import os.path import numpy as np from numpy import testing from scipy import ndimage import skimage from skimage import data_dir from skimage.util import img_as_bool from skimage.morphology import grey, selem lena = np.load(os.path.join(data_dir, 'lena_GRAY_U8.npy')) bw_lena = lena > 100 class TestMorphology(): def morph_worker(self, img, fn, morph_func, strel_func): matlab_results = np.load(os.path.join(data_dir, fn)) k = 0 for arrname in sorted(matlab_results): expected_result = matlab_results[arrname] mask = strel_func(k) actual_result = morph_func(lena, mask) testing.assert_equal(expected_result, actual_result) k = k + 1 def test_erode_diamond(self): self.morph_worker(lena, "diamond-erode-matlab-output.npz", grey.erosion, selem.diamond) def test_dilate_diamond(self): self.morph_worker(lena, "diamond-dilate-matlab-output.npz", grey.dilation, selem.diamond) def test_open_diamond(self): self.morph_worker(lena, "diamond-open-matlab-output.npz", grey.opening, selem.diamond) def test_close_diamond(self): self.morph_worker(lena, "diamond-close-matlab-output.npz", grey.closing, selem.diamond) def test_tophat_diamond(self): self.morph_worker(lena, "diamond-tophat-matlab-output.npz", grey.white_tophat, selem.diamond) def test_bothat_diamond(self): self.morph_worker(lena, "diamond-bothat-matlab-output.npz", grey.black_tophat, selem.diamond) def test_erode_disk(self): self.morph_worker(lena, "disk-erode-matlab-output.npz", grey.erosion, selem.disk) def test_dilate_disk(self): self.morph_worker(lena, "disk-dilate-matlab-output.npz", grey.dilation, selem.disk) def test_open_disk(self): self.morph_worker(lena, "disk-open-matlab-output.npz", grey.opening, selem.disk) def test_close_disk(self): self.morph_worker(lena, "disk-close-matlab-output.npz", grey.closing, selem.disk) class TestEccentricStructuringElements(): def setUp(self): self.black_pixel = 255 * np.ones((4, 4), dtype=np.uint8) self.black_pixel[1, 1] = 0 self.white_pixel = 255 - self.black_pixel self.selems = [selem.square(2), selem.rectangle(2, 2), selem.rectangle(2, 1), selem.rectangle(1, 2)] def test_dilate_erode_symmetry(self): for s in self.selems: c = grey.erosion(self.black_pixel, s) d = grey.dilation(self.white_pixel, s) assert np.all(c == (255 - d)) def test_open_black_pixel(self): for s in self.selems: grey_open = grey.opening(self.black_pixel, s) assert np.all(grey_open == self.black_pixel) def test_close_white_pixel(self): for s in self.selems: grey_close = grey.closing(self.white_pixel, s) assert np.all(grey_close == self.white_pixel) def test_open_white_pixel(self): for s in self.selems: assert np.all(grey.opening(self.white_pixel, s) == 0) def test_close_black_pixel(self): for s in self.selems: assert np.all(grey.closing(self.black_pixel, s) == 255) def test_white_tophat_white_pixel(self): for s in self.selems: tophat = grey.white_tophat(self.white_pixel, s) assert np.all(tophat == self.white_pixel) def test_black_tophat_black_pixel(self): for s in self.selems: tophat = grey.black_tophat(self.black_pixel, s) assert np.all(tophat == (255 - self.black_pixel)) def test_white_tophat_black_pixel(self): for s in self.selems: tophat = grey.white_tophat(self.black_pixel, s) assert np.all(tophat == 0) def test_black_tophat_white_pixel(self): for s in self.selems: tophat = grey.black_tophat(self.white_pixel, s) assert np.all(tophat == 0) def test_default_selem(): functions = [grey.erosion, grey.dilation, grey.opening, grey.closing, grey.white_tophat, grey.black_tophat] strel = selem.diamond(radius=1) image = np.