def test_02_01_load_one(self): folder = self.test_folder file_name = self.test_filename cpprefs.set_default_image_directory(self.test_path) workspace, module = self.make_workspace([file_name]) assert isinstance(module, L.LoadSingleImage) module.prepare_run(workspace) module.run(workspace) m = workspace.measurements self.assertTrue(isinstance(m, cpmeas.Measurements)) self.assertEqual(m.image_set_count, 1) f = m.get_all_measurements( cpmeas.IMAGE, "_".join((L.C_FILE_NAME, self.get_image_name(0)))) self.assertEqual(len(f), 1) self.assertEqual(f[0], file_name) p = m.get_all_measurements( cpmeas.IMAGE, "_".join((L.C_PATH_NAME, self.get_image_name(0)))) self.assertEqual(len(p), 1) self.assertEqual(p[0], self.test_path) s = m.get_all_measurements( cpmeas.IMAGE, "_".join((L.C_SCALING, self.get_image_name(0)))) self.assertEqual(len(s), 1) self.assertEqual(s[0], 4095) md = m.get_all_measurements( cpmeas.IMAGE, "_".join((L.C_MD5_DIGEST, self.get_image_name(0)))) self.assertEqual(len(md), 1) self.assertEqual(self.test_md5, md[0])
def test_02_01_load_one(self): path = os.path.join(example_images_directory(), "ExampleSpecklesImages") cpprefs.set_default_image_directory(path) file_name = "1-162hrh2ax2.tif" workspace, module = self.make_workspace([file_name]) assert isinstance(module, L.LoadSingleImage) module.prepare_run(workspace) module.run(workspace) m = workspace.measurements self.assertTrue(isinstance(m, cpmeas.Measurements)) self.assertEqual(m.image_set_count, 1) f = m.get_all_measurements(cpmeas.IMAGE, "_".join((L.C_FILE_NAME, self.get_image_name(0)))) self.assertEqual(len(f), 1) self.assertEqual(f[0], file_name) p = m.get_all_measurements(cpmeas.IMAGE, "_".join((L.C_PATH_NAME, self.get_image_name(0)))) self.assertEqual(len(p), 1) self.assertEqual(p[0], path) s = m.get_all_measurements(cpmeas.IMAGE, "_".join((L.C_SCALING, self.get_image_name(0)))) self.assertEqual(len(s), 1) self.assertEqual(s[0], 4095) md = m.get_all_measurements(cpmeas.IMAGE, "_".join((L.C_MD5_DIGEST, self.get_image_name(0)))) self.assertEqual(len(md), 1) md5 = hashlib.md5() image = workspace.image_set.get_image(self.get_image_name(0)) md5.update(np.ascontiguousarray(image.pixel_data).data) self.assertEqual(md5.hexdigest(), md[0])
def test_03_03_measurement_columns(self): '''Check that results of get_measurement_columns match the actual column names output''' data = 'eJztW91u2zYUph0naFqgSHexBesNd9d2iSA7SZcEQ2vPXjcPsRs0Xn8wbJgi0TEHWjQkKrU39N32GHuEXe4RJtqyJXFyJMuSJ6cSQEiH5seP5/DwHEqyWrXOWe0beCTJsFXr7HcxQfCcKKxLjf4pHFATD/dg3UAKQxqk+ilsUR3+YBFYPoDlw1P55PTgEFZk+QTEOArN1n37tHsMwJZ9vmOXovPTpiMXPIXLF4gxrF+Zm6AEdp36P+3yWjGwcknQa4VYyHQppvVNvUs7o8HspxbVLILaSt/b2D7aVv8SGebL7hTo/HyOh4hc4N+RoMK02St0jU1MdQfv9C/WzngpE3i5HXqfu3YoCHYo2eWhp563/x647UsBdnvgab/jyFjX8DXWLIVA3FeuZqPg/ckh/W34+tsAjXZtjDsOwW0J49ga21klCEfjLfjwBVBxxlsNwe0IvLx00JDtfztUVAb7ClN7SYw/DL8p4LlcR4SYEe0+T/9FcQcRcSUfrgSe7h3KUey9LejJ5Td24DDMHtKc+mX0jWPn5tnZj62IvKJ/v7NXR1y96yNGB0Qx+wvoPW99heGKPlwRtGk0vnm4MH3vCfpy+SUzLfgdoZcKmemblN3C4txnQj9cbqCuYhEGmzzIwQY2kMqoMVrKDxbFlSU58fi4JeCnxxS/7bFbNYQ36jzGyTOyJI+PvbJz4RlX2vEy6flbNF7aupfTjM/z9Et6nhaNH2U5Xnw/WlLvtOYnAHcUR7+nIJrf3wH++eFyvafoOiKVuPG0qTOkm5iNnPoo/dwV+uFyg0KdMmiZyO0nblyKmweT0n9RfjkgDiSpr+gv5Yi4uOtP9Os21VGaeSZoXl7wG03dvv1awk5fxbRT0P5oEX3fhvB9IejL5V+kJ/uPnp9//Yq+fyZ9+Xh8Xafk2U/y/snPf1Q+PF7ADnH3qUH5vvOeQtXeb5nOneAydumF8B8L/FzmdniHFMMxxOGHiWlaVGc91zjjuoYycmuSjGNx8uYbhK96/JnINX8AoKvz/HgR+y2RHyLls7h+E2THF9RAVwa1dG15vcP407q/Cto/xI3raeaDqPf7WdGvGjLOpPJBmnl6nfJB0vl8XeL/qvN+1uJEVtb7qvSTpaP/fZxpP39Jcj+2alxW9lFZm+e0909xcX/turiCgAt637RK+4xfTnEDDaL3E7Se6OVvSGVuR+uyLjzjhljX0CDF/tZlnd12XBWsZp1E7edjs9tt0TercTDXN8fluOzgwvYRnwD/uuIytRjBOvrPRiLN9b0jjIMXN35PRrFOds9a/Lxt+THHZQOXlfiS4/K4m+M+XlwV3Oznef7LcTkux+W424X7u+DixPcbXPa+N+ftf/XwBOWJJ8CfJ7isIkIGBuXfTRlSf/xxjykRqmiTr2ukM/uy6fnQhvMMQniqAk91Hg/WkM5wdzQwbDaL0b7CsCo1ndpzu7Y2reW8vRDeoPfzN/KaSKW6phijGefFtCYKX0Xgq8zj6yPFtAzE0JDZJ6k1ETsT0bWr10+2A/i88120pU8fPrh7k38B4Pcr19/+eR6Hb2OjWLgP/P/zuheCKwG/n4/9Gizm149uaD/VMavt/wXhfSus' # alternate data: 1 image, 1 object, tex scale=3, gabor angles=6 # data = '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' cpprefs.set_default_image_directory( os.path.join(example_images_directory(), "ExampleSBSImages")) fd = StringIO(zlib.decompress(base64.b64decode(data))) pipeline = cpp.Pipeline() pipeline.load(fd) module = pipeline.modules()[3] measurements = pipeline.run(image_set_end=1) for x in module.get_measurement_columns(pipeline): assert x[1] in measurements.get_feature_names( x[0] ), '%s does not match any measurement output by pipeline' % ( str(x)) for obname in measurements.get_object_names(): for m in measurements.get_feature_names(obname): if m.startswith(M.TEXTURE): assert ( obname, m, 'float' ) in module.get_measurement_columns( pipeline ), 'no entry matching %s in get_measurement_columns.' % ( (obname, m, 'float'))
def enter_batch_mode(self, workspace): '''Restore the image set list from its setting as we go into batch mode''' pipeline = workspace.pipeline assert isinstance(pipeline, cpp.Pipeline) assert not self.distributed_mode, "Distributed mode no longer supported" cpprefs.set_default_output_directory(self.custom_output_directory.value) cpprefs.set_default_image_directory(self.default_image_directory.value)
def test_03_02_pipeline_preferences(self): # # Walk the worker up through pipelines and preferences. # 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) maybe_download_example_image(["ExampleSBSImages"], "Channel1-01-A-01.tif") maybe_download_example_image(["ExampleHT29"], "AS_09125_050116030001_D03f00d0.tif") input_dir = os.path.normcase( os.path.join(example_images_directory(), "ExampleSBSImages")) output_dir = os.path.normcase( os.path.join(example_images_directory(), "ExampleHT29")) cpprefs.set_default_image_directory(input_dir) input_dir = cpprefs.get_default_image_directory() cpprefs.set_default_output_directory(output_dir) output_dir = cpprefs.get_default_output_directory() preferences = {cpprefs.DEFAULT_IMAGE_DIRECTORY: cpprefs.config_read(cpprefs.DEFAULT_IMAGE_DIRECTORY), cpprefs.DEFAULT_OUTPUT_DIRECTORY: cpprefs.config_read(cpprefs.DEFAULT_OUTPUT_DIRECTORY)} cpprefs.set_default_image_directory(example_images_directory()) cpprefs.set_default_output_directory(example_images_directory()) rep = cpanalysis.Reply( pipeline_blob = np.array(GOOD_PIPELINE), preferences = preferences) req.reply(rep) # # Get the next request so that we know the worker has # processed the preferences. # req = self.awthread.recv(self.work_socket) self.assertEqual(cpprefs.get_default_image_directory(), input_dir) self.assertEqual(cpprefs.get_default_output_directory(), output_dir) self.assertIn(self.analysis_id, self.awthread.aw.pipelines_and_preferences) pipe, prefs = self.awthread.aw.pipelines_and_preferences[ self.analysis_id] self.assertEqual(len(pipe.modules()), 7) # # Cancel and check for exit # req.reply(cpanalysis.ServerExited()) self.assertRaises(cpp.CancelledException, self.awthread.ecute)
