From b8c30bad4699e13a2c9a3eb055e11cf04990bae3 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Mon, 18 Nov 2013 21:15:04 -0600
Subject: [PATCH 01/35] Move image stack to its own module

---
 skimage/io/__init__.py     |  1 +
 skimage/io/_image_stack.py | 35 +++++++++++++++++++++++++++++++++++
 skimage/io/_io.py          | 38 ++++----------------------------------
 3 files changed, 40 insertions(+), 34 deletions(-)
 create mode 100644 skimage/io/_image_stack.py

diff --git a/skimage/io/__init__.py b/skimage/io/__init__.py
index 5e701a51..a2553c54 100644
--- a/skimage/io/__init__.py
+++ b/skimage/io/__init__.py
@@ -14,6 +14,7 @@ from .sift import *
 from .collection import *
 
 from ._io import *
+from ._image_stack import *
 from .video import *
 
 
diff --git a/skimage/io/_image_stack.py b/skimage/io/_image_stack.py
new file mode 100644
index 00000000..ca9896d5
--- /dev/null
+++ b/skimage/io/_image_stack.py
@@ -0,0 +1,35 @@
+import numpy as np
+
+
+__all__ = ['image_stack', 'push', 'pop']
+
+
+# Shared image queue
+image_stack = []
+
+
+def push(img):
+    """Push an image onto the shared image stack.
+
+    Parameters
+    ----------
+    img : ndarray
+        Image to push.
+
+    """
+    if not isinstance(img, np.ndarray):
+        raise ValueError("Can only push ndarrays to the image stack.")
+
+    image_stack.append(img)
+
+
+def pop():
+    """Pop an image from the shared image stack.
+
+    Returns
+    -------
+    img : ndarray
+        Image popped from the stack.
+
+    """
+    return image_stack.pop()
diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index eb704a6f..ae05ea77 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -1,10 +1,7 @@
-__all__ = ['Image', 'imread', 'imread_collection', 'imsave', 'imshow', 'show',
-           'push', 'pop']
-
 try:
-    from urllib.request import urlopen
+    from urllib.request import urlopen  # Python 3
 except ImportError:
-    from urllib2 import urlopen
+    from urllib2 import urlopen  # Python 2
 
 import os
 import re
@@ -19,8 +16,8 @@ from skimage.color import rgb2grey
 
 
 
-# Shared image queue
-_image_stack = []
+__all__ = ['Image', 'imread', 'imread_collection', 'imsave', 'imshow', 'show']
+
 
 URL_REGEX = re.compile(r'http://|https://|ftp://|file://|file:\\')
 
@@ -77,33 +74,6 @@ class Image(np.ndarray):
         return return_str
 
 
-def push(img):
-    """Push an image onto the shared image stack.
-
-    Parameters
-    ----------
-    img : ndarray
-        Image to push.
-
-    """
-    if not isinstance(img, np.ndarray):
-        raise ValueError("Can only push ndarrays to the image stack.")
-
-    _image_stack.append(img)
-
-
-def pop():
-    """Pop an image from the shared image stack.
-
-    Returns
-    -------
-    img : ndarray
-        Image popped from the stack.
-
-    """
-    return _image_stack.pop()
-
-
 def imread(fname, as_grey=False, plugin=None, flatten=None,
            **plugin_args):
     """Load an image from file.

From 312151b481aaa0342dd830ed402fde0a96cfbd2d Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Mon, 18 Nov 2013 21:59:46 -0600
Subject: [PATCH 02/35] Move __init__ functions to submodules.

And rename functions so we don't have to alias imports.
---
 skimage/io/__init__.py          |  40 ++---------
 skimage/io/_io.py               |   2 +-
 skimage/io/_plugins/plugin.py   | 113 ++++++++++++++++++++------------
 skimage/io/tests/test_plugin.py |  22 +++----
 4 files changed, 89 insertions(+), 88 deletions(-)

diff --git a/skimage/io/__init__.py b/skimage/io/__init__.py
index a2553c54..e19c6fe0 100644
--- a/skimage/io/__init__.py
+++ b/skimage/io/__init__.py
@@ -4,12 +4,7 @@ The following plug-ins are available:
 
 """
 
-from ._plugins import use as use_plugin
-from ._plugins import available as plugins
-from ._plugins import info as plugin_info
-from ._plugins import configuration as plugin_order
-from ._plugins import reset_plugins as _reset_plugins
-
+from ._plugins import *
 from .sift import *
 from .collection import *
 
@@ -18,34 +13,9 @@ from ._image_stack import *
 from .video import *
 
 
-available_plugins = plugins()
+reset_plugins()
 
 
-def _load_preferred_plugins():
-    # Load preferred plugin for each io function.
-    io_funcs = ['imsave', 'imshow', 'imread_collection', 'imread']
-    preferred_plugins = ['matplotlib', 'pil', 'qt', 'freeimage', 'null']
-    for func in io_funcs:
-        for plugin in preferred_plugins:
-            if plugin not in available_plugins:
-                continue
-            try:
-                use_plugin(plugin, kind=func)
-                break
-            except (ImportError, RuntimeError, OSError):
-                pass
-
-    # Use PIL as the default imread plugin, since matplotlib (1.2.x)
-    # is buggy (flips PNGs around, returns bytes as floats, etc.)
-    try:
-        use_plugin('pil', 'imread')
-    except ImportError:
-        pass
-
-def reset_plugins():
-    _reset_plugins()
-    _load_preferred_plugins()
-
 def _update_doc(doc):
     """Add a list of plugins to the module docstring, formatted as
     a ReStructuredText table.
@@ -53,7 +23,9 @@ def _update_doc(doc):
     """
     from textwrap import wrap
 
-    info = [(p, plugin_info(p)) for p in plugins() if not p == 'test']
+    info = [(p, plugin_info(p)) for p in available_plugins if not p == 'test']
+    print('test:', available_plugins, info)
+
     col_1_len = max([len(n) for (n, _) in info])
 
     wrap_len = 73
@@ -75,5 +47,3 @@ def _update_doc(doc):
     return doc
 
 __doc__ = _update_doc(__doc__)
-
-reset_plugins()
diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index ae05ea77..aa342c33 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -11,7 +11,7 @@ from io import BytesIO
 import numpy as np
 import six
 
-from skimage.io._plugins import call as call_plugin
+from skimage.io._plugins import call_plugin
 from skimage.color import rgb2grey
 
 
diff --git a/skimage/io/_plugins/plugin.py b/skimage/io/_plugins/plugin.py
index 5e04f320..dd6d4527 100644
--- a/skimage/io/_plugins/plugin.py
+++ b/skimage/io/_plugins/plugin.py
@@ -2,25 +2,26 @@
 
 """
 
-__all__ = ['use', 'available', 'call', 'info', 'configuration', 'reset_plugins']
-
 try:
-    from configparser import ConfigParser
+    from configparser import ConfigParser  # Python 3
 except ImportError:
-    from ConfigParser import ConfigParser
+    from ConfigParser import ConfigParser  # Python 2
 
 import os.path
 from glob import glob
 
 
-plugin_store = None
+__all__ = ['use_plugin', 'call_plugin', 'plugin_info', 'plugin_order',
+           'reset_plugins', 'find_available_plugins', 'available_plugins']
 
+
+plugin_store = None
 plugin_provides = {}
 plugin_module_name = {}
 plugin_meta_data = {}
 
 
-def reset_plugins():
+def _clear_plugins():
     """Clear the plugin state to the default, i.e., where no plugins are loaded
 
     """
@@ -30,8 +31,34 @@ def reset_plugins():
                     'imshow': [],
                     'imread_collection': [],
                     '_app_show': []}
+_clear_plugins()
 
-reset_plugins()
+
+def _load_preferred_plugins():
+    # Load preferred plugin for each io function.
+    io_funcs = ['imsave', 'imshow', 'imread_collection', 'imread']
+    preferred_plugins = ['matplotlib', 'pil', 'qt', 'freeimage', 'null']
+    for func in io_funcs:
+        for plugin in preferred_plugins:
+            if plugin not in available_plugins:
+                continue
+            try:
+                use_plugin(plugin, kind=func)
+                break
+            except (ImportError, RuntimeError, OSError):
+                pass
+
+    # Use PIL as the default imread plugin, since matplotlib (1.2.x)
+    # is buggy (flips PNGs around, returns bytes as floats, etc.)
+    try:
+        use_plugin('pil', 'imread')
+    except ImportError:
+        pass
+
+
+def reset_plugins():
+    _clear_plugins()
+    _load_preferred_plugins()
 
 
 def _scan_plugins():
@@ -66,7 +93,40 @@ def _scan_plugins():
 _scan_plugins()
 
 
-def call(kind, *args, **kwargs):
+def find_available_plugins(loaded=False):
+    """List available plugins.
+
+    Parameters
+    ----------
+    loaded : bool
+        If True, show only those plugins currently loaded.  By default,
+        all plugins are shown.
+
+    Returns
+    -------
+    p : dict
+        Dictionary with plugin names as keys and exposed functions as
+        values.
+
+    """
+    active_plugins = set()
+    for plugin_func in plugin_store.values():
+        for plugin, func in plugin_func:
+            active_plugins.add(plugin)
+
+    d = {}
+    for plugin in plugin_provides:
+        if not loaded or plugin in active_plugins:
+            d[plugin] = [f for f in plugin_provides[plugin] \
+                         if not f.startswith('_')]
+
+    return d
+
+
+available_plugins = find_available_plugins()
+
+
+def call_plugin(kind, *args, **kwargs):
     """Find the appropriate plugin of 'kind' and execute it.
 
     Parameters
@@ -105,7 +165,7 @@ command.  A list of all available plugins can be found using
     return func(*args, **kwargs)
 
 
-def use(name, kind=None):
+def use_plugin(name, kind=None):
     """Set the default plugin for a specified operation.  The plugin
     will be loaded if it hasn't been already.
 
@@ -158,35 +218,6 @@ def use(name, kind=None):
         plugin_store[k] = funcs
 
 
-def available(loaded=False):
-    """List available plugins.
-
-    Parameters
-    ----------
-    loaded : bool
-        If True, show only those plugins currently loaded.  By default,
-        all plugins are shown.
-
-    Returns
-    -------
-    p : dict
-        Dictionary with plugin names as keys and exposed functions as
-        values.
-
-    """
-    active_plugins = set()
-    for plugin_func in plugin_store.values():
-        for plugin, func in plugin_func:
-            active_plugins.add(plugin)
-
-    d = {}
-    for plugin in plugin_provides:
-        if not loaded or plugin in active_plugins:
-            d[plugin] = [f for f in plugin_provides[plugin] \
-                         if not f.startswith('_')]
-
-    return d
-
 
 def _load(plugin):
     """Load the given plugin.
@@ -201,7 +232,7 @@ def _load(plugin):
     plugins : List of available plugins
 
     """
-    if plugin in available(loaded=True):
+    if plugin in find_available_plugins(loaded=True):
         return
     if not plugin in plugin_module_name:
         raise ValueError("Plugin %s not found." % plugin)
@@ -222,7 +253,7 @@ def _load(plugin):
                 store.append((plugin, func))
 
 
-def info(plugin):
+def plugin_info(plugin):
     """Return plugin meta-data.
 
     Parameters
@@ -242,7 +273,7 @@ def info(plugin):
         raise ValueError('No information on plugin "%s"' % plugin)
 
 
-def configuration():
+def plugin_order():
     """Return the currently preferred plugin order.
 
     Returns
diff --git a/skimage/io/tests/test_plugin.py b/skimage/io/tests/test_plugin.py
index 5d1febe4..82d8e662 100644
--- a/skimage/io/tests/test_plugin.py
+++ b/skimage/io/tests/test_plugin.py
@@ -20,7 +20,7 @@ except RuntimeError:
 
 
 def setup_module(self):
-    plugin.use('test')  # see ../_plugins/test_plugin.py
+    plugin.use_plugin('test')  # see ../_plugins/test_plugin.py
 
 
 def teardown_module(self):
@@ -41,37 +41,37 @@ class TestPlugin:
         io.imread_collection('*.png', conserve_memory=False, plugin='test')
 
     def test_use(self):
-        plugin.use('test')
-        plugin.use('test', 'imshow')
+        plugin.use_plugin('test')
+        plugin.use_plugin('test', 'imshow')
 
     @raises(ValueError)
     def test_failed_use(self):
-        plugin.use('asd')
+        plugin.use_plugin('asd')
 
     @skipif(not PIL_available and not FI_available)
     def test_use_priority(self):
-        plugin.use(priority_plugin)
+        plugin.use_plugin(priority_plugin)
         plug, func = plugin.plugin_store['imread'][0]
         assert_equal(plug, priority_plugin)
 
-        plugin.use('test')
+        plugin.use_plugin('test')
         plug, func = plugin.plugin_store['imread'][0]
         assert_equal(plug, 'test')
 
     @skipif(not PIL_available)
     def test_use_priority_with_func(self):
-        plugin.use('pil')
+        plugin.use_plugin('pil')
         plug, func = plugin.plugin_store['imread'][0]
         assert_equal(plug, 'pil')
 
-        plugin.use('test', 'imread')
+        plugin.use_plugin('test', 'imread')
         plug, func = plugin.plugin_store['imread'][0]
         assert_equal(plug, 'test')
 
         plug, func = plugin.plugin_store['imsave'][0]
         assert_equal(plug, 'pil')
 
-        plugin.use('test')
+        plugin.use_plugin('test')
         plug, func = plugin.plugin_store['imsave'][0]
         assert_equal(plug, 'test')
 
@@ -81,8 +81,8 @@ class TestPlugin:
         assert 'test' in p['imread']
 
     def test_available(self):
-        assert 'qt' in io.plugins()
-        assert 'test' in io.plugins(loaded=True)
+        assert 'qt' in io.available_plugins
+        assert 'test' in io.find_available_plugins(loaded=True)
 
 if __name__ == "__main__":
     run_module_suite()

From 03388d49cdc403c830e03bfae93a663c9c87dd1e Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Mon, 18 Nov 2013 22:02:08 -0600
Subject: [PATCH 03/35] Use explicit imports

---
 skimage/io/tests/test_plugin.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skimage/io/tests/test_plugin.py b/skimage/io/tests/test_plugin.py
index 82d8e662..30a44414 100644
--- a/skimage/io/tests/test_plugin.py
+++ b/skimage/io/tests/test_plugin.py
@@ -1,4 +1,4 @@
-from numpy.testing import *
+from numpy.testing import assert_equal, raises
 
 from skimage import io
 from skimage.io._plugins import plugin

From 79587eaf48aa256e52b3cc162e39162f6209bfad Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Mon, 18 Nov 2013 22:04:21 -0600
Subject: [PATCH 04/35] Remove debugging statement

---
 skimage/io/__init__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/skimage/io/__init__.py b/skimage/io/__init__.py
index e19c6fe0..5fb2602b 100644
--- a/skimage/io/__init__.py
+++ b/skimage/io/__init__.py
@@ -24,7 +24,6 @@ def _update_doc(doc):
     from textwrap import wrap
 
     info = [(p, plugin_info(p)) for p in available_plugins if not p == 'test']
-    print('test:', available_plugins, info)
 
     col_1_len = max([len(n) for (n, _) in info])
 

From c820699cd85a17de608e6518c8e13cd6d880a663 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Mon, 18 Nov 2013 22:04:37 -0600
Subject: [PATCH 05/35] Remove unnecessary class

---
 skimage/io/tests/test_plugin.py | 91 +++++++++++++++++----------------
 1 file changed, 46 insertions(+), 45 deletions(-)

diff --git a/skimage/io/tests/test_plugin.py b/skimage/io/tests/test_plugin.py
index 30a44414..d91e927c 100644
--- a/skimage/io/tests/test_plugin.py
+++ b/skimage/io/tests/test_plugin.py
@@ -19,70 +19,71 @@ except RuntimeError:
     FI_available = False
 
 
-def setup_module(self):
+def setup_module():
     plugin.use_plugin('test')  # see ../_plugins/test_plugin.py
 
 
-def teardown_module(self):
+def teardown_module():
     io.reset_plugins()
 
 
-class TestPlugin:
-    def test_read(self):
-        io.imread('test.png', as_grey=True, dtype='i4', plugin='test')
+def test_read():
+    io.imread('test.png', as_grey=True, dtype='i4', plugin='test')
 
-    def test_save(self):
-        io.imsave('test.png', [1, 2, 3], plugin='test')
+def test_save():
+    io.imsave('test.png', [1, 2, 3], plugin='test')
 
