Gandlf

What's Changed
* Version update for development by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/797
* Standardizing commenting style for major functions by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/799
* Added a script to generate information useful for debugging by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/803
* Update GitHub templates by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/804
* Version update for dependency for new Google APIs by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/809
* Add schedulers monai by Ainesh06102004 in https://github.com/mlcommons/GaNDLF/pull/807
* Add default line length for linting by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/820
* Fix html rendering by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/824
* Black trailing comma config by szmazurek in https://github.com/mlcommons/GaNDLF/pull/830
* Added readme for running tests locally by VukW in https://github.com/mlcommons/GaNDLF/pull/827
* Added black trailing comma style fix by VukW in https://github.com/mlcommons/GaNDLF/pull/832
* Fixed version dicom anonymizer by VukW in https://github.com/mlcommons/GaNDLF/pull/836
* Added ability to perform stratified data splits by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/831
* Added ability to generate split CSVs using external script by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/833
* Fix code issues reported by codacy by benmalef in https://github.com/mlcommons/GaNDLF/pull/808
* Removing double print of metrics by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/838
* Version update for tagging a new release by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/837

New Contributors
* VukW made their first contribution in https://github.com/mlcommons/GaNDLF/pull/827
* benmalef made their first contribution in https://github.com/mlcommons/GaNDLF/pull/808

**Full Changelog**: https://github.com/mlcommons/GaNDLF/compare/0.0.18...0.0.19

What's Changed
* Updated version for development by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/732
* Upgrade base python and numpy versions by szmazurek in https://github.com/mlcommons/GaNDLF/pull/730
* Updated docs for new python by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/737
* Add error handling for brain age model by 1Pravi in https://github.com/mlcommons/GaNDLF/pull/710
* Updated cosign installation by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/739
* Upgrade base pandas version by Ainesh06102004 in https://github.com/mlcommons/GaNDLF/pull/740
* Making black version static by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/744
* Revert to correct download location by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/745
* Upgrade base torchmetrics version by szmazurek in https://github.com/mlcommons/GaNDLF/pull/742
* Consistent black across the codebase by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/746
* Upgrade base PyTorch version by szmazurek in https://github.com/mlcommons/GaNDLF/pull/747
* Update installation link by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/748
* Upgrade base torchio version by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/749
* Update installation instructions by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/750
* Updated the minimum and maximum python versions by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/751
* Fixed the issue where a specific library prevents training to start by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/753
* Minor documentation updates by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/754
* Bump internal version by dependabot in https://github.com/mlcommons/GaNDLF/pull/759
* Fix for sample data download by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/766
* Added documentation for extending optimizer and schedulers by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/764
* Updated min devcontainer requirement by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/769
* Ensure pip is available in environment path for devcontainers by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/770
* Sync tests with openfl develop branch by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/772
* Updated git command for speed by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/773
* Consolidated a few checks by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/774
* Added option to bias the patch extraction for label sampler by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/771
* Added option to use different weights for sampler biasing and loss by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/777
* Added option to not apply zero plane cropping for gandlf preprocess by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/779
* Add optimizers monai by Ainesh06102004 in https://github.com/mlcommons/GaNDLF/pull/781
* Rename parseconfig for consistency by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/784
* Upgrade pytorch and torchio versions by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/786
* Added flowcharts for developers by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/789
* Added an option for backwards compatibility for parseconfig by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/791
* Updated openfl tests by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/787
* Version updated for tagging by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/796

New Contributors
* szmazurek made their first contribution in https://github.com/mlcommons/GaNDLF/pull/730
* 1Pravi made their first contribution in https://github.com/mlcommons/GaNDLF/pull/710
* Ainesh06102004 made their first contribution in https://github.com/mlcommons/GaNDLF/pull/740