def test_03_03_initial_measurements(self): # # Walk to the initial measurements # 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(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() try: req.reply(cpanalysis.Reply(buf=m.file_contents())) req = self.awthread.recv(self.work_socket) # # Check that they were installed # self.assertIn(self.analysis_id, self.awthread.aw.initial_measurements) cm = self.awthread.aw.initial_measurements[self.analysis_id] for object_name in m.get_object_names(): for feature_name in m.get_feature_names(object_name): self.assertTrue(cm.has_feature(object_name, feature_name)) self.assertEqual(cm[object_name, feature_name, 1], m[object_name, feature_name, 1]) # # Cancel and check for exit # req.reply(cpanalysis.ServerExited()) self.assertRaises(cpaw.CancelledException, self.awthread.ecute) finally: m.close()
def test_01_03_unicode_directory(self): old = cpprefs.get_default_image_directory() unicode_dir = u'P125 à 144 Crible Chimiothèque HBEC' unicode_dir = tempfile.mkdtemp(prefix=unicode_dir) cpprefs.set_default_image_directory(unicode_dir) self.assertEqual(cpprefs.config_read(cpprefs.DEFAULT_IMAGE_DIRECTORY), unicode_dir) self.assertEqual(cpprefs.get_default_image_directory(), unicode_dir) cpprefs.set_default_image_directory(old)
def test_03_03_initial_measurements(self): # # Walk to the initial measurements # 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(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() try: req.reply(cpanalysis.Reply(buf = m.file_contents())) req = self.awthread.recv(self.work_socket) # # Check that they were installed # self.assertIn(self.analysis_id, self.awthread.aw.initial_measurements) cm = self.awthread.aw.initial_measurements[self.analysis_id] for object_name in m.get_object_names(): for feature_name in m.get_feature_names(object_name): self.assertTrue(cm.has_feature(object_name, feature_name)) self.assertEqual(cm[object_name, feature_name, 1], m[object_name, feature_name, 1]) # # Cancel and check for exit # req.reply(cpanalysis.ServerExited()) self.assertRaises(cpaw.CancelledException, self.awthread.ecute) finally: m.close()
def test_01_06_run_pipeline(self): import cellprofiler.pipeline as cpp import cellprofiler.cpmodule as cpm import os from cellprofiler.preferences import \ set_default_image_directory, set_default_output_directory maybe_download_fly() example_fly_dir = os.path.join(self.example_dir(), "ExampleFlyImages") set_default_image_directory(example_fly_dir) output_dir = tempfile.mkdtemp() set_default_output_directory(output_dir) try: pipeline_file = os.path.join(example_fly_dir, "ExampleFlyURL.cppipe") if not os.path.exists(pipeline_file): pipeline_file = os.path.join(example_fly_dir, "ExampleFly.cp") pipeline = cpp.Pipeline() def callback(caller, event): self.assertFalse( isinstance( event, (cpp.LoadExceptionEvent, cpp.RunExceptionEvent))) pipeline.add_listener(callback) pipeline.load(pipeline_file) while True: removed_something = False for module in reversed(pipeline.modules()): self.assertTrue(isinstance(module, cpm.CPModule)) if module.module_name in ("SaveImages", "CalculateStatistics", "ExportToSpreadsheet", "ExportToDatabase"): pipeline.remove_module(module.module_num) removed_something = True break if not removed_something: break for module in pipeline.modules(): module.show_window = False m = pipeline.run(image_set_end=1) del m finally: for file_name in os.listdir(output_dir): try: os.remove(os.path.join(output_dir, file_name)) except Exception, e: print "Failed to remove %s" % os.path.join( output_dir, file_name), e traceback.print_exc() try: os.rmdir(output_dir) except: print "Failed to remove %s" % output_dir traceback.print_exc()
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_01_06_run_pipeline(self): import cellprofiler.pipeline as cpp import cellprofiler.cpmodule as cpm import os from cellprofiler.preferences import set_default_image_directory, set_default_output_directory maybe_download_fly() example_fly_dir = os.path.join(self.example_dir(), "ExampleFlyImages") set_default_image_directory(example_fly_dir) output_dir = tempfile.mkdtemp() set_default_output_directory(output_dir) try: pipeline_file = os.path.join(example_fly_dir, "ExampleFlyURL.cppipe") if not os.path.exists(pipeline_file): pipeline_file = os.path.join(example_fly_dir, "ExampleFly.cp") pipeline = cpp.Pipeline() def callback(caller, event): self.assertFalse(isinstance(event, (cpp.LoadExceptionEvent, cpp.RunExceptionEvent))) pipeline.add_listener(callback) pipeline.load(pipeline_file) while True: removed_something = False for module in reversed(pipeline.modules()): self.assertTrue(isinstance(module, cpm.CPModule)) if module.module_name in ( "SaveImages", "CalculateStatistics", "ExportToSpreadsheet", "ExportToDatabase", ): pipeline.remove_module(module.module_num) removed_something = True break if not removed_something: break for module in pipeline.modules(): module.show_window = False m = pipeline.run(image_set_end=1) del m finally: for file_name in os.listdir(output_dir): try: os.remove(os.path.join(output_dir, file_name)) except Exception, e: print "Failed to remove %s" % os.path.join(output_dir, file_name), e traceback.print_exc() try: os.rmdir(output_dir) except: print "Failed to remove %s" % output_dir traceback.print_exc()
