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()