def test_03_08_masked_errors(self):
numpy.random.seed(38)
ground_truth = numpy.random.uniform(size=(20, 10)) > .5
test = ground_truth.copy()
mask = numpy.random.uniform(size=(20, 10)) > .5
test[~mask] = numpy.random.uniform(size=numpy.sum(~mask)) > .5
workspace, module = self.make_workspace(dict(image=ground_truth),
dict(image=test, mask=mask))
module.run(workspace)
measurements = workspace.measurements
for feature, expected in (
(cellprofiler.modules.measureimageoverlap.FTR_FALSE_POS_RATE, 0),
(cellprofiler.modules.measureimageoverlap.FTR_FALSE_NEG_RATE, 0),
(cellprofiler.modules.measureimageoverlap.FTR_TRUE_POS_RATE,
1), (cellprofiler.modules.measureimageoverlap.FTR_TRUE_NEG_RATE,
1), (cellprofiler.modules.measureimageoverlap.FTR_RECALL, 1),
(cellprofiler.modules.measureimageoverlap.FTR_PRECISION,
1), (cellprofiler.modules.measureimageoverlap.FTR_F_FACTOR, 1)):
mname = '_'.join(
(cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP,
feature, TEST_IMAGE_NAME))
value = measurements.get_current_image_measurement(mname)
self.assertAlmostEqual(expected,
value,
msg="%s is wrong" % feature)
def test_volume_and_objects(image, measurements, module, objects, workspace):
object_data = skimage.morphology.ball(3, dtype=numpy.uint8)
image.set_image(numpy.ones_like(object_data, dtype=numpy.uint8), convert=False)
image.dimensions = 3
objects.segmented = object_data
module.images[0].wants_objects.value = True
module.run(workspace)
expected = {
"Intensity_TotalIntensity_image_objects": 123.0,
"Intensity_MeanIntensity_image_objects": 1.0,
"Intensity_MedianIntensity_image_objects": 1.0,
"Intensity_StdIntensity_image_objects": 0.0,
"Intensity_MADIntensity_image_objects": 0.0,
"Intensity_MaxIntensity_image_objects": 1.0,
"Intensity_MinIntensity_image_objects": 1.0,
"Intensity_TotalArea_image_objects": 123.0,
"Intensity_PercentMaximal_image_objects": 100.0,
"Intensity_UpperQuartileIntensity_image_objects": 1.0,
"Intensity_LowerQuartileIntensity_image_objects": 1.0
}
for feature, value in expected.iteritems():
actual = measurements.get_current_measurement(
cellprofiler.measurement.IMAGE,
feature
)
assert actual == value, "{} expected {}, got {}".format(feature, value, actual)
def test_03_05_one_false_positive(self):
i, j = numpy.mgrid[0:10, 0:20]
ground_truth = ((i + j) % 2) == 0
test = ground_truth.copy()
test[0, 1] = True
workspace, module = self.make_workspace(dict(image=ground_truth),
dict(image=test))
module.run(workspace)
measurements = workspace.measurements
precision = 100.0 / 101.0
f_factor = 2 * precision / (1 + precision)
for feature, expected in (
(cellprofiler.modules.measureimageoverlap.FTR_FALSE_POS_RATE,
0.01),
(cellprofiler.modules.measureimageoverlap.FTR_FALSE_NEG_RATE, 0),
(cellprofiler.modules.measureimageoverlap.FTR_TRUE_POS_RATE,
1), (cellprofiler.modules.measureimageoverlap.FTR_TRUE_NEG_RATE,
0.99), (cellprofiler.modules.measureimageoverlap.FTR_RECALL,
1),
(cellprofiler.modules.measureimageoverlap.FTR_PRECISION,
precision),
(cellprofiler.modules.measureimageoverlap.FTR_F_FACTOR,
f_factor), (cellprofiler.modules.measureimageoverlap.
FTR_EARTH_MOVERS_DISTANCE, 0)):
mname = '_'.join(
(cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP,
feature, TEST_IMAGE_NAME))
value = measurements.get_current_image_measurement(mname)
self.assertAlmostEqual(expected,
value,
msg="%s is wrong" % feature)
def test_gray_outlines_max_possible_on_volume(self):
numpy.random.seed(0)
image = numpy.random.uniform(size=(9, 9, 9)).astype(numpy.float32)
labels = numpy.zeros_like(image)
k, i, j = numpy.mgrid[-4:5, -4:5, -4:5]
labels[k**2 + i**2 + j**2 <= 9] = 1
workspace, module = self.make_workspace(image,
labels=[labels.astype(int)],
dimensions=3)
module.blank_image.value = False
module.wants_color.value = cellprofiler.modules.overlayoutlines.WANTS_GRAYSCALE
module.max_type.value = cellprofiler.modules.overlayoutlines.MAX_POSSIBLE
module.run(workspace)
output_image = workspace.image_set.get_image(OUTPUT_IMAGE_NAME)
expected = numpy.zeros(labels.shape + (3, ))
for index, plane in enumerate(labels):
expected[index] = skimage.segmentation.mark_boundaries(
image[index], plane, color=1.0, mode="inner")
expected = skimage.color.rgb2gray(expected)
numpy.testing.assert_array_almost_equal(output_image.pixel_data,
expected)
def test_color_outlines_on_color_volume():
numpy.random.seed(0)
image = numpy.random.uniform(size=(9, 9, 9, 3)).astype(numpy.float32)
labels = numpy.zeros((9, 9, 9))
k, i, j = numpy.mgrid[-4:5, -4:5, -4:5]
labels[k**2 + i**2 + j**2 <= 9] = 1
workspace, module = make_workspace(image,
labels=[labels.astype(int)],
dimensions=3)
module.blank_image.value = False
module.wants_color.value = cellprofiler.modules.overlayoutlines.WANTS_COLOR
module.outlines[0].color.value = "Red"
module.run(workspace)
output_image = workspace.image_set.get_image(OUTPUT_IMAGE_NAME)
expected = numpy.zeros_like(image)
for index, plane in enumerate(labels):
expected[index] = skimage.segmentation.mark_boundaries(image[index],
plane,
color=(1, 0, 0),
mode="inner")
numpy.testing.assert_array_equal(output_image.pixel_data, expected)
def test_relate_zeros_with_step_parent(self):
# https://github.com/CellProfiler/CellProfiler/issues/2441
parents = numpy.zeros((10, 10), dtype=numpy.uint8)
children = numpy.zeros_like(parents)
step_parents = numpy.zeros_like(parents)
step_parents_object = cellprofiler.object.Objects()
step_parents_object.segmented = step_parents
workspace, module = self.make_workspace(parents, children)
workspace.measurements.add_measurement(
