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_image_iterator(): fname = data.CZT_peaks() st = StackIO(fname, json_discovery=False) arr = st.get_tif().asarray(memmap=True) iterator = st.image_iterator(channel_index=0, memmap=True) for a in iterator(): assert a.shape == arr.shape[-2:] # Test with channels index fname = data.CZT_peaks() st = StackIO(fname, json_discovery=False) assert_raises(TypeError, st.image_iterator, hannel_index='GFP', memmap=True) st.metadata['Channels'] = ['GFP'] it = st.image_iterator(channel_index='GFP', memmap=False, z_projection=True) assert list(it())[0].shape == arr.shape[-2:]
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()