def test_median_otsu_flow(): with TemporaryDirectory() as out_dir: data_path, _, _ = get_data('small_25') volume = nib.load(data_path).get_data() save_masked = True median_radius = 3 numpass = 3 autocrop = False vol_idx = [0] dilate = 0 mo_flow = MedianOtsuFlow() mo_flow.run(data_path, out_dir=out_dir, save_masked=save_masked, median_radius=median_radius, numpass=numpass, autocrop=autocrop, vol_idx=vol_idx, dilate=dilate) mask_name = mo_flow.last_generated_outputs['out_mask'] masked_name = mo_flow.last_generated_outputs['out_masked'] masked, mask = median_otsu(volume, median_radius, numpass, autocrop, vol_idx, dilate) result_mask_data = nib.load(join(out_dir, mask_name)).get_data() npt.assert_array_equal(result_mask_data, mask) result_masked_data = nib.load(join(out_dir, masked_name)).get_data() npt.assert_array_equal(result_masked_data, masked)
def test_force_overwrite(): with TemporaryDirectory() as out_dir: data_path, _, _ = get_data('small_25') mo_flow = MedianOtsuFlow(output_strategy='absolute') # Generate the first results mo_flow.run(data_path, out_dir=out_dir) mask_file = mo_flow.last_generated_outputs['out_mask'] first_time = os.path.getmtime(mask_file) # re-run with no force overwrite, modified time should not change mo_flow.run(data_path, out_dir=out_dir) mask_file = mo_flow.last_generated_outputs['out_mask'] second_time = os.path.getmtime(mask_file) assert first_time == second_time # re-run with force overwrite, modified time should change mo_flow = MedianOtsuFlow(output_strategy='absolute', force=True) # Make sure that at least one second elapsed, so that time-stamp is # different (sometimes measured in whole seconds) time.sleep(1) mo_flow.run(data_path, out_dir=out_dir) mask_file = mo_flow.last_generated_outputs['out_mask'] third_time = os.path.getmtime(mask_file) assert third_time != second_time
def test_median_otsu_flow(): with TemporaryDirectory() as out_dir: data_path, _, _ = get_fnames('small_25') volume = load_nifti_data(data_path) save_masked = True median_radius = 3 numpass = 3 autocrop = False vol_idx = [0] dilate = 0 mo_flow = MedianOtsuFlow() mo_flow.run(data_path, out_dir=out_dir, save_masked=save_masked, median_radius=median_radius, numpass=numpass, autocrop=autocrop, vol_idx=vol_idx, dilate=dilate) mask_name = mo_flow.last_generated_outputs['out_mask'] masked_name = mo_flow.last_generated_outputs['out_masked'] masked, mask = median_otsu(volume, vol_idx=vol_idx, median_radius=median_radius, numpass=numpass, autocrop=autocrop, dilate=dilate) result_mask_data = load_nifti_data(join(out_dir, mask_name)) npt.assert_array_equal(result_mask_data.astype(np.uint8), mask) result_masked = nib.load(join(out_dir, masked_name)) result_masked_data = np.asanyarray(result_masked.dataobj) npt.assert_array_equal(np.round(result_masked_data), masked)