"Step", cellprofiler.measurement.FF_PARENT % PARENT_OBJECTS, [])
module.step_parent_names[0].step_parent_name.value = "Step"
workspace.object_set.add_objects(step_parents_object, "Step")
module.wants_step_parent_distances.value = True
module.find_parent_child_distances.value = (
cellprofiler.modules.relateobjects.D_MINIMUM)
module.run(workspace)
expected = []
actual = workspace.measurements.get_current_measurement(
CHILD_OBJECTS,
cellprofiler.modules.relateobjects.FF_MINIMUM % "Step")
numpy.testing.assert_array_equal(actual, expected)
def test_calculate_centroid_distances_volume(self):
parents = numpy.zeros((9, 11, 11), dtype=numpy.uint8)
children = numpy.zeros_like(parents)
k, i, j = numpy.mgrid[0:9, 0:11, 0:11]
parents[(k - 4) ** 2 + (i - 5) ** 2 + (j - 5) ** 2 <= 16] = 1
children[(k - 3) ** 2 + (i - 3) ** 2 + (j - 3) ** 2 <= 4] = 1
children[(k - 4) ** 2 + (i - 7) ** 2 + (j - 7) ** 2 <= 4] = 2
workspace, module = self.make_workspace(parents, children)
module.find_parent_child_distances.value = cellprofiler.modules.relateobjects.D_CENTROID
module.run(workspace)
expected = [3, numpy.sqrt(8)]
actual = workspace.measurements.get_current_measurement(
CHILD_OBJECTS,
cellprofiler.modules.relateobjects.FF_CENTROID % PARENT_OBJECTS
)
numpy.testing.assert_array_equal(actual, expected)
def test_13_01_load_filename(self):
#
# Load a file, only specifying the FileName in the CSV
#
csv_text = '''"Image_FileName_DNA"
"%s"
''' % self.test_filename
pipeline, module, filename = self.make_pipeline(csv_text)
assert isinstance(module, cellprofiler.modules.loaddata.LoadData)
module.image_directory.dir_choice = cellprofiler.setting.ABSOLUTE_FOLDER_NAME
module.image_directory.custom_path = self.test_path
m = cellprofiler.measurement.Measurements()
workspace = cellprofiler.workspace.Workspace(pipeline, module, m, cellprofiler.object.ObjectSet(),
m, cellprofiler.image.ImageSetList())
self.assertTrue(module.prepare_run(workspace))
self.assertEqual(m.get_measurement(cellprofiler.measurement.IMAGE, "FileName_DNA", 1),
self.test_filename)
path = m.get_measurement(cellprofiler.measurement.IMAGE, "PathName_DNA", 1)
self.assertEqual(path, self.test_path)
self.assertEqual(
m.get_measurement(cellprofiler.measurement.IMAGE, "URL_DNA", 1),
cellprofiler.modules.loadimages.pathname2url(os.path.join(self.test_path, self.test_filename)))
module.prepare_group(workspace, {}, [1])
module.run(workspace)
img = workspace.image_set.get_image("DNA", must_be_grayscale=True)
self.assertEqual(tuple(img.pixel_data.shape), self.test_shape)
def test_13_03_extra_fields(self):
#
# Regression test of issue #853, extra fields
#
csv_text = '''"Image_URL_DNA"
"{cp_logo_url}", "foo"
"http:{cp_logo_url_filename}"
"bogusurl.png"
'''.format(**{
"cp_logo_url": tests.modules.cp_logo_url,
"cp_logo_url_filename": tests.modules.cp_logo_url_filename
})
pipeline, module, filename = self.make_pipeline(csv_text)
assert isinstance(module, cellprofiler.modules.loaddata.LoadData)
m = cellprofiler.measurement.Measurements()
workspace = cellprofiler.workspace.Workspace(pipeline, module, m, cellprofiler.object.ObjectSet(),
m, cellprofiler.image.ImageSetList())
self.assertTrue(module.prepare_run(workspace))
self.assertEqual(m.get_measurement(cellprofiler.measurement.IMAGE, "FileName_DNA", 1),
tests.modules.cp_logo_url_filename)
path = m.get_measurement(cellprofiler.measurement.IMAGE, "PathName_DNA", 1)
self.assertEqual(path, tests.modules.cp_logo_url_folder)
self.assertEqual(m.get_measurement(cellprofiler.measurement.IMAGE, "URL_DNA", 1),
tests.modules.cp_logo_url)
self.assertEqual(m[cellprofiler.measurement.IMAGE, "FileName_DNA", 2], tests.modules.cp_logo_url_filename)
self.assertEqual(m[cellprofiler.measurement.IMAGE, "PathName_DNA", 2], "http:")
self.assertEqual(m[cellprofiler.measurement.IMAGE, "FileName_DNA", 3], "bogusurl.png")
self.assertEqual(m[cellprofiler.measurement.IMAGE, "PathName_DNA", 3], "")
module.prepare_group(workspace, {}, [1])
module.run(workspace)
img = workspace.image_set.get_image("DNA", must_be_color=True)
self.assertEqual(tuple(img.pixel_data.shape), tests.modules.cp_logo_url_shape)
def test_manual_io_range(image, module, workspace):
data = image.pixel_data
module.rescale_method.value = "Choose specific values to be reset to a custom range"
module.wants_automatic_low.value = "Custom"
module.wants_automatic_high.value = "Custom"
module.source_scale.value = (50, 205)
module.dest_scale.value = (0.2, 0.8)
module.run(workspace)
output = workspace.image_set.get_image("RescaleIntensity")
actual = output.pixel_data
expected = skimage.exposure.rescale_intensity(1.0 * data, (50, 205), (0.2, 0.8))
numpy.testing.assert_array_equal(expected, actual)
assert numpy.any(actual == 0.2)
assert numpy.any(actual == 0.8)
def test_13_06_load_default_input_folder(self):
# Regression test of issue #1365 - load a file from the default
# input folder and check that PathName_xxx is absolute
csv_text = '''"Image_FileName_DNA","Image_PathName_DNA"\n"%s","%s"''' \
% (self.test_filename, self.test_path)
pipeline, module, filename = self.make_pipeline(csv_text)
try:
assert isinstance(module, cellprofiler.modules.loaddata.LoadData)
module.image_directory.dir_choice = cellprofiler.setting.ABSOLUTE_FOLDER_NAME
module.image_directory.custom_path = self.test_path
m = cellprofiler.measurement.Measurements()
workspace = cellprofiler.workspace.Workspace(pipeline, module, m, cellprofiler.object.ObjectSet(),
m, cellprofiler.image.ImageSetList())
self.assertTrue(module.prepare_run(workspace))
