212 lines
7.1 KiB
Python
212 lines
7.1 KiB
Python
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import numpy as np
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from skimage.segmentation import join_segmentations, relabel_sequential
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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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import pytest
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def test_join_segmentations():
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s1 = np.array([[0, 0, 1, 1],
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[0, 2, 1, 1],
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[2, 2, 2, 1]])
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s2 = np.array([[0, 1, 1, 0],
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[0, 1, 1, 0],
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[0, 1, 1, 1]])
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# test correct join
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# NOTE: technically, equality to j_ref is not required, only that there
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# is a one-to-one mapping between j and j_ref. I don't know of an easy way
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# to check this (i.e. not as error-prone as the function being tested)
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j = join_segmentations(s1, s2)
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j_ref = np.array([[0, 1, 3, 2],
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[0, 5, 3, 2],
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[4, 5, 5, 3]])
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assert_array_equal(j, j_ref)
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# test correct exception when arrays are different shapes
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s3 = np.array([[0, 0, 1, 1], [0, 2, 2, 1]])
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with testing.raises(ValueError):
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join_segmentations(s1, s3)
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def _check_maps(ar, ar_relab, fw, inv):
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assert_array_equal(fw[ar], ar_relab)
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assert_array_equal(inv[ar_relab], ar)
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def test_relabel_sequential_offset1():
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ar = np.array([1, 1, 5, 5, 8, 99, 42])
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ar_relab, fw, inv = relabel_sequential(ar)
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_check_maps(ar, ar_relab, fw, inv)
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ar_relab_ref = np.array([1, 1, 2, 2, 3, 5, 4])
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assert_array_equal(ar_relab, ar_relab_ref)
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fw_ref = np.zeros(100, int)
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fw_ref[1] = 1
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fw_ref[5] = 2
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fw_ref[8] = 3
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fw_ref[42] = 4
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fw_ref[99] = 5
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assert_array_equal(fw, fw_ref)
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inv_ref = np.array([0, 1, 5, 8, 42, 99])
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assert_array_equal(inv, inv_ref)
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def test_relabel_sequential_offset5():
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ar = np.array([1, 1, 5, 5, 8, 99, 42])
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ar_relab, fw, inv = relabel_sequential(ar, offset=5)
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_check_maps(ar, ar_relab, fw, inv)
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ar_relab_ref = np.array([5, 5, 6, 6, 7, 9, 8])
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assert_array_equal(ar_relab, ar_relab_ref)
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fw_ref = np.zeros(100, int)
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fw_ref[1] = 5
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fw_ref[5] = 6
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fw_ref[8] = 7
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fw_ref[42] = 8
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fw_ref[99] = 9
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assert_array_equal(fw, fw_ref)
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inv_ref = np.array([0, 0, 0, 0, 0, 1, 5, 8, 42, 99])
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assert_array_equal(inv, inv_ref)
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def test_relabel_sequential_offset5_with0():
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ar = np.array([1, 1, 5, 5, 8, 99, 42, 0])
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ar_relab, fw, inv = relabel_sequential(ar, offset=5)
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_check_maps(ar, ar_relab, fw, inv)
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ar_relab_ref = np.array([5, 5, 6, 6, 7, 9, 8, 0])
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assert_array_equal(ar_relab, ar_relab_ref)
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fw_ref = np.zeros(100, int)
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fw_ref[1] = 5
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fw_ref[5] = 6
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fw_ref[8] = 7
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fw_ref[42] = 8
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fw_ref[99] = 9
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assert_array_equal(fw, fw_ref)
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inv_ref = np.array([0, 0, 0, 0, 0, 1, 5, 8, 42, 99])
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assert_array_equal(inv, inv_ref)
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def test_relabel_sequential_dtype():
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ar = np.array([1, 1, 5, 5, 8, 99, 42, 0], dtype=np.uint8)
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ar_relab, fw, inv = relabel_sequential(ar, offset=5)
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_check_maps(ar.astype(int), ar_relab, fw, inv)
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ar_relab_ref = np.array([5, 5, 6, 6, 7, 9, 8, 0])
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assert_array_equal(ar_relab, ar_relab_ref)
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fw_ref = np.zeros(100, int)
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fw_ref[1] = 5
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fw_ref[5] = 6
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fw_ref[8] = 7
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fw_ref[42] = 8
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fw_ref[99] = 9
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assert_array_equal(fw, fw_ref)
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inv_ref = np.array([0, 0, 0, 0, 0, 1, 5, 8, 42, 99])
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assert_array_equal(inv, inv_ref)
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def test_relabel_sequential_signed_overflow():
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imax = np.iinfo(np.int32).max
