File size: 36,621 Bytes
a65c2f8 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 | import functools
import inspect
import sys
import warnings
from contextlib import contextmanager
import numpy as np
from ._warnings import all_warnings, warn
__all__ = [
'deprecate_func',
'get_bound_method_class',
'all_warnings',
'safe_as_int',
'check_shape_equality',
'check_nD',
'warn',
'reshape_nd',
'identity',
'slice_at_axis',
"deprecate_parameter",
"DEPRECATED",
]
def count_inner_wrappers(func):
"""Count the number of inner wrappers by unpacking ``__wrapped__``.
If a wrapped function wraps another wrapped function, then we refer to the
wrapping of the second function as an *inner wrapper*.
For example, consider this code fragment:
.. code-block:: python
@wrap_outer
@wrap_inner
def foo():
pass
Here ``@wrap_inner`` applies a wrapper to ``foo``, and ``@wrap_outer``
applies a wrapper to the result.
Parameters
----------
func : callable
The callable of which to determine the number of inner wrappers.
Returns
-------
count : int
The number of times `func` has been wrapped.
See Also
--------
count_global_wrappers
"""
unwrapped = func
count = 0
while hasattr(unwrapped, "__wrapped__"):
unwrapped = unwrapped.__wrapped__
count += 1
return count
def _warning_stacklevel(func):
"""Find stacklevel of `func` relative to its global representation.
Determine automatically with which stacklevel a warning should be raised.
Parameters
----------
func : Callable
Tries to find the global version of `func` and counts the number of
additional wrappers around `func`.
Returns
-------
stacklevel : int
The stacklevel. Minimum of 2.
"""
# Count number of wrappers around `func`
inner_wrapped_count = count_inner_wrappers(func)
global_wrapped_count = count_global_wrappers(func)
stacklevel = global_wrapped_count - inner_wrapped_count + 1
return max(stacklevel, 2)
def count_global_wrappers(func):
"""Count the total number of times a function as been wrapped globally.
Similar to :func:`count_inner_wrappers`, this counts the number of times
`func` has been wrapped. However, this function doesn't start counting
from `func` but instead tries to access the "global representation" of
`func`. This means that you could use this function from inside a wrapper
that was applied first, and still count wrappers that were applied on
top of it afterwards.
E.g., `func` might be wrapped by multiple decorators that emit
warnings. In that case, calling this function in the inner-most decorator
will still return the total count of wrappers.
Parameters
----------
func : callable
The callable of which to determine the number of wrappers. Can be a
function or method of a class.
Returns
-------
count : int
The number of times `func` has been wrapped.
See Also
--------
count_inner_wrappers
"""
if "<locals>" in func.__qualname__:
msg = (
"Cannot determine stacklevel of a function defined in another "
"function's local namespace. Set the stacklevel manually."
)
raise ValueError(msg)
first_name, *other = func.__qualname__.split(".")
global_func = func.__globals__.get(first_name, func)
# Account for `func` being a method, in which case it's an attribute of
# what we got from `func.__globals__`
for part in other:
global_func = getattr(global_func, part, global_func)
count = count_inner_wrappers(global_func)
assert count >= 0
return count
class change_default_value:
"""Decorator for changing the default value of an argument.
Parameters
----------
arg_name : str
The name of the argument to be updated.
new_value : any
The argument new value.
changed_version : str
The package version in which the change will be introduced.
warning_msg : str
Optional warning message. If None, a generic warning message
is used.
stacklevel : {None, int}, optional
If None, the decorator attempts to detect the appropriate stacklevel for the
deprecation warning automatically. This can fail, e.g., due to
decorating a closure, in which case you can set the stacklevel manually
here. The outermost decorator should have stacklevel 2, the next inner
one stacklevel 3, etc.
"""
def __init__(
self, arg_name, *, new_value, changed_version, warning_msg=None, stacklevel=None
):
self.arg_name = arg_name
self.new_value = new_value
self.warning_msg = warning_msg
self.changed_version = changed_version
self.stacklevel = stacklevel
def __call__(self, func):
parameters = inspect.signature(func).parameters
arg_idx = list(parameters.keys()).index(self.arg_name)
old_value = parameters[self.arg_name].default
if self.warning_msg is None:
self.warning_msg = (
f'The new recommended value for {self.arg_name} is '
f'{self.new_value}. Until version {self.changed_version}, '
f'the default {self.arg_name} value is {old_value}. '
f'From version {self.changed_version}, the {self.arg_name} '
f'default value will be {self.new_value}. To avoid '
f'this warning, please explicitly set {self.arg_name} value.'