self.assertEqual(m.get_measurement(cellprofiler.measurement.IMAGE, "FileName_DNA", 1),
self.test_filename)
path_out = m.get_measurement(cellprofiler.measurement.IMAGE, "PathName_DNA", 1)
self.assertEqual(self.test_path, path_out)
self.assertEqual(
m.get_measurement(cellprofiler.measurement.IMAGE, "URL_DNA", 1),
cellprofiler.modules.loadimages.pathname2url(os.path.join(self.test_path, self.test_filename)))
module.prepare_group(workspace, {}, [1])
module.run(workspace)
img = workspace.image_set.get_image("DNA", must_be_grayscale=True)
self.assertEqual(tuple(img.pixel_data.shape), self.test_shape)
finally:
os.remove(filename)
def test_volume_zeros(image, measurements, module, workspace):
image.pixel_data = numpy.zeros((10, 10, 10))
image.dimensions = 3
module.run(workspace)
expected = {
"Intensity_TotalIntensity_image": 0.0,
"Intensity_MeanIntensity_image": 0.0,
"Intensity_MedianIntensity_image": 0.0,
"Intensity_StdIntensity_image": 0.0,
"Intensity_MADIntensity_image": 0.0,
"Intensity_MaxIntensity_image": 0.0,
"Intensity_MinIntensity_image": 0.0,
"Intensity_TotalArea_image": 1000.0,
"Intensity_PercentMaximal_image": 100.0,
"Intensity_UpperQuartileIntensity_image": 0.0,
"Intensity_LowerQuartileIntensity_image": 0.0
}
for feature, value in expected.iteritems():
actual = measurements.get_current_measurement(
cellprofiler.measurement.IMAGE,
feature
)
assert actual == value, "{} expected {}, got {}".format(feature, value, actual)
def test_01_04_image_and_objects_and_mask(image, measurements, module, objects, workspace):
'''Test operation on an image masked by objects and a mask'''
numpy.random.seed(0)
pixels = numpy.random.uniform(size=(10, 10)).astype(numpy.float32)
mask = numpy.zeros((10, 10), bool)
mask[1:9, :9] = True
image.pixel_data = pixels
image.mask = mask
labels = numpy.zeros((10, 10), int)
labels[1:9, 1:5] = 1
labels[1:9, 5:] = 2
objects.segmented = labels
module.images[0].wants_objects.value = True
module.run(workspace)
assert measurements.get_current_measurement(cellprofiler.measurement.IMAGE, "Intensity_TotalArea_image_objects") == 64
assert measurements.get_current_measurement(cellprofiler.measurement.IMAGE, "Intensity_TotalIntensity_image_objects") == numpy.sum(pixels[1:9, 1:9])
assert measurements.get_current_measurement(cellprofiler.measurement.IMAGE, "Intensity_MeanIntensity_image_objects") == numpy.sum(pixels[1:9, 1:9]) / 64.0
def test_01_02_image_and_mask(image, measurements, module, workspace):
'''Test operation on a masked image'''
numpy.random.seed(0)
pixels = numpy.random.uniform(size=(10, 10)).astype(numpy.float32) * .99
pixels[1:3, 1:3] = 1
mask = numpy.zeros((10, 10), bool)
mask[1:9, 1:9] = True
image.pixel_data = pixels
image.mask = mask
module.run(workspace)
assert measurements.get_current_measurement(cellprofiler.measurement.IMAGE, "Intensity_TotalArea_image") == 64
assert measurements.get_current_measurement(cellprofiler.measurement.IMAGE, "Intensity_TotalIntensity_image") == numpy.sum(pixels[1:9, 1:9])
assert measurements.get_current_measurement(cellprofiler.measurement.IMAGE, "Intensity_MeanIntensity_image") == numpy.sum(pixels[1:9, 1:9]) / 64.0
assert measurements.get_current_measurement(cellprofiler.measurement.IMAGE, "Intensity_PercentMaximal_image") == 400. / 64.
def test_05_02_test_objects_rand_index(self):
r = numpy.random.RandomState()
r.seed(52)
base = numpy.zeros((100, 100), bool)
base[r.randint(0, 100, size=10), r.randint(0, 100, size=10)] = True
gt = base.copy()
gt[r.randint(0, 100, size=5), r.randint(0, 100, size=5)] = True
test = base.copy()
test[r.randint(0, 100, size=5), r.randint(0, 100, size=5)] = True
gt = scipy.ndimage.binary_dilation(gt, numpy.ones((5, 5), bool))
test = scipy.ndimage.binary_dilation(test, numpy.ones((5, 5), bool))
workspace, module = self.make_workspace(dict(image=gt),
dict(image=test))
module.wants_emd.value = False
module.run(workspace)
measurements = workspace.measurements
mname = '_'.join(
(cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP,
cellprofiler.modules.measureimageoverlap.FTR_RAND_INDEX,
TEST_IMAGE_NAME))
expected_rand_index = measurements.get_current_image_measurement(mname)
mname = '_'.join(
(cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP,
cellprofiler.modules.measureimageoverlap.FTR_ADJUSTED_RAND_INDEX,
TEST_IMAGE_NAME))
expected_adjusted_rand_index = \
measurements.get_current_image_measurement(mname)
def test_03_03_masked(self):
'''Test ground-truth of a masked image'''
workspace, module = self.make_workspace(
dict(image=numpy.zeros((20, 10), bool)),
dict(image=numpy.zeros((20, 10), bool),
mask=numpy.zeros((20, 10), bool)))
self.assertTrue(isinstance(module, cellprofiler.modules.measureimageoverlap.MeasureImageOverlap))
module.run(workspace)
measurements = workspace.measurements
self.assertTrue(isinstance(measurements, cellprofiler.measurement.Measurements))
for feature, expected in ((cellprofiler.modules.measureimageoverlap.FTR_FALSE_POS_RATE, 0),
(cellprofiler.modules.measureimageoverlap.FTR_FALSE_NEG_RATE, 0),
(cellprofiler.modules.measureimageoverlap.FTR_TRUE_POS_RATE, 1),
(cellprofiler.modules.measureimageoverlap.FTR_TRUE_NEG_RATE, 1),
(cellprofiler.modules.measureimageoverlap.FTR_RECALL, 1),
(cellprofiler.modules.measureimageoverlap.FTR_PRECISION, 1),
(cellprofiler.modules.measureimageoverlap.FTR_F_FACTOR, 1),
(cellprofiler.modules.measureimageoverlap.FTR_EARTH_MOVERS_DISTANCE, 0)):
mname = '_'.join((cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP, feature, TEST_IMAGE_NAME))
value = measurements.get_current_image_measurement(mname)
self.assertEqual(expected, value)
