interpolated values are requested outside of the
93
+ domain of the input data, a ValueError is raised.
94
+ If False, then `fill_value` is used.
95
+ Default is True.
96
+
97
+ fill_value : float or None, optional
98
+ The value to use for points outside of the interpolation domain.
99
+ If None, values outside the domain are extrapolated.
100
+ Default is ``np.nan``.
101
+
102
+ solver : callable, optional
103
+ Only used for methods "slinear", "cubic" and "quintic".
104
+ Sparse linear algebra solver for construction of the NdBSpline instance.
105
+ Default is the iterative solver `scipy.sparse.linalg.gcrotmk`.
106
+
107
+ .. versionadded:: 1.13
108
+
109
+ solver_args: dict, optional
110
+ Additional arguments to pass to `solver`, if any.
111
+
112
+ .. versionadded:: 1.13
113
+
114
+ Methods
115
+ -------
116
+ __call__
117
+
118
+ Attributes
119
+ ----------
120
+ grid : tuple of ndarrays
121
+ The points defining the regular grid in n dimensions.
122
+ This tuple defines the full grid via
123
+ ``np.meshgrid(*grid, indexing='ij')``
124
+ values : ndarray
125
+ Data values at the grid.
126
+ method : str
127
+ Interpolation method.
128
+ fill_value : float or ``None``
129
+ Use this value for out-of-bounds arguments to `__call__`.
130
+ bounds_error : bool
131
+ If ``True``, out-of-bounds argument raise a ``ValueError``.
132
+
133
+ Notes
134
+ -----
135
+ Contrary to `LinearNDInterpolator` and `NearestNDInterpolator`, this class
136
+ avoids expensive triangulation of the input data by taking advantage of the
137
+ regular grid structure.
138
+
139
+ In other words, this class assumes that the data is defined on a
140
+ *rectilinear* grid.
141
+
142
+ .. versionadded:: 0.14
143
+
144
+ The 'slinear'(k=1), 'cubic'(k=3), and 'quintic'(k=5) methods are
145
+ tensor-product spline interpolators, where `k` is the spline degree,
146
+ If any dimension has fewer points than `k` + 1, an error will be raised.
147
+
148
+ .. versionadded:: 1.9
149
+
150
+ If the input data is such that dimensions have incommensurate
151
+ units and differ by many orders of magnitude, the interpolant may have
152
+ numerical artifacts. Consider rescaling the data before interpolating.
153
+
154
+ **Choosing a solver for spline methods**
155
+
156
+ Spline methods, "slinear", "cubic" and "quintic" involve solving a
157
+ large sparse linear system at instantiation time. Depending on data,
158
+ the default solver may or may not be adequate. When it is not, you may
159
+ need to experiment with an optional `solver` argument, where you may
160
+ choose between the direct solver (`scipy.sparse.linalg.spsolve`) or
161
+ iterative solvers from `scipy.sparse.linalg`. You may need to supply
162
+ additional parameters via the optional `solver_args` parameter (for instance,
163
+ you may supply the starting value or target tolerance). See the
164
+ `scipy.sparse.linalg` documentation for the full list of available options.
165
+
166
+ Alternatively, you may instead use the legacy methods, "slinear_legacy",
167
+ "cubic_legacy" and "quintic_legacy". These methods allow faster construction
168
+ but evaluations will be much slower.
169
+
170
+ **Rounding rule at half points with `nearest` method**
171
+
172
+ The rounding rule with the `nearest` method at half points is rounding *down*.
173
+
174
+
175
+ Examples
176
+ --------
177
+ **Evaluate a function on the points of a 3-D grid**
178
+
179
+ As a first example, we evaluate a simple example function on the points of
180
+ a 3-D grid:
181
+
182
+ >>> from scipy.interpolate import RegularGridInterpolator
183
+ >>> import numpy as np
184
+ >>> def f(x, y, z):
185
+ ... return 2 * x**3 + 3 * y**2 - z
186
+ >>> x = np.linspace(1, 4, 11)
187
+ >>> y = np.linspace(4, 7, 22)
188
+ >>> z = np.linspace(7, 9, 33)
189
+ >>> xg, yg ,zg = np.meshgrid(x, y, z, indexing='ij', sparse=True)
190
+ >>> data = f(xg, yg, zg)
191
+
192
+ ``data`` is now a 3-D array with ``data[i, j, k] = f(x[i], y[j], z[k])``.
193
+ Next, define an interpolating function from this data:
194
+
195
+ >>> interp = RegularGridInterpolator((x, y, z), data)
196
+
197
+ Evaluate the interpolating function at the two points
198
+ ``(x,y,z) = (2.1, 6.2, 8.3)`` and ``(3.3, 5.2, 7.1)``:
199
+
200
+ >>> pts = np.array([[2.1, 6.2, 8.3],
201
+ ... [3.3, 5.2, 7.1]])
202
+ >>> interp(pts)
203
+ array([ 125.80469388, 146.30069388])
204
+
205
+ which is indeed a close approximation to
206
+
207
+ >>> f(2.1, 6.2, 8.3), f(3.3, 5.2, 7.1)
208
+ (125.54200000000002, 145.894)
209
+
210
+ **Interpolate and extrapolate a 2D dataset**
211
+
212
+ As a second example, we interpolate and extrapolate a 2D data set:
213
+
214
+ >>> x, y = np.array([-2, 0, 4]), np.array([-2, 0, 2, 5])
215
+ >>> def ff(x, y):
216
+ ... return x**2 + y**2
217
+
218
+ >>> xg, yg = np.meshgrid(x, y, indexing='ij')
219
+ >>> data = ff(xg, yg)
220
+ >>> interp = RegularGridInterpolator((x, y), data,
221
+ ... bounds_error=False, fill_value=None)
222
+
223
+ >>> import matplotlib.pyplot as plt
224
+ >>> fig = plt.figure()
225
+ >>> ax = fig.add_subplot(projection='3d')
226
+ >>> ax.scatter(xg.ravel(), yg.ravel(), data.ravel(),
227
+ ... s=60, c='k', label='data')
228
+
229
+ Evaluate and plot the interpolator on a finer grid
230
+
231
+ >>> xx = np.linspace(-4, 9, 31)
232
+ >>> yy = np.linspace(-4, 9, 31)
233
+ >>> X, Y = np.meshgrid(xx, yy, indexing='ij')
234
+
235
+ >>> # interpolator
236
+ >>> ax.plot_wireframe(X, Y, interp((X, Y)), rstride=3, cstride=3,
237
+ ... alpha=0.4, color='m', label='linear interp')
238
+
239
+ >>> # ground truth
240
+ >>> ax.plot_wireframe(X, Y, ff(X, Y), rstride=3, cstride=3,
241
+ ... alpha=0.4, label='ground truth')
242
+ >>> plt.legend()
243
+ >>> plt.show()
244
+
245
+ Other examples are given
246
+ :ref:`in the tutorial <tutorial-interpolate_regular_grid_interpolator>`.
247
+
248
+ See Also
249
+ --------
250
+ NearestNDInterpolator : Nearest neighbor interpolator on *unstructured*
251
+ data in N dimensions
252
+
253
+ LinearNDInterpolator : Piecewise linear interpolator on *unstructured* data
254
+ in N dimensions
255
+
256
+ interpn : a convenience function which wraps `RegularGridInterpolator`
257
+
258
+ scipy.ndimage.map_coordinates : interpolation on grids with equal spacing
259
+ (suitable for e.g., N-D image resampling)
260
+
261
+ References
262
+ ----------
263
+ .. [1] Python package *regulargrid* by Johannes Buchner, see
264
+ https://pypi.python.org/pypi/regulargrid/
265
+ .. [2] Wikipedia, "Trilinear interpolation",
266
+ https://en.wikipedia.org/wiki/Trilinear_interpolation
267
+ .. [3] Weiser, Alan, and Sergio E. Zarantonello. "A note on piecewise linear
268
+ and multilinear table interpolation in many dimensions." MATH.
269
+ COMPUT. 50.181 (1988): 189-196.
270
+ https://www.ams.org/journals/mcom/1988-50-181/S0025-5718-1988-0917826-0/S0025-5718-1988-0917826-0.pdf
271
+ :doi:`10.1090/S0025-5718-1988-0917826-0`
272
+
273
+ """
274
+ # this class is based on code originally programmed by Johannes Buchner,
275
+ # see https://github.com/JohannesBuchner/regulargrid
276
+
277
+ _SPLINE_DEGREE_MAP = {"slinear": 1, "cubic": 3, "quintic": 5, 'pchip': 3,
278
+ "slinear_legacy": 1, "cubic_legacy": 3, "quintic_legacy": 5,}
279
+ _SPLINE_METHODS_recursive = {"slinear_legacy", "cubic_legacy",
280
+ "quintic_legacy", "pchip"}
281
+ _SPLINE_METHODS_ndbspl = {"slinear", "cubic", "quintic"}
282
+ _SPLINE_METHODS = list(_SPLINE_DEGREE_MAP.keys())
283
+ _ALL_METHODS = ["linear", "nearest"] + _SPLINE_METHODS
284
+
285
+ # generic type compatibility with scipy-stubs
286
+ __class_getitem__ = classmethod(GenericAlias)
287
+
288
+ def __init__(self, points, values, method="linear", bounds_error=True,
289
+ fill_value=np.nan, *, solver=None, solver_args=None):
290
+ if method not in self._ALL_METHODS:
291
+ raise ValueError(f"Method '{method}' is not defined")
292
+ elif method in self._SPLINE_METHODS:
293
+ self._validate_grid_dimensions(points, method) # NB: uses np.atleast_1d
294
+
295
+ try:
296
+ xp = array_namespace(*points, values)
297
+ except Exception as e:
298
+ # either "duck-type" values or a user error?
299
+ xp = array_namespace(*points) # still forbid mixed namespaces in `points`
300
+ try:
301
+ xp_v = array_namespace(values)
302
+ except Exception:
303
+ # "duck-type" values indeed, continue with `xp` as the namespace
304
+ pass
305
+ else:
306
+ # both `points` and `values` are array API objects, check consistency
307
+ if xp_v != xp:
308
+ raise e
309
+
310
+ self._asarray = xp.asarray
311
+ self.method = method
312
+ self._spline = None
313
+ self.bounds_error = bounds_error
314
+ self._grid, self._descending_dimensions = _check_points(points)
315
+ self._values = self._check_values(values)
316
+ self._check_dimensionality(self._grid, self._values)
317
+ self.fill_value = self._check_fill_value(self._values, fill_value)
318
+ if self._descending_dimensions:
319
+ self._values = np.flip(values, axis=self._descending_dimensions)
320
+ if self.method == "pchip" and np.iscomplexobj(self._values):
321
+ msg = ("`PchipInterpolator` only works with real values. If you are trying "
322
+ "to use the real components of the passed array, use `np.real` on "
323
+ "the array before passing to `RegularGridInterpolator`.")
324
+ raise ValueError(msg)
325
+ if method in self._SPLINE_METHODS_ndbspl:
326
+ if solver_args is None:
327
+ solver_args = {}
328
+ self._spline = self._construct_spline(method, solver, **solver_args)
329
+ else:
330
+ if solver is not None or solver_args:
331
+ raise ValueError(
332
+ f"{method =} does not accept the 'solver' argument. Got "
333
+ f" {solver = } and with arguments {solver_args}."
334
+ )
335
+
336
+ def _construct_spline(self, method, solver=None, **solver_args):
337
+ if solver is None:
338
+ solver = ssl.gcrotmk
339
+ spl = make_ndbspl(
340
+ self._grid, self._values, self._SPLINE_DEGREE_MAP[method],
341
+ solver=solver, **solver_args
342
+ )
343
+ return spl
344
+
345
+ def _check_dimensionality(self, grid, values):
346
+ _check_dimensionality(grid, values)
347
+
348
+ def _check_points(self, points):
349
+ return _check_points(points)
350
+
351
+ def _check_values(self, values):
352
+ if is_array_api_obj(values):
353
+ values = np.asarray(values)
354
+
355
+ if not hasattr(values, 'ndim'):
356
+ # allow reasonable duck-typed values
357
+ values = np.asarray(values)
358
+
359
+ if hasattr(values, 'dtype') and hasattr(values, 'astype'):
360
+ if not np.issubdtype(values.dtype, np.inexact):
361
+ values = values.astype(float)
362
+
363
+ return values
364
+
365
+ def _check_fill_value(self, values, fill_value):
366
+ if fill_value is not None:
367
+ fill_value_dtype = np.asarray(fill_value).dtype
368
+ if (hasattr(values, 'dtype') and not
369
+ np.can_cast(fill_value_dtype, values.dtype,
370
+ casting='same_kind')):
371
+ raise ValueError("fill_value must be either 'None' or "
372
+ "of a type compatible with values")
373
+ return fill_value
374
+
375
+ def __call__(self, xi, method=None, *, nu=None):
376
+ """
377
+ Interpolation at coordinates.
378
+
379
+ Parameters
380
+ ----------
381
+ xi : ndarray of shape (..., ndim)
382
+ The coordinates to evaluate the interpolator at.
383
+
384
+ method : str, optional
385
+ The method of interpolation to perform. Supported are "linear",
386
+ "nearest", "slinear", "cubic", "quintic" and "pchip". Default is
387
+ the method chosen when the interpolator was created.
388
+
389
+ nu : sequence of ints, length ndim, optional
390
+ If not None, the orders of the derivatives to evaluate.
391
+ Each entry must be non-negative.
392
+ Only allowed for methods "slinear", "cubic" and "quintic".
393
+
394
+ .. versionadded:: 1.13
395
+
396
+ Returns
397
+ -------
398
+ values_x : ndarray, shape xi.shape[:-1] + values.shape[ndim:]
399
+ Interpolated values at `xi`. See notes for behaviour when
400
+ ``xi.ndim == 1``.
401
+
402
+ Notes
403
+ -----
404
+ In the case that ``xi.ndim == 1`` a new axis is inserted into
405
+ the 0 position of the returned array, values_x, so its shape is
406
+ instead ``(1,) + values.shape[ndim:]``.
407
+
408
+ Examples
409
+ --------
410
+ Here we define a nearest-neighbor interpolator of a simple function
411
+
412
+ >>> import numpy as np
413
+ >>> x, y = np.array([0, 1, 2]), np.array([1, 3, 7])
414
+ >>> def f(x, y):
415
+ ... return x**2 + y**2
416
+ >>> data = f(*np.meshgrid(x, y, indexing='ij', sparse=True))
417
+ >>> from scipy.interpolate import RegularGridInterpolator
418
+ >>> interp = RegularGridInterpolator((x, y), data, method='nearest')
419
+
420
+ By construction, the interpolator uses the nearest-neighbor
421
+ interpolation
422
+
423
+ >>> interp([[1.5, 1.3], [0.3, 4.5]])
424
+ array([2., 9.])
425
+
426
+ We can however evaluate the linear interpolant by overriding the
427
+ `method` parameter
428
+
429
+ >>> interp([[1.5, 1.3], [0.3, 4.5]], method='linear')
430
+ array([ 4.7, 24.3])
431
+ """
432
+ _spline = self._spline
433
+ method = self.method if method is None else method
434
+ is_method_changed = self.method != method
435
+ if method not in self._ALL_METHODS:
436
+ raise ValueError(f"Method '{method}' is not defined")
437
+ if is_method_changed and method in self._SPLINE_METHODS_ndbspl:
438
+ _spline = self._construct_spline(method)
439
+
440
+ if nu is not None and method not in self._SPLINE_METHODS_ndbspl:
441
+ raise ValueError(
442
+ f"Can only compute derivatives for methods "
443
+ f"{self._SPLINE_METHODS_ndbspl}, got {method =}."
444
+ )
445
+
446
+ xi, xi_shape, ndim, nans, out_of_bounds = self._prepare_xi(xi)
447
+
448
+ if method == "linear":
449
+ indices, norm_distances = self._find_indices(xi.T)
450
+ if (ndim == 2 and hasattr(self._values, 'dtype') and
451
+ self._values.ndim == 2 and self._values.flags.writeable and
452
+ self._values.dtype in (np.float64, np.complex128) and
453
+ self._values.dtype.byteorder == '='):
454
+ # until cython supports const fused types, the fast path
455
+ # cannot support non-writeable values
456
+ # a fast path
457
+ out = np.empty(indices.shape[1], dtype=self._values.dtype)
458
+ result = evaluate_linear_2d(self._values,
459
+ indices,
460
+ norm_distances,
461
+ self._grid,
462
+ out)
463
+ else:
464
+ result = self._evaluate_linear(indices, norm_distances)
465
+ elif method == "nearest":
466
+ indices, norm_distances = self._find_indices(xi.T)
467
+ result = self._evaluate_nearest(indices, norm_distances)
468
+ elif method in self._SPLINE_METHODS:
469
+ if is_method_changed:
470
+ self._validate_grid_dimensions(self._grid, method)
471
+ if method in self._SPLINE_METHODS_recursive:
472
+ result = self._evaluate_spline(xi, method)
473
+ else:
474
+ result = _spline(xi, nu=nu)
475
+
476
+ if not self.bounds_error and self.fill_value is not None:
477
+ result[out_of_bounds] = self.fill_value
478
+
479
+ # f(nan) = nan, if any
480
+ if np.any(nans):
481
+ result[nans] = np.nan
482
+ return self._asarray(result.reshape(xi_shape[:-1] + self._values.shape[ndim:]))
483
+
484
+ @property
485
+ def grid(self):
486
+ return tuple(self._asarray(p) for p in self._grid)
487
+
488
+ @property
489
+ def values(self):
490
+ return self._asarray(self._values)
491
+
492
+ def _prepare_xi(self, xi):
493
+ ndim = len(self._grid)
494
+ xi = _ndim_coords_from_arrays(xi, ndim=ndim)
495
+ if xi.shape[-1] != ndim:
496
+ raise ValueError("The requested sample points xi have dimension "
497
+ f"{xi.shape[-1]} but this "
498
+ f"RegularGridInterpolator has dimension {ndim}")
499
+
500
+ xi_shape = xi.shape
501
+ xi = xi.reshape(-1, xi_shape[-1])
502
+ xi = np.asarray(xi, dtype=float)
503
+
504
+ # find nans in input
505
+ nans = np.any(np.isnan(xi), axis=-1)
506
+
507
+ if self.bounds_error:
508
+ for i, p in enumerate(xi.T):
509
+ if not np.logical_and(np.all(self._grid[i][0] <= p),
510
+ np.all(p <= self._grid[i][-1])):
511
+ raise ValueError(
512
+ f"One of the requested xi is out of bounds in dimension {i}"
513
+ )
514
+ out_of_bounds = None
515
+ else:
516
+ out_of_bounds = self._find_out_of_bounds(xi.T)
517
+
518
+ return xi, xi_shape, ndim, nans, out_of_bounds
519
+
520
+ def _evaluate_linear(self, indices, norm_distances):
521
+ # slice for broadcasting over trailing dimensions in self._values
522
+ vslice = (slice(None),) + (None,)*(self._values.ndim - len(indices))
523
+
524
+ # Compute shifting up front before zipping everything together
525
+ shift_norm_distances = [1 - yi for yi in norm_distances]
526
+ shift_indices = [i + 1 for i in indices]
527
+
528
+ # The formula for linear interpolation in 2d takes the form:
529
+ # values = self._values[(i0, i1)] * (1 - y0) * (1 - y1) + \
530
+ # self._values[(i0, i1 + 1)] * (1 - y0) * y1 + \
531
+ # self._values[(i0 + 1, i1)] * y0 * (1 - y1) + \
532
+ # self._values[(i0 + 1, i1 + 1)] * y0 * y1
533
+ # We pair i with 1 - yi (zipped1) and i + 1 with yi (zipped2)
534
+ zipped1 = zip(indices, shift_norm_distances)
535
+ zipped2 = zip(shift_indices, norm_distances)
536
+
537
+ # Take all products of zipped1 and zipped2 and iterate over them
538
+ # to get the terms in the above formula. This corresponds to iterating
539
+ # over the vertices of a hypercube.
540
+ hypercube = itertools.product(*zip(zipped1, zipped2))
541
+ value = np.array([0.])
542
+ for h in hypercube:
543
+ edge_indices, weights = zip(*h)
544
+ weight = np.array([1.])
545
+ for w in weights:
546
+ weight = weight * w
547
+ term = np.asarray(self._values[edge_indices]) * weight[vslice]
548
+ value = value + term # cannot use += because broadcasting
549
+ return value
550
+
551
+ def _evaluate_nearest(self, indices, norm_distances):
552
+ idx_res = [np.where(yi <= .5, i, i + 1)
553
+ for i, yi in zip(indices, norm_distances)]
554
+ return self._values[tuple(idx_res)]
555
+
556
+ def _validate_grid_dimensions(self, points, method):
557
+ k = self._SPLINE_DEGREE_MAP[method]
558
+ for i, point in enumerate(points):
559
+ ndim = len(np.atleast_1d(point))
560
+ if ndim <= k:
561
+ raise ValueError(f"There are {ndim} points in dimension {i},"
562
+ f" but method {method} requires at least "
563
+ f" {k+1} points per dimension.")
564
+
565
+ def _evaluate_spline(self, xi, method):
566
+ # ensure xi is 2D list of points to evaluate (`m` is the number of
567
+ # points and `n` is the number of interpolation dimensions,
568
+ # ``n == len(self._grid)``.)
569
+ if xi.ndim == 1:
570
+ xi = xi.reshape((1, xi.size))
571
+ m, n = xi.shape
572
+
573
+ # Reorder the axes: n-dimensional process iterates over the
574
+ # interpolation axes from the last axis downwards: E.g. for a 4D grid
575
+ # the order of axes is 3, 2, 1, 0. Each 1D interpolation works along
576
+ # the 0th axis of its argument array (for 1D routine it's its ``y``
577
+ # array). Thus permute the interpolation axes of `values` *and keep
578
+ # trailing dimensions trailing*.
579
+ axes = tuple(range(self._values.ndim))
580
+ axx = axes[:n][::-1] + axes[n:]
581
+ values = self._values.transpose(axx)
582
+
583
+ if method == 'pchip':
584
+ _eval_func = self._do_pchip
585
+ else:
586
+ _eval_func = self._do_spline_fit
587
+ k = self._SPLINE_DEGREE_MAP[method]
588
+
589
+ # Non-stationary procedure: difficult to vectorize this part entirely
590
+ # into numpy-level operations. Unfortunately this requires explicit
591
+ # looping over each point in xi.
592
+
593
+ # can at least vectorize the first pass across all points in the
594
+ # last variable of xi.
595
+ last_dim = n - 1
596
+ first_values = _eval_func(self._grid[last_dim],
597
+ values,
598
+ xi[:, last_dim],
599
+ k)
600
+
601
+ # the rest of the dimensions have to be on a per point-in-xi basis
602
+ shape = (m, *self._values.shape[n:])
603
+ result = np.empty(shape, dtype=self._values.dtype)
604
+ for j in range(m):
605
+ # Main process: Apply 1D interpolate in each dimension
606
+ # sequentially, starting with the last dimension.
607
+ # These are then "folded" into the next dimension in-place.
608
+ folded_values = first_values[j, ...]
609
+ for i in range(last_dim-1, -1, -1):
610
+ # Interpolate for each 1D from the last dimensions.
611
+ # This collapses each 1D sequence into a scalar.
612
+ folded_values = _eval_func(self._grid[i],
613
+ folded_values,
614
+ xi[j, i],
615
+ k)
616
+ result[j, ...] = folded_values
617
+
618
+ return result
619
+
620
+ @staticmethod
621
+ def _do_spline_fit(x, y, pt, k):
622
+ local_interp = make_interp_spline(x, y, k=k, axis=0)
623
+ values = local_interp(pt)
624
+ return values
625
+
626
+ @staticmethod
627
+ def _do_pchip(x, y, pt, k):
628
+ local_interp = PchipInterpolator(x, y, axis=0)
629
+ values = local_interp(pt)
630
+ return values
631
+
632
+ def _find_indices(self, xi):
633
+ return find_indices(self._grid, xi)
634
+
635
+ def _find_out_of_bounds(self, xi):
636
+ # check for out of bounds xi
637
+ out_of_bounds = np.zeros((xi.shape[1]), dtype=bool)
638
+ # iterate through dimensions
639
+ for x, grid in zip(xi, self._grid):
640
+ out_of_bounds += x < grid[0]
641
+ out_of_bounds += x > grid[-1]
642
+ return out_of_bounds
643
+
644
+
645
+ def interpn(points, values, xi, method="linear", bounds_error=True,
646
+ fill_value=np.nan):
647
+ """
648
+ Multidimensional interpolation on regular or rectilinear grids.
649
+
650
+ Strictly speaking, not all regular grids are supported - this function
651
+ works on *rectilinear* grids, that is, a rectangular grid with even or
652
+ uneven spacing.
653
+
654
+ Parameters
655
+ ----------
656
+ points : tuple of ndarray of float, with shapes (m1, ), ..., (mn, )
657
+ The points defining the regular grid in n dimensions. The points in
658
+ each dimension (i.e. every elements of the points tuple) must be
659
+ strictly ascending or descending.
660
+
661
+ values : array_like, shape (m1, ..., mn, ...)
662
+ The data on the regular grid in n dimensions. Complex data is
663
+ accepted.
664
+ xi : ndarray of shape (..., ndim)
665
+ The coordinates to sample the gridded data at
666
+
667
+ method : str, optional
668
+ The method of interpolation to perform. Supported are "linear",
669
+ "nearest", "slinear", "cubic", "quintic", "pchip", and "splinef2d".
670
+ "splinef2d" is only supported for 2-dimensional data.
671
+
672
+ bounds_error : bool, optional
673
+ If True, when interpolated values are requested outside of the
674
+ domain of the input data, a ValueError is raised.
675
+ If False, then `fill_value` is used.
676
+
677
+ fill_value : number, optional
678
+ If provided, the value to use for points outside of the
679
+ interpolation domain. If None, values outside
680
+ the domain are extrapolated. Extrapolation is not supported by method
681
+ "splinef2d".
682
+
683
+ Returns
684
+ -------
685
+ values_x : ndarray, shape xi.shape[:-1] + values.shape[ndim:]
686
+ Interpolated values at `xi`. See notes for behaviour when
687
+ ``xi.ndim == 1``.
688
+
689
+ See Also
690
+ --------
691
+ NearestNDInterpolator : Nearest neighbor interpolation on unstructured
692
+ data in N dimensions
693
+ LinearNDInterpolator : Piecewise linear interpolant on unstructured data
694
+ in N dimensions
695
+ RegularGridInterpolator : interpolation on a regular or rectilinear grid
696
+ in arbitrary dimensions (`interpn` wraps this
697
+ class).
698
+ RectBivariateSpline : Bivariate spline approximation over a rectangular mesh
699
+ scipy.ndimage.map_coordinates : interpolation on grids with equal spacing
700
+ (suitable for e.g., N-D image resampling)
701
+
702
+ Notes
703
+ -----
704
+
705
+ .. versionadded:: 0.14
706
+
707
+ In the case that ``xi.ndim == 1`` a new axis is inserted into
708
+ the 0 position of the returned array, values_x, so its shape is
709
+ instead ``(1,) + values.shape[ndim:]``.
