def test_03_08_a_sad_moment(self):
#
# Run using the good pipeline, but change one of the URLs so
# an exception is thrown.
#
self.awthread = self.AWThread(self.announce_addr)
self.awthread.start()
self.set_work_socket()
self.awthread.ex(self.awthread.aw.do_job,
cpanalysis.WorkReply(
image_set_numbers = [2, 3],
worker_runs_post_group = False,
wants_dictionary = False))
#
# The worker should ask for the pipeline and preferences next.
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.PipelinePreferencesRequest)
self.assertEqual(req.analysis_id, self.analysis_id)
input_dir = os.path.join(example_images_directory(), "ExampleSBSImages")
cpprefs.set_default_image_directory(input_dir)
preferences = {cpprefs.DEFAULT_IMAGE_DIRECTORY:
cpprefs.config_read(cpprefs.DEFAULT_IMAGE_DIRECTORY) }
rep = cpanalysis.Reply(
pipeline_blob = np.array(GOOD_PIPELINE),
preferences = preferences)
req.reply(rep)
#
# The worker asks for the initial measurements.
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.InitialMeasurementsRequest)
self.assertEqual(req.analysis_id, self.analysis_id)
m = get_measurements_for_good_pipeline(nimages=3)
m[cpmeas.IMAGE, M_IMAGE_SET, 2] = np.zeros(100, np.uint8)
try:
req.reply(cpanalysis.Reply(buf = m.file_contents()))
finally:
m.close()
#
# Next, the worker asks for the shared dictionary
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.SharedDictionaryRequest)
shared_dictionaries = [{ ("foo%d" % i):"bar%d" % i} for i in range(1,8)]
rep = cpanalysis.SharedDictionaryReply(
dictionaries = shared_dictionaries)
req.reply(rep)
#
# The worker should choke somewhere in NamesAndTypes, but we
# tell the worker to skip the rest of the imageset.
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.ExceptionReport)
req.reply(cpanalysis.ExceptionPleaseDebugReply(disposition = ED_SKIP))
#
# The worker should send ImageSetSuccess for image set 2 anyway.
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.ImageSetSuccess)
self.assertEqual(req.image_set_number, 2)
req.reply(cpanalysis.Ack())
#
# And then it tells us about image set 3
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.ImageSetSuccess)
self.assertEqual(req.image_set_number, 3)
req.reply(cpanalysis.Ack())
#
# The worker should then report the measurements for both 2 and 3
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.MeasurementsReport)
self.assertSequenceEqual(req.image_set_numbers, [2, 3])
m = cpmeas.load_measurements_from_buffer(req.buf)
#
# Spot check for some expected stuff
#
self.assertTrue(m.has_feature(cpmeas.IMAGE, C_COUNT+"_Nuclei"))
self.assertTrue(m.has_feature("Nuclei", M_LOCATION_CENTER_X))
self.assertTrue(m.has_feature("Nuclei", "AreaShape_Area"))
#
# The count for the skipped image should be None
#
count = m[cpmeas.IMAGE, C_COUNT + "_Nuclei", 2]
self.assertIsNone(count)
count = m[cpmeas.IMAGE, C_COUNT + "_Nuclei", 3]
center_x = m["Nuclei", M_LOCATION_CENTER_X, 3]
self.assertEqual(count, len(center_x))
req.reply(cpanalysis.Ack())
self.awthread.ecute()
def test_03_06_the_happy_path_chapter_2(self):
#
# Give the worker image sets # 2 and 3 and tell it to run post_group
#
self.awthread = self.AWThread(self.announce_addr)
self.awthread.start()
self.set_work_socket()
self.awthread.ex(self.awthread.aw.do_job,
cpanalysis.WorkReply(
image_set_numbers = [2, 3],
worker_runs_post_group = True,
wants_dictionary = False))
