def make_workspace(self, labels, mode, distance=0, neighbors_labels=None):
'''Make a workspace for testing MeasureObjectNeighbors'''
module = M.MeasureObjectNeighbors()
module.module_num = 1
module.object_name.value = OBJECTS_NAME
module.distance_method.value = mode
module.distance.value = distance
pipeline = cpp.Pipeline()
pipeline.add_module(module)
object_set = cpo.ObjectSet()
image_set_list = cpi.ImageSetList()
image_set = image_set_list.get_image_set(0)
measurements = cpmeas.Measurements()
measurements.group_index = 1
measurements.group_number = 1
workspace = cpw.Workspace(pipeline, module, image_set, object_set,
measurements, image_set_list)
objects = cpo.Objects()
objects.segmented = labels
object_set.add_objects(objects, OBJECTS_NAME)
if neighbors_labels is None:
module.neighbors_name.value = OBJECTS_NAME
else:
module.neighbors_name.value = NEIGHBORS_NAME
objects = cpo.Objects()
objects.segmented = neighbors_labels
object_set.add_objects(objects, NEIGHBORS_NAME)
return workspace, module
def test_relate_children_volume(self):
parent_labels = numpy.zeros((30, 30, 30), dtype=numpy.uint8)
k, i, j = numpy.mgrid[-15:15, -15:15, -15:15]
parent_labels[k**2 + i**2 + j**2 <= 196] = 1
parent_object = cpo.Objects()
parent_object.segmented = parent_labels
labels = numpy.zeros((30, 30, 30), dtype=numpy.uint8)
k, i, j = numpy.mgrid[-15:15, -15:15, -7:23]
labels[k**2 + i**2 + j**2 <= 25] = 1
k, i, j = numpy.mgrid[-15:15, -15:15, -22:8]
labels[k**2 + i**2 + j**2 <= 16] = 2
labels[
0, 10:20, 10:
20] = 3 # not touching a parent, should not be counted as a child
object = cpo.Objects()
object.segmented = labels
actual_children, actual_parents = parent_object.relate_children(object)
expected_children = [2]
expected_parents = [1, 1, 0]
numpy.testing.assert_array_equal(actual_children, expected_children)
numpy.testing.assert_array_equal(actual_parents, expected_parents)
def test_05_01_overlapping(self):
'''Test object measurement with two overlapping objects in ijv format'''
i, j = np.mgrid[0:10, 0:20]
m = (i > 1) & (i < 9) & (j > 1) & (j < 19)
m1 = m & (i < j)
m2 = m & (i < 9 - j)
mlist = []
olist = []
for m in (m1, m2):
objects = cpo.Objects()
objects.segmented = m.astype(int)
olist.append(objects)
ijv = np.column_stack((
np.hstack([np.argwhere(m)[:, 0] for m in (m1, m2)]),
np.hstack([np.argwhere(m)[:, 1] for m in (m1, m2)]),
np.array([1] * np.sum(m1) + [2] * np.sum(m2))))
objects = cpo.Objects()
objects.ijv = ijv
olist.append(objects)
for objects in olist:
module = cpmoas.MeasureObjectAreaShape()
module.object_groups[0].name.value = "SomeObjects"
module.calculate_zernikes.value = True
object_set = cpo.ObjectSet()
object_set.add_objects(objects, "SomeObjects")
module.module_num = 1
image_set_list = cpi.ImageSetList()
measurements = cpmeas.Measurements()
mlist.append(measurements)
pipeline = cpp.Pipeline()
pipeline.add_module(module)
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
pipeline.add_listener(callback)
workspace = cpw.Workspace(pipeline, module,
image_set_list.get_image_set(0),
object_set, measurements, image_set_list)
module.run(workspace)
for c in module.get_measurement_columns(None):
oname, feature = c[:2]
if oname != "SomeObjects":
continue
measurements = mlist[0]
self.assertTrue(isinstance(measurements, cpmeas.Measurements))
v1 = measurements.get_current_measurement(oname, feature)
self.assertEqual(len(v1), 1)
v1 = v1[0]
measurements = mlist[1]