)
@functools.wraps(func)
def fixed_func(*args, **kwargs):
if len(args) < arg_idx + 1 and self.arg_name not in kwargs.keys():
stacklevel = (
self.stacklevel
if self.stacklevel is not None
else _warning_stacklevel(func)
)
# warn that arg_name default value changed:
warnings.warn(self.warning_msg, FutureWarning, stacklevel=stacklevel)
return func(*args, **kwargs)
return fixed_func
class PatchClassRepr(type):
"""Control class representations in rendered signatures."""
def __repr__(cls):
return f"<{cls.__name__}>"
class DEPRECATED(metaclass=PatchClassRepr):
"""Signal value to help with deprecating parameters that use None.
This is a proxy object, used to signal that a parameter has not been set.
This is useful if ``None`` is already used for a different purpose or just
to highlight a deprecated parameter in the signature.
"""
class deprecate_parameter:
"""Deprecate a parameter of a function.
Parameters
----------
deprecated_name : str
The name of the deprecated parameter.
start_version : str
The package version in which the warning was introduced.
stop_version : str
The package version in which the warning will be replaced by
an error / the deprecation is completed.
template : str, optional
If given, this message template is used instead of the default one.
new_name : str, optional
If given, the default message will recommend the new parameter name and an
error will be raised if the user uses both old and new names for the
same parameter.
modify_docstring : bool, optional
If the wrapped function has a docstring, add the deprecated parameters
to the "Other Parameters" section.
stacklevel : {None, int}, optional
If None, the decorator attempts to detect the appropriate stacklevel for the
deprecation warning automatically. This can fail, e.g., due to
decorating a closure, in which case you can set the stacklevel manually
here. The outermost decorator should have stacklevel 2, the next inner
one stacklevel 3, etc.
Notes
-----
Assign `DEPRECATED` as the new default value for the deprecated parameter.
This marks the status of the parameter also in the signature and rendered
HTML docs.
This decorator can be stacked to deprecate more than one parameter.
Examples
--------
>>> from skimage._shared.utils import deprecate_parameter, DEPRECATED
>>> @deprecate_parameter(
... "b", new_name="c", start_version="0.1", stop_version="0.3"
... )
... def foo(a, b=DEPRECATED, *, c=None):
... return a, c
Calling ``foo(1, b=2)`` will warn with::
FutureWarning: Parameter `b` is deprecated since version 0.1 and will
be removed in 0.3 (or later). To avoid this warning, please use the
parameter `c` instead. For more details, see the documentation of
`foo`.
"""
DEPRECATED = DEPRECATED # Make signal value accessible for convenience
remove_parameter_template = (
"Parameter `{deprecated_name}` is deprecated since version "
"{deprecated_version} and will be removed in {changed_version} (or "
"later). To avoid this warning, please do not use the parameter "
"`{deprecated_name}`. For more details, see the documentation of "
"`{func_name}`."
)
replace_parameter_template = (
"Parameter `{deprecated_name}` is deprecated since version "
"{deprecated_version} and will be removed in {changed_version} (or "
"later). To avoid this warning, please use the parameter `{new_name}` "
"instead. For more details, see the documentation of `{func_name}`."
)
def __init__(
self,
deprecated_name,
*,
start_version,
stop_version,
template=None,
new_name=None,
modify_docstring=True,
stacklevel=None,
):
self.deprecated_name = deprecated_name
self.new_name = new_name
self.template = template
self.start_version = start_version
self.stop_version = stop_version
self.modify_docstring = modify_docstring
self.stacklevel = stacklevel
def __call__(self, func):
parameters = inspect.signature(func).parameters
try:
deprecated_idx = list(parameters.keys()).index(self.deprecated_name)
except ValueError as e:
raise ValueError(f"{self.deprecated_name!r} not in parameters") from e
new_idx = False
if self.new_name:
try:
new_idx = list(parameters.keys()).index(self.new_name)
except ValueError as e:
raise ValueError(f"{self.new_name!r} not in parameters") from e
if parameters[self.deprecated_name].default is not DEPRECATED:
raise RuntimeError(
f"Expected `{self.deprecated_name}` to have the value {DEPRECATED!r} "
f"to indicate its status in the rendered signature."