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 1, 1, 1, 0, 0, 1, 0, 0], [0, 0, 1, 1, 1, 0, 0, 1, 0, 0], [0, 0, 1, 1, 1, 0, 0, 1, 0, 0], [0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], np.uint8) for function in functions: im_expected = function(image, strel) im_test = function(image) yield testing.assert_array_equal, im_expected, im_test def test_3d_fallback_default_selem(): # 3x3x3 cube inside a 7x7x7 image: image = np.zeros((7, 7, 7), np.bool) image[2:-2, 2:-2, 2:-2] = 1 opened = grey.opening(image) # expect a "hyper-cross" centered in the 5x5x5: image_expected = np.zeros((7, 7, 7), dtype=bool) image_expected[2:5, 2:5, 2:5] = ndimage.generate_binary_structure(3, 1) testing.assert_array_equal(opened, image_expected) def test_3d_fallback_cube_selem(): # 3x3x3 cube inside a 7x7x7 image: image = np.zeros((7, 7, 7), np.bool) image[2:-2, 2:-2, 2:-2] = 1 cube = np.ones((3, 3, 3), dtype=np.uint8) for function in [grey.closing, grey.opening]: new_image = function(image, cube) yield testing.assert_array_equal, new_image, image def test_3d_fallback_white_tophat(): image = np.zeros((7, 7, 7), dtype=bool) image[2, 2:4, 2:4] = 1 image[3, 2:5, 2:5] = 1 image[4, 3:5, 3:5] = 1 new_image = grey.white_tophat(image) footprint = ndimage.generate_binary_structure(3,1) image_expected = ndimage.white_tophat(image,footprint=footprint) testing.assert_array_equal(new_image, image_expected) def test_3d_fallback_black_tophat(): image = np.ones((7, 7, 7), dtype=bool) image[2, 2:4, 2:4] = 0 image[3, 2:5, 2:5] = 0 image[4, 3:5, 3:5] = 0 new_image = grey.black_tophat(image) footprint = ndimage.generate_binary_structure(3,1) image_expected = ndimage.black_tophat(image,footprint=footprint) testing.assert_array_equal(new_image, image_expected) def test_2d_ndimage_equivalence(): image = np.zeros((9, 9), np.uint8) image[2:-2, 2:-2] = 128 image[3:-3, 3:-3] = 196 image[4, 4] = 255 opened = grey.opening(image) closed = grey.closing(image) selem = ndimage.generate_binary_structure(2, 1) ndimage_opened = ndimage.grey_opening(image, footprint=selem) ndimage_closed = ndimage.grey_closing(image, footprint=selem) testing.assert_array_equal(opened, ndimage_opened) testing.assert_array_equal(closed, ndimage_closed) class TestDTypes(): def setUp(self): k = 5 arrname = '%03i' % k self.disk = selem.disk(k) fname_opening = os.path.join(data_dir, "disk-open-matlab-output.npz") self.expected_opening = np.load(fname_opening)[arrname] fname_closing = os.path.join(data_dir, "disk-close-matlab-output.npz") self.expected_closing = np.load(fname_closing)[arrname] def _test_image(self, image): result_opening = grey.opening(image, self.disk) testing.assert_equal(result_opening, self.expected_opening) result_closing = grey.closing(image, self.disk) testing.assert_equal(result_closing, self.expected_closing) def test_float(self): image = skimage.img_as_float(lena) self._test_image(image) @testing.decorators.skipif(True) def test_int(self): image = skimage.img_as_int(lena) self._test_image(image) def test_uint(self): image = skimage.img_as_uint(lena) self._test_image(image) def test_inplace(): selem = np.ones((3, 3)) image = np.zeros((5, 5)) out = image for f in (grey.erosion, grey.dilation, grey.white_tophat, grey.black_tophat): testing.assert_raises(NotImplementedError, f, image, selem, out=out) if __name__ == '__main__': testing.run_module_suite()