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Recent Releases of gandlf

gandlf - Lightning integration and large-scale metrics update

What's Changed

  • Update lighting integration branch by @benmalef in https://github.com/mlcommons/GaNDLF/pull/996
  • Version updated for development by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/1003
  • Lightning integration by @szmazurek in https://github.com/mlcommons/GaNDLF/pull/991
  • Updated version for action by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/1004
  • More robust CI by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/1006
  • Fix for new unit test data by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/1008
  • Fixed path for BraTS metrics config by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/1009
  • Usage document formatting updates by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/1011
  • Added sanity check for metrics by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/1012
  • Added ability to customize segmentation by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/1014
  • Added a yaml load fallback for panoptica by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/1017
  • Upgrade dependency version by @neuronflow in https://github.com/mlcommons/GaNDLF/pull/1018
  • Panoptica updated with better logic by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/1020
  • Fix brats config samples by @vpchung in https://github.com/mlcommons/GaNDLF/pull/1021
  • Updated version for release by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/1016

New Contributors

  • @neuronflow made their first contribution in https://github.com/mlcommons/GaNDLF/pull/1018
  • @vpchung made their first contribution in https://github.com/mlcommons/GaNDLF/pull/1021

Full Changelog: https://github.com/mlcommons/GaNDLF/compare/0.1.3...0.1.4

- Python
Published by sarthakpati 8 months ago

gandlf - Updated python versions for long term maintainance

What's Changed

  • Version updated for development by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/975
  • Correct spelling error by @szmazurek in https://github.com/mlcommons/GaNDLF/pull/977
  • Update versions for ossar and codeql actions by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/979
  • Update cron schedule for ossar by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/980
  • Ensure synthesis metrics have an option to take voided image by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/981
  • Updated the minimum python version by @benmalef in https://github.com/mlcommons/GaNDLF/pull/984
  • Added profiling by @pranayasinghcsmpl in https://github.com/mlcommons/GaNDLF/pull/987
  • Spellchecker corrections by @szmazurek in https://github.com/mlcommons/GaNDLF/pull/990
  • Corrected the OpenFL link in usage documentation by @naman1303 in https://github.com/mlcommons/GaNDLF/pull/989
  • Dependabot update by @dependabot in https://github.com/mlcommons/GaNDLF/pull/992
  • Update dependency version by @payalcha in https://github.com/mlcommons/GaNDLF/pull/994
  • Added configuration management using pydantic by @benmalef in https://github.com/mlcommons/GaNDLF/pull/986
  • CI updated to new python by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/1000
  • Added instance wise segmentation metrics by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/998
  • Version updated for tagging by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/1002

New Contributors

  • @naman1303 made their first contribution in https://github.com/mlcommons/GaNDLF/pull/989
  • @payalcha made their first contribution in https://github.com/mlcommons/GaNDLF/pull/994

Full Changelog: https://github.com/mlcommons/GaNDLF/compare/0.1.2...0.1.3

- Python
Published by sarthakpati 10 months ago

gandlf - Updated documentation, and dependencies, and new optimizers

What's Changed

  • Version updated for development by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/961
  • Added a faq point for the version mismatch by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/964
  • Add documentation about the log file parameter by @benmalef in https://github.com/mlcommons/GaNDLF/pull/967
  • Change the default logfile by @benmalef in https://github.com/mlcommons/GaNDLF/pull/966
  • Refactor the code related to loss computation by @szmazurek in https://github.com/mlcommons/GaNDLF/pull/965
  • Updated PyTorch to newer version by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/971
  • Update PyTorch to previous stable by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/972
  • Added new optimizers by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/970
  • Version updated for release by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/973
  • Added the ability to perform automated spell checking by @szmazurek in https://github.com/mlcommons/GaNDLF/pull/941

