Add a helper function to check for low contrast

Add a helper function to check for low contrast

Add a check for low contrast when using imsave

Use the low contrast helper in imshow and make sure warnings are always shown

Clean up parameter names and add doctests

Remove unnecessary warning context

Remove unnecessary warning context

Add dtype ranges for 64bit types

Update tests with new warnings

Fix doctest logic

Fix doctest logic

Add a low contrast test with multiple dtypes

Fix check for color images

Fix color check again

Add support for int32 types

Relax assertion for 32bit builds

Add a low contrast test with multiple dtypes

Add a low contrast test with multiple dtypes

Fix check for color images

Fix color check again

Add support for int32 types

skimage/exposure/__init__.py

@@ -1,6 +1,7 @@
 from .exposure import histogram, equalize_hist, \
                       rescale_intensity, cumulative_distribution, \
-                      adjust_gamma, adjust_sigmoid, adjust_log
+                      adjust_gamma, adjust_sigmoid, adjust_log, \
+                      is_low_contrast
 
 from ._adapthist import equalize_adapthist
 
@@ -12,4 +13,5 @@ __all__ = ['histogram',
            'cumulative_distribution',
            'adjust_gamma',
            'adjust_sigmoid',
-           'adjust_log']
+           'adjust_log',
+           'is_low_contrast']

skimage/exposure/exposure.py

@@ -1,7 +1,8 @@
+from __future__ import division
 import warnings
 import numpy as np
 
-from .. import img_as_float
+from ..color import rgb2gray
 from ..util.dtype import dtype_range, dtype_limits
 
 
@@ -463,3 +464,48 @@ def adjust_sigmoid(image, cutoff=0.5, gain=10, inv=False):
 
     out = (1 / (1 + np.exp(gain * (cutoff - image / scale)))) * scale
     return dtype(out)
+
+
+def is_low_contrast(image, fraction_threshold=0.05, lower_percentile=1,
+                    upper_percentile=99, method='linear'):
+    """Detemine if an image is low contrast.
+
+    Parameters
+    ----------
+    image : array-like
+        The image under test.
+    fraction_threshold : float, optional
+        The low contrast fraction threshold.
+    lower_bound : float, optional
+        Disregard values below this percentile when computing image contrast.
+    upper_bound : float, optional
+        Disregard values above this percentile when computing image contrast.
+    method : str, optional
+        The contrast determination method.  Right now the only available
+        option is "linear".
+
+    Returns
+    -------
+    out : bool
+        True when the image is determined to be low contrast.
+
+    Examples
+    --------
+    >>> image = np.linspace(0, 0.04, 100)
+    >>> is_low_contrast(image)
+    True
+    >>> image[-1] = 1
+    >>> is_low_contrast(image)
+    True
+    >>> is_low_contrast(image, upper_percentile=100)
+    False
+    """
+    image = np.asanyarray(image)
+    if image.ndim == 3 and image.shape[2] in [3, 4]:
+        image = rgb2gray(image)
+
+    dlimits = dtype_limits(image)
+    limits = np.percentile(image, [lower_percentile, upper_percentile])
+    ratio = (limits[1] - limits[0]) / (dlimits[1] - dlimits[0])
+
+    return ratio < fraction_threshold

skimage/exposure/tests/test_exposure.py

@@ -472,6 +472,22 @@ def test_negative():
     assert_raises(ValueError, exposure.adjust_gamma, image)
 
 
+def test_is_low_contrast():
+    image = np.linspace(0, 0.04, 100)
+    assert exposure.is_low_contrast(image)
+    image[-1] = 1
+    assert exposure.is_low_contrast(image)
+    assert not exposure.is_low_contrast(image, upper_percentile=100)
+
+    image = (image * 255).astype(np.uint8)
+    assert exposure.is_low_contrast(image)
+    assert not exposure.is_low_contrast(image, upper_percentile=100)
+
+    image = (image.astype(np.uint16)) * 2**8
+    assert exposure.is_low_contrast(image)
+    assert not exposure.is_low_contrast(image, upper_percentile=100)
+
+
 if __name__ == '__main__':
     from numpy import testing
     testing.run_module_suite()

skimage/io/_io.py

@@ -1,4 +1,5 @@
 from io import BytesIO
+import warnings
 
 import numpy as np
 import six
@@ -6,6 +7,8 @@ import six
 from ..io.manage_plugins import call_plugin
 from ..color import rgb2grey
 from .util import file_or_url_context
+from ..exposure import is_low_contrast
+from .._shared._warnings import all_warnings
 