-    def test_show(self):
-        io.imshow([1, 2, 3], plugin_arg=(1, 2), plugin='test')
+def test_show():
+    io.imshow([1, 2, 3], plugin_arg=(1, 2), plugin='test')
 
-    def test_collection(self):
-        io.imread_collection('*.png', conserve_memory=False, plugin='test')
+def test_collection():
+    io.imread_collection('*.png', conserve_memory=False, plugin='test')
 
-    def test_use(self):
-        plugin.use_plugin('test')
-        plugin.use_plugin('test', 'imshow')
+def test_use():
+    plugin.use_plugin('test')
+    plugin.use_plugin('test', 'imshow')
 
-    @raises(ValueError)
-    def test_failed_use(self):
-        plugin.use_plugin('asd')
+@raises(ValueError)
+def test_failed_use():
+    plugin.use_plugin('asd')
 
-    @skipif(not PIL_available and not FI_available)
-    def test_use_priority(self):
-        plugin.use_plugin(priority_plugin)
-        plug, func = plugin.plugin_store['imread'][0]
-        assert_equal(plug, priority_plugin)
+@skipif(not PIL_available and not FI_available)
+def test_use_priority():
+    plugin.use_plugin(priority_plugin)
+    plug, func = plugin.plugin_store['imread'][0]
+    assert_equal(plug, priority_plugin)
 
-        plugin.use_plugin('test')
-        plug, func = plugin.plugin_store['imread'][0]
-        assert_equal(plug, 'test')
+    plugin.use_plugin('test')
+    plug, func = plugin.plugin_store['imread'][0]
+    assert_equal(plug, 'test')
 
-    @skipif(not PIL_available)
-    def test_use_priority_with_func(self):
-        plugin.use_plugin('pil')
-        plug, func = plugin.plugin_store['imread'][0]
-        assert_equal(plug, 'pil')
+@skipif(not PIL_available)
+def test_use_priority_with_func():
+    plugin.use_plugin('pil')
+    plug, func = plugin.plugin_store['imread'][0]
+    assert_equal(plug, 'pil')
 
-        plugin.use_plugin('test', 'imread')
-        plug, func = plugin.plugin_store['imread'][0]
-        assert_equal(plug, 'test')
+    plugin.use_plugin('test', 'imread')
+    plug, func = plugin.plugin_store['imread'][0]
+    assert_equal(plug, 'test')
 
-        plug, func = plugin.plugin_store['imsave'][0]
-        assert_equal(plug, 'pil')
+    plug, func = plugin.plugin_store['imsave'][0]
+    assert_equal(plug, 'pil')
 
-        plugin.use_plugin('test')
-        plug, func = plugin.plugin_store['imsave'][0]
-        assert_equal(plug, 'test')
+    plugin.use_plugin('test')
+    plug, func = plugin.plugin_store['imsave'][0]
+    assert_equal(plug, 'test')
 
-    def test_plugin_order(self):
-        p = io.plugin_order()
-        assert 'imread' in p
-        assert 'test' in p['imread']
+def test_plugin_order():
+    p = io.plugin_order()
+    assert 'imread' in p
+    assert 'test' in p['imread']
+
+def test_available():
+    assert 'qt' in io.available_plugins
+    assert 'test' in io.find_available_plugins(loaded=True)
 
-    def test_available(self):
-        assert 'qt' in io.available_plugins
-        assert 'test' in io.find_available_plugins(loaded=True)
 
 if __name__ == "__main__":
+    from numpy.testing import run_module_suite
     run_module_suite()

From 552f24be8e0afdeffd3eaa32d435c140a57edaaf Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Mon, 18 Nov 2013 22:07:44 -0600
Subject: [PATCH 06/35] Remove unnecessary initialization

---
 skimage/io/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skimage/io/__init__.py b/skimage/io/__init__.py
index 5fb2602b..350ca202 100644
--- a/skimage/io/__init__.py
+++ b/skimage/io/__init__.py
@@ -1,4 +1,4 @@
-__doc__ = """Utilities to read and write images in various formats.
+"""Utilities to read and write images in various formats.
 
 The following plug-ins are available:
 

From f8ea4266082fba1210be270d6ae7607717591978 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Mon, 18 Nov 2013 22:27:34 -0600
Subject: [PATCH 07/35] Refactor io doc building code

---
 skimage/io/__init__.py | 29 ++++++++++++++++-------------
 1 file changed, 16 insertions(+), 13 deletions(-)

diff --git a/skimage/io/__init__.py b/skimage/io/__init__.py
index 350ca202..ed6df313 100644
--- a/skimage/io/__init__.py
+++ b/skimage/io/__init__.py
@@ -15,6 +15,12 @@ from .video import *
 
 reset_plugins()
 
+WRAP_LEN = 73
+
+
+def _separator(char, lengths):
+    return [char * separator_length for separator_length in lengths]
+
 
 def _update_doc(doc):
     """Add a list of plugins to the module docstring, formatted as
@@ -23,24 +29,21 @@ def _update_doc(doc):
     """
     from textwrap import wrap
 
-    info = [(p, plugin_info(p)) for p in available_plugins if not p == 'test']
+    info = [(p, plugin_info(p).get('description', 'no description'))
+            for p in available_plugins if not p == 'test']
 
     col_1_len = max([len(n) for (n, _) in info])
-
-    wrap_len = 73
-    col_2_len = wrap_len - 1 - col_1_len
+    col_2_len = WRAP_LEN - 1 - col_1_len
 
     # Insert table header
-    info.insert(0, ('=' * col_1_len, {'description': '=' * col_2_len}))
-    info.insert(1, ('Plugin', {'description': 'Description'}))
-    info.insert(2, ('-' * col_1_len, {'description': '-' * col_2_len}))
-    info.append(('=' * col_1_len, {'description': '=' * col_2_len}))
+    info.insert(0, _separator('=', (col_1_len, col_2_len)))
+    info.insert(1, ('Plugin', 'Description'))
+    info.insert(2, _separator('-', (col_1_len, col_2_len)))
+    info.append(_separator('-', (col_1_len, col_2_len)))
 
-    for (name, meta_data) in info:
-        wrapped_descr = wrap(meta_data.get('description', ''),
-                             col_2_len)
-        doc += "%s %s\n" % (name.ljust(col_1_len),
-                            '\n'.join(wrapped_descr))
+    for (name, plugin_description) in info:
+        wrapped_descr = wrap(plugin_description, col_2_len)
+        doc += "%s %s\n" % (name.ljust(col_1_len), '\n'.join(wrapped_descr))
     doc = doc.strip()
 
     return doc

From a23e31b5539d6d8db268451600ebf71293c02d15 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Mon, 18 Nov 2013 22:33:42 -0600
Subject: [PATCH 08/35] Factor out table formatting code.

---
 skimage/io/__init__.py | 30 +++++++++++++++++-------------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/skimage/io/__init__.py b/skimage/io/__init__.py
index ed6df313..31d22a3f 100644
--- a/skimage/io/__init__.py
+++ b/skimage/io/__init__.py
@@ -22,6 +22,14 @@ def _separator(char, lengths):
     return [char * separator_length for separator_length in lengths]
 
 
+def _format_plugin_info_table(info_table, column_lengths):
+    """Add separators and column titles to plugin info table."""
+    info_table.insert(0, _separator('=', column_lengths))
+    info_table.insert(1, ('Plugin', 'Description'))
+    info_table.insert(2, _separator('-', column_lengths))
+    info_table.append(_separator('-', column_lengths))
+
+
 def _update_doc(doc):
     """Add a list of plugins to the module docstring, formatted as
     a ReStructuredText table.
@@ -29,21 +37,17 @@ def _update_doc(doc):
     """
     from textwrap import wrap
 
-    info = [(p, plugin_info(p).get('description', 'no description'))
-            for p in available_plugins if not p == 'test']
+    info_table = [(p, plugin_info(p).get('description', 'no description'))
+                  for p in available_plugins if not p == 'test']
 
-    col_1_len = max([len(n) for (n, _) in info])
-    col_2_len = WRAP_LEN - 1 - col_1_len
+    name_length = max([len(n) for (n, _) in info_table])
+    description_length = WRAP_LEN - 1 - name_length
+    column_lengths = [name_length, description_length]
+    _format_plugin_info_table(info_table, column_lengths)
 
-    # Insert table header
-    info.insert(0, _separator('=', (col_1_len, col_2_len)))
-    info.insert(1, ('Plugin', 'Description'))
-    info.insert(2, _separator('-', (col_1_len, col_2_len)))
-    info.append(_separator('-', (col_1_len, col_2_len)))
-
-    for (name, plugin_description) in info:
-        wrapped_descr = wrap(plugin_description, col_2_len)
-        doc += "%s %s\n" % (name.ljust(col_1_len), '\n'.join(wrapped_descr))
+    for (name, plugin_description) in info_table:
+        wrapped_descr = wrap(plugin_description, description_length)
+        doc += "%s %s\n" % (name.ljust(name_length), '\n'.join(wrapped_descr))
     doc = doc.strip()
 
     return doc

From 1d399617575dea5d4a9ac931182a7ac53998f997 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Mon, 18 Nov 2013 22:35:32 -0600
Subject: [PATCH 09/35] Minor rename

---
 skimage/io/__init__.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/skimage/io/__init__.py b/skimage/io/__init__.py
index 31d22a3f..82a345c9 100644
--- a/skimage/io/__init__.py
+++ b/skimage/io/__init__.py
@@ -46,10 +46,11 @@ def _update_doc(doc):
     _format_plugin_info_table(info_table, column_lengths)
 
     for (name, plugin_description) in info_table:
-        wrapped_descr = wrap(plugin_description, description_length)
-        doc += "%s %s\n" % (name.ljust(name_length), '\n'.join(wrapped_descr))
+        description = wrap(plugin_description, description_length)
+        doc += "%s %s\n" % (name.ljust(name_length), '\n'.join(description))
     doc = doc.strip()
 
     return doc
 
+
 __doc__ = _update_doc(__doc__)

From 77ff0615d95d333feb905c15fe46b90316a7549e Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Mon, 18 Nov 2013 22:44:18 -0600
Subject: [PATCH 10/35] Fix wrapping of plugin descriptions

---
 skimage/io/__init__.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/skimage/io/__init__.py b/skimage/io/__init__.py
index 82a345c9..02800fbd 100644
--- a/skimage/io/__init__.py
+++ b/skimage/io/__init__.py
@@ -46,8 +46,11 @@ def _update_doc(doc):
     _format_plugin_info_table(info_table, column_lengths)
 
     for (name, plugin_description) in info_table:
-        description = wrap(plugin_description, description_length)
-        doc += "%s %s\n" % (name.ljust(name_length), '\n'.join(description))
+        description_lines = wrap(plugin_description, description_length)
+        name_column = [name]
+        name_column.extend(['' for _ in range(len(description_lines) - 1)])
+        for name, description in zip(name_column, description_lines):
+            doc += "%s %s\n" % (name.ljust(name_length), description)
     doc = doc.strip()
 
     return doc

From 8a2e88241ee31c1bdd650d8b561545f968dc64ef Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Mon, 2 Dec 2013 23:13:05 -0600
Subject: [PATCH 11/35] Factor out config-file parsing for clarity

---
 skimage/io/_plugins/plugin.py | 29 ++++++++++++++++++-----------
 1 file changed, 18 insertions(+), 11 deletions(-)

diff --git a/skimage/io/_plugins/plugin.py b/skimage/io/_plugins/plugin.py
index dd6d4527..b6e43b0f 100644
--- a/skimage/io/_plugins/plugin.py
+++ b/skimage/io/_plugins/plugin.py
@@ -61,25 +61,32 @@ def reset_plugins():
     _load_preferred_plugins()
 
 
+def _parse_config_file(filename):
+    """Return plugin name and meta-data dict from plugin config file."""
+    parser = ConfigParser()
+    parser.read(filename)
+    name = parser.sections()[0]
+
+    meta_data = {}
+    for opt in parser.options(name):
+        meta_data[opt] = parser.get(name, opt)
+
+    return name, meta_data
+
+
 def _scan_plugins():
     """Scan the plugins directory for .ini files and parse them
     to gather plugin meta-data.
 
     """
     pd = os.path.dirname(__file__)
-    ini = glob(os.path.join(pd, '*.ini'))
+    config_files = glob(os.path.join(pd, '*.ini'))
 
-    for f in ini:
-        cp = ConfigParser()
-        cp.read(f)
-        name = cp.sections()[0]
-
-        meta_data = {}
-        for opt in cp.options(name):
-            meta_data[opt] = cp.get(name, opt)
+    for filename in config_files:
+        name, meta_data = _parse_config_file(filename)
         plugin_meta_data[name] = meta_data
 
-        provides = [s.strip() for s in cp.get(name, 'provides').split(',')]
+        provides = [s.strip() for s in meta_data['provides'].split(',')]
         valid_provides = [p for p in provides if p in plugin_store]
 
         for p in provides:
@@ -88,7 +95,7 @@ def _scan_plugins():
                       " Ignoring." % (name, p))
 
         plugin_provides[name] = valid_provides
-        plugin_module_name[name] = os.path.basename(f)[:-4]
+        plugin_module_name[name] = os.path.basename(filename)[:-4]
 
 _scan_plugins()
 

From 41e62fa0875afed3100d298cdcd7e76648f3ecad Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Mon, 2 Dec 2013 23:36:12 -0600
Subject: [PATCH 12/35] Add comment for clarification

---
 skimage/io/_plugins/plugin.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/skimage/io/_plugins/plugin.py b/skimage/io/_plugins/plugin.py
index b6e43b0f..75b2f9ed 100644
--- a/skimage/io/_plugins/plugin.py
+++ b/skimage/io/_plugins/plugin.py
@@ -15,7 +15,10 @@ __all__ = ['use_plugin', 'call_plugin', 'plugin_info', 'plugin_order',
            'reset_plugins', 'find_available_plugins', 'available_plugins']
 
 
+# The plugin store will save a list of *loaded* io functions for each io type
+# (e.g. 'imread', 'imsave', etc.). Plugins are loaded as requested.
 plugin_store = None
+
 plugin_provides = {}
 plugin_module_name = {}
 plugin_meta_data = {}
@@ -225,7 +228,6 @@ def use_plugin(name, kind=None):
         plugin_store[k] = funcs
 
 
-
 def _load(plugin):
     """Load the given plugin.
 

From 86abc7c9704b75242f51392189b1d33afec34041 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Tue, 3 Dec 2013 22:16:09 -0600
Subject: [PATCH 13/35] Factor out url handling for unified file/url behavior

---
 skimage/io/_io.py  | 29 +++--------------------------
 skimage/io/util.py | 36 ++++++++++++++++++++++++++++++++++++
 2 files changed, 39 insertions(+), 26 deletions(-)
 create mode 100644 skimage/io/util.py

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index aa342c33..ce718742 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -1,11 +1,3 @@
-try:
-    from urllib.request import urlopen  # Python 3
-except ImportError:
-    from urllib2 import urlopen  # Python 2
-
-import os
-import re
-import tempfile
 from io import BytesIO
 
 import numpy as np
@@ -13,21 +5,13 @@ import six
 
 from skimage.io._plugins import call_plugin
 from skimage.color import rgb2grey
-
+from skimage._shared import six
+from .util import file_or_url_context
 
 
 __all__ = ['Image', 'imread', 'imread_collection', 'imsave', 'imshow', 'show']
 
 
-URL_REGEX = re.compile(r'http://|https://|ftp://|file://|file:\\')
-
-
-def is_url(filename):
-    """Return True if string is an http or ftp path."""
-    return (isinstance(filename, six.string_types) and
-            URL_REGEX.match(filename) is not None)
-
-
 class Image(np.ndarray):
     """Class representing Image data.
 
