def test_04_01_run_group(self):
pipeline = cpp.Pipeline()
load_images = LoadImages()
load_images.module_num = 1
load_images.images[0].channels[0].image_name.value = "Foo"
pipeline.add_module(load_images)
identify = IdentifyPrimaryObjects()
identify.module_num = 2
identify.image_name.value = "Foo"
identify.object_name.value = "dizzy"
identify.threshold_scope.value = TS_MANUAL
identify.manual_threshold.value = 0.5
identify.exclude_size.value = False
pipeline.add_module(identify)
pipeline_txt = StringIO()
pipeline.savetxt(pipeline_txt)
image = np.zeros((2, 11, 17))
image[0, 2:-2, 2:-2] = 1
image[1, 2:-2, 2:7] = 1
image[1, 2:-2, 10:-2] = 1
image_metadata = [
[
"Foo",
[
["Z", image.shape[0], image.strides[0] / 8],
["Y", image.shape[1], image.strides[1] / 8],
["X", image.shape[2], image.strides[2] / 8],
],
]
]
message = [
zmq.Frame(self.session_id),
zmq.Frame(),
zmq.Frame(RUN_GROUP_REQ_1),
zmq.Frame(pipeline_txt.getvalue()),
zmq.Frame(json.dumps(image_metadata)),
zmq.Frame(image),
]
self.socket.send_multipart(message)
response = self.socket.recv_multipart()
self.assertEqual(response.pop(0), self.session_id)
self.assertEqual(response.pop(0), "")
self.assertEqual(response.pop(0), RUN_REPLY_1)
metadata = json.loads(response.pop(0))
data = response.pop(0)
measurements = self.decode_measurements(metadata, data)
self.assertEqual(len(measurements[cpmeas.IMAGE][cpmeas.IMAGE_NUMBER]), 2)
self.assertEqual(measurements[cpmeas.IMAGE]["Count_dizzy"][0], 1)
self.assertEqual(measurements[cpmeas.IMAGE]["Count_dizzy"][1], 2)
self.assertEqual(measurements["dizzy"]["Location_Center_Y"][0], 5)
def test_04_01_run_group(self):
pipeline = cpp.Pipeline()
load_images = LoadImages()
load_images.module_num = 1
load_images.images[0].channels[0].image_name.value = "Foo"
pipeline.add_module(load_images)
identify = IdentifyPrimaryObjects()
identify.use_advanced.value = True
identify.module_num = 2
identify.x_name.value = "Foo"
identify.y_name.value = "dizzy"
identify.threshold.threshold_scope.value = TS_GLOBAL
identify.threshold.global_operation.value = TM_MANUAL
identify.threshold.manual_threshold.value = .5
identify.exclude_size.value = False
pipeline.add_module(identify)
pipeline_txt = StringIO()
pipeline.savetxt(pipeline_txt)
image = np.zeros((2, 11, 17))
image[0, 2:-2, 2:-2] = 1
image[1, 2:-2, 2:7] = 1
image[1, 2:-2, 10:-2] = 1
image_metadata = [[
"Foo",
[["Z", image.shape[0], image.strides[0] / 8],
["Y", image.shape[1], image.strides[1] / 8],
["X", image.shape[2], image.strides[2] / 8]]
]]
message = [
zmq.Frame(self.session_id),
zmq.Frame(),
zmq.Frame(RUN_GROUP_REQ_1),
zmq.Frame(pipeline_txt.getvalue()),
zmq.Frame(json.dumps(image_metadata)),
zmq.Frame(image)
]
self.socket.send_multipart(message)
response = self.socket.recv_multipart()
self.assertEqual(response.pop(0), self.session_id)
self.assertEqual(response.pop(0), "")
self.assertEqual(response.pop(0), RUN_REPLY_1)
metadata = json.loads(response.pop(0))
data = response.pop(0)
measurements = self.decode_measurements(metadata, data)
self.assertEqual(len(measurements[cpmeas.IMAGE][cpmeas.IMAGE_NUMBER]),
2)
self.assertEqual(measurements[cpmeas.IMAGE]["Count_dizzy"][0], 1)
self.assertEqual(measurements[cpmeas.IMAGE]["Count_dizzy"][1], 2)
self.assertEqual(measurements["dizzy"]["Location_Center_Y"][0], 5)
def test_02_01_pipeline_info(self):
pipeline = cpp.Pipeline()
load_images = LoadImages()
load_images.module_num = 1
load_images.add_imagecb()
load_images.images[0].channels[0].image_name.value = "Foo"
load_images.images[1].channels[0].image_name.value = "Bar"
pipeline.add_module(load_images)
identify = IdentifyPrimaryObjects()
identify.module_num = 2
identify.x_name.value = "Foo"
identify.y_name.value = "dizzy"
pipeline.add_module(identify)
pipeline_txt = StringIO()
pipeline.savetxt(pipeline_txt)
message = [
zmq.Frame(self.session_id),