for feature in (cellprofiler.modules.measureimageoverlap.FTR_RAND_INDEX, cellprofiler.modules.measureimageoverlap.FTR_ADJUSTED_RAND_INDEX):
mname = '_'.join((cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP, feature, TEST_IMAGE_NAME))
value = measurements.get_current_image_measurement(mname)
self.assertTrue(numpy.isnan(value))
def test_run_uint16(workspace, module):
module.object_name.value = "inputobjects"
module.image_name.value = "outputimage"
module.image_mode.value = "uint16"
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), (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_03_09_cropped(self):
numpy.random.seed(39)
i, j = numpy.mgrid[0:10, 0:20]
ground_truth = ((i + j) % 2) == 0
test = ground_truth.copy()
test[0, 1] = True
cropping = numpy.zeros((20, 40), bool)
cropping[10:20, 10:30] = True
big_ground_truth = numpy.random.uniform(size=(20, 40)) > .5
big_ground_truth[10:20, 10:30] = ground_truth
workspace, module = self.make_workspace(
dict(image=big_ground_truth),
dict(image=test, crop_mask=cropping))
module.run(workspace)
measurements = workspace.measurements
precision = 100.0 / 101.0
f_factor = 2 * precision / (1 + precision)
for feature, expected in ((cellprofiler.modules.measureimageoverlap.FTR_FALSE_POS_RATE, 0.01),
(cellprofiler.modules.measureimageoverlap.FTR_FALSE_NEG_RATE, 0),
(cellprofiler.modules.measureimageoverlap.FTR_TRUE_POS_RATE, 1),
(cellprofiler.modules.measureimageoverlap.FTR_TRUE_NEG_RATE, 0.99),
(cellprofiler.modules.measureimageoverlap.FTR_RECALL, 1),
(cellprofiler.modules.measureimageoverlap.FTR_PRECISION, precision),
(cellprofiler.modules.measureimageoverlap.FTR_F_FACTOR, f_factor)):
mname = '_'.join((cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP, feature, TEST_IMAGE_NAME))
value = measurements.get_current_image_measurement(mname)
self.assertAlmostEqual(expected, value,
msg="%s is wrong. Expected %f, got %f" %
(feature, expected, value))
def test_04_01_distance_centroids(self):
'''Check centroid-centroid distance calculation'''
i, j = numpy.mgrid[0:14, 0:30]
parent_labels = (i >= 7) * 1 + (j >= 15) * 2 + 1
# Centers should be at i=3 and j=7
parent_centers = numpy.array([[3, 7], [10, 7], [3, 22], [10, 22]], float)
child_labels = numpy.zeros(i.shape)
numpy.random.seed(0)
# Take 12 random points and label them
child_centers = numpy.random.permutation(numpy.prod(i.shape))[:12]
child_centers = numpy.vstack((i.flatten()[child_centers],
j.flatten()[child_centers]))
child_labels[child_centers[0], child_centers[1]] = numpy.arange(1, 13)
parent_indexes = parent_labels[child_centers[0],
child_centers[1]] - 1
expected = numpy.sqrt(numpy.sum((parent_centers[parent_indexes, :] -
child_centers.transpose()) ** 2, 1))
workspace, module = self.make_workspace(parent_labels, child_labels)
self.assertTrue(isinstance(module, cellprofiler.modules.relateobjects.Relate))
module.find_parent_child_distances.value = cellprofiler.modules.relateobjects.D_CENTROID
module.run(workspace)
self.features_and_columns_match(workspace)
meas = workspace.measurements
v = meas.get_current_measurement(CHILD_OBJECTS,
cellprofiler.modules.relateobjects.FF_CENTROID % PARENT_OBJECTS)
self.assertEqual(v.shape[0], 12)
self.assertTrue(numpy.all(numpy.abs(v - expected) < .0001))
def test_05_02_test_objects_rand_index(self):
r = numpy.random.RandomState()
r.seed(52)
base = numpy.zeros((100, 100), bool)
base[r.randint(0, 100, size=10),
r.randint(0, 100, size=10)] = True
gt = base.copy()
gt[r.randint(0, 100, size=5),
r.randint(0, 100, size=5)] = True
test = base.copy()
test[r.randint(0, 100, size=5),
r.randint(0, 100, size=5)] = True
gt = scipy.ndimage.binary_dilation(gt, numpy.ones((5, 5), bool))
test = scipy.ndimage.binary_dilation(test, numpy.ones((5, 5), bool))
workspace, module = self.make_workspace(
dict(image=gt),
dict(image=test))
module.wants_emd.value = False
module.run(workspace)
measurements = workspace.measurements
mname = '_'.join((cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP, cellprofiler.modules.measureimageoverlap.FTR_RAND_INDEX,
TEST_IMAGE_NAME))
expected_rand_index = measurements.get_current_image_measurement(mname)
mname = '_'.join((cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP, cellprofiler.modules.measureimageoverlap.FTR_ADJUSTED_RAND_INDEX,
TEST_IMAGE_NAME))
expected_adjusted_rand_index = \
measurements.get_current_image_measurement(mname)
def test_calculate_minimum_distances_volume(self):
parents = numpy.zeros((9, 11, 11), dtype=numpy.uint8)
children = numpy.zeros_like(parents)
parents[1:8, 1:10, 1:10] = 1
children[3:6, 2:3, 2:3] = 1
children[4:7, 3:8, 3:8] = 2
workspace, module = self.make_workspace(parents, children)
module.find_parent_child_distances.value = cellprofiler.modules.relateobjects.D_MINIMUM
module.run(workspace)
expected = [1, 2]
actual = workspace.measurements.get_current_measurement(
CHILD_OBJECTS,
cellprofiler.modules.relateobjects.FF_MINIMUM % PARENT_OBJECTS
)
numpy.testing.assert_array_equal(actual, expected)
def test_04_02_distance_minima(self):
'''Check centroid-perimeter distance calculation'''
i, j = numpy.mgrid[0:14, 0:30]
#
# Make the objects different sizes to exercise more code
#
parent_labels = (i >= 6) * 1 + (j >= 14) * 2 + 1
child_labels = numpy.zeros(i.shape)
numpy.random.seed(0)
# Take 12 random points and label them
child_centers = numpy.random.permutation(numpy.prod(i.shape))[:12]
child_centers = numpy.vstack((i.flatten()[child_centers],
j.flatten()[child_centers]))
child_labels[child_centers[0], child_centers[1]] = numpy.arange(1, 13)
