def test_validate_data_files_label(): """ Test the validate_data_files functions that looks for inconsistencies in the fixed/moving image and label lists. If there is any issue it will raise an error, otherwise it returns None. """ for key_file_loader, file_loader in FileLoaderDict.items(): for split in ["train", "test"]: data_dir_path = [join(DataPaths[key_file_loader], split)] common_args = dict( file_loader=file_loader, labeled=True, sample_label="all", seed=None if split == "train" else 0, ) data_loader = PairedDataLoader( data_dir_paths=data_dir_path, fixed_image_shape=fixed_image_shape, moving_image_shape=moving_image_shape, **common_args, ) assert data_loader.validate_data_files() is None data_loader.close()
def test_close(): """ Test the close function. Only needed for H5 data loaders for now. Since fixed/moving loaders are the same for unpaired data loader, only need to test the moving. """ for key_file_loader, file_loader in FileLoaderDict.items(): for split in ["train", "test"]: data_dir_path = [join(DataPaths[key_file_loader], split)] common_args = dict( file_loader=file_loader, labeled=True, sample_label="all", seed=None if split == "train" else 0, ) data_loader = PairedDataLoader( data_dir_paths=data_dir_path, fixed_image_shape=fixed_image_shape, moving_image_shape=moving_image_shape, **common_args, ) if key_file_loader == "h5": data_loader.close() for f in data_loader.loader_moving_image.h5_files.values(): assert not f.__bool__()
def test_file_loader_init(): """ check file loader is correctly called in __init__: """ loader = PairedDataLoader( file_loader=H5FileLoader, data_dir_path=data_dir_path, labeled=True, sample_label=sample_label, moving_image_shape=moving_image_shape_arr, fixed_image_shape=fixed_image_shape_arr, seed=seed, ) file_loader = H5FileLoader(dir_path=data_dir_path, name="moving_images", grouped=False) expected = ["case000025.nii.gz"] loader_got = loader.loader_moving_image.get_data_ids() file_loader_got = file_loader.get_data_ids() loader.close() file_loader.close() assert loader_got == expected, "paired_loader has loaded incorrect moving image" assert loader_got == file_loader_got, "paired_loader incorrectly calling h5_loader"
def test_init_sufficient_args(): """ check if init method of loader returns any errors when all required arguments given """ loader = PairedDataLoader( file_loader=H5FileLoader, data_dir_path=data_dir_path, labeled=True, sample_label=sample_label, moving_image_shape=moving_image_shape_arr, fixed_image_shape=fixed_image_shape_arr, seed=seed, ) loader.__init__( file_loader=H5FileLoader, data_dir_path=data_dir_path, labeled=True, sample_label=sample_label, moving_image_shape=moving_image_shape_arr, fixed_image_shape=fixed_image_shape_arr, seed=seed, ) loader.close()
def test_init(): """ Check that data loader __init__() method is correct: """ for key_file_loader, file_loader in FileLoaderDict.items(): data_dir_path = [ join(DataPaths[key_file_loader], "train"), join(DataPaths[key_file_loader], "test"), ] common_args = dict(file_loader=file_loader, labeled=True, sample_label="all", seed=None) data_loader = PairedDataLoader( data_dir_paths=data_dir_path, fixed_image_shape=fixed_image_shape, moving_image_shape=moving_image_shape, **common_args, ) # Check that file loaders are initialized correctly file_loader_method = file_loader(dir_paths=data_dir_path, name="moving_images", grouped=False) assert isinstance(data_loader.loader_moving_image, type(file_loader_method)) assert isinstance(data_loader.loader_fixed_image, type(file_loader_method)) assert isinstance(data_loader.loader_moving_label, type(file_loader_method)) assert isinstance(data_loader.loader_fixed_label, type(file_loader_method)) data_loader.close() # Check the data_dir_path variable assertion error. data_dir_path_int = [0, "1", 2, 3] with pytest.raises(AssertionError): PairedDataLoader( data_dir_paths=data_dir_path_int, fixed_image_shape=fixed_image_shape, moving_image_shape=moving_image_shape, **common_args, )
def test_init_num_images(): """ check init reads expected number of image pairs from given data path """ loader = PairedDataLoader( file_loader=H5FileLoader, data_dir_path=data_dir_path, labeled=True, sample_label=sample_label, moving_image_shape=moving_image_shape_arr, fixed_image_shape=fixed_image_shape_arr, seed=seed, ) got = loader.num_images expected = 1 loader.close() assert got == expected
def test_sample_index_generator(): """ Test to check the randomness and deterministic index generator for train/test respectively. """ for key_file_loader, file_loader in FileLoaderDict.items(): for split in ["train", "test"]: data_dir_path = [join(DataPaths[key_file_loader], split)] indices_to_compare = [] for seed in [0, 1, 0]: data_loader = PairedDataLoader( data_dir_paths=data_dir_path, fixed_image_shape=fixed_image_shape, moving_image_shape=moving_image_shape, file_loader=file_loader, labeled=True, sample_label="all", seed=seed, ) data_indices = [] for ( moving_index, fixed_index, indices, ) in data_loader.sample_index_generator(): assert isinstance(moving_index, int) assert isinstance(fixed_index, int) assert isinstance(indices, list) assert moving_index == fixed_index data_indices += indices indices_to_compare.append(data_indices) data_loader.close() if data_loader.num_images > 1: # test different seeds give different indices assert not (np.allclose(indices_to_compare[0], indices_to_compare[1])) # test same seeds give the same indices assert np.allclose(indices_to_compare[0], indices_to_compare[2])
def test_sample_index_generator(): """ check image index is expected value and format """ loader = PairedDataLoader( file_loader=H5FileLoader, data_dir_path=data_dir_path, labeled=True, sample_label=sample_label, moving_image_shape=moving_image_shape_arr, fixed_image_shape=fixed_image_shape_arr, seed=seed, ) expected = (0, 0, [0]) image_index = PairedDataLoader.sample_index_generator(loader) got = next(image_index) loader.close() assert expected == got
def test_validate_data_files_label(): """ check validate_data_files throws exception when moving and fixed label IDs vary """ loader = PairedDataLoader( file_loader=H5FileLoader, data_dir_path=data_dir_path, labeled=True, sample_label=sample_label, moving_image_shape=moving_image_shape_arr, fixed_image_shape=fixed_image_shape_arr, seed=seed, ) # alter a data ID to cause error loader.loader_moving_label.data_keys = "foo" with pytest.raises(Exception) as execinfo: PairedDataLoader.validate_data_files(loader) msg = " ".join(execinfo.value.args[0].split()) loader.close() assert "two lists are not identical" in msg