def main(in_path: str, ref_channel: str, out_dir: str, n_workers: int, tile_size: int, overlap: int, ):
if not osp.exists(out_dir):
os.makedirs(out_dir)
if n_workers == 1:
dask.config.set({'scheduler': 'synchronous'})
else:
dask.config.set({'num_workers': n_workers, 'scheduler': 'processes'})
st = datetime.now()
with tif.TiffFile(in_path, is_ome=True) as stack:
ome = stack.ome_metadata
cycle_size, ncycles, first_ref_position = get_cycle_composition(ome, ref_channel)
block_width = tile_size
block_height = tile_size
overlap = overlap
warper = Warper()
warper.block_w = block_width
warper.block_h = block_height
warper.overlap = overlap
# perform registration of full stack
register(in_path, out_dir, cycle_size, ncycles, first_ref_position, ome, warper, block_width, block_height, overlap)
fin = datetime.now()
print('time elapsed', fin - st)
def main(in_path: str, ref_channel: str, out_dir: str, n_workers: int, tile_size: int, overlap: int, method: str):
if not osp.exists(out_dir):
os.makedirs(out_dir)
if n_workers == 1:
dask.config.set({'scheduler': 'synchronous'})
else:
dask.config.set({'num_workers': n_workers, 'scheduler': 'processes'})
avail_methods = ('farneback', 'denselk', 'deepflow', 'rlof', 'pcaflow')
if method not in avail_methods:
raise ValueError('Provided opt flow method is not recognised. ' +
'\nAvailable methods: ' + str(avail_methods))
print('Using method', method)
st = datetime.now()
with tif.TiffFile(in_path, is_ome=True) as stack:
ome = stack.ome_metadata
cycle_size, ncycles, first_ref_position = get_cycle_composition(ome, ref_channel)
block_width = tile_size
block_height = tile_size
overlap = overlap
warper = Warper()
warper.block_w = block_width
warper.block_h = block_height
warper.overlap = overlap
# perform registration of full stack
register(in_path, out_dir,
cycle_size, ncycles,
first_ref_position, ome, warper,
block_width, block_height, overlap, method)
fin = datetime.now()
print('time elapsed', fin - st)