Clean up PIL plugin and handle more warnings

Use the pil plugin to load data files

Fix install_requires string formatting

Dead end commit

Make all tools executable

Remove debug print

Suppress PIL resourcewarnings

Handle a few more warnings

setup.py

@@ -149,7 +149,7 @@ if __name__ == "__main__":
 
         configuration=configuration,
         install_requires=[
-            "six>=%s" % DEPENDENCIES['six']
+            "six>=%s" % '.'.join(str(d) for d in DEPENDENCIES['six'])
         ],
         packages=setuptools.find_packages(exclude=['doc']),
         include_package_data=True,

skimage/data/__init__.py

@@ -8,7 +8,7 @@ For more images, see
 
 import os as _os
 
-from ..io import imread
+from ..io import imread, use_plugin
 from skimage import data_dir
 
 
@@ -42,6 +42,7 @@ def load(f):
     img : ndarray
         Image loaded from skimage.data_dir.
     """
+    use_plugin('pil')
     return imread(_os.path.join(data_dir, f))
 
 

skimage/io/_plugins/pil_plugin.py

@@ -7,6 +7,7 @@ from PIL import Image
 from skimage.util import img_as_ubyte, img_as_uint
 from skimage.external.tifffile import (
     imread as tif_imread, imsave as tif_imsave)
+from skimage._shared.utils import all_warnings
 
 
 def imread(fname, dtype=None, img_num=None, **kwargs):
@@ -39,7 +40,6 @@ def imread(fname, dtype=None, img_num=None, **kwargs):
     .. [2] http://pillow.readthedocs.org/en/latest/handbook/image-file-formats.html
 
     """
-    print('imread', fname)
     if hasattr(fname, 'lower') and dtype is None:
         kwargs.setdefault('key', img_num)
         if fname.lower().endswith(('.tiff', '.tif')):
@@ -54,7 +54,8 @@ def imread(fname, dtype=None, img_num=None, **kwargs):
         site = "http://pillow.readthedocs.org/en/latest/installation.html#external-libraries"
         raise ValueError('Could not load "%s"\nPlease see documentation at: %s' % (fname, site))
     else:
-        return pil_to_ndarray(im, dtype=dtype, img_num=img_num)
+        with all_warnings():  # PIL resource warnings
+            return pil_to_ndarray(im, dtype=dtype, img_num=img_num)
 
 
 def pil_to_ndarray(im, dtype=None, img_num=None):

skimage/measure/tests/test_fit.py

@@ -3,6 +3,7 @@ from numpy.testing import assert_equal, assert_raises, assert_almost_equal
 from skimage.measure import LineModel, CircleModel, EllipseModel, ransac
 from skimage.transform import AffineTransform
 from skimage.measure.fit import _dynamic_max_trials
+from skimage._shared.utils import all_warnings
 
 
 def test_line_model_invalid_input():
@@ -180,7 +181,7 @@ def test_ransac_geometric():
     model_est, inliers = ransac((src, dst), AffineTransform, 2, 20)
 
     # test whether estimated parameters equal original parameters
-    assert_almost_equal(model0._matrix, model_est._matrix)
+    assert_almost_equal(model0.params, model_est.params)
     assert np.all(np.nonzero(inliers == False)[0] == outliers)
 
 
@@ -255,7 +256,8 @@ def test_deprecated_params_attribute():
     model.params = (10, 1)
     x = np.arange(-10, 10)
     y = model.predict_y(x)
-    assert_equal(model.params, model._params)
+    with all_warnings():  # deprecation
+        assert_equal(model.params, model._params)
 
 
 if __name__ == "__main__":

skimage/measure/tests/test_regionprops.py

@@ -4,6 +4,7 @@ import numpy as np
 import math
 
 from skimage.measure._regionprops import regionprops, PROPS, perimeter
+from skimage._shared.utils import all_warnings
 
 
 SAMPLE = np.array(
@@ -25,7 +26,8 @@ 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]))
+        with all_warnings():  # deprecation warning
+            assert_equal(region[prop], getattr(region, PROPS[prop]))
 
 
 def test_dtype():
@@ -125,12 +127,14 @@ def test_equiv_diameter():
 
 
 def test_euler_number():
-    en = regionprops(SAMPLE)[0].euler_number
+    with all_warnings():  # deprecation warning
+        en = regionprops(SAMPLE)[0].euler_number
     assert en == 0
 
     SAMPLE_mod = SAMPLE.copy()
     SAMPLE_mod[7, -3] = 0
-    en = regionprops(SAMPLE_mod)[0].euler_number
+    with all_warnings():  # deprecation warning
+        en = regionprops(SAMPLE_mod)[0].euler_number
     assert en == -1
 
 
@@ -369,8 +373,9 @@ def test_equals():
     r2 = regions[0]
     r3 = regions[1]
 
-    assert_equal(r1 == r2, True, "Same regionprops are not equal")
-    assert_equal(r1 != r3, True, "Different regionprops are equal")
+    with all_warnings():  # deprecation warning
+        assert_equal(r1 == r2, True, "Same regionprops are not equal")
+        assert_equal(r1 != r3, True, "Different regionprops are equal")
 
 
 if __name__ == "__main__":

skimage/transform/tests/test_warps.py

@@ -10,6 +10,7 @@ from skimage.transform import (warp, warp_coords, rotate, resize, rescale,
                                downscale_local_mean)
 from skimage import transform as tf, data, img_as_float
 from skimage.color import rgb2gray
+from skimage._shared.utils import all_warnings
 
 
 np.random.seed(0)
@@ -196,8 +197,10 @@ def test_swirl():
     image = img_as_float(data.checkerboard())
 
     swirl_params = {'radius': 80, 'rotation': 0, 'order': 2, 'mode': 'reflect'}
-    swirled = tf.swirl(image, strength=10, **swirl_params)
-    unswirled = tf.swirl(swirled, strength=-10, **swirl_params)
+    
+    with all_warnings():  # deprecation warning
+        swirled = tf.swirl(image, strength=10, **swirl_params)
+        unswirled = tf.swirl(swirled, strength=-10, **swirl_params)
 
     assert np.mean(np.abs(image - unswirled)) < 0.01