#
# Measure the distance from the child to the edge of its parent.
# We do this using the distance transform with a background that's
# the edges of the labels
#
background = ((i != 0) & (i != 5) & (i != 6) & (i != 13) &
(j != 0) & (j != 13) & (j != 14) & (j != 29))
d = scipy.ndimage.distance_transform_edt(background)
expected = d[child_centers[0], child_centers[1]]
workspace, module = self.make_workspace(parent_labels, child_labels)
self.assertTrue(isinstance(module, cellprofiler.modules.relateobjects.Relate))
module.find_parent_child_distances.value = cellprofiler.modules.relateobjects.D_MINIMUM
module.run(workspace)
self.features_and_columns_match(workspace)
meas = workspace.measurements
v = meas.get_current_measurement(CHILD_OBJECTS,
cellprofiler.modules.relateobjects.FF_MINIMUM % PARENT_OBJECTS)
self.assertEqual(v.shape[0], 12)
self.assertTrue(numpy.all(numpy.abs(v - expected) < .0001))
def test_ijv():
numpy.random.seed(0)
image = numpy.random.uniform(size=(50, 50, 3)).astype(numpy.float32)
image[0, 0] = 1
labels0 = numpy.zeros(image.shape[:2], int)
labels0[20:30, 20:30] = 1
labels1 = numpy.zeros(image.shape[:2], int)
labels1[25:35, 25:35] = 2
labels = [labels0, labels1]
expected = image.copy()
mask = numpy.zeros(image.shape[:2], bool)
mask[20:30, 20] = True
mask[20:30, 29] = True
mask[20, 20:30] = True
mask[29, 20:30] = True
mask[25:35, 25] = True
mask[25:35, 34] = True
mask[25, 25:35] = True
mask[34, 25:35] = True
expected[mask, 0] = 1
expected[mask, 1:] = 0
workspace, module = make_workspace(image, labels=labels)
module.wants_color.value = cellprofiler.modules.overlayoutlines.WANTS_COLOR
module.outlines[0].color.value = "Red"
module.line_mode.value = "Inner"
module.run(workspace)
output_image = workspace.image_set.get_image(OUTPUT_IMAGE_NAME)
numpy.testing.assert_array_equal(output_image.pixel_data, expected)
def test_04_01_ijv(self):
numpy.random.seed(0)
image = numpy.random.uniform(size=(50, 50, 3)).astype(numpy.float32)
image[0, 0] = 1
labels0 = numpy.zeros(image.shape[:2], int)
labels0[20:30, 20:30] = 1
labels1 = numpy.zeros(image.shape[:2], int)
labels1[25:35, 25:35] = 2
labels = [labels0, labels1]
expected = image.copy()
mask = numpy.zeros(image.shape[:2], bool)
mask[20:30, 20] = True
mask[20:30, 29] = True
mask[20, 20:30] = True
mask[29, 20:30] = True
mask[25:35, 25] = True
mask[25:35, 34] = True
mask[25, 25:35] = True
mask[34, 25:35] = True
expected[mask, 0] = 1
expected[mask, 1:] = 0
workspace, module = self.make_workspace(image, labels=labels)
module.wants_color.value = cellprofiler.modules.overlayoutlines.WANTS_COLOR
module.outlines[0].color.value = "Red"
module.line_mode.value = "Inner"
module.run(workspace)
output_image = workspace.image_set.get_image(OUTPUT_IMAGE_NAME)
numpy.testing.assert_array_equal(output_image.pixel_data, expected)
def test_gray_outlines_on_blank_volume():
image = numpy.zeros((9, 9, 9))
labels = numpy.zeros_like(image)
k, i, j = numpy.mgrid[-4:5, -4:5, -4:5]
labels[k**2 + i**2 + j**2 <= 9] = 1
workspace, module = make_workspace(image,
labels=[labels.astype(int)],
dimensions=3)
module.blank_image.value = True
module.wants_color.value = cellprofiler.modules.overlayoutlines.WANTS_GRAYSCALE
module.run(workspace)
output_image = workspace.image_set.get_image(OUTPUT_IMAGE_NAME)
expected = numpy.zeros(labels.shape + (3, ))
for index, plane in enumerate(labels):
expected[index] = skimage.segmentation.mark_boundaries(image[index],
plane,
color=1.0,
mode="inner")
expected = skimage.color.rgb2gray(expected)
numpy.testing.assert_array_equal(output_image.pixel_data, expected)
def test_color_outlines_on_color_volume(self):
numpy.random.seed(0)
image = numpy.random.uniform(size=(9, 9, 9, 3)).astype(numpy.float32)
labels = numpy.zeros((9, 9, 9))
k, i, j = numpy.mgrid[-4:5, -4:5, -4:5]
labels[k ** 2 + i ** 2 + j ** 2 <= 9] = 1
workspace, module = self.make_workspace(image, labels=[labels.astype(int)], dimensions=3)
module.blank_image.value = False
module.wants_color.value = cellprofiler.modules.overlayoutlines.WANTS_COLOR
module.outlines[0].color.value = "Red"
module.run(workspace)
output_image = workspace.image_set.get_image(OUTPUT_IMAGE_NAME)
expected = numpy.zeros_like(image)
for index, plane in enumerate(labels):
expected[index] = skimage.segmentation.mark_boundaries(
image[index],
plane,
color=(1, 0, 0),
mode="inner"
)
numpy.testing.assert_array_equal(output_image.pixel_data, expected)
def test_03_04_all_right(self):
numpy.random.seed(34)
image = numpy.random.uniform(size=(10, 20)) > .5
workspace, module = self.make_workspace(dict(image=image),
dict(image=image))
module.run(workspace)
measurements = workspace.measurements
self.assertTrue(
isinstance(measurements, cellprofiler.measurement.Measurements))
for feature, expected in (
(cellprofiler.modules.measureimageoverlap.FTR_FALSE_POS_RATE, 0),
(cellprofiler.modules.measureimageoverlap.FTR_FALSE_NEG_RATE, 0),
(cellprofiler.modules.measureimageoverlap.FTR_TRUE_POS_RATE,
1), (cellprofiler.modules.measureimageoverlap.FTR_TRUE_NEG_RATE,
1), (cellprofiler.modules.measureimageoverlap.FTR_RECALL, 1),
(cellprofiler.modules.measureimageoverlap.FTR_PRECISION,
1), (cellprofiler.modules.measureimageoverlap.FTR_F_FACTOR,
1), (cellprofiler.modules.measureimageoverlap.FTR_RAND_INDEX,
1),
(cellprofiler.modules.measureimageoverlap.FTR_ADJUSTED_RAND_INDEX,
1), (cellprofiler.modules.measureimageoverlap.
FTR_EARTH_MOVERS_DISTANCE, 0)):
mname = '_'.join(
(cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP,
feature, TEST_IMAGE_NAME))
value = measurements.get_current_image_measurement(mname)
self.assertEqual(expected, value)
def test_gray_outlines_on_blank_volume(self):
image = numpy.zeros((9, 9, 9))
labels = numpy.zeros_like(image)
k, i, j = numpy.mgrid[-4:5, -4:5, -4:5]
labels[k ** 2 + i ** 2 + j ** 2 <= 9] = 1
workspace, module = self.make_workspace(image, labels=[labels.astype(int)], dimensions=3)
module.blank_image.value = True
module.wants_color.value = cellprofiler.modules.overlayoutlines.WANTS_GRAYSCALE