def test_02_02_scale(self): '''Load an image twice, as scaled and unscaled''' path = os.path.join(example_images_directory(), "ExampleSpecklesImages") cpprefs.set_default_image_directory(path) file_names = ["1-162hrh2ax2.tif", "1-162hrh2ax2.tif"] workspace, module = self.make_workspace(file_names) self.assertTrue(isinstance(module, L.LoadSingleImage)) module.file_settings[0].rescale.value = False module.file_settings[1].rescale.value = True module.run(workspace) unscaled, scaled = [workspace.image_set.get_image(self.get_image_name(i)).pixel_data for i in range(2)] np.testing.assert_almost_equal(unscaled * 65535. / 4095., scaled)
def setUp(self): # # Make a temporary directory structure # cpprefs.set_headless() directory = self.directory = tempfile.mkdtemp() for i in range(3): os.mkdir(os.path.join(directory, str(i))) for j in range(3): os.mkdir(os.path.join(directory, str(i), str(j))) for k in range(3): os.mkdir(os.path.join(directory, str(i), str(j), str(k))) cpprefs.set_default_image_directory(os.path.join(self.directory, "1"))
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 enter_batch_mode(self, workspace): '''Restore the image set list from its setting as we go into batch mode''' image_set_list = workspace.image_set_list pipeline = workspace.pipeline assert isinstance(image_set_list, cpi.ImageSetList) assert isinstance(pipeline, cpp.Pipeline) if self.distributed_mode: import tempfile try: cpprefs.set_default_output_directory(tempfile.gettempdir()) cpprefs.set_default_image_directory(tempfile.gettempdir()) except: pass else: cpprefs.set_default_output_directory(self.custom_output_directory.value) cpprefs.set_default_image_directory(self.default_image_directory.value)
def setUp(self): # # Make three temporary directory structures # cpprefs.set_headless() self.directories = [tempfile.mkdtemp() for i in range(3)] for directory in self.directories: for i in range(3): os.mkdir(os.path.join(directory, str(i))) for j in range(3): os.mkdir(os.path.join(directory, str(i), str(j))) for k in range(3): os.mkdir(os.path.join(directory, str(i), str(j), str(k))) cpprefs.set_default_image_directory(os.path.join(self.directories[0], "1")) cpprefs.set_default_output_directory(os.path.join(self.directories[1], "1")) self.root_directory = os.path.join(self.directories[2], "1")
def test_03_03_measurement_columns(self): '''Check that results of get_measurement_columns match the actual column names output''' data = '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' # alternate data: 1 image, 1 object, tex scale=3, gabor angles=6 # data = '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' cpprefs.set_default_image_directory(os.path.join(example_images_directory(),"ExampleSBSImages")) fd = StringIO(zlib.decompress(base64.b64decode(data))) pipeline = cpp.Pipeline() pipeline.load(fd) module = pipeline.modules()[3] measurements = pipeline.run(image_set_end=1) for x in module.get_measurement_columns(pipeline): assert x[1] in measurements.get_feature_names(x[0]), '%s does not match any measurement output by pipeline'%(str(x)) for obname in measurements.get_object_names(): for m in measurements.get_feature_names(obname): if m.startswith(M.TEXTURE): assert (obname, m, 'float') in module.get_measurement_columns(pipeline), 'no entry matching %s in get_measurement_columns.'%((obname, m, 'float'))
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 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 enter_batch_mode(self, workspace): '''Restore the image set list from its setting as we go into batch mode''' pipeline = workspace.pipeline assert isinstance(pipeline, cpp.Pipeline) assert not self.distributed_mode, "Distributed mode no longer supported" default_output_directory = self.custom_output_directory.value default_image_directory = self.default_image_directory.value if os.path.isdir(default_output_directory): cpprefs.set_default_output_directory(default_output_directory) else: logger.info( "Batch file default output directory, \"%s\", does not exist" % default_output_directory) if os.path.isdir(default_image_directory): cpprefs.set_default_image_directory(default_image_directory) else: logger.info( "Batch file default input directory \"%s\", does not exist" % default_image_directory)
def check_preferences(self): """Return True if preferences are OK (e.g. directories exist)""" path = self.__image_edit_box.Value if not os.path.isdir(path): if ( wx.MessageBox( ( 'The Default Input Folder is "%s", but ' "the directory does not exist. Do you want to " "create it?" ) % path, "Warning, cannot run pipeline", style=wx.YES_NO, ) == wx.NO ): return False, "Image directory does not exist" os.makedirs(path) cpprefs.set_default_image_directory(path) path = self.__output_edit_box.Value if not os.path.isdir(path): if ( wx.MessageBox( ( 'The Default Output Folder is "%s", but ' "the directory does not exist. Do you want to " "create it?" ) % path, "Warning, cannot run pipeline", style=wx.YES_NO, ) == wx.NO ): return False, "Output directory does not exist" os.makedirs(path) cpprefs.set_default_output_directory(path) return True, "OK"
def check_preferences(self): '''Return True if preferences are OK (e.g. directories exist)''' path = self.__image_edit_box.Value if not os.path.isdir(path): if wx.MessageBox(('The Default Input Folder is "%s", but ' 'the directory does not exist. Do you want to ' 'create it?') % path, "Warning, cannot run pipeline", style=wx.YES_NO) == wx.NO: return False, "Image directory does not exist" os.makedirs(path) cpprefs.set_default_image_directory(path) path = self.__output_edit_box.Value if not os.path.isdir(path): if wx.MessageBox(('The Default Output Folder is "%s", but ' 'the directory does not exist. Do you want to ' 'create it?') % path, "Warning, cannot run pipeline", style=wx.YES_NO) == wx.NO: return False, "Output directory does not exist" os.makedirs(path) cpprefs.set_default_output_directory(path) return True, "OK"