710
+
711
+ If the input data is such that input dimensions have incommensurate
712
+ units and differ by many orders of magnitude, the interpolant may have
713
+ numerical artifacts. Consider rescaling the data before interpolation.
714
+
715
+ Examples
716
+ --------
717
+ Evaluate a simple example function on the points of a regular 3-D grid:
718
+
719
+ >>> import numpy as np
720
+ >>> from scipy.interpolate import interpn
721
+ >>> def value_func_3d(x, y, z):
722
+ ... return 2 * x + 3 * y - z
723
+ >>> x = np.linspace(0, 4, 5)
724
+ >>> y = np.linspace(0, 5, 6)
725
+ >>> z = np.linspace(0, 6, 7)
726
+ >>> points = (x, y, z)
727
+ >>> values = value_func_3d(*np.meshgrid(*points, indexing='ij'))
728
+
729
+ Evaluate the interpolating function at a point
730
+
731
+ >>> point = np.array([2.21, 3.12, 1.15])
732
+ >>> print(interpn(points, values, point))
733
+ [12.63]
734
+
735
+ Compare with value at point by function
736
+
737
+ >>> value_func_3d(*point)
738
+ 12.63 # up to rounding
739
+
740
+ Since the function is linear, the interpolation is exact using linear method.
741
+
742
+ """
743
+ # sanity check 'method' kwarg
744
+ if method not in ["linear", "nearest", "cubic", "quintic", "pchip",
745
+ "splinef2d", "slinear",
746
+ "slinear_legacy", "cubic_legacy", "quintic_legacy"]:
747
+ raise ValueError("interpn only understands the methods 'linear', "
748
+ "'nearest', 'slinear', 'cubic', 'quintic', 'pchip', "
749
+ f"and 'splinef2d'. You provided {method}.")
750
+
751
+ if not hasattr(values, 'ndim'):
752
+ values = np.asarray(values)
753
+
754
+ ndim = values.ndim
755
+ if ndim > 2 and method == "splinef2d":
756
+ raise ValueError("The method splinef2d can only be used for "
757
+ "2-dimensional input data")
758
+ if not bounds_error and fill_value is None and method == "splinef2d":
759
+ raise ValueError("The method splinef2d does not support extrapolation.")
760
+
761
+ # sanity check consistency of input dimensions
762
+ if len(points) > ndim:
763
+ raise ValueError(
764
+ f"There are {len(points)} point arrays, but values has {ndim} dimensions"
765
+ )
766
+ if len(points) != ndim and method == 'splinef2d':
767
+ raise ValueError("The method splinef2d can only be used for "
768
+ "scalar data with one point per coordinate")
769
+
770
+ grid, descending_dimensions = _check_points(points)
771
+ _check_dimensionality(grid, values)
772
+
773
+ # sanity check requested xi
774
+ xi = _ndim_coords_from_arrays(xi, ndim=len(grid))
775
+ if xi.shape[-1] != len(grid):
776
+ raise ValueError(
777
+ f"The requested sample points xi have dimension {xi.shape[-1]}, "
778
+ f"but this RegularGridInterpolator has dimension {len(grid)}"
779
+ )
780
+
781
+ if bounds_error:
782
+ for i, p in enumerate(xi.T):
783
+ if not np.logical_and(np.all(grid[i][0] <= p),
784
+ np.all(p <= grid[i][-1])):
785
+ raise ValueError(
786
+ f"One of the requested xi is out of bounds in dimension {i}"
787
+ )
788
+
789
+ # perform interpolation
790
+ if method in RegularGridInterpolator._ALL_METHODS:
791
+ interp = RegularGridInterpolator(points, values, method=method,
792
+ bounds_error=bounds_error,
793
+ fill_value=fill_value)
794
+ return interp(xi)
795
+ elif method == "splinef2d":
796
+ xi_shape = xi.shape
797
+ xi = xi.reshape(-1, xi.shape[-1])
798
+
799
+ # RectBivariateSpline doesn't support fill_value; we need to wrap here
800
+ idx_valid = np.all((grid[0][0] <= xi[:, 0], xi[:, 0] <= grid[0][-1],
801
+ grid[1][0] <= xi[:, 1], xi[:, 1] <= grid[1][-1]),
802
+ axis=0)
803
+ result = np.empty_like(xi[:, 0])
804
+
805
+ # make a copy of values for RectBivariateSpline
806
+ interp = RectBivariateSpline(points[0], points[1], values[:])
807
+ result[idx_valid] = interp.ev(xi[idx_valid, 0], xi[idx_valid, 1])
808
+ result[np.logical_not(idx_valid)] = fill_value
809
+
810
+ return result.reshape(xi_shape[:-1])
811
+ else:
812
+ raise ValueError(f"unknown {method = }")
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/dfitpack.py ADDED
@@ -0,0 +1,24 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file is not meant for public use and will be removed in SciPy v2.0.0.
2
+ # Use the `scipy.interpolate` namespace for importing the functions
3
+ # included below.
4
+
5
+ from scipy._lib.deprecation import _sub_module_deprecation
6
+
7
+
8
+ __all__ = [ # noqa: F822
9
+ 'spalde',
10
+ 'splder',
11
+ 'splev',
12
+ 'splint',
13
+ 'sproot',
14
+ ]
15
+
16
+
17
+ def __dir__():
18
+ return __all__
19
+
20
+
21
+ def __getattr__(name):
22
+ return _sub_module_deprecation(sub_package="interpolate", module="dfitpack",
23
+ private_modules=["_dfitpack"], all=__all__,
24
+ attribute=name)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/fitpack.py ADDED
@@ -0,0 +1,31 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file is not meant for public use and will be removed in SciPy v2.0.0.
2
+ # Use the `scipy.interpolate` namespace for importing the functions
3
+ # included below.
4
+
5
+ from scipy._lib.deprecation import _sub_module_deprecation
6
+
7
+
8
+ __all__ = [ # noqa: F822
9
+ 'BSpline',
10
+ 'bisplev',
11
+ 'bisplrep',
12
+ 'insert',
13
+ 'spalde',
14
+ 'splantider',
15
+ 'splder',
16
+ 'splev',
17
+ 'splint',
18
+ 'splprep',
19
+ 'splrep',
20
+ 'sproot',
21
+ ]
22
+
23
+
24
+ def __dir__():
25
+ return __all__
26
+
27
+
28
+ def __getattr__(name):
29
+ return _sub_module_deprecation(sub_package="interpolate", module="fitpack",
30
+ private_modules=["_fitpack_py"], all=__all__,
31
+ attribute=name)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/fitpack2.py ADDED
@@ -0,0 +1,29 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file is not meant for public use and will be removed in SciPy v2.0.0.
2
+ # Use the `scipy.interpolate` namespace for importing the functions
3
+ # included below.
4
+
5
+ from scipy._lib.deprecation import _sub_module_deprecation
6
+
7
+
8
+ __all__ = [ # noqa: F822
9
+ 'BivariateSpline',
10
+ 'InterpolatedUnivariateSpline',
11
+ 'LSQBivariateSpline',
12
+ 'LSQSphereBivariateSpline',
13
+ 'LSQUnivariateSpline',
14
+ 'RectBivariateSpline',
15
+ 'RectSphereBivariateSpline',
16
+ 'SmoothBivariateSpline',
17
+ 'SmoothSphereBivariateSpline',
18
+ 'UnivariateSpline',
19
+ ]
20
+
21
+
22
+ def __dir__():
23
+ return __all__
24
+
25
+
26
+ def __getattr__(name):
27
+ return _sub_module_deprecation(sub_package="interpolate", module="fitpack2",
28
+ private_modules=["_fitpack2"], all=__all__,
29
+ attribute=name)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/interpnd.py ADDED
@@ -0,0 +1,21 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file is not meant for public use and will be removed in SciPy v2.0.0.
2
+ # Use the `scipy.interpolate` namespace for importing the functions
3
+ # included below.
4
+
5
+ from scipy._lib.deprecation import _sub_module_deprecation
6
+
7
+
8
+ __all__ = [ # noqa: F822
9
+ 'CloughTocher2DInterpolator',
10
+ 'LinearNDInterpolator',
11
+ ]
12
+
13
+
14
+ def __dir__():
15
+ return __all__
16
+
17
+
18
+ def __getattr__(name):
19
+ return _sub_module_deprecation(sub_package="interpolate", module="interpnd",
20
+ private_modules=["_interpnd"], all=__all__,
21
+ attribute=name, dep_version="1.17.0")
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/ndgriddata.py ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file is not meant for public use and will be removed in SciPy v2.0.0.
2
+ # Use the `scipy.interpolate` namespace for importing the functions
3
+ # included below.
4
+
5
+ from scipy._lib.deprecation import _sub_module_deprecation
6
+
7
+
8
+ __all__ = [ # noqa: F822
9
+ 'CloughTocher2DInterpolator',
10
+ 'LinearNDInterpolator',
11
+ 'NearestNDInterpolator',
12
+ 'griddata',
13
+ ]
14
+
15
+
16
+ def __dir__():
17
+ return __all__
18
+
19
+
20
+ def __getattr__(name):
21
+ return _sub_module_deprecation(sub_package="interpolate", module="ndgriddata",
22
+ private_modules=["_ndgriddata"], all=__all__,
23
+ attribute=name)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/interpolate/polyint.py ADDED
@@ -0,0 +1,24 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file is not meant for public use and will be removed in SciPy v2.0.0.
2
+ # Use the `scipy.interpolate` namespace for importing the functions
3
+ # included below.
4
+
5
+ from scipy._lib.deprecation import _sub_module_deprecation
6
+
7
+
8
+ __all__ = [ # noqa: F822
9
+ 'BarycentricInterpolator',
10
+ 'KroghInterpolator',
11
+ 'approximate_taylor_polynomial',
12
+ 'barycentric_interpolate',
13
+ 'krogh_interpolate',
14
+ ]
15
+
16
+
17
+ def __dir__():
18
+ return __all__
19
+
20
+
21
+ def __getattr__(name):
22
+ return _sub_module_deprecation(sub_package="interpolate", module="polyint",
23
+ private_modules=["_polyint"], all=__all__,
24
+ attribute=name)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/__init__.py ADDED
@@ -0,0 +1,121 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """
2
+ ==================================
3
+ Input and output (:mod:`scipy.io`)
4
+ ==================================
5
+
6
+ .. currentmodule:: scipy.io
7
+
8
+ .. toctree::
9
+ :hidden:
10
+
11
+ io.matlab
12
+
13
+ SciPy has many modules, classes, and functions available to read data
14
+ from and write data to a variety of file formats.
15
+
16
+ .. seealso:: `NumPy IO routines <https://www.numpy.org/devdocs/reference/routines.io.html>`__
17
+
18
+ MATLAB® files
19
+ =============
20
+
21
+ .. autosummary::
22
+ :toctree: generated/
23
+
24
+ loadmat - Read a MATLAB style mat file (version 4 through 7.1)
25
+ savemat - Write a MATLAB style mat file (version 4 through 7.1)
26
+ whosmat - List contents of a MATLAB style mat file (version 4 through 7.1)
27
+
28
+ For low-level MATLAB reading and writing utilities, see `scipy.io.matlab`.
29
+
30
+ IDL® files
31
+ ==========
32
+
33
+ .. autosummary::
34
+ :toctree: generated/
35
+
36
+ readsav - Read an IDL 'save' file
37
+
38
+ Matrix Market files
39
+ ===================
40
+
41
+ .. autosummary::
42
+ :toctree: generated/
43
+
44
+ mminfo - Query matrix info from Matrix Market formatted file
45
+ mmread - Read matrix from Matrix Market formatted file
46
+ mmwrite - Write matrix to Matrix Market formatted file
47
+
48
+ Unformatted Fortran files
49
+ ===============================
50
+
51
+ .. autosummary::
52
+ :toctree: generated/
53
+
54
+ FortranFile - A file object for unformatted sequential Fortran files
55
+ FortranEOFError - Exception indicating the end of a well-formed file
56
+ FortranFormattingError - Exception indicating an inappropriate end
57
+
58
+ Netcdf
59
+ ======
60
+
61
+ .. autosummary::
62
+ :toctree: generated/
63
+
64
+ netcdf_file - A file object for NetCDF data
65
+ netcdf_variable - A data object for the netcdf module
66
+
67
+ Harwell-Boeing files
68
+ ====================
69
+
70
+ .. autosummary::
71
+ :toctree: generated/
72
+
73
+ hb_read -- read H-B file
74
+ hb_write -- write H-B file
75
+
76
+ Wav sound files (:mod:`scipy.io.wavfile`)
77
+ =========================================
78
+
79
+ .. module:: scipy.io.wavfile
80
+
81
+ .. autosummary::
82
+ :toctree: generated/
83
+
84
+ read
85
+ write
86
+ WavFileWarning
87
+
88
+ Arff files (:mod:`scipy.io.arff`)
89
+ =================================
90
+
91
+ .. module:: scipy.io.arff
92
+
93
+ .. autosummary::
94
+ :toctree: generated/
95
+
96
+ loadarff
97
+ MetaData
98
+ ArffError
99
+ ParseArffError
100
+ """
101
+ # matfile read and write
102
+ from .matlab import loadmat, savemat, whosmat
103
+
104
+ # netCDF file support
105
+ from ._netcdf import netcdf_file, netcdf_variable
106
+
107
+ # Fortran file support
108
+ from ._fortran import FortranFile, FortranEOFError, FortranFormattingError
109
+
110
+ from ._fast_matrix_market import mminfo, mmread, mmwrite
111
+ from ._idl import readsav
112
+ from ._harwell_boeing import hb_read, hb_write
113
+
114
+ # Deprecated namespaces, to be removed in v2.0.0
115
+ from . import arff, harwell_boeing, idl, mmio, netcdf, wavfile
116
+
117
+ __all__ = [s for s in dir() if not s.startswith('_')]
118
+
119
+ from scipy._lib._testutils import PytestTester
120
+ test = PytestTester(__name__)
121
+ del PytestTester
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/_fortran.py ADDED
@@ -0,0 +1,354 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """
2
+ Module to read / write Fortran unformatted sequential files.
3
+
4
+ This is in the spirit of code written by Neil Martinsen-Burrell and Joe Zuntz.
5
+
6
+ """
7
+ import warnings
8
+ import numpy as np
9
+
10
+ __all__ = ['FortranFile', 'FortranEOFError', 'FortranFormattingError']
11
+
12
+
13
+ class FortranEOFError(TypeError, OSError):
14
+ """Indicates that the file ended properly.
15
+
16
+ This error descends from TypeError because the code used to raise
17
+ TypeError (and this was the only way to know that the file had
18
+ ended) so users might have ``except TypeError:``.
19
+
20
+ """
21
+ pass
22
+
23
+
24
+ class FortranFormattingError(TypeError, OSError):
25
+ """Indicates that the file ended mid-record.
26
+
27
+ Descends from TypeError for backward compatibility.
28
+
29
+ """
30
+ pass
31
+
32
+
33
+ class FortranFile:
34
+ """
35
+ A file object for unformatted sequential files from Fortran code.
36
+
37
+ Parameters
38
+ ----------
39
+ filename : file or str
40
+ Open file object or filename.
41
+ mode : {'r', 'w'}, optional
42
+ Read-write mode, default is 'r'.
43
+ header_dtype : dtype, optional
44
+ Data type of the header. Size and endianness must match the input/output file.
45
+
46
+ Notes
47
+ -----
48
+ These files are broken up into records of unspecified types. The size of
49
+ each record is given at the start (although the size of this header is not
50
+ standard) and the data is written onto disk without any formatting. Fortran
51
+ compilers supporting the BACKSPACE statement will write a second copy of
52
+ the size to facilitate backwards seeking.
53
+
54
+ This class only supports files written with both sizes for the record.
55
+ It also does not support the subrecords used in Intel and gfortran compilers
56
+ for records which are greater than 2GB with a 4-byte header.
57
+
58
+ An example of an unformatted sequential file in Fortran would be written as::
59
+
60
+ OPEN(1, FILE=myfilename, FORM='unformatted')
61
+
62
+ WRITE(1) myvariable
63
+
64
+ Since this is a non-standard file format, whose contents depend on the
65
+ compiler and the endianness of the machine, caution is advised. Files from
66
+ gfortran 4.8.0 and gfortran 4.1.2 on x86_64 are known to work.
67
+
68
+ Consider using Fortran direct-access files or files from the newer Stream
69
+ I/O, which can be easily read by `numpy.fromfile`.
70
+
71
+ Examples
72
+ --------
73
+ To create an unformatted sequential Fortran file:
74
+
75
+ >>> from scipy.io import FortranFile
76
+ >>> import numpy as np
77
+ >>> f = FortranFile('test.unf', 'w')
78
+ >>> f.write_record(np.array([1,2,3,4,5], dtype=np.int32))
79
+ >>> f.write_record(np.linspace(0,1,20).reshape((5,4)).T)
80
+ >>> f.close()
81
+
82
+ To read this file:
83
+
84
+ >>> f = FortranFile('test.unf', 'r')
85
+ >>> print(f.read_ints(np.int32))
86
+ [1 2 3 4 5]
87
+ >>> print(f.read_reals(float).reshape((5,4), order="F"))
88
+ [[0. 0.05263158 0.10526316 0.15789474]
89
+ [0.21052632 0.26315789 0.31578947 0.36842105]
90
+ [0.42105263 0.47368421 0.52631579 0.57894737]
91
+ [0.63157895 0.68421053 0.73684211 0.78947368]
92
+ [0.84210526 0.89473684 0.94736842 1. ]]
93
+ >>> f.close()
94
+
95
+ Or, in Fortran::
96
+
97
+ integer :: a(5), i
98
+ double precision :: b(5,4)
99
+ open(1, file='test.unf', form='unformatted')
100
+ read(1) a
101
+ read(1) b
102
+ close(1)
103
+ write(*,*) a
104
+ do i = 1, 5
105
+ write(*,*) b(i,:)
106
+ end do
107
+
108
+ """
109
+ def __init__(self, filename, mode='r', header_dtype=np.uint32):
110
+ if header_dtype is None:
111
+ raise ValueError('Must specify dtype')
112
+
113
+ header_dtype = np.dtype(header_dtype)
114
+ if header_dtype.kind != 'u':
115
+ warnings.warn("Given a dtype which is not unsigned.", stacklevel=2)
116
+
117
+ if mode not in 'rw' or len(mode) != 1:
118
+ raise ValueError('mode must be either r or w')
119
+
120
+ if hasattr(filename, 'seek'):
121
+ self._fp = filename
122
+ else:
123
+ self._fp = open(filename, f'{mode}b')
124
+
125
+ self._header_dtype = header_dtype
126
+
127
+ def _read_size(self, eof_ok=False):
128
+ n = self._header_dtype.itemsize
129
+ b = self._fp.read(n)
130
+ if (not b) and eof_ok:
131
+ raise FortranEOFError("End of file occurred at end of record")
132
+ elif len(b) < n:
133
+ raise FortranFormattingError(
134
+ "End of file in the middle of the record size")
135
+ return int(np.frombuffer(b, dtype=self._header_dtype, count=1)[0])
136
+
137
+ def write_record(self, *items):
138
+ """
139
+ Write a record (including sizes) to the file.
140
+
141
+ Parameters
142
+ ----------
143
+ *items : array_like
144
+ The data arrays to write.
145
+
146
+ Notes
147
+ -----
148
+ Writes data items to a file::
149
+
150
+ write_record(a.T, b.T, c.T, ...)
151
+
152
+ write(1) a, b, c, ...
153
+
154
+ Note that data in multidimensional arrays is written in
155
+ row-major order --- to make them read correctly by Fortran
156
+ programs, you need to transpose the arrays yourself when
157
+ writing them.
158
+
159
+ """
160
+ items = tuple(np.asarray(item) for item in items)
161
+ total_size = sum(item.nbytes for item in items)
162
+
163
+ nb = np.array([total_size], dtype=self._header_dtype)
164
+
165
+ nb.tofile(self._fp)
166
+ for item in items:
167
+ item.tofile(self._fp)
168
+ nb.tofile(self._fp)
169
+
170
+ def read_record(self, *dtypes, **kwargs):
171
+ """
172
+ Reads a record of a given type from the file.
173
+
174
+ Parameters
175
+ ----------
176
+ *dtypes : dtypes, optional
177
+ Data type(s) specifying the size and endianness of the data.
178
+
179
+ Returns
180
+ -------
181
+ data : ndarray
182
+ A 1-D array object.
183
+
184
+ Raises
185
+ ------
186
+ FortranEOFError
187
+ To signal that no further records are available
188
+ FortranFormattingError
189
+ To signal that the end of the file was encountered
190
+ part-way through a record
191
+
192
+ Notes
193
+ -----
194
+ If the record contains a multidimensional array, you can specify
195
+ the size in the dtype. For example::
196
+
197
+ INTEGER var(5,4)
198
+
199
+ can be read with::
200
+
201
+ read_record('(4,5)i4').T
202
+
203
+ Note that this function does **not** assume the file data is in Fortran
204
+ column major order, so you need to (i) swap the order of dimensions
205
+ when reading and (ii) transpose the resulting array.
206
+
207
+ Alternatively, you can read the data as a 1-D array and handle the
208
+ ordering yourself. For example::
209
+
210
+ read_record('i4').reshape(5, 4, order='F')
211
+
212
+ For records that contain several variables or mixed types (as opposed
213
+ to single scalar or array types), give them as separate arguments::
214
+
215
+ double precision :: a
216
+ integer :: b
217
+ write(1) a, b
218
+
219
+ record = f.read_record('<f4', '<i4')
220
+ a = record[0] # first number
221
+ b = record[1] # second number
222
+
223
+ and if any of the variables are arrays, the shape can be specified as
224
+ the third item in the relevant dtype::
225
+
226
+ double precision :: a
227
+ integer :: b(3,4)
228
+ write(1) a, b
229
+
230
+ record = f.read_record('<f4', np.dtype(('<i4', (4, 3))))
231
+ a = record[0]
232
+ b = record[1].T
233
+
234
+ NumPy also supports a short syntax for this kind of type::
235
+
236
+ record = f.read_record('<f4', '(3,3)<i4')
237
+
238
+ See Also
239
+ --------
240
+ read_reals
241
+ read_ints
242
+
243
+ """
244
+ dtype = kwargs.pop('dtype', None)
245
+ if kwargs:
246
+ raise ValueError(f"Unknown keyword arguments {tuple(kwargs.keys())}")
247
+
248
+ if dtype is not None:
249
+ dtypes = dtypes + (dtype,)
250
+ elif not dtypes:
251
+ raise ValueError('Must specify at least one dtype')
252
+
253
+ first_size = self._read_size(eof_ok=True)
254
+
255
+ dtypes = tuple(np.dtype(dtype) for dtype in dtypes)
256
+ block_size = sum(dtype.itemsize for dtype in dtypes)
257
+
258
+ num_blocks, remainder = divmod(first_size, block_size)
259
+ if remainder != 0:
260
+ raise ValueError(f'Size obtained ({first_size}) is not a multiple of the '
261
+ f'dtypes given ({block_size}).')
262
+
263
+ if len(dtypes) != 1 and first_size != block_size:
264
+ # Fortran does not write mixed type array items in interleaved order,
265
+ # and it's not possible to guess the sizes of the arrays that were written.
266
+ # The user must specify the exact sizes of each of the arrays.
267
+ raise ValueError(f'Size obtained ({first_size}) does not match with the '
268
+ f'expected size ({block_size}) of multi-item record')
269
+
270
+ data = []
271
+ for dtype in dtypes:
272
+ r = np.fromfile(self._fp, dtype=dtype, count=num_blocks)
273
+ if len(r) != num_blocks:
274
+ raise FortranFormattingError(
275
+ "End of file in the middle of a record")
276
+ if dtype.shape != ():
277
+ # Squeeze outmost block dimension for array items
278
+ if num_blocks == 1:
279
+ assert r.shape == (1,) + dtype.shape
280
+ r = r[0]
281
+
282
+ data.append(r)
283
+
284
+ second_size = self._read_size()
285
+ if first_size != second_size:
286
+ raise ValueError('Sizes do not agree in the header and footer for '
287
+ 'this record - check header dtype')
288
+
289
+ # Unpack result
290
+ if len(dtypes) == 1:
291
+ return data[0]
292
+ else:
293
+ return tuple(data)
294
+
295
+ def read_ints(self, dtype='i4'):
296
+ """
297
+ Reads a record of a given type from the file, defaulting to an integer
298
+ type (``INTEGER*4`` in Fortran).
299
+
300
+ Parameters
301
+ ----------
302
+ dtype : dtype, optional
303
+ Data type specifying the size and endianness of the data.
304
+
305
+ Returns
306
+ -------
307
+ data : ndarray
308
+ A 1-D array object.
309
+
310
+ See Also
311
+ --------
312
+ read_reals
313
+ read_record
314
+
315
+ """
316
+ return self.read_record(dtype)
317
+
318
+ def read_reals(self, dtype='f8'):
319
+ """
320
+ Reads a record of a given type from the file, defaulting to a floating
321
+ point number (``real*8`` in Fortran).
322
+
323
+ Parameters
324
+ ----------
325
+ dtype : dtype, optional
326
+ Data type specifying the size and endianness of the data.
327
+
328
+ Returns
329
+ -------
330
+ data : ndarray
331
+ A 1-D array object.
332
+
333
+ See Also
334
+ --------
335
+ read_ints
336
+ read_record
337
+
338
+ """
339
+ return self.read_record(dtype)
340
+
341
+ def close(self):
342
+ """
343
+ Closes the file. It is unsupported to call any other methods off this
344
+ object after closing it. Note that this class supports the 'with'
345
+ statement in modern versions of Python, to call this automatically
346
+
347
+ """
348
+ self._fp.close()
349
+
350
+ def __enter__(self):
351
+ return self
352
+
353
+ def __exit__(self, type, value, tb):
354
+ self.close()
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/_idl.py ADDED
@@ -0,0 +1,917 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # IDLSave - a python module to read IDL 'save' files
2
+ # Copyright (c) 2010 Thomas P. Robitaille
3
+
4
+ # Many thanks to Craig Markwardt for publishing the Unofficial Format
5
+ # Specification for IDL .sav files, without which this Python module would not
6
+ # exist (http://cow.physics.wisc.edu/~craigm/idl/savefmt).
7
+
8
+ # This code was developed by with permission from ITT Visual Information
9
+ # Systems. IDL(r) is a registered trademark of ITT Visual Information Systems,
10
+ # Inc. for their Interactive Data Language software.
11
+
12
+ # Permission is hereby granted, free of charge, to any person obtaining a
13
+ # copy of this software and associated documentation files (the "Software"),
14
+ # to deal in the Software without restriction, including without limitation
15
+ # the rights to use, copy, modify, merge, publish, distribute, sublicense,
16
+ # and/or sell copies of the Software, and to permit persons to whom the
17
+ # Software is furnished to do so, subject to the following conditions:
18
+
19
+ # The above copyright notice and this permission notice shall be included in
20
+ # all copies or substantial portions of the Software.