)
if self.template is not None:
template = self.template
elif self.new_name is not None:
template = self.replace_parameter_template
else:
template = self.remove_parameter_template
warning_message = template.format(
deprecated_name=self.deprecated_name,
deprecated_version=self.start_version,
changed_version=self.stop_version,
func_name=func.__qualname__,
new_name=self.new_name,
)
@functools.wraps(func)
def fixed_func(*args, **kwargs):
deprecated_value = DEPRECATED
new_value = DEPRECATED
# Extract value of deprecated parameter
if len(args) > deprecated_idx:
deprecated_value = args[deprecated_idx]
# Overwrite old with DEPRECATED if replacement exists
if self.new_name is not None:
args = (
args[:deprecated_idx]
+ (DEPRECATED,)
+ args[deprecated_idx + 1 :]
)
if self.deprecated_name in kwargs.keys():
deprecated_value = kwargs[self.deprecated_name]
# Overwrite old with DEPRECATED if replacement exists
if self.new_name is not None:
kwargs[self.deprecated_name] = DEPRECATED
# Extract value of new parameter (if present)
if new_idx is not False and len(args) > new_idx:
new_value = args[new_idx]
if self.new_name and self.new_name in kwargs.keys():
new_value = kwargs[self.new_name]
if deprecated_value is not DEPRECATED:
stacklevel = (
self.stacklevel
if self.stacklevel is not None
else _warning_stacklevel(func)
)
warnings.warn(
warning_message, category=FutureWarning, stacklevel=stacklevel
)
if new_value is not DEPRECATED:
raise ValueError(
f"Both deprecated parameter `{self.deprecated_name}` "
f"and new parameter `{self.new_name}` are used. Use "
f"only the latter to avoid conflicting values."
)
elif self.new_name is not None:
# Assign old value to new one
kwargs[self.new_name] = deprecated_value
return func(*args, **kwargs)
if self.modify_docstring and func.__doc__ is not None:
newdoc = _docstring_add_deprecated(
func, {self.deprecated_name: self.new_name}, self.start_version
)
fixed_func.__doc__ = newdoc
return fixed_func
def _docstring_add_deprecated(func, kwarg_mapping, deprecated_version):
"""Add deprecated kwarg(s) to the "Other Params" section of a docstring.
Parameters
----------
func : function
The function whose docstring we wish to update.
kwarg_mapping : dict
A dict containing {old_arg: new_arg} key/value pairs, see
`deprecate_parameter`.
deprecated_version : str
A major.minor version string specifying when old_arg was
deprecated.
Returns
-------
new_doc : str
The updated docstring. Returns the original docstring if numpydoc is
not available.
"""
if func.__doc__ is None:
return None
try:
from numpydoc.docscrape import FunctionDoc, Parameter
except ImportError:
# Return an unmodified docstring if numpydoc is not available.
return func.__doc__
Doc = FunctionDoc(func)
for old_arg, new_arg in kwarg_mapping.items():
desc = []
if new_arg is None:
desc.append(f'`{old_arg}` is deprecated.')
else:
desc.append(f'Deprecated in favor of `{new_arg}`.')
desc += ['', f'.. deprecated:: {deprecated_version}']
Doc['Other Parameters'].append(
Parameter(name=old_arg, type='DEPRECATED', desc=desc)
)
new_docstring = str(Doc)
# new_docstring will have a header starting with:
#
# .. function:: func.__name__
#
# and some additional blank lines. We strip these off below.
split = new_docstring.split('\n')
no_header = split[1:]
while not no_header[0].strip():
no_header.pop(0)
# Store the initial description before any of the Parameters fields.
# Usually this is a single line, but the while loop covers any case
# where it is not.
descr = no_header.pop(0)
while no_header[0].strip():
descr += '\n ' + no_header.pop(0)
descr += '\n\n'
# '\n ' rather than '\n' here to restore the original indentation.
final_docstring = descr + '\n '.join(no_header)
# strip any extra spaces from ends of lines
final_docstring = '\n'.join([line.rstrip() for line in final_docstring.split('\n')])
return final_docstring
class FailedEstimationAccessError(AttributeError):
"""Error from use of failed estimation instance
This error arises from attempts to use an instance of
:class:`FailedEstimation`.
"""
class FailedEstimation:
"""Class to indicate a failed transform estimation.