def main(args): '''Run CellProfiler args - command-line arguments, e.g. sys.argv ''' if any([arg.startswith('--work-announce') for arg in args]): # # Go headless ASAP # import cellprofiler.preferences as cpprefs cpprefs.set_headless() import cellprofiler.analysis_worker cellprofiler.analysis_worker.main() sys.exit(0) options, args = parse_args(args) set_log_level(options) if not hasattr(sys, "frozen") and options.code_statistics: print_code_statistics() return if options.print_groups_file is not None: print_groups(options.print_groups_file) return if options.batch_commands_file is not None: get_batch_commands(options.batch_commands_file) return if options.run_ilastik: run_ilastik() return # necessary to prevent matplotlib trying to use Tkinter as its backend. # has to be done before CellProfilerApp is imported from matplotlib import use as mpluse mpluse('WXAgg') if (not hasattr(sys, 'frozen')) and options.fetch_external_dependencies: import external_dependencies external_dependencies.fetch_external_dependencies( options.overwrite_external_dependencies) if (not hasattr(sys, 'frozen')) and options.build_extensions: build_extensions() if options.build_and_exit: return if options.output_html: from cellprofiler.gui.html.manual import generate_html webpage_path = options.output_directory if options.output_directory else None generate_html(webpage_path) return if options.print_measurements: print_measurements(options) return try: if options.show_gui: import wx wx.Log.EnableLogging(False) from cellprofiler.cellprofilerapp import CellProfilerApp show_splashbox = (options.pipeline_filename is None and options.workspace_filename is None and (not options.new_workspace) and options.show_splashbox) if options.workspace_filename: workspace_path = os.path.expanduser(options.workspace_filename) elif options.new_workspace: workspace_path = False else: workspace_path = None App = CellProfilerApp( 0, check_for_new_version=(options.pipeline_filename is None), show_splashbox=show_splashbox, workspace_path=workspace_path) # # Important to go headless ASAP # # cellprofiler.preferences can't be imported before we have a chance # to initialize the wx app. # import cellprofiler.preferences as cpprefs if not options.show_gui: cpprefs.set_headless() # What's there to do but run if you're running headless? # Might want to change later if there's some headless setup options.run_pipeline = True if options.plugins_directory is not None: cpprefs.set_plugin_directory(options.plugins_directory) if options.ij_plugins_directory is not None: cpprefs.set_ij_plugin_directory(options.ij_plugins_directory) if options.temp_dir is not None: cpprefs.set_temporary_directory(options.temp_dir) if options.data_file is not None: cpprefs.set_data_file(os.path.abspath(options.data_file)) if options.image_set_file is not None: cpprefs.set_image_set_file(options.image_set_file, False) from cellprofiler.utilities.version import version_string, version_number logging.root.info("Version: %s / %d" % (version_string, version_number)) if options.run_pipeline and not options.pipeline_filename: raise ValueError("You must specify a pipeline filename to run") if options.output_directory: cpprefs.set_default_output_directory(options.output_directory) if options.image_directory: cpprefs.set_default_image_directory(options.image_directory) if options.show_gui: import cellprofiler.gui.cpframe as cpgframe if options.pipeline_filename: pipeline_path = os.path.expanduser(options.pipeline_filename) try: App.frame.pipeline.load(pipeline_path) if options.run_pipeline: App.frame.Command(cpgframe.ID_FILE_ANALYZE_IMAGES) except: import wx wx.MessageBox( 'CellProfiler was unable to load the pipeline file, "%s"' % options.pipeline_filename, "Error loading pipeline", style=wx.OK | wx.ICON_ERROR) logging.root.error("Unable to load pipeline", exc_info=True) App.MainLoop() return elif options.run_pipeline: run_pipeline_headless(options, args) except Exception, e: logging.root.fatal("Uncaught exception in CellProfiler.py", exc_info=True) raise
def main(args): '''Run CellProfiler args - command-line arguments, e.g. sys.argv ''' if any([arg.startswith('--work-announce') for arg in args]): # # Go headless ASAP # import cellprofiler.preferences as cpprefs cpprefs.set_headless() for i, arg in enumerate(args): if arg == "--ij-plugins-directory" and len(args) > i+1: cpprefs.set_ij_plugin_directory(args[i+1]) break import cellprofiler.analysis_worker cellprofiler.analysis_worker.aw_parse_args() cellprofiler.analysis_worker.main() sys.exit(0) options, args = parse_args(args) if options.jvm_heap_size != None: from cellprofiler.preferences import set_jvm_heap_mb set_jvm_heap_mb(options.jvm_heap_size, False) set_log_level(options) if not hasattr(sys, "frozen") and options.code_statistics: print_code_statistics() return if options.print_groups_file is not None: print_groups(options.print_groups_file) return if options.batch_commands_file is not None: get_batch_commands(options.batch_commands_file) return if options.run_ilastik: run_ilastik() return if options.add_message_for_user: if len(args) != 3: sys.stderr.write("Usage: (for add_message-for-user)\n") sys.stderr.write("CellProfiler --add-message-for-user <caption> <message> <pipeline-or-project>\n") sys.stderr.write("where:\n") sys.stderr.write(" <caption> - the message box caption\n") sys.stderr.write(" <message> - the message displayed inside the message box\n") sys.stderr.write(" <pipeline-or-project> - the path to the pipeline or project file to modify\n") return caption = args[0] message = args[1] path = args[2] import h5py using_hdf5 = h5py.is_hdf5(path) if using_hdf5: import cellprofiler.measurements as cpmeas m = cpmeas.Measurements( filename = path, mode="r+") pipeline_text = m[cpmeas.EXPERIMENT, "Pipeline_Pipeline"] else: with open(path, "r") as fd: pipeline_text = fd.read() header, body = pipeline_text.split("\n\n", 1) pipeline_text = header + \ ("\nMessageForUser:%s|%s\n\n" % (caption, message)) + body if using_hdf5: m[cpmeas.EXPERIMENT, "Pipeline_Pipeline"] = pipeline_text m.close() else: with open(path, "w") as fd: fd.write(pipeline_text) print "Message added to %s" % path return # necessary to prevent matplotlib trying to use Tkinter as its backend. # has to be done before CellProfilerApp is imported from matplotlib import use as mpluse mpluse('WXAgg') if (not hasattr(sys, 'frozen')) and options.fetch_external_dependencies: import external_dependencies external_dependencies.fetch_external_dependencies(options.overwrite_external_dependencies) if (not hasattr(sys, 'frozen')) and options.build_extensions: