CHANGELOG.md

Changelog

0.20.0 (2024-09-20)

• Fix silenced exception in Queue when using faulty transform by @Zhack47 in #1101
• Fix RescaleIntensity by @fepegar in #1116
• Queue length modification with the use of DDP by @haughty-yeon in #1127
• Fix get_subjects_from_batch ignoring metadata by @KonoMaxi in #1131
• Fix random errors in queue test by @fepegar in #1142
• Add masking_method arg name in Mask by @lchauvin in #1137
• Enable plotting of PNG images with alpha channel by @ChristianHinge in #1150
• Fix transforms taking strings instead of sequences by @fepegar in #1153
• Improve docs for "isotropic" arg in RandomAffine by @AminAlam in #1163
• Add support to slice images and subjects by @fepegar in #1170
• Make transform return the same type as input by @haarisr in #1182
• Fix error which copying a subclass of Subject with keyword attributes by @c-winder in #1186
• Add SubjectsLoader by @fepegar in #1194

0.19.0 (2023-07-26)

• Replace p by **kwargs in all transforms by @dmus in #370
• Implementation of include/exclude args by @dmus in #373
• Remove internal self.fill, and keep padding_mode as string or number by @romainVala in #378
• Remove checks and casts to float32 by @dmus in #380
• Fix conversion to Pillow image by @fepegar in #385
• Print image path if probability map is empty by @fepegar in #386
• Remove torchvision requirement by @fepegar in #391
• Fix label sampler and improve error message by @fepegar in #394
• Fix error with invertible custom transforms, also keep include/exclude lists for inverse transforms. by @efirdc in #398
• New label transformations by @efirdc in #402
• Add transform to ensure shape multiple of N by @fepegar in #401
• Allow empty list as input to Compose. by @efirdc in #404
• Cast to float before computing mean by @fepegar in #408
• Add option to keep copies of original images by @fepegar in #413
• Delete image attribute when removing image by @fepegar in #415
• Add option to ignore intensity transforms when inverting by @fepegar in #417
• Add OneHot transform by @fepegar in #420
• Add option to modify interpolation when inverting by @fepegar in #418
• Add some label transforms for binary morphological operations by @fepegar in #424
• Small improvements for Queue by @fepegar in #423
• Fix CropOrPad for 2D images by @fepegar in #435
• Add EPISURG dataset by @fepegar in #433
• Add list of masks functionality to HistogramStandardization.train by @Linardos in #446
• Add support for custom image readers by @fepegar in #454
• Fix probabilities in label sampler by @fepegar in #459
• Use voxels rather than bounds when plotting images by @fepegar in #487
• Add input range kwarg for RescaleIntensity by @fepegar in #499
• Ignore NumPy underflows by @fepegar in #503
• Remove unused imports by @deepsource-autofix in #506
• Remove methods with unnecessary super delegation. by @deepsource-autofix in #507
• Add examples gallery to documentation by @fepegar in #508
• Fix 0 prob random sample in WeightedSampler by @TylerSpears in #511
• Avoid deprecation warnings by @fepegar in #517
• Add functions to process batches by @fepegar in #516
• Make the grid sampler compatible with the queue by @fepegar in #520
• Compress and cleanup downloaded datasets by @fepegar in #531
• Set minimum version for NumPy requirement by @fepegar in #532
• Fix unexpected exception handling by @siahuat0727 in #542
• Fix 'unraveling -1' in the weighted random sampler. by @dvolgyes in #551
• Add Mask transform by @Svdvoort in #527
• Add CopyAffine transform by @albansteff in #584
• Added Image method to convert from sitk to torchio by @mattwarkentin in #616
• Added intensity clamp transform by @mattwarkentin in #622
• Fix default pad value for label maps by @fepegar in #627
• Add tolerance for numeric checks by @justusschock in #592
• Fix syntax error for Python < 3.8 by @fepegar in #639
• Add support to pass shape and affine to Resample by @fepegar in #640
• Fix single slices metadata being lost by @fepegar in #641
• Add Resize transform by @fepegar in #642
• Raise from None to reduce error verbosity by @fepegar in #649
• Add RSNA-MICCAI brain tumor dataset by @fepegar in #650
• Fix visualization for subject with many images by @fepegar in #653
• Fix error when normalization mask is empty by @fepegar in #656
• Enable Indexing by int-Compatible type by @justusschock in #670
• Add support to crop/pad to the mask's bounding box by @fepegar in #678
• Add support to save GIFs by @fepegar in #680
• Add some Visible Human datasets by @fepegar in #679
• Add indices parameter for plotting volumes by @laynr in #683
• Remove channels_last kwarg from Image by @fepegar in #685
• Add parse_input kwarg to Transform by @fepegar in #696
• Cast translation argument to float64 for SimpleITK by @fepegar in #702
• Make Affine take RAS parameters of floating->ref by @fepegar in #712
• Rename master to main by @fepegar in #717
• Add method to show image with external viewer by @fepegar in #727
• Add kwarg to not check spatial consistency by @fepegar in #735
• Retrieve transforms history from batch dictionary by @fepegar in #745
• Add logic to invert OneHot transform by @fepegar in #748
• Fix wrong class when creating subjects from batch by @fepegar in #749
• Minor quality of life functions for inspecting scalar images and label maps by @mattwarkentin in #728
• Fix CropOrPad incorrectly storing bounds by @fepegar in #760
• Fix affine getter for multipath images by @fepegar in #763
• Check data type compatibility for custom reader by @fepegar in #770
• Use PyTorch to shuffle the queue patches by @fepegar in #776
• Fix Blur using only the first standard deviation by @fepegar in #772
• Add support to specify the interpolation type for label images by @snavalm in #791
• Fix overlapping in patches aggregator by @fepegar in #832
• Add support for torch >= 1.11 by @snipdome in #838
• Fix new SimpleITK release not being installed by @fepegar in #852
• Fix the wrong mapping in sequential labels transform by @iamSmallY in #841
• Return figure in plot_volume function by @dmus in #872
• Use PyTorch to compute Fourier transforms by @fepegar in #389
• Remove support for Python 3.6 by @fepegar in #881
• Add support to use different numbers of samples in the queue by @fepegar in #795
• Fix computation of kernels in Blur transform by @fepegar in #861
• Add support to pass label keys for dict input by @fepegar in #879
• Add support to mask 4D images with 3D masks by @fepegar in #908
• Add fftshift to fourier_transform with torch.fft by @iimog in #912
• Fix copying of subclasses of Subject by @justusschock in #794
• Use tqdm.auto by @fepegar in #926
• Add hann window function in GridAggregator as padding_mode by @LucaLumetti in #900
• Add RSNA 2022 Cervical Spine Fracture Detection dataset by @fepegar in #943
• Replace Click with Typer by @fepegar in #978
• Fix number of samples per subject in queue by @fepegar in #981
• Stop loading data when copying unloaded image by @fepegar in #982
• Add support to pass a callable as padding mode by @mueller-franzes in #959
• Use indexing instead of masked_select for faster normalization by @ramonemiliani93 in #1018
• Remove Visible Human Project datasets by @fepegar in #1026
• Add support for Python 3.11 by @fepegar in #1008
• Make subject parameter mandatory by @fepegar in #1029
• Improve support for queue in distributed training by @hsyang1222 in #1021
• Stop ignoring intensity transforms when computing inverse by @fepegar in #1039
• Add support to invert RescaleIntensity transform by @nicoloesch in #998
• Fix HistogramStandardization example by @vedal in #1022
• Add workflow to validate pull request title by @fepegar in #1042
• Add support to unload images by @fepegar in #983
• Split CI workflows by @fepegar in #1047
• Warn if 'mean' padding mode is used for label maps by @fepegar in #1065
• Fix unloaded image affine not read after CopyAffine by @fepegar in #1072
• Fix custom reader not propagated when copying by @fepegar in #1091
• Remove support for Python 3.7 by @fepegar in #1099

