def test_02_01_run_headless(self): output_directory = tempfile.mkdtemp() temp_directory = os.path.join(output_directory, "temp") os.mkdir(temp_directory) try: # # Run with a .cp file # input_directory = maybe_download_example_images(["ExampleHT29"], [ 'AS_09125_050116030001_D03f00d0.tif', 'AS_09125_050116030001_D03f00d1.tif', 'AS_09125_050116030001_D03f00d2.tif', 'ExampleHT29.cp', 'k27IllumCorrControlv1.mat' ]) pipeline_file = os.path.join(input_directory, "ExampleHT29.cp") measurements_file = os.path.join(output_directory, "Measurements.h5") done_file = os.path.join(output_directory, "Done.txt") self.run_cellprofiler("-c", "-r", "-i", input_directory, "-o", output_directory, "-p", pipeline_file, "-d", done_file, "-t", temp_directory, measurements_file) import cellprofiler.preferences as cpprefs self.assertTrue(os.path.exists(measurements_file)) self.assertTrue(os.path.exists(done_file)) # # Re-run using the measurements file. # m2_file = os.path.join(output_directory, "M2.h5") self.run_cellprofiler("-c", "-r", "-i", input_directory, "-o", output_directory, "-p", measurements_file, m2_file) self.assertTrue(os.path.exists(m2_file)) finally: shutil.rmtree(output_directory)
def test_02_02_scale(self): '''Load an image twice, as scaled and unscaled''' folder = "ExampleSpecklesImages" file_names = ["1-162hrh2ax2.tif", "1-162hrh2ax2.tif"] path = maybe_download_example_images([folder], file_names) cpprefs.set_default_image_directory(path) 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.prepare_run(workspace) 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 test_02_02_scale(self): '''Load an image twice, as scaled and unscaled''' folder = "ExampleSpecklesImages" file_names = ["1-162hrh2ax2.tif", "1-162hrh2ax2.tif"] path = maybe_download_example_images([folder], file_names) cpprefs.set_default_image_directory(path) 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.prepare_run(workspace) 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 test_02_01_run_headless(self): output_directory = tempfile.mkdtemp() temp_directory = os.path.join(output_directory, "temp") os.mkdir(temp_directory) try: # # Run with a .cp file # input_directory = maybe_download_example_images( ["ExampleHT29"], ['AS_09125_050116030001_D03f00d0.tif', 'AS_09125_050116030001_D03f00d1.tif', 'AS_09125_050116030001_D03f00d2.tif', 'ExampleHT29.cp', 'k27IllumCorrControlv1.mat']) pipeline_file = os.path.join(input_directory, "ExampleHT29.cp") measurements_file = os.path.join(output_directory, "Measurements.h5") done_file = os.path.join(output_directory, "Done.txt") self.run_cellprofiler("-c", "-r", "-i", input_directory, "-o", output_directory, "-p", pipeline_file, "-d", done_file, "-t", temp_directory, measurements_file) import cellprofiler.preferences as cpprefs self.assertTrue(os.path.exists(measurements_file)) self.assertTrue(os.path.exists(done_file)) # # Re-run using the measurements file. # m2_file = os.path.join(output_directory, "M2.h5") self.run_cellprofiler("-c", "-r", "-i", input_directory, "-o", output_directory, "-p", measurements_file, m2_file) self.assertTrue(os.path.exists(m2_file)) finally: shutil.rmtree(output_directory)