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()