**Full Changelog**: https://github.com/mlcommons/GaNDLF/compare/0.0.17...0.0.18

What's Changed
* Version update for development by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/648
* Added citation file by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/654
* Added new optimizers by AdiSir05 in https://github.com/mlcommons/GaNDLF/pull/646
* Allow histology patches to be extracted without ground truth labels by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/657
* Added metric calculation from CLI by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/663
* Added a few segmentation metrics by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/661
* Repository badges have been updated by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/667
* Added instructions on creating new tutorials by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/664
* Ensure parameters are built into the model dictionary by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/673
* Calculating penalty after all compute objects are initialized by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/675
* Add image similarity metrics by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/669
* Allow the penalty and class weights in the config to be used by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/677
* Added documentation related to OpenFL by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/683
* Add MLCube wrapper for metrics API by hasan7n in https://github.com/mlcommons/GaNDLF/pull/681
* Adding mechanism to curate each extracted patch by shubhaminnani in https://github.com/mlcommons/GaNDLF/pull/653
* Added mask to SSIM function call by FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/685
* Removed history file by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/690
* Updated the metrics output by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/687
* Update docker image name in workflow by hasan7n in https://github.com/mlcommons/GaNDLF/pull/692
* Fixed plotting function for final stats by Geeks-Sid in https://github.com/mlcommons/GaNDLF/pull/691
* Fixed import for collect stats by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/694
* HED augmentations for digital pathology image by Geeks-Sid in https://github.com/mlcommons/GaNDLF/pull/649
* Added focal loss by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/696
* Added a temporary fix for protobuf by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/702
* Use torchmetric PSNR implementation and argument ordering by FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/693
* Introduced percentile normalization for synthesis challenge metrics by FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/700
* Upgrade openvino version to latest by Geeks-Sid in https://github.com/mlcommons/GaNDLF/pull/699
* Additional PSNR evaluations for the normalized synthesis case by FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/703
* Improved formatting by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/707
* Updated checkout version and test names for clarity by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/708
* Updated default options for sgd by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/709
* Added matthews correlation coefficient loss by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/706
* Using tuples for PSNR datarange by FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/712
* Deploy model entrypoint by hasan7n in https://github.com/mlcommons/GaNDLF/pull/711
* Added parameter to toggle NCC computation by FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/717
* Adding second classification tutorial by vavali08 in https://github.com/mlcommons/GaNDLF/pull/698
* Minor code refactoring by tosemml in https://github.com/mlcommons/GaNDLF/pull/719
* Combined writing and temp file creation in a single step by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/720
* Update usage information for anonymizer by sanashah007 in https://github.com/mlcommons/GaNDLF/pull/716
* Move unit testing data to the mlcommons storage by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/722
* Fixed model saving when git repo not found by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/729
* Removing dev from version for tagging by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/731

New Contributors
* AdiSir05 made their first contribution in https://github.com/mlcommons/GaNDLF/pull/646
* shubhaminnani made their first contribution in https://github.com/mlcommons/GaNDLF/pull/653
* FelixSteinbauer made their first contribution in https://github.com/mlcommons/GaNDLF/pull/685
* vavali08 made their first contribution in https://github.com/mlcommons/GaNDLF/pull/698
* tosemml made their first contribution in https://github.com/mlcommons/GaNDLF/pull/719
* sanashah007 made their first contribution in https://github.com/mlcommons/GaNDLF/pull/716
* scap3yvt made their first contribution in https://github.com/mlcommons/GaNDLF/pull/729

