MONAI 1.6.1

What's Changed

• Update Weekly Preview Version by @ericspod in #8917
• Add docstring note that Transpose/Transposed do not update the affine matrix by @Akarsh-Doki in #8888
• Fix nnUNet test directory leakage into current working directory by @aymuos15 in #8887
• ci: mute dynamic warningregistry logs noise in pytest suite by @Priyanshu31102003 in #8893
• tests: remove duplicate and dead test cases by @aymuos15 in #8896
• Add explicit spatial_ndim tracking to MetaTensor by @aymuos15 in #8765
• Improve Affine transform documentation and add compute_w_affine tests by @engmohamedsalah in #8727
• fix: update Dockerfile and requirements-dev.txt for MONAI 1.6 tutorial compatibility by @garciadias in #8912
• Fix division by zero in clDice loss harmonic mean by @Mr-Neutr0n in #8739
• fix(losses): register buffers in GlobalMutualInformationLoss by @AlexanderSanin in #8872
• tests: remove more duplicate test cases by @aymuos15 in #8943
• Fix batched_nms for ndarray inputs by @aymuos15 in #8901
• fix: add missing stacklevel=2 to warnings.warn() in metrics/ (Fixes #8931) by @rtmalikian in #8932
• fix: add missing stacklevel=2 to warnings.warn() in losses/ (Fixes #8929) by @rtmalikian in #8930
• fix: adaptor map_names calls dict as function when inputs is a name-mapping dict by @aymuos15 in #8907
• Enabling MetaTensor Persistent Caching by @ericspod in #8940
• Use compact [1,-2,1] kernel for BendingEnergyLoss second derivatives by @vishnukannaujia in #8918
• Force GC in WSIReader tests to suppress ResourceWarning for unclosed files by @vishnukannaujia in #8919
• fix: guard division by zero in DICOMReader._get_affine for single-slice volumes (Fixes #8925) by @rtmalikian in #8926
• fix: replace raise UserWarning with warnings.warn() in verify_report_format (Fixes #8927) by @rtmalikian in #8928
• Fix FROC num_targets miscount when labels_to_exclude is set by @aymuos15 in #8951
• Remove dead and redundant code across monai/ by @aymuos15 in #8952
• docs: add Windows BUILD_MONAI install instructions by @Shizoqua in #8906
• Perf: Use a KDTree on CPU instead of full EDT for 1.5x to 16x faster metric computation by @jberg5 in #8910
• Fix nnUNet runner store_true flag command construction (#8941) by @aymuos15 in #8944
• fix: emit nnUNet store_true flags as bare CLI args in nnUNetV2Runner by @aymuos15 in #8968
• Support configurable rotation order in create_rotate by @aymuos15 in #8963
• Bump actions/checkout from 4 to 7 by @dependabot[bot] in #8965
• Bump codecov/codecov-action from 6 to 7 by @dependabot[bot] in #8966
• Bump actions/cache from 5 to 6 by @dependabot[bot] in #8964
• docs: clarify RandWeightedCrop(d) does not crop the weight map (#7851) by @aymuos15 in #8962
• Enable macOS Install Test Only by @ericspod in #8976
• Add AbsoluteVolumeDifferenceMetric to monai.metrics by @MDSALMANSHAMS in #8945
• fix(data): avoid divide-by-zero in pydicom affine for single-slice volumes by @SID-6921 in #8956
• Perf: skip redundant full-image mask on StdShiftIntensity nonzero=False path by @aymuos15 in #8975
• HyenaUnetR (SwinUnetR + HyenaND): subquadratic alternative to windowed self-attention by @farhadrgh in #8958
• Fix division by zero in Warp for singleton spatial dimensions by @VenkateswarluNagineni in #8946
• fix: warn when PydicomReader cannot determine affine from DICOM metadata (Fixes #8468) by @rtmalikian in #8922
• Warn when PydicomReader falls back to an identity affine (#8468) by @Shizoqua in #8934
• Fix non-functional jitter in Warp.get_reference_grid by @aymuos15 in #8953
• [pre-commit.ci] pre-commit suggestions by @pre-commit-ci[bot] in #8984
• Add BoundaryLoss by @txmed82 in #8916
• Make Fuzzy Gdown Argument Version-dependent by @ericspod in #8986
• Perf: faster get_largest_connected_component_mask (bincount + LUT gather) by @aymuos15 in #8978
• fix typos in docs: lazy_resampling, modules, whatsnew_1_5 by @vikashg in #9012
• docs: add documentation to CONTRIBUTING.md by @garciadias in #8878
• Fix class_labels mutation across multi-metric write_metrics_reports by @aymuos15 in #8902
• fix(MetaTensor): astype with torch dtype now returns MetaTensor preserving metadata by @AlexanderSanin in #8911
• Validate downloaded file integrity and raise ValueError on hash mismatch by @e-mny in #8833
• Fix clipping boxes with large coordinates by @Rajioba1 in #9047
• Raise OptionalImportError for unavailable explicit image readers by @minsuking in #9006
• feat: replace mypy and pytype with pyrefly for static type analysis by @garciadias in #8868
• Add NaViT: Native Resolution Vision Transformer with Patch n' Pack by @vikashg in #9011