zmq.Frame(),
zmq.Frame(PIPELINE_INFO_REQ_1),
zmq.Frame(pipeline_txt.getvalue())
]
self.socket.send_multipart(message)
message = self.socket.recv_multipart()
self.assertEqual(message.pop(0), self.session_id)
self.assertEqual(message.pop(0), "")
self.assertEqual(message.pop(0), PIPELINE_INFO_REPLY_1)
body = json.loads(message.pop(0))
self.assertEqual(len(body), 3)
channels, type_names, measurements = body
self.assertTrue("Foo" in channels)
self.assertTrue("Bar" in channels)
self.assertTrue("dizzy" in measurements)
found_location = False
found_object_number = False
for feature, idx in measurements['dizzy']:
if feature == "Location_Center_X":
self.assertEqual('java.lang.Double', type_names[idx])
found_location = True
elif feature == "Number_Object_Number":
self.assertEqual('java.lang.Integer', type_names[idx])
found_object_number = True
self.assertTrue(found_location)
self.assertTrue(found_object_number)
def test_03_01_run_something(self):
pipeline = cpp.Pipeline()
load_images = LoadImages()
load_images.module_num = 1
load_images.images[0].channels[0].image_name.value = "Foo"
pipeline.add_module(load_images)
identify = IdentifyPrimaryObjects()
identify.use_advanced.value = True
identify.module_num = 2
identify.x_name.value = "Foo"
identify.y_name.value = "dizzy"
identify.threshold.threshold_scope.value = TS_GLOBAL
identify.threshold.global_operation.value = TM_MANUAL
identify.threshold.manual_threshold.value = .5
identify.exclude_size.value = False
pipeline.add_module(identify)
pipeline_txt = StringIO()
pipeline.savetxt(pipeline_txt)
image = np.zeros((11, 17))
image[2:-2, 2:-2] = 1
image_metadata = [
["Foo",
[["Y", image.shape[0], image.strides[0] / 8],
["X", image.shape[1], image.strides[1] / 8]]]]
message = [
zmq.Frame(self.session_id),
zmq.Frame(),
zmq.Frame(RUN_REQ_1),
zmq.Frame(pipeline_txt.getvalue()),
zmq.Frame(json.dumps(image_metadata)),
zmq.Frame(image)]
self.socket.send_multipart(message)
response = self.socket.recv_multipart()
self.assertEqual(response.pop(0), self.session_id)
self.assertEqual(response.pop(0), "")
self.assertEqual(response.pop(0), RUN_REPLY_1)
metadata = json.loads(response.pop(0))
data = response.pop(0)
measurements = self.decode_measurements(metadata, data)
self.assertEqual(measurements[cpmeas.IMAGE]["Count_dizzy"][0], 1)
self.assertEqual(measurements["dizzy"]["Location_Center_Y"][0], 5)
def test_02_01_pipeline_info(self):
pipeline = cpp.Pipeline()
load_images = LoadImages()
load_images.module_num = 1
load_images.add_imagecb()
load_images.images[0].channels[0].image_name.value = "Foo"
load_images.images[1].channels[0].image_name.value = "Bar"
pipeline.add_module(load_images)
identify = IdentifyPrimaryObjects()
identify.module_num = 2
identify.image_name.value = "Foo"
identify.object_name.value = "dizzy"
pipeline.add_module(identify)
pipeline_txt = StringIO()
pipeline.savetxt(pipeline_txt)
message = [
zmq.Frame(self.session_id),
zmq.Frame(),
zmq.Frame(PIPELINE_INFO_REQ_1),
zmq.Frame(pipeline_txt.getvalue()),
]
self.socket.send_multipart(message)
message = self.socket.recv_multipart()
self.assertEqual(message.pop(0), self.session_id)
self.assertEqual(message.pop(0), "")
self.assertEqual(message.pop(0), PIPELINE_INFO_REPLY_1)
body = json.loads(message.pop(0))
self.assertEqual(len(body), 3)
channels, type_names, measurements = body
self.assertTrue("Foo" in channels)
self.assertTrue("Bar" in channels)
self.assertTrue("dizzy" in measurements)
found_location = False
found_object_number = False
for feature, idx in measurements["dizzy"]:
if feature == "Location_Center_X":
self.assertEqual("java.lang.Double", type_names[idx])
found_location = True
elif feature == "Number_Object_Number":
self.assertEqual("java.lang.Integer", type_names[idx])
found_object_number = True
self.assertTrue(found_location)