build_extensions() if options.build_and_exit: return if options.output_html: from cellprofiler.gui.html.manual import generate_html webpage_path = options.output_directory if options.output_directory else None generate_html(webpage_path) return if options.print_measurements: print_measurements(options) return if options.omero_credentials is not None: set_omero_credentials_from_string(options.omero_credentials) try: if options.show_gui: import wx wx.Log.EnableLogging(False) from cellprofiler.cellprofilerapp import CellProfilerApp from cellprofiler.workspace import is_workspace_file show_splashbox = (options.pipeline_filename is None and (not options.new_project) and options.show_splashbox) if options.pipeline_filename: if is_workspace_file(options.pipeline_filename): workspace_path = os.path.expanduser(options.pipeline_filename) pipeline_path = None else: pipeline_path = os.path.expanduser(options.pipeline_filename) workspace_path = None elif options.new_project: workspace_path = False pipeline_path = None else: workspace_path = None pipeline_path = None App = CellProfilerApp( 0, check_for_new_version = (options.pipeline_filename is None), show_splashbox = show_splashbox, workspace_path = workspace_path, pipeline_path = pipeline_path) # # Important to go headless ASAP # # cellprofiler.preferences can't be imported before we have a chance # to initialize the wx app. # import cellprofiler.preferences as cpprefs if not options.show_gui: cpprefs.set_headless() # What's there to do but run if you're running headless? # Might want to change later if there's some headless setup options.run_pipeline = True if options.plugins_directory is not None: cpprefs.set_plugin_directory(options.plugins_directory) if options.ij_plugins_directory is not None: cpprefs.set_ij_plugin_directory(options.ij_plugins_directory) if options.temp_dir is not None: if not os.path.exists(options.temp_dir): os.makedirs(options.temp_dir) cpprefs.set_temporary_directory(options.temp_dir) if options.data_file is not None: cpprefs.set_data_file(os.path.abspath(options.data_file)) if options.image_set_file is not None: cpprefs.set_image_set_file(options.image_set_file, False) from cellprofiler.utilities.version import version_string, version_number logging.root.info("Version: %s / %d" % (version_string, version_number)) if options.run_pipeline and not options.pipeline_filename: raise ValueError("You must specify a pipeline filename to run") if options.output_directory: if not os.path.exists(options.output_directory): os.makedirs(options.output_directory) cpprefs.set_default_output_directory(options.output_directory) if options.image_directory: cpprefs.set_default_image_directory(options.image_directory) if options.show_gui: if options.run_pipeline: App.frame.pipeline_controller.do_analyze_images() App.MainLoop() return elif options.run_pipeline: run_pipeline_headless(options, args) except Exception, e: logging.root.fatal("Uncaught exception in CellProfiler.py", exc_info=True) raise
def main(args): '''Run CellProfiler args - command-line arguments, e.g. sys.argv ''' if any([arg.startswith('--work-announce') for arg in args]): # # Go headless ASAP # import cellprofiler.preferences as cpprefs cpprefs.set_headless() import cellprofiler.analysis_worker cellprofiler.analysis_worker.main() sys.exit(0) options, args = parse_args(args) set_log_level(options) if not hasattr(sys, "frozen") and options.code_statistics: print_code_statistics() return if options.print_groups_file is not None: print_groups(options.print_groups_file) return if options.batch_commands_file is not None: get_batch_commands(options.batch_commands_file) return if options.run_ilastik: run_ilastik() return # necessary to prevent matplotlib trying to use Tkinter as its backend. # has to be done before CellProfilerApp is imported from matplotlib import use as mpluse mpluse('WXAgg') if (not hasattr(sys, 'frozen')) and options.fetch_external_dependencies: import external_dependencies external_dependencies.fetch_external_dependencies(options.overwrite_external_dependencies) if (not hasattr(sys, 'frozen')) and options.build_extensions: build_extensions() if options.build_and_exit: return if options.output_html: from cellprofiler.gui.html.manual import generate_html webpage_path = options.output_directory if options.output_directory else None generate_html(webpage_path) return if options.print_measurements: print_measurements(options) return try: if options.show_gui: import wx wx.Log.EnableLogging(False) from cellprofiler.cellprofilerapp import CellProfilerApp show_splashbox = (options.pipeline_filename is None and options.workspace_filename is None and (not options.new_workspace) and options.show_splashbox) if options.workspace_filename: workspace_path = os.path.expanduser(options.workspace_filename) elif options.new_workspace: workspace_path = False else: workspace_path = None App = CellProfilerApp( 0, check_for_new_version = (options.pipeline_filename is None), show_splashbox = show_splashbox, workspace_path = workspace_path) # # Important to go headless ASAP # # cellprofiler.preferences can't be imported before we have a chance # to initialize the wx app. # import cellprofiler.preferences as cpprefs if not options.show_gui: cpprefs.set_headless() # What's there to do but run if you're running headless? # Might want to change later if there's some headless setup options.run_pipeline = True if options.plugins_directory is not None: cpprefs.set_plugin_directory(options.plugins_directory) if options.ij_plugins_directory is not None: cpprefs.set_ij_plugin_directory(options.ij_plugins_directory) if options.temp_dir is not None: cpprefs.set_temporary_directory(options.temp_dir) if options.data_file is not None: cpprefs.set_data_file(os.path.abspath(options.data_file)) if options.image_set_file is not None: cpprefs.set_image_set_file(options.image_set_file, False) from cellprofiler.utilities.version import version_string, version_number logging.root.info("Version: %s / %d" % (version_string, version_number)) if options.run_pipeline and not options.pipeline_filename: raise ValueError("You must specify a pipeline filename to run") if options.output_directory: cpprefs.set_default_output_directory(options.output_directory) if options.image_directory: cpprefs.set_default_image_directory(options.image_directory) if options.show_gui: import cellprofiler.gui.cpframe as cpgframe if options.pipeline_filename: pipeline_path = os.path.expanduser(options.pipeline_filename) try: App.frame.pipeline.load(pipeline_path) if options.run_pipeline: App.frame.Command(cpgframe.ID_FILE_ANALYZE_IMAGES) except: import wx wx.MessageBox( 'CellProfiler was unable to load the pipeline file, "%s"' % options.pipeline_filename, "Error loading pipeline", style = wx.OK | wx.ICON_ERROR) logging.root.error("Unable to load pipeline", exc_info=True) App.MainLoop() return elif options.run_pipeline: run_pipeline_headless(options, args) except Exception, e: logging.root.fatal("Uncaught exception in CellProfiler.py", exc_info=True) raise
