xbeam_rechunk.py

# Copyright 2021 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Rechunk a Zarr dataset."""
from typing import Dict

from absl import app
from absl import flags
import apache_beam as beam
import xarray_beam as xbeam


INPUT_PATH = flags.DEFINE_string('input_path', None, help='input Zarr path')
OUTPUT_PATH = flags.DEFINE_string('output_path', None, help='output Zarr path')
TARGET_CHUNKS = flags.DEFINE_string(
    'target_chunks',
    '',
    help=(
        'chunks on the input Zarr dataset to change on the outputs, in the '
        'form of a comma separated dimension=size pairs, e.g., '
        "--target_chunks='x=10,y=10'. Omitted dimensions are not changed and a "
        'chunksize of -1 indicates not to chunk a dimension.'
    ),
)
RUNNER = flags.DEFINE_string('runner', None, help='beam.runners.Runner')


# pylint: disable=expression-not-assigned


def _parse_chunks_str(chunks_str: str) -> Dict[str, int]:
  chunks = {}
  parts = chunks_str.split(',')
  for part in parts:
    k, v = part.split('=')
    chunks[k] = int(v)
  return chunks


def main(argv):
  source_dataset, source_chunks = xbeam.open_zarr(INPUT_PATH.value)
  template = xbeam.make_template(source_dataset)
  target_chunks = dict(source_chunks, **_parse_chunks_str(TARGET_CHUNKS.value))
  itemsize = max(variable.dtype.itemsize for variable in template.values())

  with beam.Pipeline(runner=RUNNER.value, argv=argv) as root:
    (
        root
        | xbeam.DatasetToChunks(source_dataset, source_chunks, split_vars=True)
        | xbeam.Rechunk(  # pytype: disable=wrong-arg-types
            source_dataset.sizes,
            source_chunks,
            target_chunks,
            itemsize=itemsize,
        )
        | xbeam.ChunksToZarr(OUTPUT_PATH.value, template, target_chunks)
    )


if __name__ == '__main__':
  app.run(main)