self.assertTrue(found_object_number)
def test_02_03_clean_pipeline(self):
pipeline = cpp.Pipeline()
load_images = LoadImages()
load_images.module_num = 1
load_images.add_imagecb()
load_images.images[0].channels[0].image_name.value = "Foo"
load_images.images[1].channels[0].image_name.value = "Bar"
pipeline.add_module(load_images)
identify = IdentifyPrimaryObjects()
identify.module_num = 2
identify.x_name.value = "Foo"
identify.y_name.value = "dizzy"
pipeline.add_module(identify)
saveimages = SaveImages()
saveimages.module_num = 3
saveimages.image_name.value = "Foo"
pipeline.add_module(saveimages)
measureobjectsizeshape = MeasureObjectSizeShape()
measureobjectsizeshape.module_num = 4
measureobjectsizeshape.object_groups[0].name.value = "dizzy"
pipeline.add_module(measureobjectsizeshape)
pipeline_txt = StringIO()
pipeline.savetxt(pipeline_txt)
module_names = json.dumps([SaveImages.module_name])
message = [
zmq.Frame(self.session_id),
zmq.Frame(),
zmq.Frame(CLEAN_PIPELINE_REQ_1),
zmq.Frame(pipeline_txt.getvalue()),
zmq.Frame(module_names)
]
self.socket.send_multipart(message)
message = self.socket.recv_multipart()
self.assertEqual(message.pop(0), self.session_id)
self.assertEqual(message.pop(0), "")
self.assertEqual(message.pop(0), CLEAN_PIPELINE_REPLY_1)
pipeline_txt = message.pop(0)
pipeline = cpp.Pipeline()
pipeline.loadtxt(StringIO(pipeline_txt))
self.assertEqual(len(pipeline.modules()), 3)
self.assertIsInstance(pipeline.modules()[0], LoadImages)
self.assertIsInstance(pipeline.modules()[1], IdentifyPrimaryObjects)
self.assertIsInstance(pipeline.modules()[2], MeasureObjectSizeShape)
def test_02_03_clean_pipeline(self):
pipeline = cpp.Pipeline()
load_images = LoadImages()
load_images.module_num = 1
load_images.add_imagecb()
load_images.images[0].channels[0].image_name.value = "Foo"
load_images.images[1].channels[0].image_name.value = "Bar"
pipeline.add_module(load_images)
identify = IdentifyPrimaryObjects()
identify.module_num = 2
identify.image_name.value = "Foo"
identify.object_name.value = "dizzy"
pipeline.add_module(identify)
saveimages = SaveImages()
saveimages.module_num = 3
saveimages.image_name.value = "Foo"
pipeline.add_module(saveimages)
measureobjectsizeshape = MeasureObjectSizeShape()
measureobjectsizeshape.module_num = 4
measureobjectsizeshape.object_groups[0].name.value = "dizzy"
pipeline.add_module(measureobjectsizeshape)
pipeline_txt = StringIO()
pipeline.savetxt(pipeline_txt)
module_names = json.dumps([SaveImages.module_name])
message = [
zmq.Frame(self.session_id),
zmq.Frame(),
zmq.Frame(CLEAN_PIPELINE_REQ_1),
zmq.Frame(pipeline_txt.getvalue()),
zmq.Frame(module_names),
]
self.socket.send_multipart(message)
message = self.socket.recv_multipart()
self.assertEqual(message.pop(0), self.session_id)
self.assertEqual(message.pop(0), "")
self.assertEqual(message.pop(0), CLEAN_PIPELINE_REPLY_1)
pipeline_txt = message.pop(0)
pipeline = cpp.Pipeline()
pipeline.loadtxt(StringIO(pipeline_txt))
self.assertEqual(len(pipeline.modules()), 3)
self.assertIsInstance(pipeline.modules()[0], LoadImages)
self.assertIsInstance(pipeline.modules()[1], IdentifyPrimaryObjects)
self.assertIsInstance(pipeline.modules()[2], MeasureObjectSizeShape)
def test_04_02_bad_cellprofiler(self):
pipeline = cpp.Pipeline()
load_images = LoadImages()
load_images.module_num = 1
load_images.images[0].channels[0].image_name.value = "Foo"
pipeline.add_module(load_images)
identify = IdentifyPrimaryObjects()
identify.module_num = 2
identify.x_name.value = "Foo"
identify.y_name.value = "dizzy"
identify.threshold.threshold_scope.value = TS_GLOBAL
identify.threshold.global_operation.value = TM_MANUAL
identify.threshold.manual_threshold.value = .5
identify.exclude_size.value = False
pipeline.add_module(identify)
pipeline_txt = StringIO()
pipeline.savetxt(pipeline_txt)
image = np.zeros((11, 17))
