Biapy

Major:
- Add backward compatibility loading checkpoint

Minor:
- Change `TEST.POST_PROCESSING.MEASURE_PROPERTIES.REMOVE_BY_PROPERTIES.STAT` to `TEST.POST_PROCESSING.MEASURE_PROPERTIES.REMOVE_BY_PROPERTIES.STATS`
- Only check lr scheduler when train in enabled

Bugs fixed:
- Fix a bug in DATA.FILTER_BY_IMAGE
- Update 3D_cell_detection_zarr_tutorial.yaml with new configuration

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.4...v3.5.5

Major:
- Add BMZ exportation through configuration

Minor:
- Set automatically BMZ path and change it to `PATHS.BMZ_EXPORT_PATH`

Bugs fixed:
- Fix minor bug when loading model checkpoint
- Fix small bug in semantic seg. multiclass jaccard calculation

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.3...v3.5.4

Major:
- Update BMZ model check to support more models and increase it's robustness.

Minor:
- Add class extraction for semantic seg. BMZ models.
- Adapt instance segmentation channels to a default value depending when loading BMZ models.
- Change `LOAD_MODEL_FROM_CHECKPOINT` default value to `True`.
- Increase UNETR building process robustness

Bugs fixed:
- Fix bug when filtering by entire images.
- Prevent top-5-accuracy when classes are less than 5 in classification workflow.
- Fix bug in single data generator used in classification and SSL workflows.
- Allow BMZ/Torchvision models override completely configuration with the variables they are imposing by making `update_dependencies()` config function more generic.
- Force entire image filtering when `DATA.EXTRACT_RANDOM_PATCH` is enabled.

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.2...v3.5.3

Major:
- Add `'resunet_se'` to I2I workflow
- Extend BMZ model support
- Remove `DATA.TRAIN.MINIMUM_FOREGROUND_PER`. Now for training, validation and test a sample filtering can be made with `DATA.TRAIN.FILTER_SAMPLES`, `DATA.VAL.FILTER_SAMPLES` and `DATA.TEST.FILTER_SAMPLES` respectively.

Minor:
- Add `MODEL.LOAD_MODEL_FROM_CHECKPOINT` variable
- `DATA.PREPROCESS.MEDIAN_BLUR.FOOTPRINT` changed to `DATA.PREPROCESS.MEDIAN_BLUR.KERNEL_SIZE`
- Add robust semantic mask check using `DATA.*.CHECK_DATA`
- Divide BMZ model check into two functions so they can be reused easily by the GUI
- Change BMZ COLLECTION_URL to a new version of it

Bugs fixed:
- Fix bug in detection workflow when predicting with Zarr/H5 by chunks
- Minor fix during instance training data creation using Zarr
- Correct minor errors during BMZ model import/export

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.1...v3.5.2

Major:
- Add GRN, ConvNeXtBlock_V2 and UpConvNeXtBlock_V2 blocks

Minor:
- Change `CENTRAL_POINT_DILATION` from int to list
- Add support for fixed_zero_mean_unit_variance preprocessing for BMZ models
- Adapt BMZ model check function to work properly with models in 0.4 and 0.5 version

Bugs fixed:
- Bug in instance segmentation using only `C` channel
- Correct tags in BMZ model creation
- Adapt BMZ model check function to work properly with models in 0.4 and 0.5 version

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.0...v3.5.1

Major
- Move from Pytorch `2.2.0` to `2.4.0`
- Increase loss options
- Add options to choose train/test metrics to measure (`TRAIN.METRICS`/`TEST.METRICS`). Also added more metrics to measure in Super-resolution, Image to Image and Self-supervised workflows. Closes [86](https://github.com/BiaPyX/BiaPy/issues/86)
- Allow central point to use an ellipse footprint in Detection workflow
- Add U-NeXt V1 model
- Update BMZ code to import, finetune and export v0_4 and v0_5 spec models. Move to `bioimageio.core` version `0.6.7`
- Avoid loading entire data when creating instance labels
- Add `TEST.DET_IGNORE_POINTS_OUTSIDE_BOX` option for Detection workflow
- Remove data clipping during DA so the user is aware of the transformations
- Add `LOSS.CLASS_REBALANCE` option
- Update all notebooks with more visualization cells and descriptions.

Minor
- Remove ``TEST.EVALUATE`` option
- Organize better semantic segmentation output
- Add zoom as preprocessing in test data (only available `TEST.BY_CHUNKS == True`)
- Reorganize median filter post-processing by creating `TEST.POST_PROCESSING.MEDIAN_FILTER`, `TEST.POST_PROCESSING.MEDIAN_FILTER_AXIS` and `TEST.POST_PROCESSING.MEDIAN_FILTER_SIZE`. Removing ``TEST.POST_PROCESSING.YZ_FILTERING``, `TEST.POST_PROCESSING.YZ_FILTERING_SIZE`, ``TEST.POST_PROCESSING.Z_FILTERING`` and `TEST.POST_PROCESSING.Z_FILTERING_SIZE`
- Go back to use channel 0 as semantic mask to grow the instances in `BC `channels. Also fix resolution and channel order in `edt()` call in ``BP``.
- Remove contrast/brightness EM transformations as they were not used
- Be more permissive with provided csv file during point mask creation in detection workflow
- Add `-v` option to consult BiaPy's version

Fixes
- Fix `resunet++` issue. Closes [95](https://github.com/BiaPyX/BiaPy/issues/95)
- Number of residual groups in `RCAN`.
- Correctly read result images when reusing results. Closes [94](https://github.com/BiaPyX/BiaPy/issues/94)
- Avoid loading entire data when creating instance labels. Closes [92](https://github.com/BiaPyX/BiaPy/issues/92)
- Add load checkpoint after training again (last epoch training model has been using before)

New Contributors
* anepaniagua made their first contribution in https://github.com/BiaPyX/BiaPy/pull/85

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.4.6...v3.5.0