def make_workspace(self, image1, image2, objects=None):
'''Make a workspace for testing Threshold'''
module = M.MeasureColocalization()
image_set_list = cpi.ImageSetList()
image_set = image_set_list.get_image_set(0)
for image_group, name, image in zip(module.image_groups,
(IMAGE1_NAME, IMAGE2_NAME),
(image1, image2)):
image_group.image_name.value = name
image_set.add(name, image)
object_set = cpo.ObjectSet()
if objects is None:
module.images_or_objects.value = M.M_IMAGES
else:
module.images_or_objects.value = M.M_IMAGES_AND_OBJECTS
module.object_groups[0].object_name.value = OBJECTS_NAME
object_set.add_objects(objects, OBJECTS_NAME)
pipeline = cpp.Pipeline()
workspace = cpw.Workspace(pipeline,
module,
image_set,
object_set,
cpmeas.Measurements(),
image_set_list)
return workspace, module
def test_02_04_03_get_measurement_columns_both(self):
module = M.MeasureColocalization()
module.image_groups[0].image_name.value = IMAGE1_NAME
module.image_groups[1].image_name.value = IMAGE2_NAME
module.object_groups[0].object_name.value = OBJECTS_NAME
module.images_or_objects.value = M.M_IMAGES_AND_OBJECTS
columns = module.get_measurement_columns(None)
expected = [
(cpmeas.IMAGE,
ftr % (IMAGE1_NAME, IMAGE2_NAME),
cpmeas.COLTYPE_FLOAT)
for ftr in self.all_image_measurement_formats] + [
(cpmeas.IMAGE,
ftr % (IMAGE2_NAME, IMAGE1_NAME),
cpmeas.COLTYPE_FLOAT)
for ftr in self.asymmetrical_measurement_formats] + [
(OBJECTS_NAME,
ftr % (IMAGE1_NAME, IMAGE2_NAME),
cpmeas.COLTYPE_FLOAT)
for ftr in self.all_object_measurement_formats] + [
(OBJECTS_NAME,
ftr % (IMAGE2_NAME, IMAGE1_NAME),
cpmeas.COLTYPE_FLOAT)
for ftr in self.asymmetrical_measurement_formats]
self.assertEqual(len(columns), len(expected))
for column in columns:
self.assertTrue(any([all([cf == ef for cf, ef in zip(column, ex)])
for ex in expected]))
def test_02_02_get_measurements(self):
'''Test the get_measurements function for some different cases'''
module = M.MeasureColocalization()
module.image_groups[0].image_name.value = IMAGE1_NAME
module.image_groups[1].image_name.value = IMAGE2_NAME
module.object_groups[0].object_name.value = OBJECTS_NAME
module.images_or_objects.value = M.M_IMAGES
def meas(name):
ans = list(module.get_measurements(None, name, "Correlation"))
ans.sort()
if name == "Image":
mf = self.all_image_measurement_formats
else:
mf = self.all_object_measurement_formats
expected = sorted([_.split("_")[1] for _ in mf])
return ans == expected
self.assertTrue(meas("Image"))
self.assertFalse(meas(OBJECTS_NAME))
module.images_or_objects.value = M.M_OBJECTS
self.assertFalse(meas("Image"))
self.assertTrue(meas(OBJECTS_NAME))
module.images_or_objects.value = M.M_IMAGES_AND_OBJECTS
self.assertTrue(meas("Image"))
self.assertTrue(meas(OBJECTS_NAME))
def test_02_03_get_measurement_images(self):
'''Test the get_measurment_images function for some different cases'''
for iocase, names in (
(M.M_IMAGES, [cpmeas.IMAGE]),
(M.M_OBJECTS, [OBJECTS_NAME]),
(M.M_IMAGES_AND_OBJECTS, [cpmeas.IMAGE, OBJECTS_NAME])):
module = M.MeasureColocalization()
module.image_groups[0].image_name.value = IMAGE1_NAME
module.image_groups[1].image_name.value = IMAGE2_NAME
module.object_groups[0].object_name.value = OBJECTS_NAME
module.images_or_objects.value = iocase
for name, mfs in ((cpmeas.IMAGE, self.all_image_measurement_formats),
(OBJECTS_NAME, self.all_object_measurement_formats)):
if name not in names:
continue
for mf in mfs:
ftr = mf.split("_")[1]
ans = module.get_measurement_images(
None, name, "Correlation", ftr)
expected = ["%s_%s" % (i1, i2) for i1, i2 in
((IMAGE1_NAME, IMAGE2_NAME),
(IMAGE2_NAME, IMAGE1_NAME))]
if mf in self.asymmetrical_measurement_formats:
self.assertTrue(all([e in ans for e in expected]))
else:
self.assertTrue(any([e in ans for e in expected]))
def test_02_01_get_categories(self):
'''Test the get_categories function for some different cases'''
module = M.MeasureColocalization()
module.image_groups[0].image_name.value = IMAGE1_NAME
module.image_groups[1].image_name.value = IMAGE2_NAME
module.object_groups[0].object_name.value = OBJECTS_NAME
module.images_or_objects.value = M.M_IMAGES
def cat(name):
return module.get_categories(None, name) == ["Correlation"]
self.assertTrue(cat("Image"))
self.assertFalse(cat(OBJECTS_NAME))
module.images_or_objects.value = M.M_OBJECTS
self.assertFalse(cat("Image"))
self.assertTrue(cat(OBJECTS_NAME))
module.images_or_objects.value = M.M_IMAGES_AND_OBJECTS
self.assertTrue(cat("Image"))
self.assertTrue(cat(OBJECTS_NAME))