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Version 3.5.13

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@danifranco danifranco released this 30 Apr 10:01
· 597 commits to master since this release
v3.5.13
89e5132

Major:

  • Completely restructure the inference by chunks (closing #91):
    • A custom Pytorch dataloader is used to speed up the process taking into account number of workers and multiple GPUs
    • Now this inference always creates a Zarr, even if the inputs are H5 files, thus, TEST.BY_CHUNKS.FORMAT was removed
    • Now to division mask is needed, speeding up the process and saving disk space
  • Complete synapse detection pipeline by adding metrics, debug files, etc. Now it should not be experimental anymore
  • Add remove close points by distance+mask as post-processing for the synapses (remove_close_points_by_mask function)

Minor:

  • Add two optional cells in the inference notebook to transform 3D images/videos into 2D images, and the inverse task after prediction. This allows the users to process 3D data using a 2D model (closing #115)
  • Add B channel in synapse segmentation
  • Merge train/test/val instance creation into one function
  • Add zarr_to_tif.py utility script
  • Change SYSTEM.NUM_WORKERS default value to -1 and remove it from all templates (closing #114).
  • Make ensure_3d_shape function more robust and write_chunked_data to write in 'ZYXC' axes order always
  • Move activations into model_call function, removing redundant code (closing #110)
  • Add new losses description in SR, SSL and I2I workflows
  • Add option to ignore a value in instance masks (still experimental)
  • Add TEST.DET_TH_TYPE option
  • Add PROBLEM.INSTANCE_SEG.SYNAPSES.TH_TYPE option
  • Add a new feature to export the calculated metrics into a CSV file (closing #116 and #117)
  • Change the way saved cfg in checkpoint is merged with the current cfg (now it is more robust as the cfg is always translated into the current version)
  • Move to bioimageio.core==0.8.0 version
  • Update notebooks:
    • Move installation up to restart notebook after reinstalling numpy
    • Update BMZ cell with latest fields

Bugs fixed:

  • Disable norm by image when using Zarr/H5 images
  • Fix error when instances were generated using a Zarr/H5, as the axes need to be modified always in the next runs so the user does not need to know how the data was created/axes order
  • Solve minor bug in blocks.py that lead to errors while building U-Next models.
  • Ensure only the input cfg is copied one time in DDP setting
  • Solve problem in during shape mismatch check
  • Avoid copying gt_associated_id always, reducing the amount of memory for training
  • Make ensemble functions work as before returning a torch.Tensor
  • Reduce the code in I2I workflow reusing predict_batches_in_test
  • Remove convert_old_model_cfg_to_current_version from misc.py so to use the one from biapy.engine.check_configuration instead
  • Add MODEL.BMZ.EXPORT.DATASET_INFO when converting the an old cfg into the current version
  • Fix error during old cfg conversion with PATHS.LWR_Y_FILE old key
  • Relax test25 constraints and fix Dapi_dataset path
  • Correct load_data_from_dir function converting it to the way we load data before by just giving a path (closing #109)
  • Solve diff_between_configs function
  • Solve edge problem with by_chunks_collate_fn function
  • Adapt chunks size of the of the Zarr to be created in by chunks setting by transposing the axes into the Zarr axe order

Full Changelog: v3.5.12...v3.5.13

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