The ``from_estimate`` class method of each transform type may return an
instance of this class to indicate some failure in the estimation process.
Parameters
----------
message : str
Message indicating reason for failed estimation.
Attributes
----------
message : str
Message above.
Raises
------
FailedEstimationAccessError
Exception raised for missing attributes or if the instance is used as a
callable.
"""
error_cls = FailedEstimationAccessError
hint = (
"You can check for a failed estimation by truth testing the returned "
"object. For failed estimations, `bool(estimation_result)` will be `False`. "
"E.g.\n\n"
" if not estimation_result:\n"
" raise RuntimeError(f'Failed estimation: {estimation_result}')"
)
def __init__(self, message):
self.message = message
def __bool__(self):
return False
def __repr__(self):
return f"{type(self).__name__}({self.message!r})"
def __str__(self):
return self.message
def __call__(self, *args, **kwargs):
msg = (
f'{type(self).__name__} is not callable. {self.message}\n\n'
f'Hint: {self.hint}'
)
raise self.error_cls(msg)
def __getattr__(self, name):
msg = (
f'{type(self).__name__} has no attribute {name!r}. {self.message}\n\n'
f'Hint: {self.hint}'
)
raise self.error_cls(msg)
@contextmanager
def _ignore_deprecated_estimate_warning():
"""Filter warnings about the deprecated `estimate` method.
Use either as decorator or context manager.
"""
with warnings.catch_warnings():
warnings.filterwarnings(
action="ignore",
category=FutureWarning,
message="`estimate` is deprecated",
module="skimage",
)
yield
class channel_as_last_axis:
"""Decorator for automatically making channels axis last for all arrays.
This decorator reorders axes for compatibility with functions that only
support channels along the last axis. After the function call is complete
the channels axis is restored back to its original position.
Parameters
----------
channel_arg_positions : tuple of int, optional
Positional arguments at the positions specified in this tuple are
assumed to be multichannel arrays. The default is to assume only the
first argument to the function is a multichannel array.
channel_kwarg_names : tuple of str, optional
A tuple containing the names of any keyword arguments corresponding to
multichannel arrays.
multichannel_output : bool, optional
A boolean that should be True if the output of the function is not a
multichannel array and False otherwise. This decorator does not
currently support the general case of functions with multiple outputs
where some or all are multichannel.
"""
def __init__(
self,
channel_arg_positions=(0,),
channel_kwarg_names=(),
multichannel_output=True,
):
self.arg_positions = set(channel_arg_positions)
self.kwarg_names = set(channel_kwarg_names)
self.multichannel_output = multichannel_output
def __call__(self, func):
@functools.wraps(func)
def fixed_func(*args, **kwargs):
channel_axis = kwargs.get('channel_axis', None)
if channel_axis is None:
return func(*args, **kwargs)
# TODO: convert scalars to a tuple in anticipation of eventually
# supporting a tuple of channel axes. Right now, only an
# integer or a single-element tuple is supported, though.
if np.isscalar(channel_axis):
channel_axis = (channel_axis,)
if len(channel_axis) > 1:
raise ValueError("only a single channel axis is currently supported")
if channel_axis == (-1,) or channel_axis == -1:
return func(*args, **kwargs)
if self.arg_positions:
new_args = []
for pos, arg in enumerate(args):
if pos in self.arg_positions:
new_args.append(np.moveaxis(arg, channel_axis[0], -1))
else:
new_args.append(arg)
new_args = tuple(new_args)
else:
new_args = args
for name in self.kwarg_names:
kwargs[name] = np.moveaxis(kwargs[name], channel_axis[0], -1)
# now that we have moved the channels axis to the last position,
# change the channel_axis argument to -1
kwargs["channel_axis"] = -1
# Call the function with the fixed arguments
out = func(*new_args, **kwargs)
if self.multichannel_output:
out = np.moveaxis(out, -1, channel_axis[0])
return out
return fixed_func
class deprecate_func:
"""Decorate a deprecated function and warn when it is called.
Adapted from <http://wiki.python.org/moin/PythonDecoratorLibrary>.
Parameters
----------
deprecated_version : str
The package version when the deprecation was introduced.
removed_version : str
The package version in which the deprecated function will be removed.
hint : str, optional
A hint on how to address this deprecation,
e.g., "Use `skimage.submodule.alternative_func` instead."
stacklevel : {None, int}, optional
If None, the decorator attempts to detect the appropriate stacklevel for the
deprecation warning automatically. This can fail, e.g., due to
decorating a closure, in which case you can set the stacklevel manually
here. The outermost decorator should have stacklevel 2, the next inner
one stacklevel 3, etc.
