Extend plugins with imshow_collection

A first implementation is made for Matplotlib.

skimage/io/_io.py

@@ -10,7 +10,8 @@ from ..exposure import is_low_contrast
 from .._shared.utils import all_warnings, warn
 
 
-__all__ = ['imread', 'imread_collection', 'imsave', 'imshow', 'show']
+__all__ = ['imread', 'imsave', 'imshow', 'show',
+           'imread_collection', 'imshow_collection']
 
 
 def imread(fname, as_grey=False, plugin=None, flatten=None,
@@ -155,6 +156,26 @@ def imshow(arr, plugin=None, **plugin_args):
     return call_plugin('imshow', arr, plugin=plugin, **plugin_args)
 
 
+def imshow_collection(ic, plugin=None, **plugin_args):
+    """Display an image.
+
+    Parameters
+    ----------
+    ic : ImageCollection
+        Collection to display.
+    plugin : str
+        Name of plugin to use.  By default, the different plugins are
+        tried until a suitable candidate is found.
+
+    Other parameters
+    ----------------
+    plugin_args : keywords
+        Passed to the given plugin.
+
+    """
+    return call_plugin('imshow_collection', ic, plugin=plugin, **plugin_args)
+
+
 def show():
     '''Display pending images.
 

skimage/io/_plugins/matplotlib_plugin.ini

@@ -1,4 +1,3 @@
 [matplotlib]
 description = Display or save images using Matplotlib
-provides = imshow, imread, _app_show
-
+provides = imshow, imread, imshow_collection, _app_show

skimage/io/_plugins/matplotlib_plugin.py

@@ -147,6 +147,7 @@ def imshow(im, ax=None, show_cbar=None, **kwargs):
     if kwargs.get('cmap', None) == 'viridis':
         kwargs['cmap'] = viridis
     lo, hi, cmap = _get_display_range(im)
+
     kwargs.setdefault('interpolation', 'nearest')
     kwargs.setdefault('cmap', cmap)
     kwargs.setdefault('vmin', lo)
@@ -160,8 +161,20 @@ def imshow(im, ax=None, show_cbar=None, **kwargs):
         plt.colorbar(ax_im, cax=cax)
     ax.set_adjustable('box-forced')
     ax.get_figure().tight_layout()
+
     return ax_im
 
+
+def imshow_collection(ic, *args, **kwargs):
+    """Display all images in the collection.
+
+    """
+    fig, axes = plt.subplots(1, len(ic))
+    for n, image in enumerate(ic):
+        kwargs['axis'] = axes[n]
+        imshow(image, *args, **kwargs)
+
+
 imread = plt.imread
 show = plt.show
 

skimage/io/_plugins/test_plugin.ini

@@ -1,3 +1,3 @@
 [test]
 description = Test plugin
-provides = imsave, imshow, imread, imread_collection
+provides = imsave, imshow, imread, imread_collection, imshow_collection

skimage/io/_plugins/test_plugin.py

@@ -1,6 +1,8 @@
 # This mock-up is called by ../tests/test_plugin.py
 # to verify the behaviour of the plugin infrastructure
 
+from skimage.io import ImageCollection
+
 
 def imread(fname, dtype=None):
     assert fname == 'test.png'
@@ -20,3 +22,8 @@ def imshow(arr, plugin_arg=None):
 def imread_collection(x, conserve_memory=True):
     assert conserve_memory == False
     assert x == '*.png'
+    return ImageCollection([0, 1], load_func=lambda x: x)
+
+
+def imshow_collection(x):
+    assert len(x) == 2

skimage/io/manage_plugins.py

@@ -46,7 +46,8 @@ plugin_meta_data = {}
 preferred_plugins = {
     # Default plugins for all types (overridden by specific types below).
     'all': ['pil', 'matplotlib', 'qt', 'freeimage'],
-    'imshow': ['matplotlib']
+    'imshow': ['matplotlib'],
+    'imshow_collection': ['matplotlib']
 }
 
 
@@ -59,13 +60,15 @@ def _clear_plugins():
                     'imsave': [],
                     'imshow': [],
                     'imread_collection': [],
+                    'imshow_collection': [],
                     '_app_show': []}
 _clear_plugins()
 
 
 def _load_preferred_plugins():
     # Load preferred plugin for each io function.
-    io_types = ['imsave', 'imshow', 'imread_collection', 'imread']
+    io_types = ['imsave', 'imshow', 'imread_collection', 'imshow_collection',
+                'imread']
     for p_type in io_types:
         _set_plugin(p_type, preferred_plugins['all'])
 
@@ -190,8 +193,8 @@ def call_plugin(kind, *args, **kwargs):
     if len(plugin_funcs) == 0:
         msg = ("No suitable plugin registered for %s.\n\n"
                "You may load I/O plugins with the `skimage.io.use_plugin` "
-               "command.  A list of all available plugins can be found using "
-               "`skimage.io.plugins()`.")
+               "command.  A list of all available plugins are shown in the "
+               "`skimage.io` docstring.")
         raise RuntimeError(msg % kind)
 
     plugin = kwargs.pop('plugin', None)
@@ -216,7 +219,7 @@ def use_plugin(name, kind=None):
     ----------
     name : str
         Name of plugin.
-    kind : {'imsave', 'imread', 'imshow', 'imread_collection'}, optional
+    kind : {'imsave', 'imread', 'imshow', 'imread_collection', 'imshow_collection'}, optional
         Set the plugin for this function.  By default,
         the plugin is set for all functions.
 

skimage/io/tests/test_plugin.py

@@ -41,7 +41,8 @@ def test_show():
 
 
 def test_collection():
-    io.imread_collection('*.png', conserve_memory=False, plugin='test')
+    ic = io.imread_collection('*.png', conserve_memory=False, plugin='test')
+    io.imshow_collection(ic)
 
 
 def test_use():