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import numpy | ||
import numpy.random | ||
import numpy.testing | ||
import pytest | ||
import cellprofiler.object | ||
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import constrainobjects | ||
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instance = constrainobjects.ConstrainObjects | ||
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@pytest.fixture(scope="function") | ||
def reference_empty(): | ||
obj = cellprofiler.object.Objects() | ||
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return obj | ||
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@pytest.fixture(scope="function") | ||
def object_set_empty(objects_empty, reference_empty): | ||
objects_set = cellprofiler.object.ObjectSet() | ||
objects_set.add_objects(objects_empty, "InputObjects") | ||
objects_set.add_objects(reference_empty, "ReferenceObjects") | ||
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return objects_set | ||
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@pytest.fixture(scope="function") | ||
def image_labels(): | ||
labels = numpy.zeros((20, 20), dtype=numpy.uint16) | ||
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# Make some child objects | ||
labels[2:7, 2:7] = 1 | ||
labels[2:7, 14:19] = 2 | ||
labels[14:19, 2:7] = 3 | ||
labels[14:20, 14:20] = 4 | ||
# One protruding object | ||
labels[9:13, 9:13] = 5 | ||
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return labels | ||
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@pytest.fixture(scope="function") | ||
def image_reference(): | ||
labels = numpy.zeros((20, 20), dtype=numpy.uint16) | ||
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# Make some parent objects | ||
labels[1:8, 1:8] = 1 | ||
labels[1:8, 13:20] = 2 | ||
labels[13:20, 1:8] = 3 | ||
labels[10:18, 10:18] = 4 | ||
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return labels | ||
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def test_2d_ignore(image_labels, image_reference, module, object_set_empty, objects_empty, | ||
reference_empty, workspace_empty): | ||
labels = image_labels.copy() | ||
reference = image_reference.copy() | ||
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objects_empty.segmented = labels | ||
reference_empty.segmented = reference | ||
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module.x_name.value = "InputObjects" | ||
module.y_name.value = "OutputObjects" | ||
module.reference_name.value = "ReferenceObjects" | ||
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module.run(workspace_empty) | ||
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actual = object_set_empty.get_objects("OutputObjects").segmented | ||
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expected = labels.copy() | ||
# The piece of object 4 outside of the parent should be removed | ||
# and object 5 should be ignored | ||
expected[14:20, 18:20] = 0 | ||
expected[18:20, 14:20] = 0 | ||
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numpy.testing.assert_array_equal(actual, expected) | ||
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def test_2d_remove_protrude(image_labels, image_reference, module, object_set_empty, objects_empty, | ||
reference_empty, workspace_empty): | ||
labels = image_labels.copy() | ||
reference = image_reference.copy() | ||
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objects_empty.segmented = labels | ||
reference_empty.segmented = reference | ||
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module.x_name.value = "InputObjects" | ||
module.y_name.value = "OutputObjects" | ||
module.reference_name.value = "ReferenceObjects" | ||
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module.coersion_method.value = constrainobjects.METHOD_REMOVE | ||
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module.run(workspace_empty) | ||
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actual = object_set_empty.get_objects("OutputObjects").segmented | ||
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expected = labels.copy() | ||
# The piece of object 4 outside of the parent should be removed | ||
# and the part of object 5 inside object 4 should be removed | ||
expected[14:20, 18:20] = 0 | ||
expected[18:20, 14:20] = 0 | ||
expected[10:13, 10:13] = 0 | ||
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numpy.testing.assert_array_equal(actual, expected) | ||
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def test_2d_remove_orphans(image_labels, image_reference, module, object_set_empty, objects_empty, | ||
reference_empty, workspace_empty): | ||
labels = image_labels.copy() | ||
reference = image_reference.copy() | ||
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objects_empty.segmented = labels | ||
reference_empty.segmented = reference | ||
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module.x_name.value = "InputObjects" | ||
module.y_name.value = "OutputObjects" | ||
module.reference_name.value = "ReferenceObjects" | ||
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module.remove_orphans.value = True | ||
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module.run(workspace_empty) | ||
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actual = object_set_empty.get_objects("OutputObjects").segmented | ||