Examples
--------
>>> @deprecate_func(
... deprecated_version="1.0.0",
... removed_version="1.2.0",
... hint="Use `bar` instead."
... )
... def foo():
... pass
Calling ``foo`` will warn with::
FutureWarning: `foo` is deprecated since version 1.0.0
and will be removed in version 1.2.0. Use `bar` instead.
"""
def __init__(
self, *, deprecated_version, removed_version=None, hint=None, stacklevel=None
):
self.deprecated_version = deprecated_version
self.removed_version = removed_version
self.hint = hint
self.stacklevel = stacklevel
def __call__(self, func):
message = (
f"`{func.__name__}` is deprecated since version {self.deprecated_version}"
)
if self.removed_version:
message += f" and will be removed in version {self.removed_version}."
if self.hint:
# Prepend space and make sure it closes with "."
message += f" {self.hint.rstrip('.')}."
@functools.wraps(func)
def wrapped(*args, **kwargs):
stacklevel = (
self.stacklevel
if self.stacklevel is not None
else _warning_stacklevel(func)
)
warnings.warn(message, category=FutureWarning, stacklevel=stacklevel)
return func(*args, **kwargs)
# modify docstring to display deprecation warning
doc = f'**Deprecated:** {message}'
if wrapped.__doc__ is None:
wrapped.__doc__ = doc
else:
wrapped.__doc__ = doc + '\n\n ' + wrapped.__doc__
return wrapped
def _deprecate_estimate(func, class_name=None):
"""Deprecate ``estimate`` method."""
class_name = func.__qualname__.split('.')[0] if class_name is None else class_name
return deprecate_func(
deprecated_version="0.26",
removed_version="2.2",
hint=f"Please use `{class_name}.from_estimate` class constructor instead.",
stacklevel=2,
)(func)
def _deprecate_inherited_estimate(cls):
"""Deprecate inherited ``estimate`` instance method.
This needs a class decorator so we can correctly specify the class of the
`from_estimate` class method in the deprecation message.
"""
def estimate(self, *args, **kwargs):
return self._estimate(*args, **kwargs) is None
# The inherited method will always be wrapped by deprecator.
inherited_meth = getattr(cls, 'estimate').__wrapped__
estimate.__doc__ = inherited_meth.__doc__
estimate.__signature__ = inspect.signature(inherited_meth)
cls.estimate = _deprecate_estimate(estimate, cls.__name__)
return cls
def _update_from_estimate_docstring(cls):
"""Fix docstring for inherited ``from_estimate`` class method.
Even for classes that inherit the `from_estimate` method, and do not
override it, we nevertheless need to change the *docstring* of the
`from_estimate` method to point the user to the current (inheriting) class,
rather than the class in which the method is defined (the inherited class).
This needs a class decorator so we can modify the docstring of the new
class method. CPython currently does not allow us to modify class method
docstrings by updating ``__doc__``.
"""
inherited_cmeth = getattr(cls, 'from_estimate')
def from_estimate(cls, *args, **kwargs):
return inherited_cmeth(*args, **kwargs)
inherited_class_name = inherited_cmeth.__qualname__.split('.')[-2]
from_estimate.__doc__ = inherited_cmeth.__doc__.replace(
inherited_class_name, cls.__name__
)
from_estimate.__signature__ = inspect.signature(inherited_cmeth)
cls.from_estimate = classmethod(from_estimate)
return cls
def get_bound_method_class(m):
"""Return the class for a bound method."""
return m.im_class if sys.version < '3' else m.__self__.__class__
def safe_as_int(val, atol=1e-3):
"""
Attempt to safely cast values to integer format.
Parameters
----------
val : scalar or iterable of scalars
Number or container of numbers which are intended to be interpreted as
integers, e.g., for indexing purposes, but which may not carry integer
type.
atol : float
Absolute tolerance away from nearest integer to consider values in
``val`` functionally integers.
Returns
-------
val_int : NumPy scalar or ndarray of dtype `np.int64`
Returns the input value(s) coerced to dtype `np.int64` assuming all
were within ``atol`` of the nearest integer.