@@ -110,14 +94,7 @@ def imread(fname, as_grey=False, plugin=None, flatten=None,
     if flatten is not None:
         as_grey = flatten
 
-    if is_url(fname):
-        _, ext = os.path.splitext(fname)
-        with tempfile.NamedTemporaryFile(delete=False, suffix=ext) as f:
-            u = urlopen(fname)
-            f.write(u.read())
-        img = call_plugin('imread', f.name, plugin=plugin, **plugin_args)
-        os.remove(f.name)
-    else:
+    with file_or_url_context(fname) as fname:
         img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
 
     if as_grey and getattr(img, 'ndim', 0) >= 3:
diff --git a/skimage/io/util.py b/skimage/io/util.py
new file mode 100644
index 00000000..06f5a5b5
--- /dev/null
+++ b/skimage/io/util.py
@@ -0,0 +1,36 @@
+try:
+    from urllib.request import urlopen  # Python 3
+except ImportError:
+    from urllib2 import urlopen  # Python 2
+
+import os
+import re
+import tempfile
+from contextlib import contextmanager
+
+from skimage._shared import six
+
+
+URL_REGEX = re.compile(r'http://|https://|ftp://|file://|file:\\')
+
+
+def is_url(filename):
+    """Return True if string is an http or ftp path."""
+    return (isinstance(filename, six.string_types) and
+            URL_REGEX.match(filename) is not None)
+
+
+@contextmanager
+def file_or_url_context(resource_name):
+    """Yield name of file from the given resource (i.e. file or url)."""
+    if is_url(resource_name):
+        _, ext = os.path.splitext(resource_name)
+        with tempfile.NamedTemporaryFile(delete=False, suffix=ext) as f:
+            u = urlopen(resource_name)
+            f.write(u.read())
+        try:
+            yield f.name
+        finally:
+            os.remove(f.name)
+    else:
+        yield resource_name

From 318781bca1973f34d3a6b00b5b9253cef5190f58 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Tue, 3 Dec 2013 22:27:00 -0600
Subject: [PATCH 14/35] Add test that error gets raised when no plugin
 available

---
 skimage/io/tests/test_io.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/skimage/io/tests/test_io.py b/skimage/io/tests/test_io.py
index 8049860a..51b9a336 100644
--- a/skimage/io/tests/test_io.py
+++ b/skimage/io/tests/test_io.py
@@ -4,6 +4,7 @@ from numpy.testing import assert_array_equal, raises, run_module_suite
 import numpy as np
 
 import skimage.io as io
+from skimage.io._plugins.plugin import plugin_store
 from skimage import data_dir
 
 
@@ -28,5 +29,13 @@ def test_imread_url():
     assert image.shape == (512, 512)
 
 
+@raises(RuntimeError)
+def test_imread_no_plugin():
+    # tweak data path so that file URI works on both unix and windows.
+    image_path = os.path.join(data_dir, 'lena.png')
+    plugin_store['imread'] = []
+    io.imread(image_path)
+
+
 if __name__ == "__main__":
     run_module_suite()

From 90f1e791d80f2b195c7e2818c200a7016ea78afc Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Tue, 3 Dec 2013 22:30:56 -0600
Subject: [PATCH 15/35] PEP8

---
 skimage/io/_plugins/plugin.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/skimage/io/_plugins/plugin.py b/skimage/io/_plugins/plugin.py
index 75b2f9ed..ec8ed7c9 100644
--- a/skimage/io/_plugins/plugin.py
+++ b/skimage/io/_plugins/plugin.py
@@ -155,11 +155,11 @@ def call_plugin(kind, *args, **kwargs):
 
     plugin_funcs = plugin_store[kind]
     if len(plugin_funcs) == 0:
-        raise RuntimeError('''No suitable plugin registered for %s.
-
-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()`.''' % kind)
+        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()`.")
+        raise RuntimeError(msg % kind)
 
     plugin = kwargs.pop('plugin', None)
     if plugin is None:

From db45127fa93b495337df3e39a1c4622fce297ada Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Tue, 3 Dec 2013 23:16:50 -0600
Subject: [PATCH 16/35] Fix test so it doesn't have side-effects

---
 skimage/io/tests/test_io.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/skimage/io/tests/test_io.py b/skimage/io/tests/test_io.py
index 51b9a336..6b74ae34 100644
--- a/skimage/io/tests/test_io.py
+++ b/skimage/io/tests/test_io.py
@@ -33,8 +33,12 @@ def test_imread_url():
 def test_imread_no_plugin():
     # tweak data path so that file URI works on both unix and windows.
     image_path = os.path.join(data_dir, 'lena.png')
+    plugins = plugin_store['imread']
     plugin_store['imread'] = []
-    io.imread(image_path)
+    try:
+        io.imread(image_path)
+    finally:
+        plugin_store['imread'] = plugins
 
 
 if __name__ == "__main__":

From e04066de7ef7c0f1a337fa390ce2e5714b6d5952 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Tue, 3 Dec 2013 23:24:16 -0600
Subject: [PATCH 17/35] Change InheritedConfig so a key is contained if a
 parent key is contained

---
 skimage/io/inherited_config.py | 159 +++++++++++++++++++++++++++++++++
 1 file changed, 159 insertions(+)
 create mode 100644 skimage/io/inherited_config.py

diff --git a/skimage/io/inherited_config.py b/skimage/io/inherited_config.py
new file mode 100644
index 00000000..6b989b66
--- /dev/null
+++ b/skimage/io/inherited_config.py
@@ -0,0 +1,159 @@
+class InheritedConfig(dict):
+    """Configuration dictionary where non-existent keys can inherit values.
+
+    This class allows you to define parameter names that can match exactly, but
+    if it doesn't, parameter names will be searched based on key inheritance.
+    For example, the key 'size.text' will default to 'size'.
+
+    Note that indexing into the dictionary will raise an error if it doesn't
+    match exactly, while `InheritedConfig.get` will look up values based on
+    inheritance.
+
+    Parameters
+    ----------
+    config_values : dict or list of (key, value) pairs
+        Default values for a configuration, where keys are the parameter names
+        and values are the associated value.
+    cascade_map : dict
+        Dictionary defining cascading defaults. If a parameter name is not
+        found, indexing `cascade_map` with the parameter name will return
+        the parameter to look for.
+    kwargs : dict
+        Keyword arguments for initializing dict.
+    """
+
+    _separator = '.'
+
+    def __init__(self, config_values=None, **kwargs):
+        assert 'config_values' not in kwargs
+
+        if config_values is None:
+            config_values = {}
+
+        super(InheritedConfig, self).__init__(config_values, **kwargs)
+
+    def get(self, key, default=None, _prev=None):
+        """Return best matching config value for `key`.
+
+        Get value from configuration. The search for `key` is in the following
+        order:
+
+            - `self` (Value in global configuration)
+            - `default`
+            - Alternate key specified by `self.cascade_map`
+
+        This method supports the pattern commonly used for optional keyword
+        arguments to a function. For example::
+
+            >>> def print_value(key, **kwargs):
+            ...     print kwargs.get(key, 0)
+            >>> print_value('size')
+            0
+            >>> print_value('size', size=1)
+            1
+
+        Instead, you would create a config class and write::
+
+            >>> config = InheritedConfig(size=0)
+            >>> def print_value(key, **kwargs):
+            ...     print kwargs.get(key, config.get(key))
+            >>> print_value('size')
+            0
+            >>> print_value('size', size=1)
+            1
+            >>> print_value('non-existent')
+            None
+            >>> print_value('size.text')
+            0
+
+        See examples below for a demonstration of the cascading of
+        configuration names.
+
+        Parameters
+        ----------
+        key : str
+            Name of config value you want.
+        default : object
+            Default value if `key` doesn't exist in instance.
+
+        Examples
+        --------
+        >>> config = InheritedConfig(size=0)
+        >>> config.get('size')
+        0
+        >>> top_choice={'size': 1}
+        >>> top_choice.get('size', config.get('size'))
+        1
+        >>> config.get('non-existent', 'unknown')
+        'unknown'
+        >>> config.get('size.text')
+        0
+        >>> config.get('size.text', 2)
+        2
+        >>> top_choice.get('size', config.get('size.text'))
+        1
+        """
+        if key in self.keys():
+            return self[key]
+        elif default is not None:
+            return default
+        elif self._separator in key:
+            return self.get(self._parent(key))
+        else:
+            return None
+
+    def _parent(self, key):
+        """Return parent key."""
+        parts = key.split(self._separator)
+        return self._separator.join(parts[:-1])
+
+    def __contains__(self, key):
+        if key in self.keys():
+            return True
+        elif self._separator in key:
+            return self.__contains__(self._parent(key))
+        else:
+            return False
+
+
+def test_get_non_existent():
+    config = InheritedConfig()
+    assert config.get('size') is None
+
+
+def test_get_simple():
+    config = InheritedConfig({'imread': 'matplotlib'})
+    assert config.get('imread') == 'matplotlib'
+
+
+def test_get_default():
+    config = InheritedConfig()
+    assert config.get('size', 10) == 10
+
+
+def test_get_best():
+    config = InheritedConfig({'size': 0, 'size.text': 1})
+    assert config.get('size.text') == 1
+
+
+def test_get_multi_level():
+    config = InheritedConfig({'size': 0})
+    assert config.get('size.text.title') == 0
+    config['size.text'] = 1
+    assert config.get('size.text.title') == 1
+    config['size.text.title'] = 2
+    assert config.get('size.text.title') == 2
+
+
+def test_contains():
+    config = InheritedConfig({'imread': 'matplotlib'})
+    assert 'imread' in config
+    assert 'imread.jpg' in config
+
+
+if __name__ == '__main__':
+    import doctest
+    from numpy import testing
+
+    doctest.testmod()
+    testing.run_module_suite()

From fabe4fa0ccb32aa3ea381e40e17c271dffcce9e6 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Tue, 3 Dec 2013 23:28:27 -0600
Subject: [PATCH 18/35] Move tests to separate file.

---
 skimage/io/inherited_config.py            | 37 --------------------
 skimage/io/tests/test_inherited_config.py | 41 +++++++++++++++++++++++
 2 files changed, 41 insertions(+), 37 deletions(-)
 create mode 100644 skimage/io/tests/test_inherited_config.py

diff --git a/skimage/io/inherited_config.py b/skimage/io/inherited_config.py
index 6b989b66..446e6db7 100644
--- a/skimage/io/inherited_config.py
+++ b/skimage/io/inherited_config.py
@@ -116,44 +116,7 @@ class InheritedConfig(dict):
             return False
 
 
-def test_get_non_existent():
-    config = InheritedConfig()
-    assert config.get('size') is None
-
-
-def test_get_simple():
-    config = InheritedConfig({'imread': 'matplotlib'})
-    assert config.get('imread') == 'matplotlib'
-
-
-def test_get_default():
-    config = InheritedConfig()
-    assert config.get('size', 10) == 10
-
-
-def test_get_best():
-    config = InheritedConfig({'size': 0, 'size.text': 1})
-    assert config.get('size.text') == 1
-
-
-def test_get_multi_level():
-    config = InheritedConfig({'size': 0})
-    assert config.get('size.text.title') == 0
-    config['size.text'] = 1
-    assert config.get('size.text.title') == 1
-    config['size.text.title'] = 2
-    assert config.get('size.text.title') == 2
-
-
-def test_contains():
-    config = InheritedConfig({'imread': 'matplotlib'})
-    assert 'imread' in config
-    assert 'imread.jpg' in config
-
-
 if __name__ == '__main__':
     import doctest
-    from numpy import testing
 
     doctest.testmod()
-    testing.run_module_suite()
diff --git a/skimage/io/tests/test_inherited_config.py b/skimage/io/tests/test_inherited_config.py
new file mode 100644
index 00000000..5521da0b
--- /dev/null
+++ b/skimage/io/tests/test_inherited_config.py
@@ -0,0 +1,41 @@
+from skimage.io.inherited_config import InheritedConfig
+
+
+def test_get_non_existent():
+    config = InheritedConfig()
+    assert config.get('size') is None
+
+
+def test_get_simple():
+    config = InheritedConfig({'imread': 'matplotlib'})
+    assert config.get('imread') == 'matplotlib'
+
+
+def test_get_default():
+    config = InheritedConfig()
+    assert config.get('size', 10) == 10
+
+
+def test_get_best():
+    config = InheritedConfig({'size': 0, 'size.text': 1})
+    assert config.get('size.text') == 1
+
+
+def test_get_multi_level():
+    config = InheritedConfig({'size': 0})
+    assert config.get('size.text.title') == 0
+    config['size.text'] = 1
+    assert config.get('size.text.title') == 1
+    config['size.text.title'] = 2
+    assert config.get('size.text.title') == 2
+
+
+def test_contains():
+    config = InheritedConfig({'imread': 'matplotlib'})
+    assert 'imread' in config
+    assert 'imread.jpg' in config
+
+
+if __name__ == '__main__':
+    from numpy import testing
+    testing.run_module_suite()

From f1dce4be9d18a2787ef5b29b40640e3f41a01a3d Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Tue, 3 Dec 2013 23:32:06 -0600
Subject: [PATCH 19/35] Change plugin_store to use InheritedConfig

---
 skimage/io/_plugins/plugin.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/skimage/io/_plugins/plugin.py b/skimage/io/_plugins/plugin.py
index ec8ed7c9..2ff2f938 100644
--- a/skimage/io/_plugins/plugin.py
+++ b/skimage/io/_plugins/plugin.py
@@ -9,6 +9,7 @@ except ImportError:
 
 import os.path
 from glob import glob
+from skimage.io.inherited_config import InheritedConfig
 
 
 __all__ = ['use_plugin', 'call_plugin', 'plugin_info', 'plugin_order',
@@ -29,11 +30,11 @@ def _clear_plugins():
 
     """
     global plugin_store
-    plugin_store = {'imread': [],
-                    'imsave': [],
-                    'imshow': [],
-                    'imread_collection': [],
-                    '_app_show': []}
+    plugin_store = InheritedConfig({'imread': [],
+                                    'imsave': [],
+                                    'imshow': [],
+                                    'imread_collection': [],
+                                    '_app_show': []})
 _clear_plugins()
 
 

From 860c6b5cb56d1744385c37d05b7b7005709c483f Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Tue, 3 Dec 2013 23:57:19 -0600
Subject: [PATCH 20/35] Use InheritedConfig for plugin_store

---
 skimage/io/_io.py                         | 11 +++++++++--
 skimage/io/inherited_config.py            |  9 +++++++--
 skimage/io/tests/test_inherited_config.py |  6 ++++++
 3 files changed, 22 insertions(+), 4 deletions(-)

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index ce718742..1a938408 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -1,3 +1,4 @@
+import os
 from io import BytesIO
 
 import numpy as np
@@ -5,7 +6,6 @@ import six
 
 from skimage.io._plugins import call_plugin
 from skimage.color import rgb2grey
-from skimage._shared import six
 from .util import file_or_url_context
 
 
@@ -95,7 +95,14 @@ def imread(fname, as_grey=False, plugin=None, flatten=None,
         as_grey = flatten
 
     with file_or_url_context(fname) as fname:
-        img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
+        function = 'imread'
+        # TODO: This should probably use imghdr to get the image format.
+        try:
+            _, extension = os.path.splitext(fname)
+            function = function + extension
+        except AttributeError:  # Buffers don't work with splitext
+            pass
+        img = call_plugin(function, fname, plugin=plugin, **plugin_args)
 
     if as_grey and getattr(img, 'ndim', 0) >= 3:
         img = rgb2grey(img)
diff --git a/skimage/io/inherited_config.py b/skimage/io/inherited_config.py
index 446e6db7..9cbc7857 100644
--- a/skimage/io/inherited_config.py
+++ b/skimage/io/inherited_config.py
@@ -32,7 +32,10 @@ class InheritedConfig(dict):
 
         super(InheritedConfig, self).__init__(config_values, **kwargs)
 
-    def get(self, key, default=None, _prev=None):
+    def __getitem__(self, key):
+        return self.get(key, _raise=True)
+
+    def get(self, key, default=None, _raise=False):
         """Return best matching config value for `key`.
 
         Get value from configuration. The search for `key` is in the following
@@ -94,11 +97,13 @@ class InheritedConfig(dict):
         1
         """
         if key in self.keys():
-            return self[key]
+            return super(InheritedConfig, self).__getitem__(key)
         elif default is not None:
             return default
         elif self._separator in key:
             return self.get(self._parent(key))
+        elif _raise:
+            raise KeyError('%r not in %s' % (key, self.__class__.__name__))
         else:
             return None
 
diff --git a/skimage/io/tests/test_inherited_config.py b/skimage/io/tests/test_inherited_config.py
index 5521da0b..207d3cf1 100644
--- a/skimage/io/tests/test_inherited_config.py
+++ b/skimage/io/tests/test_inherited_config.py
@@ -36,6 +36,12 @@ def test_contains():
     assert 'imread.jpg' in config
 
 
+def test_getitem():
+    config = InheritedConfig({'imread': 'a'})
+    assert config['imread'] == 'a'
+    assert config['imread.png'] == 'a'
+
+
 if __name__ == '__main__':
     from numpy import testing
     testing.run_module_suite()

From 6994bc53b987903946678c684ae46fc35002afa7 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Wed, 4 Dec 2013 22:54:38 -0600
Subject: [PATCH 21/35] Add test for loading preferred plugins.

