Added class for preprocessing persistence diagrams

[raphaelreinauer]

Reference issues/PRs

Added requested feature issues#65 [enhancement] Add preprocessing module for persistence diagrams

Types of changes

• [ ] Bug fix (non-breaking change which fixes an issue)
• [X] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to change)

Description

I added a Python module for extracting features from persistence diagrams, which can be used to preprocess persistence diagrams. The class is derived from Hugginfaces FeatureExtractionMixin which allows to store the parameters used for feature extraction in a JSON file, which allows to easily reproduce experiments. I have implemented normalization of the points in the persistence diagram, padding with zeros, and filtering points by persistence.

Checklist

• [X] I have read the guidelines for contributing.
• [X] My code follows the code style of this project. I used flake8 to check my Python changes.
• [X] My change requires a change to the documentation.
• [X] I have updated the documentation accordingly.
• [X] I have added tests to cover my changes.
• [X] All new and existing tests passed. I used pytest to check this on Python tests.

[matteocao]

I see there are many conflicts: Have you pulled master before pushing this fix?

[raphaelreinauer]

I see there are many conflicts: Have you pulled master before pushing this fix?

Yes, I did. The conflicts are because I have put all the constants outside of the gdeep.utils.utility in the gdeep.utils namespace.

[matteocao]

Still, I do not understand why they appear as conflicts rather than simple updates: a conflict usually happens when git cannot "play" your commits on top of the existing code. If you are changing the code starting from master, there should be no conflicts, just a normal commit. Anyway, no matter the cause, they need to be solved before we can merge. But it is not super urgent as we need to discuss about #70 first and this will probably entail some changes anyway.

[raphaelreinauer]

Still, I do not understand why they appear as conflicts rather than simple updates: a conflict usually happens when git cannot "play" your commits on top of the existing code. If you are changing the code starting from master, there should be no conflicts, just a normal commit. Anyway, no matter the cause, they need to be solved before we can merge. But it is not super urgent as we need to discuss about #70 first and this will probably entail some changes anyway.

I think it's because I merged some files from another branch. Okay, let me resolve the conflicts.

[raphaelreinauer]

Still, I do not understand why they appear as conflicts rather than simple updates: a conflict usually happens when git cannot "play" your commits on top of the existing code. If you are changing the code starting from master, there should be no conflicts, just a normal commit. Anyway, no matter the cause, they need to be solved before we can merge. But it is not super urgent as we need to discuss about #70 first and this will probably entail some changes anyway.

I think it's because I merged some files from another branch. Okay, let me resolve the conflicts.

Okay, done!