def test_overlap_merge(self, objects_x, objects_y, module, workspace):
# Test handling of overlapping objects in 'merge' mode
segment_x = numpy.zeros((10, 10))
segment_x[2][2] = 1
segment_x[2][3] = 1
segment_x[3][2] = 1
segment_x[3][3] = 1
objects_x.segmented = segment_x
segment_y = numpy.zeros((10, 10))
segment_y[3][3] = 1
segment_y[3][4] = 1
segment_y[4][3] = 1
segment_y[4][4] = 1
objects_y.segmented = segment_y
module.merge_method.value = "Merge"
module.run(workspace)
merged = workspace.get_objects("merged")
assert len(merged.indices) == 1
expected_segment = numpy.zeros_like(segment_x)
expected_segment[segment_y > 0] = 1
expected_segment[segment_x > 0] = 1
assert (merged.segmented == expected_segment).all()
def test_run_binary(workspace, module):
module.object_name.value = "inputobjects"
module.image_name.value = "outputimage"
module.image_mode.value = "Binary (black & white)"
module.run(workspace)
image = workspace.image_set.get_image("outputimage")
objects = workspace.get_objects("inputobjects")
assert image.dimensions == objects.segmented.ndim
pixel_data = image.pixel_data
assert pixel_data.shape == objects.shape
if objects.segmented.ndim == 2:
assert not pixel_data[0, 0]
assert numpy.all(pixel_data[:, 1:])
assert numpy.all(pixel_data[1:, :])
else:
assert not numpy.all(pixel_data[:, 0, 0])
assert numpy.all(pixel_data[:, :, 1:])
assert numpy.all(pixel_data[:, 1:, :])
def test_run_grayscale(workspace, module):
module.object_name.value = "inputobjects"
module.image_name.value = "outputimage"
module.image_mode.value = "Grayscale"
module.run(workspace)
image = workspace.image_set.get_image("outputimage")
objects = workspace.get_objects("inputobjects")
assert image.dimensions == objects.segmented.ndim
pixel_data = image.pixel_data
assert pixel_data.shape == objects.shape
expected = numpy.reshape(
numpy.arange(256).astype(numpy.float32) / 255, (16, 16))
if objects.segmented.ndim == 3:
expected = numpy.tile(expected, (3, 1))
expected = numpy.reshape(expected, (3, 16, 16))
assert numpy.all(pixel_data == expected)
def test_one_object_second_image(self, objects_y, module, workspace,
merge_methods):
# Test merge methods with one object in target set
segment = numpy.zeros((10, 10))
segment[2:4, 2:4] = 1
objects_y.segmented = segment
for method in merge_methods:
module.merge_method.value = method
module.output_object.value = method
module.run(workspace)
numpy.testing.assert_array_equal(
workspace.get_objects(method).segmented, segment)
def test_duplicate_object(self, objects_x, objects_y, module,
workspace, merge_methods):
# Test merge methods with same object in both sets
segment = numpy.zeros((10, 10))
segment[2:4, 2:4] = 1
objects_x.segmented = segment
objects_y.segmented = segment
for method in merge_methods:
module.merge_method.value = method
module.output_object.value = method
module.run(workspace)
numpy.testing.assert_array_equal(
workspace.get_objects(method).segmented, segment)
def test_one_object_first_image(self, objects_x, module, workspace,
merge_methods):
# Test merge methods with one object in initial set
segment = numpy.zeros((10, 10))
segment[2][2] = 1
segment[2][3] = 1
segment[3][2] = 1
segment[3][3] = 1
objects_x.segmented = segment
for method in merge_methods:
module.merge_method.value = method
module.output_object.value = method
module.run(workspace)
assert (
workspace.get_objects(method).segmented == segment).all()
def test_duplicate_object(self, objects_x, module, workspace,
merge_methods):
# Test merge methods with same object in both sets
segment = numpy.zeros((10, 10))
segment[2][2] = 1
segment[2][3] = 1
segment[3][2] = 1
segment[3][3] = 1
objects_x.segmented = segment
objects_y.segmented = segment
for method in merge_methods:
module.merge_method.value = method
module.output_object.value = method
module.run(workspace)
assert (
workspace.get_objects(method).segmented == segment).all()
def test_overlap_discard(self, objects_x, objects_y, module,
workspace):
# Test handling of overlapping objects in 'discard' mode
segment_x = numpy.zeros((10, 10))
segment_x[2:4, 2:4] = 1
objects_x.segmented = segment_x
segment_y = numpy.zeros((10, 10))