---
 skimage/io/_plugins/plugin.py   |  3 ++-
 skimage/io/tests/test_plugin.py | 17 +++++++++++++++++
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/skimage/io/_plugins/plugin.py b/skimage/io/_plugins/plugin.py
index 2ff2f938..5352a511 100644
--- a/skimage/io/_plugins/plugin.py
+++ b/skimage/io/_plugins/plugin.py
@@ -24,6 +24,8 @@ plugin_provides = {}
 plugin_module_name = {}
 plugin_meta_data = {}
 
+preferred_plugins = ['matplotlib', 'pil', 'qt', 'freeimage', 'null']
+
 
 def _clear_plugins():
     """Clear the plugin state to the default, i.e., where no plugins are loaded
@@ -41,7 +43,6 @@ _clear_plugins()
 def _load_preferred_plugins():
     # Load preferred plugin for each io function.
     io_funcs = ['imsave', 'imshow', 'imread_collection', 'imread']
-    preferred_plugins = ['matplotlib', 'pil', 'qt', 'freeimage', 'null']
     for func in io_funcs:
         for plugin in preferred_plugins:
             if plugin not in available_plugins:
diff --git a/skimage/io/tests/test_plugin.py b/skimage/io/tests/test_plugin.py
index d91e927c..4be829ca 100644
--- a/skimage/io/tests/test_plugin.py
+++ b/skimage/io/tests/test_plugin.py
@@ -30,23 +30,29 @@ def teardown_module():
 def test_read():
     io.imread('test.png', as_grey=True, dtype='i4', plugin='test')
 
+
 def test_save():
     io.imsave('test.png', [1, 2, 3], plugin='test')
 
+
 def test_show():
     io.imshow([1, 2, 3], plugin_arg=(1, 2), plugin='test')
 
+
 def test_collection():
     io.imread_collection('*.png', conserve_memory=False, plugin='test')
 
+
 def test_use():
     plugin.use_plugin('test')
     plugin.use_plugin('test', 'imshow')
 
+
 @raises(ValueError)
 def test_failed_use():
     plugin.use_plugin('asd')
 
+
 @skipif(not PIL_available and not FI_available)
 def test_use_priority():
     plugin.use_plugin(priority_plugin)
@@ -57,6 +63,7 @@ def test_use_priority():
     plug, func = plugin.plugin_store['imread'][0]
     assert_equal(plug, 'test')
 
+
 @skipif(not PIL_available)
 def test_use_priority_with_func():
     plugin.use_plugin('pil')
@@ -74,16 +81,26 @@ def test_use_priority_with_func():
     plug, func = plugin.plugin_store['imsave'][0]
     assert_equal(plug, 'test')
 
+
 def test_plugin_order():
     p = io.plugin_order()
     assert 'imread' in p
     assert 'test' in p['imread']
 
+
 def test_available():
     assert 'qt' in io.available_plugins
     assert 'test' in io.find_available_plugins(loaded=True)
 
 
+def test_load_preferred_plugins():
+    from skimage.io._plugins import null_plugin
+    plugin.preferred_plugins = ['null']
+    plugin.reset_plugins()
+    plug, func = plugin.plugin_store['imshow'][0]
+    assert func == null_plugin.imshow
+
+
 if __name__ == "__main__":
     from numpy.testing import run_module_suite
     run_module_suite()

From ac4eb5ae7b0856712fa01c9dc4c460d25782fcb8 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Wed, 4 Dec 2013 22:58:35 -0600
Subject: [PATCH 22/35] Make preferred_plugins a dict

---
 skimage/io/_plugins/plugin.py   | 7 ++++---
 skimage/io/tests/test_plugin.py | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/skimage/io/_plugins/plugin.py b/skimage/io/_plugins/plugin.py
index 5352a511..6657ebbc 100644
--- a/skimage/io/_plugins/plugin.py
+++ b/skimage/io/_plugins/plugin.py
@@ -24,8 +24,9 @@ plugin_provides = {}
 plugin_module_name = {}
 plugin_meta_data = {}
 
-preferred_plugins = ['matplotlib', 'pil', 'qt', 'freeimage', 'null']
-
+preferred_plugins = {
+    'io': ['matplotlib', 'pil', 'qt', 'freeimage', 'null']
+}
 
 def _clear_plugins():
     """Clear the plugin state to the default, i.e., where no plugins are loaded
@@ -44,7 +45,7 @@ def _load_preferred_plugins():
     # Load preferred plugin for each io function.
     io_funcs = ['imsave', 'imshow', 'imread_collection', 'imread']
     for func in io_funcs:
-        for plugin in preferred_plugins:
+        for plugin in preferred_plugins['io']:
             if plugin not in available_plugins:
                 continue
             try:
diff --git a/skimage/io/tests/test_plugin.py b/skimage/io/tests/test_plugin.py
index 4be829ca..53f105a2 100644
--- a/skimage/io/tests/test_plugin.py
+++ b/skimage/io/tests/test_plugin.py
@@ -95,7 +95,7 @@ def test_available():
 
 def test_load_preferred_plugins():
     from skimage.io._plugins import null_plugin
-    plugin.preferred_plugins = ['null']
+    plugin.preferred_plugins['io'] = ['null']
     plugin.reset_plugins()
     plug, func = plugin.plugin_store['imshow'][0]
     assert func == null_plugin.imshow

From 0922ccf92315f0c4bdd60ac4ee71d1a84cdcea80 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Thu, 5 Dec 2013 22:56:58 -0600
Subject: [PATCH 23/35] Refactor load_preferred_plugins

---
 skimage/io/_plugins/null_plugin.ini |  2 +-
 skimage/io/_plugins/null_plugin.py  |  7 ++++-
 skimage/io/_plugins/plugin.py       | 40 +++++++++++++++++------------
 skimage/io/tests/test_plugin.py     | 39 ++++++++++++++++++++++++----
 4 files changed, 64 insertions(+), 24 deletions(-)

diff --git a/skimage/io/_plugins/null_plugin.ini b/skimage/io/_plugins/null_plugin.ini
index ddc45f33..9703aab0 100644
--- a/skimage/io/_plugins/null_plugin.ini
+++ b/skimage/io/_plugins/null_plugin.ini
@@ -1,3 +1,3 @@
 [null]
 description = Default plugin that does nothing
-provides = imshow, imread, _app_show
+provides = imshow, imread, imsave, _app_show
diff --git a/skimage/io/_plugins/null_plugin.py b/skimage/io/_plugins/null_plugin.py
index 70bfd5d8..4eb7adf3 100644
--- a/skimage/io/_plugins/null_plugin.py
+++ b/skimage/io/_plugins/null_plugin.py
@@ -1,4 +1,4 @@
-__all__ = ['imshow', 'imread', '_app_show']
+__all__ = ['imshow', 'imread', 'imsave', '_app_show']
 
 import warnings
 
@@ -17,4 +17,9 @@ def imshow(*args, **kwargs):
 def imread(*args, **kwargs):
     warnings.warn(RuntimeWarning(message))
 
+
+def imsave(*args, **kwargs):
+    warnings.warn(RuntimeWarning(message))
+
+
 _app_show = imshow
diff --git a/skimage/io/_plugins/plugin.py b/skimage/io/_plugins/plugin.py
index 6657ebbc..42cf448e 100644
--- a/skimage/io/_plugins/plugin.py
+++ b/skimage/io/_plugins/plugin.py
@@ -25,9 +25,14 @@ plugin_module_name = {}
 plugin_meta_data = {}
 
 preferred_plugins = {
-    'io': ['matplotlib', 'pil', 'qt', 'freeimage', 'null']
+    'all': ['matplotlib', 'pil', 'qt', 'freeimage', 'null'],
+    # Use PIL as the default imread plugin, since matplotlib (1.2.x)
+    # is buggy (flips PNGs around, returns bytes as floats, etc.)
+    'imread': ['pil'],
+    'imread.tiff': ['tifffile'],
 }
 
+
 def _clear_plugins():
     """Clear the plugin state to the default, i.e., where no plugins are loaded
 
@@ -43,23 +48,24 @@ _clear_plugins()
 
 def _load_preferred_plugins():
     # Load preferred plugin for each io function.
-    io_funcs = ['imsave', 'imshow', 'imread_collection', 'imread']
-    for func in io_funcs:
-        for plugin in preferred_plugins['io']:
-            if plugin not in available_plugins:
-                continue
-            try:
-                use_plugin(plugin, kind=func)
-                break
-            except (ImportError, RuntimeError, OSError):
-                pass
+    io_types = ['imsave', 'imshow', 'imread_collection', 'imread']
+    for p_type in io_types:
+        _set_plugin(p_type, preferred_plugins['all'])
 
-    # Use PIL as the default imread plugin, since matplotlib (1.2.x)
-    # is buggy (flips PNGs around, returns bytes as floats, etc.)
-    try:
-        use_plugin('pil', 'imread')
-    except ImportError:
-        pass
+    plugin_types = (p for p in preferred_plugins.keys() if p != 'all')
+    for p_type in plugin_types:
+        _set_plugin(p_type, preferred_plugins[p_type])
+
+
+def _set_plugin(plugin_type, plugin_list):
+    for plugin in plugin_list:
+        if plugin not in available_plugins:
+            continue
+        try:
+            use_plugin(plugin, kind=plugin_type)
+            break
+        except (ImportError, RuntimeError, OSError):
+            pass
 
 
 def reset_plugins():
diff --git a/skimage/io/tests/test_plugin.py b/skimage/io/tests/test_plugin.py
index 53f105a2..fba1c5d0 100644
--- a/skimage/io/tests/test_plugin.py
+++ b/skimage/io/tests/test_plugin.py
@@ -1,3 +1,5 @@
+from contextlib import contextmanager
+
 from numpy.testing import assert_equal, raises
 
 from skimage import io
@@ -27,6 +29,16 @@ def teardown_module():
     io.reset_plugins()
 
 
+@contextmanager
+def protect_preferred_plugins():
+    """Contexts where `preferred_plugins` can be modified w/o side-effects."""
+    preferred_plugins = plugin.preferred_plugins.copy()
+    try:
+        yield
+    finally:
+        plugin.preferred_plugins = preferred_plugins
+
+
 def test_read():
     io.imread('test.png', as_grey=True, dtype='i4', plugin='test')
 
@@ -93,12 +105,29 @@ def test_available():
     assert 'test' in io.find_available_plugins(loaded=True)
 
 
-def test_load_preferred_plugins():
+def test_load_preferred_plugins_all():
     from skimage.io._plugins import null_plugin
-    plugin.preferred_plugins['io'] = ['null']
-    plugin.reset_plugins()
-    plug, func = plugin.plugin_store['imshow'][0]
-    assert func == null_plugin.imshow
+
+    with protect_preferred_plugins():
+        plugin.preferred_plugins = {'all': ['null']}
+        plugin.reset_plugins()
+
+        for plugin_type in ('imread', 'imsave', 'imshow'):
+            plug, func = plugin.plugin_store[plugin_type][0]
+            assert func == getattr(null_plugin, plugin_type)
+
+
+def test_load_preferred_plugins_imread():
+    from skimage.io._plugins import null_plugin
+
+    with protect_preferred_plugins():
+        plugin.preferred_plugins['imread'] = ['null']
+        plugin.reset_plugins()
+
+        plug, func = plugin.plugin_store['imread'][0]
+        assert func == null_plugin.imread
+        plug, func = plugin.plugin_store['imshow'][0]
+        assert func != null_plugin.imshow
 
 
 if __name__ == "__main__":

From 99aa5a823836126c08a811860b7ba39d631b83c4 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Thu, 5 Dec 2013 23:18:09 -0600
Subject: [PATCH 24/35] Move io._plugins.plugin to io.manage_plugins

---
 skimage/io/__init__.py                        |  3 +-
 skimage/io/_io.py                             |  2 +-
 skimage/io/_plugins/__init__.py               |  1 -
 .../{_plugins/plugin.py => manage_plugins.py} |  4 +-
 skimage/io/tests/test_io.py                   |  2 +-
 skimage/io/tests/test_plugin.py               | 50 +++++++++----------
 6 files changed, 32 insertions(+), 30 deletions(-)
 rename skimage/io/{_plugins/plugin.py => manage_plugins.py} (98%)

diff --git a/skimage/io/__init__.py b/skimage/io/__init__.py
index 02800fbd..316253ca 100644
--- a/skimage/io/__init__.py
+++ b/skimage/io/__init__.py
@@ -4,7 +4,7 @@ The following plug-ins are available:
 
 """
 
-from ._plugins import *
+from .manage_plugins import *
 from .sift import *
 from .collection import *
 
@@ -37,6 +37,7 @@ def _update_doc(doc):
     """
     from textwrap import wrap
 
+
     info_table = [(p, plugin_info(p).get('description', 'no description'))
                   for p in available_plugins if not p == 'test']
 
diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index 1a938408..0f5087a1 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -4,7 +4,7 @@ from io import BytesIO
 import numpy as np
 import six
 
-from skimage.io._plugins import call_plugin
+from skimage.io.manage_plugins import call_plugin
 from skimage.color import rgb2grey
 from .util import file_or_url_context
 
diff --git a/skimage/io/_plugins/__init__.py b/skimage/io/_plugins/__init__.py
index 48aad58e..e69de29b 100644
--- a/skimage/io/_plugins/__init__.py
+++ b/skimage/io/_plugins/__init__.py
@@ -1 +0,0 @@
-from .plugin import *
diff --git a/skimage/io/_plugins/plugin.py b/skimage/io/manage_plugins.py
similarity index 98%
rename from skimage/io/_plugins/plugin.py
rename to skimage/io/manage_plugins.py
index 42cf448e..ebc55b6a 100644
--- a/skimage/io/_plugins/plugin.py
+++ b/skimage/io/manage_plugins.py
@@ -9,6 +9,7 @@ except ImportError:
 
 import os.path
 from glob import glob
+
 from skimage.io.inherited_config import InheritedConfig
 
 
@@ -25,6 +26,7 @@ plugin_module_name = {}
 plugin_meta_data = {}
 
 preferred_plugins = {
+    # Default plugins for all types (overridden by specific types below).
     'all': ['matplotlib', 'pil', 'qt', 'freeimage', 'null'],
     # Use PIL as the default imread plugin, since matplotlib (1.2.x)
     # is buggy (flips PNGs around, returns bytes as floats, etc.)
@@ -92,7 +94,7 @@ def _scan_plugins():
 
     """
     pd = os.path.dirname(__file__)
-    config_files = glob(os.path.join(pd, '*.ini'))
+    config_files = glob(os.path.join(pd, '_plugins', '*.ini'))
 
     for filename in config_files:
         name, meta_data = _parse_config_file(filename)
diff --git a/skimage/io/tests/test_io.py b/skimage/io/tests/test_io.py
index 6b74ae34..14879e64 100644
--- a/skimage/io/tests/test_io.py
+++ b/skimage/io/tests/test_io.py
@@ -4,7 +4,7 @@ from numpy.testing import assert_array_equal, raises, run_module_suite
 import numpy as np
 
 import skimage.io as io
-from skimage.io._plugins.plugin import plugin_store
+from skimage.io.manage_plugins import plugin_store
 from skimage import data_dir
 
 
diff --git a/skimage/io/tests/test_plugin.py b/skimage/io/tests/test_plugin.py
index fba1c5d0..06f3a600 100644
--- a/skimage/io/tests/test_plugin.py
+++ b/skimage/io/tests/test_plugin.py
@@ -3,7 +3,7 @@ from contextlib import contextmanager
 from numpy.testing import assert_equal, raises
 
 from skimage import io
-from skimage.io._plugins import plugin
+from skimage.io import manage_plugins
 from numpy.testing.decorators import skipif
 
 try:
@@ -22,7 +22,7 @@ except RuntimeError:
 
 
 def setup_module():
-    plugin.use_plugin('test')  # see ../_plugins/test_plugin.py
+    manage_plugins.use_plugin('test')  # see ../_plugins/test_plugin.py
 
 
 def teardown_module():
@@ -32,11 +32,11 @@ def teardown_module():
 @contextmanager
 def protect_preferred_plugins():
     """Contexts where `preferred_plugins` can be modified w/o side-effects."""
-    preferred_plugins = plugin.preferred_plugins.copy()
+    preferred_plugins = manage_plugins.preferred_plugins.copy()
     try:
         yield
     finally:
-        plugin.preferred_plugins = preferred_plugins
+        manage_plugins.preferred_plugins = preferred_plugins
 
 
 def test_read():
@@ -56,41 +56,41 @@ def test_collection():
 
 
 def test_use():
-    plugin.use_plugin('test')
-    plugin.use_plugin('test', 'imshow')
+    manage_plugins.use_plugin('test')
+    manage_plugins.use_plugin('test', 'imshow')
 
 
 @raises(ValueError)
 def test_failed_use():
-    plugin.use_plugin('asd')
+    manage_plugins.use_plugin('asd')
 