v2 = measurements.get_current_measurement(oname, feature)
self.assertEqual(len(v2), 1)
v2 = v2[0]
expected = (v1, v2)
v = mlist[2].get_current_measurement(oname, feature)
self.assertEqual(tuple(v), expected)
def test_05_01_relate_zero_parents_and_children(self):
"""Test the relate method if both parent and child label matrices are zeros"""
x = cpo.Objects()
x.segmented = np.zeros((10, 10), int)
y = cpo.Objects()
y.segmented = np.zeros((10, 10), int)
children_per_parent, parents_of_children = x.relate_children(y)
self.assertEqual(np.product(children_per_parent.shape), 0)
self.assertEqual(np.product(parents_of_children.shape), 0)
def test_05_03_relate_one_parent_no_children(self):
x = cpo.Objects()
labels = np.zeros((10, 10), int)
labels[3:6, 3:6] = 1
x.segmented = labels
y = cpo.Objects()
y.segmented = np.zeros((10, 10), int)
children_per_parent, parents_of_children = x.relate_children(y)
self.assertEqual(np.product(children_per_parent.shape), 1)
self.assertEqual(children_per_parent[0], 0)
self.assertEqual(np.product(parents_of_children.shape), 0)
def make_workspace(
self,
labels,
overlap_choice,
masking_objects=None,
masking_image=None,
renumber=True,
):
module = M.MaskObjects()
module.module_num = 1
module.object_name.value = INPUT_OBJECTS
module.remaining_objects.value = OUTPUT_OBJECTS
module.mask_choice.value = (M.MC_OBJECTS if masking_objects is not None
else M.MC_IMAGE)
module.masking_image.value = MASKING_IMAGE
module.masking_objects.value = MASKING_OBJECTS
module.retain_or_renumber.value = M.R_RENUMBER if renumber else M.R_RETAIN
module.overlap_choice.value = overlap_choice
pipeline = cpp.Pipeline()
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
pipeline.add_listener(callback)
pipeline.add_module(module)
object_set = cpo.ObjectSet()
io = cpo.Objects()
io.segmented = labels
object_set.add_objects(io, INPUT_OBJECTS)
if masking_objects is not None:
oo = cpo.Objects()
oo.segmented = masking_objects
object_set.add_objects(oo, MASKING_OBJECTS)
image_set_list = cpi.ImageSetList()
image_set = image_set_list.get_image_set(0)
if masking_image is not None:
mi = cpi.Image(masking_image)
image_set.add(MASKING_IMAGE, mi)
workspace = cpw.Workspace(
pipeline,
module,
image_set,
object_set,
cpmeas.Measurements(),
image_set_list,
)
return workspace, module
def test_06_05_last_object_masked(self):
# Regression test of issue #1553
# MeasureColocalization was truncating the measurements
# if the last had no pixels or all pixels masked.
#
r = np.random.RandomState()
r.seed(65)
image1 = r.uniform(size=(20, 20))
image2 = r.uniform(size=(20, 20))
labels = np.zeros((20, 20), int)
labels[3:8, 3:8] = 1
labels[13:18, 13:18] = 2
mask = labels != 2
objects = cpo.Objects()
objects.segmented = labels
for mask1, mask2 in ((mask, None), (None, mask), (mask, mask)):
workspace, module = self.make_workspace(
cpi.Image(image1, mask=mask1),
cpi.Image(image2, mask=mask2),
objects)
module.run(workspace)
m = workspace.measurements
feature = M.F_CORRELATION_FORMAT % (IMAGE1_NAME, IMAGE2_NAME)
values = m[OBJECTS_NAME, feature]
self.assertEqual(len(values), 2)
self.assertTrue(np.isnan(values[1]))
def test_06_03_no_objects(self):
'''Test images with no objects'''
labels = np.zeros((10, 10), int)
i, j = np.mgrid[0:10, 0:10]
image1 = ((i + j) % 2).astype(float)
image2 = image1.copy()
i1 = cpi.Image(image1)
i2 = cpi.Image(image2)
o = cpo.Objects()
o.segmented = labels