**Full Changelog**: https://github.com/mlcommons/GaNDLF/compare/0.0.16...0.0.17

What's Changed
* Implemented a common copyright message for CLI and updated links & email by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/512
* Change python-test.yml to pass on docs-only by AlexanderGetka-cbica in https://github.com/mlcommons/GaNDLF/pull/517
* Making the flowchart a bit more generic to showcase inference by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/514
* Updated install verification logic by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/520
* Updated implementation for augmentations that need std-dev by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/521
* Ability to generate multiple training configurations using a specific strategy by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/525
* Updated patch divisibility logic by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/523
* Added sanity check for `norm_type` for non-vgg network architectures by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/528
* Fixing requirement for SimpleITK for a problematic version by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/537
* Preprocessing is now working when a random set of metadata columns are present by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/535
* Added ability to combine classification inference results from different architectures by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/531
* Added ability to save `initial` and `latest` models in addition to `best` by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/539
* Latest model is now saved correctly by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/546
* Consideration of `scaling_factor` has been moved to loss/metrics by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/541
* Added ability to specify testing data csv in main cli by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/545
* added more information for 529 by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/549
* Add docker docs by AlexanderGetka-cbica in https://github.com/mlcommons/GaNDLF/pull/550
* Added more details to documentation specifically related to training customization by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/552
* Added more details about Docker by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/554
* Separate `modelDir` and `outputDir` parameters for inference to cohesiveness by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/557
* The logs now include metric headers from `overall_stats` by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/558
* Fix parseConfig separately from my other PR by AlexanderGetka-cbica in https://github.com/mlcommons/GaNDLF/pull/561


**Full Changelog**: https://github.com/mlcommons/GaNDLF/compare/0.0.5...0.0.16

What's Changed
* Python 3.8 fixes by AlexanderGetka-cbica in https://github.com/CBICA/GaNDLF/pull/453
* Version updated for development by sarthakpati in https://github.com/CBICA/GaNDLF/pull/452
* Fixing the `stride_size` check for histology inference by sarthakpati in https://github.com/CBICA/GaNDLF/pull/455
* Update CI (PyTest to 3.8, and Docker Image creation) by AlexanderGetka-cbica in https://github.com/CBICA/GaNDLF/pull/461
* Bump numpy from 1.21.0 to 1.22.0 by dependabot in https://github.com/CBICA/GaNDLF/pull/460
* Add collectStats functionality for classification tasks by garvm7 in https://github.com/CBICA/GaNDLF/pull/463
* Ensuring params are populated correctly even if only testing data is invoked by sarthakpati in https://github.com/CBICA/GaNDLF/pull/466
* Added blending probability maps with original WSI by sarthakpati in https://github.com/CBICA/GaNDLF/pull/465
* Update data type for stride size by sarthakpati in https://github.com/CBICA/GaNDLF/pull/458
* Add FP16 option for model optimization by junwenwu in https://github.com/CBICA/GaNDLF/pull/457
* Added option to not pick up pretrained weights for `imagenet_vgg` by sarthakpati in https://github.com/CBICA/GaNDLF/pull/469
* Added ability to print model size and summary at run-time by sarthakpati in https://github.com/CBICA/GaNDLF/pull/468
* Better handling of large WSIs by sarthakpati in https://github.com/CBICA/GaNDLF/pull/472
* Added exception testing for histology classification by sarthakpati in https://github.com/CBICA/GaNDLF/pull/477
* Fixing reported Codacy fixes by sarthakpati in https://github.com/CBICA/GaNDLF/pull/474
* Formatting fixes for readability by sarthakpati in https://github.com/CBICA/GaNDLF/pull/478
* Completely excising VIPS from GaNDLF by sarthakpati in https://github.com/CBICA/GaNDLF/pull/480
* Update test workflow with file path filtering by AlexanderGetka-cbica in https://github.com/CBICA/GaNDLF/pull/473
* Saving report for failure cases from `pytest` as a separate log by sarthakpati in https://github.com/CBICA/GaNDLF/pull/482
* New metric added to calculated per-class accuracy by sarthakpati in https://github.com/CBICA/GaNDLF/pull/486
* Single utility function to return array from tensor/image by sarthakpati in https://github.com/CBICA/GaNDLF/pull/483
* Increasing unit test coverage by sarthakpati in https://github.com/CBICA/GaNDLF/pull/487
* Fixed the order of coordinates in `predictions.csv` for WSI inference by sarthakpati in https://github.com/CBICA/GaNDLF/pull/490
* Added ability to call specific post processing algorithms after reverse one-hot encoding by sarthakpati in https://github.com/CBICA/GaNDLF/pull/494
* Adding Largest connected component analysis as a post-processing step by Geeks-Sid in https://github.com/CBICA/GaNDLF/pull/467
* Dedicated rescaling preprocessing function added for increased flexibility by sarthakpati in https://github.com/CBICA/GaNDLF/pull/496
* Fixes multi-batch issue for `per_label_accuracy` by sarthakpati in https://github.com/CBICA/GaNDLF/pull/498
* Included classification-specific metrics using overall predictions and ground truths by sarthakpati in https://github.com/CBICA/GaNDLF/pull/500
* version update for tagging by sarthakpati in https://github.com/CBICA/GaNDLF/pull/501

