def test_03_04_object_measurement_columns(self):
module = L.LoadSingleImage()
module.file_settings[0].image_objects_choice.value = L.IO_OBJECTS
module.file_settings[0].objects_name.value = OBJECTS_NAME
columns = module.get_measurement_columns(None)
expected_columns = ((cpmeas.IMAGE,
L.C_OBJECTS_FILE_NAME + "_" + OBJECTS_NAME),
(cpmeas.IMAGE,
L.C_OBJECTS_PATH_NAME + "_" + OBJECTS_NAME),
(cpmeas.IMAGE, L.C_COUNT + "_" + OBJECTS_NAME),
(OBJECTS_NAME,
L.C_LOCATION + "_" + L.FTR_CENTER_X),
(OBJECTS_NAME,
L.C_LOCATION + "_" + L.FTR_CENTER_Y),
(OBJECTS_NAME,
L.C_NUMBER + "_" + L.FTR_OBJECT_NUMBER))
for expected_column in expected_columns:
self.assertTrue(
any([
column[0] == expected_column[0]
and column[1] == expected_column[1] for column in columns
]))
for column in columns:
self.assertTrue(
any([
column[0] == expected_column[0]
and column[1] == expected_column[1]
for expected_column in expected_columns
]))
def test_04_01_load_objects(self):
r = np.random.RandomState()
r.seed(41)
labels = np.random.randint(0, 10, size=(30, 40))
filename = "myobjects.png"
directory = tempfile.mkdtemp()
cpprefs.set_default_image_directory(directory)
pilimage = PIL.Image.fromarray(labels.astype(np.uint8), "L")
pilimage.save(os.path.join(directory, filename))
del pilimage
try:
module = L.LoadSingleImage()
module.module_num = 1
module.directory.set_dir_choice(L.DEFAULT_INPUT_FOLDER_NAME)
fs = module.file_settings[0]
fs.file_name.value = filename
fs.image_objects_choice.value = L.IO_OBJECTS
fs.objects_name.value = OBJECTS_NAME
pipeline = cpp.Pipeline()
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
pipeline.add_listener(callback)
pipeline.add_module(module)
m = cpmeas.Measurements()
object_set = cpo.ObjectSet()
image_set_list = cpi.ImageSetList()
image_set = image_set_list.get_image_set(0)
workspace = cpw.Workspace(pipeline, module, image_set, object_set,
m, image_set_list)
module.prepare_run(workspace)
module.run(workspace)
o = object_set.get_objects(OBJECTS_NAME)
np.testing.assert_equal(labels, o.segmented)
self.assertEqual(
m.get_current_image_measurement("_".join(
(L.C_COUNT, OBJECTS_NAME))), 9)
self.assertEqual(
m.get_current_image_measurement("_".join(
(L.C_OBJECTS_FILE_NAME, OBJECTS_NAME))), filename)
self.assertEqual(
m.get_current_image_measurement("_".join(
(L.C_OBJECTS_PATH_NAME, OBJECTS_NAME))), directory)
for feature in (M_LOCATION_CENTER_X, M_LOCATION_CENTER_Y,
M_NUMBER_OBJECT_NUMBER):
values = m.get_current_measurement(OBJECTS_NAME, feature)
self.assertEqual(len(values), 9)
finally:
try:
os.remove(os.path.join(directory, filename))
os.rmdir(directory)
except:
print "Failed to delete directory " + directory
def test_03_05_object_categories(self):
module = L.LoadSingleImage()
module.file_settings[0].image_objects_choice.value = L.IO_OBJECTS
module.file_settings[0].objects_name.value = OBJECTS_NAME
for object_name, expected_categories in (
(cpmeas.IMAGE, (L.C_COUNT, L.C_OBJECTS_FILE_NAME, L.C_OBJECTS_PATH_NAME)),
(OBJECTS_NAME, (L.C_NUMBER, L.C_LOCATION))):
categories = module.get_categories(None, object_name)
self.assertTrue(all([category in expected_categories
for category in categories]))
self.assertTrue(all([expected_category in categories
for expected_category in expected_categories]))
def test_03_06_object_measurements(self):
module = L.LoadSingleImage()
module.file_settings[0].image_objects_choice.value = L.IO_OBJECTS
module.file_settings[0].objects_name.value = OBJECTS_NAME
for object_name, category, expected_features in (
(cpmeas.IMAGE, L.C_COUNT, (OBJECTS_NAME,)),
(cpmeas.IMAGE, L.C_OBJECTS_FILE_NAME, (OBJECTS_NAME,)),
(cpmeas.IMAGE, L.C_OBJECTS_PATH_NAME, (OBJECTS_NAME,)),
(OBJECTS_NAME, L.C_NUMBER, (L.FTR_OBJECT_NUMBER, )),
(OBJECTS_NAME, L.C_LOCATION, (L.FTR_CENTER_X, L.FTR_CENTER_Y))):
features = module.get_measurements(None, object_name, category)
self.assertTrue(all([feature in expected_features
for feature in features]))
self.assertTrue(all([expected_feature in features
for expected_feature in expected_features]))
def test_02_03_prepare_run(self):
