# ndx-pinto-metadata
The NWB extension for storing ViRMEN experimental metadata for the Pinto lab.
## Installation
```bash
pip install ndx_pinto_metadata
```
## Usage
```python
from uuid import uuid4
from datetime import datetime
from dateutil.tz import tzlocal
import numpy as np
from pynwb import NWBFile, NWBHDF5IO
from hdmf.common.table import DynamicTable
from ndx_pinto_metadata import LabMetaDataExtension, MazeExtension
# Create NWBFile
nwbfile = NWBFile(
session_description="session_description",
identifier=str(uuid4()),
session_start_time=datetime(1970, 1, 1, tzinfo=tzlocal()),
)
# Add MazeExtension
maze_extension = MazeExtension(name="mazes", description="Holds information about the mazes for this task.")
# Add row for each maze
maze_extension.add_row(
antiFraction=0,
cueDensityPerM=3,
cueDuration=np.nan,
cueProbability=np.inf,
cueVisibleAt=10,
hideHintUntil=-15,
lContext=10,
lCue=45,
lMemory=10,
lStart=5,
maxTrialDuration=180,
turnHint=1,
numTrials=80,
numTrialsPerMin=2,
criteriaNTrials=100,
numSessions=1,
performance=np.inf,
maxBias=0.2,
easyBlock=np.nan,
easyBlockNTrials=10,
numBlockTrials=40,
blockPerform=0.55,
geoDistP=np.nan,
geoDistPEasy=np.nan,
)
# Create table for storing stimulus protocol parameters
stimulus_protocol = DynamicTable(name="stimulus_protocol", description="Holds information about the stimulus protocol.")
protocol_dict = dict(
stimulus_code="TowersTaskSwitchStimulusTrain",
numMazesInProtocol=11,
trialDraw="EradeCapped",
stimDraw="LeftOneOnly",
cueMinSeparation=12,
totalRepeatProbability=0.05,
numRepeatTrials=2,
visualcolor=np.array([0, 0, 1]),
memorycolor=np.array([0.5, 0.5, 0.]),
princetonImplementation=1,
)
for protocol_name in protocol_dict:
stimulus_protocol.add_column(
name=protocol_name,
description="stimulus protocol parameter.",
)
stimulus_protocol.add_row(**protocol_dict)
# Create LabMetaData
lab_meta_data = LabMetaDataExtension(
name="LabMetaData",
experiment_name="TowersTaskSwitchEasy",
experiment_code="TowersTaskSwitchEasy",
session_index=49,
total_reward=0.925,
surface_quality=74.22,
rig="VR_Widefield",
num_trials=242,
num_iterations=430233,
session_duration=3838.5730088,
advance=0,
mazes=maze_extension,
stimulus_protocol=stimulus_protocol,
)
# Add to NWBFile
nwbfile.add_lab_meta_data(lab_meta_data=lab_meta_data)
# Write LabMetaData to NWB file
nwbfile_path = "virmen_metadata.nwb"
with NWBHDF5IO(nwbfile_path, mode="w") as io:
io.write(nwbfile)
# Check LabMetaData was added to the NWB file
with NWBHDF5IO(nwbfile_path, mode="r", load_namespaces=True) as io:
read_nwbfile = io.read()
read_nwbfile_lab_metadata = read_nwbfile.lab_meta_data["LabMetaData"]
```
---
This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).
Raw data
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