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CHANGELOG.md

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Changelog

0.4.0

Released on May 31, 2022

  • Added extensive documentation, which is available on ReadTheDocs
  • Added a unit testing suite for the backend API, which has 100% code coverage
  • Polished and extended the scripts for generating a random test project and a real-world project
  • Updated all external dependencies of the frontend to their latest version
  • Replaced the deprecated THREE.Geometry with THREE.BufferedGeometry in the embedding renderer
  • Introduced linting using PyLint and Flake8 and fixed all linting warnings
  • Fixed many smaller bugs
    • The add_border function of the image_processing module added a border of ones when it was requested to add a zero border
    • Fixed a bug in the center_ crop function of the image_processing module, which in some situations cut off too much
    • Renamed blue-black-yellow color map to black-yellow for consistency
    • Fixed the return type of the render_superimposed_heatmap function, the return type was PIL.Image and is now numpy.ndarray
    • Renamed the raw_heatmap parameters to attribution_data in all relevant heatmap rendering functions of the image_processing module (raw heatmap is a term, which I used to use for attribution data, but attribution data is the common term)
    • Added validation for the label_index_regex and the label_word_net_id_regex parameters of the constructor of the ImageDirectoryDataset class
    • Fixed the parsing of label indices (they were not converted to integers) in the get_sample method of the ImageDirectoryDataset class
    • Fixed a NumPy warning (bool should be used instead numpy.bool)
    • Fixed the exception caught when retrieving samples from an Hdf5Dataset in the get_sample (this would cause the get_sample method to pass through the IndexError instead of raising a LookupError itself, when the sample was not found)
    • In the Project class some methods did not fail when the project was closed and others failed with wrong exceptions when the project was closed
    • Fixed index bound checks when retrieving attributions using the get_attribution method of the AttributionDatabase (also indirectly affected the get_attribution method of the Project class)
    • When retrieving analyses using the get_analysis method of the AnalysisDatabase class, NumPy Arrays are now returned, where previously HDF5 datasets were returned
    • In the Project class, the check whether a project contains a dataset, attributions, or analyses was incorrect and is now fixed
    • If a project has no dataset, then retrieving samples now fails with an informative exception
    • Removed the base_embedding and base_embedding_axes_indices from embeddings, because these were not specification compliant, and the feature was never used (this was feature was also removed from the Angular Frontend)
    • Renamed instances of eigen_value variable names in Python code and eigenValue variable names in TypeScript to eigenvalue
    • Simplified the code in the get_attribution_heatmap method of the Server class (previously it was tested twice whether the heatmap is to be superimposed onto the input image, now this check is only performed once)
    • Removed multiple instances of dead code (code that never ran, because the conditions to run the code were always false)
    • Fixed multiple docstrings in classes, methods, and functions (this fixes incorrect documentation, typos, or partially missing documentation)
    • Fixed a bug in the heatmap rendering, where the resulting heatmap had an extra dimension, which caused the conversion to a PNG to fail
    • Fixed a bug in the eigenvalue plot in the frontend, where, when an embedding did not use eigenvalue decomposition or there are no eigenvalues available for the embedding, then the ViRelAy frontend raised an error, now the eigenvalue plot is simply not displayed when an embedding has no eigenvalues
    • Fixed a bug in the overlay image mode of ViRelAy, when there was no negative component in an attribution, then the heatmap was displayed instead of the heatmap superimposed onto the input image
    • When superimposing a heatmap onto an input image, the negative and positive components are now weighted equally, thus making the negative and positive attribution parts comparable

v0.3.1

Released on July 5, 2021

  • PyPI release
  • updated example in README
  • updated paper reference in README

v0.3.0

Released on June 24, 2021

  • Added a license (AGPL)
  • Added a share button, which generates a link that restores the entire current state

v0.2.0

Released on June 24, 2021

  • Initial stable public release