segment_y[3, 3:5] = 1
objects_y.segmented = segment_y
module.merge_method.value = "Discard"
module.run(workspace)
merged = workspace.get_objects("merged")
assert len(merged.indices) == 1
expected_segment = segment_x
numpy.testing.assert_array_equal(merged.segmented,
expected_segment)
def test_not_touching(self, objects_x, objects_y, module, workspace,
merge_methods):
# Test merge methods with two distinct objects
segment_x = numpy.zeros((10, 10))
segment_x[2:4, 2:4] = 1
objects_x.segmented = segment_x
segment_y = numpy.zeros((10, 10))
segment_y[8:10, 8:10] = 1
objects_y.segmented = segment_y
for method in merge_methods:
module.merge_method.value = method
module.output_object.value = method
module.run(workspace)
combined = workspace.get_objects(method)
assert len(combined.indices) == 2
numpy.testing.assert_array_equal(combined.segmented,
segment_x + 2 * segment_y)
def test_overlap_segment(self, objects_x, objects_y, module,
workspace):
# Test handling of overlapping objects in 'segment' mode
segment_x = numpy.zeros((10, 10))
segment_x[1:5, 1:6] = 1
objects_x.segmented = segment_x
segment_y = numpy.zeros((10, 10))
segment_y[1:6, 4:9] = 1
objects_y.segmented = segment_y
module.merge_method.value = "Segment"
module.run(workspace)
merged = workspace.get_objects("merged")
assert len(merged.indices) == 2
expected_segment = numpy.zeros_like(segment_x)
expected_segment[1:6, 4:9] = 2
expected_segment[1:5, 1:5] = 1
assert (merged.segmented == expected_segment).all()
def test_overlap_preserve(self, objects_x, objects_y, module,
workspace):
# Test handling of overlapping objects in 'preserve' mode
segment_x = numpy.zeros((10, 10))
segment_x[2:4, 2:4] = 1
objects_x.segmented = segment_x
segment_y = numpy.zeros((10, 10))
segment_y[3, 3:5] = 1
objects_y.segmented = segment_y
module.merge_method.value = "Preserve"
module.run(workspace)
merged = workspace.get_objects("merged")
assert len(merged.indices) == 2
expected_segment = numpy.zeros_like(segment_x)
expected_segment[segment_y > 0] = 2
expected_segment[segment_x > 0] = 1
numpy.testing.assert_array_equal(merged.segmented,
expected_segment)
def test_run_color(workspace, module):
for color in [
"Default",
"autumn",
"bone",
"colorcube",
"cool",
"copper",
"flag",
"gray",
"hot",
"hsv",
"jet",
"lines",
"pink",
"prism",
"spring",
"summer",
"white",
"winter",
]:
module.object_name.value = "inputobjects"
module.image_name.value = "outputimage"
module.image_mode.value = "Color"
module.colormap.value = color
module.run(workspace)
image = workspace.image_set.get_image("outputimage")
objects = workspace.get_objects("inputobjects")
assert image.dimensions == objects.segmented.ndim
pixel_data = image.pixel_data
assert pixel_data.shape == objects.shape + (3, )
def test_for_inappropriate_merge(self, objects_x, objects_y, module,
workspace, merge_methods):
# Test that adjacent objects in the source set aren't merged inappropriately.
segmentation_x = numpy.zeros((10, 10))
segmentation_x[2, 2:4] = 1
segmentation_x[3, 2:4] = 2
segmentation_y = numpy.zeros((10, 10))
segmentation_y[6, 6] = 3
objects_x.segmented = segmentation_x
objects_y.segmented = segmentation_y
segmentation_expected = segmentation_x + segmentation_y
for method in merge_methods:
module.merge_method.value = method
module.output_object.value = method
module.run(workspace)
merged = workspace.get_objects(method)
assert len(merged.indices) == 3
numpy.testing.assert_array_equal(merged.segmented,
segmentation_expected)
def test_not_touching(self, objects_x, objects_y, module, workspace,
merge_methods):
# Test merge methods with two distinct objects
segment_x = numpy.zeros((10, 10))
segment_x[2][2] = 1
segment_x[2][3] = 1
segment_x[3][2] = 1
segment_x[3][3] = 1
objects_x.segmented = segment_x
segment_y = numpy.zeros((10, 10))
segment_y[8][8] = 1
segment_y[8][9] = 1
segment_y[9][8] = 1
segment_y[9][9] = 1
objects_y.segmented = segment_y
for method in merge_methods:
module.merge_method.value = method
module.output_object.value = method
module.run(workspace)
combined = workspace.get_objects(method)
assert len(combined.indices) == 2
assert (combined.segmented == segment_x + 2 * segment_y).all()