New Contributors
* garvm7 made their first contribution in https://github.com/CBICA/GaNDLF/pull/463

**Full Changelog**: https://github.com/CBICA/GaNDLF/compare/0.0.14...0.0.15

What's Changed
* updated version for development by sarthakpati in https://github.com/CBICA/GaNDLF/pull/259
* Fix for `get_final_layer` use in `GANDLF.utils` by sarthakpati in https://github.com/CBICA/GaNDLF/pull/260
* Add functionality to save training patches by sarthakpati in https://github.com/CBICA/GaNDLF/pull/263
* Updates to integrate new OPM APIs by sarthakpati in https://github.com/CBICA/GaNDLF/pull/261
* Added option to print per-label segmentation scores by sarthakpati in https://github.com/CBICA/GaNDLF/pull/264
* updated initialization for dicts by sarthakpati in https://github.com/CBICA/GaNDLF/pull/267
* Motion artifact separated by sarthakpati in https://github.com/CBICA/GaNDLF/pull/270
* added `black` and `opencv-python` as an explicit requirements by sarthakpati in https://github.com/CBICA/GaNDLF/pull/271
* Bump numpy from 1.19.2 to 1.21.0 by dependabot in https://github.com/CBICA/GaNDLF/pull/272
* Added capability to use `InstanceNorm` in `DenseNet` by sarthakpati in https://github.com/CBICA/GaNDLF/pull/274
* Updated implementations of `VGG` and `DenseNet` to use `ModelBase` for consistency by sarthakpati in https://github.com/CBICA/GaNDLF/pull/276
* Added git hash to model save by sarthakpati in https://github.com/CBICA/GaNDLF/pull/277
* Added FAQ by sarthakpati in https://github.com/CBICA/GaNDLF/pull/279
* Update to how `git_hash` is saved by sarthakpati in https://github.com/CBICA/GaNDLF/pull/280
* Documentation updated for new module structure by sarthakpati in https://github.com/CBICA/GaNDLF/pull/283
* Accuracy is now standardized from torchmetrics by sarthakpati in https://github.com/CBICA/GaNDLF/pull/287
* Adding automated linting check for `black` by sarthakpati in https://github.com/CBICA/GaNDLF/pull/284
* Post-processing module added by sarthakpati in https://github.com/CBICA/GaNDLF/pull/289
* Added a `GANDLF.anonymize` module by sarthakpati in https://github.com/CBICA/GaNDLF/pull/291
* Updated documentation (faq and usage) by sarthakpati in https://github.com/CBICA/GaNDLF/pull/294
* Git submodule update is now integrate in setup by sarthakpati in https://github.com/CBICA/GaNDLF/pull/296
* Ensure `colorjitter` works with defaults by sarthakpati in https://github.com/CBICA/GaNDLF/pull/297
* More progress bars for better feedback by sarthakpati in https://github.com/CBICA/GaNDLF/pull/301
* Update usage.md - plot final results by anishshriram in https://github.com/CBICA/GaNDLF/pull/305
* Using `Resample` and `Resize` from TorchIO by Geeks-Sid in https://github.com/CBICA/GaNDLF/pull/293
* Ensure hole filling output is int by sarthakpati in https://github.com/CBICA/GaNDLF/pull/306
* Added instructions for dependency management by sarthakpati in https://github.com/CBICA/GaNDLF/pull/307
* Minor fix for `reset_prev` by sarthakpati in https://github.com/CBICA/GaNDLF/pull/310
* added captk and fets links by sarthakpati in https://github.com/CBICA/GaNDLF/pull/311
* Updates documentation based on SB's notes by sarthakpati in https://github.com/CBICA/GaNDLF/pull/313
* Added script to verify installation by sarthakpati in https://github.com/CBICA/GaNDLF/pull/315
