# -*- coding: utf-8 -*-
# ======================================================================================
# Copyright (©) 2015-2023 LCS - Laboratoire Catalyse et Spectrochimie, Caen, France.
# CeCILL-B FREE SOFTWARE LICENSE AGREEMENT
# See full LICENSE agreement in the root directory.
# ======================================================================================
__all__ = ["read_zip"]
__dataset_methods__ = __all__
from spectrochempy.core.readers.importer import (
ALIAS,
FILETYPES,
Importer,
_importer_method,
_openfid,
read,
)
from spectrochempy.utils.docstrings import _docstring
# ======================================================================================
# Public functions
# ======================================================================================
_docstring.delete_params("Importer.see_also", "read_zip")
[docs]@_docstring.dedent
def read_zip(*paths, **kwargs):
"""
Open a zipped list of data files.
Parameters
----------
%(Importer.parameters)s
Returns
--------
%(Importer.returns)s
Other Parameters
----------------
%(Importer.other_parameters)s
See Also
---------
%(Importer.see_also.no_read_zip)s
Examples
--------
>>> A = scp.read_zip('agirdata/P350/FTIR/FTIR.zip', only=50, origin='omnic')
>>> print(A)
NDDataset: [float64] a.u. (shape: (y:50, x:2843))
"""
kwargs["filetypes"] = ["Compressed files (*.zip)"]
# TODO: allows other type of compressed files
kwargs["protocol"] = ["zip"]
importer = Importer()
return importer(*paths, **kwargs)
# ======================================================================================
# Private functions
# ======================================================================================
@_importer_method
def _read_zip(*args, **kwargs):
# Below we assume that files to read are in a unique directory
import zipfile
# read zip file
_, filename = args
fid, kwargs = _openfid(filename, **kwargs)
with zipfile.ZipFile(fid) as zf:
filelist = zf.filelist
only = kwargs.pop("only", len(filelist))
datasets = []
files = []
dirs = []
for file in filelist:
if "__MACOSX" in file.filename:
continue # bypass non-data files
if ".DS_Store" in file.filename:
continue
# make a pathlib object (python > 3.7)
file = zipfile.Path(zf, at=file.filename)
# seek the parent directory containing the files to read
if not file.is_dir():
files.append(file)
else:
dirs.append(file)
def extract(children, **kwargs):
extension = children.name.split(".")[-1]
if extension.lower() not in list(zip(*(ALIAS + FILETYPES)))[0]:
return
origin = kwargs.get("origin", "")
return read(children.name, content=children.read_bytes(), origin=origin)
# We assume that we have only a single dir with not subdir
if dirs:
# a single directory
count = 0
for children in dirs[0].iterdir():
if count == only:
# limits to only this number of files
break
elif "__MACOSX" in str(children.name):
continue # bypass non-data files
elif ".DS_Store" in str(children.name):
continue
else:
# print(count, children)
# TODO: why this pose problem in pycharm-debug?????
d = extract(children, **kwargs)
if d is not None:
datasets.append(d)
count += 1
else:
for file in files:
d = extract(file, **kwargs)
if d is not None:
datasets.append(d)
if len(datasets) == 1:
return datasets[0]
else:
return datasets