21
+
22
+ # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
23
+ # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
24
+ # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
25
+ # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
26
+ # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
27
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
28
+ # DEALINGS IN THE SOFTWARE.
29
+
30
+ __all__ = ['readsav']
31
+
32
+ import struct
33
+ import numpy as np
34
+ import tempfile
35
+ import zlib
36
+ import warnings
37
+
38
+ # Define the different data types that can be found in an IDL save file
39
+ DTYPE_DICT = {1: '>u1',
40
+ 2: '>i2',
41
+ 3: '>i4',
42
+ 4: '>f4',
43
+ 5: '>f8',
44
+ 6: '>c8',
45
+ 7: '|O',
46
+ 8: '|O',
47
+ 9: '>c16',
48
+ 10: '|O',
49
+ 11: '|O',
50
+ 12: '>u2',
51
+ 13: '>u4',
52
+ 14: '>i8',
53
+ 15: '>u8'}
54
+
55
+ # Define the different record types that can be found in an IDL save file
56
+ RECTYPE_DICT = {0: "START_MARKER",
57
+ 1: "COMMON_VARIABLE",
58
+ 2: "VARIABLE",
59
+ 3: "SYSTEM_VARIABLE",
60
+ 6: "END_MARKER",
61
+ 10: "TIMESTAMP",
62
+ 12: "COMPILED",
63
+ 13: "IDENTIFICATION",
64
+ 14: "VERSION",
65
+ 15: "HEAP_HEADER",
66
+ 16: "HEAP_DATA",
67
+ 17: "PROMOTE64",
68
+ 19: "NOTICE",
69
+ 20: "DESCRIPTION"}
70
+
71
+ # Define a dictionary to contain structure definitions
72
+ STRUCT_DICT = {}
73
+
74
+
75
+ def _align_32(f):
76
+ '''Align to the next 32-bit position in a file'''
77
+
78
+ pos = f.tell()
79
+ if pos % 4 != 0:
80
+ f.seek(pos + 4 - pos % 4)
81
+ return
82
+
83
+
84
+ def _skip_bytes(f, n):
85
+ '''Skip `n` bytes'''
86
+ f.read(n)
87
+ return
88
+
89
+
90
+ def _read_bytes(f, n):
91
+ '''Read the next `n` bytes'''
92
+ return f.read(n)
93
+
94
+
95
+ def _read_byte(f):
96
+ '''Read a single byte'''
97
+ return np.uint8(struct.unpack('>B', f.read(4)[:1])[0])
98
+
99
+
100
+ def _read_long(f):
101
+ '''Read a signed 32-bit integer'''
102
+ return np.int32(struct.unpack('>l', f.read(4))[0])
103
+
104
+
105
+ def _read_int16(f):
106
+ '''Read a signed 16-bit integer'''
107
+ return np.int16(struct.unpack('>h', f.read(4)[2:4])[0])
108
+
109
+
110
+ def _read_int32(f):
111
+ '''Read a signed 32-bit integer'''
112
+ return np.int32(struct.unpack('>i', f.read(4))[0])
113
+
114
+
115
+ def _read_int64(f):
116
+ '''Read a signed 64-bit integer'''
117
+ return np.int64(struct.unpack('>q', f.read(8))[0])
118
+
119
+
120
+ def _read_uint16(f):
121
+ '''Read an unsigned 16-bit integer'''
122
+ return np.uint16(struct.unpack('>H', f.read(4)[2:4])[0])
123
+
124
+
125
+ def _read_uint32(f):
126
+ '''Read an unsigned 32-bit integer'''
127
+ return np.uint32(struct.unpack('>I', f.read(4))[0])
128
+
129
+
130
+ def _read_uint64(f):
131
+ '''Read an unsigned 64-bit integer'''
132
+ return np.uint64(struct.unpack('>Q', f.read(8))[0])
133
+
134
+
135
+ def _read_float32(f):
136
+ '''Read a 32-bit float'''
137
+ return np.float32(struct.unpack('>f', f.read(4))[0])
138
+
139
+
140
+ def _read_float64(f):
141
+ '''Read a 64-bit float'''
142
+ return np.float64(struct.unpack('>d', f.read(8))[0])
143
+
144
+
145
+ class Pointer:
146
+ '''Class used to define pointers'''
147
+
148
+ def __init__(self, index):
149
+ self.index = index
150
+ return
151
+
152
+
153
+ class ObjectPointer(Pointer):
154
+ '''Class used to define object pointers'''
155
+ pass
156
+
157
+
158
+ def _read_string(f):
159
+ '''Read a string'''
160
+ length = _read_long(f)
161
+ if length > 0:
162
+ chars = _read_bytes(f, length).decode('latin1')
163
+ _align_32(f)
164
+ else:
165
+ chars = ''
166
+ return chars
167
+
168
+
169
+ def _read_string_data(f):
170
+ '''Read a data string (length is specified twice)'''
171
+ length = _read_long(f)
172
+ if length > 0:
173
+ length = _read_long(f)
174
+ string_data = _read_bytes(f, length)
175
+ _align_32(f)
176
+ else:
177
+ string_data = ''
178
+ return string_data
179
+
180
+
181
+ def _read_data(f, dtype):
182
+ '''Read a variable with a specified data type'''
183
+ if dtype == 1:
184
+ if _read_int32(f) != 1:
185
+ raise Exception("Error occurred while reading byte variable")
186
+ return _read_byte(f)
187
+ elif dtype == 2:
188
+ return _read_int16(f)
189
+ elif dtype == 3:
190
+ return _read_int32(f)
191
+ elif dtype == 4:
192
+ return _read_float32(f)
193
+ elif dtype == 5:
194
+ return _read_float64(f)
195
+ elif dtype == 6:
196
+ real = _read_float32(f)
197
+ imag = _read_float32(f)
198
+ return np.complex64(real + imag * 1j)
199
+ elif dtype == 7:
200
+ return _read_string_data(f)
201
+ elif dtype == 8:
202
+ raise Exception("Should not be here - please report this")
203
+ elif dtype == 9:
204
+ real = _read_float64(f)
205
+ imag = _read_float64(f)
206
+ return np.complex128(real + imag * 1j)
207
+ elif dtype == 10:
208
+ return Pointer(_read_int32(f))
209
+ elif dtype == 11:
210
+ return ObjectPointer(_read_int32(f))
211
+ elif dtype == 12:
212
+ return _read_uint16(f)
213
+ elif dtype == 13:
214
+ return _read_uint32(f)
215
+ elif dtype == 14:
216
+ return _read_int64(f)
217
+ elif dtype == 15:
218
+ return _read_uint64(f)
219
+ else:
220
+ raise Exception(f"Unknown IDL type: {dtype} - please report this")
221
+
222
+
223
+ def _read_structure(f, array_desc, struct_desc):
224
+ '''
225
+ Read a structure, with the array and structure descriptors given as
226
+ `array_desc` and `structure_desc` respectively.
227
+ '''
228
+
229
+ nrows = array_desc['nelements']
230
+ columns = struct_desc['tagtable']
231
+
232
+ dtype = []
233
+ for col in columns:
234
+ if col['structure'] or col['array']:
235
+ dtype.append(((col['name'].lower(), col['name']), np.object_))
236
+ else:
237
+ if col['typecode'] in DTYPE_DICT:
238
+ dtype.append(((col['name'].lower(), col['name']),
239
+ DTYPE_DICT[col['typecode']]))
240
+ else:
241
+ raise Exception(f"Variable type {col['typecode']} not implemented")
242
+
243
+ structure = np.rec.recarray((nrows, ), dtype=dtype)
244
+
245
+ for i in range(nrows):
246
+ for col in columns:
247
+ dtype = col['typecode']
248
+ if col['structure']:
249
+ structure[col['name']][i] = _read_structure(f,
250
+ struct_desc['arrtable'][col['name']],
251
+ struct_desc['structtable'][col['name']])
252
+ elif col['array']:
253
+ structure[col['name']][i] = _read_array(f, dtype,
254
+ struct_desc['arrtable'][col['name']])
255
+ else:
256
+ structure[col['name']][i] = _read_data(f, dtype)
257
+
258
+ # Reshape structure if needed
259
+ if array_desc['ndims'] > 1:
260
+ dims = array_desc['dims'][:int(array_desc['ndims'])]
261
+ dims.reverse()
262
+ structure = structure.reshape(dims)
263
+
264
+ return structure
265
+
266
+
267
+ def _read_array(f, typecode, array_desc):
268
+ '''
269
+ Read an array of type `typecode`, with the array descriptor given as
270
+ `array_desc`.
271
+ '''
272
+
273
+ if typecode in [1, 3, 4, 5, 6, 9, 13, 14, 15]:
274
+
275
+ if typecode == 1:
276
+ nbytes = _read_int32(f)
277
+ if nbytes != array_desc['nbytes']:
278
+ warnings.warn("Not able to verify number of bytes from header",
279
+ stacklevel=3)
280
+
281
+ # Read bytes as numpy array
282
+ array = np.frombuffer(f.read(array_desc['nbytes']),
283
+ dtype=DTYPE_DICT[typecode])
284
+
285
+ elif typecode in [2, 12]:
286
+
287
+ # These are 2 byte types, need to skip every two as they are not packed
288
+
289
+ array = np.frombuffer(f.read(array_desc['nbytes']*2),
290
+ dtype=DTYPE_DICT[typecode])[1::2]
291
+
292
+ else:
293
+
294
+ # Read bytes into list
295
+ array = []
296
+ for i in range(array_desc['nelements']):
297
+ dtype = typecode
298
+ data = _read_data(f, dtype)
299
+ array.append(data)
300
+
301
+ array = np.array(array, dtype=np.object_)
302
+
303
+ # Reshape array if needed
304
+ if array_desc['ndims'] > 1:
305
+ dims = array_desc['dims'][:int(array_desc['ndims'])]
306
+ dims.reverse()
307
+ array = array.reshape(dims)
308
+
309
+ # Go to next alignment position
310
+ _align_32(f)
311
+
312
+ return array
313
+
314
+
315
+ def _read_record(f):
316
+ '''Function to read in a full record'''
317
+
318
+ record = {'rectype': _read_long(f)}
319
+
320
+ nextrec = _read_uint32(f)
321
+ nextrec += _read_uint32(f).astype(np.int64) * 2**32
322
+
323
+ _skip_bytes(f, 4)
324
+
325
+ if record['rectype'] not in RECTYPE_DICT:
326
+ raise Exception(f"Unknown RECTYPE: {record['rectype']}")
327
+
328
+ record['rectype'] = RECTYPE_DICT[record['rectype']]
329
+
330
+ if record['rectype'] in ["VARIABLE", "HEAP_DATA"]:
331
+
332
+ if record['rectype'] == "VARIABLE":
333
+ record['varname'] = _read_string(f)
334
+ else:
335
+ record['heap_index'] = _read_long(f)
336
+ _skip_bytes(f, 4)
337
+
338
+ rectypedesc = _read_typedesc(f)
339
+
340
+ if rectypedesc['typecode'] == 0:
341
+
342
+ if nextrec == f.tell():
343
+ record['data'] = None # Indicates NULL value
344
+ else:
345
+ raise ValueError("Unexpected type code: 0")
346
+
347
+ else:
348
+
349
+ varstart = _read_long(f)
350
+ if varstart != 7:
351
+ raise Exception("VARSTART is not 7")
352
+
353
+ if rectypedesc['structure']:
354
+ record['data'] = _read_structure(f, rectypedesc['array_desc'],
355
+ rectypedesc['struct_desc'])
356
+ elif rectypedesc['array']:
357
+ record['data'] = _read_array(f, rectypedesc['typecode'],
358
+ rectypedesc['array_desc'])
359
+ else:
360
+ dtype = rectypedesc['typecode']
361
+ record['data'] = _read_data(f, dtype)
362
+
363
+ elif record['rectype'] == "TIMESTAMP":
364
+
365
+ _skip_bytes(f, 4*256)
366
+ record['date'] = _read_string(f)
367
+ record['user'] = _read_string(f)
368
+ record['host'] = _read_string(f)
369
+
370
+ elif record['rectype'] == "VERSION":
371
+
372
+ record['format'] = _read_long(f)
373
+ record['arch'] = _read_string(f)
374
+ record['os'] = _read_string(f)
375
+ record['release'] = _read_string(f)
376
+
377
+ elif record['rectype'] == "IDENTIFICATON":
378
+
379
+ record['author'] = _read_string(f)
380
+ record['title'] = _read_string(f)
381
+ record['idcode'] = _read_string(f)
382
+
383
+ elif record['rectype'] == "NOTICE":
384
+
385
+ record['notice'] = _read_string(f)
386
+
387
+ elif record['rectype'] == "DESCRIPTION":
388
+
389
+ record['description'] = _read_string_data(f)
390
+
391
+ elif record['rectype'] == "HEAP_HEADER":
392
+
393
+ record['nvalues'] = _read_long(f)
394
+ record['indices'] = [_read_long(f) for _ in range(record['nvalues'])]
395
+
396
+ elif record['rectype'] == "COMMONBLOCK":
397
+
398
+ record['nvars'] = _read_long(f)
399
+ record['name'] = _read_string(f)
400
+ record['varnames'] = [_read_string(f) for _ in range(record['nvars'])]
401
+
402
+ elif record['rectype'] == "END_MARKER":
403
+
404
+ record['end'] = True
405
+
406
+ elif record['rectype'] == "UNKNOWN":
407
+
408
+ warnings.warn("Skipping UNKNOWN record", stacklevel=3)
409
+
410
+ elif record['rectype'] == "SYSTEM_VARIABLE":
411
+
412
+ warnings.warn("Skipping SYSTEM_VARIABLE record", stacklevel=3)
413
+
414
+ else:
415
+
416
+ raise Exception(f"record['rectype']={record['rectype']} not implemented")
417
+
418
+ f.seek(nextrec)
419
+
420
+ return record
421
+
422
+
423
+ def _read_typedesc(f):
424
+ '''Function to read in a type descriptor'''
425
+
426
+ typedesc = {'typecode': _read_long(f), 'varflags': _read_long(f)}
427
+
428
+ if typedesc['varflags'] & 2 == 2:
429
+ raise Exception("System variables not implemented")
430
+
431
+ typedesc['array'] = typedesc['varflags'] & 4 == 4
432
+ typedesc['structure'] = typedesc['varflags'] & 32 == 32
433
+
434
+ if typedesc['structure']:
435
+ typedesc['array_desc'] = _read_arraydesc(f)
436
+ typedesc['struct_desc'] = _read_structdesc(f)
437
+ elif typedesc['array']:
438
+ typedesc['array_desc'] = _read_arraydesc(f)
439
+
440
+ return typedesc
441
+
442
+
443
+ def _read_arraydesc(f):
444
+ '''Function to read in an array descriptor'''
445
+
446
+ arraydesc = {'arrstart': _read_long(f)}
447
+
448
+ if arraydesc['arrstart'] == 8:
449
+
450
+ _skip_bytes(f, 4)
451
+
452
+ arraydesc['nbytes'] = _read_long(f)
453
+ arraydesc['nelements'] = _read_long(f)
454
+ arraydesc['ndims'] = _read_long(f)
455
+
456
+ _skip_bytes(f, 8)
457
+
458
+ arraydesc['nmax'] = _read_long(f)
459
+
460
+ arraydesc['dims'] = [_read_long(f) for _ in range(arraydesc['nmax'])]
461
+
462
+ elif arraydesc['arrstart'] == 18:
463
+
464
+ warnings.warn("Using experimental 64-bit array read", stacklevel=3)
465
+
466
+ _skip_bytes(f, 8)
467
+
468
+ arraydesc['nbytes'] = _read_uint64(f)
469
+ arraydesc['nelements'] = _read_uint64(f)
470
+ arraydesc['ndims'] = _read_long(f)
471
+
472
+ _skip_bytes(f, 8)
473
+
474
+ arraydesc['nmax'] = 8
475
+
476
+ arraydesc['dims'] = []
477
+ for d in range(arraydesc['nmax']):
478
+ v = _read_long(f)
479
+ if v != 0:
480
+ raise Exception("Expected a zero in ARRAY_DESC")
481
+ arraydesc['dims'].append(_read_long(f))
482
+
483
+ else:
484
+ raise Exception(f"Unknown ARRSTART: {arraydesc['arrstart']}")
485
+
486
+ return arraydesc
487
+
488
+
489
+ def _read_structdesc(f):
490
+ '''Function to read in a structure descriptor'''
491
+
492
+ structdesc = {}
493
+
494
+ structstart = _read_long(f)
495
+ if structstart != 9:
496
+ raise Exception("STRUCTSTART should be 9")
497
+
498
+ structdesc['name'] = _read_string(f)
499
+ predef = _read_long(f)
500
+ structdesc['ntags'] = _read_long(f)
501
+ structdesc['nbytes'] = _read_long(f)
502
+
503
+ structdesc['predef'] = predef & 1
504
+ structdesc['inherits'] = predef & 2
505
+ structdesc['is_super'] = predef & 4
506
+
507
+ if not structdesc['predef']:
508
+
509
+ structdesc['tagtable'] = [_read_tagdesc(f)
510
+ for _ in range(structdesc['ntags'])]
511
+
512
+ for tag in structdesc['tagtable']:
513
+ tag['name'] = _read_string(f)
514
+
515
+ structdesc['arrtable'] = {tag['name']: _read_arraydesc(f)
516
+ for tag in structdesc['tagtable']
517
+ if tag['array']}
518
+
519
+ structdesc['structtable'] = {tag['name']: _read_structdesc(f)
520
+ for tag in structdesc['tagtable']
521
+ if tag['structure']}
522
+
523
+ if structdesc['inherits'] or structdesc['is_super']:
524
+ structdesc['classname'] = _read_string(f)
525
+ structdesc['nsupclasses'] = _read_long(f)
526
+ structdesc['supclassnames'] = [
527
+ _read_string(f) for _ in range(structdesc['nsupclasses'])]
528
+ structdesc['supclasstable'] = [
529
+ _read_structdesc(f) for _ in range(structdesc['nsupclasses'])]
530
+
531
+ STRUCT_DICT[structdesc['name']] = structdesc
532
+
533
+ else:
534
+
535
+ if structdesc['name'] not in STRUCT_DICT:
536
+ raise Exception("PREDEF=1 but can't find definition")
537
+
538
+ structdesc = STRUCT_DICT[structdesc['name']]
539
+
540
+ return structdesc
541
+
542
+
543
+ def _read_tagdesc(f):
544
+ '''Function to read in a tag descriptor'''
545
+
546
+ tagdesc = {'offset': _read_long(f)}
547
+
548
+ if tagdesc['offset'] == -1:
549
+ tagdesc['offset'] = _read_uint64(f)
550
+
551
+ tagdesc['typecode'] = _read_long(f)
552
+ tagflags = _read_long(f)
553
+
554
+ tagdesc['array'] = tagflags & 4 == 4
555
+ tagdesc['structure'] = tagflags & 32 == 32
556
+ tagdesc['scalar'] = tagdesc['typecode'] in DTYPE_DICT
557
+ # Assume '10'x is scalar
558
+
559
+ return tagdesc
560
+
561
+
562
+ def _replace_heap(variable, heap):
563
+
564
+ if isinstance(variable, Pointer):
565
+
566
+ while isinstance(variable, Pointer):
567
+
568
+ if variable.index == 0:
569
+ variable = None
570
+ else:
571
+ if variable.index in heap:
572
+ variable = heap[variable.index]
573
+ else:
574
+ warnings.warn("Variable referenced by pointer not found "
575
+ "in heap: variable will be set to None",
576
+ stacklevel=3)
577
+ variable = None
578
+
579
+ replace, new = _replace_heap(variable, heap)
580
+
581
+ if replace:
582
+ variable = new
583
+
584
+ return True, variable
585
+
586
+ elif isinstance(variable, np.rec.recarray):
587
+
588
+ # Loop over records
589
+ for ir, record in enumerate(variable):
590
+
591
+ replace, new = _replace_heap(record, heap)
592
+
593
+ if replace:
594
+ variable[ir] = new
595
+
596
+ return False, variable
597
+
598
+ elif isinstance(variable, np.record):
599
+
600
+ # Loop over values
601
+ for iv, value in enumerate(variable):
602
+
603
+ replace, new = _replace_heap(value, heap)
604
+
605
+ if replace:
606
+ variable[iv] = new
607
+
608
+ return False, variable
609
+
610
+ elif isinstance(variable, np.ndarray):
611
+
612
+ # Loop over values if type is np.object_
613
+ if variable.dtype.type is np.object_:
614
+
615
+ for iv in range(variable.size):
616
+
617
+ replace, new = _replace_heap(variable.item(iv), heap)
618
+
619
+ if replace:
620
+ variable.reshape(-1)[iv] = new
621
+
622
+ return False, variable
623
+
624
+ else:
625
+
626
+ return False, variable
627
+
628
+
629
+ class AttrDict(dict):
630
+ '''
631
+ A case-insensitive dictionary with access via item, attribute, and call
632
+ notations:
633
+
634
+ >>> from scipy.io._idl import AttrDict
635
+ >>> d = AttrDict()
636
+ >>> d['Variable'] = 123
637
+ >>> d['Variable']
638
+ 123
639
+ >>> d.Variable
640
+ 123
641
+ >>> d.variable
642
+ 123
643
+ >>> d('VARIABLE')
644
+ 123
645
+ >>> d['missing']
646
+ Traceback (most recent error last):
647
+ ...
648
+ KeyError: 'missing'
649
+ >>> d.missing
650
+ Traceback (most recent error last):
651
+ ...
652
+ AttributeError: 'AttrDict' object has no attribute 'missing'
653
+ '''
654
+
655
+ def __init__(self, init=None):
656
+ if init is None:
657
+ init = {}
658
+ dict.__init__(self, init)
659
+
660
+ def __getitem__(self, name):
661
+ return super().__getitem__(name.lower())
662
+
663
+ def __setitem__(self, key, value):
664
+ return super().__setitem__(key.lower(), value)
665
+
666
+ def __getattr__(self, name):
667
+ try:
668
+ return self.__getitem__(name)
669
+ except KeyError:
670
+ raise AttributeError(
671
+ f"'{type(self)}' object has no attribute '{name}'") from None
672
+
673
+ __setattr__ = __setitem__
674
+ __call__ = __getitem__
675
+
676
+
677
+ def readsav(file_name, idict=None, python_dict=False,
678
+ uncompressed_file_name=None, verbose=False):
679
+ """
680
+ Read an IDL .sav file.
681
+
682
+ Parameters
683
+ ----------
684
+ file_name : str
685
+ Name of the IDL save file.
686
+ idict : dict, optional
687
+ Dictionary in which to insert .sav file variables.
688
+ python_dict : bool, optional
689
+ By default, the object return is not a Python dictionary, but a
690
+ case-insensitive dictionary with item, attribute, and call access
691
+ to variables. To get a standard Python dictionary, set this option
692
+ to True.
693
+ uncompressed_file_name : str, optional
694
+ This option only has an effect for .sav files written with the
695
+ /compress option. If a file name is specified, compressed .sav
696
+ files are uncompressed to this file. Otherwise, readsav will use
697
+ the `tempfile` module to determine a temporary filename
698
+ automatically, and will remove the temporary file upon successfully
699
+ reading it in.
700
+ verbose : bool, optional
701
+ Whether to print out information about the save file, including
702
+ the records read, and available variables.
703
+
704
+ Returns
705
+ -------
706
+ idl_dict : AttrDict or dict
707
+ If `python_dict` is set to False (default), this function returns a
708
+ case-insensitive dictionary with item, attribute, and call access
709
+ to variables. If `python_dict` is set to True, this function
710
+ returns a Python dictionary with all variable names in lowercase.
711
+ If `idict` was specified, then variables are written to the
712
+ dictionary specified, and the updated dictionary is returned.
713
+
714
+ Examples
715
+ --------
716
+ >>> from os.path import dirname, join as pjoin
717
+ >>> import scipy.io as sio
718
+ >>> from scipy.io import readsav
719
+
720
+ Get the filename for an example .sav file from the tests/data directory.
721
+
722
+ >>> data_dir = pjoin(dirname(sio.__file__), 'tests', 'data')
723
+ >>> sav_fname = pjoin(data_dir, 'array_float32_1d.sav')
724
+
725
+ Load the .sav file contents.
726
+
727
+ >>> sav_data = readsav(sav_fname)
728
+
729
+ Get keys of the .sav file contents.
730
+
731
+ >>> print(sav_data.keys())
732
+ dict_keys(['array1d'])
733
+
734
+ Access a content with a key.
735
+
736
+ >>> print(sav_data['array1d'])
737
+ [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
738
+ 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
739
+ 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
740
+ 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
741
+ 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
742
+ 0. 0. 0.]
743
+
744
+ """
745
+
746
+ # Initialize record and variable holders
747
+ records = []
748
+ if python_dict or idict:
749
+ variables = {}
750
+ else:
751
+ variables = AttrDict()
752
+
753
+ # Open the IDL file
754
+ f = open(file_name, 'rb')
755
+
756
+ # Read the signature, which should be 'SR'
757
+ signature = _read_bytes(f, 2)
758
+ if signature != b'SR':
759
+ raise Exception(f"Invalid SIGNATURE: {signature}")
760
+
761
+ # Next, the record format, which is '\x00\x04' for normal .sav
762
+ # files, and '\x00\x06' for compressed .sav files.
