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import warnings
import numpy as np
from .._shared.utils import warn, deprecate_func, deprecate_parameter, DEPRECATED
from .._shared.version_requirements import require
from ..exposure import is_low_contrast
from ..color.colorconv import rgb2gray, rgba2rgb
from ..io.manage_plugins import call_plugin, _hide_plugin_deprecation_warnings
from .util import file_or_url_context
__all__ = [
'imread',
'imsave',
'imshow',
'show',
'imread_collection',
'imshow_collection',
]
_remove_plugin_param_template = (
"The plugin infrastructure in `skimage.io` and the parameter "
"`{deprecated_name}` are 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}`. Instead, use `imageio` "
"or other I/O packages directly. See also `{func_name}`."
)
@deprecate_parameter(
"plugin",
start_version="0.25",
stop_version="0.27",
template=_remove_plugin_param_template,
)
def imread(fname, as_gray=False, plugin=DEPRECATED, **plugin_args):
"""Load an image from file.
Parameters
----------
fname : str or pathlib.Path
Image file name, e.g. ``test.jpg`` or URL.
as_gray : bool, optional
If True, convert color images to gray-scale (64-bit floats).
Images that are already in gray-scale format are not converted.
Other Parameters
----------------
plugin_args : DEPRECATED
The plugin infrastructure is deprecated.
Returns
-------
img_array : ndarray
The different color bands/channels are stored in the
third dimension, such that a gray-image is MxN, an
RGB-image MxNx3 and an RGBA-image MxNx4.
"""
if plugin is DEPRECATED:
plugin = None
if plugin_args:
msg = (
"The plugin infrastructure in `skimage.io` is deprecated since "
"version 0.25 and will be removed in 0.27 (or later). To avoid "
"this warning, please do not pass additional keyword arguments "
"for plugins (`**plugin_args`). Instead, use `imageio` or other "
"I/O packages directly. See also `skimage.io.imread`."
)
warnings.warn(msg, category=FutureWarning, stacklevel=3)
if isinstance(fname, pathlib.Path):
fname = str(fname.resolve())
if plugin is None and hasattr(fname, 'lower'):
if fname.lower().endswith(('.tiff', '.tif')):
plugin = 'tifffile'
with file_or_url_context(fname) as fname, _hide_plugin_deprecation_warnings():
img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
if not hasattr(img, 'ndim'):
return img
if img.ndim > 2:
if img.shape[-1] not in (3, 4) and img.shape[-3] in (3, 4):
img = np.swapaxes(img, -1, -3)
img = np.swapaxes(img, -2, -3)
if as_gray:
if img.shape[2] == 4:
img = rgba2rgb(img)
img = rgb2gray(img)
return img
@deprecate_parameter(
"plugin",
start_version="0.25",
stop_version="0.27",
template=_remove_plugin_param_template,
)
def imread_collection(
load_pattern, conserve_memory=True, plugin=DEPRECATED, **plugin_args
):
"""
Load a collection of images.
Parameters
----------
load_pattern : str or list
List of objects to load. These are usually filenames, but may
vary depending on the currently active plugin. See :class:`ImageCollection`
for the default behaviour of this parameter.
conserve_memory : bool, optional
If True, never keep more than one in memory at a specific
time. Otherwise, images will be cached once they are loaded.
Returns
-------
ic : :class:`ImageCollection`
Collection of images.
Other Parameters
----------------
plugin_args : DEPRECATED
The plugin infrastructure is deprecated.
"""
if plugin is DEPRECATED:
plugin = None
if plugin_args:
msg = (
"The plugin infrastructure in `skimage.io` is deprecated since "
"version 0.25 and will be removed in 0.27 (or later). To avoid "
"this warning, please do not pass additional keyword arguments "
"for plugins (`**plugin_args`). Instead, use `imageio` or other "
"I/O packages directly. See also `skimage.io.imread_collection`."