# regression test for issue #673 and #1161
#
# If LoadSingleImage appears first, pathname data does not show
# up in the measurements.
#
maybe_download_sbs()
folder = "ExampleSBSImages"
path = os.path.join(example_images_directory(), folder)
filename = "Channel1-01-A-01.tif"
pipeline = cpp.Pipeline()
lsi = L.LoadSingleImage()
lsi.module_num = 1
lsi.directory.dir_choice = cps.ABSOLUTE_FOLDER_NAME
lsi.directory.custom_path = path
lsi.file_settings[0].image_name.value = self.get_image_name(0)
lsi.file_settings[0].file_name.value = filename
pipeline.add_module(lsi)
li = LI.LoadImages()
li.module_num = 2
pipeline.add_module(li)
li.match_method.value = LI.MS_EXACT_MATCH
li.location.dir_choice = cps.ABSOLUTE_FOLDER_NAME
li.location.custom_path = path
li.images[0].common_text.value = "Channel2-"
m = cpmeas.Measurements()
workspace = cpw.Workspace(pipeline, lsi, m, cpo.ObjectSet(), m,
cpi.ImageSetList())
self.assertTrue(pipeline.prepare_run(workspace))
self.assertGreater(m.image_set_count, 1)
pipeline.prepare_group(workspace, {}, m.get_image_numbers())
#
# Skip to the second image set
#
m.next_image_set(2)
lsi.run(workspace)
#
# Are the measurements populated?
#
m_file = "_".join((cpmeas.C_FILE_NAME, self.get_image_name(0)))
self.assertEqual(m[cpmeas.IMAGE, m_file, 2], filename)
#
# Can we retrieve the image?
#
pixel_data = m.get_image(self.get_image_name(0)).pixel_data
self.assertFalse(np.isscalar(pixel_data))
def test_04_02_object_outlines(self):
labels = np.zeros((30, 40), int)
labels[10:15, 20:30] = 1
expected_outlines = labels != 0
expected_outlines[11:14, 21:29] = False
filename = "myobjects.png"
directory = tempfile.mkdtemp()
cpprefs.set_default_image_directory(directory)
pilimage = PIL.Image.fromarray(labels.astype(np.uint8), "L")
pilimage.save(os.path.join(directory, filename))
del pilimage
try:
module = L.LoadSingleImage()
module.module_num = 1
module.directory.set_dir_choice(L.DEFAULT_INPUT_FOLDER_NAME)
fs = module.file_settings[0]
fs.file_name.value = filename
fs.image_objects_choice.value = L.IO_OBJECTS
fs.objects_name.value = OBJECTS_NAME
fs.wants_outlines.value = True
fs.outlines_name.value = OUTLINES_NAME
pipeline = cpp.Pipeline()
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
pipeline.add_listener(callback)
pipeline.add_module(module)
m = cpmeas.Measurements()
object_set = cpo.ObjectSet()
image_set_list = cpi.ImageSetList()
image_set = image_set_list.get_image_set(0)
workspace = cpw.Workspace(pipeline, module, image_set, object_set,
m, image_set_list)
module.prepare_run(workspace)
module.run(workspace)
outlines = image_set.get_image(OUTLINES_NAME)
np.testing.assert_equal(outlines.pixel_data, expected_outlines)
finally:
try:
os.remove(os.path.join(directory, filename))
os.rmdir(directory)
except:
print "Failed to delete directory " + directory
def make_workspace(self, file_names):
module = L.LoadSingleImage()
module.module_num = 1
for i, file_name in enumerate(file_names):
if i > 0:
module.add_file()
module.file_settings[i].image_name.value = self.get_image_name(i)
module.file_settings[i].file_name.value = file_name
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()
workspace = cpw.Workspace(pipeline, module,
image_set_list.get_image_set(0),
cpo.ObjectSet(), cpmeas.Measurements(),
image_set_list)
return workspace, module