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expected = labels.copy() | ||
# The piece of object 4 outside of the parent should be removed | ||
expected[14:20, 18:20] = 0 | ||
expected[18:20, 14:20] = 0 | ||
# Object 5 should be removed altogether | ||
expected[expected == 5] = 0 | ||
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numpy.testing.assert_array_equal(actual, expected) | ||
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@pytest.fixture(scope="function") | ||
def volume_labels(): | ||
labels = numpy.zeros((10, 20, 20), dtype=numpy.uint16) | ||
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# Make some child objects | ||
labels[2:7, 2:7, 2:7] = 1 | ||
labels[2:5, 2:7, 14:19] = 2 | ||
labels[5:9, 14:19, 2:7] = 3 | ||
labels[3:8, 14:20, 14:20] = 4 | ||
# One protruding object | ||
labels[0:9, 9:13, 9:13] = 5 | ||
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return labels | ||
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@pytest.fixture(scope="function") | ||
def volume_reference(): | ||
labels = numpy.zeros((10, 20, 20), dtype=numpy.uint16) | ||
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# Make some parent objects | ||
labels[2:7, 1:8, 1:8] = 1 | ||
labels[2:5, 1:8, 13:20] = 2 | ||
labels[5:9, 13:20, 1:8] = 3 | ||
labels[3:8, 10:18, 10:18] = 4 | ||
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return labels | ||
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def test_3d_ignore(volume_labels, volume_reference, module, object_set_empty, objects_empty, | ||
reference_empty, workspace_empty): | ||
labels = volume_labels.copy() | ||
reference = volume_reference.copy() | ||
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objects_empty.segmented = labels | ||
reference_empty.segmented = reference | ||
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module.x_name.value = "InputObjects" | ||
module.y_name.value = "OutputObjects" | ||
module.reference_name.value = "ReferenceObjects" | ||
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module.run(workspace_empty) | ||
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actual = object_set_empty.get_objects("OutputObjects").segmented | ||
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expected = labels.copy() | ||
# The piece of object 4 outside of the parent should be removed | ||
# and object 5 should be ignored | ||
expected[3:8, 14:20, 18:20] = 0 | ||
expected[3:8, 18:20, 14:20] = 0 | ||
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numpy.testing.assert_array_equal(actual, expected) | ||
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def test_3d_remove_protrude(volume_labels, volume_reference, module, object_set_empty, objects_empty, | ||
reference_empty, workspace_empty): | ||
labels = volume_labels.copy() | ||
reference = volume_reference.copy() | ||
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objects_empty.segmented = labels | ||
reference_empty.segmented = reference | ||
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module.x_name.value = "InputObjects" | ||
module.y_name.value = "OutputObjects" | ||
module.reference_name.value = "ReferenceObjects" | ||
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module.coersion_method.value = constrainobjects.METHOD_REMOVE | ||
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module.run(workspace_empty) | ||
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actual = object_set_empty.get_objects("OutputObjects").segmented | ||
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expected = labels.copy() | ||
# The piece of object 4 outside of the parent should be removed | ||
# and the part of object 5 inside object 4 should be removed | ||
expected[3:8, 14:20, 18:20] = 0 | ||
expected[3:8, 18:20, 14:20] = 0 | ||
expected[3:8, 10:13, 10:13] = 0 | ||
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numpy.testing.assert_array_equal(actual, expected) | ||
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def test_3d_remove_orphans(volume_labels, volume_reference, module, object_set_empty, objects_empty, | ||
reference_empty, workspace_empty): | ||
labels = volume_labels.copy() | ||
reference = volume_reference.copy() | ||
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objects_empty.segmented = labels | ||
reference_empty.segmented = reference | ||
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module.x_name.value = "InputObjects" | ||
module.y_name.value = "OutputObjects" | ||
module.reference_name.value = "ReferenceObjects" | ||
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module.remove_orphans.value = True | ||
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module.run(workspace_empty) | ||
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actual = object_set_empty.get_objects("OutputObjects").segmented | ||
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expected = labels.copy() | ||
# The piece of object 4 outside of the parent should be removed | ||
expected[3:8, 14:20, 18:20] = 0 | ||
expected[3:8, 18:20, 14:20] = 0 | ||
# Object 5 should be removed altogether | ||
expected[expected == 5] = 0 | ||
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numpy.testing.assert_array_equal(actual, expected) |