* Added ability to save preprocessed files with data augmentation by sarthakpati in https://github.com/CBICA/GaNDLF/pull/317
* Added ResNet with multiple configurations by Sofia-Mouchtaris in https://github.com/CBICA/GaNDLF/pull/319
* Bug fix in parameters for `gandlf_collectStats` by dlang95 in https://github.com/CBICA/GaNDLF/pull/321
* `Resample_Min` added to ensure a baseline resolution for all images getting processed by sarthakpati in https://github.com/CBICA/GaNDLF/pull/325
* Added final predictions for classification by sarthakpati in https://github.com/CBICA/GaNDLF/pull/328
* Ensuring cropping zero planes are applied for preprocessing by sarthakpati in https://github.com/CBICA/GaNDLF/pull/329
* Typo fixed for `hd95` by sarthakpati in https://github.com/CBICA/GaNDLF/pull/331
* Using `TiffSlide` instead of `OpenSlide` for a better deployment by sarthakpati in https://github.com/CBICA/GaNDLF/pull/303
* Histology anonymization added by Geeks-Sid in https://github.com/CBICA/GaNDLF/pull/281
* Bug fix for `gandlf_collectStats` by sarthakpati in https://github.com/CBICA/GaNDLF/pull/335
* Adding `resize_image` as a separate option as compared to `resize_patch` by sarthakpati in https://github.com/CBICA/GaNDLF/pull/337
* Sanity checking is now softer with a threshold by sarthakpati in https://github.com/CBICA/GaNDLF/pull/340
* Added ability to resume with and without updating parameters and/or data by sarthakpati in https://github.com/CBICA/GaNDLF/pull/344
* Reverse one-hot logic is now updated to output unique labels by sarthakpati in https://github.com/CBICA/GaNDLF/pull/342
* Added EfficientNet with multiple configurations by Sofia-Mouchtaris in https://github.com/CBICA/GaNDLF/pull/327
* Links added for current networks by sarthakpati in https://github.com/CBICA/GaNDLF/pull/346
* Add Dockerfiles and Docker Hub CI by AlexanderGetka-cbica in https://github.com/CBICA/GaNDLF/pull/353
* Add GitHub Packages upload step, refine Docker CI further by AlexanderGetka-cbica in https://github.com/CBICA/GaNDLF/pull/355
* Added Docker Image builds by sarthakpati in https://github.com/CBICA/GaNDLF/pull/354
* docker ci badge position change by sarthakpati in https://github.com/CBICA/GaNDLF/pull/356
* Docker CI: Fix login requirement -- no need to log in for PRs (oops!) by AlexanderGetka-cbica in https://github.com/CBICA/GaNDLF/pull/359
* Added some checks for inference mode by sarthakpati in https://github.com/CBICA/GaNDLF/pull/358
* Fix for invalid classification accuracy in training by orhunguley in https://github.com/CBICA/GaNDLF/pull/361
* Post-training optimization using OpenVINO added by junwenwu in https://github.com/CBICA/GaNDLF/pull/312
* Enabling inference without having access to the ground truth by sarthakpati in https://github.com/CBICA/GaNDLF/pull/363
* Ensure ONNX-related print only happens once during training by sarthakpati in https://github.com/CBICA/GaNDLF/pull/364
* Fixed issue with `balanced_accuracy` parsing by sarthakpati in https://github.com/CBICA/GaNDLF/pull/366
* Hard requirement of PyTorch to LTS by sarthakpati in https://github.com/CBICA/GaNDLF/pull/369
* Added post-processing step to map predicted labels to new values by sarthakpati in https://github.com/CBICA/GaNDLF/pull/367
* Fix Docker CI on PRs again (meta information missing causing a rebuild -> out of space) by AlexanderGetka-cbica in https://github.com/CBICA/GaNDLF/pull/371
