From 782ba46a4ce84ff6c7ed9e23747cd1d0c2cd060d Mon Sep 17 00:00:00 2001 From: Steven Silvester Date: Mon, 22 Dec 2014 06:36:59 -0600 Subject: [PATCH] Handle more warnings Punt on the issue of warnings with the minimum build Handle warnings in measure pkg Fix the rank filter test by forcing a random seed in the function Compare as boolean in imread test Import loadmat in test_setup to avoid warning Use a setup method for imread plugin test Revoke unintended changes Fix indentation to appease jni More indentation fixes Fix unintentional comment out --- ...lot_circular_elliptical_hough_transform.py | 0 doc/gh-pages.py | 0 doc/release/contribs.py | 0 doc/source/coverage_generator.py | 0 doc/source/user_guide/parallelization.txt | 0 setup.py | 2 +- skimage/_shared/testing.py | 8 ++++-- skimage/filters/rank/tests/test_rank.py | 28 +++++++++---------- skimage/io/_plugins/pil_plugin.py | 3 +- skimage/io/tests/test_imread.py | 9 ++++-- skimage/measure/__init__.py | 0 skimage/measure/_find_contours.py | 0 skimage/measure/tests/__init__.py | 2 ++ skimage/scripts/skivi | 0 14 files changed, 29 insertions(+), 23 deletions(-) mode change 100644 => 100755 doc/examples/plot_circular_elliptical_hough_transform.py mode change 100644 => 100755 doc/gh-pages.py mode change 100644 => 100755 doc/release/contribs.py mode change 100644 => 100755 doc/source/coverage_generator.py mode change 100644 => 100755 doc/source/user_guide/parallelization.txt mode change 100644 => 100755 setup.py mode change 100644 => 100755 skimage/measure/__init__.py mode change 100644 => 100755 skimage/measure/_find_contours.py create mode 100644 skimage/measure/tests/__init__.py mode change 100644 => 100755 skimage/scripts/skivi diff --git a/doc/examples/plot_circular_elliptical_hough_transform.py b/doc/examples/plot_circular_elliptical_hough_transform.py old mode 100644 new mode 100755 diff --git a/doc/gh-pages.py b/doc/gh-pages.py old mode 100644 new mode 100755 diff --git a/doc/release/contribs.py b/doc/release/contribs.py old mode 100644 new mode 100755 diff --git a/doc/source/coverage_generator.py b/doc/source/coverage_generator.py old mode 100644 new mode 100755 diff --git a/doc/source/user_guide/parallelization.txt b/doc/source/user_guide/parallelization.txt old mode 100644 new mode 100755 diff --git a/setup.py b/setup.py old mode 100644 new mode 100755 index 2317c36f..01b69620 --- a/setup.py +++ b/setup.py @@ -149,7 +149,7 @@ if __name__ == "__main__": configuration=configuration, install_requires=[ - "six>=%s" % '.'.join(str(d) for d in DEPENDENCIES['six']) + "six>=%s" % DEPENDENCIES['six'] ], packages=setuptools.find_packages(exclude=['doc']), include_package_data=True, diff --git a/skimage/_shared/testing.py b/skimage/_shared/testing.py index 7712c0ae..44ffb62d 100644 --- a/skimage/_shared/testing.py +++ b/skimage/_shared/testing.py @@ -179,12 +179,14 @@ def mono_check(plugin, fmt='png'): def setup_test(): - warnings.simplefilter('error') - with all_warnings(): + warnings.simplefilter('error') + with all_warnings(): from scipy import signal, ndimage, special, optimize, linalg + from scipy.io import loadmat from skimage import filter, viewer, data data.moon() - + if os.environ.get('TRAVIS_PYTHON_VERSION', None) == '2.7': + warnings.simplefilter('default') if __name__ == '__main__': color_check('pil') diff --git a/skimage/filters/rank/tests/test_rank.py b/skimage/filters/rank/tests/test_rank.py index f2d91ff0..d245d3f4 100644 --- a/skimage/filters/rank/tests/test_rank.py +++ b/skimage/filters/rank/tests/test_rank.py @@ -13,12 +13,12 @@ np.random.seed(0) def test_all(): - - with all_warnings(): # precision loss - check_all() + with all_warnings(): # precision loss + check_all() def check_all(): + np.random.seed(0) image = np.random.rand(25, 25) selem = morphology.disk(1) refs = np.load(os.path.join(skimage.data_dir, "rank_filter_tests.npz")) @@ -159,7 +159,7 @@ def test_bitdepth(): for i in range(5): image = np.ones((100, 100), dtype=np.uint16) * 255 * 2 ** i