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()
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 main(args=None): '''Run CellProfiler args - command-line arguments, e.g. sys.argv ''' if args is None: args = sys.argv import cellprofiler.preferences as cpprefs cpprefs.set_awt_headless(True) exit_code = 0 switches = ('--work-announce', '--knime-bridge-address') if any([any([arg.startswith(switch) for switch in switches]) for arg in args]): # # Go headless ASAP # cpprefs.set_headless() for i, arg in enumerate(args): if arg == "--ij-plugins-directory" and len(args) > i + 1: cpprefs.set_ij_plugin_directory(args[i + 1]) break import cellprofiler.analysis_worker cellprofiler.analysis_worker.aw_parse_args() cellprofiler.analysis_worker.main() sys.exit(exit_code) options, args = parse_args(args) if options.print_version: from cellprofiler.utilities.version import \ dotted_version, version_string, git_hash, version_number print "CellProfiler %s" % dotted_version print "Git %s" % git_hash print "Version %s" % version_number print "Built %s" % version_string.split(" ")[0] sys.exit(exit_code) # # Important to go headless ASAP # if (not options.show_gui) or options.write_schema_and_exit: import cellprofiler.preferences as cpprefs cpprefs.set_headless() # What's there to do but run if you're running headless? # Might want to change later if there's some headless setup options.run_pipeline = True if options.jvm_heap_size is not None: from cellprofiler.preferences import set_jvm_heap_mb set_jvm_heap_mb(options.jvm_heap_size, False) set_log_level(options) if options.print_groups_file is not None: print_groups(options.print_groups_file) return if options.batch_commands_file is not None: get_batch_commands(options.batch_commands_file) return if options.run_ilastik: run_ilastik() return if options.add_message_for_user: if len(args) != 3: sys.stderr.write("Usage: (for add_message-for-user)\n") sys.stderr.write("CellProfiler --add-message-for-user <caption> <message> <pipeline-or-project>\n") sys.stderr.write("where:\n") sys.stderr.write(" <caption> - the message box caption\n") sys.stderr.write(" <message> - the message displayed inside the message box\n") sys.stderr.write(" <pipeline-or-project> - the path to the pipeline or project file to modify\n") return caption = args[0] message = args[1] path = args[2] import h5py using_hdf5 = h5py.is_hdf5(path) if using_hdf5: import cellprofiler.measurements as cpmeas m = cpmeas.Measurements( filename=path, mode="r+") pipeline_text = m[cpmeas.EXPERIMENT, "Pipeline_Pipeline"] else: with open(path, "r") as fd: pipeline_text = fd.read() header, body = pipeline_text.split("\n\n", 1) pipeline_text = header + \ ("\nMessageForUser:%s|%s\n\n" % (caption, message)) + body if using_hdf5: m[cpmeas.EXPERIMENT, "Pipeline_Pipeline"] = pipeline_text m.close() else: with open(path, "w") as fd: fd.write(pipeline_text) print "Message added to %s" % path return # necessary to prevent matplotlib trying to use Tkinter as its backend. # has to be done before CellProfilerApp is imported from matplotlib import use as mpluse mpluse('WXAgg') if options.omero_credentials is not None: set_omero_credentials_from_string(options.omero_credentials) if options.plugins_directory is not None: cpprefs.set_plugin_directory(options.plugins_directory, globally=False) if options.ij_plugins_directory is not None: cpprefs.set_ij_plugin_directory(options.ij_plugins_directory, globally=False) if options.temp_dir is not None: if not os.path.exists(options.temp_dir): os.makedirs(options.temp_dir) cpprefs.set_temporary_directory(options.temp_dir, globally=False) if not options.allow_schema_write: cpprefs.set_allow_schema_write(False) # # After the crucial preferences are established, we can start the VM # from cellprofiler.utilities.cpjvm import cp_start_vm cp_start_vm() # # Not so crucial preferences... # if options.image_set_file is not None: cpprefs.set_image_set_file(options.image_set_file) try: # --------------------------------------- # # Handle command-line tasks that that need to load the modules to run # if options.output_html: from cellprofiler.gui.html.manual import generate_html webpage_path = options.output_directory if options.output_directory else None generate_html(webpage_path) return if options.print_measurements: print_measurements(options) return if not hasattr(sys, "frozen") and options.code_statistics: print_code_statistics() return if options.write_schema_and_exit: write_schema(options.pipeline_filename) return # # ------------------------------------------ if options.show_gui: import wx wx.Log.EnableLogging(False) from cellprofiler.gui.app import App from cellprofiler.workspace import is_workspace_file if options.pipeline_filename: if is_workspace_file(options.pipeline_filename): workspace_path = os.path.expanduser(options.pipeline_filename) pipeline_path = None else: pipeline_path = os.path.expanduser(options.pipeline_filename) workspace_path = None elif options.new_project: workspace_path = False pipeline_path = None else: workspace_path = None pipeline_path = None app = App(0, workspace_path=workspace_path, pipeline_path=pipeline_path) if options.data_file is not None: cpprefs.set_data_file(os.path.abspath(options.data_file)) from cellprofiler.utilities.version import version_string, version_number logging.root.info("Version: %s / %d" % (version_string, version_number)) if options.run_pipeline and not options.pipeline_filename: raise ValueError("You must specify a pipeline filename to run") if options.output_directory: if not os.path.exists(options.output_directory): os.makedirs(options.output_directory) cpprefs.set_default_output_directory(options.output_directory) if options.image_directory: cpprefs.set_default_image_directory(options.image_directory) if options.show_gui: if options.run_pipeline: app.frame.pipeline_controller.do_analyze_images() app.MainLoop() return elif options.run_pipeline: run_pipeline_headless(options, args) except Exception, e: logging.root.fatal("Uncaught exception in CellProfiler.py", exc_info=True) exit_code = -1