Full Changelog: https://github.com/mlcommons/GaNDLF/compare/0.1.1...0.1.2

- Python
Published by sarthakpati over 1 year ago

gandlf - New logo, updated DICOM support for WSI, and DP

What's Changed

  • Version updated for development by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/948
  • Upload code coverage only from master by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/950
  • Added functionality related to DP training by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/945
  • Added documentation on private model training by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/952
  • Automatic set strides kernels in dynunet by @benmalef in https://github.com/mlcommons/GaNDLF/pull/955
  • Add Huggingface Integration by @pranayasinghcsmpl in https://github.com/mlcommons/GaNDLF/pull/916
  • Standardized dependency installation for GitHub actions by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/921
  • Added logo by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/958
  • Add support for DICOM WSI by using OpenSlide by @benmalef in https://github.com/mlcommons/GaNDLF/pull/959
  • Getting ready to tag new version with update dependencies by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/960

Full Changelog: https://github.com/mlcommons/GaNDLF/compare/0.1.0...0.1.1

- Python
Published by sarthakpati over 1 year ago

gandlf - 0.1.0: new version to kickstart the process of updating APIs

What's Changed

  • Entrypoints and new gandlf cli command by @VukW in https://github.com/mlcommons/GaNDLF/pull/818
  • Trigger tests for pull requests to all branches by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/855
  • Update PyTorch dependency by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/857
  • Updated CLI options for new API by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/853
  • Add a new optimizer by @pranayasinghcsmpl in https://github.com/mlcommons/GaNDLF/pull/874
  • Minor typos removed by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/882
  • Add dynunet model by @benmalef in https://github.com/mlcommons/GaNDLF/pull/873
  • Hardcoding pip version for workflows by @benmalef in https://github.com/mlcommons/GaNDLF/pull/887
  • Adding function to get augmentation transforms by @szmazurek in https://github.com/mlcommons/GaNDLF/pull/889
  • Cleaning setup by @VukW in https://github.com/mlcommons/GaNDLF/pull/890
  • Added metrics for BraTS Path challenge by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/885
  • Metrics library updated to support comma separate inputs by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/900
  • Added output path for optimize model by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/896
  • Add logging final version by @benmalef in https://github.com/mlcommons/GaNDLF/pull/893
  • Adding proper parameter usage in the class constructor by @szmazurek in https://github.com/mlcommons/GaNDLF/pull/908
  • Updated version check for nightly builds by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/910
  • Ensure all build commands are in single step by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/911
  • New command line API functionality by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/845
  • Added programmatic pip list by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/864
  • Fix binary auroc error by @VukW in https://github.com/mlcommons/GaNDLF/pull/914
  • Update sample configuration for classification by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/917
  • Torch version updated by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/919
  • Updated GaNDLF documentation for clarity by @Linardos in https://github.com/mlcommons/GaNDLF/pull/915
  • Fixed bug in inference by @vahluw in https://github.com/mlcommons/GaNDLF/pull/922
  • Add log file parameter to cli commands by @benmalef in https://github.com/mlcommons/GaNDLF/pull/912
  • Updated docs for clarity by @Linardos in https://github.com/mlcommons/GaNDLF/pull/927
  • Changed warning message by @Linardos in https://github.com/mlcommons/GaNDLF/pull/933
  • Fix spurious errors in OpenFL Github Actions workflow by @psfoley in https://github.com/mlcommons/GaNDLF/pull/934
  • Added the ademamix optimizer by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/936
  • Added itcr connectivity map by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/938
  • Assert messages to flush to the log file by @benmalef in https://github.com/mlcommons/GaNDLF/pull/923
  • Added migration guide by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/939
  • Update requests version by @benmalef in https://github.com/mlcommons/GaNDLF/pull/943
  • Added the option to upload coverage to codacy by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/946
  • Version updated for tagging by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/947

New Contributors

  • @pranayasinghcsmpl made their first contribution in https://github.com/mlcommons/GaNDLF/pull/874
  • @Linardos made their first contribution in https://github.com/mlcommons/GaNDLF/pull/915

