Cellseg-models-pytorch

Fixes

- Fix SCE loss bug.
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Features

- Add a Wandb artifact table callback for loading a table of test data metrics and insights to wandb.

Fixes

- Symmetric CE loss fixed.

- Add option to return binary and instance labelled mask from the dataloader. Previously binary was returned with `return_inst` flag which was confusing.
- Fix the `SegmentationExperiment` to return preds and masks at test time.

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Fixes

- Wandb Callback bugs fixed.
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Test

- Update loss tests

Fixes

- Add a conv block `BasicConvOld` to enable `Dippa` to cellseg conversion of models.
- Fix `inst_key`, `aux_key` bug in `MultiTaskUnet`
- Add a type_map > 0 masking for the `inst_map`s in post-processing

- Modify the optimizer adjustment utility function to adjust any optim/weight params.

- Modify lit `SegmentationExperiment` according to new changes.

Features

- Add optional spectral decoupliing to all losses
- Add optional Label smoothing to all losses
- Add optional Spatially varying label smoothing to all losses

- Add mse, ssim and iqi torchmetrics for metric logging.
- Add wandb per class metric callback for logging.
- Add `from_yaml` init classmethod to initialize from yaml files.

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Test

- Update tests for Inferes and mask utils.
- Add tests for the benchmarkers.

Fixes

- init and typing fixes

Docs

- Typo fies in docs

Features

- Add numba parallellized median filter and majority voting for post-processing
- Add support for own semantic and type seg post-proc funcs in Inferers

- Add segmentation performance benchmarking helper class.
- Add segmentation latency benchmarking helper class.

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Fixes

- Update `save2db` & `save2folder` for optional type_map and sem_map args.
- Pre-processing (`pre-proc`) callable arg for `_get_tiles` method. This enables the Lizard datamodule.
- Fix- padding bug with sliding window inference.

Features

- Lizard datamodule (https://arxiv.org/abs/2108.11195)

- Add a universal multi-task U-net model builder (experimental)

Test

- Update dataset tests.

- Update tests for multi-task U-Net

Type Hints

- Fix incorrect type hints.

Examples

- Add cellpose training with Lizard dataset notebook.