image[2:-2, 2:-2] = 1
# Get the strides wrong (I broke it accidentally this way before...)
# And there's more wrong in this one.
image_metadata = [[
"Foo",
[["Y", image.shape[0], image.strides[0]],
["X", image.shape[1], image.strides[1]]]
]]
message = [
zmq.Frame(self.session_id),
zmq.Frame(),
zmq.Frame(RUN_GROUP_REQ_1),
zmq.Frame(pipeline_txt.getvalue()),
zmq.Frame(json.dumps(image_metadata)),
zmq.Frame(image)
]
self.socket.send_multipart(message)
response = self.socket.recv_multipart()
self.assertEqual(response.pop(0), self.session_id)
self.assertEqual(response.pop(0), "")
self.assertEqual(response.pop(0), CELLPROFILER_EXCEPTION_1)
def execute_merge_files(self, mm):
input_files = []
output_fd, output_file = tempfile.mkstemp(".mat")
pipeline = cpp.Pipeline()
li = LoadImages()
li.module_num = 1
pipeline.add_module(li)
for m in mm:
input_fd, input_file = tempfile.mkstemp(".mat")
pipeline.save_measurements(input_file, m)
input_files.append((input_fd, input_file))
M.MergeOutputFiles.merge_files(output_file, [x[1] for x in input_files])
m = cpmeas.load_measurements(output_file)
os.close(output_fd)
os.remove(output_file)
for fd, filename in input_files:
os.close(fd)
os.remove(filename)
return m
def test_04_02_bad_cellprofiler(self):
pipeline = cpp.Pipeline()
load_images = LoadImages()
load_images.module_num = 1
load_images.images[0].channels[0].image_name.value = "Foo"
pipeline.add_module(load_images)
identify = IdentifyPrimaryObjects()
identify.module_num = 2
identify.x_name.value = "Foo"
identify.y_name.value = "dizzy"
identify.threshold.threshold_scope.value = TS_GLOBAL
identify.threshold.global_operation.value = TM_MANUAL
identify.threshold.manual_threshold.value = .5
identify.exclude_size.value = False
pipeline.add_module(identify)
pipeline_txt = StringIO()
pipeline.savetxt(pipeline_txt)
image = np.zeros((11, 17))
image[2:-2, 2:-2] = 1
# Get the strides wrong (I broke it accidentally this way before...)
# And there's more wrong in this one.
image_metadata = [
["Foo",
[["Y", image.shape[0], image.strides[0]],
["X", image.shape[1], image.strides[1]]]]]
message = [
zmq.Frame(self.session_id),
zmq.Frame(),
zmq.Frame(RUN_GROUP_REQ_1),
zmq.Frame(pipeline_txt.getvalue()),
zmq.Frame(json.dumps(image_metadata)),
zmq.Frame(image)]
self.socket.send_multipart(message)
response = self.socket.recv_multipart()
self.assertEqual(response.pop(0), self.session_id)
self.assertEqual(response.pop(0), "")
self.assertEqual(response.pop(0), CELLPROFILER_EXCEPTION_1)
def test_03_03_run_missing_measurement(self):
# Regression test of knime-bridge issue #6
#
# Missing measurement causes exception
#
pipeline = cpp.Pipeline()
load_images = LoadImages()
load_images.module_num = 1
load_images.images[0].channels[0].image_name.value = "Foo"
pipeline.add_module(load_images)
identify = IdentifyPrimaryObjects()
identify.module_num = 2
identify.use_advanced.value = True
identify.x_name.value = "Foo"
identify.y_name.value = "dizzy"
identify.threshold.threshold_scope.value = TS_GLOBAL
identify.threshold.global_operation.value = TM_MANUAL
identify.threshold.manual_threshold.value = .5
identify.exclude_size.value = False
pipeline.add_module(identify)
flag_module = FlagImage()
flag_module.module_num = 3
flag = flag_module.flags[0]
flag.wants_skip.value = True
criterion = flag.measurement_settings[0]
criterion.source_choice.value = S_IMAGE
criterion.measurement.value = "Count_dizzy"