0.18.0 (2020-11-29)

• Add FPG dataset
• Optimize cropping in samplers
• Optimize implementation of UniformSampler and WeightedSampler
• Fix non integer labels in Colin 27 version 2008 (#223)
• Add RandomAnisotropy transform
• Add RandomGamma transform
• Add ScalarImage and LabelMap classes
• Add RandomLabelsToImage transform
• Add support for more input types in Transform
• Add support for 4D images
• Add ICBM dataset
• Add support to specify axes as anatomical labels
• Add SpatialTransform and IntensityTransform
• Replace ImagesDataset with SubjectsDataset
• Add support to pass multiple paths to Image
• Refactor reproducibility features
• Add deterministic versions of all random transforms
• Add support to invert transforms
• Add support for SimpleITK > 1
• Add pre-commit to help contributions and improve code quality
• Add DICOM data for testing
• Add some visualization support (Subject.plot, Image.plot)
• Add support to pass parameters per axis, e.g. for RandomAffine (#346)
• Remove deprecated transforms Resample and CenterCropOrPad

0.17.0 (2020-06-23)

• Add transforms history to Subject attributes to improve traceability
• Add support to use an initial transformation in Resample
• Add support to use an image file as target in Resample
• Add mean argument to RandomNoise
• Add tensor support for transforms
• Add support to use strings as interpolation argument
• Add support for 2D images
• Add attribute access to Subject and Image
• Add MNI and 3D Slicer datasets
• Add intensity argument to RandomGhosting
• Add translation argument to RandomAffine
• Add shape, spacing and orientation attributes to Image and Subject
• Refactor samplers
• Refactor inference classes
• Add 3D Slicer extension
• Add ITK-SNAP datasets
• Add support to take NumPy arrays as transforms input
• Optimize cropping using PyTorch
• Optimizing transforms by reducing number of tensor copying
• Improve representation (repr()) of Image
• Use lazy loading in Image

0.16.0 (2020-04-21)

• Add advanced padding options for RandomAffine
• Add reference space options in Resample
• Add probability argument to all transforms
• Add OneOf and Compose transforms to improve composability

0.15.0 (2020-04-07)

• Refactor RandomElasticDeformation transform
• Make Subject inherit from dict

0.14.0 (2020-03-31)

• Add datasets module
• Add support for DICOM files
• Add documentation
• Add CropOrPad transform

0.13.0 (2020-02-24)

• Add Subject class
• Add random blur transform
• Add lambda transform
• Add random patches swapping transform
• Add MRI k-space ghosting artefact augmentation

0.12.0 (2020-01-21)

• Add ToCanonical transform
• Add CenterCropOrPad transform

0.11.0 (2020-01-15)

• Add Resample transform

0.10.0 (2020-01-15)

• Add Pad transform
• Add Crop transform

0.9.0 (2020-01-14)

• Add CLI tool to transform an image from file

0.8.0 (2020-01-11)

• Add Image class

0.7.0 (2020-01-02)

• Make transforms use PyTorch tensors consistently

0.6.0 (2020-01-02)

• Add support for NRRD

0.5.0 (2020-01-01)

• Add bias field transform

0.4.0 (2019-12-29)

• Add MRI k-space motion artefact augmentation

0.3.0 (2019-12-21)

• Add Rescale transform
• Add support for multimodal data and missing modalities

0.2.0 (2019-12-06)

• First release on PyPI.