1import numpy as np 2import pytest 3from scipy import ndimage as ndi 4from numpy.testing import assert_allclose, assert_array_equal, assert_equal 5 6from skimage import color, data, transform 7from skimage._shared._warnings import expected_warnings 8from skimage._shared.testing import TestCase, fetch 9from skimage.morphology import gray, footprints 10from skimage.util import img_as_uint, img_as_ubyte 11 12 13class TestMorphology(): 14 15 # These expected outputs were generated with skimage v0.12.1 16 # using: 17 # 18 # from skimage.morphology.tests.test_gray import TestMorphology 19 # import numpy as np 20 # output = TestMorphology()._build_expected_output() 21 # np.savez_compressed('gray_morph_output.npz', **output) 22 23 def _build_expected_output(self): 24 funcs = (gray.erosion, gray.dilation, gray.opening, gray.closing, 25 gray.white_tophat, gray.black_tophat) 26 footprints_2D = (footprints.square, footprints.diamond, 27 footprints.disk, footprints.star) 28 29 image = img_as_ubyte(transform.downscale_local_mean( 30 color.rgb2gray(data.coffee()), (20, 20))) 31 32 output = {} 33 for n in range(1, 4): 34 for strel in footprints_2D: 35 for func in funcs: 36 key = f'{strel.__name__}_{n}_{func.__name__}' 37 output[key] = func(image, strel(n)) 38 39 return output 40 41 def test_gray_morphology(self): 42 expected = dict(np.load(fetch('data/gray_morph_output.npz'))) 43 calculated = self._build_expected_output() 44 assert_equal(expected, calculated) 45 46 47class TestEccentricStructuringElements(TestCase): 48 def setUp(self): 49 self.black_pixel = 255 * np.ones((4, 4), dtype=np.uint8) 50 self.black_pixel[1, 1] = 0 51 self.white_pixel = 255 - self.black_pixel 52 self.footprints = [footprints.square(2), footprints.rectangle(2, 2), 53 footprints.rectangle(2, 1), 54 footprints.rectangle(1, 2)] 55 56 def test_dilate_erode_symmetry(self): 57 for s in self.footprints: 58 c = gray.erosion(self.black_pixel, s) 59 d = gray.dilation(self.white_pixel, s) 60 assert np.all(c == (255 - d)) 61 62 def test_open_black_pixel(self): 63 for s in self.footprints: 64 gray_open = gray.opening(self.black_pixel, s) 65 assert np.all(gray_open == self.black_pixel) 66 67 def test_close_white_pixel(self): 68 for s in self.footprints: 69 gray_close = gray.closing(self.white_pixel, s) 70 assert np.all(gray_close == self.white_pixel) 71 72 def test_open_white_pixel(self): 73 for s in self.footprints: 74 assert np.all(gray.opening(self.white_pixel, s) == 0) 75 76 def test_close_black_pixel(self): 77 for s in self.footprints: 78 assert np.all(gray.closing(self.black_pixel, s) == 255) 79 80 def test_white_tophat_white_pixel(self): 81 for s in self.footprints: 82 tophat = gray.white_tophat(self.white_pixel, s) 83 assert np.all(tophat == self.white_pixel) 84 85 def test_black_tophat_black_pixel(self): 86 for s in self.footprints: 87 tophat = gray.black_tophat(self.black_pixel, s) 88 assert np.all(tophat == (255 - self.black_pixel)) 89 90 def test_white_tophat_black_pixel(self): 91 for s in self.footprints: 92 tophat = gray.white_tophat(self.black_pixel, s) 93 assert np.all(tophat == 0) 94 95 def test_black_tophat_white_pixel(self): 96 for s in self.footprints: 97 tophat = gray.black_tophat(self.white_pixel, s) 98 assert np.all(tophat == 0) 99 100 101gray_functions = [gray.erosion, gray.dilation, 102 gray.opening, gray.closing, 103 gray.white_tophat, gray.black_tophat] 104 105 106@pytest.mark.parametrize("function", gray_functions) 107def test_default_footprint(function): 108 strel = footprints.diamond(radius=1) 109 image = np.