Notes
-----
This operation calculates ``val`` modulo 1, which returns the mantissa of
all values. Then all mantissas greater than 0.5 are subtracted from one.
Finally, the absolute tolerance from zero is calculated. If it is less
than ``atol`` for all value(s) in ``val``, they are rounded and returned
in an integer array. Or, if ``val`` was a scalar, a NumPy scalar type is
returned.
If any value(s) are outside the specified tolerance, an informative error
is raised.
Examples
--------
>>> safe_as_int(7.0)
7
>>> safe_as_int([9, 4, 2.9999999999])
array([9, 4, 3])
>>> safe_as_int(53.1)
Traceback (most recent call last):
...
ValueError: Integer argument required but received 53.1, check inputs.
>>> safe_as_int(53.01, atol=0.01)
53
"""
mod = np.asarray(val) % 1 # Extract mantissa
# Check for and subtract any mod values > 0.5 from 1
if mod.ndim == 0: # Scalar input, cannot be indexed
if mod > 0.5:
mod = 1 - mod
else: # Iterable input, now ndarray
mod[mod > 0.5] = 1 - mod[mod > 0.5] # Test on each side of nearest int
if not np.allclose(mod, 0, atol=atol):
raise ValueError(f'Integer argument required but received {val}, check inputs.')
return np.round(val).astype(np.int64)
def check_shape_equality(*images):
"""Check that all images have the same shape"""
image0 = images[0]
if not all(image0.shape == image.shape for image in images[1:]):
raise ValueError('Input images must have the same dimensions.')
return
def slice_at_axis(sl, axis):
"""
Construct tuple of slices to slice an array in the given dimension.
Parameters
----------
sl : slice
The slice for the given dimension.
axis : int
The axis to which `sl` is applied. All other dimensions are left
"unsliced".
Returns
-------
sl : tuple of slices
A tuple with slices matching `shape` in length.
Examples
--------
>>> slice_at_axis(slice(None, 3, -1), 1)
(slice(None, None, None), slice(None, 3, -1), Ellipsis)
"""
return (slice(None),) * axis + (sl,) + (...,)
def reshape_nd(arr, ndim, dim):
"""Reshape a 1D array to have n dimensions, all singletons but one.
Parameters
----------
arr : array, shape (N,)
Input array
ndim : int
Number of desired dimensions of reshaped array.
dim : int
Which dimension/axis will not be singleton-sized.
Returns
-------
arr_reshaped : array, shape ([1, ...], N, [1,...])
View of `arr` reshaped to the desired shape.
Examples
--------
>>> rng = np.random.default_rng()
>>> arr = rng.random(7)
>>> reshape_nd(arr, 2, 0).shape
(7, 1)
>>> reshape_nd(arr, 3, 1).shape
(1, 7, 1)
>>> reshape_nd(arr, 4, -1).shape
(1, 1, 1, 7)
"""
if arr.ndim != 1:
raise ValueError("arr must be a 1D array")
new_shape = [1] * ndim
new_shape[dim] = -1
return np.reshape(arr, new_shape)
def check_nD(array, ndim, arg_name='image'):
"""
Verify an array meets the desired ndims and array isn't empty.
Parameters
----------
array : array-like
Input array to be validated
ndim : int or iterable of ints
Allowable ndim or ndims for the array.
arg_name : str, optional
The name of the array in the original function.
"""
array = np.asanyarray(array)
msg_incorrect_dim = "The parameter `%s` must be a %s-dimensional array"
msg_empty_array = "The parameter `%s` cannot be an empty array"
if isinstance(ndim, int):
ndim = [ndim]
if array.size == 0:
raise ValueError(msg_empty_array % (arg_name))
if array.ndim not in ndim:
raise ValueError(
msg_incorrect_dim % (arg_name, '-or-'.join([str(n) for n in ndim]))
)
def convert_to_float(image, preserve_range):
"""Convert input image to float image with the appropriate range.
Parameters
----------
image : ndarray
Input image.
preserve_range : bool
Determines if the range of the image should be kept or transformed
using img_as_float. Also see
https://scikit-image.org/docs/dev/user_guide/data_types.html
Notes
-----
* Input images with `float32` data type are not upcast.
Returns
-------
image : ndarray
Transformed version of the input.
