Skip to main content

Convert data to nwb

Project description

# nwbext_ecog: An NWB extension for ECoG data

Author: Ben Dichter

There are three data types, `Surface`, `CorticalSurfaces`, and `ECoGSubject`. `CorticalSurfaces` is simply a group (like a folder) to put `Surface` objects into. `Surface` holds surface mesh data (vertices and triangular faces) for sections of cortex. `ECoGSubject` is an extension of `Subject` that allows you to add the `CorticalSurfaces` object to `/general/subject`.

## Usage

### python

install:
```bash
pip install nwbext_ecog.git
```

write:
```python
import pynwb
from nwbext_ecog import CorticalSurfaces, ECoGSubject

nwbfile = pynwb.NWBFile(...)

...

cortical_surfaces = CorticalSurfaces()
## loop me
cortical_surfaces.create_surface(name=name, faces=faces, vertices=veritices)
##
nwbfile.subject = ECoGSubject(cortical_surfaces=cortical_surfaces)
```

You can optionally attach images of the subject's brain:
```python
from pynwb.base import Images
from pynwb.image import GrayscaleImage

subject.images = Images(name='subject images', images=[GrayscaleImage('image1', data=image_data)])
```

read:
```python
import nwbext_ecog
from pynwb import NWBHDF5IO
io = NWBHDF5IO('path_to_file.nwb','r')
nwb = io.read()
nwb.subject.cortical_surfaces
```

### MATLAB
install:
```matlab
generateExtension('/path/to/nwbext_ecog/nwbext_ecog/ecog.namespace.yaml');
```

write:
```matlab
cortical_surfaces = types.ecog.CorticalSurfaces;

%%% loop me
surf = types.ecog.Surface('faces', faces, 'vertices', vertices);
cortical_surfaces.surface.set(surface_name, surf);
%%%

file.subject = types.ecog.ECoGSubject(name, cortical_surfaces);
```


Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for nwbext-ecog, version 0.7.2
Filename, size File type Python version Upload date Hashes
Filename, size nwbext_ecog-0.7.2-py2.py3-none-any.whl (7.3 kB) File type Wheel Python version py2.py3 Upload date Hashes View
Filename, size nwbext_ecog-0.7.2.tar.gz (4.3 kB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page