def test_13_01_load_filename(self): # # Load a file, only specifying the FileName in the CSV # dir = os.path.join(example_images_directory(), "ExampleSBSImages") file_name = 'Channel2-01-A-01.tif' csv_text = '''"Image_FileName_DNA" "%s" '''% file_name pipeline, module, filename = self.make_pipeline(csv_text) assert isinstance(module, L.LoadData) module.image_directory.dir_choice = cps.ABSOLUTE_FOLDER_NAME module.image_directory.custom_path = dir m = cpmeas.Measurements(mode="memory") workspace = cpw.Workspace(pipeline, module, m, cpo.ObjectSet(), m, cpi.ImageSetList()) self.assertTrue(module.prepare_run(workspace)) self.assertEqual(m.get_measurement(cpmeas.IMAGE, "FileName_DNA", 1), file_name) path = m.get_measurement(cpmeas.IMAGE, "PathName_DNA", 1) self.assertEqual(path, dir) self.assertEqual(m.get_measurement(cpmeas.IMAGE, "URL_DNA", 1), L.pathname2url(os.path.join(dir, file_name))) module.prepare_group(workspace, {}, [1]) module.run(workspace) img = workspace.image_set.get_image("DNA", must_be_grayscale=True) self.assertEqual(tuple(img.pixel_data.shape), (640, 640))
def test_13_01_load_filename(self): # # Load a file, only specifying the FileName in the CSV # dir = os.path.join(example_images_directory(), "ExampleSBSImages") file_name = 'Channel2-01-A-01.tif' csv_text = '''"Image_FileName_DNA" "%s" ''' % file_name pipeline, module, filename = self.make_pipeline(csv_text) assert isinstance(module, L.LoadData) module.image_directory.dir_choice = cps.ABSOLUTE_FOLDER_NAME module.image_directory.custom_path = dir m = cpmeas.Measurements(mode="memory") workspace = cpw.Workspace(pipeline, module, m, cpo.ObjectSet(), m, cpi.ImageSetList()) self.assertTrue(module.prepare_run(workspace)) self.assertEqual(m.get_measurement(cpmeas.IMAGE, "FileName_DNA", 1), file_name) path = m.get_measurement(cpmeas.IMAGE, "PathName_DNA", 1) self.assertEqual(path, dir) self.assertEqual(m.get_measurement(cpmeas.IMAGE, "URL_DNA", 1), L.pathname2url(os.path.join(dir, file_name))) module.prepare_group(workspace, {}, [1]) module.run(workspace) img = workspace.image_set.get_image("DNA", must_be_grayscale=True) self.assertEqual(tuple(img.pixel_data.shape), (640, 640))
def test_13_06_load_default_input_folder(self): # Regression test of issue #1365 - load a file from the default # input folder and check that PathName_xxx is absolute csv_text = '''"Image_FileName_DNA","Image_PathName_DNA"\n"%s","%s"''' \ % (self.test_filename, self.test_path) pipeline, module, filename = self.make_pipeline(csv_text) try: assert isinstance(module, L.LoadData) module.image_directory.dir_choice = cps.ABSOLUTE_FOLDER_NAME module.image_directory.custom_path = self.test_path m = cpmeas.Measurements() workspace = cpw.Workspace(pipeline, module, m, cpo.ObjectSet(), m, cpi.ImageSetList()) self.assertTrue(module.prepare_run(workspace)) self.assertEqual(m.get_measurement(cpmeas.IMAGE, "FileName_DNA", 1), self.test_filename) path_out = m.get_measurement(cpmeas.IMAGE, "PathName_DNA", 1) self.assertEqual(self.test_path, path_out) self.assertEqual( m.get_measurement(cpmeas.IMAGE, "URL_DNA", 1), L.pathname2url(os.path.join(self.test_path, self.test_filename))) module.prepare_group(workspace, {}, [1]) module.run(workspace) img = workspace.image_set.get_image("DNA", must_be_grayscale=True) self.assertEqual(tuple(img.pixel_data.shape), self.test_shape) finally: os.remove(filename)
def test_13_06_load_default_input_folder(self): # Regression test of issue #1365 - load a file from the default # input folder and check that PathName_xxx is absolute csv_text = '''"Image_FileName_DNA","Image_PathName_DNA"\n"%s","%s"''' \ % (self.test_filename, self.test_path) pipeline, module, filename = self.make_pipeline(csv_text) try: assert isinstance(module, L.LoadData) module.image_directory.dir_choice = cps.ABSOLUTE_FOLDER_NAME module.image_directory.custom_path = self.test_path m = cpmeas.Measurements() workspace = cpw.Workspace(pipeline, module, m, cpo.ObjectSet(), m, cpi.ImageSetList()) self.assertTrue(module.prepare_run(workspace)) self.assertEqual( m.get_measurement(cpmeas.IMAGE, "FileName_DNA", 1), self.test_filename) path_out = m.get_measurement(cpmeas.IMAGE, "PathName_DNA", 1) self.assertEqual(self.test_path, path_out) self.assertEqual( m.get_measurement(cpmeas.IMAGE, "URL_DNA", 1), L.pathname2url(os.path.join(self.test_path, self.test_filename))) module.prepare_group(workspace, {}, [1]) module.run(workspace) img = workspace.image_set.get_image("DNA", must_be_grayscale=True) self.assertEqual(tuple(img.pixel_data.shape), self.test_shape) finally: os.remove(filename)