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Refactor segmentation and aggregation codes to avoid simplify code and avoid code duplication

Ghislain Durifrequested to merge
refactor_segmentation_aggregation into dev

Merging refactor_segmentation_aggregation into dev

Introduced modifications:

  • additional debugging

  • final minor fixes after segmentation/aggregation refactoring, unit tests are passing (note: some warnings raised by dependencies still present but we will manage that later)

  • fix typo when calling super.init() method

  • avoid warning about regex group not being captured

  • fix segmentation class (especially issues raised during testing)

  • fix several issues raised during testing + add new helper function

  • fix issue with indentation

  • remove useless import

  • fix indexing + add check on barcode (if needed) in test helper function

  • WIP (to be run): re-implement unit tests following refactoring of Segmentation, ImageSegmentation and VisiumSegmentation class

  • WIP (to be tested): use new implementation of Segmentation class to simplify code

  • WIP (to be tested): refactor segmentation and aggregation to avoid copied-pasted code in ImageSegmentation and VisiumSegmentation

  • minor

  • use image from test dir in dev script

Co-authored-by: Ghislain Durif gd.dev@libertymail.net

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