workspace, module = self.make_workspace(i1, i2, o)
module.run(workspace)
m = workspace.measurements
mi = module.get_measurement_images(None, OBJECTS_NAME,
"Correlation", "Correlation")
corr = m.get_current_measurement(OBJECTS_NAME, "Correlation_Correlation_%s" % mi[0])
self.assertEqual(len(corr), 0)
self.assertEqual(len(m.get_object_names()), 2)
self.assertTrue(OBJECTS_NAME in m.get_object_names())
columns = module.get_measurement_columns(None)
image_features = m.get_feature_names(cpmeas.IMAGE)
object_features = m.get_feature_names(OBJECTS_NAME)
self.assertEqual(len(columns), len(image_features) + len(object_features))
for column in columns:
if column[0] == cpmeas.IMAGE:
self.assertTrue(column[1] in image_features)
else:
self.assertEqual(column[0], OBJECTS_NAME)
self.assertTrue(column[1] in object_features)
def make_workspace(self,
labels,
operation,
iterations=1,
wants_outlines=False,
wants_fill_holes=False):
object_set = cpo.ObjectSet()
objects = cpo.Objects()
objects.segmented = labels
object_set.add_objects(objects, INPUT_NAME)
module = E.ExpandOrShrink()
module.object_name.value = INPUT_NAME
module.output_object_name.value = OUTPUT_NAME
module.outlines_name.value = OUTLINES_NAME
module.operation.value = operation
module.iterations.value = iterations
module.wants_outlines.value = wants_outlines
module.wants_fill_holes.value = wants_fill_holes
module.module_num = 1
pipeline = cpp.Pipeline()
pipeline.add_module(module)
image_set_list = cpi.ImageSetList()
workspace = cpw.Workspace(pipeline,
module,
image_set_list.get_image_set(0),
object_set,
cpmeas.Measurements(),
image_set_list)
return workspace, module
def test_04_02_masked_edge(self):
# Regression test of issue #1115
labels = np.zeros((20, 50), int)
labels[15:25, 15:25] = 1
image = np.random.uniform(size=labels.shape).astype(np.float32)
#
# Mask the edge of the object
#
mask = ~cpmo.outline(labels).astype(bool)
m = cpmeas.Measurements()
m.add(IMAGE_NAME, cpi.Image(image, mask=mask))
object_set = cpo.ObjectSet()
o = cpo.Objects()
o.segmented = labels
object_set.add_objects(o, OBJECT_NAME)
pipeline = P.Pipeline()
def callback(caller, event):
self.assertFalse(isinstance(event, P.RunExceptionEvent))
pipeline.add_listener(callback)
module = MOI.MeasureObjectIntensity()
module.module_num = 1
module.images[0].name.value = IMAGE_NAME
module.objects[0].name.value = OBJECT_NAME
pipeline.add_module(module)
workspace = cpw.Workspace(pipeline, module, m, object_set, m, None)
module.run(workspace)
def run(self, workspace):
image_name = self.image_name.value
objects_name = self.objects_name.value
image = workspace.image_set.get_image(image_name)
pixel_data = image.pixel_data
labels = workspace.interaction_request(
self, pixel_data, workspace.measurements.image_set_number)
if labels is None:
# User cancelled. Soldier on as best we can.
workspace.cancel_request()
labels = np.zeros(pixel_data.shape[:2], int)
objects = cpo.Objects()
objects.segmented = labels
workspace.object_set.add_objects(objects, objects_name)
##################
#
# Add measurements
#
m = workspace.measurements
#
# The object count
#
object_count = np.max(labels)
I.add_object_count_measurements(m, objects_name, object_count)
#
# The object locations
#
I.add_object_location_measurements(m, objects_name, labels)
workspace.display_data.labels = labels
workspace.display_data.pixel_data = pixel_data
def test_06_05_ijv_three_overlapping(self):