#
# The worker should ask for the pipeline and preferences next.
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.PipelinePreferencesRequest)
self.assertEqual(req.analysis_id, self.analysis_id)
input_dir = os.path.join(example_images_directory(), "ExampleSBSImages")
cpprefs.set_default_image_directory(input_dir)
preferences = {cpprefs.DEFAULT_IMAGE_DIRECTORY:
cpprefs.config_read(cpprefs.DEFAULT_IMAGE_DIRECTORY) }
rep = cpanalysis.Reply(
pipeline_blob = np.array(DISPLAY_PIPELINE),
preferences = preferences)
req.reply(rep)
#
# The worker asks for the initial measurements.
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.InitialMeasurementsRequest)
self.assertEqual(req.analysis_id, self.analysis_id)
m = get_measurements_for_good_pipeline(nimages=3)
try:
req.reply(cpanalysis.Reply(buf = m.file_contents()))
finally:
m.close()
#
# In group mode, the worker issues a display request and constructs
# its own dictonaries
#
for image_number in (2, 3):
#
# The worker sends a display request for FlipAndRotate
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.DisplayRequest)
req.reply(cpanalysis.Ack())
#
# The worker sends ImageSetSuccess.
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.ImageSetSuccess)
self.assertEqual(req.image_set_number, image_number)
req.reply(cpanalysis.Ack())
#
# The worker sends a DisplayPostGroup request for FlipAndRotate
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.DisplayPostGroupRequest)
self.assertEqual(req.image_set_number, 3)
req.reply(cpanalysis.Ack())
#
# The worker sends a measurement report for image sets 2 and 3
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.MeasurementsReport)
self.assertSequenceEqual(req.image_set_numbers, [2, 3])
m = cpmeas.load_measurements_from_buffer(req.buf)
#
# Spot check for some expected stuff
#
self.assertTrue(m.has_feature(cpmeas.IMAGE, C_COUNT+"_Nuclei"))
self.assertTrue(m.has_feature("Nuclei", M_LOCATION_CENTER_X))
self.assertTrue(m.has_feature("Nuclei", "AreaShape_Area"))
req.reply(cpanalysis.Ack())
self.awthread.ecute()
def test_03_07_a_sad_ending(self):
#
# Run using the bad pipeline and lead the analysis worker
# through debug post-mortem
#
self.awthread = self.AWThread(self.announce_addr)
self.awthread.start()
self.set_work_socket()
self.awthread.ex(self.awthread.aw.do_job,
cpanalysis.WorkReply(
image_set_numbers = [2],
worker_runs_post_group = False,
wants_dictionary = False))
#
# The worker should ask for the pipeline and preferences next.
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.PipelinePreferencesRequest)
self.assertEqual(req.analysis_id, self.analysis_id)
input_dir = os.path.join(example_images_directory(), "ExampleSBSImages")
cpprefs.set_default_image_directory(input_dir)
preferences = {cpprefs.DEFAULT_IMAGE_DIRECTORY:
cpprefs.config_read(cpprefs.DEFAULT_IMAGE_DIRECTORY) }
rep = cpanalysis.Reply(
pipeline_blob = np.array(BAD_PIPELINE),
preferences = preferences)
req.reply(rep)
#
# The worker asks for the initial measurements.
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.InitialMeasurementsRequest)
self.assertEqual(req.analysis_id, self.analysis_id)
m = get_measurements_for_good_pipeline(nimages=2)
try:
req.reply(cpanalysis.Reply(buf = m.file_contents()))
finally:
m.close()
#
# Next, the worker asks for the shared dictionary
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.SharedDictionaryRequest)
shared_dictionaries = [{ ("foo%d" % i):"bar%d" % i} for i in range(1,8)]
rep = cpanalysis.SharedDictionaryReply(
dictionaries = shared_dictionaries)
req.reply(rep)
#
# The worker should choke somewhere in NamesAndTypes
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.ExceptionReport)
password = "******"
req.reply(cpanalysis.ExceptionPleaseDebugReply(
disposition='DEBUG',
verification_hash = hashlib.sha1(password).hexdigest()))
#
# Next, the worker sends DebugWaiting once it binds to a port
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.DebugWaiting)
handle = None
telnet_socket = socket.socket(socket.AF_INET,
proto = socket.IPPROTO_TCP)
telnet_socket.connect(("127.0.0.1", req.port))
try:
req.reply(cpanalysis.Ack())
