v0.1.26

0.1.26 — 2025-05-07

Removed

• Removed datamodules module
• Removed datasets module

Refactor

• Refactored the whole model interface to be more user-friendly.

Features

• Added a new wsi module, including:

  • A SlideReader class to read patches from a WSI slide.
    • Backends: Openslide, CUCIM
    • Adapted the reader class from HistoPrep library. Props to Jopo666
  • get_sub_grids function to get subgrids from a WSI slide. Can be used to filter the patches. Based on connected components.

• Added a new torch_datasets module, including:

  • WSIDatasetInfer class to run inference directly from WSIs.
    • Adapted the class from HistoPrep library. Props to Jopo666
  • TrainDatasetH5 class to handle training data for the models from a h5 file.
  • TrainDatasetFolder class to handle training data for the models from img and label folders.

• Added a new inference.WsiSegmenter-class to handle the segmentation of WSIs.

• Added a new wsi.inst_merger.InstMerger-class to handle the merging of instance masks at image boundaries.

• Added inst2gdf and sem2gdf functions to utils.vectorize module. These functions convert efficiently instance and semantic masks to GeoDataFrame objects.

• Added FileHandler.to_mat and FileHandler.to_gson save functions that take in a dictionary of model output masks (output from the Inferer-classes) and save it to a .mat or '.feather', '.geojson', '.parquet' files.

Added Dependencies

• Added libpysal dependency
• Added networkx dependency

Removed Dependencies

• Removed lightning dependency
• Removed albumentations dependency

Chore

• Move FolderDatasetInferto torch_datasets module