763
+ recfmt = _read_bytes(f, 2)
764
+
765
+ if recfmt == b'\x00\x04':
766
+ pass
767
+
768
+ elif recfmt == b'\x00\x06':
769
+
770
+ if verbose:
771
+ print("IDL Save file is compressed")
772
+
773
+ if uncompressed_file_name:
774
+ fout = open(uncompressed_file_name, 'w+b')
775
+ else:
776
+ fout = tempfile.NamedTemporaryFile(suffix='.sav')
777
+
778
+ if verbose:
779
+ print(f" -> expanding to {fout.name}")
780
+
781
+ # Write header
782
+ fout.write(b'SR\x00\x04')
783
+
784
+ # Cycle through records
785
+ while True:
786
+
787
+ # Read record type
788
+ rectype = _read_long(f)
789
+ fout.write(struct.pack('>l', int(rectype)))
790
+
791
+ # Read position of next record and return as int
792
+ nextrec = _read_uint32(f)
793
+ nextrec += _read_uint32(f).astype(np.int64) * 2**32
794
+
795
+ # Read the unknown 4 bytes
796
+ unknown = f.read(4)
797
+
798
+ # Check if the end of the file has been reached
799
+ if RECTYPE_DICT[rectype] == 'END_MARKER':
800
+ modval = np.int64(2**32)
801
+ fout.write(struct.pack('>I', int(nextrec) % modval))
802
+ fout.write(
803
+ struct.pack('>I', int((nextrec - (nextrec % modval)) / modval))
804
+ )
805
+ fout.write(unknown)
806
+ break
807
+
808
+ # Find current position
809
+ pos = f.tell()
810
+
811
+ # Decompress record
812
+ rec_string = zlib.decompress(f.read(nextrec-pos))
813
+
814
+ # Find new position of next record
815
+ nextrec = fout.tell() + len(rec_string) + 12
816
+
817
+ # Write out record
818
+ fout.write(struct.pack('>I', int(nextrec % 2**32)))
819
+ fout.write(struct.pack('>I', int((nextrec - (nextrec % 2**32)) / 2**32)))
820
+ fout.write(unknown)
821
+ fout.write(rec_string)
822
+
823
+ # Close the original compressed file
824
+ f.close()
825
+
826
+ # Set f to be the decompressed file, and skip the first four bytes
827
+ f = fout
828
+ f.seek(4)
829
+
830
+ else:
831
+ raise Exception(f"Invalid RECFMT: {recfmt}")
832
+
833
+ # Loop through records, and add them to the list
834
+ while True:
835
+ r = _read_record(f)
836
+ records.append(r)
837
+ if 'end' in r:
838
+ if r['end']:
839
+ break
840
+
841
+ # Close the file
842
+ f.close()
843
+
844
+ # Find heap data variables
845
+ heap = {}
846
+ for r in records:
847
+ if r['rectype'] == "HEAP_DATA":
848
+ heap[r['heap_index']] = r['data']
849
+
850
+ # Find all variables
851
+ for r in records:
852
+ if r['rectype'] == "VARIABLE":
853
+ replace, new = _replace_heap(r['data'], heap)
854
+ if replace:
855
+ r['data'] = new
856
+ variables[r['varname'].lower()] = r['data']
857
+
858
+ if verbose:
859
+
860
+ # Print out timestamp info about the file
861
+ for record in records:
862
+ if record['rectype'] == "TIMESTAMP":
863
+ print("-"*50)
864
+ print(f"Date: {record['date']}")
865
+ print(f"User: {record['user']}")
866
+ print(f"Host: {record['host']}")
867
+ break
868
+
869
+ # Print out version info about the file
870
+ for record in records:
871
+ if record['rectype'] == "VERSION":
872
+ print("-"*50)
873
+ print(f"Format: {record['format']}")
874
+ print(f"Architecture: {record['arch']}")
875
+ print(f"Operating System: {record['os']}")
876
+ print(f"IDL Version: {record['release']}")
877
+ break
878
+
879
+ # Print out identification info about the file
880
+ for record in records:
881
+ if record['rectype'] == "IDENTIFICATON":
882
+ print("-"*50)
883
+ print(f"Author: {record['author']}")
884
+ print(f"Title: {record['title']}")
885
+ print(f"ID Code: {record['idcode']}")
886
+ break
887
+
888
+ # Print out descriptions saved with the file
889
+ for record in records:
890
+ if record['rectype'] == "DESCRIPTION":
891
+ print("-"*50)
892
+ print(f"Description: {record['description']}")
893
+ break
894
+
895
+ print("-"*50)
896
+ print(f"Successfully read {len(records)} records of which:")
897
+
898
+ # Create convenience list of record types
899
+ rectypes = [r['rectype'] for r in records]
900
+
901
+ for rt in set(rectypes):
902
+ if rt != 'END_MARKER':
903
+ print(f" - {rectypes.count(rt)} are of type {rt}")
904
+ print("-"*50)
905
+
906
+ if 'VARIABLE' in rectypes:
907
+ print("Available variables:")
908
+ for var in variables:
909
+ print(f" - {var} [{type(variables[var])}]")
910
+ print("-"*50)
911
+
912
+ if idict:
913
+ for var in variables:
914
+ idict[var] = variables[var]
915
+ return idict
916
+ else:
917
+ return variables
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/_mmio.py ADDED
@@ -0,0 +1,968 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """
2
+ Matrix Market I/O in Python.
3
+ See http://math.nist.gov/MatrixMarket/formats.html
4
+ for information about the Matrix Market format.
5
+ """
6
+ #
7
+ # Author: Pearu Peterson <pearu@cens.ioc.ee>
8
+ # Created: October, 2004
9
+ #
10
+ # References:
11
+ # http://math.nist.gov/MatrixMarket/
12
+ #
13
+ import os
14
+
15
+ import numpy as np
16
+ from numpy import (asarray, real, imag, conj, zeros, ndarray, concatenate,
17
+ ones, can_cast)
18
+
19
+ from scipy.sparse import coo_array, issparse, coo_matrix
20
+
21
+ __all__ = ['mminfo', 'mmread', 'mmwrite', 'MMFile']
22
+
23
+
24
+ # -----------------------------------------------------------------------------
25
+ def asstr(s):
26
+ if isinstance(s, bytes):
27
+ return s.decode('latin1')
28
+ return str(s)
29
+
30
+
31
+ def mminfo(source):
32
+ """
33
+ Return size and storage parameters from Matrix Market file-like 'source'.
34
+
35
+ Parameters
36
+ ----------
37
+ source : str or file-like
38
+ Matrix Market filename (extension .mtx) or open file-like object
39
+
40
+ Returns
41
+ -------
42
+ rows : int
43
+ Number of matrix rows.
44
+ cols : int
45
+ Number of matrix columns.
46
+ entries : int
47
+ Number of non-zero entries of a sparse matrix
48
+ or rows*cols for a dense matrix.
49
+ format : str
50
+ Either 'coordinate' or 'array'.
51
+ field : str
52
+ Either 'real', 'complex', 'pattern', or 'integer'.
53
+ symmetry : str
54
+ Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
55
+
56
+ Examples
57
+ --------
58
+ >>> from io import StringIO
59
+ >>> from scipy.io import mminfo
60
+
61
+ >>> text = '''%%MatrixMarket matrix coordinate real general
62
+ ... 5 5 7
63
+ ... 2 3 1.0
64
+ ... 3 4 2.0
65
+ ... 3 5 3.0
66
+ ... 4 1 4.0
67
+ ... 4 2 5.0
68
+ ... 4 3 6.0
69
+ ... 4 4 7.0
70
+ ... '''
71
+
72
+
73
+ ``mminfo(source)`` returns the number of rows, number of columns,
74
+ format, field type and symmetry attribute of the source file.
75
+
76
+ >>> mminfo(StringIO(text))
77
+ (5, 5, 7, 'coordinate', 'real', 'general')
78
+ """
79
+ return MMFile.info(source)
80
+
81
+ # -----------------------------------------------------------------------------
82
+
83
+
84
+ def mmread(source, *, spmatrix=True):
85
+ """
86
+ Reads the contents of a Matrix Market file-like 'source' into a matrix.
87
+
88
+ Parameters
89
+ ----------
90
+ source : str or file-like
91
+ Matrix Market filename (extensions .mtx, .mtz.gz)
92
+ or open file-like object.
93
+ spmatrix : bool, optional (default: True)
94
+ If ``True``, return sparse matrix. Otherwise return sparse array.
95
+
96
+ Returns
97
+ -------
98
+ a : ndarray or coo_array or coo_matrix
99
+ Dense or sparse array depending on the matrix format in the
100
+ Matrix Market file.
101
+
102
+ Examples
103
+ --------
104
+ >>> from io import StringIO
105
+ >>> from scipy.io import mmread
106
+
107
+ >>> text = '''%%MatrixMarket matrix coordinate real general
108
+ ... 5 5 7
109
+ ... 2 3 1.0
110
+ ... 3 4 2.0
111
+ ... 3 5 3.0
112
+ ... 4 1 4.0
113
+ ... 4 2 5.0
114
+ ... 4 3 6.0
115
+ ... 4 4 7.0
116
+ ... '''
117
+
118
+ ``mmread(source)`` returns the data as sparse matrix in COO format.
119
+
120
+ >>> m = mmread(StringIO(text), spmatrix=False)
121
+ >>> m
122
+ <COOrdinate sparse array of dtype 'float64'
123
+ with 7 stored elements and shape (5, 5)>
124
+ >>> m.toarray()
125
+ array([[0., 0., 0., 0., 0.],
126
+ [0., 0., 1., 0., 0.],
127
+ [0., 0., 0., 2., 3.],
128
+ [4., 5., 6., 7., 0.],
129
+ [0., 0., 0., 0., 0.]])
130
+ """
131
+ return MMFile().read(source, spmatrix=spmatrix)
132
+
133
+ # -----------------------------------------------------------------------------
134
+
135
+
136
+ def mmwrite(target, a, comment='', field=None, precision=None, symmetry=None):
137
+ r"""
138
+ Writes the sparse or dense array `a` to Matrix Market file-like `target`.
139
+
140
+ Parameters
141
+ ----------
142
+ target : str or file-like
143
+ Matrix Market filename (extension .mtx) or open file-like object.
144
+ a : array like
145
+ Sparse or dense 2-D array.
146
+ comment : str, optional
147
+ Comments to be prepended to the Matrix Market file.
148
+ field : None or str, optional
149
+ Either 'real', 'complex', 'pattern', or 'integer'.
150
+ precision : None or int, optional
151
+ Number of digits to display for real or complex values.
152
+ symmetry : None or str, optional
153
+ Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
154
+ If symmetry is None the symmetry type of 'a' is determined by its
155
+ values.
156
+
157
+ Returns
158
+ -------
159
+ None
160
+
161
+ Examples
162
+ --------
163
+ >>> from io import BytesIO
164
+ >>> import numpy as np
165
+ >>> from scipy.sparse import coo_array
166
+ >>> from scipy.io import mmwrite
167
+
168
+ Write a small NumPy array to a matrix market file. The file will be
169
+ written in the ``'array'`` format.
170
+
171
+ >>> a = np.array([[1.0, 0, 0, 0], [0, 2.5, 0, 6.25]])
172
+ >>> target = BytesIO()
173
+ >>> mmwrite(target, a)
174
+ >>> print(target.getvalue().decode('latin1'))
175
+ %%MatrixMarket matrix array real general
176
+ %
177
+ 2 4
178
+ 1
179
+ 0
180
+ 0
181
+ 2.5
182
+ 0
183
+ 0
184
+ 0
185
+ 6.25
186
+
187
+ Add a comment to the output file, and set the precision to 3.
188
+
189
+ >>> target = BytesIO()
190
+ >>> mmwrite(target, a, comment='\n Some test data.\n', precision=3)
191
+ >>> print(target.getvalue().decode('latin1'))
192
+ %%MatrixMarket matrix array real general
193
+ %
194
+ % Some test data.
195
+ %
196
+ 2 4
197
+ 1.00e+00
198
+ 0.00e+00
199
+ 0.00e+00
200
+ 2.50e+00
201
+ 0.00e+00
202
+ 0.00e+00
203
+ 0.00e+00
204
+ 6.25e+00
205
+
206
+ Convert to a sparse matrix before calling ``mmwrite``. This will
207
+ result in the output format being ``'coordinate'`` rather than
208
+ ``'array'``.
209
+
210
+ >>> target = BytesIO()
211
+ >>> mmwrite(target, coo_array(a), precision=3)
212
+ >>> print(target.getvalue().decode('latin1'))
213
+ %%MatrixMarket matrix coordinate real general
214
+ %
215
+ 2 4 3
216
+ 1 1 1.00e+00
217
+ 2 2 2.50e+00
218
+ 2 4 6.25e+00
219
+
220
+ Write a complex Hermitian array to a matrix market file. Note that
221
+ only six values are actually written to the file; the other values
222
+ are implied by the symmetry.
223
+
224
+ >>> z = np.array([[3, 1+2j, 4-3j], [1-2j, 1, -5j], [4+3j, 5j, 2.5]])
225
+ >>> z
226
+ array([[ 3. +0.j, 1. +2.j, 4. -3.j],
227
+ [ 1. -2.j, 1. +0.j, -0. -5.j],
228
+ [ 4. +3.j, 0. +5.j, 2.5+0.j]])
229
+
230
+ >>> target = BytesIO()
231
+ >>> mmwrite(target, z, precision=2)
232
+ >>> print(target.getvalue().decode('latin1'))
233
+ %%MatrixMarket matrix array complex hermitian
234
+ %
235
+ 3 3
236
+ 3.0e+00 0.0e+00
237
+ 1.0e+00 -2.0e+00
238
+ 4.0e+00 3.0e+00
239
+ 1.0e+00 0.0e+00
240
+ 0.0e+00 5.0e+00
241
+ 2.5e+00 0.0e+00
242
+
243
+ """
244
+ MMFile().write(target, a, comment, field, precision, symmetry)
245
+
246
+
247
+ ###############################################################################
248
+ class MMFile:
249
+ __slots__ = ('_rows',
250
+ '_cols',
251
+ '_entries',
252
+ '_format',
253
+ '_field',
254
+ '_symmetry')
255
+
256
+ @property
257
+ def rows(self):
258
+ return self._rows
259
+
260
+ @property
261
+ def cols(self):
262
+ return self._cols
263
+
264
+ @property
265
+ def entries(self):
266
+ return self._entries
267
+
268
+ @property
269
+ def format(self):
270
+ return self._format
271
+
272
+ @property
273
+ def field(self):
274
+ return self._field
275
+
276
+ @property
277
+ def symmetry(self):
278
+ return self._symmetry
279
+
280
+ @property
281
+ def has_symmetry(self):
282
+ return self._symmetry in (self.SYMMETRY_SYMMETRIC,
283
+ self.SYMMETRY_SKEW_SYMMETRIC,
284
+ self.SYMMETRY_HERMITIAN)
285
+
286
+ # format values
287
+ FORMAT_COORDINATE = 'coordinate'
288
+ FORMAT_ARRAY = 'array'
289
+ FORMAT_VALUES = (FORMAT_COORDINATE, FORMAT_ARRAY)
290
+
291
+ @classmethod
292
+ def _validate_format(self, format):
293
+ if format not in self.FORMAT_VALUES:
294
+ msg = f'unknown format type {format}, must be one of {self.FORMAT_VALUES}'
295
+ raise ValueError(msg)
296
+
297
+ # field values
298
+ FIELD_INTEGER = 'integer'
299
+ FIELD_UNSIGNED = 'unsigned-integer'
300
+ FIELD_REAL = 'real'
301
+ FIELD_COMPLEX = 'complex'
302
+ FIELD_PATTERN = 'pattern'
303
+ FIELD_VALUES = (FIELD_INTEGER, FIELD_UNSIGNED, FIELD_REAL, FIELD_COMPLEX,
304
+ FIELD_PATTERN)
305
+
306
+ @classmethod
307
+ def _validate_field(self, field):
308
+ if field not in self.FIELD_VALUES:
309
+ msg = f'unknown field type {field}, must be one of {self.FIELD_VALUES}'
310
+ raise ValueError(msg)
311
+
312
+ # symmetry values
313
+ SYMMETRY_GENERAL = 'general'
314
+ SYMMETRY_SYMMETRIC = 'symmetric'
315
+ SYMMETRY_SKEW_SYMMETRIC = 'skew-symmetric'
316
+ SYMMETRY_HERMITIAN = 'hermitian'
317
+ SYMMETRY_VALUES = (SYMMETRY_GENERAL, SYMMETRY_SYMMETRIC,
318
+ SYMMETRY_SKEW_SYMMETRIC, SYMMETRY_HERMITIAN)
319
+
320
+ @classmethod
321
+ def _validate_symmetry(self, symmetry):
322
+ if symmetry not in self.SYMMETRY_VALUES:
323
+ raise ValueError(f'unknown symmetry type {symmetry}, '
324
+ f'must be one of {self.SYMMETRY_VALUES}')
325
+
326
+ DTYPES_BY_FIELD = {FIELD_INTEGER: 'intp',
327
+ FIELD_UNSIGNED: 'uint64',
328
+ FIELD_REAL: 'd',
329
+ FIELD_COMPLEX: 'D',
330
+ FIELD_PATTERN: 'd'}
331
+
332
+ # -------------------------------------------------------------------------
333
+ @staticmethod
334
+ def reader():
335
+ pass
336
+
337
+ # -------------------------------------------------------------------------
338
+ @staticmethod
339
+ def writer():
340
+ pass
341
+
342
+ # -------------------------------------------------------------------------
343
+ @classmethod
344
+ def info(self, source):
345
+ """
346
+ Return size, storage parameters from Matrix Market file-like 'source'.
347
+
348
+ Parameters
349
+ ----------
350
+ source : str or file-like
351
+ Matrix Market filename (extension .mtx) or open file-like object
352
+
353
+ Returns
354
+ -------
355
+ rows : int
356
+ Number of matrix rows.
357
+ cols : int
358
+ Number of matrix columns.
359
+ entries : int
360
+ Number of non-zero entries of a sparse matrix
361
+ or rows*cols for a dense matrix.
362
+ format : str
363
+ Either 'coordinate' or 'array'.
364
+ field : str
365
+ Either 'real', 'complex', 'pattern', or 'integer'.
366
+ symmetry : str
367
+ Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
368
+ """
369
+
370
+ stream, close_it = self._open(source)
371
+
372
+ try:
373
+
374
+ # read and validate header line
375
+ line = stream.readline()
376
+ mmid, matrix, format, field, symmetry = \
377
+ (asstr(part.strip()) for part in line.split())
378
+ if not mmid.startswith('%%MatrixMarket'):
379
+ raise ValueError('source is not in Matrix Market format')
380
+ if not matrix.lower() == 'matrix':
381
+ raise ValueError("Problem reading file header: " + line)
382
+
383
+ # http://math.nist.gov/MatrixMarket/formats.html
384
+ if format.lower() == 'array':
385
+ format = self.FORMAT_ARRAY
386
+ elif format.lower() == 'coordinate':
387
+ format = self.FORMAT_COORDINATE
388
+
389
+ # skip comments
390
+ # line.startswith('%')
391
+ while line:
392
+ if line.lstrip() and line.lstrip()[0] in ['%', 37]:
393
+ line = stream.readline()
394
+ else:
395
+ break
396
+
397
+ # skip empty lines
398
+ while not line.strip():
399
+ line = stream.readline()
400
+
401
+ split_line = line.split()
402
+ if format == self.FORMAT_ARRAY:
403
+ if not len(split_line) == 2:
404
+ raise ValueError("Header line not of length 2: " +
405
+ line.decode('ascii'))
406
+ rows, cols = map(int, split_line)
407
+ entries = rows * cols
408
+ else:
409
+ if not len(split_line) == 3:
410
+ raise ValueError("Header line not of length 3: " +
411
+ line.decode('ascii'))
412
+ rows, cols, entries = map(int, split_line)
413
+
414
+ return (rows, cols, entries, format, field.lower(),
415
+ symmetry.lower())
416
+
417
+ finally:
418
+ if close_it:
419
+ stream.close()
420
+
421
+ # -------------------------------------------------------------------------
422
+ @staticmethod
423
+ def _open(filespec, mode='rb'):
424
+ """ Return an open file stream for reading based on source.
425
+
426
+ If source is a file name, open it (after trying to find it with mtx and
427
+ gzipped mtx extensions). Otherwise, just return source.
428
+
429
+ Parameters
430
+ ----------
431
+ filespec : str or file-like
432
+ String giving file name or file-like object
433
+ mode : str, optional
434
+ Mode with which to open file, if `filespec` is a file name.
435
+
436
+ Returns
437
+ -------
438
+ fobj : file-like
439
+ Open file-like object.
440
+ close_it : bool
441
+ True if the calling function should close this file when done,
442
+ false otherwise.
443
+ """
444
+ # If 'filespec' is path-like (str, pathlib.Path, os.DirEntry, other class
445
+ # implementing a '__fspath__' method), try to convert it to str. If this
446
+ # fails by throwing a 'TypeError', assume it's an open file handle and
447
+ # return it as-is.
448
+ try:
449
+ filespec = os.fspath(filespec)
450
+ except TypeError:
451
+ return filespec, False
452
+
453
+ # 'filespec' is definitely a str now
454
+
455
+ # open for reading
456
+ if mode[0] == 'r':
457
+
458
+ # determine filename plus extension
459
+ if not os.path.isfile(filespec):
460
+ if os.path.isfile(filespec+'.mtx'):
461
+ filespec = filespec + '.mtx'
462
+ elif os.path.isfile(filespec+'.mtx.gz'):
463
+ filespec = filespec + '.mtx.gz'
464
+ elif os.path.isfile(filespec+'.mtx.bz2'):
465
+ filespec = filespec + '.mtx.bz2'
466
+ # open filename
467
+ if filespec.endswith('.gz'):
468
+ import gzip
469
+ stream = gzip.open(filespec, mode)
470
+ elif filespec.endswith('.bz2'):
471
+ import bz2
472
+ stream = bz2.BZ2File(filespec, 'rb')
473
+ else:
474
+ stream = open(filespec, mode)
475
+
476
+ # open for writing
477
+ else:
478
+ if filespec[-4:] != '.mtx':
479
+ filespec = filespec + '.mtx'
480
+ stream = open(filespec, mode)
481
+
482
+ return stream, True
483
+
484
+ # -------------------------------------------------------------------------
485
+ @staticmethod
486
+ def _get_symmetry(a):
487
+ m, n = a.shape
488
+ if m != n:
489
+ return MMFile.SYMMETRY_GENERAL
490
+ issymm = True
491
+ isskew = True
492
+ isherm = a.dtype.char in 'FD'
493
+
494
+ # sparse input
495
+ if issparse(a):
496
+ # check if number of nonzero entries of lower and upper triangle
497
+ # matrix are equal
498
+ a = a.tocoo()
499
+ (row, col) = a.nonzero()
500
+ if (row < col).sum() != (row > col).sum():
501
+ return MMFile.SYMMETRY_GENERAL
502
+
503
+ # define iterator over symmetric pair entries
504
+ a = a.todok()
505
+
506
+ def symm_iterator():
507
+ for ((i, j), aij) in a.items():
508
+ if i > j:
509
+ aji = a[j, i]
510
+ yield (aij, aji, False)
511
+ elif i == j:
512
+ yield (aij, aij, True)
513
+
514
+ # non-sparse input
515
+ else:
516
+ # define iterator over symmetric pair entries
517
+ def symm_iterator():
518
+ for j in range(n):
519
+ for i in range(j, n):
520
+ aij, aji = a[i][j], a[j][i]
521
+ yield (aij, aji, i == j)
522
+
523
+ # check for symmetry
524
+ # yields aij, aji, is_diagonal
525
+ for (aij, aji, is_diagonal) in symm_iterator():
526
+ if isskew and is_diagonal and aij != 0:
527
+ isskew = False
528
+ else:
529
+ if issymm and aij != aji:
530
+ issymm = False
531
+ with np.errstate(over="ignore"):
532
+ # This can give a warning for uint dtypes, so silence that
533
+ if isskew and aij != -aji:
534
+ isskew = False
535
+ if isherm and aij != conj(aji):
536
+ isherm = False
537
+ if not (issymm or isskew or isherm):
538
+ break
539
+
540
+ # return symmetry value
541
+ if issymm:
542
+ return MMFile.SYMMETRY_SYMMETRIC
543
+ if isskew:
544
+ return MMFile.SYMMETRY_SKEW_SYMMETRIC
545
+ if isherm:
546
+ return MMFile.SYMMETRY_HERMITIAN
547
+ return MMFile.SYMMETRY_GENERAL
548
+
549
+ # -------------------------------------------------------------------------
550
+ @staticmethod
551
+ def _field_template(field, precision):
552
+ return {MMFile.FIELD_REAL: '%%.%ie\n' % precision,
553
+ MMFile.FIELD_INTEGER: '%i\n',
554
+ MMFile.FIELD_UNSIGNED: '%u\n',
555
+ MMFile.FIELD_COMPLEX: '%%.%ie %%.%ie\n' %
556
+ (precision, precision)
557
+ }.get(field, None)
558
+
559
+ # -------------------------------------------------------------------------
560
+ def __init__(self, **kwargs):
561
+ self._init_attrs(**kwargs)
562
+
563
+ # -------------------------------------------------------------------------
564
+ def read(self, source, *, spmatrix=True):
565
+ """
566
+ Reads the contents of a Matrix Market file-like 'source' into a matrix.
567
+
568
+ Parameters
569
+ ----------
570
+ source : str or file-like
571
+ Matrix Market filename (extensions .mtx, .mtz.gz)
572
+ or open file object.
573
+ spmatrix : bool, optional (default: True)
574
+ If ``True``, return sparse matrix. Otherwise return sparse array.
575
+
576
+ Returns
577
+ -------
578
+ a : ndarray or coo_array or coo_matrix
579
+ Dense or sparse array depending on the matrix format in the
580
+ Matrix Market file.
581
+ """
582
+ stream, close_it = self._open(source)
583
+
584
+ try:
585
+ self._parse_header(stream)
586
+ data = self._parse_body(stream)
587
+
588
+ finally:
589
+ if close_it:
590
+ stream.close()
591
+ if spmatrix and isinstance(data, coo_array):
592
+ data = coo_matrix(data)
593
+ return data
594
+
595
+
596
+ # -------------------------------------------------------------------------
597
+ def write(self, target, a, comment='', field=None, precision=None,
598
+ symmetry=None):
599
+ """
600
+ Writes sparse or dense array `a` to Matrix Market file-like `target`.
601
+
602
+ Parameters
603
+ ----------
604
+ target : str or file-like
605
+ Matrix Market filename (extension .mtx) or open file-like object.
606
+ a : array like
607
+ Sparse or dense 2-D array.
608
+ comment : str, optional
609
+ Comments to be prepended to the Matrix Market file.
610
+ field : None or str, optional
611
+ Either 'real', 'complex', 'pattern', or 'integer'.
612
+ precision : None or int, optional
613
+ Number of digits to display for real or complex values.
614
+ symmetry : None or str, optional
615
+ Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
616
+ If symmetry is None the symmetry type of 'a' is determined by its
617
+ values.
618
+ """
619
+
620
+ stream, close_it = self._open(target, 'wb')
621
+
622
+ try:
623
+ self._write(stream, a, comment, field, precision, symmetry)
624
+
625
+ finally:
626
+ if close_it:
627
+ stream.close()
628
+ else:
629
+ stream.flush()
630
+
631
+ # -------------------------------------------------------------------------
632
+ def _init_attrs(self, **kwargs):
633
+ """
634
+ Initialize each attributes with the corresponding keyword arg value
635
+ or a default of None
636
+ """
637
+
638
+ attrs = self.__class__.__slots__
639
+ public_attrs = [attr[1:] for attr in attrs]
640
+ invalid_keys = set(kwargs.keys()) - set(public_attrs)
641
+
642
+ if invalid_keys:
643
+ raise ValueError(f"found {tuple(invalid_keys)} invalid keyword "
644
+ f"arguments, please only use {public_attrs}")
645
+
646
+ for attr in attrs:
647
+ setattr(self, attr, kwargs.get(attr[1:], None))
648
+
649
+ # -------------------------------------------------------------------------
650
+ def _parse_header(self, stream):
651
+ rows, cols, entries, format, field, symmetry = \
652
+ self.__class__.info(stream)
653
+ self._init_attrs(rows=rows, cols=cols, entries=entries, format=format,
654
+ field=field, symmetry=symmetry)
655
+
656
+ # -------------------------------------------------------------------------
657
+ def _parse_body(self, stream):
658
+ rows, cols, entries, format, field, symm = (self.rows, self.cols,
659
+ self.entries, self.format,
660
+ self.field, self.symmetry)
661
+
662
+ dtype = self.DTYPES_BY_FIELD.get(field, None)
663
+
664
+ has_symmetry = self.has_symmetry
665
+ is_integer = field == self.FIELD_INTEGER
666
+ is_unsigned_integer = field == self.FIELD_UNSIGNED
667
+ is_complex = field == self.FIELD_COMPLEX
668
+ is_skew = symm == self.SYMMETRY_SKEW_SYMMETRIC
669
+ is_herm = symm == self.SYMMETRY_HERMITIAN
670
+ is_pattern = field == self.FIELD_PATTERN
671
+
672
+ if format == self.FORMAT_ARRAY:
673
+ a = zeros((rows, cols), dtype=dtype)
674
+ line = 1
675
+ i, j = 0, 0
676
+ if is_skew:
677
+ a[i, j] = 0
678
+ if i < rows - 1:
679
+ i += 1
680
+ while line:
681
+ line = stream.readline()
682
+ # line.startswith('%')
683
+ if not line or line[0] in ['%', 37] or not line.strip():
684
+ continue
685
+ if is_integer:
686
+ aij = int(line)
687
+ elif is_unsigned_integer:
688
+ aij = int(line)
689
+ elif is_complex:
690
+ aij = complex(*map(float, line.split()))
691
+ else:
692
+ aij = float(line)
693
+ a[i, j] = aij
694
+ if has_symmetry and i != j:
695
+ if is_skew:
696
+ a[j, i] = -aij
697
+ elif is_herm:
698
+ a[j, i] = conj(aij)
699
+ else:
700
+ a[j, i] = aij
701
+ if i < rows-1:
702
+ i = i + 1
703
+ else:
704
+ j = j + 1
705
+ if not has_symmetry:
706
+ i = 0
707
+ else:
708
+ i = j
709
+ if is_skew:
710
+ a[i, j] = 0
711
+ if i < rows-1:
712
+ i += 1
713
+
714
+ if is_skew:
715
+ if not (i in [0, j] and j == cols - 1):
716
+ raise ValueError("Parse error, did not read all lines.")
