def export_to_tmds(meta: source.MetaData, source_file: Any,
export_path: pathlib.Path) -> None:
"""Exports the valid data slices into a new TDMS file on disk.
Don't mind the nested for loops, the sizes of the iterators of the first
and second stage are very small.
Arguments:
meta: meta data of source file
source_file: Tdms file, that passed all consistency checks
export_path: File path for the corrected TDMS file.
"""
index_ranges = prepare_data_correction(source_file)
with nptdms.TdmsWriter(export_path) as tdms_writer:
for group in source_file.tdms_operator.groups():
for channel in group.channels():
if len(channel) > 0:
write_chunks_to_file(
tdms_writer,
index_ranges,
group,
channel,
meta.segment_size,
)
def capture_chunk(self, in_data, frame_count, time_info, status):
self.data = np.fromstring(in_data, dtype=np.float32)
if self._has_runner:
data_chunk = nptdms.ChannelObject(self.group_name,
self.channel_name,
self.data,
properties={})
if self.filepath is not None:
with nptdms.TdmsWriter(self.filepath, 'a') as writer:
writer.write_segment([data_chunk])
return (self.data, pyaudio.paContinue)
def copy_tdms(nwb, in_path, out_path, nrois):
num_all_rois = nwb['/processing/Acquired_ROIs/roi_spec'].shape[0]
print('Copying {} of {} ROIs from {} to {}'.format(
nrois, num_all_rois, in_path, out_path))
in_tdms = nptdms.TdmsFile(in_path)
group_name = 'Functional Imaging Data'
with nptdms.TdmsWriter(out_path) as out_tdms:
root, group = in_tdms.object(), in_tdms.object(group_name)
out_tdms.write_segment([root, group])
for ch, channel in {'0': 'Red', '1': 'Green'}.items():
ch_name = 'Channel {} Data'.format(ch)
ch_obj = in_tdms.object(group_name, ch_name)
shape = (cycles_per_trial(nwb), num_all_rois, -1)
ch_data = ch_obj.data.reshape(shape)
subset = ch_data[:, :nrois, :].reshape(-1)
new_obj = nptdms.ChannelObject(group_name, ch_name, subset, properties={})
out_tdms.write_segment([new_obj])
def write(self):
"""write the tdms segment set with root object, group objects and channel objects into one tdms file"""
with nptdms.TdmsWriter(self.tdms_file_path) as writer:
writer.write_segment(self.tdms_object_set)