 
 __all__ = ['Image', 'imread', 'imread_collection', 'imsave', 'imshow', 'show']
@@ -152,6 +155,8 @@ def imsave(fname, arr, plugin=None, **plugin_args):
         Passed to the given plugin.
 
     """
+    if is_low_contrast(arr):
+        warnings.warn('%s is a low contrast image' % fname)
     return call_plugin('imsave', fname, arr, plugin=plugin, **plugin_args)
 
 

skimage/io/_plugins/matplotlib_plugin.py

@@ -2,7 +2,9 @@ from collections import namedtuple
 import numpy as np
 import warnings
 import matplotlib.pyplot as plt
-from skimage.util import dtype as dtypes
+from ...util import dtype as dtypes
+from ...exposure import is_low_contrast
+from ..._shared._warnings import all_warnings
 
 
 _default_colormap = 'gray'
@@ -49,7 +51,7 @@ def _get_image_properties(image):
     out_of_range_float = (np.issubdtype(image.dtype, np.float) and
                           (immin < lo or immax > hi))
     low_dynamic_range = (immin != immax and
-                         (float(immax - immin) / (hi - lo)) < (1. / 255))
+                         is_low_contrast(image))
     unsupported_dtype = image.dtype not in dtypes._supported_types
 
     return ImageProperties(signed, out_of_range_float,
@@ -72,8 +74,8 @@ def _raise_warnings(image_properties):
         warnings.warn("Low image dynamic range; displaying image with "
                       "stretched contrast.")
     if ip.out_of_range_float:
-        warnings.warn("Float image out of standard range; displaying image "
-                      "with stretched contrast.")
+        warnings.warn("Float image out of standard range; displaying "
+                      "image with stretched contrast.")
 
 
 def _get_display_range(image):

skimage/io/tests/test_mpl_imshow.py

@@ -87,7 +87,8 @@ def test_outside_standard_range():
 
 def test_nonstandard_type():
     plt.figure()
-    with expected_warnings(["Non-standard image type"]):
+    with expected_warnings(["Non-standard image type",
+                            "Low image dynamic range"]):
         ax_im = io.imshow(im64)
     assert ax_im.get_clim() == (im64.min(), im64.max())
     assert n_subplots(ax_im) == 2

skimage/io/tests/test_pil.py

@@ -147,7 +147,8 @@ def test_imsave_filelike():
     s = BytesIO()
 
     # save to file-like object
-    with expected_warnings(['precision loss|unclosed file']):
+    with expected_warnings(['precision loss|unclosed file',
+                            'is a low contrast image']):
         imsave(s, image)
 
     # read from file-like object

skimage/measure/tests/test_regionprops.py

@@ -26,7 +26,7 @@ INTENSITY_SAMPLE[1, 9:11] = 2
 def test_all_props():
     region = regionprops(SAMPLE, INTENSITY_SAMPLE)[0]
     for prop in PROPS:
-        assert_equal(region[prop], getattr(region, PROPS[prop]))
+        assert_almost_equal(region[prop], getattr(region, PROPS[prop]))
 
 
 def test_dtype():

skimage/util/dtype.py

@@ -11,6 +11,10 @@ dtype_range = {np.bool_: (False, True),
                np.uint16: (0, 65535),
                np.int8: (-128, 127),
                np.int16: (-32768, 32767),
+               np.int64: (-2**63, 2**63 - 1),
+               np.uint64: (0, 2**64 - 1),
+               np.int32: (-2**31, 2**31 - 1),
+               np.uint32: (0, 2**32 - 1),
                np.float32: (-1, 1),
                np.float64: (-1, 1)}