image_mask=moremat['mask'][:, :, idx],
roi_status=neuron_status_dict.get(moremat['badROIs01'][idx]),
fitness=moremat['fitness'][idx],
neuron_type=neuron_type_dict.get(neuron_type[idx], 'unknown'),
roi2surr_sig=roi2surr_sig[idx],
offsets_ch1_pix=offsets_ch1_pix[idx])
# create a ROI region table
roi_region = plane_segmentation.create_roi_table_region(
description='good roi region table',
region=(np.where(moremat['badROIs01'] == 0)[0]).tolist())
# ------ Trial Segmentation processing module ------
trial_seg_mod = nwbfile.create_processing_module(
'Trial-based-Segmentation', 'Trial-segmented data based on different event markers')
dF_F = nwb_ophys.DfOverF(name='deconvolved dF-over-F')
trial_seg_mod.add_data_interface(dF_F)
# ingest each trial-based dataset, time-lock to different event types
for data_name in ('firstSideTryAl', 'firstSideTryAl_COM', 'goToneAl', 'rewardAl', 'commitIncorrAl',
'initToneAl', 'stimAl_allTrs', 'stimAl_noEarlyDec', 'stimOffAl'):
try:
dF_F.add_roi_response_series(
nwb_ophys.RoiResponseSeries(
name=data_name,
data=postmat[data_name].traces.transpose([1, 0, 2]),
unit='',
rois=roi_region,
timestamps=postmat[data_name].time,
description=f'(ROIs x time x trial), aligned to event_id: {postmat[data_name].eventI}'))
except Exception as e:
offsets_ch1_pix=offsets_ch1_pix[idx])
# create a ROI region table
roi_region = plane_segmentation.create_roi_table_region(
description='good roi region table',
region=(np.where(moremat['badROIs01'] == 0)[0]).tolist())
# ------ Trial Segmentation processing module ------
trial_seg_mod = nwbfile.create_processing_module(
'Trial-based-Segmentation', 'Trial-segmented data based on different event markers')
# ingest each trial-based dataset, time-lock to different event types
for data_name in ('firstSideTryAl', 'firstSideTryAl_COM', 'goToneAl', 'rewardAl', 'commitIncorrAl',
'initToneAl', 'stimAl_allTrs', 'stimAl_noEarlyDec', 'stimOffAl'):
try:
dF_F = nwb_ophys.DfOverF(name = f'dFoF_{data_name}')
for tr_idx, d in enumerate(postmat[data_name].traces.transpose([2, 1, 0])):
dF_F.add_roi_response_series(
nwb_ophys.RoiResponseSeries(
name=f'Trial_{tr_idx:02d}',
data=d,
unit='',
rois=roi_region,
timestamps=postmat[data_name].time,
description=f'(ROIs x time), aligned to event_id: {postmat[data_name].eventI}'))
trial_seg_mod.add_data_interface(dF_F)
except Exception as e:
print(f'Error adding roi_response_series: {data_name}\n\t\tErrorMsg: {str(e)}\n', file=sys.stderr)
# ------ Behavior processing module ------
behavior_mod = nwbfile.create_processing_module(