Documentation for development

[adam2392]

Setting up Environment

• devcontainer.json for vscode to help w/ development, by starting container in containers folder, and also install vs-code extensions
  • e.g. prettiercode, and better-comments
  • can mount the container and see the internal workings
  • just need vscode and docker
  • can change workspaceMount.
• dockercompose for running the application
• vscode -> open project -> auto-mount and auto-extension
• add to contribute.rst

Main API JS endpoints

routes:

• brain/:subject
• electrodes/:subject
• anatomy/:subject
• /:subject (e.g. ct/t1)

template pages:

• Brain_3D.jsx: pull in data API and brain API -> load in as GLTF files

Main Data Structures

1. BIDS electrodes.tsv and coordsystem.json
2. BIDS-Derivatives annotations.tsv
3. data views

Data is organized in BIDS:

The data files should be named and organized as: derivatives/seekviz/sub-<subject>/[ses-<session>]/sub-<subject>_ses-<session>_task-<task>_seek.json

Data View Abstraction

1. 2D array of data with metadata json
2. kwarg to determine if "connectivity" data or not

abstraction of data views:

• we’re account for a list here for multiple overlaid multiple views
  • by default. the anatomy and electrodes are overlaid
• for time series, only have 1 data view connectivity data view:
• LA1_LA2 example
• static
  • or just “value”
• then is a 2D array

[adam2392]

@TheBrainChain some messy notes here, but todo is to highlevel document these and then get working on #14 for me.