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()
if not options.last_image_set.isdigit(): raise ValueError("The --last-image-set option takes a numeric argument") else: image_set_end = int(options.last_image_set) if image_set_start is None: image_set_numbers = np.arange(1, image_set_end+1) else: image_set_numbers = np.arange(image_set_start, image_set_end+1) else: image_set_end = None if options.output_directory: cpprefs.set_default_output_directory(options.output_directory) if options.image_directory: cpprefs.set_default_image_directory(options.image_directory) if options.show_gui: import cellprofiler.gui.cpframe as cpgframe if options.pipeline_filename: try: App.frame.pipeline.load(os.path.expanduser(options.pipeline_filename)) if options.run_pipeline: App.frame.Command(cpgframe.ID_FILE_ANALYZE_IMAGES) except: import wx wx.MessageBox( 'CellProfiler was unable to load the pipeline file, "%s"' % options.pipeline_filename, "Error loading pipeline", style = wx.OK | wx.ICON_ERROR) logging.root.error("Unable to load pipeline", exc_info=True)
def test_03_09_flag_image_abort(self): # # Regression test of issue #1210 # Make a pipeline that aborts during FlagImage # data = r"""CellProfiler Pipeline: http://www.cellprofiler.org Version:3 DateRevision:20140918122611 GitHash:ded6939 ModuleCount:6 HasImagePlaneDetails:False Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] : Filter images?:Images only Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "\x5B\\\\\\\\\\\\\\\\/\x5D\\\\\\\\.") Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Extract metadata?:No Metadata data type:Text Metadata types:{} Extraction method count:1 Metadata extraction method:Extract from file/folder names Metadata source:File name Regular expression:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)_w(?P<ChannelNumber>\x5B0-9\x5D) Regular expression:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$ Extract metadata from:All images Select the filtering criteria:and (file does contain "") Metadata file location: Match file and image metadata:\x5B\x5D Use case insensitive matching?:No NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Assign a name to:All images Select the image type:Grayscale image Name to assign these images:DNA Match metadata:\x5B\x5D Image set matching method:Order Set intensity range from:Image metadata Assignments count:1 Single images count:0 Select the rule criteria:and (file does contain "") Name to assign these images:DNA Name to assign these objects:Cell Select the image type:Grayscale image Set intensity range from:Image metadata Retain outlines of loaded objects?:No Name the outline image:LoadedOutlines Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Do you want to group your images?:No grouping metadata count:1 Metadata category:None FlagImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Hidden:1 Hidden:1 Name the flag\'s category:Metadata Name the flag:QCFlag Flag if any, or all, measurement(s) fails to meet the criteria?:Flag if any fail Skip image set if flagged?:Yes Flag is based on:Whole-image measurement Select the object to be used for flagging:None Which measurement?:Height_DNA Flag images based on low values?:No Minimum value:0.0 Flag images based on high values?:Yes Maximum value:1.0 Rules file location:Elsewhere...\x7C Rules file name:rules.txt Class number: MeasureImageIntensity:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Select the image to measure:DNA Measure the intensity only from areas enclosed by objects?:No Select the input objects:None """ 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(data), 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() pipeline = cpp.Pipeline() pipeline.loadtxt(StringIO(data)) pipeline.write_pipeline_measurement(m) 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(1,7)] rep = cpanalysis.SharedDictionaryReply( dictionaries = shared_dictionaries) req.reply(rep) # # MeasureImageIntensity follows FlagImage and it is poised to ask # for a display. So if we get that, we know the module has been run # and we fail the test. # req = self.awthread.recv(self.work_socket) self.assertFalse(isinstance(req, cpanalysis.DisplayRequest)) self.assertFalse(isinstance(req, cpanalysis.ExceptionReport))
image_set_start = None if not options.last_image_set is None: if not options.last_image_set.isdigit(): raise ValueError( "The --last-image-set option takes a numeric argument") else: image_set_end = int(options.last_image_set) else: image_set_end = None if options.output_directory: cpprefs.set_default_output_directory(options.output_directory) if options.image_directory: cpprefs.set_default_image_directory(options.image_directory) if options.show_gui: import cellprofiler.gui.cpframe as cpgframe if options.pipeline_filename: try: App.frame.pipeline.load( os.path.expanduser(options.pipeline_filename)) if options.run_pipeline: App.frame.Command(cpgframe.ID_FILE_ANALYZE_IMAGES) except: import wx wx.MessageBox( 'CellProfiler was unable to load the pipeline file, "%s"' % options.pipeline_filename, "Error loading pipeline",
