ndx-tank-metadata

NWB LabMetaData extension for Tank lab.

Install

$ pip install ndx-tank-metadata

Usage

This extension is built for extending the LabMetaData schema with custom fields requested for the conversion of Virmen metadata. The extension is built into the Tank lab conversion pipeline (tank-lab-to-nwb) and is not necessary to be installed separately. Alternatively, it can be used from a python script as demonstrated below.

import os
from pynwb import NWBFile, NWBHDF5IO
from datetime import datetime

from ndx_tank_metadata import LabMetaDataExtension, RigExtension, MazeExtension

nwbfile = NWBFile('description', 'id', datetime.now().astimezone())

# Add rig information
rig = {'name': 'rig',
       'rig': 'VRTrain6',
       'simulationMode': 0,
       'hasDAQ': 1,
       'hasSyncComm': 0,
       'minIterationDT': 0.01,
       'arduinoPort': 'COM5',
       'sensorDotsPerRev': [1967.6, 1967.6, 1967.6, 1967.6],
       'ballCircumference': 63.8,
       'toroidXFormP1': 0.5193,
       'toroidXFormP2': 0.5171,
       'colorAdjustment': [0., 0.4, 0.5],
       'soundAdjustment': 0.2,
       'nidaqDevice': 1,
       'nidaqPort': 1,
       'nidaqLines': [0, 11],
       'syncClockChannel': 5,
       'syncDataChannel': 6,
       'rewardChannel': 0,
       'rewardSize': 0.004,
       'rewardDuration': 0.05,
       'laserChannel': 1,
       'rightPuffChannel': 2,
       'leftPuffChannel': 3,
       'webcam_name': 'Live! Cam Sync HD VF0770'}
rig_extension = RigExtension(**rig)

# Create mazes table
maze_extension = MazeExtension(name='mazes',
                               description='description of the mazes')

maze_dict = {'world': 1,
             'lStart': '5',
             'lCue': '45',
             'lMemory': '10',
             'cueDuration': 'NaN',
             'cueVisibleAt': 'Inf',
             'cueProbability': 'Inf',
             'cueDensityPerM': '3',
             'nCueSlots': '3',
             'tri_turnHint': 1,
             'color': [],
             'turnHint_Mem': 0,
             'numTrials': 10,
             'numTrialsPerMin': 2,
             'criteriaNTrials': 1,
             'warmupNTrials': [],
             'numSessions': 0,
             'performance': 0, 
             'maxBias': 1,
             'warmupMaze': [],
             'warmupPerform': [],
             'warmupBias': [],
             'warmupMotor': [],
             'easyBlock': 0,
             'easyBlockNTrials': 10,
             'numBlockTrials': 20,
             'blockPerform': 0.7}

# Add each maze to extension
maze_extension.add_row(**maze_dict)

# Create LabMetaData container
lab_metadata_dict = dict(
    name='LabMetaData',
    experiment_name='test',
    world_file_name='test',
    protocol_name='test',
    stimulus_bank_path='test',
    commit_id='test',
    location='test',
    num_trials=245,
    session_end_time=datetime.utcnow().isoformat(),
    rig=rig_extension,
    mazes=maze_extension
)

# Populate metadata extension 
lab_metadata = LabMetaDataExtension(**lab_metadata_dict)

# Add to file
nwbfile.add_lab_meta_data(lab_metadata)

filename = 'test_labmetadata.nwb'
with NWBHDF5IO(filename, 'w') as io:
    io.write(nwbfile)