"""
if image.dtype == np.float16:
return image.astype(np.float32)
if preserve_range:
# Convert image to double only if it is not single or double
# precision float
if image.dtype.char not in 'df':
image = image.astype(float)
else:
from ..util.dtype import img_as_float
image = img_as_float(image)
return image
def _validate_interpolation_order(image_dtype, order):
"""Validate and return spline interpolation's order.
Parameters
----------
image_dtype : dtype
Image dtype.
order : {None, int}, optional
The order of the spline interpolation. The order has to be in the range
0-5. If ``None`` assume order 0 for Boolean images, otherwise 1. See
`skimage.transform.warp` for detail.
Returns
-------
order : int
if input order is None, returns 0 if image_dtype is bool and 1
otherwise. Otherwise, image_dtype is checked and input order
is validated accordingly (order > 0 is not supported for bool
image dtype)
"""
if order is None:
return 0 if image_dtype == bool else 1
if order < 0 or order > 5:
raise ValueError("Spline interpolation order has to be in the range 0-5.")
if image_dtype == bool and order != 0:
raise ValueError(
"Input image dtype is bool. Interpolation is not defined "
"with bool data type. Please set order to 0 or explicitly "
"cast input image to another data type."
)
return order
def _to_np_mode(mode):
"""Convert padding modes from `ndi.correlate` to `np.pad`."""
mode_translation_dict = dict(nearest='edge', reflect='symmetric', mirror='reflect')
if mode in mode_translation_dict:
mode = mode_translation_dict[mode]
return mode
def _to_ndimage_mode(mode):
"""Convert from `numpy.pad` mode name to the corresponding ndimage mode."""
mode_translation_dict = dict(
constant='constant',
edge='nearest',
symmetric='reflect',
reflect='mirror',
wrap='wrap',
)
if mode not in mode_translation_dict:
raise ValueError(
f"Unknown mode: '{mode}', or cannot translate mode. The "
f"mode should be one of 'constant', 'edge', 'symmetric', "
f"'reflect', or 'wrap'. See the documentation of numpy.pad for "
f"more info."
)
return _fix_ndimage_mode(mode_translation_dict[mode])
def _fix_ndimage_mode(mode):
# SciPy 1.6.0 introduced grid variants of constant and wrap which
# have less surprising behavior for images. Use these when available
grid_modes = {'constant': 'grid-constant', 'wrap': 'grid-wrap'}
return grid_modes.get(mode, mode)
new_float_type = {
# preserved types
np.float32().dtype.char: np.float32,
np.float64().dtype.char: np.float64,
np.complex64().dtype.char: np.complex64,
np.complex128().dtype.char: np.complex128,
# altered types
np.float16().dtype.char: np.float32,
'g': np.float64, # np.float128 ; doesn't exist on windows
'G': np.complex128, # np.complex256 ; doesn't exist on windows
}
def _supported_float_type(input_dtype, allow_complex=False):
"""Return an appropriate floating-point dtype for a given dtype.
float32, float64, complex64, complex128 are preserved.
float16 is promoted to float32.
complex256 is demoted to complex128.
Other types are cast to float64.
Parameters
----------
input_dtype : np.dtype or tuple of np.dtype
The input dtype. If a tuple of multiple dtypes is provided, each
dtype is first converted to a supported floating point type and the
final dtype is then determined by applying `np.result_type` on the
sequence of supported floating point types.
allow_complex : bool, optional
If False, raise a ValueError on complex-valued inputs.
Returns
-------
float_type : dtype
Floating-point dtype for the image.
"""
if isinstance(input_dtype, tuple):
return np.result_type(*(_supported_float_type(d) for d in input_dtype))
input_dtype = np.dtype(input_dtype)
if not allow_complex and input_dtype.kind == 'c':
raise ValueError("complex valued input is not supported")
return new_float_type.get(input_dtype.char, np.float64)
def identity(image, *args, **kwargs):
"""Returns the first argument unmodified."""
return image
def as_binary_ndarray(array, *, variable_name):
"""Return `array` as a numpy.ndarray of dtype bool.
Raises
------
ValueError:
An error including the given `variable_name` if `array` can not be
safely cast to a boolean array.
"""
array = np.asarray(array)
if array.dtype != bool:
if np.any((array != 1) & (array != 0)):
raise ValueError(
f"{variable_name} array is not of dtype boolean or "
f"contains values other than 0 and 1 so cannot be "
f"safely cast to boolean array."
)
return np.asarray(array, dtype=bool)
|