# Copyright (c) 2021. Lucas G. S. Jeub
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
from pathlib import Path
from dask import delayed
from dask.distributed import secede, rejoin
import numpy as np
from local2global.utils import local_error
from local2global_embedding.patches import rolling_window_graph
from local2global_embedding.run.scripts.utils import aligned_coords, num_patches, num_nodes
[docs]
def global_align_errors(patches, output_file, window=14, scale=True, verbose=False, use_tmp=False):
output_file = Path(output_file)
if not output_file.is_file():
pg = delayed(rolling_window_graph)(num_patches(patches), window)
secede()
n_nodes = num_nodes(patches).compute()
aligned = aligned_coords(patches, pg, verbose=verbose, scale=scale, use_tmp=use_tmp).compute()
rejoin()
workfile = output_file.with_suffix('.tmp.npy')
ref_file = workfile.with_name(workfile.name.replace('error', 'reference'))
try:
errors = np.lib.format.open_memmap(workfile, mode='w+', dtype=float, shape=(n_nodes, len(aligned.patches)))
reference = np.lib.format.open_memmap(ref_file, mode='w+', dtype=float, shape=(n_nodes, aligned.shape[1]))
reference[:, :] = np.nan
errors[:, :] = np.nan
reference[aligned.nodes] = aligned.coordinates
for i, p in enumerate(aligned.patches):
errors[p.nodes, i] = local_error(p, reference)
errors.flush()
reference.flush()
workfile.replace(output_file)
ref_file.replace(ref_file.with_name(ref_file.name.replace('.tmp', '')))
finally:
workfile.unlink(missing_ok=True)
ref_file.unlink(missing_ok=True)
return output_file