Exemplo n.º 1
0
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)
Exemplo n.º 2
0
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)