* Fixing docker builds by sarthakpati in https://github.com/CBICA/GaNDLF/pull/372
* ROCm Docker builds are no longer valid since we are only supporting PyTorch LTS by sarthakpati in https://github.com/CBICA/GaNDLF/pull/370
* Custom inference loop added for histo classification by sarthakpati in https://github.com/CBICA/GaNDLF/pull/374
* UNet and Light UNet with varying depth by Sofia-Mouchtaris in https://github.com/CBICA/GaNDLF/pull/357
* Create codacy-coverage-reporter.yml by sarthakpati in https://github.com/CBICA/GaNDLF/pull/368
* added a comment about padding options by sarthakpati in https://github.com/CBICA/GaNDLF/pull/376
* Improved penalty calculation and added ImageNet-specific VGG by Geeks-Sid in https://github.com/CBICA/GaNDLF/pull/365
* Error checks added to ImageNet VGG by sarthakpati in https://github.com/CBICA/GaNDLF/pull/377
* updated config comment for `num_channels` by sarthakpati in https://github.com/CBICA/GaNDLF/pull/378
* Logic fixed for step scheduler by sarthakpati in https://github.com/CBICA/GaNDLF/pull/379
* Add option to save model at every epoch by sarthakpati in https://github.com/CBICA/GaNDLF/pull/381
* Added note for classification/regression tasks by sarthakpati in https://github.com/CBICA/GaNDLF/pull/385
* Added RGBA to RGB conversion in preprocessing by sarthakpati in https://github.com/CBICA/GaNDLF/pull/384
* Improved default `step_size` calculation by sarthakpati in https://github.com/CBICA/GaNDLF/pull/386
* Added a key for `exp` scheduler by sarthakpati in https://github.com/CBICA/GaNDLF/pull/387
* Documentation updates by sarthakpati in https://github.com/CBICA/GaNDLF/pull/388
* Fixing tests on named venv by sarthakpati in https://github.com/CBICA/GaNDLF/pull/382
* Fixing pytorch version dependency for macOS by sarthakpati in https://github.com/CBICA/GaNDLF/pull/390
* Add option to strategize the final aggregation for segmentation by sarthakpati in https://github.com/CBICA/GaNDLF/pull/392
* Fixing per-label metrics display by sarthakpati in https://github.com/CBICA/GaNDLF/pull/393
* Added submodule to hand template-matching based normalization by sarthakpati in https://github.com/CBICA/GaNDLF/pull/394
* Added RGB to RGBA conversion for preprocessing by sarthakpati in https://github.com/CBICA/GaNDLF/pull/397
* A new transformer-based segmentation arch (`UNetR`) has been added by Sofia-Mouchtaris in https://github.com/CBICA/GaNDLF/pull/398
* Fixing different device issue on multi-layer `UNet` and `UNETR` by sarthakpati in https://github.com/CBICA/GaNDLF/pull/399
* Added sigmoid multiplier for UNet model output by sarthakpati in https://github.com/CBICA/GaNDLF/pull/400
* Documentation update for installation by sarthakpati in https://github.com/CBICA/GaNDLF/pull/403
* More inference mode options added by sarthakpati in https://github.com/CBICA/GaNDLF/pull/405
* Update `one_hot` and `reverse_one_hot` logic for succinctness by sarthakpati in https://github.com/CBICA/GaNDLF/pull/404
* moving get_final_layer method functionality to GANDLF.utils to avoid by brandon-edwards in https://github.com/CBICA/GaNDLF/pull/407
* API updates to make GaNDLF's compute objects callable outside the tool by sarthakpati in https://github.com/CBICA/GaNDLF/pull/401
* Added memory usage for cuda under `verbose` by sarthakpati in https://github.com/CBICA/GaNDLF/pull/409