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labels = np.array([0, 1, 99, 42, 42], dtype=np.int32)
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output, fw, inv = relabel_sequential(labels, offset=imax)
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reference = np.array([0, imax, imax + 2, imax + 1, imax + 1],
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dtype=np.uint32)
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assert_array_equal(output, reference)
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assert output.dtype == reference.dtype
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def test_very_large_labels():
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imax = np.iinfo(np.int64).max
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labels = np.array([0, 1, imax, 42, 42], dtype=np.int64)
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output, fw, inv = relabel_sequential(labels, offset=imax)
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assert np.max(output) == imax + 2
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@pytest.mark.parametrize('dtype', (np.byte, np.short, np.intc, np.int_,
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np.longlong, np.ubyte, np.ushort,
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np.uintc, np.uint, np.ulonglong))
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@pytest.mark.parametrize('data_already_sequential', (False, True))
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def test_relabel_sequential_int_dtype_stability(data_already_sequential,
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dtype):
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if data_already_sequential:
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ar = np.array([1, 3, 0, 2, 5, 4], dtype=dtype)
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else:
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ar = np.array([1, 1, 5, 5, 8, 99, 42, 0], dtype=dtype)
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assert all(a.dtype == dtype for a in relabel_sequential(ar))
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def test_relabel_sequential_int_dtype_overflow():
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ar = np.array([1, 3, 0, 2, 5, 4], dtype=np.uint8)
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offset = 254
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ar_relab, fw, inv = relabel_sequential(ar, offset=offset)
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_check_maps(ar, ar_relab, fw, inv)
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assert all(a.dtype == np.uint16 for a in (ar_relab, fw))
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assert inv.dtype == ar.dtype
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ar_relab_ref = np.where(ar > 0, ar.astype(np.int) + offset - 1, 0)
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assert_array_equal(ar_relab, ar_relab_ref)
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def test_relabel_sequential_negative_values():
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ar = np.array([1, 1, 5, -5, 8, 99, 42, 0])
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with pytest.raises(ValueError):
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relabel_sequential(ar)
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@pytest.mark.parametrize('offset', (0, -3))
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@pytest.mark.parametrize('data_already_sequential', (False, True))
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def test_relabel_sequential_nonpositive_offset(data_already_sequential,
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offset):
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if data_already_sequential:
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ar = np.array([1, 3, 0, 2, 5, 4])
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else:
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ar = np.array([1, 1, 5, 5, 8, 99, 42, 0])
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with pytest.raises(ValueError):
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relabel_sequential(ar, offset=offset)
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@pytest.mark.parametrize('offset', (1, 5))
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@pytest.mark.parametrize('with0', (False, True))
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@pytest.mark.parametrize('input_starts_at_offset', (False, True))
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def test_relabel_sequential_already_sequential(offset, with0,
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input_starts_at_offset):
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if with0:
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ar = np.array([1, 3, 0, 2, 5, 4])
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else:
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ar = np.array([1, 3, 2, 5, 4])
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if input_starts_at_offset:
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ar[ar > 0] += offset - 1
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ar_relab, fw, inv = relabel_sequential(ar, offset=offset)
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_check_maps(ar, ar_relab, fw, inv)
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if input_starts_at_offset:
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ar_relab_ref = ar
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else:
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ar_relab_ref = np.where(ar > 0, ar + offset - 1, 0)
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assert_array_equal(ar_relab, ar_relab_ref)
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def test_incorrect_input_dtype():
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labels = np.array([0, 2, 2, 1, 1, 8], dtype=float)
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with testing.raises(TypeError):
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_ = relabel_sequential(labels)
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def test_arraymap_call():
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ar = np.array([1, 1, 5, 5, 8, 99, 42, 0], dtype=np.intp)
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relabeled, fw, inv = relabel_sequential(ar)
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testing.assert_array_equal(relabeled, fw(ar))
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testing.assert_array_equal(ar, inv(relabeled))
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def test_arraymap_len():
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ar = np.array([1, 1, 5, 5, 8, 99, 42, 0], dtype=np.intp)
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relabeled, fw, inv = relabel_sequential(ar)
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assert len(fw) == 100
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assert len(fw) == len(np.array(fw))
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assert len(inv) == 6
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assert len(inv) == len(np.array(inv))
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def test_arraymap_set():
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ar = np.array([1, 1, 5, 5, 8, 99, 42, 0], dtype=np.intp)
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relabeled, fw, inv = relabel_sequential(ar)
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fw[72] = 6
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assert fw[72] == 6
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