133 lines
3 KiB
Python
133 lines
3 KiB
Python
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import numpy as np
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from skimage.measure import find_contours
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from skimage._shared import testing
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from skimage._shared.testing import assert_array_equal
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from pytest import raises
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a = np.ones((8, 8), dtype=np.float32)
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a[1:-1, 1] = 0
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a[1, 1:-1] = 0
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x, y = np.mgrid[-1:1:5j, -1:1:5j]
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r = np.sqrt(x**2 + y**2)
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def test_binary():
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ref = [[6. , 1.5],
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[5. , 1.5],
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[4. , 1.5],
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[3. , 1.5],
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[2. , 1.5],
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[1.5, 2. ],
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[1.5, 3. ],
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[1.5, 4. ],
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[1.5, 5. ],
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[1.5, 6. ],
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[1. , 6.5],
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[0.5, 6. ],
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[0.5, 5. ],
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[0.5, 4. ],
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[0.5, 3. ],
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[0.5, 2. ],
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[0.5, 1. ],
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[1. , 0.5],
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[2. , 0.5],
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[3. , 0.5],
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[4. , 0.5],
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[5. , 0.5],
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[6. , 0.5],
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[6.5, 1. ],
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[6. , 1.5]]
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contours = find_contours(a, 0.5, positive_orientation='high')
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assert len(contours) == 1
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assert_array_equal(contours[0][::-1], ref)
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# target contour for mask tests
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mask_contour = [
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[6. , 0.5],
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[5. , 0.5],
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[4. , 0.5],
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[3. , 0.5],
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[2. , 0.5],
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[1. , 0.5],
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[0.5, 1. ],
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[0.5, 2. ],
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[0.5, 3. ],
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[0.5, 4. ],
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[0.5, 5. ],
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[0.5, 6. ],
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[1. , 6.5],
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[1.5, 6. ],
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[1.5, 5. ],
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[1.5, 4. ],
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[1.5, 3. ],
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[1.5, 2. ],
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[2. , 1.5],
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[3. , 1.5],
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[4. , 1.5],
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[5. , 1.5],
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[6. , 1.5],
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]
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mask = np.ones((8, 8), dtype=bool)
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# Some missing data that should result in a hole in the contour:
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mask[7, 0:3] = False
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def test_nodata():
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# Test missing data via NaNs in input array
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b = np.copy(a)
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b[~mask] = np.nan
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contours = find_contours(b, 0.5, positive_orientation='high')
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assert len(contours) == 1
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assert_array_equal(contours[0], mask_contour)
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def test_mask():
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# Test missing data via explicit masking
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contours = find_contours(a, 0.5, positive_orientation='high', mask=mask)
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assert len(contours) == 1
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assert_array_equal(contours[0], mask_contour)
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def test_mask_shape():
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bad_mask = np.ones((8, 7), dtype=bool)
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with raises(ValueError, match='shape'):
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find_contours(a, 0, mask=bad_mask)
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def test_mask_dtype():
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bad_mask = np.ones((8,8), dtype=np.uint8)
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with raises(TypeError, match='binary'):
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find_contours(a, 0, mask=bad_mask)
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def test_float():
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contours = find_contours(r, 0.5)
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assert len(contours) == 1
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assert_array_equal(contours[0],
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[[ 2., 3.],
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[ 1., 2.],
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[ 2., 1.],
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[ 3., 2.],
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[ 2., 3.]])
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def test_memory_order():
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contours = find_contours(np.ascontiguousarray(r), 0.5)
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assert len(contours) == 1
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contours = find_contours(np.asfortranarray(r), 0.5)
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assert len(contours) == 1
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def test_invalid_input():
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with testing.raises(ValueError):
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find_contours(r, 0.5, 'foo', 'bar')
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with testing.raises(ValueError):
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find_contours(r[..., None], 0.5)
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