module.run(workspace)
output_image = workspace.image_set.get_image(OUTPUT_IMAGE_NAME)
expected = numpy.zeros(labels.shape + (3,))
for index, plane in enumerate(labels):
expected[index] = skimage.segmentation.mark_boundaries(
image[index],
plane,
color=1.0,
mode="inner"
)
expected = skimage.color.rgb2gray(expected)
numpy.testing.assert_array_equal(output_image.pixel_data, expected)
def test_03_07_one_false_negative_and_mask(self):
i, j = numpy.mgrid[0:10, 0:20]
ground_truth = ((i + j) % 2) == 0
test = ground_truth.copy()
test[0, 0] = False
mask = j < 10
workspace, module = self.make_workspace(dict(image=ground_truth),
dict(image=test, mask=mask))
module.run(workspace)
measurements = workspace.measurements
recall = 0.98
f_factor = 2 * recall / (1 + recall)
for feature, expected in (
(cellprofiler.modules.measureimageoverlap.FTR_FALSE_POS_RATE,
0), (cellprofiler.modules.measureimageoverlap.FTR_FALSE_NEG_RATE,
0.02),
(cellprofiler.modules.measureimageoverlap.FTR_TRUE_POS_RATE, 0.98),
(cellprofiler.modules.measureimageoverlap.FTR_TRUE_NEG_RATE,
1), (cellprofiler.modules.measureimageoverlap.FTR_RECALL, recall),
(cellprofiler.modules.measureimageoverlap.FTR_PRECISION, 1),
(cellprofiler.modules.measureimageoverlap.FTR_F_FACTOR, f_factor)):
mname = '_'.join(
(cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP,
feature, TEST_IMAGE_NAME))
value = measurements.get_current_image_measurement(mname)
self.assertAlmostEqual(expected,
value,
msg="%s is wrong" % feature)
def test_calculate_centroid_distances_volume(self):
parents = numpy.zeros((9, 11, 11), dtype=numpy.uint8)
children = numpy.zeros_like(parents)
k, i, j = numpy.mgrid[0:9, 0:11, 0:11]
parents[(k - 4)**2 + (i - 5)**2 + (j - 5)**2 <= 16] = 1
children[(k - 3)**2 + (i - 3)**2 + (j - 3)**2 <= 4] = 1
children[(k - 4)**2 + (i - 7)**2 + (j - 7)**2 <= 4] = 2
workspace, module = self.make_workspace(parents, children)
module.find_parent_child_distances.value = (
cellprofiler.modules.relateobjects.D_CENTROID)
module.run(workspace)
expected = [3, numpy.sqrt(8)]
actual = workspace.measurements.get_current_measurement(
CHILD_OBJECTS,
cellprofiler.modules.relateobjects.FF_CENTROID % PARENT_OBJECTS)
numpy.testing.assert_array_equal(actual, expected)
def test_03_09_cropped(self):
numpy.random.seed(39)
i, j = numpy.mgrid[0:10, 0:20]
ground_truth = ((i + j) % 2) == 0
test = ground_truth.copy()
test[0, 1] = True
cropping = numpy.zeros((20, 40), bool)
cropping[10:20, 10:30] = True
big_ground_truth = numpy.random.uniform(size=(20, 40)) > .5
big_ground_truth[10:20, 10:30] = ground_truth
workspace, module = self.make_workspace(
dict(image=big_ground_truth), dict(image=test, crop_mask=cropping))
module.run(workspace)
measurements = workspace.measurements
precision = 100.0 / 101.0
f_factor = 2 * precision / (1 + precision)
for feature, expected in (
(cellprofiler.modules.measureimageoverlap.FTR_FALSE_POS_RATE,
0.01),
(cellprofiler.modules.measureimageoverlap.FTR_FALSE_NEG_RATE, 0),
(cellprofiler.modules.measureimageoverlap.FTR_TRUE_POS_RATE,
1), (cellprofiler.modules.measureimageoverlap.FTR_TRUE_NEG_RATE,
0.99), (cellprofiler.modules.measureimageoverlap.FTR_RECALL,
1),
(cellprofiler.modules.measureimageoverlap.FTR_PRECISION,
precision),
(cellprofiler.modules.measureimageoverlap.FTR_F_FACTOR, f_factor)):
mname = '_'.join(
(cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP,
feature, TEST_IMAGE_NAME))
value = measurements.get_current_image_measurement(mname)
self.assertAlmostEqual(expected,
value,
msg="%s is wrong. Expected %f, got %f" %
(feature, expected, value))
def test_calculate_minimum_distances_volume(self):
parents = numpy.zeros((9, 11, 11), dtype=numpy.uint8)
children = numpy.zeros_like(parents)
parents[1:8, 1:10, 1:10] = 1
children[3:6, 2:3, 2:3] = 1
children[4:7, 3:8, 3:8] = 2
workspace, module = self.make_workspace(parents, children)
module.find_parent_child_distances.value = (
cellprofiler.modules.relateobjects.D_MINIMUM)
module.run(workspace)
expected = [1, 2]
actual = workspace.measurements.get_current_measurement(
CHILD_OBJECTS,
cellprofiler.modules.relateobjects.FF_MINIMUM % PARENT_OBJECTS)
numpy.testing.assert_array_equal(actual, expected)
def test_11_02_invert_binary_invert(self):
#
# Regression for issue #1329
#
r = numpy.random.RandomState()
r.seed(1102)
m = cellprofiler.measurement.Measurements()
pixel_data = r.uniform(size=(20, 20)) > .5
m.add("inputimage", cellprofiler.image.Image(pixel_data))
module = cellprofiler.modules.imagemath.ImageMath()
module.images[0].image_name.value = "inputimage"
module.output_image_name.value = "intermediateimage"
module.operation.value = cellprofiler.modules.imagemath.O_INVERT
module.module_num = 1
pipeline = cellprofiler.pipeline.Pipeline()
pipeline.add_module(module)
module = cellprofiler.modules.imagemath.ImageMath()
module.images[0].image_name.value = "intermediateimage"
module.output_image_name.value = "outputimage"
module.operation.value = cellprofiler.modules.imagemath.O_INVERT
module.module_num = 2
pipeline = cellprofiler.pipeline.Pipeline()
workspace = cellprofiler.workspace.Workspace(pipeline, module, m, None,
m, None)
for module in pipeline.modules():
module.run(workspace)
numpy.testing.assert_array_equal(
pixel_data,
m.get_image("inputimage").pixel_data > .5)
def test_03_01_zeros(self):
'''Test ground-truth of zeros and image of zeros'''
workspace, module = self.make_workspace(
dict(image=numpy.ones((20, 10), bool)),
dict(image=numpy.ones((20, 10), bool)))
self.assertTrue(
isinstance(
module,
cellprofiler.modules.measureimageoverlap.MeasureImageOverlap))
module.run(workspace)
measurements = workspace.measurements
self.assertTrue(
isinstance(measurements, cellprofiler.measurement.Measurements))
self.assertEqual(
measurements.get_current_image_measurement(
"Overlap_FalseNegRate_test"), 0)
features = measurements.get_feature_names(
cellprofiler.measurement.IMAGE)
for feature in cellprofiler.modules.measureimageoverlap.FTR_ALL + [
cellprofiler.modules.measureimageoverlap.