#
# This is a regression test of a bug where a segmentation consists
# of only one point, labeled three times yielding two planes instead
# of three.
#
ijv = np.array([[4, 5, 1],
[4, 5, 2],
[4, 5, 3]])
x = cpo.Objects()
x.set_ijv(ijv, (8, 9))
labels = []
indices = np.zeros(3, bool)
for l, i in x.get_labels():
labels.append(l)
self.assertEqual(len(i), 1)
self.assertTrue(i[0] in (1, 2, 3))
indices[i[0] - 1] = True
self.assertTrue(np.all(indices))
self.assertEqual(len(labels), 3)
lstacked = np.dstack(labels)
i, j, k = np.mgrid[0:lstacked.shape[0],
0:lstacked.shape[1],
0:lstacked.shape[2]]
self.assertTrue(np.all(lstacked[(i != 4) | (j != 5)] == 0))
self.assertEqual((1, 2, 3), tuple(sorted(lstacked[4, 5, :])))
def test_non_overlapping_object_intensity(self):
# https://github.com/CellProfiler/CellProfiler/issues/2764
image1 = np.random.rand(10, 10)
image1[:5, :] = 0
image2 = np.random.rand(10, 10)
image2[5:, :] = 0
objects = cpo.Objects()
objects.segmented = np.ones_like(image1, dtype=np.uint8)
workspace, module = self.make_workspace(cpi.Image(image1),
cpi.Image(image2), objects)
module.run(workspace)
m = workspace.measurements
feature = M.F_OVERLAP_FORMAT % (IMAGE1_NAME, IMAGE2_NAME)
values = m[OBJECTS_NAME, feature]
assert len(values) == 1
assert values[0] == 0.0
def make_workspace(self, primary_labels, secondary_labels):
"""Make a workspace that has objects for the input labels
returns a workspace with the following
object_set - has object with name "primary" containing
the primary labels
has object with name "secondary" containing
the secondary labels
"""
isl = cpi.ImageSetList()
module = cpmit.IdentifyTertiarySubregion()
module.module_num = 1
module.primary_objects_name.value = PRIMARY
module.secondary_objects_name.value = SECONDARY
module.subregion_objects_name.value = TERTIARY
workspace = cpw.Workspace(cpp.Pipeline(), module, isl.get_image_set(0),
cpo.ObjectSet(), cpm.Measurements(), isl)
workspace.pipeline.add_module(module)
for labels, name in ((primary_labels, PRIMARY), (secondary_labels,
SECONDARY)):
objects = cpo.Objects()
objects.segmented = labels
workspace.object_set.add_objects(objects, name)
return workspace
def run(self, workspace):
'''Find the outlines on the current image set
workspace - The workspace contains
pipeline - instance of cpp for this run
image_set - the images in the image set being processed
object_set - the objects (labeled masks) in this image set
measurements - the measurements for this run
frame - the parent frame to whatever frame is created. None means don't draw.
'''
gridding = workspace.get_grid(self.grid_name.value)
if self.shape_choice == SHAPE_RECTANGLE:
labels = self.run_rectangle(workspace, gridding)
elif self.shape_choice == SHAPE_CIRCLE_FORCED:
labels = self.run_forced_circle(workspace, gridding)
elif self.shape_choice == SHAPE_CIRCLE_NATURAL:
labels = self.run_natural_circle(workspace, gridding)
elif self.shape_choice == SHAPE_NATURAL:
labels = self.run_natural(workspace, gridding)
objects = cpo.Objects()
objects.segmented = labels
object_count = gridding.rows * gridding.columns
workspace.object_set.add_objects(objects,
self.output_objects_name.value)
add_object_location_measurements(workspace.measurements,
self.output_objects_name.value,
labels, object_count)
add_object_count_measurements(workspace.measurements,
self.output_objects_name.value,
object_count)
if self.show_window:
workspace.display_data.gridding = gridding
workspace.display_data.labels = labels
def make_workspace(self, gridding, labels=None):
module = I.IdentifyObjectsInGrid()
module.module_num = 1
module.grid_name.value = GRID_NAME
module.output_objects_name.value = OUTPUT_OBJECTS_NAME
module.guiding_object_name.value = GUIDING_OBJECTS_NAME
image_set_list = cpi.ImageSetList()
object_set = cpo.ObjectSet()
if labels is not None:
my_objects = cpo.Objects()
my_objects.segmented = labels
object_set.add_objects(my_objects, GUIDING_OBJECTS_NAME)
pipeline = cpp.Pipeline()
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
pipeline.add_listener(callback)
pipeline.add_module(module)
workspace = cpw.Workspace(
pipeline,
module,
image_set_list.get_image_set(0),
object_set,
cpmeas.Measurements(),
image_set_list,
)
workspace.set_grid(GRID_NAME, gridding)
return workspace, module
def rruunn(self,
input_labels,
relabel_option,
merge_option=cellprofiler.modules.splitormergeobjects.
UNIFY_DISTANCE,
unify_method=cellprofiler.modules.splitormergeobjects.
