bids_explorer 0.1.0

A simple bids dataset explorer without being too strict

Tool for exploring BIDS datasets which allows more flexibility than mne-bids or pybids (which are both amazing tools I use very often but sometimes lack flexibility).

Introduction

BidsArchitecture is the primary object for managing BIDS dataset structures. When provided with a directory (root) containing a BIDS dataset, an instance of BidsArchitecture extracts key information about the dataset's structure and populates a pandas DataFrame with relevant details, such as subject identifiers, sessions, and other metadata.

Once initialized, the instance supports various operations to filter and select subsets of the dataset based on criteria like sessions, tasks, and other BIDS entities.

It is assumed that the dataset adheres to the BIDS specification, following a directory tree structure similar to the example below:

root
├── sub-01
│   ├── ses-01
│   │   └── eeg
│   │       └── sub-01_ses-01_task-aTask_eeg.edf
│   └── ses-02
│       └── eeg
│           └── sub-01_ses-02_task-aTask_eeg.edf
└── sub-02
    │   └── eeg
    │       └── sub-02_ses-01_task-aTask_eeg.edf
    └── ses-02
        └── eeg
            └── sub-02_ses-02_task-aTask_eeg.edf

Installation

For the moment this module is not published on pypi so the installation will require you to follow these steps:

1. Make sure poetry is installed on your machine (or the remote machine you are working on). Poetry is a dependancies and environment manager which make easier python deployment. It is very straightforward to install, just follow the instruction on their website
2. Go to your projects folder cd ~/projects (or wherever it is)
3. Clone this repository git clone https://github.com/Sam54000/bids_explorer.git.
4. Move to the cloned repository cd ./bids_explorer
5. Run poetry install

Quick start

The main class is BidsArchitecture.

import bids_explorer

# Create an instance of BidsArchitecture
bids = bids_explorer.BidsArchitecture(root="path/to/bids/dataset")

The dataset will be represented by the attribute database, which is a pandas DataFrame containing all the individual files within the dataset.

The BidsArchitecture instance also provides several attributes corresponding to BIDS entities, such as:

• subjects
• sessions
• tasks
• acquisitions
• runs
• description
• suffixes
• extension
• datatype

>>> bids.subjects
["01","02"]
>>> bids.sessions
["01","02"]

In this example:

• bids.subjects returns a list of all subject identifiers.
• bids.sessions returns a list of all session identifiers.

Selecting files

ou can select files based on BIDS entities. For example, to retrieve files only for subject "01":

selected_files = bids.select(subject="01")

This will return a new instance of BidsArchitecture containing only the selected files.

Performing operations between two BidsArchitecture instances

Performing operations between two BidsArchitecture instances is possible. The available operations are + and - and * (intersection).

bids1 = bids_explorer.BidsArchitecture(root="path/to/bids/dataset1")
bids2 = bids_explorer.BidsArchitecture(root="path/to/bids/dataset2")

Add 2 Architectures:

merged_architecture = bids1 + bids2

Subtract 2 Architectures:

subtracted_architecture = bids1 - bids2

Intersection of 2 Architectures:

intersection_architecture = bids1 * bids2

Removing entries from the BidsArchitecture instance

It is possible to remove entries from the BidsArchitecture instance.

bids = bids.remove(subject="01", session="01")

This will return a new instance of BidsArchitecture with the specified files removed.

Error logging

A nice feature of BidsArchitecture is its errors attributes which is a panda DataFrame that lists all the files that doesn't follow BIDS format within the dataset.