 
 @skipif(not PIL_available and not FI_available)
 def test_use_priority():
-    plugin.use_plugin(priority_plugin)
-    plug, func = plugin.plugin_store['imread'][0]
+    manage_plugins.use_plugin(priority_plugin)
+    plug, func = manage_plugins.plugin_store['imread'][0]
     assert_equal(plug, priority_plugin)
 
-    plugin.use_plugin('test')
-    plug, func = plugin.plugin_store['imread'][0]
+    manage_plugins.use_plugin('test')
+    plug, func = manage_plugins.plugin_store['imread'][0]
     assert_equal(plug, 'test')
 
 
 @skipif(not PIL_available)
 def test_use_priority_with_func():
-    plugin.use_plugin('pil')
-    plug, func = plugin.plugin_store['imread'][0]
+    manage_plugins.use_plugin('pil')
+    plug, func = manage_plugins.plugin_store['imread'][0]
     assert_equal(plug, 'pil')
 
-    plugin.use_plugin('test', 'imread')
-    plug, func = plugin.plugin_store['imread'][0]
+    manage_plugins.use_plugin('test', 'imread')
+    plug, func = manage_plugins.plugin_store['imread'][0]
     assert_equal(plug, 'test')
 
-    plug, func = plugin.plugin_store['imsave'][0]
+    plug, func = manage_plugins.plugin_store['imsave'][0]
     assert_equal(plug, 'pil')
 
-    plugin.use_plugin('test')
-    plug, func = plugin.plugin_store['imsave'][0]
+    manage_plugins.use_plugin('test')
+    plug, func = manage_plugins.plugin_store['imsave'][0]
     assert_equal(plug, 'test')
 
 
@@ -109,11 +109,11 @@ def test_load_preferred_plugins_all():
     from skimage.io._plugins import null_plugin
 
     with protect_preferred_plugins():
-        plugin.preferred_plugins = {'all': ['null']}
-        plugin.reset_plugins()
+        manage_plugins.preferred_plugins = {'all': ['null']}
+        manage_plugins.reset_plugins()
 
         for plugin_type in ('imread', 'imsave', 'imshow'):
-            plug, func = plugin.plugin_store[plugin_type][0]
+            plug, func = manage_plugins.plugin_store[plugin_type][0]
             assert func == getattr(null_plugin, plugin_type)
 
 
@@ -121,12 +121,12 @@ def test_load_preferred_plugins_imread():
     from skimage.io._plugins import null_plugin
 
     with protect_preferred_plugins():
-        plugin.preferred_plugins['imread'] = ['null']
-        plugin.reset_plugins()
+        manage_plugins.preferred_plugins['imread'] = ['null']
+        manage_plugins.reset_plugins()
 
-        plug, func = plugin.plugin_store['imread'][0]
+        plug, func = manage_plugins.plugin_store['imread'][0]
         assert func == null_plugin.imread
-        plug, func = plugin.plugin_store['imshow'][0]
+        plug, func = manage_plugins.plugin_store['imshow'][0]
         assert func != null_plugin.imshow
 
 

From e59daf474c38aa744c3f3f3ee3cf20d930501082 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Thu, 5 Dec 2013 23:38:13 -0600
Subject: [PATCH 25/35] Modest attempt at normalizing file extensions

---
 skimage/io/_io.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index 0f5087a1..d38e7ac0 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -99,7 +99,7 @@ def imread(fname, as_grey=False, plugin=None, flatten=None,
         # TODO: This should probably use imghdr to get the image format.
         try:
             _, extension = os.path.splitext(fname)
-            function = function + extension
+            function = function + extension.lower()
         except AttributeError:  # Buffers don't work with splitext
             pass
         img = call_plugin(function, fname, plugin=plugin, **plugin_args)

From 0f88bed41d94717ebe8cdaec355e1aef55424c6d Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Fri, 6 Dec 2013 22:26:20 -0600
Subject: [PATCH 26/35] Remove inherited config and file-type-specific code.

This functionality needs to fleshed out a bit more. This commit can be
reverted after the initial refactor PR.
---
 skimage/io/_io.py                         |  10 +-
 skimage/io/inherited_config.py            | 127 ----------------------
 skimage/io/manage_plugins.py              |  13 +--
 skimage/io/tests/test_inherited_config.py |  47 --------
 4 files changed, 6 insertions(+), 191 deletions(-)
 delete mode 100644 skimage/io/inherited_config.py
 delete mode 100644 skimage/io/tests/test_inherited_config.py

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index d38e7ac0..97f8718e 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -1,4 +1,3 @@
-import os
 from io import BytesIO
 
 import numpy as np
@@ -95,14 +94,7 @@ def imread(fname, as_grey=False, plugin=None, flatten=None,
         as_grey = flatten
 
     with file_or_url_context(fname) as fname:
-        function = 'imread'
-        # TODO: This should probably use imghdr to get the image format.
-        try:
-            _, extension = os.path.splitext(fname)
-            function = function + extension.lower()
-        except AttributeError:  # Buffers don't work with splitext
-            pass
-        img = call_plugin(function, fname, plugin=plugin, **plugin_args)
+        img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
 
     if as_grey and getattr(img, 'ndim', 0) >= 3:
         img = rgb2grey(img)
diff --git a/skimage/io/inherited_config.py b/skimage/io/inherited_config.py
deleted file mode 100644
index 9cbc7857..00000000
--- a/skimage/io/inherited_config.py
+++ /dev/null
@@ -1,127 +0,0 @@
-class InheritedConfig(dict):
-    """Configuration dictionary where non-existent keys can inherit values.
-
-    This class allows you to define parameter names that can match exactly, but
-    if it doesn't, parameter names will be searched based on key inheritance.
-    For example, the key 'size.text' will default to 'size'.
-
-    Note that indexing into the dictionary will raise an error if it doesn't
-    match exactly, while `InheritedConfig.get` will look up values based on
-    inheritance.
-
-    Parameters
-    ----------
-    config_values : dict or list of (key, value) pairs
-        Default values for a configuration, where keys are the parameter names
-        and values are the associated value.
-    cascade_map : dict
-        Dictionary defining cascading defaults. If a parameter name is not
-        found, indexing `cascade_map` with the parameter name will return
-        the parameter to look for.
-    kwargs : dict
-        Keyword arguments for initializing dict.
-    """
-
-    _separator = '.'
-
-    def __init__(self, config_values=None, **kwargs):
-        assert 'config_values' not in kwargs
-
-        if config_values is None:
-            config_values = {}
-
-        super(InheritedConfig, self).__init__(config_values, **kwargs)
-
-    def __getitem__(self, key):
-        return self.get(key, _raise=True)
-
-    def get(self, key, default=None, _raise=False):
-        """Return best matching config value for `key`.
-
-        Get value from configuration. The search for `key` is in the following
-        order:
-
-            - `self` (Value in global configuration)
-            - `default`
-            - Alternate key specified by `self.cascade_map`
-
-        This method supports the pattern commonly used for optional keyword
-        arguments to a function. For example::
-
-            >>> def print_value(key, **kwargs):
-            ...     print kwargs.get(key, 0)
-            >>> print_value('size')
-            0
-            >>> print_value('size', size=1)
-            1
-
-        Instead, you would create a config class and write::
-
-            >>> config = InheritedConfig(size=0)
-            >>> def print_value(key, **kwargs):
-            ...     print kwargs.get(key, config.get(key))
-            >>> print_value('size')
-            0
-            >>> print_value('size', size=1)
-            1
-            >>> print_value('non-existent')
-            None
-            >>> print_value('size.text')
-            0
-
-        See examples below for a demonstration of the cascading of
-        configuration names.
-
-        Parameters
-        ----------
-        key : str
-            Name of config value you want.
-        default : object
-            Default value if `key` doesn't exist in instance.
-
-        Examples
-        --------
-        >>> config = InheritedConfig(size=0)
-        >>> config.get('size')
-        0
-        >>> top_choice={'size': 1}
-        >>> top_choice.get('size', config.get('size'))
-        1
-        >>> config.get('non-existent', 'unknown')
-        'unknown'
-        >>> config.get('size.text')
-        0
-        >>> config.get('size.text', 2)
-        2
-        >>> top_choice.get('size', config.get('size.text'))
-        1
-        """
-        if key in self.keys():
-            return super(InheritedConfig, self).__getitem__(key)
-        elif default is not None:
-            return default
-        elif self._separator in key:
-            return self.get(self._parent(key))
-        elif _raise:
-            raise KeyError('%r not in %s' % (key, self.__class__.__name__))
-        else:
-            return None
-
-    def _parent(self, key):
-        """Return parent key."""
-        parts = key.split(self._separator)
-        return self._separator.join(parts[:-1])
-
-    def __contains__(self, key):
-        if key in self.keys():
-            return True
-        elif self._separator in key:
-            return self.__contains__(self._parent(key))
-        else:
-            return False
-
-
-if __name__ == '__main__':
-    import doctest
-
-    doctest.testmod()
diff --git a/skimage/io/manage_plugins.py b/skimage/io/manage_plugins.py
index ebc55b6a..e68594a2 100644
--- a/skimage/io/manage_plugins.py
+++ b/skimage/io/manage_plugins.py
@@ -10,8 +10,6 @@ except ImportError:
 import os.path
 from glob import glob
 
-from skimage.io.inherited_config import InheritedConfig
-
 
 __all__ = ['use_plugin', 'call_plugin', 'plugin_info', 'plugin_order',
            'reset_plugins', 'find_available_plugins', 'available_plugins']
@@ -31,7 +29,6 @@ preferred_plugins = {
     # Use PIL as the default imread plugin, since matplotlib (1.2.x)
     # is buggy (flips PNGs around, returns bytes as floats, etc.)
     'imread': ['pil'],
-    'imread.tiff': ['tifffile'],
 }
 
 
@@ -40,11 +37,11 @@ def _clear_plugins():
 
     """
     global plugin_store
-    plugin_store = InheritedConfig({'imread': [],
-                                    'imsave': [],
-                                    'imshow': [],
-                                    'imread_collection': [],
-                                    '_app_show': []})
+    plugin_store = {'imread': [],
+                    'imsave': [],
+                    'imshow': [],
+                    'imread_collection': [],
+                    '_app_show': []}
 _clear_plugins()
 
 
diff --git a/skimage/io/tests/test_inherited_config.py b/skimage/io/tests/test_inherited_config.py
deleted file mode 100644
index 207d3cf1..00000000
--- a/skimage/io/tests/test_inherited_config.py
+++ /dev/null
@@ -1,47 +0,0 @@
-from skimage.io.inherited_config import InheritedConfig
-
-
-def test_get_non_existent():
-    config = InheritedConfig()
-    assert config.get('size') is None
-
-
-def test_get_simple():
-    config = InheritedConfig({'imread': 'matplotlib'})
-    assert config.get('imread') == 'matplotlib'
-
-
-def test_get_default():
-    config = InheritedConfig()
-    assert config.get('size', 10) == 10
-
-
-def test_get_best():
-    config = InheritedConfig({'size': 0, 'size.text': 1})
-    assert config.get('size.text') == 1
-
-
-def test_get_multi_level():
-    config = InheritedConfig({'size': 0})
-    assert config.get('size.text.title') == 0
-    config['size.text'] = 1
-    assert config.get('size.text.title') == 1
-    config['size.text.title'] = 2
-    assert config.get('size.text.title') == 2
-
-
-def test_contains():
-    config = InheritedConfig({'imread': 'matplotlib'})
-    assert 'imread' in config
-    assert 'imread.jpg' in config
-
-
-def test_getitem():
-    config = InheritedConfig({'imread': 'a'})
-    assert config['imread'] == 'a'
-    assert config['imread.png'] == 'a'
-
-
-if __name__ == '__main__':
-    from numpy import testing
-    testing.run_module_suite()

From c329ff14bc024cd29264370a9fe4fc736d2a09a1 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Fri, 6 Dec 2013 22:40:37 -0600
Subject: [PATCH 27/35] Fix failing doctest on systems w/o PIL

---
 skimage/io/manage_plugins.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/skimage/io/manage_plugins.py b/skimage/io/manage_plugins.py
index e68594a2..ace57d8f 100644
--- a/skimage/io/manage_plugins.py
+++ b/skimage/io/manage_plugins.py
@@ -197,15 +197,19 @@ def use_plugin(name, kind=None):
 
     See Also
     --------
-    plugins : List of available plugins
+    available_plugins : List of available plugins
 
     Examples
     --------
 
-    Use the Python Imaging Library to read images:
+    To use a plugin named 'null' as the default image reader, you would write:
 
-    >>> from skimage.io import use_plugin
-    >>> use_plugin('pil', 'imread')
+    >>> from skimage import io
+    >>> io.use_plugin('null', 'imread')
+
+    To see a list of available plugins run ``io.available_plugins``. Note that
+    this lists plugins that are defined, but the full list may not be usable
+    if your system does not have the required libraries installed.
 
     """
     if kind is None:

From 99c5ba409a3a03d0a0156302b4b6e7b5324b8a40 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Fri, 6 Dec 2013 23:43:56 -0600
Subject: [PATCH 28/35] Slight clean up of tests

---
 skimage/io/tests/test_collection.py  | 153 ++++++++-------------------
 skimage/io/tests/test_multi_image.py |  69 ++++++++++++
 2 files changed, 114 insertions(+), 108 deletions(-)
 create mode 100644 skimage/io/tests/test_multi_image.py

diff --git a/skimage/io/tests/test_collection.py b/skimage/io/tests/test_collection.py
index cf5ef820..1e9fea73 100644
--- a/skimage/io/tests/test_collection.py
+++ b/skimage/io/tests/test_collection.py
@@ -1,88 +1,72 @@
-import sys
 import os.path
 
 import numpy as np
-from numpy.testing import (assert_raises,
-                           assert_equal,
-                           assert_array_almost_equal,
-                           )
-from numpy.testing.decorators import skipif
+from numpy.testing import assert_raises, assert_equal, assert_allclose
 
 from skimage import data_dir
-from skimage.io import ImageCollection, MultiImage
-from skimage.io.collection import alphanumeric_key
-from skimage.io import Image as ioImage
-
-import six
+from skimage.io.collection import ImageCollection, alphanumeric_key
 
 
-try:
-    from PIL import Image
-except ImportError:
-    PIL_available = False
-else:
-    PIL_available = True
+def test_string_split():
+    test_string = 'z23a'
+    test_str_result = ['z', 23, 'a']
+    assert_equal(alphanumeric_key(test_string), test_str_result)
 
 
-class TestAlphanumericKey():
-    def setUp(self):
-        self.test_string = 'z23a'
-        self.test_str_result = ['z', 23, 'a']
-        self.filenames = ['f9.10.png', 'f9.9.png', 'f10.10.png', 'f10.9.png',
-            'e9.png', 'e10.png', 'em.png']
-        self.sorted_filenames = \
-            ['e9.png', 'e10.png', 'em.png', 'f9.9.png', 'f9.10.png',
-            'f10.9.png', 'f10.10.png']
-
-    def test_string_split(self):
-        assert_equal(alphanumeric_key(self.test_string), self.test_str_result)
-
-    def test_string_sort(self):
-        sorted_filenames = sorted(self.filenames, key=alphanumeric_key)
-        assert_equal(sorted_filenames, self.sorted_filenames)
+def test_string_sort():
+    filenames = ['f9.10.png', 'f9.9.png', 'f10.10.png', 'f10.9.png',
+                 'e9.png', 'e10.png', 'em.png']
+    sorted_filenames = ['e9.png', 'e10.png', 'em.png', 'f9.9.png',
+                        'f9.10.png', 'f10.9.png', 'f10.10.png']
+    sorted_filenames = sorted(filenames, key=alphanumeric_key)
+    assert_equal(sorted_filenames, sorted_filenames)
 
 
 class TestImageCollection():
-    pattern = [os.path.join(data_dir, pic) for pic in ['camera.png',
-                                                       'color.png']]
-    pattern_matched = [os.path.join(data_dir, pic) for pic in 
-                                                    ['camera.png', 'moon.png']]
+
+    pattern = [os.path.join(data_dir, pic)
+               for pic in ['camera.png', 'color.png']]
+
+    pattern_matched = [os.path.join(data_dir, pic)
+                       for pic in ['camera.png', 'moon.png']]
 
     def setUp(self):
-        self.collection = ImageCollection(self.pattern)
-        self.collection_matched = ImageCollection(self.pattern_matched)
+        # Generic image collection with images of different shapes.
+        self.images = ImageCollection(self.pattern)
+        # Image collection with images having shapes that match.
+        self.images_matched = ImageCollection(self.pattern_matched)
 
     def test_len(self):
-        assert len(self.collection) == 2
+        assert len(self.images) == 2
 
     def test_getitem(self):
-        num = len(self.collection)
+        num = len(self.images)
         for i in range(-num, num):
-            assert type(self.collection[i]) is np.ndarray
-        assert_array_almost_equal(self.collection[0],
-                                  self.collection[-num])
+            assert type(self.images[i]) is np.ndarray
+        assert_allclose(self.images[0],
+                                  self.images[-num])
 
