Metadata-Version: 2.1
Name: ndx-ecog
Version: 0.1.0
Summary: An NWB extension for storing the cortical surface of subjects in ECoG experiments
Home-page: UNKNOWN
Author: Ben Dichter
Author-email: ben.dichter@gmail.com
License: BSD 3-Clause
Description: # ndx-ecog Extension for NWB:N
        
        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 ndx_ecog
        ```
        
        write:
        ```python
        import pynwb
        from ndx_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/ndx-ecog/spec/ndx-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);
        ```
        
Platform: UNKNOWN
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Description-Content-Type: text/markdown