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 110 [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 111 [0, 0, 1, 1, 1, 1, 1, 1, 0, 0], 112 [0, 0, 1, 1, 1, 1, 1, 1, 0, 0], 113 [0, 0, 1, 1, 1, 1, 1, 1, 0, 0], 114 [0, 0, 1, 1, 1, 0, 0, 1, 0, 0], 115 [0, 0, 1, 1, 1, 0, 0, 1, 0, 0], 116 [0, 0, 1, 1, 1, 0, 0, 1, 0, 0], 117 [0, 0, 1, 1, 1, 1, 1, 1, 0, 0], 118 [0, 0, 1, 1, 1, 1, 1, 1, 0, 0], 119 [0, 0, 1, 1, 1, 1, 1, 1, 0, 0], 120 [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 121 [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], np.uint8) 122 im_expected = function(image, strel) 123 im_test = function(image) 124 assert_array_equal(im_expected, im_test) 125 126 127def test_3d_fallback_default_footprint(): 128 # 3x3x3 cube inside a 7x7x7 image: 129 image = np.zeros((7, 7, 7), bool) 130 image[2:-2, 2:-2, 2:-2] = 1 131 132 opened = gray.opening(image) 133 134 # expect a "hyper-cross" centered in the 5x5x5: 135 image_expected = np.zeros((7, 7, 7), dtype=bool) 136 image_expected[2:5, 2:5, 2:5] = ndi.generate_binary_structure(3, 1) 137 assert_array_equal(opened, image_expected) 138 139 140gray_3d_fallback_functions = [gray.closing, gray.opening] 141 142 143@pytest.mark.parametrize("function", gray_3d_fallback_functions) 144def test_3d_fallback_cube_footprint(function): 145 # 3x3x3 cube inside a 7x7x7 image: 146 image = np.zeros((7, 7, 7), bool) 147 image[2:-2, 2:-2, 2:-2] = 1 148 149 cube = np.ones((3, 3, 3), dtype=np.uint8) 150 151 new_image = function(image, cube) 152 assert_array_equal(new_image, image) 153 154 155def test_3d_fallback_white_tophat(): 156 image = np.zeros((7, 7, 7), dtype=bool) 157 image[2, 2:4, 2:4] = 1 158 image[3, 2:5, 2:5] = 1 159 image[4, 3:5, 3:5] = 1 160 161 with expected_warnings([r'operator.*deprecated|\A\Z']): 162 new_image = gray.white_tophat(image) 163 footprint = ndi.generate_binary_structure(3, 1) 164 with expected_warnings([r'operator.*deprecated|\A\Z']): 165 image_expected = ndi.white_tophat( 166 image.view(dtype=np.uint8), footprint=footprint) 167 assert_array_equal(new_image, image_expected) 168 169 170def test_3d_fallback_black_tophat(): 171 image = np.ones((7, 7, 7), dtype=bool) 172 image[2, 2:4, 2:4] = 0 173 image[3, 2:5, 2:5] = 0 174 image[4, 3:5, 3:5] = 0 175 176 with expected_warnings([r'operator.*deprecated|\A\Z']): 177 new_image = gray.black_tophat(image) 178 footprint = ndi.generate_binary_structure(3, 1) 179 with expected_warnings([r'operator.