-        #assert_raises expects a callable, hence this do-very-little func
+        # assert_raises expects a callable, hence this thin wrapper function.
         def return_img(n):
-            return self.collection[n]
+            return self.images[n]
         assert_raises(IndexError, return_img, num)
         assert_raises(IndexError, return_img, -num - 1)
 
     def test_slicing(self):
-        assert type(self.collection[:]) is ImageCollection
-        assert len(self.collection[:]) == 2
-        assert len(self.collection[:1]) == 1
-        assert len(self.collection[1:]) == 1
-        assert_array_almost_equal(self.collection[0], self.collection[:1][0])
-        assert_array_almost_equal(self.collection[1], self.collection[1:][0])
-        assert_array_almost_equal(self.collection[1], self.collection[::-1][0])
-        assert_array_almost_equal(self.collection[0], self.collection[::-1][1])
+        assert type(self.images[:]) is ImageCollection
+        assert len(self.images[:]) == 2
+        assert len(self.images[:1]) == 1
+        assert len(self.images[1:]) == 1
+        assert_allclose(self.images[0], self.images[:1][0])
+        assert_allclose(self.images[1], self.images[1:][0])
+        assert_allclose(self.images[1], self.images[::-1][0])
+        assert_allclose(self.images[0], self.images[::-1][1])
 
     def test_files_property(self):
-        assert isinstance(self.collection.files, list)
+        assert isinstance(self.images.files, list)
 
         def set_files(f):
-            self.collection.files = f
+            self.images.files = f
         assert_raises(AttributeError, set_files, 'newfiles')
 
     def test_custom_load(self):
@@ -95,59 +79,12 @@ class TestImageCollection():
         assert_equal(ic[1], (2, 'two'))
 
     def test_concatenate(self):
-        ar = self.collection_matched.concatenate()
-        assert_equal(ar.shape, (len(self.collection_matched),) + 
-                                self.collection[0].shape)
-        assert_raises(ValueError, self.collection.concatenate)
+        array = self.images_matched.concatenate()
+        expected_shape = (len(self.images_matched),) + self.images[0].shape
+        assert_equal(array.shape, expected_shape)
 
-
-class TestMultiImage():
-
-    def setUp(self):
-        # This multipage TIF file was created with imagemagick:
-        # convert im1.tif im2.tif -adjoin multipage.tif
-        if PIL_available:
-            self.img = MultiImage(os.path.join(data_dir, 'multipage.tif'))
-
-    @skipif(not PIL_available)
-    def test_len(self):
-        assert len(self.img) == 2
-
-    @skipif(not PIL_available)
-    def test_getitem(self):
-        num = len(self.img)
-        for i in range(-num, num):
-            assert type(self.img[i]) is np.ndarray
-        assert_array_almost_equal(self.img[0],
-                                  self.img[-num])
-
-        #assert_raises expects a callable, hence this do-very-little func
-        def return_img(n):
-            return self.img[n]
-        assert_raises(IndexError, return_img, num)
-        assert_raises(IndexError, return_img, -num - 1)
-
-    @skipif(not PIL_available)
-    def test_files_property(self):
-        assert isinstance(self.img.filename, six.string_types)
-
-        def set_filename(f):
-            self.img.filename = f
-        assert_raises(AttributeError, set_filename, 'newfile')
-
-    @skipif(not PIL_available)
-    def test_conserve_memory_property(self):
-        assert isinstance(self.img.conserve_memory, bool)
-
-        def set_mem(val):
-            self.img.conserve_memory = val
-        assert_raises(AttributeError, set_mem, True)
-
-    @skipif(not PIL_available)
-    def test_concatenate(self):
-        ar = self.img.concatenate()
-        assert_equal(ar.shape, (len(self.img),) + 
-                                self.img[0].shape)
+    def test_concatentate_mismatched_image_shapes(self):
+        assert_raises(ValueError, self.images.concatenate)
 
 
 if __name__ == "__main__":
diff --git a/skimage/io/tests/test_multi_image.py b/skimage/io/tests/test_multi_image.py
new file mode 100644
index 00000000..ebaa71dc
--- /dev/null
+++ b/skimage/io/tests/test_multi_image.py
@@ -0,0 +1,69 @@
+import os
+
+import numpy as np
+from numpy.testing.decorators import skipif
+from numpy.testing import assert_raises, assert_equal, assert_allclose
+
+from skimage import data_dir
+from skimage.io.collection import MultiImage
+
+try:
+    from PIL import Image
+except ImportError:
+    PIL_available = False
+else:
+    PIL_available = True
+
+import six
+
+
+class TestMultiImage():
+
+    def setUp(self):
+        # This multipage TIF file was created with imagemagick:
+        # convert im1.tif im2.tif -adjoin multipage.tif
+        if PIL_available:
+            self.img = MultiImage(os.path.join(data_dir, 'multipage.tif'))
+
+    @skipif(not PIL_available)
+    def test_len(self):
+        assert len(self.img) == 2
+
+    @skipif(not PIL_available)
+    def test_getitem(self):
+        num = len(self.img)
+        for i in range(-num, num):
+            assert type(self.img[i]) is np.ndarray
+        assert_allclose(self.img[0], self.img[-num])
+
+        # assert_raises expects a callable, hence this thin wrapper function.
+        def return_img(n):
+            return self.img[n]
+        assert_raises(IndexError, return_img, num)
+        assert_raises(IndexError, return_img, -num - 1)
+
+    @skipif(not PIL_available)
+    def test_files_property(self):
+        assert isinstance(self.img.filename, six.string_types)
+
+        def set_filename(f):
+            self.img.filename = f
+        assert_raises(AttributeError, set_filename, 'newfile')
+
+    @skipif(not PIL_available)
+    def test_conserve_memory_property(self):
+        assert isinstance(self.img.conserve_memory, bool)
+
+        def set_mem(val):
+            self.img.conserve_memory = val
+        assert_raises(AttributeError, set_mem, True)
+
+    @skipif(not PIL_available)
+    def test_concatenate(self):
+        array = self.img.concatenate()
+        assert_equal(array.shape, (len(self.img),) + self.img[0].shape)
+
+
+if __name__ == "__main__":
+    from numpy.testing import run_module_suite
+    run_module_suite()

From c09f1bfd326876e4f6523a8cee3468e18455bb09 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 7 Dec 2013 00:01:32 -0600
Subject: [PATCH 29/35] Revert previous 3 commits to test Travis CI failures.

---
 skimage/io/_io.py                         |  10 +-
 skimage/io/inherited_config.py            | 127 ++++++++++++++++++
 skimage/io/manage_plugins.py              |  25 ++--
 skimage/io/tests/test_collection.py       | 153 +++++++++++++++-------
 skimage/io/tests/test_inherited_config.py |  47 +++++++
 skimage/io/tests/test_multi_image.py      |  69 ----------
 6 files changed, 303 insertions(+), 128 deletions(-)
 create mode 100644 skimage/io/inherited_config.py
 create mode 100644 skimage/io/tests/test_inherited_config.py
 delete mode 100644 skimage/io/tests/test_multi_image.py

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index 97f8718e..d38e7ac0 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -1,3 +1,4 @@
+import os
 from io import BytesIO
 
 import numpy as np
@@ -94,7 +95,14 @@ def imread(fname, as_grey=False, plugin=None, flatten=None,
         as_grey = flatten
 
     with file_or_url_context(fname) as fname:
-        img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
+        function = 'imread'
+        # TODO: This should probably use imghdr to get the image format.
+        try:
+            _, extension = os.path.splitext(fname)
+            function = function + extension.lower()
+        except AttributeError:  # Buffers don't work with splitext
+            pass
+        img = call_plugin(function, fname, plugin=plugin, **plugin_args)
 
     if as_grey and getattr(img, 'ndim', 0) >= 3:
         img = rgb2grey(img)
diff --git a/skimage/io/inherited_config.py b/skimage/io/inherited_config.py
new file mode 100644
index 00000000..9cbc7857
--- /dev/null
+++ b/skimage/io/inherited_config.py
@@ -0,0 +1,127 @@
+class InheritedConfig(dict):
+    """Configuration dictionary where non-existent keys can inherit values.
+
+    This class allows you to define parameter names that can match exactly, but
+    if it doesn't, parameter names will be searched based on key inheritance.
+    For example, the key 'size.text' will default to 'size'.
+
+    Note that indexing into the dictionary will raise an error if it doesn't
+    match exactly, while `InheritedConfig.get` will look up values based on
+    inheritance.
+
+    Parameters
+    ----------
+    config_values : dict or list of (key, value) pairs
+        Default values for a configuration, where keys are the parameter names
+        and values are the associated value.
+    cascade_map : dict
+        Dictionary defining cascading defaults. If a parameter name is not
+        found, indexing `cascade_map` with the parameter name will return
+        the parameter to look for.
+    kwargs : dict
+        Keyword arguments for initializing dict.
+    """
+
+    _separator = '.'
+
+    def __init__(self, config_values=None, **kwargs):
+        assert 'config_values' not in kwargs
+
+        if config_values is None:
+            config_values = {}
+
+        super(InheritedConfig, self).__init__(config_values, **kwargs)
+
+    def __getitem__(self, key):
+        return self.get(key, _raise=True)
+
+    def get(self, key, default=None, _raise=False):
+        """Return best matching config value for `key`.
+
+        Get value from configuration. The search for `key` is in the following
+        order:
+
+            - `self` (Value in global configuration)
+            - `default`
+            - Alternate key specified by `self.cascade_map`
+
+        This method supports the pattern commonly used for optional keyword
+        arguments to a function. For example::
+
+            >>> def print_value(key, **kwargs):
+            ...     print kwargs.get(key, 0)
+            >>> print_value('size')
+            0
+            >>> print_value('size', size=1)
+            1
+
+        Instead, you would create a config class and write::
+
+            >>> config = InheritedConfig(size=0)
+            >>> def print_value(key, **kwargs):
+            ...     print kwargs.get(key, config.get(key))
+            >>> print_value('size')
+            0
+            >>> print_value('size', size=1)
+            1
+            >>> print_value('non-existent')
+            None
+            >>> print_value('size.text')
+            0
+
+        See examples below for a demonstration of the cascading of
+        configuration names.
+
+        Parameters
+        ----------
+        key : str
+            Name of config value you want.
+        default : object
+            Default value if `key` doesn't exist in instance.
+
+        Examples
+        --------
+        >>> config = InheritedConfig(size=0)
+        >>> config.get('size')
+        0
+        >>> top_choice={'size': 1}
+        >>> top_choice.get('size', config.get('size'))
+        1
+        >>> config.get('non-existent', 'unknown')
+        'unknown'
+        >>> config.get('size.text')
+        0
+        >>> config.get('size.text', 2)
+        2
+        >>> top_choice.get('size', config.get('size.text'))
+        1
+        """
+        if key in self.keys():
+            return super(InheritedConfig, self).__getitem__(key)
+        elif default is not None:
+            return default
+        elif self._separator in key:
+            return self.get(self._parent(key))
+        elif _raise:
+            raise KeyError('%r not in %s' % (key, self.__class__.__name__))
+        else:
+            return None
+
+    def _parent(self, key):
+        """Return parent key."""
+        parts = key.split(self._separator)
+        return self._separator.join(parts[:-1])
+
+    def __contains__(self, key):
+        if key in self.keys():
+            return True
+        elif self._separator in key:
+            return self.__contains__(self._parent(key))
+        else:
+            return False
+
+
+if __name__ == '__main__':
+    import doctest
+
+    doctest.testmod()
diff --git a/skimage/io/manage_plugins.py b/skimage/io/manage_plugins.py
index ace57d8f..ebc55b6a 100644
--- a/skimage/io/manage_plugins.py
+++ b/skimage/io/manage_plugins.py
@@ -10,6 +10,8 @@ except ImportError:
 import os.path
 from glob import glob
 
+from skimage.io.inherited_config import InheritedConfig
+
 
 __all__ = ['use_plugin', 'call_plugin', 'plugin_info', 'plugin_order',
            'reset_plugins', 'find_available_plugins', 'available_plugins']
@@ -29,6 +31,7 @@ preferred_plugins = {
     # Use PIL as the default imread plugin, since matplotlib (1.2.x)
     # is buggy (flips PNGs around, returns bytes as floats, etc.)
     'imread': ['pil'],
+    'imread.tiff': ['tifffile'],
 }
 
 
@@ -37,11 +40,11 @@ def _clear_plugins():
 
     """
     global plugin_store
-    plugin_store = {'imread': [],
-                    'imsave': [],
-                    'imshow': [],
-                    'imread_collection': [],
-                    '_app_show': []}
+    plugin_store = InheritedConfig({'imread': [],
+                                    'imsave': [],
+                                    'imshow': [],
+                                    'imread_collection': [],
+                                    '_app_show': []})
 _clear_plugins()
 
 
@@ -197,19 +200,15 @@ def use_plugin(name, kind=None):
 
     See Also
     --------
-    available_plugins : List of available plugins
+    plugins : List of available plugins
 
     Examples
     --------
 
-    To use a plugin named 'null' as the default image reader, you would write:
+    Use the Python Imaging Library to read images:
 
-    >>> from skimage import io
-    >>> io.use_plugin('null', 'imread')
-
-    To see a list of available plugins run ``io.available_plugins``. Note that
-    this lists plugins that are defined, but the full list may not be usable
-    if your system does not have the required libraries installed.
+    >>> from skimage.io import use_plugin
+    >>> use_plugin('pil', 'imread')
 
     """
     if kind is None:
diff --git a/skimage/io/tests/test_collection.py b/skimage/io/tests/test_collection.py
index 1e9fea73..cf5ef820 100644
--- a/skimage/io/tests/test_collection.py
+++ b/skimage/io/tests/test_collection.py
@@ -1,72 +1,88 @@
+import sys
 import os.path
 
 import numpy as np
-from numpy.testing import assert_raises, assert_equal, assert_allclose
+from numpy.testing import (assert_raises,
+                           assert_equal,
+                           assert_array_almost_equal,
+                           )
+from numpy.testing.decorators import skipif
 
 from skimage import data_dir
-from skimage.io.collection import ImageCollection, alphanumeric_key
+from skimage.io import ImageCollection, MultiImage
+from skimage.io.collection import alphanumeric_key
+from skimage.io import Image as ioImage
+
+import six
 
 
-def test_string_split():
-    test_string = 'z23a'
-    test_str_result = ['z', 23, 'a']
-    assert_equal(alphanumeric_key(test_string), test_str_result)
+try:
+    from PIL import Image
+except ImportError:
+    PIL_available = False
+else:
+    PIL_available = True
 
 
-def test_string_sort():
-    filenames = ['f9.10.png', 'f9.9.png', 'f10.10.png', 'f10.9.png',
-                 'e9.png', 'e10.png', 'em.png']
-    sorted_filenames = ['e9.png', 'e10.png', 'em.png', 'f9.9.png',
-                        'f9.10.png', 'f10.9.png', 'f10.10.png']
-    sorted_filenames = sorted(filenames, key=alphanumeric_key)
-    assert_equal(sorted_filenames, sorted_filenames)
+class TestAlphanumericKey():
+    def setUp(self):
+        self.test_string = 'z23a'
+        self.test_str_result = ['z', 23, 'a']
+        self.filenames = ['f9.10.png', 'f9.9.png', 'f10.10.png', 'f10.9.png',
+            'e9.png', 'e10.png', 'em.png']
+        self.sorted_filenames = \
+            ['e9.png', 'e10.png', 'em.png', 'f9.9.png', 'f9.10.png',
+            'f10.9.png', 'f10.10.png']
+
+    def test_string_split(self):
+        assert_equal(alphanumeric_key(self.test_string), self.test_str_result)
+
+    def test_string_sort(self):
+        sorted_filenames = sorted(self.filenames, key=alphanumeric_key)
+        assert_equal(sorted_filenames, self.sorted_filenames)
 
 
 class TestImageCollection():
-
-    pattern = [os.path.join(data_dir, pic)
-               for pic in ['camera.png', 'color.png']]
-
-    pattern_matched = [os.path.join(data_dir, pic)
-                       for pic in ['camera.png', 'moon.png']]
+    pattern = [os.path.join(data_dir, pic) for pic in ['camera.png',
+                                                       'color.png']]
+    pattern_matched = [os.path.join(data_dir, pic) for pic in 
+                                                    ['camera.png', 'moon.png']]
 
     def setUp(self):
-        # Generic image collection with images of different shapes.
-        self.images = ImageCollection(self.pattern)
-        # Image collection with images having shapes that match.
-        self.images_matched = ImageCollection(self.pattern_matched)
+        self.collection = ImageCollection(self.pattern)
+        self.collection_matched = ImageCollection(self.pattern_matched)
 
     def test_len(self):
-        assert len(self.images) == 2
+        assert len(self.collection) == 2
 
     def test_getitem(self):
-        num = len(self.images)
+        num = len(self.collection)
         for i in range(-num, num):
-            assert type(self.images[i]) is np.ndarray
-        assert_allclose(self.images[0],
-                                  self.images[-num])
+            assert type(self.collection[i]) is np.ndarray
+        assert_array_almost_equal(self.collection[0],
+                                  self.collection[-num])
 