717
+ else:
718
+ if not (i in [0, j] and j == cols):
719
+ raise ValueError("Parse error, did not read all lines.")
720
+
721
+ elif format == self.FORMAT_COORDINATE:
722
+ # Read sparse COOrdinate format
723
+
724
+ if entries == 0:
725
+ # empty matrix
726
+ return coo_array((rows, cols), dtype=dtype)
727
+
728
+ I = zeros(entries, dtype='intc')
729
+ J = zeros(entries, dtype='intc')
730
+ if is_pattern:
731
+ V = ones(entries, dtype='int8')
732
+ elif is_integer:
733
+ V = zeros(entries, dtype='intp')
734
+ elif is_unsigned_integer:
735
+ V = zeros(entries, dtype='uint64')
736
+ elif is_complex:
737
+ V = zeros(entries, dtype='complex')
738
+ else:
739
+ V = zeros(entries, dtype='float')
740
+
741
+ entry_number = 0
742
+ for line in stream:
743
+ # line.startswith('%')
744
+ if not line or line[0] in ['%', 37] or not line.strip():
745
+ continue
746
+
747
+ if entry_number+1 > entries:
748
+ raise ValueError("'entries' in header is smaller than "
749
+ "number of entries")
750
+ l = line.split()
751
+ I[entry_number], J[entry_number] = map(int, l[:2])
752
+
753
+ if not is_pattern:
754
+ if is_integer:
755
+ V[entry_number] = int(l[2])
756
+ elif is_unsigned_integer:
757
+ V[entry_number] = int(l[2])
758
+ elif is_complex:
759
+ V[entry_number] = complex(*map(float, l[2:]))
760
+ else:
761
+ V[entry_number] = float(l[2])
762
+ entry_number += 1
763
+ if entry_number < entries:
764
+ raise ValueError("'entries' in header is larger than "
765
+ "number of entries")
766
+
767
+ I -= 1 # adjust indices (base 1 -> base 0)
768
+ J -= 1
769
+
770
+ if has_symmetry:
771
+ mask = (I != J) # off diagonal mask
772
+ od_I = I[mask]
773
+ od_J = J[mask]
774
+ od_V = V[mask]
775
+
776
+ I = concatenate((I, od_J))
777
+ J = concatenate((J, od_I))
778
+
779
+ if is_skew:
780
+ od_V *= -1
781
+ elif is_herm:
782
+ od_V = od_V.conjugate()
783
+
784
+ V = concatenate((V, od_V))
785
+
786
+ a = coo_array((V, (I, J)), shape=(rows, cols), dtype=dtype)
787
+ else:
788
+ raise NotImplementedError(format)
789
+
790
+ return a
791
+
792
+ # ------------------------------------------------------------------------
793
+ def _write(self, stream, a, comment='', field=None, precision=None,
794
+ symmetry=None):
795
+ if isinstance(a, list) or isinstance(a, ndarray) or \
796
+ isinstance(a, tuple) or hasattr(a, '__array__'):
797
+ rep = self.FORMAT_ARRAY
798
+ a = asarray(a)
799
+ if len(a.shape) != 2:
800
+ raise ValueError('Expected 2 dimensional array')
801
+ rows, cols = a.shape
802
+
803
+ if field is not None:
804
+
805
+ if field == self.FIELD_INTEGER:
806
+ if not can_cast(a.dtype, 'intp'):
807
+ raise OverflowError("mmwrite does not support integer "
808
+ "dtypes larger than native 'intp'.")
809
+ a = a.astype('intp')
810
+ elif field == self.FIELD_REAL:
811
+ if a.dtype.char not in 'fd':
812
+ a = a.astype('d')
813
+ elif field == self.FIELD_COMPLEX:
814
+ if a.dtype.char not in 'FD':
815
+ a = a.astype('D')
816
+
817
+ else:
818
+ if not issparse(a):
819
+ raise ValueError(f'unknown matrix type: {type(a)}')
820
+
821
+ rep = 'coordinate'
822
+ rows, cols = a.shape
823
+
824
+ typecode = a.dtype.char
825
+
826
+ if precision is None:
827
+ if typecode in 'fF':
828
+ precision = 8
829
+ else:
830
+ precision = 16
831
+ if field is None:
832
+ kind = a.dtype.kind
833
+ if kind == 'i':
834
+ if not can_cast(a.dtype, 'intp'):
835
+ raise OverflowError("mmwrite does not support integer "
836
+ "dtypes larger than native 'intp'.")
837
+ field = 'integer'
838
+ elif kind == 'f':
839
+ field = 'real'
840
+ elif kind == 'c':
841
+ field = 'complex'
842
+ elif kind == 'u':
843
+ field = 'unsigned-integer'
844
+ else:
845
+ raise TypeError('unexpected dtype kind ' + kind)
846
+
847
+ if symmetry is None:
848
+ symmetry = self._get_symmetry(a)
849
+
850
+ # validate rep, field, and symmetry
851
+ self.__class__._validate_format(rep)
852
+ self.__class__._validate_field(field)
853
+ self.__class__._validate_symmetry(symmetry)
854
+
855
+ # write initial header line
856
+ data = f'%%MatrixMarket matrix {rep} {field} {symmetry}\n'
857
+ stream.write(data.encode('latin1'))
858
+
859
+ # write comments
860
+ for line in comment.split('\n'):
861
+ data = f'%{line}\n'
862
+ stream.write(data.encode('latin1'))
863
+
864
+ template = self._field_template(field, precision)
865
+ # write dense format
866
+ if rep == self.FORMAT_ARRAY:
867
+ # write shape spec
868
+ data = '%i %i\n' % (rows, cols)
869
+ stream.write(data.encode('latin1'))
870
+
871
+ if field in (self.FIELD_INTEGER, self.FIELD_REAL,
872
+ self.FIELD_UNSIGNED):
873
+ if symmetry == self.SYMMETRY_GENERAL:
874
+ for j in range(cols):
875
+ for i in range(rows):
876
+ data = template % a[i, j]
877
+ stream.write(data.encode('latin1'))
878
+
879
+ elif symmetry == self.SYMMETRY_SKEW_SYMMETRIC:
880
+ for j in range(cols):
881
+ for i in range(j + 1, rows):
882
+ data = template % a[i, j]
883
+ stream.write(data.encode('latin1'))
884
+
885
+ else:
886
+ for j in range(cols):
887
+ for i in range(j, rows):
888
+ data = template % a[i, j]
889
+ stream.write(data.encode('latin1'))
890
+
891
+ elif field == self.FIELD_COMPLEX:
892
+
893
+ if symmetry == self.SYMMETRY_GENERAL:
894
+ for j in range(cols):
895
+ for i in range(rows):
896
+ aij = a[i, j]
897
+ data = template % (real(aij), imag(aij))
898
+ stream.write(data.encode('latin1'))
899
+ else:
900
+ for j in range(cols):
901
+ for i in range(j, rows):
902
+ aij = a[i, j]
903
+ data = template % (real(aij), imag(aij))
904
+ stream.write(data.encode('latin1'))
905
+
906
+ elif field == self.FIELD_PATTERN:
907
+ raise ValueError('pattern type inconsisted with dense format')
908
+
909
+ else:
910
+ raise TypeError(f'Unknown field type {field}')
911
+
912
+ # write sparse format
913
+ else:
914
+ coo = a.tocoo() # convert to COOrdinate format
915
+
916
+ # if symmetry format used, remove values above main diagonal
917
+ if symmetry != self.SYMMETRY_GENERAL:
918
+ lower_triangle_mask = coo.row >= coo.col
919
+ coo = coo_array((coo.data[lower_triangle_mask],
920
+ (coo.row[lower_triangle_mask],
921
+ coo.col[lower_triangle_mask])),
922
+ shape=coo.shape)
923
+
924
+ # write shape spec
925
+ data = '%i %i %i\n' % (rows, cols, coo.nnz)
926
+ stream.write(data.encode('latin1'))
927
+
928
+ template = self._field_template(field, precision-1)
929
+
930
+ if field == self.FIELD_PATTERN:
931
+ for r, c in zip(coo.row+1, coo.col+1):
932
+ data = "%i %i\n" % (r, c)
933
+ stream.write(data.encode('latin1'))
934
+ elif field in (self.FIELD_INTEGER, self.FIELD_REAL,
935
+ self.FIELD_UNSIGNED):
936
+ for r, c, d in zip(coo.row+1, coo.col+1, coo.data):
937
+ data = ("%i %i " % (r, c)) + (template % d)
938
+ stream.write(data.encode('latin1'))
939
+ elif field == self.FIELD_COMPLEX:
940
+ for r, c, d in zip(coo.row+1, coo.col+1, coo.data):
941
+ data = ("%i %i " % (r, c)) + (template % (d.real, d.imag))
942
+ stream.write(data.encode('latin1'))
943
+ else:
944
+ raise TypeError(f'Unknown field type {field}')
945
+
946
+
947
+ def _is_fromfile_compatible(stream):
948
+ """
949
+ Check whether `stream` is compatible with numpy.fromfile.
950
+
951
+ Passing a gzipped file object to ``fromfile/fromstring`` doesn't work with
952
+ Python 3.
953
+ """
954
+
955
+ bad_cls = []
956
+ try:
957
+ import gzip
958
+ bad_cls.append(gzip.GzipFile)
959
+ except ImportError:
960
+ pass
961
+ try:
962
+ import bz2
963
+ bad_cls.append(bz2.BZ2File)
964
+ except ImportError:
965
+ pass
966
+
967
+ bad_cls = tuple(bad_cls)
968
+ return not isinstance(stream, bad_cls)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/_netcdf.py ADDED
@@ -0,0 +1,1104 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """
2
+ NetCDF reader/writer module.
3
+
4
+ This module is used to read and create NetCDF files. NetCDF files are
5
+ accessed through the `netcdf_file` object. Data written to and from NetCDF
6
+ files are contained in `netcdf_variable` objects. Attributes are given
7
+ as member variables of the `netcdf_file` and `netcdf_variable` objects.
8
+
9
+ This module implements the Scientific.IO.NetCDF API to read and create
10
+ NetCDF files. The same API is also used in the PyNIO and pynetcdf
11
+ modules, allowing these modules to be used interchangeably when working
12
+ with NetCDF files.
13
+
14
+ Only NetCDF3 is supported here; for NetCDF4 see
15
+ `netCDF4-python <http://unidata.github.io/netcdf4-python/>`__,
16
+ which has a similar API.
17
+
18
+ """
19
+
20
+ # TODO:
21
+ # * properly implement ``_FillValue``.
22
+ # * fix character variables.
23
+ # * implement PAGESIZE for Python 2.6?
24
+
25
+ # The Scientific.IO.NetCDF API allows attributes to be added directly to
26
+ # instances of ``netcdf_file`` and ``netcdf_variable``. To differentiate
27
+ # between user-set attributes and instance attributes, user-set attributes
28
+ # are automatically stored in the ``_attributes`` attribute by overloading
29
+ #``__setattr__``. This is the reason why the code sometimes uses
30
+ #``obj.__dict__['key'] = value``, instead of simply ``obj.key = value``;
31
+ # otherwise the key would be inserted into userspace attributes.
32
+
33
+
34
+ __all__ = ['netcdf_file', 'netcdf_variable']
35
+
36
+
37
+ import warnings
38
+ import weakref
39
+ from operator import mul
40
+ from platform import python_implementation
41
+
42
+ import mmap as mm
43
+
44
+ import numpy as np
45
+ from numpy import frombuffer, dtype, empty, array, asarray
46
+ from numpy import little_endian as LITTLE_ENDIAN
47
+ from functools import reduce
48
+
49
+
50
+ IS_PYPY = python_implementation() == 'PyPy'
51
+
52
+ ABSENT = b'\x00\x00\x00\x00\x00\x00\x00\x00'
53
+ ZERO = b'\x00\x00\x00\x00'
54
+ NC_BYTE = b'\x00\x00\x00\x01'
55
+ NC_CHAR = b'\x00\x00\x00\x02'
56
+ NC_SHORT = b'\x00\x00\x00\x03'
57
+ NC_INT = b'\x00\x00\x00\x04'
58
+ NC_FLOAT = b'\x00\x00\x00\x05'
59
+ NC_DOUBLE = b'\x00\x00\x00\x06'
60
+ NC_DIMENSION = b'\x00\x00\x00\n'
61
+ NC_VARIABLE = b'\x00\x00\x00\x0b'
62
+ NC_ATTRIBUTE = b'\x00\x00\x00\x0c'
63
+ FILL_BYTE = b'\x81'
64
+ FILL_CHAR = b'\x00'
65
+ FILL_SHORT = b'\x80\x01'
66
+ FILL_INT = b'\x80\x00\x00\x01'
67
+ FILL_FLOAT = b'\x7C\xF0\x00\x00'
68
+ FILL_DOUBLE = b'\x47\x9E\x00\x00\x00\x00\x00\x00'
69
+
70
+ TYPEMAP = {NC_BYTE: ('b', 1),
71
+ NC_CHAR: ('c', 1),
72
+ NC_SHORT: ('h', 2),
73
+ NC_INT: ('i', 4),
74
+ NC_FLOAT: ('f', 4),
75
+ NC_DOUBLE: ('d', 8)}
76
+
77
+ FILLMAP = {NC_BYTE: FILL_BYTE,
78
+ NC_CHAR: FILL_CHAR,
79
+ NC_SHORT: FILL_SHORT,
80
+ NC_INT: FILL_INT,
81
+ NC_FLOAT: FILL_FLOAT,
82
+ NC_DOUBLE: FILL_DOUBLE}
83
+
84
+ REVERSE = {('b', 1): NC_BYTE,
85
+ ('B', 1): NC_CHAR,
86
+ ('c', 1): NC_CHAR,
87
+ ('h', 2): NC_SHORT,
88
+ ('i', 4): NC_INT,
89
+ ('f', 4): NC_FLOAT,
90
+ ('d', 8): NC_DOUBLE,
91
+
92
+ # these come from asarray(1).dtype.char and asarray('foo').dtype.char,
93
+ # used when getting the types from generic attributes.
94
+ ('l', 4): NC_INT,
95
+ ('S', 1): NC_CHAR}
96
+
97
+
98
+ class netcdf_file:
99
+ """
100
+ A file object for NetCDF data.
101
+
102
+ A `netcdf_file` object has two standard attributes: `dimensions` and
103
+ `variables`. The values of both are dictionaries, mapping dimension
104
+ names to their associated lengths and variable names to variables,
105
+ respectively. Application programs should never modify these
106
+ dictionaries.
107
+
108
+ All other attributes correspond to global attributes defined in the
109
+ NetCDF file. Global file attributes are created by assigning to an
110
+ attribute of the `netcdf_file` object.
111
+
112
+ Parameters
113
+ ----------
114
+ filename : string or file-like
115
+ string -> filename
116
+ mode : {'r', 'w', 'a'}, optional
117
+ read-write-append mode, default is 'r'
118
+ mmap : None or bool, optional
119
+ Whether to mmap `filename` when reading. Default is True
120
+ when `filename` is a file name, False when `filename` is a
121
+ file-like object. Note that when mmap is in use, data arrays
122
+ returned refer directly to the mmapped data on disk, and the
123
+ file cannot be closed as long as references to it exist.
124
+ version : {1, 2}, optional
125
+ version of netcdf to read / write, where 1 means *Classic
126
+ format* and 2 means *64-bit offset format*. Default is 1. See
127
+ `here <https://docs.unidata.ucar.edu/nug/current/netcdf_introduction.html#select_format>`__
128
+ for more info.
129
+ maskandscale : bool, optional
130
+ Whether to automatically scale and/or mask data based on attributes.
131
+ Default is False.
132
+
133
+ Notes
134
+ -----
135
+ This module is derived from
136
+ `pupynere <https://bitbucket.org/robertodealmeida/pupynere/>`_.
137
+ The major advantage of this module over other modules is that it doesn't
138
+ require the code to be linked to the NetCDF libraries. However, for a more
139
+ recent version of the NetCDF standard and additional features, please consider
140
+ the permissively-licensed
141
+ `netcdf4-python <https://unidata.github.io/netcdf4-python/>`_.
142
+
143
+ NetCDF files are a self-describing binary data format. The file contains
144
+ metadata that describes the dimensions and variables in the file. More
145
+ details about NetCDF files can be found `here
146
+ <https://www.unidata.ucar.edu/software/netcdf/guide_toc.html>`__. There
147
+ are three main sections to a NetCDF data structure:
148
+
149
+ 1. Dimensions
150
+ 2. Variables
151
+ 3. Attributes
152
+
153
+ The dimensions section records the name and length of each dimension used
154
+ by the variables. The variables would then indicate which dimensions it
155
+ uses and any attributes such as data units, along with containing the data
156
+ values for the variable. It is good practice to include a
157
+ variable that is the same name as a dimension to provide the values for
158
+ that axes. Lastly, the attributes section would contain additional
159
+ information such as the name of the file creator or the instrument used to
160
+ collect the data.
161
+
162
+ When writing data to a NetCDF file, there is often the need to indicate the
163
+ 'record dimension'. A record dimension is the unbounded dimension for a
164
+ variable. For example, a temperature variable may have dimensions of
165
+ latitude, longitude and time. If one wants to add more temperature data to
166
+ the NetCDF file as time progresses, then the temperature variable should
167
+ have the time dimension flagged as the record dimension.
168
+
169
+ In addition, the NetCDF file header contains the position of the data in
170
+ the file, so access can be done in an efficient manner without loading
171
+ unnecessary data into memory. It uses the ``mmap`` module to create
172
+ Numpy arrays mapped to the data on disk, for the same purpose.
173
+
174
+ Note that when `netcdf_file` is used to open a file with mmap=True
175
+ (default for read-only), arrays returned by it refer to data
176
+ directly on the disk. The file should not be closed, and cannot be cleanly
177
+ closed when asked, if such arrays are alive. You may want to copy data arrays
178
+ obtained from mmapped Netcdf file if they are to be processed after the file
179
+ is closed, see the example below.
180
+
181
+ Examples
182
+ --------
183
+ To create a NetCDF file:
184
+
185
+ >>> from scipy.io import netcdf_file
186
+ >>> import numpy as np
187
+ >>> f = netcdf_file('simple.nc', 'w')
188
+ >>> f.history = 'Created for a test'
189
+ >>> f.createDimension('time', 10)
190
+ >>> time = f.createVariable('time', 'i', ('time',))
191
+ >>> time[:] = np.arange(10)
192
+ >>> time.units = 'days since 2008-01-01'
193
+ >>> f.close()
194
+
195
+ Note the assignment of ``arange(10)`` to ``time[:]``. Exposing the slice
196
+ of the time variable allows for the data to be set in the object, rather
197
+ than letting ``arange(10)`` overwrite the ``time`` variable.
198
+
199
+ To read the NetCDF file we just created:
200
+
201
+ >>> from scipy.io import netcdf_file
202
+ >>> f = netcdf_file('simple.nc', 'r')
203
+ >>> print(f.history)
204
+ b'Created for a test'
205
+ >>> time = f.variables['time']
206
+ >>> print(time.units)
207
+ b'days since 2008-01-01'
208
+ >>> print(time.shape)
209
+ (10,)
210
+ >>> print(time[-1])
211
+ 9
212
+
213
+ NetCDF files, when opened read-only, return arrays that refer
214
+ directly to memory-mapped data on disk:
215
+
216
+ >>> data = time[:]
217
+
218
+ If the data is to be processed after the file is closed, it needs
219
+ to be copied to main memory:
220
+
221
+ >>> data = time[:].copy()
222
+ >>> del time
223
+ >>> f.close()
224
+ >>> data.mean()
225
+ 4.5
226
+
227
+ A NetCDF file can also be used as context manager:
228
+
229
+ >>> from scipy.io import netcdf_file
230
+ >>> with netcdf_file('simple.nc', 'r') as f:
231
+ ... print(f.history)
232
+ b'Created for a test'
233
+
234
+ """
235
+ def __init__(self, filename, mode='r', mmap=None, version=1,
236
+ maskandscale=False):
237
+ """Initialize netcdf_file from fileobj (str or file-like)."""
238
+ if mode not in 'rwa':
239
+ raise ValueError("Mode must be either 'r', 'w' or 'a'.")
240
+
241
+ if hasattr(filename, 'seek'): # file-like
242
+ self.fp = filename
243
+ self.filename = 'None'
244
+ if mmap is None:
245
+ mmap = False
246
+ elif mmap and not hasattr(filename, 'fileno'):
247
+ raise ValueError('Cannot use file object for mmap')
248
+ else: # maybe it's a string
249
+ self.filename = filename
250
+ omode = 'r+' if mode == 'a' else mode
251
+ self.fp = open(self.filename, f'{omode}b')
252
+ if mmap is None:
253
+ # Mmapped files on PyPy cannot be usually closed
254
+ # before the GC runs, so it's better to use mmap=False
255
+ # as the default.
256
+ mmap = (not IS_PYPY)
257
+
258
+ if mode != 'r':
259
+ # Cannot read write-only files
260
+ mmap = False
261
+
262
+ self.use_mmap = mmap
263
+ self.mode = mode
264
+ self.version_byte = version
265
+ self.maskandscale = maskandscale
266
+
267
+ self.dimensions = {}
268
+ self.variables = {}
269
+
270
+ self._dims = []
271
+ self._recs = 0
272
+ self._recsize = 0
273
+
274
+ self._mm = None
275
+ self._mm_buf = None
276
+ if self.use_mmap:
277
+ self._mm = mm.mmap(self.fp.fileno(), 0, access=mm.ACCESS_READ)
278
+ self._mm_buf = np.frombuffer(self._mm, dtype=np.int8)
279
+
280
+ self._attributes = {}
281
+
282
+ if mode in 'ra':
283
+ self._read()
284
+
285
+ def __setattr__(self, attr, value):
286
+ # Store user defined attributes in a separate dict,
287
+ # so we can save them to file later.
288
+ try:
289
+ self._attributes[attr] = value
290
+ except AttributeError:
291
+ pass
292
+ self.__dict__[attr] = value
293
+
294
+ def close(self):
295
+ """Closes the NetCDF file."""
296
+ if hasattr(self, 'fp') and not self.fp.closed:
297
+ try:
298
+ self.flush()
299
+ finally:
300
+ self.variables = {}
301
+ if self._mm_buf is not None:
302
+ ref = weakref.ref(self._mm_buf)
303
+ self._mm_buf = None
304
+ if ref() is None:
305
+ # self._mm_buf is gc'd, and we can close the mmap
306
+ self._mm.close()
307
+ else:
308
+ # we cannot close self._mm, since self._mm_buf is
309
+ # alive and there may still be arrays referring to it
310
+ warnings.warn(
311
+ "Cannot close a netcdf_file opened with mmap=True, when "
312
+ "netcdf_variables or arrays referring to its data still "
313
+ "exist. All data arrays obtained from such files refer "
314
+ "directly to data on disk, and must be copied before the "
315
+ "file can be cleanly closed. "
316
+ "(See netcdf_file docstring for more information on mmap.)",
317
+ category=RuntimeWarning, stacklevel=2,
318
+ )
319
+ self._mm = None
320
+ self.fp.close()
321
+ __del__ = close
322
+
323
+ def __enter__(self):
324
+ return self
325
+
326
+ def __exit__(self, type, value, traceback):
327
+ self.close()
328
+
329
+ def createDimension(self, name, length):
330
+ """
331
+ Adds a dimension to the Dimension section of the NetCDF data structure.
332
+
333
+ Note that this function merely adds a new dimension that the variables can
334
+ reference. The values for the dimension, if desired, should be added as
335
+ a variable using `createVariable`, referring to this dimension.
336
+
337
+ Parameters
338
+ ----------
339
+ name : str
340
+ Name of the dimension (Eg, 'lat' or 'time').
341
+ length : int
342
+ Length of the dimension.
343
+
344
+ See Also
345
+ --------
346
+ createVariable
347
+
348
+ """
349
+ if length is None and self._dims:
350
+ raise ValueError("Only first dimension may be unlimited!")
351
+
352
+ self.dimensions[name] = length
353
+ self._dims.append(name)
354
+
355
+ def createVariable(self, name, type, dimensions):
356
+ """
357
+ Create an empty variable for the `netcdf_file` object, specifying its data
358
+ type and the dimensions it uses.
359
+
360
+ Parameters
361
+ ----------
362
+ name : str
363
+ Name of the new variable.
364
+ type : dtype or str
365
+ Data type of the variable.
366
+ dimensions : sequence of str
367
+ List of the dimension names used by the variable, in the desired order.
368
+
369
+ Returns
370
+ -------
371
+ variable : netcdf_variable
372
+ The newly created ``netcdf_variable`` object.
373
+ This object has also been added to the `netcdf_file` object as well.
374
+
375
+ See Also
376
+ --------
377
+ createDimension
378
+
379
+ Notes
380
+ -----
381
+ Any dimensions to be used by the variable should already exist in the
382
+ NetCDF data structure or should be created by `createDimension` prior to
383
+ creating the NetCDF variable.
