def setup(): global stack_iter global metadata image_path_list = data.stack_list() metadata = {"PhysicalSizeX": 0.42, "PhysicalSizeY": 0.42, "PhysicalSizeZ": 1.5, "TimeIncrement": 3, "FileName": '', "Shape": [1, 1, 512, 512], "DimensionOrder": "TZYX"} metadata['FileName'] = image_path_list[0] stack_io = StackIO(image_path_list=image_path_list, metadata=metadata) im0 = stack_io.get_tif().asarray() correct_metadata = {'FileName': os.path.basename(image_path_list[0]), 'SizeX': im0.shape[2], 'SizeY': im0.shape[1], 'SizeZ': im0.shape[0], 'SizeT': len(image_path_list), 'Shape': (len(image_path_list), im0.shape[2], im0.shape[1], im0.shape[0])} stack_io.metadata.update(correct_metadata) metadata = stack_io.metadata stack_iter = stack_io.list_iterator()
def test_stackio_list_iterator(): metadata = { 'SizeC': 1, 'TimeIncrement': 10.0, 'DimensionOrder': ['C', 'T', 'Z', 'Y', 'X'], 'SizeT': 4, 'AcquisitionDate': '2014-03-24T11:25:14', 'SizeX': 56, 'SizeY': 48, 'SizeZ': 4, 'PhysicalSizeY': 0.065, 'PhysicalSizeX': 0.065, 'Shape': (1, 4, 4, 48, 56), 'PhysicalSizeZ': 1.0 } file_list = data.stack_list() stackio = StackIO(image_path_list=file_list, metadata=metadata) stack_iter = stackio.list_iterator() for n, stack in enumerate(stack_iter()): assert stack.shape == (5, 172, 165) assert n == 3 file_list = data.stack_list() stackio = StackIO(image_path_list=file_list, metadata=metadata, base_dir=os.path.dirname(file_list[0])) assert len(stackio.image_path_list) == 4
def setup(): global stack_iter global metadata image_path_list = data.stack_list() metadata = { "PhysicalSizeX": 0.42, "PhysicalSizeY": 0.42, "PhysicalSizeZ": 1.5, "TimeIncrement": 3, "FileName": '', "Shape": [1, 1, 512, 512], "DimensionOrder": "TZYX" } metadata['FileName'] = image_path_list[0] stack_io = StackIO(image_path_list=image_path_list, metadata=metadata) im0 = stack_io.get_tif().asarray() correct_metadata = { 'FileName': os.path.basename(image_path_list[0]), 'SizeX': im0.shape[2], 'SizeY': im0.shape[1], 'SizeZ': im0.shape[0], 'SizeT': len(image_path_list), 'Shape': (len(image_path_list), im0.shape[2], im0.shape[1], im0.shape[0]) } stack_io.metadata.update(correct_metadata) metadata = stack_io.metadata stack_iter = stack_io.list_iterator()