-        # assert_raises expects a callable, hence this thin wrapper function.
+        #assert_raises expects a callable, hence this do-very-little func
         def return_img(n):
-            return self.images[n]
+            return self.collection[n]
         assert_raises(IndexError, return_img, num)
         assert_raises(IndexError, return_img, -num - 1)
 
     def test_slicing(self):
-        assert type(self.images[:]) is ImageCollection
-        assert len(self.images[:]) == 2
-        assert len(self.images[:1]) == 1
-        assert len(self.images[1:]) == 1
-        assert_allclose(self.images[0], self.images[:1][0])
-        assert_allclose(self.images[1], self.images[1:][0])
-        assert_allclose(self.images[1], self.images[::-1][0])
-        assert_allclose(self.images[0], self.images[::-1][1])
+        assert type(self.collection[:]) is ImageCollection
+        assert len(self.collection[:]) == 2
+        assert len(self.collection[:1]) == 1
+        assert len(self.collection[1:]) == 1
+        assert_array_almost_equal(self.collection[0], self.collection[:1][0])
+        assert_array_almost_equal(self.collection[1], self.collection[1:][0])
+        assert_array_almost_equal(self.collection[1], self.collection[::-1][0])
+        assert_array_almost_equal(self.collection[0], self.collection[::-1][1])
 
     def test_files_property(self):
-        assert isinstance(self.images.files, list)
+        assert isinstance(self.collection.files, list)
 
         def set_files(f):
-            self.images.files = f
+            self.collection.files = f
         assert_raises(AttributeError, set_files, 'newfiles')
 
     def test_custom_load(self):
@@ -79,12 +95,59 @@ class TestImageCollection():
         assert_equal(ic[1], (2, 'two'))
 
     def test_concatenate(self):
-        array = self.images_matched.concatenate()
-        expected_shape = (len(self.images_matched),) + self.images[0].shape
-        assert_equal(array.shape, expected_shape)
+        ar = self.collection_matched.concatenate()
+        assert_equal(ar.shape, (len(self.collection_matched),) + 
+                                self.collection[0].shape)
+        assert_raises(ValueError, self.collection.concatenate)
 
-    def test_concatentate_mismatched_image_shapes(self):
-        assert_raises(ValueError, self.images.concatenate)
+
+class TestMultiImage():
+
+    def setUp(self):
+        # This multipage TIF file was created with imagemagick:
+        # convert im1.tif im2.tif -adjoin multipage.tif
+        if PIL_available:
+            self.img = MultiImage(os.path.join(data_dir, 'multipage.tif'))
+
+    @skipif(not PIL_available)
+    def test_len(self):
+        assert len(self.img) == 2
+
+    @skipif(not PIL_available)
+    def test_getitem(self):
+        num = len(self.img)
+        for i in range(-num, num):
+            assert type(self.img[i]) is np.ndarray
+        assert_array_almost_equal(self.img[0],
+                                  self.img[-num])
+
+        #assert_raises expects a callable, hence this do-very-little func
+        def return_img(n):
+            return self.img[n]
+        assert_raises(IndexError, return_img, num)
+        assert_raises(IndexError, return_img, -num - 1)
+
+    @skipif(not PIL_available)
+    def test_files_property(self):
+        assert isinstance(self.img.filename, six.string_types)
+
+        def set_filename(f):
+            self.img.filename = f
+        assert_raises(AttributeError, set_filename, 'newfile')
+
+    @skipif(not PIL_available)
+    def test_conserve_memory_property(self):
+        assert isinstance(self.img.conserve_memory, bool)
+
+        def set_mem(val):
+            self.img.conserve_memory = val
+        assert_raises(AttributeError, set_mem, True)
+
+    @skipif(not PIL_available)
+    def test_concatenate(self):
+        ar = self.img.concatenate()
+        assert_equal(ar.shape, (len(self.img),) + 
+                                self.img[0].shape)
 
 
 if __name__ == "__main__":
diff --git a/skimage/io/tests/test_inherited_config.py b/skimage/io/tests/test_inherited_config.py
new file mode 100644
index 00000000..207d3cf1
--- /dev/null
+++ b/skimage/io/tests/test_inherited_config.py
@@ -0,0 +1,47 @@
+from skimage.io.inherited_config import InheritedConfig
+
+
+def test_get_non_existent():
+    config = InheritedConfig()
+    assert config.get('size') is None
+
+
+def test_get_simple():
+    config = InheritedConfig({'imread': 'matplotlib'})
+    assert config.get('imread') == 'matplotlib'
+
+
+def test_get_default():
+    config = InheritedConfig()
+    assert config.get('size', 10) == 10
+
+
+def test_get_best():
+    config = InheritedConfig({'size': 0, 'size.text': 1})
+    assert config.get('size.text') == 1
+
+
+def test_get_multi_level():
+    config = InheritedConfig({'size': 0})
+    assert config.get('size.text.title') == 0
+    config['size.text'] = 1
+    assert config.get('size.text.title') == 1
+    config['size.text.title'] = 2
+    assert config.get('size.text.title') == 2
+
+
+def test_contains():
+    config = InheritedConfig({'imread': 'matplotlib'})
+    assert 'imread' in config
+    assert 'imread.jpg' in config
+
+
+def test_getitem():
+    config = InheritedConfig({'imread': 'a'})
+    assert config['imread'] == 'a'
+    assert config['imread.png'] == 'a'
+
+
+if __name__ == '__main__':
+    from numpy import testing
+    testing.run_module_suite()
diff --git a/skimage/io/tests/test_multi_image.py b/skimage/io/tests/test_multi_image.py
deleted file mode 100644
index ebaa71dc..00000000
--- a/skimage/io/tests/test_multi_image.py
+++ /dev/null
@@ -1,69 +0,0 @@
-import os
-
-import numpy as np
-from numpy.testing.decorators import skipif
-from numpy.testing import assert_raises, assert_equal, assert_allclose
-
-from skimage import data_dir
-from skimage.io.collection import MultiImage
-
-try:
-    from PIL import Image
-except ImportError:
-    PIL_available = False
-else:
-    PIL_available = True
-
-import six
-
-
-class TestMultiImage():
-
-    def setUp(self):
-        # This multipage TIF file was created with imagemagick:
-        # convert im1.tif im2.tif -adjoin multipage.tif
-        if PIL_available:
-            self.img = MultiImage(os.path.join(data_dir, 'multipage.tif'))
-
-    @skipif(not PIL_available)
-    def test_len(self):
-        assert len(self.img) == 2
-
-    @skipif(not PIL_available)
-    def test_getitem(self):
-        num = len(self.img)
-        for i in range(-num, num):
-            assert type(self.img[i]) is np.ndarray
-        assert_allclose(self.img[0], self.img[-num])
-
-        # assert_raises expects a callable, hence this thin wrapper function.
-        def return_img(n):
-            return self.img[n]
-        assert_raises(IndexError, return_img, num)
-        assert_raises(IndexError, return_img, -num - 1)
-
-    @skipif(not PIL_available)
-    def test_files_property(self):
-        assert isinstance(self.img.filename, six.string_types)
-
-        def set_filename(f):
-            self.img.filename = f
-        assert_raises(AttributeError, set_filename, 'newfile')
-
-    @skipif(not PIL_available)
-    def test_conserve_memory_property(self):
-        assert isinstance(self.img.conserve_memory, bool)
-
-        def set_mem(val):
-            self.img.conserve_memory = val
-        assert_raises(AttributeError, set_mem, True)
-
-    @skipif(not PIL_available)
-    def test_concatenate(self):
-        array = self.img.concatenate()
-        assert_equal(array.shape, (len(self.img),) + self.img[0].shape)
-
-
-if __name__ == "__main__":
-    from numpy.testing import run_module_suite
-    run_module_suite()

From 27bab6390029e94626950ec88908761f55ed35d6 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 7 Dec 2013 00:22:34 -0600
Subject: [PATCH 30/35] Un-revert "Fix failing doctest on systems w/o PIL"
 commit

---
 skimage/io/manage_plugins.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/skimage/io/manage_plugins.py b/skimage/io/manage_plugins.py
index ebc55b6a..c5334c4a 100644
--- a/skimage/io/manage_plugins.py
+++ b/skimage/io/manage_plugins.py
@@ -200,16 +200,19 @@ def use_plugin(name, kind=None):
 
     See Also
     --------
-    plugins : List of available plugins
+    available_plugins : List of available plugins
 
     Examples
     --------
 
-    Use the Python Imaging Library to read images:
+    To use a plugin named 'null' as the default image reader, you would write:
 
-    >>> from skimage.io import use_plugin
-    >>> use_plugin('pil', 'imread')
+    >>> from skimage import io
+    >>> io.use_plugin('null', 'imread')
 
+    To see a list of available plugins run ``io.available_plugins``. Note that
+    this lists plugins that are defined, but the full list may not be usable
+    if your system does not have the required libraries installed.
     """
     if kind is None:
         kind = plugin_store.keys()

From 6a751045f1a6d22c775754388b217182f33da3df Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 7 Dec 2013 01:04:40 -0600
Subject: [PATCH 31/35] Un-revert commits added to test Travis CI failures

---
 skimage/io/_io.py                         |  10 +-
 skimage/io/inherited_config.py            | 127 ------------------
 skimage/io/manage_plugins.py              |  14 +-
 skimage/io/tests/test_collection.py       | 153 +++++++---------------
 skimage/io/tests/test_inherited_config.py |  47 -------
 skimage/io/tests/test_multi_image.py      |  69 ++++++++++
 6 files changed, 121 insertions(+), 299 deletions(-)
 delete mode 100644 skimage/io/inherited_config.py
 delete mode 100644 skimage/io/tests/test_inherited_config.py
 create mode 100644 skimage/io/tests/test_multi_image.py

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index d38e7ac0..97f8718e 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -1,4 +1,3 @@
-import os
 from io import BytesIO
 
 import numpy as np
@@ -95,14 +94,7 @@ def imread(fname, as_grey=False, plugin=None, flatten=None,
         as_grey = flatten
 
     with file_or_url_context(fname) as fname:
-        function = 'imread'
-        # TODO: This should probably use imghdr to get the image format.
-        try:
-            _, extension = os.path.splitext(fname)
-            function = function + extension.lower()
-        except AttributeError:  # Buffers don't work with splitext
-            pass
-        img = call_plugin(function, fname, plugin=plugin, **plugin_args)
+        img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
 
     if as_grey and getattr(img, 'ndim', 0) >= 3:
         img = rgb2grey(img)
diff --git a/skimage/io/inherited_config.py b/skimage/io/inherited_config.py
deleted file mode 100644
index 9cbc7857..00000000
--- a/skimage/io/inherited_config.py
+++ /dev/null
@@ -1,127 +0,0 @@
-class InheritedConfig(dict):
-    """Configuration dictionary where non-existent keys can inherit values.
-
-    This class allows you to define parameter names that can match exactly, but
-    if it doesn't, parameter names will be searched based on key inheritance.
-    For example, the key 'size.text' will default to 'size'.
-
-    Note that indexing into the dictionary will raise an error if it doesn't
-    match exactly, while `InheritedConfig.get` will look up values based on
-    inheritance.
-
-    Parameters
-    ----------
-    config_values : dict or list of (key, value) pairs
-        Default values for a configuration, where keys are the parameter names
-        and values are the associated value.
-    cascade_map : dict
-        Dictionary defining cascading defaults. If a parameter name is not
-        found, indexing `cascade_map` with the parameter name will return
-        the parameter to look for.
-    kwargs : dict
-        Keyword arguments for initializing dict.
-    """
-
-    _separator = '.'
-
-    def __init__(self, config_values=None, **kwargs):
-        assert 'config_values' not in kwargs
-
-        if config_values is None:
-            config_values = {}
-
-        super(InheritedConfig, self).__init__(config_values, **kwargs)
-
-    def __getitem__(self, key):
-        return self.get(key, _raise=True)
-
-    def get(self, key, default=None, _raise=False):
-        """Return best matching config value for `key`.
-
-        Get value from configuration. The search for `key` is in the following
-        order:
-
-            - `self` (Value in global configuration)
-            - `default`
-            - Alternate key specified by `self.cascade_map`
-
-        This method supports the pattern commonly used for optional keyword
-        arguments to a function. For example::
-
-            >>> def print_value(key, **kwargs):
-            ...     print kwargs.get(key, 0)
-            >>> print_value('size')
-            0
-            >>> print_value('size', size=1)
-            1
-
-        Instead, you would create a config class and write::
-
-            >>> config = InheritedConfig(size=0)
-            >>> def print_value(key, **kwargs):
-            ...     print kwargs.get(key, config.get(key))
-            >>> print_value('size')
-            0
-            >>> print_value('size', size=1)
-            1
-            >>> print_value('non-existent')
-            None
-            >>> print_value('size.text')
-            0
-
-        See examples below for a demonstration of the cascading of
-        configuration names.
-
-        Parameters
-        ----------
-        key : str
-            Name of config value you want.
-        default : object
-            Default value if `key` doesn't exist in instance.
-
-        Examples
-        --------
-        >>> config = InheritedConfig(size=0)
-        >>> config.get('size')
-        0
-        >>> top_choice={'size': 1}
-        >>> top_choice.get('size', config.get('size'))
-        1
-        >>> config.get('non-existent', 'unknown')
-        'unknown'
-        >>> config.get('size.text')
-        0
-        >>> config.get('size.text', 2)
-        2
-        >>> top_choice.get('size', config.get('size.text'))
-        1
-        """
-        if key in self.keys():
-            return super(InheritedConfig, self).__getitem__(key)
-        elif default is not None:
-            return default
-        elif self._separator in key:
-            return self.get(self._parent(key))
-        elif _raise:
-            raise KeyError('%r not in %s' % (key, self.__class__.__name__))
-        else:
-            return None
-
-    def _parent(self, key):
-        """Return parent key."""
-        parts = key.split(self._separator)
-        return self._separator.join(parts[:-1])
-
-    def __contains__(self, key):
-        if key in self.keys():
-            return True
-        elif self._separator in key:
-            return self.__contains__(self._parent(key))
-        else:
-            return False
-
-
-if __name__ == '__main__':
-    import doctest
-
-    doctest.testmod()
diff --git a/skimage/io/manage_plugins.py b/skimage/io/manage_plugins.py
index c5334c4a..ace57d8f 100644
--- a/skimage/io/manage_plugins.py
+++ b/skimage/io/manage_plugins.py
@@ -10,8 +10,6 @@ except ImportError:
 import os.path
 from glob import glob
 
-from skimage.io.inherited_config import InheritedConfig
-
 
 __all__ = ['use_plugin', 'call_plugin', 'plugin_info', 'plugin_order',
            'reset_plugins', 'find_available_plugins', 'available_plugins']
@@ -31,7 +29,6 @@ preferred_plugins = {
     # Use PIL as the default imread plugin, since matplotlib (1.2.x)
     # is buggy (flips PNGs around, returns bytes as floats, etc.)
     'imread': ['pil'],
-    'imread.tiff': ['tifffile'],
 }
 
 
@@ -40,11 +37,11 @@ def _clear_plugins():
 
     """
     global plugin_store
-    plugin_store = InheritedConfig({'imread': [],
-                                    'imsave': [],
-                                    'imshow': [],
-                                    'imread_collection': [],
-                                    '_app_show': []})
+    plugin_store = {'imread': [],
+                    'imsave': [],
+                    'imshow': [],
+                    'imread_collection': [],
+                    '_app_show': []}
 _clear_plugins()
 
