"""Repack (similar to h5repack) .rtdc files"""
from __future__ import annotations
import argparse
import pathlib
import h5py
from ..rtdc_dataset import rtdc_copy
from .._version import version
from . import common
[docs]
def repack(
path_in: str | pathlib.Path = None,
path_out: str | pathlib.Path = None,
strip_basins: bool = False,
strip_logs: bool = False,
check_suffix: bool = True):
"""Repack/recreate an .rtdc file, optionally stripping the logs
Parameters
----------
path_in: str or pathlib.Path
file to compress
path_out: str or pathlib
output file path
strip_basins: bool
do not write basin information to the output file
strip_logs: bool
do not write logs to the output file
check_suffix: bool
check suffixes for input and output files
Returns
-------
path_out: pathlib.Path
output path (with possibly corrected suffix)
"""
if path_in is None and path_out is None:
parser = repack_parser()
args = parser.parse_args()
path_in = args.input
path_out = args.output
strip_basins = args.strip_basins
strip_logs = args.strip_logs
allowed_input_suffixes = [".rtdc"]
if not check_suffix:
allowed_input_suffixes.append(pathlib.Path(path_in).suffix)
path_in, path_out, path_temp = common.setup_task_paths(
path_in, path_out, allowed_input_suffixes=allowed_input_suffixes)
with h5py.File(path_in) as h5, h5py.File(path_temp, "w") as hc:
rtdc_copy(src_h5file=h5,
dst_h5file=hc,
features="all",
include_basins=not strip_basins,
include_logs=not strip_logs,
include_tables=True,
meta_prefix="")
# Finally, rename temp to out
path_temp.rename(path_out)
return path_out
def repack_parser():
descr = "Repack an .rtdc file. The difference to dclab-compress " \
+ "is that no logs are added. Other logs can optionally be " \
+ "stripped away. Repacking also gets rid of old clutter " \
+ "data (e.g. previous metadata stored in the HDF5 file)."
parser = argparse.ArgumentParser(description=descr)
parser.add_argument('input', metavar="INPUT", type=str,
help='Input path (.rtdc file)')
parser.add_argument('output', metavar="OUTPUT", type=str,
help='Output path (.rtdc file)')
parser.add_argument('--strip-basins',
dest='strip_basins',
action='store_true',
help='Do not copy any basin information to the '
'output file.')
parser.set_defaults(strip_basins=False)
parser.add_argument('--strip-logs',
dest='strip_logs',
action='store_true',
help='Do not copy any logs to the output file.')
parser.set_defaults(strip_logs=False)
parser.add_argument('--version', action='version',
version=f'dclab-repack {version}')
return parser