• Fix GHSA-873f-pvrv-4x83: warn before executing a bundle's config in load()/run() by @garciadias in #9057
• Modernising Build Process by @ericspod in #9010
• Safe eval by @ericspod in #8936
• fix(safeeval): evaluate rewritten AST instead of original string by @chhayankjain in #9063
• Lazily import onnx so a broken onnx does not block 'import monai' (#8455) by @Shizoqua in #8937
• Fix ClipIntensityPercentiles metadata accumulation by @engmohamedsalah in #9003
• Fix NaN gradient in PerceptualLoss normalize_tensor by @Shizoqua in #8982
• Fix dot-notation read on $@ref-backed ConfigParser proxies by @VenkateswarluNagineni in #8994
• fix: address Dependabot alerts for mlflow, transformers, setuptools by @garciadias in #9032
• Weekly Preview Fix by @ericspod in #9075
• Fix GHSA-x6pr-233j-x5cw: warn before executing an FL-provisioned bundle config by @garciadias in #9078
• SwinUNETR: optional flash attention (scaled_dot_product_attention) in WindowAttention by @aymuos15 in #8977
• fix(transforms): make Crop.compute_slices torch.compile-friendly by @aymuos15 in #8960
• Update CodeQL Action by @ericspod in #9079
• Precommit Autofixing by @ericspod in #9061
• Warn before instantiating target from algo_object.json by @garciadias in #9085
• Reject non-finite DICOM affine metadata in PydicomReader by @garciadias in #9087
• Harden download/deserialize integrity (weights_only, hash checks, path confinement) by @garciadias in #9088
• Harden nnUNetV2Runner against code execution by @garciadias in #9086
• Fixing Git Dependency Weekly Build Issue by @ericspod in #9081
• Check Environment Script by @ericspod in #9038
• ci: add local pre-commit DCO hook and setup command by @garciadias in #9094
• Declare ruff's vendored-file excludes once in pyproject.toml by @hjmjohnson in #9090
• Route runtests.sh ruff invocations through PY_EXE by @hjmjohnson in #9089
• Fix VarAutoEncoder reparameterize returning mu+std at inference (#8413) by @Shizoqua in #8933
• Clarify CUDA/CuPy install requirements in docs (#8106) by @Shizoqua in #8983
• Fix tracing-state leak after transform exceptions by @yinkev in #9019
• Fix QuickNAT indexed skip connections by @yinkev in #9021
• feat(losses/metrics): implement ignore_index support across dice and … by @Rusheel86 in #8757
• Actions Permission and Other CodeQL Fixes by @ericspod in #9098
• Fix AutoRunner to honor num_fold when generating folds by @mattlin1124 in #9110
• Fix three malformed error messages by @hjmjohnson in #9065
• Fix 1/N floor in effective-rank collapse score after mean-centering by @rubenG1009 in #8997
• Add affine-aware landmark heatmap generation by @mustafamm072 in #8957
• Add GPU-accelerated dcm image decoding by @MMelQin in #8954
• tests: remove the temporary directory make_nifti_image creates by @aymuos15 in #9042
• Adding MedNeXt to documentation by @id-b3 in #9074
• Report a missing nnunetv2 as an optional dependency in nnUNetV2Runner by @Kirscher in #9054
• fix: confine nnUNet postprocessing pickle loads to the results directory (GHSA-8f32) by @garciadias in #9113
• Improve/writer error messages by @skdas20 in #8753
• fix: screen logging.conf class=/args= before fileConfig (GHSA-wvpx) by @garciadias in #9114
• fix: restrict algo_from_json target to Algo subclasses (GHSA-2wx3) by @garciadias in #9115
• Add Tool-Assisted Contribution Policy by @ericspod in #9106
• Release 1.6.1 Docs Updates by @ericspod in #9120

New Contributors

• @Akarsh-Doki made their first contribution in #8888
• @Priyanshu31102003 made their first contribution in #8893
• @Mr-Neutr0n made their first contribution in #8739
• @rtmalikian made their first contribution in #8932
• @vishnukannaujia made their first contribution in #8918
• @Shizoqua made their first contribution in #8906
• @jberg5 made their first contribution in #8910
• @MDSALMANSHAMS made their first contribution in #8945
• @SID-6921 made their first contribution in #8956
• @farhadrgh made their first contribution in #8958
• @VenkateswarluNagineni made their first contribution in #8946
• @txmed82 made their first contribution in #8916
• @vikashg made their first contribution in #9012
• @Rajioba1 made their first contribution in #9047
• @minsuking made their first contribution in #9006
• @yinkev made their first contribution in #9019
• @Rusheel86 made their first contribution in #8757
• @mustafamm072 made their first contribution in #8957
• @MMelQin made their first contribution in #8954
• @id-b3 made their first contribution in #9074
• @skdas20 made their first contribution in #8753

Full Changelog: 1.6.0...1.6.1