Biapy

Minor:
- Avoid copying a temporal file to merge updated cfg with the input one
- Add a new function to know the differences between input config and current one
- Add BiaPy version to log

Bugs fixed:
- Always translate input configuration to the current version
- Allow BMZ affinity model consumption
- Fix area calculation in instance segmentation stats
- Add xarray version constraint as the latest `xarray-2025.3.0` is crashing in `bioimageio.core` imports

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.11...v3.5.12

Major:
- Adapt `DFCAN` to 3D and add SSIM-based loss
- Adapt `RCAN` to 3D
- Ensure appropiate data range when calculating metrics in `SR`, `SSL` and `I2I` workflows.
- Implement more data/sample filtering methods: `'target_mean'`, `'target_min'`, `'target_max'`, `'diff'`, `'diff_by_min_max_ratio'`, `'diff_by_target_min_max_ratio'`
- Distribute better loading data code into classes
- Add in all most code Typing checks for Pydantic/Pylance
- Rename `'custom'` normalization into `'zero_mean_unit_variance'`
- Separate into a class the normalization module to reduce repeated code
- Avoid doing normalization for test GT data in `I2I`, `SR`, `SSL` and `Denoising`
- Organize metrics for `I2I`, `SR` and `SSL` depending on train and test
- Avoid creating X data during `Instance segmentation` saving disk space
- Improve `Detection` workflow when multihead output is created
- Add `SSIM`, `W_MAE_SSIM` and `W_MSE_SSIM` losses for `I2I`, `SR` and `SSL` workflows
- Move some variables from `TEST.BY_CHUNKS` to `DATA.TEST`

Minor:
- Change 2D image load to be more robust
- BMZ connection:
- Add task description option
- Add model version
- Change `env.yaml` created
- Change BMZ model import message error
- Add more `Instance segmentation` model support when consuming BMZ models
- Allow multiple ddp runs without closing the process group initialization
- Add script to change a parameter in the RDF file of a BMZ model
- Update DDP messages and wait points
- Remove mixed precision in evaluation
- Add `find_unused_parameters` when using `resunet_se` with DDP
- Add more information while gathering training/validation data
- Add more options to tune `RCAN` model
- Add script for blur estimation
- Add script to measure similarity metrics common in `I2I` and `SR` workflows
- Add tensor conversion in metric calculation
- Add changes to `convert_old_model_cfg_to_current_version` in order to convert old configurations into new
- Upgrade filtering saving examples of the patches/images filtered so the user can check them
- Change `DATA.FILTER_BY_IMAGE` default value to `False`
- Wrap rotate function to allow `float16`

Bugs fixed:
- Fix minor bug in instance segmentation when test is not enabled and test path does not exist
- Instance masks folder name update to not set always contour info
- Solve bugs in `U-Next V1` and `U-Next V2` models when using more than one channel
- Fix 3D `U-NeXt` models
- BMZ connection:
- Resize cover to ensure the shape
- Avoid adding duplicate tags
- Ensure only a patch is taken for BMZ input when working with H5/Zarr files
- Ensure only `pytorch_state_dict` models are consumed
- Correct `C` channel activation during `Instance segmentation` when it is used alone.
- Fix minor error during `MODEL.BMZ.EXPORT.DATASET_INFO` check
- Solve minor bug in `convert_old_model_cfg_to_current_version` function
- Fix conversion to RGB in generators
- Fix problem with `TEST.REDUCE_MEMORY`
- Calculate metrics when reusing predictions (`TEST.REUSE_PREDICTIONS`). They are calculated as `"merge_patches"`
- Allow `SSL` pretrainings during model check
- Add restrictions in `SR`, `SSL` and `I2I` workflows to not use `wdsr` in 3D

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.10...v3.5.11

Minor:
- Disable mixed precision calls
- Move data IO management to biapy/data and create `imread`/`imwrite` functions to avoid using `skimage.io` as they are deprecating these functions
- Change `timm.optim` call to avoid warning of future deprecation
- BioImage Model Zoo related (BMZ) changes:
- Add function to autogenerate a `documentation.md`
- Move BMZ related functions to `bmz_utils.py`
- Add test_model at the end of BMZ model creation with a larger tolerance than the default so the differences due to casting are allowed
- Create cover extracting a patch containing mask information
- Add argument to provide the dataset id when exporting a BMZ model
- Ensure `weights_only=True` during checkpoint loading stage when building a BMZ model

Bugs fixed:
- Checkpoint load on DDP right after training fixed
- Update installation restricting torchmetric version to avoid an issue in classification workflow

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.9...v3.5.10

Major:
- Add synapse segmentation options for instance segmentation (in experimental state)

Minor:
- Add script to convert instance segmentation datasets into detection workflow format
- Print a better message when shapes does not match between samples
- Some variables for detection has been modified and now don't need to be set per class values:
- Change `TEST.POST_PROCESSING.REMOVE_CLOSE_POINTS_RADIUS` default value to `0`
- Change `TEST.POST_PROCESSING.DET_WATERSHED_FIRST_DILATION` default value to `[-1,-1]`
- Change `TEST.DET_MIN_TH_TO_BE_PEAK` default value to `0.2`
- Change `TEST.DET_TOLERANCE` default value to `10`
- Add instance segmentation multihead test in `run_checks.py`
- Update `convert_old_model_cfg_to_current_version` function to cover new changes

Bugs fixed:
- Handle multiple data within Zarr/H5 during test
- Delete channel restriction when ensuring 3D shape ([convert_instance_data_to_detection.py](https://github.com/BiaPyX/BiaPy/blob/master/biapy/utils/scripts/convert_instance_data_to_detection.py))
- Fix class prediction to the points in detection
- Fix error with `diplib` package
- Fix issue between `TRAIN.PATIENCE` and `TRAIN.LR_SCHEDULER.REDUCEONPLATEAU_PATIENCE`
- Solve issues with data type during detection watershed so the instance properties can be measured with `diplib` as it does not support int64 data type
- Fix issue when multiple raw images (lightmycells case) were provided
- Fix issue with BMZ model exportation
- Solve issues with `run_checks.py` due to recent changes. Now it is correctly reporting when a test crashes as it will crash too.

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.8...v3.5.9

Bugs fixed:
- Fix Torchvision calls for semantic seg, detection and instance segmentation workflows

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.7...v3.5.8

Major:
- Rebuilt CartoCell tutorial organization and update notebooks.
- Update templates to follow the same configuration as in the notebooks, which achieve good results in the example datasets.

Minor:
- Improve robustness loading 3D images
- Make SurfaceArea only requested in 3D images
- Update example dataset paths to `raw` and `label` in most cases to be consistent

Bugs fixed:
- Fix bug during `TEST.REDUCE_MEMORY`
- Fix errors while loading H5 nested data
- Solve bug when loading Zarr/H5 files into memory for training
- Fix missing import in some workflows
- Changes in instance segmentation's statistic calculation:
- Add `diplib` library as a dependency to calculate surface area more precisely and enable `elongation` for 3D which is P2A in `diplib`
- Correct centroid coordinates
- Make `SurfaceArea` only requested in 3D images to accelerate the process
- Fix bug in the filtering while predicting by chunks

**Full Changelog**: https://github.com/BiaPyX/BiaPy/compare/v3.5.6...v3.5.7