*deprecated|\A\Z']): 180 image_expected = ndi.black_tophat( 181 image.view(dtype=np.uint8), footprint=footprint) 182 assert_array_equal(new_image, image_expected) 183 184 185def test_2d_ndimage_equivalence(): 186 image = np.zeros((9, 9), np.uint8) 187 image[2:-2, 2:-2] = 128 188 image[3:-3, 3:-3] = 196 189 image[4, 4] = 255 190 191 opened = gray.opening(image) 192 closed = gray.closing(image) 193 194 footprint = ndi.generate_binary_structure(2, 1) 195 ndimage_opened = ndi.grey_opening(image, footprint=footprint) 196 ndimage_closed = ndi.grey_closing(image, footprint=footprint) 197 198 assert_array_equal(opened, ndimage_opened) 199 assert_array_equal(closed, ndimage_closed) 200 201 202# float test images 203im = np.array([[ 0.55, 0.72, 0.6 , 0.54, 0.42], 204 [ 0.65, 0.44, 0.89, 0.96, 0.38], 205 [ 0.79, 0.53, 0.57, 0.93, 0.07], 206 [ 0.09, 0.02, 0.83, 0.78, 0.87], 207 [ 0.98, 0.8 , 0.46, 0.78, 0.12]]) 208 209eroded = np.array([[ 0.55, 0.44, 0.54, 0.42, 0.38], 210 [ 0.44, 0.44, 0.44, 0.38, 0.07], 211 [ 0.09, 0.02, 0.53, 0.07, 0.07], 212 [ 0.02, 0.02, 0.02, 0.78, 0.07], 213 [ 0.09, 0.02, 0.46, 0.12, 0.12]]) 214 215dilated = np.array([[ 0.72, 0.72, 0.89, 0.96, 0.54], 216 [ 0.79, 0.89, 0.96, 0.96, 0.96], 217 [ 0.79, 0.79, 0.93, 0.96, 0.93], 218 [ 0.98, 0.83, 0.83, 0.93, 0.87], 219 [ 0.98, 0.98, 0.83, 0.78, 0.87]]) 220 221opened = np.array([[ 0.55, 0.55, 0.54, 0.54, 0.42], 222 [ 0.55, 0.44, 0.54, 0.44, 0.38], 223 [ 0.44, 0.53, 0.53, 0.78, 0.07], 224 [ 0.09, 0.02, 0.78, 0.78, 0.78], 225 [ 0.09, 0.46, 0.46, 0.78, 0.12]]) 226 227closed = np.array([[ 0.72, 0.72, 0.72, 0.54, 0.54], 228 [ 0.72, 0.72, 0.89, 0.96, 0.54], 229 [ 0.79, 0.79, 0.79, 0.93, 0.87], 230 [ 0.79, 0.79, 0.83, 0.78, 0.87], 231 [ 0.98, 0.83, 0.78, 0.78, 0.78]]) 232 233 234def test_float(): 235 assert_allclose(gray.erosion(im), eroded) 236 assert_allclose(gray.dilation(im), dilated) 237 assert_allclose(gray.opening(im), opened) 238 assert_allclose(gray.closing(im), closed) 239 240 241def test_uint16(): 242 im16, eroded16, dilated16, opened16, closed16 = ( 243 map(img_as_uint, [im, eroded, dilated, opened, closed])) 244 assert_allclose(gray.erosion(im16), eroded16) 245 assert_allclose(gray.dilation(im16), dilated16) 246 assert_allclose(gray.opening(im16), opened16) 247 assert_allclose(gray.closing(im16), closed16) 248 249 250def test_discontiguous_out_array(): 251 image = np.array([[5, 6, 2], 252 [7, 2, 2], 253 [3, 5, 1]], np.uint8) 254 out_array_big = np.zeros((5, 5), np.uint8) 255 out_array = out_array_big[::2, ::2] 256 expected_dilation = np.array([[7, 0, 6, 0, 6], 257 [0, 0, 0, 0, 0], 258 [7, 0, 7, 0, 2], 259 [0, 0, 0, 0, 0], 260 [7, 0, 5, 0, 5]], np.uint8) 261 expected_erosion = np.array([[5, 0, 2, 0, 2], 262 [0, 0, 0, 0, 0], 263 [2, 0, 2, 0, 1], 264 [0, 0, 0, 0, 0], 265 [3, 0, 1, 0, 1]], np.uint8) 266 gray.dilation(image, out=out_array) 267 assert_array_equal(out_array_big, expected_dilation) 268 gray.erosion(image, out=out_array) 269 assert_array_equal(out_array_big, expected_erosion) 270 271 272def test_1d_erosion(): 273 image = np.array([1, 2, 3, 2, 1]) 274 expected = np.array([1, 1, 2, 1, 1]) 275 eroded = gray.erosion(image) 276 assert_array_equal(eroded, expected) 277 278 279def test_deprecated_import(): 280 msg = "Importing from skimage.morphology.grey is deprecated." 281 with expected_warnings([msg + r"|\A\Z"]): 282 from skimage.morphology.grey import erosion 283 284 285@pytest.mark.parametrize( 286 'function', ['erosion', 'dilation', 'closing', 'opening', 'white_tophat', 287 'black_tophat'], 288) 289def test_selem_kwarg_deprecation(function): 290 with expected_warnings(["`selem` is a deprecated argument name"]): 291 getattr(gray, function)(np.zeros((4, 4)), selem=np.ones((3, 3))) 292