def main(args=None): '''Run CellProfiler args - command-line arguments, e.g. sys.argv ''' if args is None: args = sys.argv import cellprofiler.preferences as cpprefs cpprefs.set_awt_headless(True) exit_code = 0 switches = ('--work-announce', '--knime-bridge-address') if any( [any([arg.startswith(switch) for switch in switches]) for arg in args]): # # Go headless ASAP # cpprefs.set_headless() for i, arg in enumerate(args): if arg == "--ij-plugins-directory" and len(args) > i + 1: cpprefs.set_ij_plugin_directory(args[i + 1]) break import cellprofiler.worker cellprofiler.worker.aw_parse_args() cellprofiler.worker.main() sys.exit(exit_code) options, args = parse_args(args) if options.print_version: from cellprofiler.utilities.version import \ dotted_version, version_string, git_hash, version_number print "CellProfiler %s" % dotted_version print "Git %s" % git_hash print "Version %s" % version_number print "Built %s" % version_string.split(" ")[0] sys.exit(exit_code) # # Important to go headless ASAP # if (not options.show_gui) or options.write_schema_and_exit: import cellprofiler.preferences as cpprefs cpprefs.set_headless() # What's there to do but run if you're running headless? # Might want to change later if there's some headless setup options.run_pipeline = True if options.jvm_heap_size is not None: from cellprofiler.preferences import set_jvm_heap_mb set_jvm_heap_mb(options.jvm_heap_size, False) set_log_level(options) if options.print_groups_file is not None: print_groups(options.print_groups_file) return if options.batch_commands_file is not None: get_batch_commands(options.batch_commands_file) return if options.add_message_for_user: if len(args) != 3: sys.stderr.write("Usage: (for add_message-for-user)\n") sys.stderr.write( "CellProfiler --add-message-for-user <caption> <message> <pipeline-or-project>\n" ) sys.stderr.write("where:\n") sys.stderr.write(" <caption> - the message box caption\n") sys.stderr.write( " <message> - the message displayed inside the message box\n" ) sys.stderr.write( " <pipeline-or-project> - the path to the pipeline or project file to modify\n" ) return caption = args[0] message = args[1] path = args[2] import h5py using_hdf5 = h5py.is_hdf5(path) if using_hdf5: import cellprofiler.measurement as cpmeas m = cpmeas.Measurements(filename=path, mode="r+") pipeline_text = m[cpmeas.EXPERIMENT, "Pipeline_Pipeline"] else: with open(path, "r") as fd: pipeline_text = fd.read() header, body = pipeline_text.split("\n\n", 1) pipeline_text = header + \ ("\nMessageForUser:%s|%s\n\n" % (caption, message)) + body if using_hdf5: m[cpmeas.EXPERIMENT, "Pipeline_Pipeline"] = pipeline_text m.close() else: with open(path, "w") as fd: fd.write(pipeline_text) print "Message added to %s" % path return # necessary to prevent matplotlib trying to use Tkinter as its backend. # has to be done before CellProfilerApp is imported from matplotlib import use as mpluse mpluse('WXAgg') if options.omero_credentials is not None: set_omero_credentials_from_string(options.omero_credentials) if options.plugins_directory is not None: cpprefs.set_plugin_directory(options.plugins_directory, globally=False) if options.ij_plugins_directory is not None: cpprefs.set_ij_plugin_directory(options.ij_plugins_directory, globally=False) if options.temp_dir is not None: if not os.path.exists(options.temp_dir): os.makedirs(options.temp_dir) cpprefs.set_temporary_directory(options.temp_dir, globally=False) if not options.allow_schema_write: cpprefs.set_allow_schema_write(False) # # After the crucial preferences are established, we can start the VM # from cellprofiler.utilities.cpjvm import cp_start_vm cp_start_vm() # # Not so crucial preferences... # if options.image_set_file is not None: cpprefs.set_image_set_file(options.image_set_file) try: # --------------------------------------- # # Handle command-line tasks that that need to load the modules to run # if options.output_html: from cellprofiler.gui.html.manual import generate_html webpage_path = options.output_directory if options.output_directory else None generate_html(webpage_path) return if options.print_measurements: print_measurements(options) return if not hasattr(sys, "frozen") and options.code_statistics: print_code_statistics() return if options.write_schema_and_exit: write_schema(options.pipeline_filename) return # # ------------------------------------------ if options.show_gui: import wx wx.Log.EnableLogging(False) from cellprofiler.gui.app import App from cellprofiler.workspace import is_workspace_file if options.pipeline_filename: if is_workspace_file(options.pipeline_filename): workspace_path = os.path.expanduser( options.pipeline_filename) pipeline_path = None else: pipeline_path = os.path.expanduser( options.pipeline_filename) workspace_path = None elif options.new_project: workspace_path = False pipeline_path = None else: workspace_path = None pipeline_path = None app = App(0, workspace_path=workspace_path, pipeline_path=pipeline_path) if options.data_file is not None: cpprefs.set_data_file(os.path.abspath(options.data_file)) from cellprofiler.utilities.version import version_string, version_number logging.root.info("Version: %s / %d" % (version_string, version_number)) if options.run_pipeline and not options.pipeline_filename: raise ValueError("You must specify a pipeline filename to run") if options.output_directory: if not os.path.exists(options.output_directory): os.makedirs(options.output_directory) cpprefs.set_default_output_directory(options.output_directory) if options.image_directory: cpprefs.set_default_image_directory(options.image_directory) if options.show_gui: if options.run_pipeline: app.frame.pipeline_controller.do_analyze_images() app.MainLoop() return elif options.run_pipeline: run_pipeline_headless(options, args) except Exception, e: logging.root.fatal("Uncaught exception in CellProfiler.py", exc_info=True) exit_code = -1
def test_03_04_shared_dictionary_request(self): # # The SharedDictionaryRequest # 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) rep = cpanalysis.SharedDictionaryReply( dictionaries = [{ ("foo%d" % i):"bar%d" % i} for i in range(1,8)]) req.reply(rep) # # Sneaky way to get pipeline. First, synchronize with the next message # req = self.awthread.recv(self.work_socket) pipe, prefs = self.awthread.aw.pipelines_and_preferences[ self.analysis_id] for d, module in zip(rep.dictionaries, pipe.modules()): self.assertDictEqual(module.get_dictionary(), d) # # Might as well torpedo the app. It should be stalled waiting # for the FlipAndRotate display. # self.cancel() self.awthread.ecute()