FTR_EARTH_MOVERS_DISTANCE
]:
field = '_'.join(
(cellprofiler.modules.measureimageoverlap.C_IMAGE_OVERLAP,
feature, TEST_IMAGE_NAME))
self.assertTrue(field in features, "Missing feature: %s" % feature)
ftr_emd = module.measurement_name(
cellprofiler.modules.measureimageoverlap.FTR_EARTH_MOVERS_DISTANCE)
self.assertEqual(measurements[cellprofiler.measurement.IMAGE, ftr_emd],
0)
def test_enhance(accuracy, image, module, workspace):
data = numpy.zeros((20, 30))
expected = numpy.zeros((20, 30))
i, j = numpy.mgrid[-10:10, -10:20]
data[i ** 2 + j ** 2 <= 7 ** 2] = 1
i, j = numpy.mgrid[-10:10, -25:5]
data[i ** 2 + j ** 2 <= 9] = 1
expected[i ** 2 + j ** 2 <= 9] = 1
image.pixel_data = data
module.method.value = "Enhance"
module.enhance_method.value = "Speckles"
module.speckle_accuracy.value = accuracy
module.object_size.value = 14
module.run(workspace)
output = workspace.image_set.get_image("output")
actual = output.pixel_data
numpy.testing.assert_array_equal(expected, actual)
def test_enhance_circles_volume(image, module, workspace):
k, i, j = numpy.mgrid[-15:16, -15:16, -15:16]
data = numpy.abs(numpy.sqrt(k * k + i * i + j * j) - 6) <= 1.5
data = data.astype(float)
image.pixel_data = data
image.dimensions = 3
module.method.value = "Enhance"
module.enhance_method.value = "Circles"
module.object_size.value = 12
module.run(workspace)
actual = workspace.image_set.get_image("output").pixel_data
expected = numpy.zeros_like(data)
for index, plane in enumerate(data):
expected[index] = skimage.transform.hough_circle(plane, 6)[0]
numpy.testing.assert_array_almost_equal(expected, actual)
def test_enhance_neurites_tubeness_negative(image, module, workspace):
data = numpy.ones((20, 30))
data[5:15, 10:20] -= numpy.identity(10)
image.pixel_data = data
module.method.value = "Enhance"
module.enhance_method.value = "Neurites"
module.neurite_choice.value = "Tubeness"
module.smoothing.value = 1.0
module.run(workspace)
output = workspace.image_set.get_image("output")
actual = output.pixel_data
expected = centrosome.filter.hessian(
scipy.ndimage.gaussian_filter(data, 1.0),
return_hessian=False,
return_eigenvectors=False
)
expected = -expected[:, :, 0] * (expected[:, :, 0] < 0)
expected = skimage.exposure.rescale_intensity(expected)
numpy.testing.assert_array_almost_equal(expected, actual, decimal=5)
def test_enhance_circles_masked(image, module, workspace):
data = numpy.zeros((31, 62))
mask = numpy.ones_like(data, dtype=numpy.bool)
i, j = numpy.mgrid[-15:16, -15:16]
circle = numpy.abs(numpy.sqrt(i * i + j * j) - 6) <= 1.5
data[:, :31] = circle
data[:, 31:] = circle
mask[:, 31:][circle] = False
image.pixel_data = data
image.mask = mask
module.method.value = "Enhance"
module.enhance_method.value = "Circles"
module.object_size.value = 12
module.run(workspace)
actual = workspace.image_set.get_image("output").pixel_data
assert actual[15, 15] == 1
assert actual[15, 15 + 31] == 0
def test_suppress_masked_volume(image, module, workspace):
data = numpy.zeros((20, 20, 30))
mask = numpy.ones_like(data, dtype=numpy.bool)
k, i, j = numpy.mgrid[-10:10, -10:10, -10:20]
data[k ** 2 + i ** 2 + j ** 2 <= 7 ** 2] = 1
k, i, j = numpy.mgrid[-10:10, -10:10, -25:5]
data[k ** 2 + i ** 2 + j ** 2 <= 9] = 1
mask[k ** 2 + i ** 2 + j ** 2 <= 9] = False
expected = data
image.pixel_data = data
image.mask = mask
image.dimensions = 3
module.method.value = "Suppress"
module.object_size.value = 14
module.run(workspace)
output = workspace.image_set.get_image("output")
actual = output.pixel_data
numpy.testing.assert_array_equal(expected, actual)
def test_enhance_neurites_gradient_volume(image, module, workspace):
resources = os.path.realpath(os.path.join(os.path.dirname(__file__), "..", "resources"))
data = numpy.load(os.path.join(resources, "neurite.npy"))
data = skimage.exposure.rescale_intensity(1.0 * data)
data = numpy.tile(data, (3, 1)).reshape(3, *data.shape)
image.pixel_data = data
image.dimensions = 3
module.method.value = "Enhance"
module.enhance_method.value = "Neurites"
module.neurite_choice.value = "Line structures"
module.object_size.value = 8
module.run(workspace)
output = workspace.image_set.get_image("output")
actual = output.pixel_data
expected = numpy.load(os.path.join(resources, "enhanced_neurite.npy"))
expected = numpy.tile(expected, (3, 1)).reshape(3, *expected.shape)
numpy.testing.assert_array_almost_equal(expected, actual)
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_05_02_test_objects_rand_index(self):
r = numpy.random.RandomState()
r.seed(52)
base = numpy.zeros((100, 100), bool)
base[r.randint(0, 100, size=10),
r.randint(0, 100, size=10)] = True
gt = base.copy()
gt[r.randint(0, 100, size=5),
r.randint(0, 100, size=5)] = True
test = base.copy()
test[r.randint(0, 100, size=5),
r.randint(0, 100, size=5)] = True
gt = scipy.ndimage.binary_dilation(gt, numpy.ones((5, 5), bool))
test = scipy.ndimage.binary_dilation(test, numpy.ones((5, 5), bool))
gt_labels, _ = scipy.ndimage.label(gt, numpy.ones((3, 3), bool))
test_labels, _ = scipy.ndimage.label(test, numpy.ones((3, 3), bool))
workspace, module = self.make_obj_workspace(
gt_labels, test_labels,
dict(image=numpy.ones(gt_labels.shape)),
dict(image=numpy.ones(test_labels.shape)))
module.run(workspace)
measurements = workspace.measurements
mname = '_'.join((cellprofiler.modules.measureobjectoverlap.C_IMAGE_OVERLAP, cellprofiler.modules.measureobjectoverlap.FTR_RAND_INDEX,
GROUND_TRUTH_OBJ, ID_OBJ))
expected_rand_index = measurements.get_current_image_measurement(mname)
rand_index = measurements.get_current_image_measurement(mname)
self.assertAlmostEqual(rand_index, expected_rand_index)
mname = '_'.join((cellprofiler.modules.measureobjectoverlap.C_IMAGE_OVERLAP, cellprofiler.modules.measureobjectoverlap.FTR_ADJUSTED_RAND_INDEX,
GROUND_TRUTH_OBJ, ID_OBJ))
adjusted_rand_index = \
measurements.get_current_image_measurement(mname)
def test_01_02_image_and_mask(image, measurements, module, workspace):
'''Test operation on a masked image'''
numpy.random.seed(0)
pixels = numpy.random.uniform(size=(10, 10)).astype(numpy.float32) * .99
pixels[1:3, 1:3] = 1
mask = numpy.zeros((10, 10), bool)
mask[1:9, 1:9] = True
image.pixel_data = pixels
image.mask = mask
module.run(workspace)
assert measurements.get_current_measurement(
cellprofiler.measurement.IMAGE, "Intensity_TotalArea_image") == 64
assert measurements.get_current_measurement(
cellprofiler.measurement.IMAGE,
"Intensity_TotalIntensity_image") == numpy.sum(pixels[1:9, 1:9])
assert measurements.get_current_measurement(
cellprofiler.measurement.IMAGE,
"Intensity_MeanIntensity_image") == numpy.sum(pixels[1:9, 1:9]) / 64.0
assert measurements.get_current_measurement(
cellprofiler.measurement.IMAGE,
"Intensity_PercentMaximal_image") == 400. / 64.
