DeMapper: A Deconstructed Mapper (TDA) Toolbox for MATLAB

DeMapper is a simple toolbox to run Mapper techniques (from Topological Data Analysis) in MATLAB.

Find the documentation at: https://braindynamicslab.github.io/demapper/

There are many examples on how to use the tool, as tests: https://github.com/braindynamicslab/demapper/tree/master/tests

Similarly, the code is documented with the main entrypoints:

• code.mapper.mapper: run one mapper on one matrix
• code.analysis:run_main: run many mappers and many analyses on "many" matrices in parallel
• code.analysis:run_preprocess: run one preprocessing step on one matrix
• code.analysis:run_analysis: run one analysis on one matrix

Cite

This toolbox was published as Hasegan et al., Network Neuroscience, 2024. If you use this toolbox, please cite the paper.

@article{hasegan2024demapper,
  title={Deconstructing the Mapper algorithm to extract richer topological and temporal features from functional neuroimaging data},
  author={Hasegan, Daniel and Geniesse, Caleb and Chowdhury, Samir and Saggar, Manish},
  journal={Network Neuroscience},
  year={2024},
}

The code of the analysis that was presented in the paper, can be found within the folder hasegan_et_al_netneuro_2024/.

Tests

Once we make the repository public, activate the workflow to run the tests automatically. For now, run in MATLAB within the main folder:

addpath(genpath('code'))
addpath(genpath('tests'))
tests

Generating Documentation

Install sphinx

pip install -r docs/requirements.txt

Then build the sphinx documentation

sphinx-build -b html docs/source docs/build

To generate for the website, please run the following instead:

git co website                                  # Check out the website branch
git merge master                                # Merge the master branch            
                                                # Resolve any issues with the merge
sphinx-build -b html docs/source docs           # Build the documentation
git add docs                                    # Add the documentation to the staging area
git ci -m "Update documentation"                # Commit the changes
git push                                        # Push the changes to the website branch

Authors

Created and maintained by the Brain Dynamics Lab

Authors:

• Daniel Hasegan
• Caleb Geniesse
• Samir Chowdhury
• Manish Saggar