Metadata-Version: 2.1
Name: ndx-whisk
Version: 0.1.1
Summary: NWB extension to store whisker tracking measurements computed with Whisk (Janelia Whisker Tracker) or other video-based whisker tracking methods.
Home-page: 
Author: Vincent Prevosto
Author-email: prevosto@mit.edu
License: BSD-3
Keywords: NeurodataWithoutBorders,NWB,nwb-extension,ndx-extension
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Description-Content-Type: text/markdown; charset=UTF-8
License-File: LICENSE.txt

# ndx-whisk Extension for NWB

ndx-whisk is an [NWB](https://www.nwb.org/) extension to store whisker tracking measurements. It is intended to convert `.whiskers` and `.measurements` files generated by [whisk (Janelia Whisker Tracker)](https://github.com/nclack/whisk/), or saved to `hdf5` with [WhiskiWrap](https://github.com/cxrodgers/WhiskiWrap), but can be used with other whisker tracking methods.

## Installation

`pip install ndx-whisk`

## Usage

See test script `test_whiskermeasurement.py` in `src/pynwb/tests`.  

```python
from pynwb import NWBHDF5IO, NWBFile
from ndx_whisk import WhiskerMeasurementTable
import numpy as np

# Load your data
whisker_data = read_whisker_measurement_table('tracked_data.whiskers')

# Create a WhiskerMeasurementTable
whisker_meas = WhiskerMeasurementTable(
    name='name',
    description='description'
)

# Add data to the WhiskerMeasurementTable
for i in range(np.shape(whisker_data['frame_id'])[0]):
    whisker_meas.add_row({k: whisker_data[k][i] for k in whisker_data.keys()})
    
# Set up a NWB file
nwbfile = set_up_nwbfile()
path = 'tracked_data.nwb'

# Add a ProcessingModule for behavioral data
behavior_module = nwbfile.create_processing_module(
    name="behavior", description="Processed behavioral data"
)

# Add the WhiskerMeasurementTable
nwbfile.processing['behavior'].add(whisker_meas)

# Save to NWB file
with NWBHDF5IO(path, mode='w') as io:
    io.write(nwbfile)
```

---
This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).