criterion.wants_minimum.value = True
criterion.minimum_value.value = 1000
pipeline.add_module(flag_module)
measureobjectsizeshape = MeasureObjectSizeShape()
measureobjectsizeshape.module_num = 4
measureobjectsizeshape.object_groups[0].name.value = "dizzy"
pipeline.add_module(measureobjectsizeshape)
pipeline_txt = StringIO()
pipeline.savetxt(pipeline_txt)
image = np.zeros((11, 17))
image[2:-2, 2:-2] = 1
image_metadata = [[
"Foo",
[["Y", image.shape[0], image.strides[0] / 8],
["X", image.shape[1], image.strides[1] / 8]]
]]
message = [
zmq.Frame(self.session_id),
zmq.Frame(),
zmq.Frame(RUN_REQ_1),
zmq.Frame(pipeline_txt.getvalue()),
zmq.Frame(json.dumps(image_metadata)),
zmq.Frame(image)
]
self.socket.send_multipart(message)
response = self.socket.recv_multipart()
self.assertEqual(response.pop(0), self.session_id)
self.assertEqual(response.pop(0), "")
self.assertEqual(response.pop(0), RUN_REPLY_1)
metadata = json.loads(response.pop(0))
data = response.pop(0)
measurements = self.decode_measurements(metadata, data)
self.assertEqual(measurements[cpmeas.IMAGE]["Count_dizzy"][0], 1)
self.assertEqual(measurements["dizzy"]["Location_Center_Y"][0], 5)
self.assertEqual(len(measurements["dizzy"]["AreaShape_Area"]), 0)
def test_03_03_run_missing_measurement(self):
# Regression test of knime-bridge issue #6
#
# Missing measurement causes exception
#
pipeline = cpp.Pipeline()
load_images = LoadImages()
load_images.module_num = 1
load_images.images[0].channels[0].image_name.value = "Foo"
pipeline.add_module(load_images)
identify = IdentifyPrimaryObjects()
identify.module_num = 2
identify.use_advanced.value = True
identify.x_name.value = "Foo"
identify.y_name.value = "dizzy"
identify.threshold.threshold_scope.value = TS_GLOBAL
identify.threshold.global_operation.value = TM_MANUAL
identify.threshold.manual_threshold.value = .5
identify.exclude_size.value = False
pipeline.add_module(identify)
flag_module = FlagImage()
flag_module.module_num = 3
flag = flag_module.flags[0]
flag.wants_skip.value = True
criterion = flag.measurement_settings[0]
criterion.source_choice.value = S_IMAGE
criterion.measurement.value = "Count_dizzy"
criterion.wants_minimum.value = True
criterion.minimum_value.value = 1000
pipeline.add_module(flag_module)
measureobjectsizeshape = MeasureObjectSizeShape()
measureobjectsizeshape.module_num = 4
measureobjectsizeshape.object_groups[0].name.value = "dizzy"
pipeline.add_module(measureobjectsizeshape)
pipeline_txt = StringIO()
pipeline.savetxt(pipeline_txt)
image = np.zeros((11, 17))
image[2:-2, 2:-2] = 1
image_metadata = [
["Foo",
[["Y", image.shape[0], image.strides[0] / 8],
["X", image.shape[1], image.strides[1] / 8]]]]
message = [
zmq.Frame(self.session_id),
zmq.Frame(),
zmq.Frame(RUN_REQ_1),
zmq.Frame(pipeline_txt.getvalue()),
zmq.Frame(json.dumps(image_metadata)),
zmq.Frame(image)]
self.socket.send_multipart(message)
response = self.socket.recv_multipart()
self.assertEqual(response.pop(0), self.session_id)
self.assertEqual(response.pop(0), "")
self.assertEqual(response.pop(0), RUN_REPLY_1)
metadata = json.loads(response.pop(0))
data = response.pop(0)
measurements = self.decode_measurements(metadata, data)
self.assertEqual(measurements[cpmeas.IMAGE]["Count_dizzy"][0], 1)
self.assertEqual(measurements["dizzy"]["Location_Center_Y"][0], 5)
self.assertEqual(len(measurements["dizzy"]["AreaShape_Area"]), 0)