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 add_tdms_ch(self, grp_name, ch_name: str, ch_properties: dict,
data: list) -> None:
"""
add a channel object to the segment set that will eventually be added to the tdms object
:param grp_name: name of the parent group
:param ch_name: name of the channel
:param ch_properties: dictionary of the channel properties
:param data: dictionary of the channel data
"""
channel = nptdms.ChannelObject(grp_name,
ch_name,
data,
properties=ch_properties.copy())
self.tdms_object_set.update({channel})
def write_chunks_to_file(
tdms_writer: nptdms.TdmsWriter,
index_ranges: List[Tuple[int, int]],
group,
channel,
segment_size: int,
):
"""Writes correct data slice per slice to disk.
Arguments:
tdms_writer: Tdms handle for the new file
index_ranges: Chunk Indices that point to valid data slices
group: TDMS Group inside the old tdms file
channel: TDMS Channel inside group
segment_size: Sets size of each segment written to a TDMS file
"""
clean_data = []
clean_data_nbytes = 0
for (offset, length) in tqdm.tqdm(index_ranges):
data = channel.read_data(offset=offset, length=length)
clean_data.append(data)
clean_data_nbytes += data.nbytes
# When segment_size is reached, a new segment is written to file
if clean_data_nbytes > segment_size * 1_000_000_000:
new_channel = nptdms.ChannelObject(group.name, channel.name,
np.concatenate(clean_data))
tdms_writer.write_segment([new_channel])
clean_data = []
clean_data_nbytes = 0
# The remaining chunks are written to file as a last smaller segment
if clean_data:
new_channel = nptdms.ChannelObject(group.name, channel.name,
np.concatenate(clean_data))
tdms_writer.write_segment([new_channel])
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])