Full Changelog: https://github.com/mlcommons/GaNDLF/compare/0.0.20...0.1.0

- Python
Published by sarthakpati over 1 year ago

gandlf - Last tag with older API - no new functionality to be added after this

What's Changed

  • Version updated for development by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/839
  • Updated version checking mechanism by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/841
  • PR title regex fix by @VukW in https://github.com/mlcommons/GaNDLF/pull/844
  • Deprecated pkg resources by @VukW in https://github.com/mlcommons/GaNDLF/pull/846
  • Fixing data split logic by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/847
  • Commenting out auroc by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/850
  • Ensure a float tensor is passed for augmentations by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/860
  • Refactor inference manager code to save correct files by @Geeks-Sid in https://github.com/mlcommons/GaNDLF/pull/865
  • Made train batches order same as gt by @VukW in https://github.com/mlcommons/GaNDLF/pull/870
  • Downgrade requests from newest version by @VukW in https://github.com/mlcommons/GaNDLF/pull/871
  • Update black action with specific version by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/876
  • Create CODEOWNERS by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/867
  • Fixed pip version for CI tests by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/898
  • Corrected forward operations order by @hongbozheng in https://github.com/mlcommons/GaNDLF/pull/897
  • Fix train metrics by @VukW in https://github.com/mlcommons/GaNDLF/pull/868
  • Updated version for release by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/904

New Contributors

  • @hongbozheng made their first contribution in https://github.com/mlcommons/GaNDLF/pull/897

Full Changelog: https://github.com/mlcommons/GaNDLF/compare/0.0.19...0.0.20

- Python
Published by sarthakpati over 1 year ago

gandlf - Tagging before major API overhaul

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

- Python
Published by sarthakpati almost 2 years ago

gandlf - A major release with multiple updated dependencies

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

- Python
Published by sarthakpati about 2 years ago

gandlf - New version before major dependency updates

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

- Python
Published by sarthakpati over 2 years ago

gandlf - Major release with the paper

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

- Python
Published by sarthakpati almost 3 years ago

gandlf - Major release before dependency updates.

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

- Python
Published by AlexanderGetka-cbica over 3 years ago

gandlf - Major release with lots of new functionality

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 getfinallayer 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 getclassimbalance_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

- Python
Published by sarthakpati over 3 years ago

gandlf - Documentation updates and minor bugfixes

From History:

  • Deep supervision added
  • Documentation updated
  • Model IO is now standardized

- Python
Published by sarthakpati about 4 years ago

gandlf - Multiple new features for training

From History:

  • New Network: Light-UNet
  • Misc bugfixes
  • Automatic check-pointing of the model has been added
  • Extending the codebase has been simplified
  • New optimizers added
  • New metrics added
  • Affine augmentation can now be significantly fine-tuned
  • Update logic for penalty calculation
  • RGB-specific augmentation added
  • Cropping added

- Python
Published by sarthakpati over 4 years ago

gandlf - New metric calculation mechanism

Changelog:

  • Misc bugfixes for segmentation and classification
  • DFU 2021 parameter file added
  • Added SDNet for supervised learning - https://doi.org/10.1016/j.media.2019.101535
  • Added option to re-orient all images to canonical
  • Preprocessing and augmentation made into separate submodules

- Python
Published by sarthakpati over 4 years ago

gandlf - Updated feature set for segmentation and classification

Changelog:

  • Half-time epoch loss and metric output added for increased information
  • Gradient clipping added
  • Per-epoch details in validation output added
  • Different types of normalization layer options added
  • Hausdorff as a validation metric has been added
  • New option to save preprocessed data before the training starts

- Python
Published by sarthakpati over 4 years ago

gandlf - Major refactor finished

  • First level of code re-organization
  • No API changes for config files

- Python
Published by sarthakpati over 4 years ago

gandlf - Final tag before major refactor

- Python
Published by sarthakpati almost 5 years ago