384
+
385
+ """
386
+ shape = tuple([self.dimensions[dim] for dim in dimensions])
387
+ shape_ = tuple([dim or 0 for dim in shape]) # replace None with 0 for NumPy
388
+
389
+ type = dtype(type)
390
+ typecode, size = type.char, type.itemsize
391
+ if (typecode, size) not in REVERSE:
392
+ raise ValueError(f"NetCDF 3 does not support type {type}")
393
+
394
+ # convert to big endian always for NetCDF 3
395
+ data = empty(shape_, dtype=type.newbyteorder("B"))
396
+ self.variables[name] = netcdf_variable(
397
+ data, typecode, size, shape, dimensions,
398
+ maskandscale=self.maskandscale)
399
+ return self.variables[name]
400
+
401
+ def flush(self):
402
+ """
403
+ Perform a sync-to-disk flush if the `netcdf_file` object is in write mode.
404
+
405
+ See Also
406
+ --------
407
+ sync : Identical function
408
+
409
+ """
410
+ if hasattr(self, 'mode') and self.mode in 'wa':
411
+ self._write()
412
+ sync = flush
413
+
414
+ def _write(self):
415
+ self.fp.seek(0)
416
+ self.fp.write(b'CDF')
417
+ self.fp.write(array(self.version_byte, '>b').tobytes())
418
+
419
+ # Write headers and data.
420
+ self._write_numrecs()
421
+ self._write_dim_array()
422
+ self._write_gatt_array()
423
+ self._write_var_array()
424
+
425
+ def _write_numrecs(self):
426
+ # Get highest record count from all record variables.
427
+ for var in self.variables.values():
428
+ if var.isrec and len(var.data) > self._recs:
429
+ self.__dict__['_recs'] = len(var.data)
430
+ self._pack_int(self._recs)
431
+
432
+ def _write_dim_array(self):
433
+ if self.dimensions:
434
+ self.fp.write(NC_DIMENSION)
435
+ self._pack_int(len(self.dimensions))
436
+ for name in self._dims:
437
+ self._pack_string(name)
438
+ length = self.dimensions[name]
439
+ self._pack_int(length or 0) # replace None with 0 for record dimension
440
+ else:
441
+ self.fp.write(ABSENT)
442
+
443
+ def _write_gatt_array(self):
444
+ self._write_att_array(self._attributes)
445
+
446
+ def _write_att_array(self, attributes):
447
+ if attributes:
448
+ self.fp.write(NC_ATTRIBUTE)
449
+ self._pack_int(len(attributes))
450
+ for name, values in attributes.items():
451
+ self._pack_string(name)
452
+ self._write_att_values(values)
453
+ else:
454
+ self.fp.write(ABSENT)
455
+
456
+ def _write_var_array(self):
457
+ if self.variables:
458
+ self.fp.write(NC_VARIABLE)
459
+ self._pack_int(len(self.variables))
460
+
461
+ # Sort variable names non-recs first, then recs.
462
+ def sortkey(n):
463
+ v = self.variables[n]
464
+ if v.isrec:
465
+ return (-1,)
466
+ return v._shape
467
+ variables = sorted(self.variables, key=sortkey, reverse=True)
468
+
469
+ # Set the metadata for all variables.
470
+ for name in variables:
471
+ self._write_var_metadata(name)
472
+ # Now that we have the metadata, we know the vsize of
473
+ # each record variable, so we can calculate recsize.
474
+ self.__dict__['_recsize'] = sum([
475
+ var._vsize for var in self.variables.values()
476
+ if var.isrec])
477
+ # Set the data for all variables.
478
+ for name in variables:
479
+ self._write_var_data(name)
480
+ else:
481
+ self.fp.write(ABSENT)
482
+
483
+ def _write_var_metadata(self, name):
484
+ var = self.variables[name]
485
+
486
+ self._pack_string(name)
487
+ self._pack_int(len(var.dimensions))
488
+ for dimname in var.dimensions:
489
+ dimid = self._dims.index(dimname)
490
+ self._pack_int(dimid)
491
+
492
+ self._write_att_array(var._attributes)
493
+
494
+ nc_type = REVERSE[var.typecode(), var.itemsize()]
495
+ self.fp.write(nc_type)
496
+
497
+ if not var.isrec:
498
+ vsize = var.data.size * var.data.itemsize
499
+ vsize += -vsize % 4
500
+ else: # record variable
501
+ try:
502
+ vsize = var.data[0].size * var.data.itemsize
503
+ except IndexError:
504
+ vsize = 0
505
+ rec_vars = len([v for v in self.variables.values()
506
+ if v.isrec])
507
+ if rec_vars > 1:
508
+ vsize += -vsize % 4
509
+ self.variables[name].__dict__['_vsize'] = vsize
510
+ self._pack_int(vsize)
511
+
512
+ # Pack a bogus begin, and set the real value later.
513
+ self.variables[name].__dict__['_begin'] = self.fp.tell()
514
+ self._pack_begin(0)
515
+
516
+ def _write_var_data(self, name):
517
+ var = self.variables[name]
518
+
519
+ # Set begin in file header.
520
+ the_beguine = self.fp.tell()
521
+ self.fp.seek(var._begin)
522
+ self._pack_begin(the_beguine)
523
+ self.fp.seek(the_beguine)
524
+
525
+ # Write data.
526
+ if not var.isrec:
527
+ self.fp.write(var.data.tobytes())
528
+ count = var.data.size * var.data.itemsize
529
+ self._write_var_padding(var, var._vsize - count)
530
+ else: # record variable
531
+ # Handle rec vars with shape[0] < nrecs.
532
+ if self._recs > len(var.data):
533
+ shape = (self._recs,) + var.data.shape[1:]
534
+ # Resize in-place does not always work since
535
+ # the array might not be single-segment
536
+ try:
537
+ var.data.resize(shape)
538
+ except ValueError:
539
+ dtype = var.data.dtype
540
+ var.__dict__['data'] = np.resize(var.data, shape).astype(dtype)
541
+
542
+ pos0 = pos = self.fp.tell()
543
+ for rec in var.data:
544
+ # Apparently scalars cannot be converted to big endian. If we
545
+ # try to convert a ``=i4`` scalar to, say, '>i4' the dtype
546
+ # will remain as ``=i4``.
547
+ if not rec.shape and (rec.dtype.byteorder == '<' or
548
+ (rec.dtype.byteorder == '=' and LITTLE_ENDIAN)):
549
+ rec = rec.byteswap()
550
+ self.fp.write(rec.tobytes())
551
+ # Padding
552
+ count = rec.size * rec.itemsize
553
+ self._write_var_padding(var, var._vsize - count)
554
+ pos += self._recsize
555
+ self.fp.seek(pos)
556
+ self.fp.seek(pos0 + var._vsize)
557
+
558
+ def _write_var_padding(self, var, size):
559
+ encoded_fill_value = var._get_encoded_fill_value()
560
+ num_fills = size // len(encoded_fill_value)
561
+ self.fp.write(encoded_fill_value * num_fills)
562
+
563
+ def _write_att_values(self, values):
564
+ if hasattr(values, 'dtype'):
565
+ nc_type = REVERSE[values.dtype.char, values.dtype.itemsize]
566
+ else:
567
+ types = [(int, NC_INT), (float, NC_FLOAT), (str, NC_CHAR)]
568
+
569
+ # bytes index into scalars in py3k. Check for "string" types
570
+ if isinstance(values, str | bytes):
571
+ sample = values
572
+ else:
573
+ try:
574
+ sample = values[0] # subscriptable?
575
+ except TypeError:
576
+ sample = values # scalar
577
+
578
+ for class_, nc_type in types:
579
+ if isinstance(sample, class_):
580
+ break
581
+
582
+ typecode, size = TYPEMAP[nc_type]
583
+ dtype_ = f'>{typecode}'
584
+ # asarray() dies with bytes and '>c' in py3k. Change to 'S'
585
+ dtype_ = 'S' if dtype_ == '>c' else dtype_
586
+
587
+ values = asarray(values, dtype=dtype_)
588
+
589
+ self.fp.write(nc_type)
590
+
591
+ if values.dtype.char == 'S':
592
+ nelems = values.itemsize
593
+ else:
594
+ nelems = values.size
595
+ self._pack_int(nelems)
596
+
597
+ if not values.shape and (values.dtype.byteorder == '<' or
598
+ (values.dtype.byteorder == '=' and LITTLE_ENDIAN)):
599
+ values = values.byteswap()
600
+ self.fp.write(values.tobytes())
601
+ count = values.size * values.itemsize
602
+ self.fp.write(b'\x00' * (-count % 4)) # pad
603
+
604
+ def _read(self):
605
+ # Check magic bytes and version
606
+ magic = self.fp.read(3)
607
+ if not magic == b'CDF':
608
+ raise TypeError(f"Error: {self.filename} is not a valid NetCDF 3 file")
609
+ self.__dict__['version_byte'] = frombuffer(self.fp.read(1), '>b')[0]
610
+
611
+ # Read file headers and set data.
612
+ self._read_numrecs()
613
+ self._read_dim_array()
614
+ self._read_gatt_array()
615
+ self._read_var_array()
616
+
617
+ def _read_numrecs(self):
618
+ self.__dict__['_recs'] = self._unpack_int()
619
+
620
+ def _read_dim_array(self):
621
+ header = self.fp.read(4)
622
+ if header not in [ZERO, NC_DIMENSION]:
623
+ raise ValueError("Unexpected header.")
624
+ count = self._unpack_int()
625
+
626
+ for dim in range(count):
627
+ name = self._unpack_string().decode('latin1')
628
+ length = self._unpack_int() or None # None for record dimension
629
+ self.dimensions[name] = length
630
+ self._dims.append(name) # preserve order
631
+
632
+ def _read_gatt_array(self):
633
+ for k, v in self._read_att_array().items():
634
+ self.__setattr__(k, v)
635
+
636
+ def _read_att_array(self):
637
+ header = self.fp.read(4)
638
+ if header not in [ZERO, NC_ATTRIBUTE]:
639
+ raise ValueError("Unexpected header.")
640
+ count = self._unpack_int()
641
+
642
+ attributes = {}
643
+ for attr in range(count):
644
+ name = self._unpack_string().decode('latin1')
645
+ attributes[name] = self._read_att_values()
646
+ return attributes
647
+
648
+ def _read_var_array(self):
649
+ header = self.fp.read(4)
650
+ if header not in [ZERO, NC_VARIABLE]:
651
+ raise ValueError("Unexpected header.")
652
+
653
+ begin = 0
654
+ dtypes = {'names': [], 'formats': []}
655
+ rec_vars = []
656
+ count = self._unpack_int()
657
+ for var in range(count):
658
+ (name, dimensions, shape, attributes,
659
+ typecode, size, dtype_, begin_, vsize) = self._read_var()
660
+ # https://www.unidata.ucar.edu/software/netcdf/guide_toc.html
661
+ # Note that vsize is the product of the dimension lengths
662
+ # (omitting the record dimension) and the number of bytes
663
+ # per value (determined from the type), increased to the
664
+ # next multiple of 4, for each variable. If a record
665
+ # variable, this is the amount of space per record. The
666
+ # netCDF "record size" is calculated as the sum of the
667
+ # vsize's of all the record variables.
668
+ #
669
+ # The vsize field is actually redundant, because its value
670
+ # may be computed from other information in the header. The
671
+ # 32-bit vsize field is not large enough to contain the size
672
+ # of variables that require more than 2^32 - 4 bytes, so
673
+ # 2^32 - 1 is used in the vsize field for such variables.
674
+ if shape and shape[0] is None: # record variable
675
+ rec_vars.append(name)
676
+ # The netCDF "record size" is calculated as the sum of
677
+ # the vsize's of all the record variables.
678
+ self.__dict__['_recsize'] += vsize
679
+ if begin == 0:
680
+ begin = begin_
681
+ dtypes['names'].append(name)
682
+ dtypes['formats'].append(str(shape[1:]) + dtype_)
683
+
684
+ # Handle padding with a virtual variable.
685
+ if typecode in 'bch':
686
+ actual_size = reduce(mul, (1,) + shape[1:]) * size
687
+ padding = -actual_size % 4
688
+ if padding:
689
+ dtypes['names'].append(f'_padding_{var}')
690
+ dtypes['formats'].append(f'({padding},)>b')
691
+
692
+ # Data will be set later.
693
+ data = None
694
+ else: # not a record variable
695
+ # Calculate size to avoid problems with vsize (above)
696
+ a_size = reduce(mul, shape, 1) * size
697
+ if self.use_mmap:
698
+ data = self._mm_buf[begin_:begin_+a_size].view(dtype=dtype_)
699
+ data = data.reshape(shape)
700
+ else:
701
+ pos = self.fp.tell()
702
+ self.fp.seek(begin_)
703
+ data = frombuffer(self.fp.read(a_size), dtype=dtype_
704
+ ).copy()
705
+ data = data.reshape(shape)
706
+ self.fp.seek(pos)
707
+
708
+ # Add variable.
709
+ self.variables[name] = netcdf_variable(
710
+ data, typecode, size, shape, dimensions, attributes,
711
+ maskandscale=self.maskandscale)
712
+
713
+ if rec_vars:
714
+ # Remove padding when only one record variable.
715
+ if len(rec_vars) == 1:
716
+ dtypes['names'] = dtypes['names'][:1]
717
+ dtypes['formats'] = dtypes['formats'][:1]
718
+
719
+ # Build rec array.
720
+ if self.use_mmap:
721
+ buf = self._mm_buf[begin:begin+self._recs*self._recsize]
722
+ rec_array = buf.view(dtype=dtypes)
723
+ rec_array = rec_array.reshape((self._recs,))
724
+ else:
725
+ pos = self.fp.tell()
726
+ self.fp.seek(begin)
727
+ rec_array = frombuffer(self.fp.read(self._recs*self._recsize),
728
+ dtype=dtypes).copy()
729
+ rec_array = rec_array.reshape((self._recs,))
730
+ self.fp.seek(pos)
731
+
732
+ for var in rec_vars:
733
+ self.variables[var].__dict__['data'] = rec_array[var]
734
+
735
+ def _read_var(self):
736
+ name = self._unpack_string().decode('latin1')
737
+ dimensions = []
738
+ shape = []
739
+ dims = self._unpack_int()
740
+
741
+ for i in range(dims):
742
+ dimid = self._unpack_int()
743
+ dimname = self._dims[dimid]
744
+ dimensions.append(dimname)
745
+ dim = self.dimensions[dimname]
746
+ shape.append(dim)
747
+ dimensions = tuple(dimensions)
748
+ shape = tuple(shape)
749
+
750
+ attributes = self._read_att_array()
751
+ nc_type = self.fp.read(4)
752
+ vsize = self._unpack_int()
753
+ begin = [self._unpack_int, self._unpack_int64][self.version_byte-1]()
754
+
755
+ typecode, size = TYPEMAP[nc_type]
756
+ dtype_ = f'>{typecode}'
757
+
758
+ return name, dimensions, shape, attributes, typecode, size, dtype_, begin, vsize
759
+
760
+ def _read_att_values(self):
761
+ nc_type = self.fp.read(4)
762
+ n = self._unpack_int()
763
+
764
+ typecode, size = TYPEMAP[nc_type]
765
+
766
+ count = n*size
767
+ values = self.fp.read(int(count))
768
+ self.fp.read(-count % 4) # read padding
769
+
770
+ if typecode != 'c':
771
+ values = frombuffer(values, dtype=f'>{typecode}').copy()
772
+ if values.shape == (1,):
773
+ values = values[0]
774
+ else:
775
+ values = values.rstrip(b'\x00')
776
+ return values
777
+
778
+ def _pack_begin(self, begin):
779
+ if self.version_byte == 1:
780
+ self._pack_int(begin)
781
+ elif self.version_byte == 2:
782
+ self._pack_int64(begin)
783
+
784
+ def _pack_int(self, value):
785
+ self.fp.write(array(value, '>i').tobytes())
786
+ _pack_int32 = _pack_int
787
+
788
+ def _unpack_int(self):
789
+ return int(frombuffer(self.fp.read(4), '>i')[0])
790
+ _unpack_int32 = _unpack_int
791
+
792
+ def _pack_int64(self, value):
793
+ self.fp.write(array(value, '>q').tobytes())
794
+
795
+ def _unpack_int64(self):
796
+ return frombuffer(self.fp.read(8), '>q')[0]
797
+
798
+ def _pack_string(self, s):
799
+ count = len(s)
800
+ self._pack_int(count)
801
+ self.fp.write(s.encode('latin1'))
802
+ self.fp.write(b'\x00' * (-count % 4)) # pad
803
+
804
+ def _unpack_string(self):
805
+ count = self._unpack_int()
806
+ s = self.fp.read(count).rstrip(b'\x00')
807
+ self.fp.read(-count % 4) # read padding
808
+ return s
809
+
810
+
811
+ class netcdf_variable:
812
+ """
813
+ A data object for netcdf files.
814
+
815
+ `netcdf_variable` objects are constructed by calling the method
816
+ `netcdf_file.createVariable` on the `netcdf_file` object. `netcdf_variable`
817
+ objects behave much like array objects defined in numpy, except that their
818
+ data resides in a file. Data is read by indexing and written by assigning
819
+ to an indexed subset; the entire array can be accessed by the index ``[:]``
820
+ or (for scalars) by using the methods `getValue` and `assignValue`.
821
+ `netcdf_variable` objects also have attribute `shape` with the same meaning
822
+ as for arrays, but the shape cannot be modified. There is another read-only
823
+ attribute `dimensions`, whose value is the tuple of dimension names.
824
+
825
+ All other attributes correspond to variable attributes defined in
826
+ the NetCDF file. Variable attributes are created by assigning to an
827
+ attribute of the `netcdf_variable` object.
828
+
829
+ Parameters
830
+ ----------
831
+ data : array_like
832
+ The data array that holds the values for the variable.
833
+ Typically, this is initialized as empty, but with the proper shape.
834
+ typecode : dtype character code
835
+ Desired data-type for the data array.
836
+ size : int
837
+ Desired element size for the data array.
838
+ shape : sequence of ints
839
+ The shape of the array. This should match the lengths of the
840
+ variable's dimensions.
841
+ dimensions : sequence of strings
842
+ The names of the dimensions used by the variable. Must be in the
843
+ same order of the dimension lengths given by `shape`.
844
+ attributes : dict, optional
845
+ Attribute values (any type) keyed by string names. These attributes
846
+ become attributes for the netcdf_variable object.
847
+ maskandscale : bool, optional
848
+ Whether to automatically scale and/or mask data based on attributes.
849
+ Default is False.
850
+
851
+
852
+ Attributes
853
+ ----------
854
+ dimensions : list of str
855
+ List of names of dimensions used by the variable object.
856
+ isrec, shape
857
+ Properties
858
+
859
+ See also
860
+ --------
861
+ isrec, shape
862
+
863
+ Notes
864
+ -----
865
+ For a more recent version of the NetCDF standard and additional features, please
866
+ consider the permissively-licensed
867
+ `netcdf4-python <https://unidata.github.io/netcdf4-python/>`_.
868
+
869
+ """
870
+ def __init__(self, data, typecode, size, shape, dimensions,
871
+ attributes=None,
872
+ maskandscale=False):
873
+ self.data = data
874
+ self._typecode = typecode
875
+ self._size = size
876
+ self._shape = shape
877
+ self.dimensions = dimensions
878
+ self.maskandscale = maskandscale
879
+
880
+ self._attributes = attributes or {}
881
+ for k, v in self._attributes.items():
882
+ self.__dict__[k] = v
883
+
884
+ def __setattr__(self, attr, value):
885
+ # Store user defined attributes in a separate dict,
886
+ # so we can save them to file later.
887
+ try:
888
+ self._attributes[attr] = value
889
+ except AttributeError:
890
+ pass
891
+ self.__dict__[attr] = value
892
+
893
+ def isrec(self):
894
+ """Returns whether the variable has a record dimension or not.
895
+
896
+ A record dimension is a dimension along which additional data could be
897
+ easily appended in the netcdf data structure without much rewriting of
898
+ the data file. This attribute is a read-only property of the
899
+ `netcdf_variable`.
900
+
901
+ """
902
+ return bool(self.data.shape) and not self._shape[0]
903
+ isrec = property(isrec)
904
+
905
+ def shape(self):
906
+ """Returns the shape tuple of the data variable.
907
+
908
+ This is a read-only attribute and can not be modified in the
909
+ same manner of other numpy arrays.
910
+ """
911
+ return self.data.shape
912
+ shape = property(shape)
913
+
914
+ def getValue(self):
915
+ """
916
+ Retrieve a scalar value from a `netcdf_variable` of length one.
917
+
918
+ Raises
919
+ ------
920
+ ValueError
921
+ If the netcdf variable is an array of length greater than one,
922
+ this exception will be raised.
923
+
924
+ """
925
+ return self.data.item()
926
+
927
+ def assignValue(self, value):
928
+ """
929
+ Assign a scalar value to a `netcdf_variable` of length one.
930
+
931
+ Parameters
932
+ ----------
933
+ value : scalar
934
+ Scalar value (of compatible type) to assign to a length-one netcdf
935
+ variable. This value will be written to file.
936
+
937
+ Raises
938
+ ------
939
+ ValueError
940
+ If the input is not a scalar, or if the destination is not a length-one
941
+ netcdf variable.
942
+
943
+ """
944
+ if not self.data.flags.writeable:
945
+ # Work-around for a bug in NumPy. Calling itemset() on a read-only
946
+ # memory-mapped array causes a seg. fault.
947
+ # See NumPy ticket #1622, and SciPy ticket #1202.
948
+ # This check for `writeable` can be removed when the oldest version
949
+ # of NumPy still supported by scipy contains the fix for #1622.
950
+ raise RuntimeError("variable is not writeable")
951
+
952
+ self.data[:] = value
953
+
954
+ def typecode(self):
955
+ """
956
+ Return the typecode of the variable.
957
+
958
+ Returns
959
+ -------
960
+ typecode : char
961
+ The character typecode of the variable (e.g., 'i' for int).
962
+
963
+ """
964
+ return self._typecode
965
+
966
+ def itemsize(self):
967
+ """
968
+ Return the itemsize of the variable.
969
+
970
+ Returns
971
+ -------
972
+ itemsize : int
973
+ The element size of the variable (e.g., 8 for float64).
974
+
975
+ """
976
+ return self._size
977
+
978
+ def __getitem__(self, index):
979
+ if not self.maskandscale:
980
+ return self.data[index]
981
+
982
+ data = self.data[index].copy()
983
+ missing_value = self._get_missing_value()
984
+ data = self._apply_missing_value(data, missing_value)
985
+ scale_factor = self._attributes.get('scale_factor')
986
+ add_offset = self._attributes.get('add_offset')
987
+ if add_offset is not None or scale_factor is not None:
988
+ data = data.astype(np.float64)
989
+ if scale_factor is not None:
990
+ data = data * scale_factor
991
+ if add_offset is not None:
992
+ data += add_offset
993
+
994
+ return data
995
+
996
+ def __setitem__(self, index, data):
997
+ if self.maskandscale:
998
+ missing_value = (
999
+ self._get_missing_value() or
1000
+ getattr(data, 'fill_value', 999999))
1001
+ self._attributes.setdefault('missing_value', missing_value)
1002
+ self._attributes.setdefault('_FillValue', missing_value)
1003
+ data = ((data - self._attributes.get('add_offset', 0.0)) /
1004
+ self._attributes.get('scale_factor', 1.0))
1005
+ data = np.ma.asarray(data).filled(missing_value)
1006
+ if self._typecode not in 'fd' and data.dtype.kind == 'f':
1007
+ data = np.round(data)
1008
+
1009
+ # Expand data for record vars?
1010
+ if self.isrec:
1011
+ if isinstance(index, tuple):
1012
+ rec_index = index[0]
1013
+ else:
1014
+ rec_index = index
1015
+ if isinstance(rec_index, slice):
1016
+ recs = (rec_index.start or 0) + len(data)
1017
+ else:
1018
+ recs = rec_index + 1
1019
+ if recs > len(self.data):
1020
+ shape = (recs,) + self._shape[1:]
1021
+ # Resize in-place does not always work since
1022
+ # the array might not be single-segment
1023
+ try:
1024
+ self.data.resize(shape)
1025
+ except ValueError:
1026
+ dtype = self.data.dtype
1027
+ self.__dict__['data'] = np.resize(self.data, shape).astype(dtype)
1028
+ self.data[index] = data
1029
+
1030
+ def _default_encoded_fill_value(self):
1031
+ """
1032
+ The default encoded fill-value for this Variable's data type.
1033
+ """
1034
+ nc_type = REVERSE[self.typecode(), self.itemsize()]
1035
+ return FILLMAP[nc_type]
1036
+
1037
+ def _get_encoded_fill_value(self):
1038
+ """
1039
+ Returns the encoded fill value for this variable as bytes.
1040
+
1041
+ This is taken from either the _FillValue attribute, or the default fill
1042
+ value for this variable's data type.
1043
+ """
1044
+ if '_FillValue' in self._attributes:
1045
+ fill_value = np.array(self._attributes['_FillValue'],
1046
+ dtype=self.data.dtype).tobytes()
1047
+ if len(fill_value) == self.itemsize():
1048
+ return fill_value
1049
+ else:
1050
+ return self._default_encoded_fill_value()
1051
+ else:
1052
+ return self._default_encoded_fill_value()
1053
+
1054
+ def _get_missing_value(self):
1055
+ """
1056
+ Returns the value denoting "no data" for this variable.
1057
+
1058
+ If this variable does not have a missing/fill value, returns None.
1059
+
1060
+ If both _FillValue and missing_value are given, give precedence to
1061
+ _FillValue. The netCDF standard gives special meaning to _FillValue;
1062
+ missing_value is just used for compatibility with old datasets.
1063
+ """
1064
+
1065
+ if '_FillValue' in self._attributes:
1066
+ missing_value = self._attributes['_FillValue']
1067
+ elif 'missing_value' in self._attributes:
1068
+ missing_value = self._attributes['missing_value']
1069
+ else:
1070
+ missing_value = None
1071
+
1072
+ return missing_value
1073
+
1074
+ @staticmethod
1075
+ def _apply_missing_value(data, missing_value):
1076
+ """
1077
+ Applies the given missing value to the data array.
1078
+
1079
+ Returns a numpy.ma array, with any value equal to missing_value masked
1080
+ out (unless missing_value is None, in which case the original array is
1081
+ returned).
1082
+ """
1083
+
1084
+ if missing_value is None:
1085
+ newdata = data
1086
+ else:
1087
+ try:
1088
+ missing_value_isnan = np.isnan(missing_value)
1089
+ except (TypeError, NotImplementedError):
1090
+ # some data types (e.g., characters) cannot be tested for NaN
1091
+ missing_value_isnan = False
1092
+
1093
+ if missing_value_isnan:
1094
+ mymask = np.isnan(data)
1095
+ else:
1096
+ mymask = (data == missing_value)
1097
+
1098
+ newdata = np.ma.masked_where(mymask, data)
1099
+
1100
+ return newdata
1101
+
1102
+
1103
+ NetCDFFile = netcdf_file
1104
+ NetCDFVariable = netcdf_variable
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/harwell_boeing.py ADDED
@@ -0,0 +1,17 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file is not meant for public use and will be removed in SciPy v2.0.0.
2
+ # Use the `scipy.io` namespace for importing the functions
3
+ # included below.
