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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

pip install nwbext_ecog.git

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:
from pynwb.base import Images
from pynwb.image import GrayscaleImage

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

import nwbext_ecog
from pynwb import NWBHDF5IO
io = NWBHDF5IO('path_to_file.nwb','r')
nwb =


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);

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