* Fixes to model getting sent to device twice by sarthakpati in https://github.com/CBICA/GaNDLF/pull/411
* Upgrade to OpenVINO 2022.1 by junwenwu in https://github.com/CBICA/GaNDLF/pull/410
* Model device location fixed for inference by sarthakpati in https://github.com/CBICA/GaNDLF/pull/412
* Fixed type passed to get_class_imbalance_weights by psfoley in https://github.com/CBICA/GaNDLF/pull/414
* Updated OpenVINO installation for CI by sarthakpati in https://github.com/CBICA/GaNDLF/pull/415
* Reducing dataframe iteration by sarthakpati in https://github.com/CBICA/GaNDLF/pull/416
* Documentation update to use pip instead of conda, per our CI by sarthakpati in https://github.com/CBICA/GaNDLF/pull/419
* Taking care of case where `0` is absent from `class_list` for segmentation by sarthakpati in https://github.com/CBICA/GaNDLF/pull/418
* Providing train/val split should not result in another training by sarthakpati in https://github.com/CBICA/GaNDLF/pull/420
* Fix typo torch summary by katesedykh in https://github.com/CBICA/GaNDLF/pull/421
* Added a preprocessing dict for `resize_image` by sarthakpati in https://github.com/CBICA/GaNDLF/pull/423
* Create pytorch objects inference fix by psfoley in https://github.com/CBICA/GaNDLF/pull/422
* Figure added from manuscript by sarthakpati in https://github.com/CBICA/GaNDLF/pull/426
* Checking dimensionality of computations and raising run-time error by sarthakpati in https://github.com/CBICA/GaNDLF/pull/429
* Supporting JPG for writing segmentation output by sarthakpati in https://github.com/CBICA/GaNDLF/pull/432
* Histology inference logic updated by Geeks-Sid in https://github.com/CBICA/GaNDLF/pull/433
* Bug fix for OpenVINO iGPU model craching by junwenwu in https://github.com/CBICA/GaNDLF/pull/436
* Simplified logic for histology inference by sarthakpati in https://github.com/CBICA/GaNDLF/pull/435
* Links updated to remove redundant highlights by sarthakpati in https://github.com/CBICA/GaNDLF/pull/440
* Trying to fix Out-of-Memory on unit tests (with TransNet changes) by AlexanderGetka-cbica in https://github.com/CBICA/GaNDLF/pull/444
* Improving code coverage by reducing number of lines of code by sarthakpati in https://github.com/CBICA/GaNDLF/pull/446
* Enable patch size calculation in microns for histology images by sarthakpati in https://github.com/CBICA/GaNDLF/pull/439
* Improved masking functionality for histology inference by Geeks-Sid in https://github.com/CBICA/GaNDLF/pull/448
* version update for tagging by sarthakpati in https://github.com/CBICA/GaNDLF/pull/449

New Contributors
* dependabot made their first contribution in https://github.com/CBICA/GaNDLF/pull/272
* anishshriram made their first contribution in https://github.com/CBICA/GaNDLF/pull/305
* Sofia-Mouchtaris made their first contribution in https://github.com/CBICA/GaNDLF/pull/319
* dlang95 made their first contribution in https://github.com/CBICA/GaNDLF/pull/321
* AlexanderGetka-cbica made their first contribution in https://github.com/CBICA/GaNDLF/pull/353
* brandon-edwards made their first contribution in https://github.com/CBICA/GaNDLF/pull/407
* psfoley made their first contribution in https://github.com/CBICA/GaNDLF/pull/414
* katesedykh made their first contribution in https://github.com/CBICA/GaNDLF/pull/421

**Full Changelog**: https://github.com/CBICA/GaNDLF/compare/0.0.13...0.0.14