UM_DISCONNECTED,
distance_threshold=5,
minimum_intensity_fraction=.9,
where_algorithm=cellprofiler.modules.splitormergeobjects.
CA_CLOSEST_POINT,
image=None,
parent_object="Parent_object",
parents_of=None):
'''Run the SplitOrMergeObjects module
returns the labels matrix and the workspace.
'''
module = cellprofiler.modules.splitormergeobjects.SplitOrMergeObjects()
module.module_num = 1
module.objects_name.value = INPUT_OBJECTS_NAME
module.output_objects_name.value = OUTPUT_OBJECTS_NAME
module.relabel_option.value = relabel_option
module.merge_option.value = merge_option
module.merging_method.value = unify_method
module.parent_object.value = parent_object
module.distance_threshold.value = distance_threshold
module.minimum_intensity_fraction.value = minimum_intensity_fraction
module.wants_image.value = (image is not None)
module.where_algorithm.value = where_algorithm
pipeline = cpp.Pipeline()
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
pipeline.add_listener(callback)
pipeline.add_module(module)
image_set_list = cpi.ImageSetList()
image_set = image_set_list.get_image_set(0)
if image is not None:
img = cpi.Image(image)
image_set.add(IMAGE_NAME, img)
module.image_name.value = IMAGE_NAME
object_set = cpo.ObjectSet()
o = cpo.Objects()
o.segmented = input_labels
object_set.add_objects(o, INPUT_OBJECTS_NAME)
workspace = cpw.Workspace(pipeline, module, image_set, object_set,
cpmeas.Measurements(), image_set_list)
if parents_of is not None:
m = workspace.measurements
ftr = cellprofiler.measurement.FF_PARENT % parent_object
m[INPUT_OBJECTS_NAME, ftr] = parents_of
module.run(workspace)
output_objects = workspace.object_set.get_objects(OUTPUT_OBJECTS_NAME)
return output_objects.segmented, workspace
def test_zero_valued_intensity(self):
# https://github.com/CellProfiler/CellProfiler/issues/2680
image1 = np.zeros((10, 10), dtype=np.float32)
image2 = np.random.rand(10, 10).astype(np.float32)
labels = np.zeros_like(image1, dtype=np.uint8)
labels[5, 5] = 1
objects = cpo.Objects()
objects.segmented = labels
workspace, module = self.make_workspace(cpi.Image(image1), cpi.Image(image2), objects)
module.run(workspace)
m = workspace.measurements
feature = M.F_CORRELATION_FORMAT % (IMAGE1_NAME, IMAGE2_NAME)
values = m[OBJECTS_NAME, feature]
assert len(values) == 1
assert np.isnan(values[0])
def test_06_04_ijv_to_labels_overlapping(self):
'''Convert an ijv representation with overlap to labels'''
ijv = np.array([[1, 1, 1],
[1, 2, 1],
[2, 1, 1],
[2, 2, 1],
[1, 3, 2],
[2, 3, 2],
[2, 3, 3],
[4, 4, 4],
[4, 5, 4],
[4, 5, 5],
[5, 5, 5]])
x = cpo.Objects()
x.ijv = ijv
labels = x.get_labels()
self.assertEqual(len(labels), 2)
unique_a = np.unique(labels[0][0])[1:]
unique_b = np.unique(labels[1][0])[1:]
for a in unique_a:
self.assertTrue(a not in unique_b)
for b in unique_b:
self.assertTrue(b not in unique_a)
for i, j, v in ijv:
mylabels = labels[0][0] if v in unique_a else labels[1][0]
self.assertEqual(mylabels[i, j], v)
def test_06_02_cropped_objects(self):
'''Test images and objects with a cropping mask'''
np.random.seed(0)
image1 = np.random.uniform(size=(20, 20))
i1 = cpi.Image(image1)
crop_mask = np.zeros((20, 20), bool)
crop_mask[5:15, 5:15] = True
i2 = cpi.Image(image1[5:15, 5:15], crop_mask=crop_mask)
labels = np.zeros((10, 10), int)
labels[:4, :4] = 1
labels[6:, 6:] = 2
o = cpo.Objects()
o.segmented = labels
#
# Make the objects have the cropped image as a parent
#
o.parent_image = i2
workspace, module = self.make_workspace(i1, i2, o)
