def setUp(self):
context = zmq.Context.instance()
self.notify_addr = "inproc://" + uuid.uuid4().hex
self.socket_addr = "inproc://" + uuid.uuid4().hex
self.kill_pub = context.socket(zmq.PUB)
self.kill_pub.bind(self.notify_addr)
self.server = KnimeBridgeServer(context, self.socket_addr,
self.notify_addr, NOTIFY_STOP)
self.server.start()
self.session_id = uuid.uuid4().hex
self.socket = context.socket(zmq.REQ)
self.socket.connect(self.socket_addr)
def setUp(self):
context = zmq.Context.instance()
self.notify_addr = "inproc://" + uuid.uuid4().hex
self.socket_addr = "inproc://" + uuid.uuid4().hex
self.kill_pub = context.socket(zmq.PUB)
self.kill_pub.bind(self.notify_addr)
self.server = KnimeBridgeServer(context, self.socket_addr, self.notify_addr, NOTIFY_STOP)
self.server.start()
self.session_id = uuid.uuid4().hex
self.socket = context.socket(zmq.REQ)
self.socket.connect(self.socket_addr)
def main():
#
# For OS/X set up the UI elements that users expect from
# an app.
#
if sys.platform == "darwin":
import os.path
icon_path = pkg_resources.resource_filename(
"cellprofiler", os.path.join("data", "icons", "CellProfiler.png"))
os.environ["APP_NAME_%d" % os.getpid()] = "CellProfilerWorker"
os.environ["APP_ICON_%d" % os.getpid()] = icon_path
# Start the JVM
from cellprofiler_core.utilities.java import start_java, stop_java
start_java()
deadman_start_socket = the_zmq_context.socket(zmq.PAIR)
deadman_start_socket.bind(DEADMAN_START_ADDR)
# Start the deadman switch thread.
start_daemon_thread(target=exit_on_stdin_close, name="exit_on_stdin_close")
deadman_start_socket.recv()
deadman_start_socket.close()
from cellprofiler.knime_bridge import KnimeBridgeServer
with Worker(work_announce_address) as worker:
worker_thread = threading.Thread(target=worker.run,
name="WorkerThread")
worker_thread.setDaemon(True)
worker_thread.start()
with KnimeBridgeServer(the_zmq_context, knime_bridge_address,
NOTIFY_ADDR, NOTIFY_STOP):
worker_thread.join()
#
# Shutdown - need to handle some global cleanup here
#
try:
stop_java()
except:
logging.warning("Failed to stop the JVM", exc_info=True)
def main():
#
# For OS/X set up the UI elements that users expect from
# an app.
#
if sys.platform == "darwin":
from cellprofiler.icons import get_builtin_images_path
icon_path = os.path.join(get_builtin_images_path(), "artwork/CellProfilerIcon.png")
os.environ["APP_NAME_%d" % os.getpid()] = "CellProfilerWorker"
os.environ["APP_ICON_%d" % os.getpid()] = icon_path
# Start the JVM
from cellprofiler.utilities.cpjvm import cp_start_vm, cp_stop_vm
cp_start_vm()
deadman_start_socket = the_zmq_context.socket(zmq.PAIR)
deadman_start_socket.bind(DEADMAN_START_ADDR)
# Start the deadman switch thread.
start_daemon_thread(target=exit_on_stdin_close,
name="exit_on_stdin_close")
deadman_start_socket.recv()
deadman_start_socket.close()
from cellprofiler.knime_bridge import KnimeBridgeServer
with AnalysisWorker(work_announce_address) as worker:
worker_thread = threading.Thread(target=worker.run,
name="WorkerThread")
worker_thread.setDaemon(True)
worker_thread.start()
with KnimeBridgeServer(the_zmq_context,
knime_bridge_address,
NOTIFY_ADDR, NOTIFY_STOP):
worker_thread.join()
#
# Shutdown - need to handle some global cleanup here
#
try:
cp_stop_vm()
except:
logger.warn("Failed to stop the JVM", exc_info=1)
class TestKnimeBridge(unittest.TestCase):
def setUp(self):
context = zmq.Context.instance()
self.notify_addr = "inproc://" + uuid.uuid4().hex
self.socket_addr = "inproc://" + uuid.uuid4().hex
self.kill_pub = context.socket(zmq.PUB)
self.kill_pub.bind(self.notify_addr)
self.server = KnimeBridgeServer(context, self.socket_addr,
self.notify_addr, NOTIFY_STOP)
self.server.start()
self.session_id = uuid.uuid4().hex
self.socket = context.socket(zmq.REQ)
self.socket.connect(self.socket_addr)
def tearDown(self):
self.kill_pub.send(NOTIFY_STOP)
self.server.join()
self.kill_pub.close()
self.socket.close()
def test_01_01_do_nothing(self):
# test KB thread lifecycle
pass
def test_01_02_connect(self):
message = [
zmq.Frame(self.session_id),
zmq.Frame(),
zmq.Frame(CONNECT_REQ_1)
]
self.socket.send_multipart(message)
reply = self.socket.recv_multipart()
self.assertEqual(reply.pop(0), self.session_id)
self.assertEqual(reply.pop(0), "")
self.assertEqual(reply.pop(0), CONNECT_REPLY_1)
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_02_02_bad_pipeline(self):
message = [
zmq.Frame(self.session_id),
zmq.Frame(),
zmq.Frame(PIPELINE_INFO_REQ_1),
zmq.Frame("Freckles is a good dog but a bad pipeline")
]
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_EXCEPTION_1)
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_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_03_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...)