)
warnings.warn(msg, category=FutureWarning, stacklevel=3)
with _hide_plugin_deprecation_warnings():
return call_plugin(
'imread_collection',
load_pattern,
conserve_memory,
plugin=plugin,
**plugin_args,
)
@deprecate_parameter(
"plugin",
start_version="0.25",
stop_version="0.27",
template=_remove_plugin_param_template,
)
def imsave(fname, arr, plugin=DEPRECATED, *, check_contrast=True, **plugin_args):
"""Save an image to file.
Parameters
----------
fname : str or pathlib.Path
Target filename.
arr : ndarray of shape (M,N) or (M,N,3) or (M,N,4)
Image data.
check_contrast : bool, optional
Check for low contrast and print warning (default: True).
Other Parameters
----------------
plugin_args : DEPRECATED
The plugin infrastructure is deprecated.
"""
if plugin is DEPRECATED:
plugin = None
if plugin_args:
msg = (
"The plugin infrastructure in `skimage.io` is deprecated since "
"version 0.25 and will be removed in 0.27 (or later). To avoid "
"this warning, please do not pass additional keyword arguments "
"for plugins (`**plugin_args`). Instead, use `imageio` or other "
"I/O packages directly. See also `skimage.io.imsave`."
)
warnings.warn(msg, category=FutureWarning, stacklevel=3)
if isinstance(fname, pathlib.Path):
fname = str(fname.resolve())
if plugin is None and hasattr(fname, 'lower'):
if fname.lower().endswith(('.tiff', '.tif')):
plugin = 'tifffile'
if arr.dtype == bool:
warn(
f'{fname} is a boolean image: setting True to 255 and False to 0. '
'To silence this warning, please convert the image using '
'img_as_ubyte.',
stacklevel=3,
)
arr = arr.astype('uint8') * 255
if check_contrast and is_low_contrast(arr):
warn(f'{fname} is a low contrast image')
with _hide_plugin_deprecation_warnings():
return call_plugin('imsave', fname, arr, plugin=plugin, **plugin_args)
@deprecate_func(
deprecated_version="0.25",
removed_version="0.27",
hint="Please use `matplotlib`, `napari`, etc. to visualize images.",
)
def imshow(arr, plugin=None, **plugin_args):
"""Display an image.
Parameters
----------
arr : ndarray or str
Image data or name of image file.
plugin : str
Name of plugin to use. By default, the different plugins are
tried (starting with imageio) until a suitable candidate is found.
Other Parameters
----------------
plugin_args : keywords
Passed to the given plugin.
"""
if isinstance(arr, str):
arr = call_plugin('imread', arr, plugin=plugin)
with _hide_plugin_deprecation_warnings():
return call_plugin('imshow', arr, plugin=plugin, **plugin_args)
@deprecate_func(
deprecated_version="0.25",
removed_version="0.27",
hint="Please use `matplotlib`, `napari`, etc. to visualize images.",
)
def imshow_collection(ic, plugin=None, **plugin_args):
"""Display a collection of images.
Parameters
----------
ic : :class:`ImageCollection`
Collection to display.
Other Parameters
----------------
plugin_args : keywords
Passed to the given plugin.
"""
with _hide_plugin_deprecation_warnings():
return call_plugin('imshow_collection', ic, plugin=plugin, **plugin_args)
@require("matplotlib", ">=3.3")
@deprecate_func(
deprecated_version="0.25",
removed_version="0.27",
hint="Please use `matplotlib`, `napari`, etc. to visualize images.",
)
def show():
"""Display pending images.
Launch the event loop of the current GUI plugin, and display all
pending images, queued via `imshow`. This is required when using
`imshow` from non-interactive scripts.
A call to `show` will block execution of code until all windows
have been closed.
Examples
--------
>>> import skimage.io as io
>>> rng = np.random.default_rng()
>>> for i in range(4):
... ax_im = io.imshow(rng.random((50, 50))) # doctest: +SKIP
>>> io.show() # doctest: +SKIP
"""
with _hide_plugin_deprecation_warnings():
return call_plugin('_app_show')
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