4
+
5
+ from scipy._lib.deprecation import _sub_module_deprecation
6
+
7
+ __all__ = ["hb_read", "hb_write"] # noqa: F822
8
+
9
+
10
+ def __dir__():
11
+ return __all__
12
+
13
+
14
+ def __getattr__(name):
15
+ return _sub_module_deprecation(sub_package="io", module="harwell_boeing",
16
+ private_modules=["_harwell_boeing"], all=__all__,
17
+ attribute=name)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/idl.py ADDED
@@ -0,0 +1,17 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file is not meant for public use and will be removed in SciPy v2.0.0.
2
+ # Use the `scipy.io` namespace for importing the functions
3
+ # included below.
4
+
5
+ from scipy._lib.deprecation import _sub_module_deprecation
6
+
7
+ __all__ = ["readsav"] # noqa: F822
8
+
9
+
10
+ def __dir__():
11
+ return __all__
12
+
13
+
14
+ def __getattr__(name):
15
+ return _sub_module_deprecation(sub_package="io", module="idl",
16
+ private_modules=["_idl"], all=__all__,
17
+ attribute=name)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/mmio.py ADDED
@@ -0,0 +1,17 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file is not meant for public use and will be removed in SciPy v2.0.0.
2
+ # Use the `scipy.io` namespace for importing the functions
3
+ # included below.
4
+
5
+ from scipy._lib.deprecation import _sub_module_deprecation
6
+
7
+ __all__ = ["mminfo", "mmread", "mmwrite"] # noqa: F822
8
+
9
+
10
+ def __dir__():
11
+ return __all__
12
+
13
+
14
+ def __getattr__(name):
15
+ return _sub_module_deprecation(sub_package="io", module="mmio",
16
+ private_modules=["_mmio"], all=__all__,
17
+ attribute=name)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/netcdf.py ADDED
@@ -0,0 +1,17 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file is not meant for public use and will be removed in SciPy v2.0.0.
2
+ # Use the `scipy.io` namespace for importing the functions
3
+ # included below.
4
+
5
+ from scipy._lib.deprecation import _sub_module_deprecation
6
+
7
+ __all__ = ["netcdf_file", "netcdf_variable"] # noqa: F822
8
+
9
+
10
+ def __dir__():
11
+ return __all__
12
+
13
+
14
+ def __getattr__(name):
15
+ return _sub_module_deprecation(sub_package="io", module="netcdf",
16
+ private_modules=["_netcdf"], all=__all__,
17
+ attribute=name)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/io/wavfile.py ADDED
@@ -0,0 +1,944 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """
2
+ Module to read / write wav files using NumPy arrays
3
+
4
+ Functions
5
+ ---------
6
+ `read`: Return the sample rate (in samples/sec) and data from a WAV file.
7
+
8
+ `write`: Write a NumPy array as a WAV file.
9
+
10
+ """
11
+ import io
12
+ import os
13
+ import sys
14
+ import numpy as np
15
+ import struct
16
+ import warnings
17
+ from enum import IntEnum
18
+
19
+
20
+ __all__ = [
21
+ 'WavFileWarning',
22
+ 'read',
23
+ 'write'
24
+ ]
25
+
26
+
27
+ class WavFileWarning(UserWarning):
28
+ """
29
+ Warning for WAV files with format issues that can still be read.
30
+
31
+ Raised when a WAV file has problems like missing metadata or
32
+ non-standard formatting, but can still be processed successfully.
33
+ """
34
+ pass
35
+
36
+
37
+ class SeekEmulatingReader:
38
+ """
39
+ Tracks stream position, provides tell(), and emulates only those
40
+ seeks that can be supported by reading forward. Other seeks raise
41
+ io.UnsupportedOperation. Note that this class implements only the
42
+ minimum necessary to keep wavfile.read() happy.
43
+ """
44
+ def __init__(self, reader):
45
+ self.reader = reader
46
+ self.pos = 0
47
+
48
+ def read(self, size=-1, /):
49
+ data = self.reader.read(size)
50
+ self.pos += len(data)
51
+ return data
52
+
53
+ def seek(self, offset, whence=os.SEEK_SET, /):
54
+ match whence:
55
+ case os.SEEK_SET if offset >= self.pos:
56
+ self.read(offset - self.pos) # convert to relative
57
+ case os.SEEK_CUR if offset >= 0:
58
+ self.read(offset) # advance by offset
59
+ case os.SEEK_END if offset == 0:
60
+ self.read() # advance to end of stream
61
+ case _:
62
+ raise io.UnsupportedOperation("SeekEmulatingReader was asked to emulate"
63
+ " a seek operation it does not support.")
64
+ return self.pos
65
+
66
+ def tell(self):
67
+ return self.pos
68
+
69
+ def close(self):
70
+ self.reader.close()
71
+
72
+ # np.fromfile expects to be able to call flush(), and _read_data_chunk
73
+ # expects to catch io.UnsupportedOperation if np.fromfile fails.
74
+ def flush(self):
75
+ raise io.UnsupportedOperation("SeekEmulatingReader can't flush.")
76
+
77
+
78
+ class WAVE_FORMAT(IntEnum):
79
+ """
80
+ WAVE form wFormatTag IDs
81
+
82
+ Complete list is in mmreg.h in Windows 10 SDK. ALAC and OPUS are the
83
+ newest additions, in v10.0.14393 2016-07
84
+ """
85
+ UNKNOWN = 0x0000
86
+ PCM = 0x0001
87
+ ADPCM = 0x0002
88
+ IEEE_FLOAT = 0x0003
89
+ VSELP = 0x0004
90
+ IBM_CVSD = 0x0005
91
+ ALAW = 0x0006
92
+ MULAW = 0x0007
93
+ DTS = 0x0008
94
+ DRM = 0x0009
95
+ WMAVOICE9 = 0x000A
96
+ WMAVOICE10 = 0x000B
97
+ OKI_ADPCM = 0x0010
98
+ DVI_ADPCM = 0x0011
99
+ IMA_ADPCM = 0x0011 # Duplicate
100
+ MEDIASPACE_ADPCM = 0x0012
101
+ SIERRA_ADPCM = 0x0013
102
+ G723_ADPCM = 0x0014
103
+ DIGISTD = 0x0015
104
+ DIGIFIX = 0x0016
105
+ DIALOGIC_OKI_ADPCM = 0x0017
106
+ MEDIAVISION_ADPCM = 0x0018
107
+ CU_CODEC = 0x0019
108
+ HP_DYN_VOICE = 0x001A
109
+ YAMAHA_ADPCM = 0x0020
110
+ SONARC = 0x0021
111
+ DSPGROUP_TRUESPEECH = 0x0022
112
+ ECHOSC1 = 0x0023
113
+ AUDIOFILE_AF36 = 0x0024
114
+ APTX = 0x0025
115
+ AUDIOFILE_AF10 = 0x0026
116
+ PROSODY_1612 = 0x0027
117
+ LRC = 0x0028
118
+ DOLBY_AC2 = 0x0030
119
+ GSM610 = 0x0031
120
+ MSNAUDIO = 0x0032
121
+ ANTEX_ADPCME = 0x0033
122
+ CONTROL_RES_VQLPC = 0x0034
123
+ DIGIREAL = 0x0035
124
+ DIGIADPCM = 0x0036
125
+ CONTROL_RES_CR10 = 0x0037
126
+ NMS_VBXADPCM = 0x0038
127
+ CS_IMAADPCM = 0x0039
128
+ ECHOSC3 = 0x003A
129
+ ROCKWELL_ADPCM = 0x003B
130
+ ROCKWELL_DIGITALK = 0x003C
131
+ XEBEC = 0x003D
132
+ G721_ADPCM = 0x0040
133
+ G728_CELP = 0x0041
134
+ MSG723 = 0x0042
135
+ INTEL_G723_1 = 0x0043
136
+ INTEL_G729 = 0x0044
137
+ SHARP_G726 = 0x0045
138
+ MPEG = 0x0050
139
+ RT24 = 0x0052
140
+ PAC = 0x0053
141
+ MPEGLAYER3 = 0x0055
142
+ LUCENT_G723 = 0x0059
143
+ CIRRUS = 0x0060
144
+ ESPCM = 0x0061
145
+ VOXWARE = 0x0062
146
+ CANOPUS_ATRAC = 0x0063
147
+ G726_ADPCM = 0x0064
148
+ G722_ADPCM = 0x0065
149
+ DSAT = 0x0066
150
+ DSAT_DISPLAY = 0x0067
151
+ VOXWARE_BYTE_ALIGNED = 0x0069
152
+ VOXWARE_AC8 = 0x0070
153
+ VOXWARE_AC10 = 0x0071
154
+ VOXWARE_AC16 = 0x0072
155
+ VOXWARE_AC20 = 0x0073
156
+ VOXWARE_RT24 = 0x0074
157
+ VOXWARE_RT29 = 0x0075
158
+ VOXWARE_RT29HW = 0x0076
159
+ VOXWARE_VR12 = 0x0077
160
+ VOXWARE_VR18 = 0x0078
161
+ VOXWARE_TQ40 = 0x0079
162
+ VOXWARE_SC3 = 0x007A
163
+ VOXWARE_SC3_1 = 0x007B
164
+ SOFTSOUND = 0x0080
165
+ VOXWARE_TQ60 = 0x0081
166
+ MSRT24 = 0x0082
167
+ G729A = 0x0083
168
+ MVI_MVI2 = 0x0084
169
+ DF_G726 = 0x0085
170
+ DF_GSM610 = 0x0086
171
+ ISIAUDIO = 0x0088
172
+ ONLIVE = 0x0089
173
+ MULTITUDE_FT_SX20 = 0x008A
174
+ INFOCOM_ITS_G721_ADPCM = 0x008B
175
+ CONVEDIA_G729 = 0x008C
176
+ CONGRUENCY = 0x008D
177
+ SBC24 = 0x0091
178
+ DOLBY_AC3_SPDIF = 0x0092
179
+ MEDIASONIC_G723 = 0x0093
180
+ PROSODY_8KBPS = 0x0094
181
+ ZYXEL_ADPCM = 0x0097
182
+ PHILIPS_LPCBB = 0x0098
183
+ PACKED = 0x0099
184
+ MALDEN_PHONYTALK = 0x00A0
185
+ RACAL_RECORDER_GSM = 0x00A1
186
+ RACAL_RECORDER_G720_A = 0x00A2
187
+ RACAL_RECORDER_G723_1 = 0x00A3
188
+ RACAL_RECORDER_TETRA_ACELP = 0x00A4
189
+ NEC_AAC = 0x00B0
190
+ RAW_AAC1 = 0x00FF
191
+ RHETOREX_ADPCM = 0x0100
192
+ IRAT = 0x0101
193
+ VIVO_G723 = 0x0111
194
+ VIVO_SIREN = 0x0112
195
+ PHILIPS_CELP = 0x0120
196
+ PHILIPS_GRUNDIG = 0x0121
197
+ DIGITAL_G723 = 0x0123
198
+ SANYO_LD_ADPCM = 0x0125
199
+ SIPROLAB_ACEPLNET = 0x0130
200
+ SIPROLAB_ACELP4800 = 0x0131
201
+ SIPROLAB_ACELP8V3 = 0x0132
202
+ SIPROLAB_G729 = 0x0133
203
+ SIPROLAB_G729A = 0x0134
204
+ SIPROLAB_KELVIN = 0x0135
205
+ VOICEAGE_AMR = 0x0136
206
+ G726ADPCM = 0x0140
207
+ DICTAPHONE_CELP68 = 0x0141
208
+ DICTAPHONE_CELP54 = 0x0142
209
+ QUALCOMM_PUREVOICE = 0x0150
210
+ QUALCOMM_HALFRATE = 0x0151
211
+ TUBGSM = 0x0155
212
+ MSAUDIO1 = 0x0160
213
+ WMAUDIO2 = 0x0161
214
+ WMAUDIO3 = 0x0162
215
+ WMAUDIO_LOSSLESS = 0x0163
216
+ WMASPDIF = 0x0164
217
+ UNISYS_NAP_ADPCM = 0x0170
218
+ UNISYS_NAP_ULAW = 0x0171
219
+ UNISYS_NAP_ALAW = 0x0172
220
+ UNISYS_NAP_16K = 0x0173
221
+ SYCOM_ACM_SYC008 = 0x0174
222
+ SYCOM_ACM_SYC701_G726L = 0x0175
223
+ SYCOM_ACM_SYC701_CELP54 = 0x0176
224
+ SYCOM_ACM_SYC701_CELP68 = 0x0177
225
+ KNOWLEDGE_ADVENTURE_ADPCM = 0x0178
226
+ FRAUNHOFER_IIS_MPEG2_AAC = 0x0180
227
+ DTS_DS = 0x0190
228
+ CREATIVE_ADPCM = 0x0200
229
+ CREATIVE_FASTSPEECH8 = 0x0202
230
+ CREATIVE_FASTSPEECH10 = 0x0203
231
+ UHER_ADPCM = 0x0210
232
+ ULEAD_DV_AUDIO = 0x0215
233
+ ULEAD_DV_AUDIO_1 = 0x0216
234
+ QUARTERDECK = 0x0220
235
+ ILINK_VC = 0x0230
236
+ RAW_SPORT = 0x0240
237
+ ESST_AC3 = 0x0241
238
+ GENERIC_PASSTHRU = 0x0249
239
+ IPI_HSX = 0x0250
240
+ IPI_RPELP = 0x0251
241
+ CS2 = 0x0260
242
+ SONY_SCX = 0x0270
243
+ SONY_SCY = 0x0271
244
+ SONY_ATRAC3 = 0x0272
245
+ SONY_SPC = 0x0273
246
+ TELUM_AUDIO = 0x0280
247
+ TELUM_IA_AUDIO = 0x0281
248
+ NORCOM_VOICE_SYSTEMS_ADPCM = 0x0285
249
+ FM_TOWNS_SND = 0x0300
250
+ MICRONAS = 0x0350
251
+ MICRONAS_CELP833 = 0x0351
252
+ BTV_DIGITAL = 0x0400
253
+ INTEL_MUSIC_CODER = 0x0401
254
+ INDEO_AUDIO = 0x0402
255
+ QDESIGN_MUSIC = 0x0450
256
+ ON2_VP7_AUDIO = 0x0500
257
+ ON2_VP6_AUDIO = 0x0501
258
+ VME_VMPCM = 0x0680
259
+ TPC = 0x0681
260
+ LIGHTWAVE_LOSSLESS = 0x08AE
261
+ OLIGSM = 0x1000
262
+ OLIADPCM = 0x1001
263
+ OLICELP = 0x1002
264
+ OLISBC = 0x1003
265
+ OLIOPR = 0x1004
266
+ LH_CODEC = 0x1100
267
+ LH_CODEC_CELP = 0x1101
268
+ LH_CODEC_SBC8 = 0x1102
269
+ LH_CODEC_SBC12 = 0x1103
270
+ LH_CODEC_SBC16 = 0x1104
271
+ NORRIS = 0x1400
272
+ ISIAUDIO_2 = 0x1401
273
+ SOUNDSPACE_MUSICOMPRESS = 0x1500
274
+ MPEG_ADTS_AAC = 0x1600
275
+ MPEG_RAW_AAC = 0x1601
276
+ MPEG_LOAS = 0x1602
277
+ NOKIA_MPEG_ADTS_AAC = 0x1608
278
+ NOKIA_MPEG_RAW_AAC = 0x1609
279
+ VODAFONE_MPEG_ADTS_AAC = 0x160A
280
+ VODAFONE_MPEG_RAW_AAC = 0x160B
281
+ MPEG_HEAAC = 0x1610
282
+ VOXWARE_RT24_SPEECH = 0x181C
283
+ SONICFOUNDRY_LOSSLESS = 0x1971
284
+ INNINGS_TELECOM_ADPCM = 0x1979
285
+ LUCENT_SX8300P = 0x1C07
286
+ LUCENT_SX5363S = 0x1C0C
287
+ CUSEEME = 0x1F03
288
+ NTCSOFT_ALF2CM_ACM = 0x1FC4
289
+ DVM = 0x2000
290
+ DTS2 = 0x2001
291
+ MAKEAVIS = 0x3313
292
+ DIVIO_MPEG4_AAC = 0x4143
293
+ NOKIA_ADAPTIVE_MULTIRATE = 0x4201
294
+ DIVIO_G726 = 0x4243
295
+ LEAD_SPEECH = 0x434C
296
+ LEAD_VORBIS = 0x564C
297
+ WAVPACK_AUDIO = 0x5756
298
+ OGG_VORBIS_MODE_1 = 0x674F
299
+ OGG_VORBIS_MODE_2 = 0x6750
300
+ OGG_VORBIS_MODE_3 = 0x6751
301
+ OGG_VORBIS_MODE_1_PLUS = 0x676F
302
+ OGG_VORBIS_MODE_2_PLUS = 0x6770
303
+ OGG_VORBIS_MODE_3_PLUS = 0x6771
304
+ ALAC = 0x6C61
305
+ _3COM_NBX = 0x7000 # Can't have leading digit
306
+ OPUS = 0x704F
307
+ FAAD_AAC = 0x706D
308
+ AMR_NB = 0x7361
309
+ AMR_WB = 0x7362
310
+ AMR_WP = 0x7363
311
+ GSM_AMR_CBR = 0x7A21
312
+ GSM_AMR_VBR_SID = 0x7A22
313
+ COMVERSE_INFOSYS_G723_1 = 0xA100
314
+ COMVERSE_INFOSYS_AVQSBC = 0xA101
315
+ COMVERSE_INFOSYS_SBC = 0xA102
316
+ SYMBOL_G729_A = 0xA103
317
+ VOICEAGE_AMR_WB = 0xA104
318
+ INGENIENT_G726 = 0xA105
319
+ MPEG4_AAC = 0xA106
320
+ ENCORE_G726 = 0xA107
321
+ ZOLL_ASAO = 0xA108
322
+ SPEEX_VOICE = 0xA109
323
+ VIANIX_MASC = 0xA10A
324
+ WM9_SPECTRUM_ANALYZER = 0xA10B
325
+ WMF_SPECTRUM_ANAYZER = 0xA10C
326
+ GSM_610 = 0xA10D
327
+ GSM_620 = 0xA10E
328
+ GSM_660 = 0xA10F
329
+ GSM_690 = 0xA110
330
+ GSM_ADAPTIVE_MULTIRATE_WB = 0xA111
331
+ POLYCOM_G722 = 0xA112
332
+ POLYCOM_G728 = 0xA113
333
+ POLYCOM_G729_A = 0xA114
334
+ POLYCOM_SIREN = 0xA115
335
+ GLOBAL_IP_ILBC = 0xA116
336
+ RADIOTIME_TIME_SHIFT_RADIO = 0xA117
337
+ NICE_ACA = 0xA118
338
+ NICE_ADPCM = 0xA119
339
+ VOCORD_G721 = 0xA11A
340
+ VOCORD_G726 = 0xA11B
341
+ VOCORD_G722_1 = 0xA11C
342
+ VOCORD_G728 = 0xA11D
343
+ VOCORD_G729 = 0xA11E
344
+ VOCORD_G729_A = 0xA11F
345
+ VOCORD_G723_1 = 0xA120
346
+ VOCORD_LBC = 0xA121
347
+ NICE_G728 = 0xA122
348
+ FRACE_TELECOM_G729 = 0xA123
349
+ CODIAN = 0xA124
350
+ FLAC = 0xF1AC
351
+ EXTENSIBLE = 0xFFFE
352
+ DEVELOPMENT = 0xFFFF
353
+
354
+
355
+ KNOWN_WAVE_FORMATS = {WAVE_FORMAT.PCM, WAVE_FORMAT.IEEE_FLOAT}
356
+
357
+
358
+ def _raise_bad_format(format_tag):
359
+ try:
360
+ format_name = WAVE_FORMAT(format_tag).name
361
+ except ValueError:
362
+ format_name = f'{format_tag:#06x}'
363
+ raise ValueError(f"Unknown wave file format: {format_name}. Supported "
364
+ "formats: " +
365
+ ', '.join(x.name for x in KNOWN_WAVE_FORMATS))
366
+
367
+
368
+ def _read_fmt_chunk(fid, is_big_endian):
369
+ """
370
+ Returns
371
+ -------
372
+ size : int
373
+ size of format subchunk in bytes (minus 8 for "fmt " and itself)
374
+ format_tag : int
375
+ PCM, float, or compressed format
376
+ channels : int
377
+ number of channels
378
+ fs : int
379
+ sampling frequency in samples per second
380
+ bytes_per_second : int
381
+ overall byte rate for the file
382
+ block_align : int
383
+ bytes per sample, including all channels
384
+ bit_depth : int
385
+ bits per sample
386
+
387
+ Notes
388
+ -----
389
+ Assumes file pointer is immediately after the 'fmt ' id
390
+ """
391
+ if is_big_endian:
392
+ fmt = '>'
393
+ else:
394
+ fmt = '<'
395
+
396
+ size = struct.unpack(fmt+'I', fid.read(4))[0]
397
+
398
+ if size < 16:
399
+ raise ValueError("Binary structure of wave file is not compliant")
400
+
401
+ res = struct.unpack(fmt+'HHIIHH', fid.read(16))
402
+ bytes_read = 16
403
+
404
+ format_tag, channels, fs, bytes_per_second, block_align, bit_depth = res
405
+
406
+ if format_tag == WAVE_FORMAT.EXTENSIBLE and size >= (16+2):
407
+ ext_chunk_size = struct.unpack(fmt+'H', fid.read(2))[0]
408
+ bytes_read += 2
409
+ if ext_chunk_size >= 22:
410
+ extensible_chunk_data = fid.read(22)
411
+ bytes_read += 22
412
+ raw_guid = extensible_chunk_data[2+4:2+4+16]
413
+ # GUID template {XXXXXXXX-0000-0010-8000-00AA00389B71} (RFC-2361)
414
+ # MS GUID byte order: first three groups are native byte order,
415
+ # rest is Big Endian
416
+ if is_big_endian:
417
+ tail = b'\x00\x00\x00\x10\x80\x00\x00\xAA\x00\x38\x9B\x71'
418
+ else:
419
+ tail = b'\x00\x00\x10\x00\x80\x00\x00\xAA\x00\x38\x9B\x71'
420
+ if raw_guid.endswith(tail):
421
+ format_tag = struct.unpack(fmt+'I', raw_guid[:4])[0]
422
+ else:
423
+ raise ValueError("Binary structure of wave file is not compliant")
424
+
425
+ if format_tag not in KNOWN_WAVE_FORMATS:
426
+ _raise_bad_format(format_tag)
427
+
428
+ # move file pointer to next chunk
429
+ if size > bytes_read:
430
+ fid.read(size - bytes_read)
431
+
432
+ # fmt should always be 16, 18 or 40, but handle it just in case
433
+ _handle_pad_byte(fid, size)
434
+
435
+ if format_tag == WAVE_FORMAT.PCM:
436
+ if bytes_per_second != fs * block_align:
437
+ raise ValueError("WAV header is invalid: nAvgBytesPerSec must"
438
+ " equal product of nSamplesPerSec and"
439
+ " nBlockAlign, but file has nSamplesPerSec ="
440
+ f" {fs}, nBlockAlign = {block_align}, and"
441
+ f" nAvgBytesPerSec = {bytes_per_second}")
442
+
443
+ return (size, format_tag, channels, fs, bytes_per_second, block_align,
444
+ bit_depth)
445
+
446
+
447
+ def _read_data_chunk(fid, format_tag, channels, bit_depth, is_big_endian, is_rf64,
448
+ block_align, mmap=False, rf64_chunk_size=None):
449
+ """
450
+ Notes
451
+ -----
452
+ Assumes file pointer is immediately after the 'data' id
453
+
454
+ It's possible to not use all available bits in a container, or to store
455
+ samples in a container bigger than necessary, so bytes_per_sample uses
456
+ the actual reported container size (nBlockAlign / nChannels). Real-world
457
+ examples:
458
+
459
+ Adobe Audition's "24-bit packed int (type 1, 20-bit)"
460
+
461
+ nChannels = 2, nBlockAlign = 6, wBitsPerSample = 20
462
+
463
+ http://www-mmsp.ece.mcgill.ca/Documents/AudioFormats/WAVE/Samples/AFsp/M1F1-int12-AFsp.wav
464
+ is:
465
+
466
+ nChannels = 2, nBlockAlign = 4, wBitsPerSample = 12
467
+
468
+ http://www-mmsp.ece.mcgill.ca/Documents/AudioFormats/WAVE/Docs/multichaudP.pdf
469
+ gives an example of:
470
+
471
+ nChannels = 2, nBlockAlign = 8, wBitsPerSample = 20
472
+ """
473
+ if is_big_endian:
474
+ fmt = '>'
475
+ else:
476
+ fmt = '<'
477
+
478
+ # Size of the data subchunk in bytes
479
+ if not is_rf64:
480
+ size = struct.unpack(fmt+'I', fid.read(4))[0]
481
+ else:
482
+ # chunk size is stored in global file header for RF64
483
+ size = rf64_chunk_size
484
+ # skip data chunk size as it is 0xFFFFFFF
485
+ fid.read(4)
486
+
487
+ # Number of bytes per sample (sample container size)
488
+ bytes_per_sample = block_align // channels
489
+ n_samples = size // bytes_per_sample
490
+
491
+ if format_tag == WAVE_FORMAT.PCM:
492
+ if 1 <= bit_depth <= 8:
493
+ dtype = 'u1' # WAV of 8-bit integer or less are unsigned
494
+ elif bytes_per_sample in {3, 5, 6, 7}:
495
+ # No compatible dtype. Load as raw bytes for reshaping later.
496
+ dtype = 'V1'
497
+ elif bit_depth <= 64:
498
+ # Remaining bit depths can map directly to signed numpy dtypes
499
+ dtype = f'{fmt}i{bytes_per_sample}'
500
+ else:
501
+ raise ValueError("Unsupported bit depth: the WAV file "
502
+ f"has {bit_depth}-bit integer data.")
503
+ elif format_tag == WAVE_FORMAT.IEEE_FLOAT:
504
+ if bit_depth in {32, 64}:
505
+ dtype = f'{fmt}f{bytes_per_sample}'
506
+ else:
507
+ raise ValueError("Unsupported bit depth: the WAV file "
508
+ f"has {bit_depth}-bit floating-point data.")
509
+ else:
510
+ _raise_bad_format(format_tag)
511
+
512
+ start = fid.tell()
513
+ if not mmap:
514
+ try:
515
+ count = size if dtype == 'V1' else n_samples
516
+ data = np.fromfile(fid, dtype=dtype, count=count)
517
+ except io.UnsupportedOperation: # not a C-like file
518
+ fid.seek(start, 0) # just in case it seeked, though it shouldn't
519
+ data = np.frombuffer(fid.read(size), dtype=dtype)
520
+
521
+ if dtype == 'V1':
522
+ # Rearrange raw bytes into smallest compatible numpy dtype
523
+ dt = f'{fmt}i4' if bytes_per_sample == 3 else f'{fmt}i8'
524
+ a = np.zeros((len(data) // bytes_per_sample, np.dtype(dt).itemsize),
525
+ dtype='V1')
526
+ if is_big_endian:
527
+ a[:, :bytes_per_sample] = data.reshape((-1, bytes_per_sample))
528
+ else:
529
+ a[:, -bytes_per_sample:] = data.reshape((-1, bytes_per_sample))
530
+ data = a.view(dt).reshape(a.shape[:-1])
531
+ else:
532
+ if bytes_per_sample in {1, 2, 4, 8}:
533
+ start = fid.tell()
534
+ data = np.memmap(fid, dtype=dtype, mode='c', offset=start,
535
+ shape=(n_samples,))
536
+ fid.seek(start + size)
537
+ else:
538
+ raise ValueError("mmap=True not compatible with "
539
+ f"{bytes_per_sample}-byte container size.")