def test_volume_zeros(image, measurements, module, workspace):
image.pixel_data = numpy.zeros((10, 10, 10))
image.dimensions = 3
module.run(workspace)
expected = {
"Intensity_TotalIntensity_image": 0.0,
"Intensity_MeanIntensity_image": 0.0,
"Intensity_MedianIntensity_image": 0.0,
"Intensity_StdIntensity_image": 0.0,
"Intensity_MADIntensity_image": 0.0,
"Intensity_MaxIntensity_image": 0.0,
"Intensity_MinIntensity_image": 0.0,
"Intensity_TotalArea_image": 1000.0,
"Intensity_PercentMaximal_image": 100.0,
"Intensity_UpperQuartileIntensity_image": 0.0,
"Intensity_LowerQuartileIntensity_image": 0.0
}
for feature, value in expected.iteritems():
actual = measurements.get_current_measurement(
cellprofiler.measurement.IMAGE, feature)
assert actual == value, "{} expected {}, got {}".format(
feature, value, actual)
def test_volume_and_objects(image, measurements, module, objects, workspace):
object_data = skimage.morphology.ball(3, dtype=numpy.uint8)
image.set_image(numpy.ones_like(object_data, dtype=numpy.uint8),
convert=False)
image.dimensions = 3
objects.segmented = object_data
module.images[0].wants_objects.value = True
module.run(workspace)
expected = {
"Intensity_TotalIntensity_image_objects": 123.0,
"Intensity_MeanIntensity_image_objects": 1.0,
"Intensity_MedianIntensity_image_objects": 1.0,
"Intensity_StdIntensity_image_objects": 0.0,
"Intensity_MADIntensity_image_objects": 0.0,
"Intensity_MaxIntensity_image_objects": 1.0,
"Intensity_MinIntensity_image_objects": 1.0,
"Intensity_TotalArea_image_objects": 123.0,
"Intensity_PercentMaximal_image_objects": 100.0,
"Intensity_UpperQuartileIntensity_image_objects": 1.0,
"Intensity_LowerQuartileIntensity_image_objects": 1.0
}
for feature, value in expected.iteritems():
actual = measurements.get_current_measurement(
cellprofiler.measurement.IMAGE, feature)
assert actual == value, "{} expected {}, got {}".format(
feature, value, actual)
def test_01_01_image(image, measurements, module, workspace):
'''Test operation on a single unmasked image'''
numpy.random.seed(0)
pixels = numpy.random.uniform(size=(10, 10)).astype(numpy.float32) * .99
pixels[0:2, 0:2] = 1
image.pixel_data = pixels
module.run(workspace)
assert measurements.get_current_measurement(
cellprofiler.measurement.IMAGE, "Intensity_TotalArea_image") == 100
assert measurements.get_current_measurement(
cellprofiler.measurement.IMAGE,
"Intensity_TotalIntensity_image") == numpy.sum(pixels)
assert measurements.get_current_measurement(
cellprofiler.measurement.IMAGE,
"Intensity_MeanIntensity_image") == numpy.sum(pixels) / 100.0
assert measurements.get_current_image_measurement(
'Intensity_MinIntensity_image') == numpy.min(pixels)
assert measurements.get_current_image_measurement(
'Intensity_MaxIntensity_image') == numpy.max(pixels)
assert measurements.get_current_image_measurement(
'Intensity_PercentMaximal_image') == 4.0
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 is 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_uint16(workspace, module):
module.object_name.value = "inputobjects"
module.image_name.value = "outputimage"
module.image_mode.value = "uint16"
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), (16, 16))
if objects.segmented.ndim is 3:
expected = numpy.tile(expected, (3, 1))
expected = numpy.reshape(expected, (3, 16, 16))
assert numpy.all(pixel_data == expected)
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_enhance_texture_volume(image, module, workspace):
r = numpy.random.RandomState()
r.seed(81)
data = r.uniform(size=(8, 19, 24))
image.pixel_data = data
image.dimensions = 3
sigma = 2.1
module.method.value = "Enhance"
module.enhance_method.value = "Texture"
module.smoothing.value = sigma
module.run(workspace)
gaussian_mask = skimage.filters.gaussian(numpy.ones_like(data), sigma, mode='constant')
gaussian = skimage.filters.gaussian(data, sigma, mode='constant') / gaussian_mask
squared_gaussian = skimage.filters.gaussian(data ** 2, sigma, mode='constant') / gaussian_mask
expected = squared_gaussian - gaussian ** 2
actual = workspace.image_set.get_image("output").pixel_data
numpy.testing.assert_almost_equal(expected, actual)
def test_volume(image, measurements, module, workspace):
image.set_image(skimage.morphology.ball(3), convert=False)
image.dimensions = 3
module.run(workspace)
expected = {
"Intensity_TotalIntensity_image": 123.0,
"Intensity_MeanIntensity_image": 0.358600583090379,
"Intensity_MedianIntensity_image": 0.0,
"Intensity_StdIntensity_image": 0.47958962134059907,
"Intensity_MADIntensity_image": 0.0,
"Intensity_MaxIntensity_image": 1.0,
"Intensity_MinIntensity_image": 0.0,
"Intensity_TotalArea_image": 343.0,
"Intensity_PercentMaximal_image": 35.8600583090379,
"Intensity_UpperQuartileIntensity_image": 1.0,
"Intensity_LowerQuartileIntensity_image": 0.0
}
for feature, value in expected.iteritems():
actual = measurements.get_current_measurement(
cellprofiler.measurement.IMAGE, feature)
assert actual == value, "{} expected {}, got {}".format(
feature, value, actual)
def test_volume(image, measurements, module, workspace):
image.set_image(skimage.morphology.ball(3), convert=False)
image.dimensions = 3
module.run(workspace)
expected = {
"Intensity_TotalIntensity_image": 123.0,
"Intensity_MeanIntensity_image": 0.358600583090379,
"Intensity_MedianIntensity_image": 0.0,
"Intensity_StdIntensity_image": 0.47958962134059907,
"Intensity_MADIntensity_image": 0.0,
"Intensity_MaxIntensity_image": 1.0,
"Intensity_MinIntensity_image": 0.0,
"Intensity_TotalArea_image": 343.0,
"Intensity_PercentMaximal_image": 35.8600583090379,
"Intensity_UpperQuartileIntensity_image": 1.0,
"Intensity_LowerQuartileIntensity_image": 0.0
}
for feature, value in expected.iteritems():
actual = measurements.get_current_measurement(
cellprofiler.measurement.IMAGE,
feature
)
assert actual == value, "{} expected {}, got {}".format(feature, value, actual)
def test_03_01_binary_ijv(self):
workspace, module, ijv = self.make_workspace_ijv()
self.assertTrue(isinstance(module, cellprofiler.modules.convertobjectstoimage.ConvertObjectsToImage))
module.image_mode.value = "Binary (black & white)"
module.run(workspace)
pixel_data = workspace.image_set.get_image(IMAGE_NAME).pixel_data
self.assertEqual(len(numpy.unique(ijv[:, 0] + ijv[:, 1] * pixel_data.shape[0])),
numpy.sum(pixel_data))
self.assertTrue(numpy.all(pixel_data[ijv[:, 0], ijv[:, 1]]))