with all_warnings(): # bit depth - rank.mean_percentile(image=image, selem=elem, mask=mask, + rank.mean_percentile(image=image, selem=elem, mask=mask, out=out, shift_x=0, shift_y=0, p0=.1, p1=.9) @@ -270,7 +270,7 @@ def test_compare_ubyte_vs_float(): func = getattr(rank, method) out_u = func(image_uint, disk(3)) with all_warnings(): # precision loss - out_f = func(image_float, disk(3)) + out_f = func(image_float, disk(3)) assert_equal(out_u, out_f) @@ -283,9 +283,9 @@ def test_compare_8bit_unsigned_vs_signed(): image[image > 127] = 0 image_s = image.astype(np.int8) with all_warnings(): # precision loss - image_u = img_as_ubyte(image_s) + image_u = img_as_ubyte(image_s) - assert_equal(image_u, img_as_ubyte(image_s)) + assert_equal(image_u, img_as_ubyte(image_s)) methods = ['autolevel', 'bottomhat', 'equalize', 'gradient', 'maximum', 'mean', 'subtract_mean', 'median', 'minimum', 'modal', @@ -295,8 +295,8 @@ def test_compare_8bit_unsigned_vs_signed(): func = getattr(rank, method) with all_warnings(): # sign loss - out_u = func(image_u, disk(3)) - out_s = func(image_s, disk(3)) + out_u = func(image_u, disk(3)) + out_s = func(image_s, disk(3)) assert_equal(out_u, out_s) @@ -487,11 +487,11 @@ def test_entropy(): data = np.tile( np.reshape(np.arange(4096), (64, 64)), (2, 2)).astype(np.uint16) with all_warnings(): # bitdepth - assert(np.max(rank.entropy(data, selem)) == 12) + assert(np.max(rank.entropy(data, selem)) == 12) # make sure output is of dtype double with all_warnings(): # bitdepth - out = rank.entropy(data, np.ones((16, 16), dtype=np.uint8)) + out = rank.entropy(data, np.ones((16, 16), dtype=np.uint8)) assert out.dtype == np.double @@ -523,9 +523,9 @@ def test_16bit(): value = 2 ** bitdepth - 1 image[10, 10] = value with all_warnings(): # bitdepth - assert rank.minimum(image, selem)[10, 10] == 0 - assert rank.maximum(image, selem)[10, 10] == value - assert rank.mean(image, selem)[10, 10] == int(value / selem.size) + assert rank.minimum(image, selem)[10, 10] == 0 + assert rank.maximum(image, selem)[10, 10] == value + assert rank.mean(image, selem)[10, 10] == int(value / selem.size) def test_bilateral(): diff --git a/skimage/io/_plugins/pil_plugin.py b/skimage/io/_plugins/pil_plugin.py index 05b8b9cb..3146cbbc 100644 --- a/skimage/io/_plugins/pil_plugin.py +++ b/skimage/io/_plugins/pil_plugin.py @@ -48,8 +48,7 @@ def imread(fname, dtype=None, img_num=None, **kwargs): im = Image.open(fname) try: # this will raise an IOError if the file is not readable - #im.getdata()[0] - pass + im.getdata()[0] except IOError: site = "http://pillow.readthedocs.org/en/latest/installation.html#external-libraries" raise ValueError('Could not load "%s"\nPlease see documentation at: %s' % (fname, site)) diff --git a/skimage/io/tests/test_imread.py b/skimage/io/tests/test_imread.py index a2c32b79..759e8c67 100644 --- a/skimage/io/tests/test_imread.py +++ b/skimage/io/tests/test_imread.py @@ -11,13 +11,16 @@ import skimage.io as sio try: import imread as _imread - use_plugin('imread') except ImportError: imread_available = False else: imread_available = True -np.random.seed(0) + +def setup(): + if imread_available: + np.random.seed(0) + use_plugin('imread') def teardown(): @@ -54,7 +57,7 @@ def test_bilevel(): expected[::2] = 1 img = imread(os.path.join(data_dir, 'checker_bilevel.png')) - assert_array_equal(img, expected) + assert_array_equal(img.astype(bool), expected) class TestSave: diff --git a/skimage/measure/__init__.py b/skimage/measure/__init__.py old mode 100644 new mode 100755 diff --git a/skimage/measure/_find_contours.py b/skimage/measure/_find_contours.py old mode 100644 new mode 100755 diff --git a/skimage/measure/tests/__init__.py b/skimage/measure/tests/__init__.py new file mode 100644 index 00000000..c098c64d --- /dev/null +++ b/skimage/measure/tests/__init__.py @@ -0,0 +1,2 @@ +from skimage._shared.testing import setup_test +setup_test() diff --git a/skimage/scripts/skivi b/skimage/scripts/skivi old mode 100644 new mode 100755