NWB:N extension for storing metadata for Tank lab
Project description
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)
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