def convert(inFileOrFolder, overwrite=False, fileType=None, outputMetadata=False, outputFeedbackChannel=False, multipleGroupsPerFile=False, compression=True):
"""
Convert the given file to a NeuroDataWithoutBorders file using pynwb
Supported fileformats:
- ABF v2 files created by Clampex
- DAT files created by Patchmaster v2x90
:param inFileOrFolder: path to a file or folder
:param overwrite: overwrite output file, defaults to `False`
:param fileType: file type to be converted, must be passed iff `inFileOrFolder` refers to a folder
:param outputMetadata: output metadata of the file, helpful for debugging
:param outputFeedbackChannel: Output ADC data which stems from stimulus feedback channels (ignored for DAT files)
:param multipleGroupsPerFile: Write all Groups in the DAT file into one NWB
file. By default we create one NWB per Group (ignored for ABF files).
:param compression: Toggle compression for HDF5 datasets
:return: path of the created NWB file
"""
if not os.path.exists(inFileOrFolder):
raise ValueError(f"The file {inFileOrFolder} does not exist.")
if os.path.isfile(inFileOrFolder):
root, ext = os.path.splitext(inFileOrFolder)
if os.path.isdir(inFileOrFolder):
if not fileType:
raise ValueError("Missing fileType when passing a folder")
inFileOrFolder = os.path.normpath(inFileOrFolder)
inFileOrFolder = os.path.realpath(inFileOrFolder)
ext = fileType
root = os.path.join(inFileOrFolder, "..",
os.path.basename(inFileOrFolder))
outFile = root + ".nwb"
if not outputMetadata and os.path.exists(outFile):
if overwrite:
os.remove(outFile)
else:
raise ValueError(f"The output file {outFile} does already exist.")
if ext == ".abf":
if outputMetadata:
ABFConverter.outputMetadata(inFileOrFolder)
else:
ABFConverter(inFileOrFolder, outFile, outputFeedbackChannel=outputFeedbackChannel, compression=compression)
elif ext == ".dat":
if outputMetadata:
DatConverter.outputMetadata(inFileOrFolder)
else:
DatConverter(inFileOrFolder, outFile, multipleGroupsPerFile=multipleGroupsPerFile, compression=compression)
else:
raise ValueError(f"The extension {ext} is currently not supported.")
return outFile
df
df = pd.read_csv(
'/Volumes/easystore5T/data/DANDI/nwb_lizhou/recieved/lizhou_meta_denormalized.csv'
)
src_dir = '/Volumes/easystore5T/data/DANDI/nwb_lizhou/recieved/*/*.abf'
src_paths = glob(src_dir)
overwrite = False
for src_path in tqdm(list(src_paths)):
#try:
src_fname = os.path.split(src_path)[1]
dest_fname = src_fname[:-3] + 'nwb'
dest_path = '/'.join(src_path.split('/')[:6] + ['nwb', dest_fname])
abf_num = int(src_fname[:-4])
metadata = get_metadata(abf_num, df)
if os.path.isfile(dest_path) and not overwrite:
print('skipping {}.'.format(src_fname))
else:
print('converting {}.'.format(src_fname))
kwargs = dict()
if metadata is None:
print('no metadata found for {}.'.format(src_fname))
else:
kwargs.update(metadata=metadata)
ABFConverter(src_path, dest_path, outputFeedbackChannel=True, **kwargs)