#
# Should say, "Verification: ", but it could change...
#
prompt = telnet_socket.recv(20)
telnet_socket.send("corned beef\n")
pdb = telnet_socket.recv(4000)
telnet_socket.send("exit\n")
finally:
telnet_socket.close()
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.DebugComplete)
req.reply(cpanalysis.ExceptionPleaseDebugReply(disposition = ED_STOP))
def test_03_05_the_happy_path_chapter_1(self):
#
# Run the worker clear through to the end
# for the first imageset
#
self.awthread = self.AWThread(self.announce_addr)
self.awthread.start()
self.set_work_socket()
self.awthread.ex(self.awthread.aw.do_job,
cpanalysis.WorkReply(
image_set_numbers = [1],
worker_runs_post_group = False,
wants_dictionary = True))
#
# The worker should ask for the pipeline and preferences next.
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.PipelinePreferencesRequest)
self.assertEqual(req.analysis_id, self.analysis_id)
input_dir = os.path.join(example_images_directory(), "ExampleSBSImages")
cpprefs.set_default_image_directory(input_dir)
preferences = {cpprefs.DEFAULT_IMAGE_DIRECTORY:
cpprefs.config_read(cpprefs.DEFAULT_IMAGE_DIRECTORY) }
rep = cpanalysis.Reply(
pipeline_blob = np.array(DISPLAY_PIPELINE),
preferences = preferences)
req.reply(rep)
#
# The worker asks for the initial measurements.
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.InitialMeasurementsRequest)
self.assertEqual(req.analysis_id, self.analysis_id)
m = get_measurements_for_good_pipeline()
try:
req.reply(cpanalysis.Reply(buf = m.file_contents()))
finally:
m.close()
#
# Next, the worker asks for the shared dictionary
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.SharedDictionaryRequest)
shared_dictionaries = [{ ("foo%d" % i):"bar%d" % i} for i in range(1,8)]
rep = cpanalysis.SharedDictionaryReply(
dictionaries = shared_dictionaries)
req.reply(rep)
#
# The worker sends a display request for FlipAndRotate
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.DisplayRequest)
self.assertEqual(req.image_set_number, 1)
d = req.display_data_dict
# Possibly, this will break if someone edits FlipAndRotate. Sorry.
self.assertItemsEqual(d.keys(),
['vmax', 'output_image_pixel_data',
'image_pixel_data', 'vmin'])
self.assertIsInstance(d['output_image_pixel_data'], np.ndarray)
req.reply(cpanalysis.Ack())
#
# The worker sends ImageSetSuccessWithDictionary.
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.ImageSetSuccessWithDictionary)
self.assertEqual(req.image_set_number, 1)
for expected, actual in zip(shared_dictionaries, req.shared_dicts):
self.assertDictEqual(expected, actual)
req.reply(cpanalysis.Ack())
#
# The worker sends the measurement report
#
req = self.awthread.recv(self.work_socket)
self.assertIsInstance(req, cpanalysis.MeasurementsReport)
self.assertSequenceEqual(req.image_set_numbers, [1])
m = cpmeas.load_measurements_from_buffer(req.buf)
#
# Spot check for some expected stuff
#
self.assertTrue(m.has_feature(cpmeas.IMAGE, C_COUNT+"_Nuclei"))
self.assertTrue(m.has_feature("Nuclei", M_LOCATION_CENTER_X))
self.assertTrue(m.has_feature("Nuclei", "AreaShape_Area"))
req.reply(cpanalysis.Ack())
self.awthread.ecute()
