Releases: BiaPyX/BiaPy
Releases · BiaPyX/BiaPy
Version 3.4.3
Minor:
- Improve the messaging of some errors to make them more comprehensible for the end user.
- Restrict
TEST.POST_PROCESSING.REPARE_LARGE_BLOBS_SIZE
usage to instance segmentation workflow andBP
channels. - Allow detection and denoising workflows use
unetr
andmultiresunet
models. - Change affine
AUGMENTOR.AFFINE_MODE
toreflect
by default. - Now the grid in the aumented samples saved take into account the image size to alway create 5x5 grid.
- Adapt MAE's grid mask to be operative in 3D.
Bug fixes:
- 3D stack metric values.
- Fix errors in
DATA.PROBABILITY_MAP
. - Prevent
TEST.POST_PROCESSING.CLEAR_BORDER
remove all instances in 2D. - Fix minor bugs during some of the instance segmentation post-processing due image shape mismatch.
- Now
TEST.POST_PROCESSING.CLEAR_BORDER
andTEST.POST_PROCESSING.VORONOI_ON_MASK
are aboveTEST.POST_PROCESSING.MEASURE_PROPERTIES.REMOVE_BY_PROPERTIES
so the instances can be repaired before filtering and stats. - Minor bugs in detection watershed
- Fix bug during detection mask creation for Zarr images with more than one channel
- Fix process_sample_by_chunks() function call in multi-gpu setting due to recent changes
- Fix errors in percentile clipping
- Avoid stuck processes to jump into inference phase in multi-gpu configuration when setting patience during training
- Fix cross-validation errors: 1) when using it in SR workflow due to its upsampling ; 2) in classification
- Fix bug in grid masking using mae in SSL workflow
- Add preprocessing function into classification
- Minor bug when
C
is not the last channel using Zarr inference
Full Changelog: v3.4.2...v3.4.3
Version 3.4.2
Fix:
- Downgrade scikit-image version to avoid reloading the kernel in Colab notebooks
- I2I workflow inference edge case fixed when multiple images in multiple directories where found leading to an infinite loop.
Full Changelog: v3.4.1...v3.4.2
Version 3.4.1
Minor:
- Add BiaPy version into YAML files
Fix:
- Update pyproject.toml specifiying a few libraries more to not be that restrictive and so BiaPy is smoothly installed in Colab
Full Changelog: v3.4.0...v3.4.1
Version 3.4.0
Major:
- Allow to train with large Zarr/H5 files without loading data in memory
- Adapt by_chunks to multichannel data
- Add option to reuse predictions in test
Minor:
- Calculate detection metrics in by_chunks setting
- Add DATA.NORMALIZATION.CUSTOM_MODE option
- Add percentile normalization
Fix:
- Correct bug when discading samples from training when using TRAIN.MINIMUM_FOREGROUND_PER
- Fix PSNR calculation in I2I and SR workflows
- Update notebooks and correct errors related to gdown package
- Correct validation paths in generators when in memory is False
Full Changelog: v3.3.14...v3.4.0
Version 3.3.15
Fix:
- Preprocessing checking
- PSNR calculation in I2I and SR workflows
Full Changelog: v3.3.14...v3.3.15
Version 3.3.14
New functionality:
- Add multithread detection
Fix:
dense
contour creation in 3D- Add grid masking to MAE
- Ensure validation logs prints metric/loss in the same order as with training data
- Solve problems in recently added Image to Image (I2I) workflow
- Correct TTA errors produced by recent changes when added multihead models
Full Changelog: v3.3.13...v3.3.14
Version 3.3.13
Fix:
- Fix normalization issue during test image reconstruction in SSL and SR workflows
Full Changelog: v3.3.11...v3.3.12
Version 3.3.12
Fix:
- Fix semantic segmentation multiclass edge error when a batch is compose by just one sample
- Correct minor error in SSL workflow using
masking
(MAE) during inference - Fix some SR scale problems due to recent changes
Full Changelog: v3.3.11...v3.3.12
Version 3.3.11
Fix:
- Correct few scale problems due to recent changes in SR workflow
Full Changelog: v3.3.10...v3.3.11
Version 3.3.10
Fixes:
- Fix typo in base_workflow.py due to recent changes that crash during inference
- Convert
PROBLEM.SUPER_RESOLUTION.UPSCALING
to a tuple to use one per dimension - Add
TRAIN.OPT_BETAS
- Change
TRAIN.W_DECAY
default value to0.02
- Fix bug when in
DATA.TRAIN.REPLICATE
- Correct 3D SR workflow
Full Changelog: v3.3.9...v3.3.10