540
+
541
+ _handle_pad_byte(fid, size)
542
+
543
+ if channels > 1:
544
+ data = data.reshape(-1, channels)
545
+ return data
546
+
547
+
548
+ def _skip_unknown_chunk(fid, is_big_endian):
549
+ if is_big_endian:
550
+ fmt = '>I'
551
+ else:
552
+ fmt = '<I'
553
+
554
+ data = fid.read(4)
555
+ # call unpack() and seek() only if we have really read data from file
556
+ # otherwise empty read at the end of the file would trigger
557
+ # unnecessary exception at unpack() call
558
+ # in case data equals somehow to 0, there is no need for seek() anyway
559
+ if data:
560
+ size = struct.unpack(fmt, data)[0]
561
+ fid.seek(size, 1)
562
+ _handle_pad_byte(fid, size)
563
+
564
+
565
+ def _read_riff_chunk(fid):
566
+ str1 = fid.read(4) # File signature
567
+ if str1 == b'RIFF':
568
+ is_rf64 = False
569
+ is_big_endian = False
570
+ fmt = '<I'
571
+ elif str1 == b'RIFX':
572
+ is_rf64 = False
573
+ is_big_endian = True
574
+ fmt = '>I'
575
+ elif str1 == b'RF64':
576
+ is_rf64 = True
577
+ is_big_endian = False
578
+ fmt = '<Q'
579
+ else:
580
+ # There are also .wav files with "FFIR" or "XFIR" signatures?
581
+ raise ValueError(f"File format {repr(str1)} not understood. Only "
582
+ "'RIFF', 'RIFX', and 'RF64' supported.")
583
+ # Size of entire file
584
+ if not is_rf64:
585
+ file_size = struct.unpack(fmt, fid.read(4))[0] + 8
586
+ rf64_chunk_size = None
587
+ str2 = fid.read(4)
588
+ else:
589
+ # Skip 0xFFFFFFFF (-1) bytes
590
+ fid.read(4)
591
+ str2 = fid.read(4)
592
+ str3 = fid.read(4)
593
+ if str3 != b'ds64':
594
+ raise ValueError("Invalid RF64 file: ds64 chunk not found.")
595
+ ds64_size = struct.unpack("<I", fid.read(4))[0]
596
+ file_size = struct.unpack(fmt, fid.read(8))[0] + 8
597
+ rf64_chunk_size = struct.unpack('<Q', fid.read(8))[0]
598
+ # Ignore additional attributes of ds64 chunk like sample count, tables, etc.
599
+ # and just skip to the next chunk
600
+ fid.seek(ds64_size - 16, 1)
601
+
602
+ if str2 != b'WAVE':
603
+ raise ValueError(f"Not a WAV file. RIFF form type is {repr(str2)}.")
604
+
605
+ return file_size, is_big_endian, is_rf64, rf64_chunk_size
606
+
607
+
608
+ def _handle_pad_byte(fid, size):
609
+ # "If the chunk size is an odd number of bytes, a pad byte with value zero
610
+ # is written after ckData." So we need to seek past this after each chunk.
611
+ if size % 2:
612
+ fid.seek(1, 1)
613
+
614
+
615
+ def read(filename, mmap=False):
616
+ """
617
+ Open a WAV file.
618
+
619
+ Return the sample rate (in samples/sec) and data from an LPCM WAV file.
620
+
621
+ Parameters
622
+ ----------
623
+ filename : string or open file handle
624
+ Input WAV file.
625
+ mmap : bool, optional
626
+ Whether to read data as memory-mapped (default: False). Not compatible
627
+ with some bit depths; see Notes. Only to be used on real files.
628
+
629
+ .. versionadded:: 0.12.0
630
+
631
+ Returns
632
+ -------
633
+ rate : int
634
+ Sample rate of WAV file.
635
+ data : numpy array
636
+ Data read from WAV file. Data-type is determined from the file;
637
+ see Notes. Data is 1-D for 1-channel WAV, or 2-D of shape
638
+ (Nsamples, Nchannels) otherwise. If a file-like input without a
639
+ C-like file descriptor (e.g., :class:`python:io.BytesIO`) is
640
+ passed, this will not be writeable.
641
+
642
+ Notes
643
+ -----
644
+ Common data types: [1]_
645
+
646
+ ===================== =========== =========== =============
647
+ WAV format Min Max NumPy dtype
648
+ ===================== =========== =========== =============
649
+ 32-bit floating-point -1.0 +1.0 float32
650
+ 32-bit integer PCM -2147483648 +2147483647 int32
651
+ 24-bit integer PCM -2147483648 +2147483392 int32
652
+ 16-bit integer PCM -32768 +32767 int16
653
+ 8-bit integer PCM 0 255 uint8
654
+ ===================== =========== =========== =============
655
+
656
+ WAV files can specify arbitrary bit depth, and this function supports
657
+ reading any integer PCM depth from 1 to 64 bits. Data is returned in the
658
+ smallest compatible numpy int type, in left-justified format. 8-bit and
659
+ lower is unsigned, while 9-bit and higher is signed.
660
+
661
+ For example, 24-bit data will be stored as int32, with the MSB of the
662
+ 24-bit data stored at the MSB of the int32, and typically the least
663
+ significant byte is 0x00. (However, if a file actually contains data past
664
+ its specified bit depth, those bits will be read and output, too. [2]_)
665
+
666
+ This bit justification and sign matches WAV's native internal format, which
667
+ allows memory mapping of WAV files that use 1, 2, 4, or 8 bytes per sample
668
+ (so 24-bit files cannot be memory-mapped, but 32-bit can).
669
+
670
+ IEEE float PCM in 32- or 64-bit format is supported, with or without mmap.
671
+ Values exceeding [-1, +1] are not clipped.
672
+
673
+ Non-linear PCM (mu-law, A-law) is not supported.
674
+
675
+ References
676
+ ----------
677
+ .. [1] IBM Corporation and Microsoft Corporation, "Multimedia Programming
678
+ Interface and Data Specifications 1.0", section "Data Format of the
679
+ Samples", August 1991
680
+ http://www.tactilemedia.com/info/MCI_Control_Info.html
681
+ .. [2] Adobe Systems Incorporated, "Adobe Audition 3 User Guide", section
682
+ "Audio file formats: 24-bit Packed Int (type 1, 20-bit)", 2007
683
+
684
+ Examples
685
+ --------
686
+ >>> from os.path import dirname, join as pjoin
687
+ >>> from scipy.io import wavfile
688
+ >>> import scipy.io
689
+
690
+ Get the filename for an example .wav file from the tests/data directory.
691
+
692
+ >>> data_dir = pjoin(dirname(scipy.io.__file__), 'tests', 'data')
693
+ >>> wav_fname = pjoin(data_dir, 'test-44100Hz-2ch-32bit-float-be.wav')
694
+
695
+ Load the .wav file contents.
696
+
697
+ >>> samplerate, data = wavfile.read(wav_fname)
698
+ >>> print(f"number of channels = {data.shape[1]}")
699
+ number of channels = 2
700
+ >>> length = data.shape[0] / samplerate
701
+ >>> print(f"length = {length}s")
702
+ length = 0.01s
703
+
704
+ Plot the waveform.
705
+
706
+ >>> import matplotlib.pyplot as plt
707
+ >>> import numpy as np
708
+ >>> time = np.linspace(0., length, data.shape[0])
709
+ >>> plt.plot(time, data[:, 0], label="Left channel")
710
+ >>> plt.plot(time, data[:, 1], label="Right channel")
711
+ >>> plt.legend()
712
+ >>> plt.xlabel("Time [s]")
713
+ >>> plt.ylabel("Amplitude")
714
+ >>> plt.show()
715
+
716
+ """
717
+ if hasattr(filename, 'read'):
718
+ fid = filename
719
+ mmap = False
720
+ else:
721
+ fid = open(filename, 'rb')
722
+
723
+ if not (was_seekable := fid.seekable()):
724
+ fid = SeekEmulatingReader(fid)
725
+
726
+ try:
727
+ file_size, is_big_endian, is_rf64, rf64_chunk_size = _read_riff_chunk(fid)
728
+ fmt_chunk_received = False
729
+ data_chunk_received = False
730
+ while fid.tell() < file_size:
731
+ # read the next chunk
732
+ chunk_id = fid.read(4)
733
+
734
+ if not chunk_id:
735
+ if data_chunk_received:
736
+ # End of file but data successfully read
737
+ warnings.warn(
738
+ f"Reached EOF prematurely; finished at {fid.tell():d} bytes, "
739
+ f"expected {file_size:d} bytes from header.",
740
+ WavFileWarning, stacklevel=2)
741
+ break
742
+ else:
743
+ raise ValueError("Unexpected end of file.")
744
+ elif len(chunk_id) < 4:
745
+ msg = f"Incomplete chunk ID: {repr(chunk_id)}"
746
+ # If we have the data, ignore the broken chunk
747
+ if fmt_chunk_received and data_chunk_received:
748
+ warnings.warn(msg + ", ignoring it.", WavFileWarning,
749
+ stacklevel=2)
750
+ else:
751
+ raise ValueError(msg)
752
+
753
+ if chunk_id == b'fmt ':
754
+ fmt_chunk_received = True
755
+ fmt_chunk = _read_fmt_chunk(fid, is_big_endian)
756
+ format_tag, channels, fs = fmt_chunk[1:4]
757
+ bit_depth = fmt_chunk[6]
758
+ block_align = fmt_chunk[5]
759
+ elif chunk_id == b'fact':
760
+ _skip_unknown_chunk(fid, is_big_endian)
761
+ elif chunk_id == b'data':
762
+ data_chunk_received = True
763
+ if not fmt_chunk_received:
764
+ raise ValueError("No fmt chunk before data")
765
+ data = _read_data_chunk(fid, format_tag, channels, bit_depth,
766
+ is_big_endian, is_rf64, block_align,
767
+ mmap, rf64_chunk_size)
768
+ elif chunk_id == b'LIST':
769
+ # Someday this could be handled properly but for now skip it
770
+ _skip_unknown_chunk(fid, is_big_endian)
771
+ elif chunk_id in {b'JUNK', b'Fake'}:
772
+ # Skip alignment chunks without warning
773
+ _skip_unknown_chunk(fid, is_big_endian)
774
+ else:
775
+ warnings.warn("Chunk (non-data) not understood, skipping it.",
776
+ WavFileWarning, stacklevel=2)
777
+ _skip_unknown_chunk(fid, is_big_endian)
778
+ finally:
779
+ if not hasattr(filename, 'read'):
780
+ fid.close()
781
+ elif was_seekable:
782
+ # Rewind, if we are able, so that caller can do something
783
+ # else with the raw WAV stream.
784
+ fid.seek(0)
785
+
786
+ return fs, data
787
+
788
+
789
+ def write(filename, rate, data):
790
+ """
791
+ Write a NumPy array as a WAV file.
792
+
793
+ Parameters
794
+ ----------
795
+ filename : string or open file handle
796
+ Output wav file.
797
+ rate : int
798
+ The sample rate (in samples/sec).
799
+ data : ndarray
800
+ A 1-D or 2-D NumPy array of either integer or float data-type.
801
+
802
+ Notes
803
+ -----
804
+ * Writes a simple uncompressed WAV file.
805
+ * To write multiple-channels, use a 2-D array of shape
806
+ (Nsamples, Nchannels).
807
+ * The bits-per-sample and PCM/float will be determined by the data-type.
808
+
809
+ Common data types: [1]_
810
+
811
+ ===================== =========== =========== =============
812
+ WAV format Min Max NumPy dtype
813
+ ===================== =========== =========== =============
814
+ 32-bit floating-point -1.0 +1.0 float32
815
+ 32-bit PCM -2147483648 +2147483647 int32
816
+ 16-bit PCM -32768 +32767 int16
817
+ 8-bit PCM 0 255 uint8
818
+ ===================== =========== =========== =============
819
+
820
+ Note that 8-bit PCM is unsigned.
821
+
822
+ References
823
+ ----------
824
+ .. [1] IBM Corporation and Microsoft Corporation, "Multimedia Programming
825
+ Interface and Data Specifications 1.0", section "Data Format of the
826
+ Samples", August 1991
827
+ http://www.tactilemedia.com/info/MCI_Control_Info.html
828
+
829
+ Examples
830
+ --------
831
+ Create a 100Hz sine wave, sampled at 44100Hz.
832
+ Write to 16-bit PCM, Mono.
833
+
834
+ >>> from scipy.io.wavfile import write
835
+ >>> import numpy as np
836
+ >>> samplerate = 44100; fs = 100
837
+ >>> t = np.linspace(0., 1., samplerate)
838
+ >>> amplitude = np.iinfo(np.int16).max
839
+ >>> data = amplitude * np.sin(2. * np.pi * fs * t)
840
+ >>> write("example.wav", samplerate, data.astype(np.int16))
841
+
842
+ """
843
+ if hasattr(filename, 'write'):
844
+ fid = filename
845
+ else:
846
+ fid = open(filename, 'wb')
847
+
848
+ fs = rate
849
+
850
+ try:
851
+ dkind = data.dtype.kind
852
+ allowed_dtypes = ['float32', 'float64',
853
+ 'uint8', 'int16', 'int32', 'int64']
854
+ if data.dtype.name not in allowed_dtypes:
855
+ raise ValueError(f"Unsupported data type '{data.dtype}'")
856
+
857
+ header_data = b''
858
+
859
+ header_data += b'RIFF'
860
+ header_data += b'\x00\x00\x00\x00'
861
+ header_data += b'WAVE'
862
+
863
+ # fmt chunk
864
+ header_data += b'fmt '
865
+ if dkind == 'f':
866
+ format_tag = WAVE_FORMAT.IEEE_FLOAT
867
+ else:
868
+ format_tag = WAVE_FORMAT.PCM
869
+ if data.ndim == 1:
870
+ channels = 1
871
+ else:
872
+ channels = data.shape[1]
873
+ bit_depth = data.dtype.itemsize * 8
874
+ bytes_per_second = fs*(bit_depth // 8)*channels
875
+ block_align = channels * (bit_depth // 8)
876
+
877
+ fmt_chunk_data = struct.pack('<HHIIHH', format_tag, channels, fs,
878
+ bytes_per_second, block_align, bit_depth)
879
+ if not (dkind == 'i' or dkind == 'u'):
880
+ # add cbSize field for non-PCM files
881
+ fmt_chunk_data += b'\x00\x00'
882
+
883
+ header_data += struct.pack('<I', len(fmt_chunk_data))
884
+ header_data += fmt_chunk_data
885
+
886
+ # check data size (needs to be immediately before the data chunk)
887
+ # if too large for standard RIFF, use RF64 instead
888
+ resulting_file_size = len(header_data) + 4 + 4 + data.nbytes
889
+ is_rf64 = (resulting_file_size - 8) > 0xFFFFFFFF
890
+ if is_rf64:
891
+ header_data = b''
892
+ header_data += b'RF64'
893
+ header_data += b'\xFF\xFF\xFF\xFF'
894
+ header_data += b'WAVE'
895
+ header_data += b'ds64'
896
+ # size of ds64 chunk
897
+ header_data += struct.pack('<I', 28)
898
+ # will be filled later with real file size
899
+ header_data += struct.pack('<Q', 0)
900
+ header_data += struct.pack('<Q', data.nbytes)
901
+ header_data += struct.pack('<Q', data.shape[0])
902
+ # ignore 'table' field for now
903
+ header_data += struct.pack('<I', 0)
904
+ header_data += b'fmt '
905
+ header_data += struct.pack('<I', len(fmt_chunk_data))
906
+ header_data += fmt_chunk_data
907
+
908
+ # fact chunk (non-PCM files)
909
+ if not (dkind == 'i' or dkind == 'u'):
910
+ header_data += b'fact'
911
+ header_data += struct.pack('<II', 4, data.shape[0])
912
+
913
+ fid.write(header_data)
914
+
915
+ # data chunk
916
+ fid.write(b'data')
917
+ # write data chunk size, unless its too big in which case 0xFFFFFFFF is written
918
+ fid.write(struct.pack('<I', min(data.nbytes, 4294967295)))
919
+
920
+ if data.dtype.byteorder == '>' or (data.dtype.byteorder == '=' and
921
+ sys.byteorder == 'big'):
922
+ data = data.byteswap()
923
+ _array_tofile(fid, data)
924
+
925
+ # Determine file size and place it in correct
926
+ # position at start of the file or the data chunk.
927
+ size = fid.tell()
928
+ if not is_rf64:
929
+ fid.seek(4)
930
+ fid.write(struct.pack('<I', size-8))
931
+ else:
932
+ fid.seek(20)
933
+ fid.write(struct.pack('<Q', size-8))
934
+
935
+ finally:
936
+ if not hasattr(filename, 'write'):
937
+ fid.close()
938
+ else:
939
+ fid.seek(0)
940
+
941
+
942
+ def _array_tofile(fid, data):
943
+ # ravel gives a c-contiguous buffer
944
+ fid.write(data.ravel().view('b').data)
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/linalg/__init__.pxd ADDED
@@ -0,0 +1 @@
 
 
1
+ from scipy.linalg cimport cython_blas, cython_lapack
data/conda_envs/evalclaw/lib/python3.11/site-packages/scipy/linalg/__init__.py ADDED
@@ -0,0 +1,234 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """
2
+ ====================================
3
+ Linear algebra (:mod:`scipy.linalg`)
4
+ ====================================
5
+
6
+ .. currentmodule:: scipy.linalg
7
+
8
+ .. toctree::
9
+ :hidden:
10
+
11
+ linalg.blas
12
+ linalg.cython_blas
13
+ linalg.cython_lapack
14
+ linalg.interpolative
15
+ linalg.lapack
16
+
17
+ Linear algebra functions.
18
+
19
+ .. eventually, we should replace the numpy.linalg HTML link with just `numpy.linalg`
20
+
21
+ .. seealso::
22
+
23
+ `numpy.linalg <https://www.numpy.org/devdocs/reference/routines.linalg.html>`__
24
+ for more linear algebra functions. Note that identically named
25
+ functions from `scipy.linalg` may offer more or slightly differing
26
+ functionality.
27
+
28
+
29
+ Basics
30
+ ======
31
+
32
+ .. autosummary::
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+ :toctree: generated/
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+
35
+ inv - Find the inverse of a square matrix
36
+ solve - Solve a linear system of equations
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+ solve_banded - Solve a banded linear system
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+ solveh_banded - Solve a Hermitian or symmetric banded system
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+ solve_circulant - Solve a circulant system
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+ solve_triangular - Solve a triangular matrix
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+ solve_toeplitz - Solve a toeplitz matrix
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+ matmul_toeplitz - Multiply a Toeplitz matrix with an array.
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+ det - Find the determinant of a square matrix
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+ norm - Matrix and vector norm
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+ lstsq - Solve a linear least-squares problem
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+ pinv - Pseudo-inverse (Moore-Penrose) using lstsq
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+ pinvh - Pseudo-inverse of hermitian matrix
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+ khatri_rao - Khatri-Rao product of two arrays
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+ orthogonal_procrustes - Solve an orthogonal Procrustes problem
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+ matrix_balance - Balance matrix entries with a similarity transformation
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+ subspace_angles - Compute the subspace angles between two matrices
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+ bandwidth - Return the lower and upper bandwidth of an array
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+ issymmetric - Check if a square 2D array is symmetric
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+ ishermitian - Check if a square 2D array is Hermitian
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+ LinAlgError
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+ LinAlgWarning
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+
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+ Eigenvalue Problems
59
+ ===================
60
+
61
+ .. autosummary::
62
+ :toctree: generated/
63
+
64
+ eig - Find the eigenvalues and eigenvectors of a square matrix
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+ eigvals - Find just the eigenvalues of a square matrix
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+ eigh - Find the e-vals and e-vectors of a Hermitian or symmetric matrix
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+ eigvalsh - Find just the eigenvalues of a Hermitian or symmetric matrix
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+ eig_banded - Find the eigenvalues and eigenvectors of a banded matrix
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+ eigvals_banded - Find just the eigenvalues of a banded matrix
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+ eigh_tridiagonal - Find the eigenvalues and eigenvectors of a tridiagonal matrix
71
+ eigvalsh_tridiagonal - Find just the eigenvalues of a tridiagonal matrix
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+
73
+ Decompositions
74
+ ==============
75
+
76
+ .. autosummary::
77
+ :toctree: generated/
78
+
79
+ lu - LU decomposition of a matrix
80
+ lu_factor - LU decomposition returning unordered matrix and pivots
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+ lu_solve - Solve Ax=b using back substitution with output of lu_factor
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+ svd - Singular value decomposition of a matrix
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+ svdvals - Singular values of a matrix
84
+ diagsvd - Construct matrix of singular values from output of svd
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+ orth - Construct orthonormal basis for the range of A using svd
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+ null_space - Construct orthonormal basis for the null space of A using svd
87
+ ldl - LDL.T decomposition of a Hermitian or a symmetric matrix.
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+ cholesky - Cholesky decomposition of a matrix
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+ cholesky_banded - Cholesky decomp. of a sym. or Hermitian banded matrix
90
+ cho_factor - Cholesky decomposition for use in solving a linear system
91
+ cho_solve - Solve previously factored linear system
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+ cho_solve_banded - Solve previously factored banded linear system
93
+ polar - Compute the polar decomposition.
94
+ qr - QR decomposition of a matrix
95
+ qr_multiply - QR decomposition and multiplication by Q
96
+ qr_update - Rank k QR update
97
+ qr_delete - QR downdate on row or column deletion
98
+ qr_insert - QR update on row or column insertion
99
+ rq - RQ decomposition of a matrix
100
+ qz - QZ decomposition of a pair of matrices
101
+ ordqz - QZ decomposition of a pair of matrices with reordering
102
+ schur - Schur decomposition of a matrix
103
+ rsf2csf - Real to complex Schur form
104
+ hessenberg - Hessenberg form of a matrix
105
+ cdf2rdf - Complex diagonal form to real diagonal block form
106
+ cossin - Cosine sine decomposition of a unitary or orthogonal matrix
107
+
108
+ .. seealso::
109
+
110
+ `scipy.linalg.interpolative` -- Interpolative matrix decompositions
111
+
112
+
113
+ Matrix Functions
114
+ ================
115
+
116
+ .. autosummary::
117
+ :toctree: generated/
118
+
119
+ expm - Matrix exponential
120
+ logm - Matrix logarithm
121
+ cosm - Matrix cosine
122
+ sinm - Matrix sine
123
+ tanm - Matrix tangent
124
+ coshm - Matrix hyperbolic cosine
125
+ sinhm - Matrix hyperbolic sine
126
+ tanhm - Matrix hyperbolic tangent
127
+ signm - Matrix sign
128
+ sqrtm - Matrix square root
129
+ funm - Evaluating an arbitrary matrix function
130
+ expm_frechet - Frechet derivative of the matrix exponential
131
+ expm_cond - Relative condition number of expm in the Frobenius norm
132
+ fractional_matrix_power - Fractional matrix power
133
+
134
+
135
+ Matrix Equation Solvers
136
+ =======================
137
+
138
+ .. autosummary::
139
+ :toctree: generated/
140
+
141
+ solve_sylvester - Solve the Sylvester matrix equation
142
+ solve_continuous_are - Solve the continuous-time algebraic Riccati equation
143
+ solve_discrete_are - Solve the discrete-time algebraic Riccati equation
144
+ solve_continuous_lyapunov - Solve the continuous-time Lyapunov equation
145
+ solve_discrete_lyapunov - Solve the discrete-time Lyapunov equation
146
+
147
+
148
+ Sketches and Random Projections
149
+ ===============================
150
+
151
+ .. autosummary::
152
+ :toctree: generated/
153
+
154
+ clarkson_woodruff_transform - Applies the Clarkson Woodruff Sketch (a.k.a CountMin Sketch)
155
+
156
+ Special Matrices
157
+ ================
158
+
159
+ .. autosummary::
160
+ :toctree: generated/
161
+
162
+ block_diag - Construct a block diagonal matrix from submatrices
163
+ circulant - Circulant matrix
164
+ companion - Companion matrix
165
+ convolution_matrix - Convolution matrix
166
+ dft - Discrete Fourier transform matrix
167
+ fiedler - Fiedler matrix
168
+ fiedler_companion - Fiedler companion matrix
169
+ hadamard - Hadamard matrix of order 2**n
170
+ hankel - Hankel matrix
171
+ helmert - Helmert matrix
172
+ hilbert - Hilbert matrix
173
+ invhilbert - Inverse Hilbert matrix
174
+ leslie - Leslie matrix
175
+ pascal - Pascal matrix
176
+ invpascal - Inverse Pascal matrix
177
+ toeplitz - Toeplitz matrix
178
+
179
+ Low-level routines
180
+ ==================
181
+
182
+ .. autosummary::
183
+ :toctree: generated/
184
+
185
+ get_blas_funcs
186
+ get_lapack_funcs
187
+ find_best_blas_type
188
+
189
+ .. seealso::
190
+
191
+ `scipy.linalg.blas` -- Low-level BLAS functions
192
+
193
+ `scipy.linalg.lapack` -- Low-level LAPACK functions
194
+
195
+ `scipy.linalg.cython_blas` -- Low-level BLAS functions for Cython
196
+
197
+ `scipy.linalg.cython_lapack` -- Low-level LAPACK functions for Cython
198
+
199
+ """ # noqa: E501
200
+
201
+ from ._misc import *
202
+ from ._cythonized_array_utils import *
203
+ from ._basic import *
204
+ from ._decomp import *
205
+ from ._decomp_lu import *
206
+ from ._decomp_ldl import *
207
+ from ._decomp_cholesky import *
208
+ from ._decomp_qr import *
209
+ from ._decomp_qz import *
210
+ from ._decomp_svd import *
211
+ from ._decomp_schur import *
212
+ from ._decomp_polar import *
213
+ from ._matfuncs import *
214
+ from .blas import *
215
+ from .lapack import *
216
+ from ._special_matrices import *
217
+ from ._solvers import *
218
+ from ._procrustes import *
219
+ from ._decomp_update import *
220
+ from ._sketches import *
221
+ from ._decomp_cossin import *
222
+
223
+ # Deprecated namespaces, to be removed in v2.0.0
224
+ from . import (
225
+ decomp, decomp_cholesky, decomp_lu, decomp_qr, decomp_svd, decomp_schur,
226
+ basic, misc, special_matrices, matfuncs,
227
+ )
228
+
229
+ __all__ = [s for s in dir() if not s.startswith('_')]
230
+
231
+
232
+ from scipy._lib._testutils import PytestTester
233
+ test = PytestTester(__name__)
234
+ del PytestTester