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_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_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_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 decode_measurements(self, metadata, data):
offset = 0
ddata = {}
self.assertEqual(len(metadata), 4)
for object_name, md in metadata[0]:
items = {}
ddata[object_name] = items
for feature, count in md:
next_offset = offset + count * 8
items[feature] = np.frombuffer(data[offset:next_offset],
np.float64)
offset = next_offset
for object_name, md in metadata[1]:
if object_name not in ddata:
items = {}
ddata[object_name] = items
else:
items = ddata[object_name]
for feature, count in md:
next_offset = offset + count * 4
items[feature] = np.frombuffer(data[offset:next_offset],
np.float32)
offset = next_offset
for object_name, md in metadata[2]:
if object_name not in ddata:
items = {}
ddata[object_name] = items
else:
items = ddata[object_name]
for feature, count in md:
next_offset = offset + count * 4
items[feature] = np.frombuffer(data[offset:next_offset],
np.int32)
offset = next_offset
return ddata
class TestKnimeBridge(unittest.TestCase):
def setUp(self):
context = zmq.Context.instance()
self.notify_addr = "inproc://" + uuid.uuid4().hex
self.socket_addr = "inproc://" + uuid.uuid4().hex
self.kill_pub = context.socket(zmq.PUB)
self.kill_pub.bind(self.notify_addr)
self.server = KnimeBridgeServer(
context, self.socket_addr, self.notify_addr, NOTIFY_STOP)
self.server.start()
self.session_id = uuid.uuid4().hex
self.socket = context.socket(zmq.REQ)
self.socket.connect(self.socket_addr)
def tearDown(self):
self.kill_pub.send(NOTIFY_STOP)
self.server.join()
self.kill_pub.close()
self.socket.close()
def test_01_01_do_nothing(self):
# test KB thread lifecycle
pass
def test_01_02_connect(self):
message = [
zmq.Frame(self.session_id),
zmq.Frame(),
zmq.Frame(CONNECT_REQ_1)]
self.socket.send_multipart(message)
reply = self.socket.recv_multipart()
self.assertEqual(reply.pop(0), self.session_id)
self.assertEqual(reply.pop(0), "")
self.assertEqual(reply.pop(0), CONNECT_REPLY_1)
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_02_02_bad_pipeline(self):
message = [zmq.Frame(self.session_id),
zmq.Frame(),
zmq.Frame(PIPELINE_INFO_REQ_1),
zmq.Frame("Freckles is a good dog but a bad pipeline")]
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_EXCEPTION_1)
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_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_03_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...)
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_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_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_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 decode_measurements(self, metadata, data):
offset = 0
ddata = {}
self.assertEqual(len(metadata), 4)
for object_name, md in metadata[0]:
items = {}
ddata[object_name] = items
for feature, count in md:
next_offset = offset + count * 8
items[feature] = np.frombuffer(
data[offset:next_offset], np.float64)
offset = next_offset
for object_name, md in metadata[1]:
if object_name not in ddata:
items = {}
ddata[object_name] = items
else:
items = ddata[object_name]
for feature, count in md:
next_offset = offset + count * 4
items[feature] = np.frombuffer(
data[offset:next_offset], np.float32)
offset = next_offset
for object_name, md in metadata[2]:
if object_name not in ddata:
items = {}
ddata[object_name] = items
else:
items = ddata[object_name]
for feature, count in md:
next_offset = offset + count * 4
items[feature] = np.frombuffer(
data[offset:next_offset], np.int32)
offset = next_offset
return ddata
def main():
#
# For Windows build with Ilastik, look for site-packages
# in order to find Ilastik sources.
#
if hasattr(sys, 'frozen') and sys.platform == "win32":
root = os.path.split(sys.argv[0])[0]
if len(root) == 0:
root = os.curdir
root = os.path.abspath(root)
site_packages = os.path.join(root, 'site-packages').encode('utf-8')
if os.path.exists(site_packages) and os.path.isdir(site_packages):
import site
site.addsitedir(site_packages)
#
# For OS/X set up the UI elements that users expect from
# an app.
#
if sys.platform == "darwin":
from cellprofiler.icons import get_builtin_images_path
icon_path = os.path.join(get_builtin_images_path(),
"artwork/CellProfilerIcon.png")
os.environ["APP_NAME_%d" % os.getpid()] = "CellProfilerWorker"
os.environ["APP_ICON_%d" % os.getpid()] = icon_path
# Start the JVM
from cellprofiler.utilities.cpjvm import cp_start_vm, cp_stop_vm
cp_start_vm()
deadman_start_socket = the_zmq_context.socket(zmq.PAIR)
deadman_start_socket.bind(DEADMAN_START_ADDR)
# Start the deadman switch thread.
start_daemon_thread(target=exit_on_stdin_close, name="exit_on_stdin_close")
deadman_start_socket.recv()
deadman_start_socket.close()
# Limit Ilastik to one job thread.
try:
from ilastik.core.jobMachine import GLOBAL_WM
try:
GLOBAL_WM.set_thread_count(1)
except:
GLOBAL_WM.setThreadCount(1)
except:
pass
from cellprofiler.knime_bridge import KnimeBridgeServer
with AnalysisWorker(work_announce_address) as worker:
worker_thread = threading.Thread(target=worker.run,
name="WorkerThread")
worker_thread.setDaemon(True)
worker_thread.start()
with KnimeBridgeServer(the_zmq_context, knime_bridge_address,
NOTIFY_ADDR, NOTIFY_STOP):
enter_run_loop()
worker_thread.join()
#
# Shutdown - need to handle some global cleanup here
#
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.stopWorkers()
except:
logger.warn("Failed to stop Ilastik")
try:
cp_stop_vm()
except:
logger.warn("Failed to stop the JVM", exc_info=1)
