import os import retinotopic_mapping.DisplayLogAnalysis as dla import NeuroAnalysisTools.NwbTools as nt curr_folder = os.path.dirname(os.path.realpath(__file__)) os.chdir(curr_folder) nwb_fn = [f for f in os.listdir(curr_folder) if f[-4:] == '.nwb'][0] nwb_f = nt.RecordedFile(nwb_fn) stim_pkl_fn = [f for f in os.listdir(curr_folder) if f[-4:] == '.pkl'][0] stim_log = dla.DisplayLogAnalyzer(stim_pkl_fn) nwb_f.add_visual_display_log_retinotopic_mapping(stim_log=stim_log) nwb_f.close()
notebook_path = os.path.join(curr_folder, 'notebook.txt')
with open(notebook_path, 'r') as ff:
notes = ff.read()
general = nt.DEFAULT_GENERAL
general['experimenter'] = experimenter
general['subject']['subject_id'] = mouse_id
general['subject']['genotype'] = genotype
general['subject']['sex'] = sex
general['subject']['age'] = age
general['optophysiology'].update({'imaging_plane_0': {}})
general['optophysiology']['imaging_plane_0'].update({'indicator': indicator})
general['optophysiology']['imaging_plane_0'].update(
{'imaging_rate': imaging_rate})
general['optophysiology']['imaging_plane_0'].update(
{'imaging_depth': imaging_depth})
general['optophysiology']['imaging_plane_0'].update(
{'location': imaging_location})
general['optophysiology']['imaging_plane_0'].update({'device': imaging_device})
general['optophysiology']['imaging_plane_0'].update(
{'excitation_lambda': imaging_excitation_lambda})
general['notes'] = notes
file_name = date_recorded + '_M' + mouse_id + '_' + sess_num + '.nwb'
rf = nt.RecordedFile(os.path.join(curr_folder, file_name),
identifier=file_name[:-4],
description='')
rf.add_general(general=general)
rf.close()
background=background) # ================================================================================= # ======================= Set Stimuli Sequence ==================================== all_stim = [uc, fc, sl, sn, lsn, dgc, sgc, si, ss] stim_seq = [all_stim[stim_ind] for stim_ind in cs_stim_ind_sequence] cs.set_stimuli(stimuli=stim_seq, static_images_path=static_images_path) # ================================================================================= # =============================== display ========================================= ds.set_stim(cs) log_path, log_dict = ds.trigger_display() # =============================== display ========================================= # =============================== convert log to .nwb ============================= import os import WarpedVisualStim.DisplayLogAnalysis as dla import NeuroAnalysisTools.NwbTools as nt log_folder, log_fn = os.path.split(log_path) log_nwb_path = os.path.splitext(log_path)[0] + '.nwb' save_f = nt.RecordedFile(filename=log_nwb_path, identifier=os.path.splitext(log_fn)[0], description='') stim_log = dla.DisplayLogAnalyzer(log_path) save_f.add_visual_display_log_retinotopic_mapping(stim_log=stim_log) save_f.close() # =============================== convert log to .nwb ============================= # =============================== show plot======================================== plt.show() # =================================================================================