 
@@ -213,6 +210,7 @@ def use_plugin(name, kind=None):
     To see a list of available plugins run ``io.available_plugins``. Note that
     this lists plugins that are defined, but the full list may not be usable
     if your system does not have the required libraries installed.
+
     """
     if kind is None:
         kind = plugin_store.keys()
diff --git a/skimage/io/tests/test_collection.py b/skimage/io/tests/test_collection.py
index cf5ef820..1e9fea73 100644
--- a/skimage/io/tests/test_collection.py
+++ b/skimage/io/tests/test_collection.py
@@ -1,88 +1,72 @@
-import sys
 import os.path
 
 import numpy as np
-from numpy.testing import (assert_raises,
-                           assert_equal,
-                           assert_array_almost_equal,
-                           )
-from numpy.testing.decorators import skipif
+from numpy.testing import assert_raises, assert_equal, assert_allclose
 
 from skimage import data_dir
-from skimage.io import ImageCollection, MultiImage
-from skimage.io.collection import alphanumeric_key
-from skimage.io import Image as ioImage
-
-import six
+from skimage.io.collection import ImageCollection, alphanumeric_key
 
 
-try:
-    from PIL import Image
-except ImportError:
-    PIL_available = False
-else:
-    PIL_available = True
+def test_string_split():
+    test_string = 'z23a'
+    test_str_result = ['z', 23, 'a']
+    assert_equal(alphanumeric_key(test_string), test_str_result)
 
 
-class TestAlphanumericKey():
-    def setUp(self):
-        self.test_string = 'z23a'
-        self.test_str_result = ['z', 23, 'a']
-        self.filenames = ['f9.10.png', 'f9.9.png', 'f10.10.png', 'f10.9.png',
-            'e9.png', 'e10.png', 'em.png']
-        self.sorted_filenames = \
-            ['e9.png', 'e10.png', 'em.png', 'f9.9.png', 'f9.10.png',
-            'f10.9.png', 'f10.10.png']
-
-    def test_string_split(self):
-        assert_equal(alphanumeric_key(self.test_string), self.test_str_result)
-
-    def test_string_sort(self):
-        sorted_filenames = sorted(self.filenames, key=alphanumeric_key)
-        assert_equal(sorted_filenames, self.sorted_filenames)
+def test_string_sort():
+    filenames = ['f9.10.png', 'f9.9.png', 'f10.10.png', 'f10.9.png',
+                 'e9.png', 'e10.png', 'em.png']
+    sorted_filenames = ['e9.png', 'e10.png', 'em.png', 'f9.9.png',
+                        'f9.10.png', 'f10.9.png', 'f10.10.png']
+    sorted_filenames = sorted(filenames, key=alphanumeric_key)
+    assert_equal(sorted_filenames, sorted_filenames)
 
 
 class TestImageCollection():
-    pattern = [os.path.join(data_dir, pic) for pic in ['camera.png',
-                                                       'color.png']]
-    pattern_matched = [os.path.join(data_dir, pic) for pic in 
-                                                    ['camera.png', 'moon.png']]
+
+    pattern = [os.path.join(data_dir, pic)
+               for pic in ['camera.png', 'color.png']]
+
+    pattern_matched = [os.path.join(data_dir, pic)
+                       for pic in ['camera.png', 'moon.png']]
 
     def setUp(self):
-        self.collection = ImageCollection(self.pattern)
-        self.collection_matched = ImageCollection(self.pattern_matched)
+        # Generic image collection with images of different shapes.
+        self.images = ImageCollection(self.pattern)
+        # Image collection with images having shapes that match.
+        self.images_matched = ImageCollection(self.pattern_matched)
 
     def test_len(self):
-        assert len(self.collection) == 2
+        assert len(self.images) == 2
 
     def test_getitem(self):
-        num = len(self.collection)
+        num = len(self.images)
         for i in range(-num, num):
-            assert type(self.collection[i]) is np.ndarray
-        assert_array_almost_equal(self.collection[0],
-                                  self.collection[-num])
+            assert type(self.images[i]) is np.ndarray
+        assert_allclose(self.images[0],
+                                  self.images[-num])
 
-        #assert_raises expects a callable, hence this do-very-little func
+        # assert_raises expects a callable, hence this thin wrapper function.
         def return_img(n):
-            return self.collection[n]
+            return self.images[n]
         assert_raises(IndexError, return_img, num)
         assert_raises(IndexError, return_img, -num - 1)
 
     def test_slicing(self):
-        assert type(self.collection[:]) is ImageCollection
-        assert len(self.collection[:]) == 2
-        assert len(self.collection[:1]) == 1
-        assert len(self.collection[1:]) == 1
-        assert_array_almost_equal(self.collection[0], self.collection[:1][0])
-        assert_array_almost_equal(self.collection[1], self.collection[1:][0])
-        assert_array_almost_equal(self.collection[1], self.collection[::-1][0])
-        assert_array_almost_equal(self.collection[0], self.collection[::-1][1])
+        assert type(self.images[:]) is ImageCollection
+        assert len(self.images[:]) == 2
+        assert len(self.images[:1]) == 1
+        assert len(self.images[1:]) == 1
+        assert_allclose(self.images[0], self.images[:1][0])
+        assert_allclose(self.images[1], self.images[1:][0])
+        assert_allclose(self.images[1], self.images[::-1][0])
+        assert_allclose(self.images[0], self.images[::-1][1])
 
     def test_files_property(self):
-        assert isinstance(self.collection.files, list)
+        assert isinstance(self.images.files, list)
 
         def set_files(f):
-            self.collection.files = f
+            self.images.files = f
         assert_raises(AttributeError, set_files, 'newfiles')
 
     def test_custom_load(self):
@@ -95,59 +79,12 @@ class TestImageCollection():
         assert_equal(ic[1], (2, 'two'))
 
     def test_concatenate(self):
-        ar = self.collection_matched.concatenate()
-        assert_equal(ar.shape, (len(self.collection_matched),) + 
-                                self.collection[0].shape)
-        assert_raises(ValueError, self.collection.concatenate)
+        array = self.images_matched.concatenate()
+        expected_shape = (len(self.images_matched),) + self.images[0].shape
+        assert_equal(array.shape, expected_shape)
 
-
-class TestMultiImage():
-
-    def setUp(self):
-        # This multipage TIF file was created with imagemagick:
-        # convert im1.tif im2.tif -adjoin multipage.tif
-        if PIL_available:
-            self.img = MultiImage(os.path.join(data_dir, 'multipage.tif'))
-
-    @skipif(not PIL_available)
-    def test_len(self):
-        assert len(self.img) == 2
-
-    @skipif(not PIL_available)
-    def test_getitem(self):
-        num = len(self.img)
-        for i in range(-num, num):
-            assert type(self.img[i]) is np.ndarray
-        assert_array_almost_equal(self.img[0],
-                                  self.img[-num])
-
-        #assert_raises expects a callable, hence this do-very-little func
-        def return_img(n):
-            return self.img[n]
-        assert_raises(IndexError, return_img, num)
-        assert_raises(IndexError, return_img, -num - 1)
-
-    @skipif(not PIL_available)
-    def test_files_property(self):
-        assert isinstance(self.img.filename, six.string_types)
-
-        def set_filename(f):
-            self.img.filename = f
-        assert_raises(AttributeError, set_filename, 'newfile')
-
-    @skipif(not PIL_available)
-    def test_conserve_memory_property(self):
-        assert isinstance(self.img.conserve_memory, bool)
-
-        def set_mem(val):
-            self.img.conserve_memory = val
-        assert_raises(AttributeError, set_mem, True)
-
-    @skipif(not PIL_available)
-    def test_concatenate(self):
-        ar = self.img.concatenate()
-        assert_equal(ar.shape, (len(self.img),) + 
-                                self.img[0].shape)
+    def test_concatentate_mismatched_image_shapes(self):
+        assert_raises(ValueError, self.images.concatenate)
 
 
 if __name__ == "__main__":
diff --git a/skimage/io/tests/test_inherited_config.py b/skimage/io/tests/test_inherited_config.py
deleted file mode 100644
index 207d3cf1..00000000
--- a/skimage/io/tests/test_inherited_config.py
+++ /dev/null
@@ -1,47 +0,0 @@
-from skimage.io.inherited_config import InheritedConfig
-
-
-def test_get_non_existent():
-    config = InheritedConfig()
-    assert config.get('size') is None
-
-
-def test_get_simple():
-    config = InheritedConfig({'imread': 'matplotlib'})
-    assert config.get('imread') == 'matplotlib'
-
-
-def test_get_default():
-    config = InheritedConfig()
-    assert config.get('size', 10) == 10
-
-
-def test_get_best():
-    config = InheritedConfig({'size': 0, 'size.text': 1})
-    assert config.get('size.text') == 1
-
-
-def test_get_multi_level():
-    config = InheritedConfig({'size': 0})
-    assert config.get('size.text.title') == 0
-    config['size.text'] = 1
-    assert config.get('size.text.title') == 1
-    config['size.text.title'] = 2
-    assert config.get('size.text.title') == 2
-
-
-def test_contains():
-    config = InheritedConfig({'imread': 'matplotlib'})
-    assert 'imread' in config
-    assert 'imread.jpg' in config
-
-
-def test_getitem():
-    config = InheritedConfig({'imread': 'a'})
-    assert config['imread'] == 'a'
-    assert config['imread.png'] == 'a'
-
-
-if __name__ == '__main__':
-    from numpy import testing
-    testing.run_module_suite()
diff --git a/skimage/io/tests/test_multi_image.py b/skimage/io/tests/test_multi_image.py
new file mode 100644
index 00000000..ebaa71dc
--- /dev/null
+++ b/skimage/io/tests/test_multi_image.py
@@ -0,0 +1,69 @@
+import os
+
+import numpy as np
+from numpy.testing.decorators import skipif
+from numpy.testing import assert_raises, assert_equal, assert_allclose
+
+from skimage import data_dir
+from skimage.io.collection import MultiImage
+
+try:
+    from PIL import Image
+except ImportError:
+    PIL_available = False
+else:
+    PIL_available = True
+
+import six
+
+
+class TestMultiImage():
+
+    def setUp(self):
+        # This multipage TIF file was created with imagemagick:
+        # convert im1.tif im2.tif -adjoin multipage.tif
+        if PIL_available:
+            self.img = MultiImage(os.path.join(data_dir, 'multipage.tif'))
+
+    @skipif(not PIL_available)
+    def test_len(self):
+        assert len(self.img) == 2
+
+    @skipif(not PIL_available)
+    def test_getitem(self):
+        num = len(self.img)
+        for i in range(-num, num):
+            assert type(self.img[i]) is np.ndarray
+        assert_allclose(self.img[0], self.img[-num])
+
+        # assert_raises expects a callable, hence this thin wrapper function.
+        def return_img(n):
+            return self.img[n]
+        assert_raises(IndexError, return_img, num)
+        assert_raises(IndexError, return_img, -num - 1)
+
+    @skipif(not PIL_available)
+    def test_files_property(self):
+        assert isinstance(self.img.filename, six.string_types)
+
+        def set_filename(f):
+            self.img.filename = f
+        assert_raises(AttributeError, set_filename, 'newfile')
+
+    @skipif(not PIL_available)
+    def test_conserve_memory_property(self):
+        assert isinstance(self.img.conserve_memory, bool)
+
+        def set_mem(val):
+            self.img.conserve_memory = val
+        assert_raises(AttributeError, set_mem, True)
+
+    @skipif(not PIL_available)
+    def test_concatenate(self):
+        array = self.img.concatenate()
+        assert_equal(array.shape, (len(self.img),) + self.img[0].shape)
+
+
+if __name__ == "__main__":
+    from numpy.testing import run_module_suite
+    run_module_suite()

From f04e14272f1b45c827701b61e4a0df04a0f571fc Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 7 Dec 2013 01:07:17 -0600
Subject: [PATCH 32/35] Fix doctest which causes side-effects.

I'm not sure that there's a safe way to write this example as a doctest,
but I think this will pass on Travis (although it still has side-effects.
---
 skimage/io/manage_plugins.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/skimage/io/manage_plugins.py b/skimage/io/manage_plugins.py
index ace57d8f..08bf1703 100644
--- a/skimage/io/manage_plugins.py
+++ b/skimage/io/manage_plugins.py
@@ -202,10 +202,10 @@ def use_plugin(name, kind=None):
     Examples
     --------
 
-    To use a plugin named 'null' as the default image reader, you would write:
+    To use Matplotlib as the default image reader, you would write:
 
     >>> from skimage import io
-    >>> io.use_plugin('null', 'imread')
+    >>> io.use_plugin('matplotlib', 'imread')
 
     To see a list of available plugins run ``io.available_plugins``. Note that
     this lists plugins that are defined, but the full list may not be usable

From b715b79c31c891ab1e91c1ac54738131cfdb4bf3 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 7 Dec 2013 10:26:56 -0600
Subject: [PATCH 33/35] Test Image._repr_png_

---
 skimage/io/tests/test_image.py | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/skimage/io/tests/test_image.py b/skimage/io/tests/test_image.py
index 6c54695b..ef63ef95 100644
--- a/skimage/io/tests/test_image.py
+++ b/skimage/io/tests/test_image.py
@@ -1,7 +1,12 @@
-from skimage.io import Image
+from io import BytesIO
+
+import numpy as np
+from skimage import img_as_ubyte
+from skimage.io import Image, imread
 
 from numpy.testing import assert_equal, assert_array_equal
 
+
 def test_tags():
     f = Image([1, 2, 3], foo='bar', sigma='delta')
     g = Image([3, 2, 1], sun='moon')
@@ -11,7 +16,17 @@ def test_tags():
     assert_array_equal((g + 2).tags['sun'], 'moon')
     assert_equal(h.tags, {})
 
+
+def test_repr_png_roundtrip():
+    original_array = 255 * np.ones((3, 3), dtype=np.uint8)
+    image = Image(original_array)
+    array = imread(BytesIO(image._repr_png_()))
+    # Force output to ubyte range for plugin compatibility.
+    # For example, Matplotlib will return floats even if the image is uint8.
+    assert_array_equal(img_as_ubyte(array), original_array)
+    # Note that PIL breaks with `_repr_jpeg_`.
+
+
 if __name__ == "__main__":
     from numpy.testing import run_module_suite
     run_module_suite()
-

From f7fa4049f55b1bfc7818ca89694127ef044a5f30 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 7 Dec 2013 10:41:03 -0600
Subject: [PATCH 34/35] Test null plugin

---
 skimage/io/tests/test_null.py | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 skimage/io/tests/test_null.py

diff --git a/skimage/io/tests/test_null.py b/skimage/io/tests/test_null.py
new file mode 100644
index 00000000..6d3913d9
--- /dev/null
+++ b/skimage/io/tests/test_null.py
@@ -0,0 +1,35 @@
+import os
+import warnings
+
+import numpy as np
+from numpy.testing import raises
+
+from skimage import io
+from skimage import data_dir
+
+
+@raises(Warning)
+def test_null_imread():
+    path = os.path.join(data_dir, 'color.png')
+    with warnings.catch_warnings():  # Temporarily set warnings as errors.
+        warnings.filterwarnings('error')
+        io.imread(path, plugin='null')
+
+
+@raises(Warning)
+def test_null_imsave():
+    with warnings.catch_warnings():  # Temporarily set warnings as errors.
+        warnings.filterwarnings('error')
+        io.imsave('dummy.png', np.zeros((3, 3)), plugin='null')
+
+
+@raises(Warning)
+def test_null_imshow():
+    with warnings.catch_warnings():  # Temporarily set warnings as errors.
+        warnings.filterwarnings('error')
+        io.imshow(np.zeros((3, 3)), plugin='null')
+
+
+if __name__ == '__main__':
+    from numpy.testing import run_module_suite
+    run_module_suite()

From d7cf60ef0b554a458a20bf8803e376a1a45a1cf4 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 7 Dec 2013 11:45:37 -0600
Subject: [PATCH 35/35] Attempt to fix failing test on Python 3 buildbot

---
 skimage/io/tests/test_image.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/skimage/io/tests/test_image.py b/skimage/io/tests/test_image.py
index ef63ef95..b74c973e 100644
--- a/skimage/io/tests/test_image.py
+++ b/skimage/io/tests/test_image.py
@@ -18,7 +18,8 @@ def test_tags():
 
 
 def test_repr_png_roundtrip():
-    original_array = 255 * np.ones((3, 3), dtype=np.uint8)
+    # Use RGB-like shape since some backends convert grayscale to RGB
+    original_array = 255 * np.ones((5, 5, 3), dtype=np.uint8)
     image = Image(original_array)
     array = imread(BytesIO(image._repr_png_()))
     # Force output to ubyte range for plugin compatibility.