module.run(workspace)
m = workspace.measurements
mi = module.get_measurement_images(None, OBJECTS_NAME, "Correlation",
"Correlation")
corr = m.get_current_measurement(OBJECTS_NAME,
"Correlation_Correlation_%s" % mi[0])
self.assertAlmostEqual(corr[0], 1)
self.assertAlmostEqual(corr[1], 1)
def test_07_01_make_ijv_outlines(self):
np.random.seed(70)
x = cpo.Objects()
ii, jj = np.mgrid[0:10, 0:20]
masks = [(ii - ic) ** 2 + (jj - jc) ** 2 < r ** 2
for ic, jc, r in ((4, 5, 5), (4, 12, 5), (6, 8, 5))]
i = np.hstack([ii[mask] for mask in masks])
j = np.hstack([jj[mask] for mask in masks])
v = np.hstack([[k + 1] * np.sum(mask) for k, mask in enumerate(masks)])
x.set_ijv(np.column_stack((i, j, v)), ii.shape)
x.parent_image = cpi.Image(np.zeros((10, 20)))
colors = np.random.uniform(size=(3, 3)).astype(np.float32)
image = x.make_ijv_outlines(colors)
i1 = [i for i, color in enumerate(colors) if np.all(color == image[0, 5, :])]
self.assertEqual(len(i1), 1)
i2 = [i for i, color in enumerate(colors) if np.all(color == image[0, 12, :])]
self.assertEqual(len(i2), 1)
i3 = [i for i, color in enumerate(colors) if np.all(color == image[-1, 8, :])]
self.assertEqual(len(i3), 1)
self.assertNotEqual(i1[0], i2[0])
self.assertNotEqual(i2[0], i3[0])
colors = colors[np.array([i1[0], i2[0], i3[0]])]
outlines = np.zeros((10, 20, 3), np.float32)
alpha = np.zeros((10, 20))
for i, (color, mask) in enumerate(zip(colors, masks)):
my_outline = outline(mask)
outlines[my_outline] += color
alpha[my_outline] += 1
alpha[alpha == 0] = 1
outlines /= alpha[:, :, np.newaxis]
np.testing.assert_almost_equal(outlines, image)
def test_03_01_non_contiguous(self):
'''make sure MeasureObjectAreaShape doesn't crash if fed non-contiguous objects'''
module = cpmoas.MeasureObjectAreaShape()
module.object_groups[0].name.value = "SomeObjects"
module.calculate_zernikes.value = True
object_set = cpo.ObjectSet()
labels = np.zeros((10, 20), int)
labels[1:9, 1:5] = 1
labels[4:6, 6:19] = 1
objects = cpo.Objects()
objects.segmented = labels
object_set.add_objects(objects, "SomeObjects")
module.module_num = 1
image_set_list = cpi.ImageSetList()
measurements = cpmeas.Measurements()
pipeline = cpp.Pipeline()
pipeline.add_module(module)
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
pipeline.add_listener(callback)
workspace = cpw.Workspace(pipeline, module,
image_set_list.get_image_set(0),
object_set, measurements, image_set_list)
module.run(workspace)
values = measurements.get_current_measurement("SomeObjects",
"AreaShape_Perimeter")
self.assertEqual(len(values), 1)
self.assertEqual(values[0], 54)
def test_04_01_wrong_image_size(self):
'''Regression test of IMG-961 - object and image size differ'''
np.random.seed(41)
labels = np.ones((20, 50), int)
image = np.random.uniform(size=(30, 40)).astype(np.float32)
image_set_list = cpi.ImageSetList()
image_set = image_set_list.get_image_set(0)
image_set.add('MyImage', cpi.Image(image))
object_set = cpo.ObjectSet()
o = cpo.Objects()
o.segmented = labels
object_set.add_objects(o, "MyObjects")
pipeline = P.Pipeline()
def callback(caller, event):
self.assertFalse(isinstance(event, P.RunExceptionEvent))
pipeline.add_listener(callback)
module = MOI.MeasureObjectIntensity()
module.module_num = 1
module.images[0].name.value = "MyImage"
module.objects[0].name.value = "MyObjects"
pipeline.add_module(module)
workspace = cpw.Workspace(pipeline, module, image_set, object_set,
cpmeas.Measurements(), image_set_list)
module.run(workspace)
feature_name = '%s_%s_%s' % (MOI.INTENSITY, MOI.INTEGRATED_INTENSITY,
