"""Create .rtdc files with scalar-only features"""
import argparse
import pathlib
import warnings
import hdf5plugin
from ..rtdc_dataset import new_dataset, RTDCWriter
from .._version import version
from . import common
[docs]def condense(path_out=None, path_in=None, check_suffix=True):
"""Create a new dataset with all (ancillary) scalar-only features"""
cmp_kw = hdf5plugin.Zstd(clevel=5)
if path_out is None or path_in is None:
parser = condense_parser()
args = parser.parse_args()
path_in = args.input
path_out = args.output
allowed_input_suffixes = [".rtdc", ".tdms"]
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)
logs = {}
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
with new_dataset(path_in) as ds:
ds.export.hdf5(path=path_temp,
features=ds.features_scalar,
# We do not need filtering, because we are
# only interested in the scalar features.
filtered=False,
compression_kwargs=cmp_kw,
override=True)
logs.update(ds.logs)
# command log
logs["dclab-condense"] = common.get_command_log(paths=[path_in])
# warnings log
if w:
logs["dclab-condense-warnings"] = common.assemble_warnings(w)
# Write log file
with RTDCWriter(path_temp, compression_kwargs=cmp_kw) as hw:
for name in logs:
hw.store_log(name, logs[name])
# Finally, rename temp to out
path_temp.rename(path_out)
def condense_parser():
descr = "Reduce an RT-DC measurement to its scalar-only features " \
+ "(i.e. without `contour`, `image`, `mask`, or `trace`). " \
+ "All available ancillary features are computed."
parser = argparse.ArgumentParser(description=descr)
parser.add_argument('input', metavar="INPUT", type=str,
help='Input path (.tdms or .rtdc file)')
parser.add_argument('output', metavar="OUTPUT", type=str,
help='Output path (.rtdc file)')
parser.add_argument('--version', action='version',
version=f'dclab-condense {version}')
return parser