main_select_modality.py

from add_calcium_imaging import add_calcium_imaging_thorlabs
from add_stimulus import add_stimulus_optophysiology
from add_electrophysiology import add_ephys
from add_processedROI import add_processedROI
from add_metadata import add_metadata
from add_axon_imaging import add_axon_datasets
from metadata_gui import display_metadata_nwb
from pynwb import NWBHDF5IO
import os

# Konstantinos Nasiotis


folder_name = r"C:\NWB project\Ed\Jack"
excel_fname = r"C:\NWB project\Ed\Ruthazer lab datasets.xlsx"


# 1. Initiate nwb_file and add metadata
nwbfile, single_excel_entry = add_metadata(folder_name, excel_fname)

# Display NWB metadata -  This is a standalone function - Set to False to continue to the nwb conversion
display_the_metadata = True
if display_the_metadata:
    display_metadata_nwb(nwbfile)


if single_excel_entry['experiment_type'] == 'calcium imaging':

    # 2. Add Calcium imaging
    save_raw_files_in_nwb = False
    nwbfile = add_calcium_imaging_thorlabs(nwbfile, folder_name, save_raw_files_in_nwb)

    # 3. Add timeseries of the ROIs
    nwbfile = add_processedROI(nwbfile, folder_name, save_raw_files_in_nwb, single_excel_entry)

    # 4. Add stimuli presentation events
    nwbfile = add_stimulus_optophysiology(nwbfile, folder_name, single_excel_entry)


elif single_excel_entry['experiment_type'] == 'ephys':

    # 2. Add Electrophysiology recording
    nwbfile = add_ephys(nwbfile, folder_name)


elif 'axon imaging' in single_excel_entry['experiment_type']:
    nwbfile = add_axon_datasets(nwbfile, folder_name, single_excel_entry)

# *. Close the file
identifier = os.path.basename(folder_name)  # Grab the folder name

with NWBHDF5IO(os.path.join(folder_name, identifier+'.nwb'), 'w') as io:
    io.write(nwbfile)
    print('[*] Saved ' + identifier + '.nwb file')