"MyImage")
m = workspace.measurements.get_current_measurement(
"MyObjects", feature_name)
self.assertEqual(len(m), 1)
self.assertAlmostEqual(m[0], np.sum(image[:20, :40]), 4)
def test_04_01_extent(self):
module = cpmoas.MeasureObjectAreaShape()
module.object_groups[0].name.value = "SomeObjects"
module.calculate_zernikes.value = True
object_set = cpo.ObjectSet()
labels = np.zeros((10, 20), int)
# 3/4 of a square is covered
labels[5:7, 5:10] = 1
labels[7:9, 5:15] = 1
objects = cpo.Objects()
objects.segmented = labels
object_set.add_objects(objects, "SomeObjects")
module.module_num = 1
image_set_list = cpi.ImageSetList()
measurements = cpmeas.Measurements()
pipeline = cpp.Pipeline()
pipeline.add_module(module)
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
pipeline.add_listener(callback)
workspace = cpw.Workspace(pipeline, module,
image_set_list.get_image_set(0),
object_set, measurements, image_set_list)
module.run(workspace)
values = measurements.get_current_measurement(
"SomeObjects", "_".join((cpmoas.AREA_SHAPE, cpmoas.F_EXTENT)))
self.assertEqual(len(values), 1)
self.assertAlmostEqual(values[0], .75)
def make_workspace(self, image, labels):
module = D.DefineGrid()
module.module_num = 1
module.grid_image.value = GRID_NAME
module.manual_image.value = INPUT_IMAGE_NAME
module.display_image_name.value = INPUT_IMAGE_NAME
module.object_name.value = OBJECTS_NAME
module.save_image_name.value = OUTPUT_IMAGE_NAME
image_set_list = cpi.ImageSetList()
image_set = image_set_list.get_image_set(0)
image_set.add(INPUT_IMAGE_NAME, cpi.Image(image))
object_set = cpo.ObjectSet()
objects = cpo.Objects()
objects.segmented = labels
object_set.add_objects(objects, OBJECTS_NAME)
pipeline = cpp.Pipeline()
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.LoadExceptionEvent))
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
pipeline.add_listener(callback)
pipeline.add_module(module)
measurements = cpmeas.Measurements()
workspace = cpw.Workspace(pipeline, module, image_set, object_set,
measurements, image_set_list)
return workspace, module
def test_05_06_relate_one_parent_two_children(self):
x = cpo.Objects()
labels = np.zeros((10, 10), int)
labels[3:6, 3:9] = 1
x.segmented = labels
y = cpo.Objects()
labels = np.zeros((10, 10), int)
labels[3:6, 3:6] = 1
labels[3:6, 7:9] = 2
y.segmented = labels
children_per_parent, parents_of_children = x.relate_children(y)
self.assertEqual(np.product(children_per_parent.shape), 1)
self.assertEqual(children_per_parent[0], 2)
self.assertEqual(np.product(parents_of_children.shape), 2)
self.assertEqual(parents_of_children[0], 1)
self.assertEqual(parents_of_children[1], 1)
def run(self, workspace: cpw.Workspace) -> None:
# Prepare inputs
image_name: str = self.image_name.value
image: cpi.Image = workspace.image_set.get_image(image_name)
input_pixels: np.ndarray = image.pixel_data
params = self.get_mask_params(workspace)
self.save_mask_params(workspace, params)
# Transform from microns to pixels before processing
mpp = params.pop("MPP")
params["RadialOffset"] /= mpp
params["Thickness"] /= mpp
# Construct wedge object and place in workspace
mask = make_wedge_mask(params, shape=input_pixels.shape[:2])
mask_obj = cpo.Objects()
mask_obj.segmented = mask
workspace.object_set.add_objects(mask_obj, self.wedge_mask_name.value)
if self.show_window:
# Construct merged image
image_rgb = (np.copy(input_pixels) if image.multichannel else
skimage.color.gray2rgb(input_pixels))
