# 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).
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"description": "# ndx-whisk Extension for NWB\n\nndx-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.\n\n## Installation\n\n`pip install ndx-whisk`\n\n## Usage\n\nSee test script `test_whiskermeasurement.py` in `src/pynwb/tests`. \n\n```python\nfrom pynwb import NWBHDF5IO, NWBFile\nfrom ndx_whisk import WhiskerMeasurementTable\nimport numpy as np\n\n# Load your data\nwhisker_data = read_whisker_measurement_table('tracked_data.whiskers')\n\n# Create a WhiskerMeasurementTable\nwhisker_meas = WhiskerMeasurementTable(\n name='name',\n description='description'\n)\n\n# Add data to the WhiskerMeasurementTable\nfor i in range(np.shape(whisker_data['frame_id'])[0]):\n whisker_meas.add_row({k: whisker_data[k][i] for k in whisker_data.keys()})\n \n# Set up a NWB file\nnwbfile = set_up_nwbfile()\npath = 'tracked_data.nwb'\n\n# Add a ProcessingModule for behavioral data\nbehavior_module = nwbfile.create_processing_module(\n name=\"behavior\", description=\"Processed behavioral data\"\n)\n\n# Add the WhiskerMeasurementTable\nnwbfile.processing['behavior'].add(whisker_meas)\n\n# Save to NWB file\nwith NWBHDF5IO(path, mode='w') as io:\n io.write(nwbfile)\n```\n\n---\nThis extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).\n",
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