| import pathlib |
| 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') |
|
|