color = tuple(c / 255.0 for c in self.mask_color.to_rgb())
blended_image = blend_image_and_mask(image_rgb, mask, color)
workspace.display_data.blended_image = blended_image
def make_workspace(self, image, outline=None, labels=None):
'''Make a workspace for testing ApplyThreshold'''
m = cpmeas.Measurements()
object_set = cpo.ObjectSet()
module = O.OverlayOutlines()
module.blank_image.value = False
module.image_name.value = INPUT_IMAGE_NAME
module.output_image_name.value = OUTPUT_IMAGE_NAME
if outline is not None:
module.outlines[0].outline_name.value = OUTLINE_NAME
m.add(OUTLINE_NAME, cpi.Image(outline))
module.outlines[0].outline_choice.value = O.FROM_IMAGES
if labels is not None:
objects = cpo.Objects()
if len(labels) > 1:
ijv = np.vstack([
np.column_stack(list(np.where(l > 0)) + [l[l > 0]])
for l in labels
])
objects.set_ijv(ijv, shape=labels[0].shape)
else:
objects.segmented = labels[0]
object_set.add_objects(objects, OBJECTS_NAME)
module.outlines[0].outline_choice.value = O.FROM_OBJECTS
module.outlines[0].objects_name.value = OBJECTS_NAME
pipeline = cpp.Pipeline()
workspace = cpw.Workspace(pipeline, module, m, object_set, m, None)
m.add(INPUT_IMAGE_NAME, cpi.Image(image))
return workspace, module
def test_01_00_zeros(self):
"""Run on an empty labels matrix"""
object_set = cpo.ObjectSet()
labels = np.zeros((10, 20), int)
objects = cpo.Objects()
objects.segmented = labels
object_set.add_objects(objects, "SomeObjects")
module = cpmoas.MeasureObjectAreaShape()
settings = ["SomeObjects", "Yes"]
module.set_settings_from_values(settings, 1, module.module_class())
module.module_num = 1
image_set_list = cpi.ImageSetList()
measurements = cpmeas.Measurements()
pipeline = cpp.Pipeline()
pipeline.add_module(module)
workspace = cpw.Workspace(pipeline, module,
image_set_list.get_image_set(0),
object_set, measurements, image_set_list)
module.run(workspace)
for f in (cpmoas.F_AREA, cpmoas.F_CENTER_X, cpmoas.F_CENTER_Y,
cpmoas.F_ECCENTRICITY, cpmoas.F_EULER_NUMBER,
cpmoas.F_EXTENT, cpmoas.F_FORM_FACTOR,
cpmoas.F_MAJOR_AXIS_LENGTH, cpmoas.F_MINOR_AXIS_LENGTH,
cpmoas.F_ORIENTATION, cpmoas.F_PERIMETER,
cpmoas.F_SOLIDITY, cpmoas.F_COMPACTNESS,
cpmoas.F_MAXIMUM_RADIUS, cpmoas.F_MEAN_RADIUS,
cpmoas.F_MEDIAN_RADIUS,
cpmoas.F_MIN_FERET_DIAMETER, cpmoas.F_MAX_FERET_DIAMETER):
m = cpmoas.AREA_SHAPE + "_" + f
a = measurements.get_current_measurement('SomeObjects', m)
self.assertEqual(len(a), 0)
def make_workspace(self, image, mask=None, labels=None, binary_image=None):
'''Make a workspace and IdentifyPrimaryObjects module
image - the intensity image for thresholding
mask - if present, the "don't analyze" mask of the intensity image
labels - if thresholding per-object, the labels matrix needed
binary_image - if thresholding using a binary image, the image
'''
module = YS.IdentifyYeastCells()
module.module_num = 1
module.input_image_name.value = IMAGE_NAME
module.object_name.value = OBJECTS_NAME
module.binary_image.value = BINARY_IMAGE_NAME
module.masking_objects.value = MASKING_OBJECTS_NAME
pipeline = cellprofiler.pipeline.Pipeline()
pipeline.add_module(module)
m = cpmeas.Measurements()
cpimage = cpi.Image(image, mask=mask)
m.add(IMAGE_NAME, cpimage)
if binary_image is not None:
m.add(BINARY_IMAGE_NAME, cpi.Image(binary_image))
object_set = cpo.ObjectSet()
if labels is not None:
o = cpo.Objects()
o.segmented = labels
object_set.add_objects(o, MASKING_OBJECTS_NAME)
workspace = cellprofiler.workspace.Workspace(pipeline, module, m,
object_set, m, None)
return workspace, module