Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Port towards config file-based training #90

Merged
merged 67 commits into from
Mar 7, 2024
Merged

Port towards config file-based training #90

merged 67 commits into from
Mar 7, 2024

Commits on Nov 29, 2023

  1. port code towards config file-based training

    @naga-karthik
    naga-karthik committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    718cb5e View commit details
    Browse the repository at this point in the history

  2. fix/update imports

    @naga-karthik
    naga-karthik committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    35d7093 View commit details
    Browse the repository at this point in the history

  3. create function for argument parser

    @naga-karthik
    naga-karthik committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    893106a View commit details
    Browse the repository at this point in the history

  4. minor code improvements

    @naga-karthik
    naga-karthik committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    c03a962 View commit details
    Browse the repository at this point in the history

  5. add configs folder with soft_all config yaml

    @naga-karthik
    naga-karthik committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    28e99cc View commit details
    Browse the repository at this point in the history

Commits on Jan 24, 2024

  1. add citation bibtex info

    @naga-karthik
    naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    1382696 View commit details
    Browse the repository at this point in the history

  2. add arxiv badge

    @naga-karthik
    naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    b1b37c3 View commit details
    Browse the repository at this point in the history

  3. minor edit

    @naga-karthik
    naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    44b7b42 View commit details
    Browse the repository at this point in the history

  4. Fixed typo

    @jcohenadad @naga-karthik
    jcohenadad authored and naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    c829090 View commit details
    Browse the repository at this point in the history

  5. Fixed wrong file name 

    #92
    @jcohenadad @naga-karthik
    jcohenadad authored and naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    ace417a View commit details
    Browse the repository at this point in the history

  6. clarify help for checkpoint folder

    @naga-karthik
    naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    1de1e8a View commit details
    Browse the repository at this point in the history

  7. Added setup.py

    @jcohenadad @naga-karthik
    jcohenadad authored and naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    ae95bad View commit details
    Browse the repository at this point in the history

  8. Do not install requirements 

    The line "--extra-index-url" makes it tricky to run requirements via setup.py,
so the strategy is to simply run pip install once for the requirements, and
another time for the package install
    @jcohenadad @naga-karthik
    jcohenadad authored and naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    37258e8 View commit details
    Browse the repository at this point in the history

  9. Get parser arguments from within main 

    Required by #94
    @jcohenadad @naga-karthik
    jcohenadad authored and naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    31372e9 View commit details
    Browse the repository at this point in the history

  10. Instruct to download repos

    @jcohenadad @naga-karthik
    jcohenadad authored and naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    40fbaaf View commit details
    Browse the repository at this point in the history

  11. Fixed path to install package

    @jcohenadad @naga-karthik
    jcohenadad authored and naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    f7c20a1 View commit details
    Browse the repository at this point in the history

  12. Added info to download model

    @jcohenadad @naga-karthik
    jcohenadad authored and naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    902fc78 View commit details
    Browse the repository at this point in the history

  13. Updated README with install instructions

    @jcohenadad @naga-karthik
    jcohenadad authored and naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    3405c18 View commit details
    Browse the repository at this point in the history

  14. Updated README with correct syntax

    @jcohenadad @naga-karthik
    jcohenadad authored and naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    1613fb5 View commit details
    Browse the repository at this point in the history

  15. add code to dump train/val/test subjects into yaml file

    @naga-karthik
    naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    8db546a View commit details
    Browse the repository at this point in the history

  16. add data splits yaml

    @naga-karthik
    naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    eb3f1ff View commit details
    Browse the repository at this point in the history

  17. add info about finding train/val/test splits yaml file

    @naga-karthik
    naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    ceab9a3 View commit details
    Browse the repository at this point in the history

  18. simplify prepare_data function

    @naga-karthik
    naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    2d9899d View commit details
    Browse the repository at this point in the history

  19. remove unused input arg

    @naga-karthik
    naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    1b6056a View commit details
    Browse the repository at this point in the history

  20. binarize preds with 0.5 threshold

    @naga-karthik
    naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    c3a9fc0 View commit details
    Browse the repository at this point in the history

  21. remove unused import

    @naga-karthik
    naga-karthik committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    998fe5e View commit details
    Browse the repository at this point in the history

Commits on Jan 28, 2024

  1. fix checkpoint name while loading

    @naga-karthik
    naga-karthik committed Jan 28, 2024
    Configuration menu
    Copy the full SHA
    8d19401 View commit details
    Browse the repository at this point in the history

Commits on Jan 29, 2024

  1. add binrarized soft labels

    @naga-karthik
    naga-karthik committed Jan 29, 2024
    Configuration menu
    Copy the full SHA
    91e57fa View commit details
    Browse the repository at this point in the history

Commits on Jan 31, 2024

  1. add script for generating binarized soft labels

    @naga-karthik
    naga-karthik committed Jan 31, 2024
    Configuration menu
    Copy the full SHA
    1b3e351 View commit details
    Browse the repository at this point in the history

  2. remove unused function

    @naga-karthik
    naga-karthik committed Jan 31, 2024
    Configuration menu
    Copy the full SHA
    dcb42af View commit details
    Browse the repository at this point in the history

Commits on Feb 2, 2024

  1. add option to create datalist for offline binarized soft labels

    @naga-karthik
    naga-karthik committed Feb 2, 2024
    Configuration menu
    Copy the full SHA
    70938c6 View commit details
    Browse the repository at this point in the history

  2. add script to compare csa across training GT

    @naga-karthik
    naga-karthik committed Feb 2, 2024
    Configuration menu
    Copy the full SHA
    edae2ee View commit details
    Browse the repository at this point in the history

Commits on Feb 3, 2024

  1. change variable name to softseg_soft

    @naga-karthik
    naga-karthik committed Feb 3, 2024
    Configuration menu
    Copy the full SHA
    f5ec0f4 View commit details
    Browse the repository at this point in the history

  2. add script to generate csa violin plots for diff training label types

    @naga-karthik
    naga-karthik committed Feb 3, 2024
    Configuration menu
    Copy the full SHA
    5740888 View commit details
    Browse the repository at this point in the history

Commits on Feb 5, 2024

  1. rename training config file

    @naga-karthik
    naga-karthik committed Feb 5, 2024
    Configuration menu
    Copy the full SHA
    1aab0d4 View commit details
    Browse the repository at this point in the history

  2. revert to orignal version; no label binarization

    @naga-karthik
    naga-karthik committed Feb 5, 2024
    Configuration menu
    Copy the full SHA
    5960989 View commit details
    Browse the repository at this point in the history

  3. add pycache

    @naga-karthik
    naga-karthik committed Feb 5, 2024
    Configuration menu
    Copy the full SHA
    e78cb74 View commit details
    Browse the repository at this point in the history

  4. add joblib splits file for datalist creation

    @naga-karthik
    naga-karthik committed Feb 5, 2024
    Configuration menu
    Copy the full SHA
    009d207 View commit details
    Browse the repository at this point in the history

  5. add script for nnunet inference

    @naga-karthik
    naga-karthik committed Feb 5, 2024
    Configuration menu
    Copy the full SHA
    97d0a09 View commit details
    Browse the repository at this point in the history

  6. add script for reproducing training

    @naga-karthik
    naga-karthik committed Feb 5, 2024
    Configuration menu
    Copy the full SHA
    b26862f View commit details
    Browse the repository at this point in the history

  7. add script for running inference and generating csa plots

    @naga-karthik
    naga-karthik committed Feb 5, 2024
    Configuration menu
    Copy the full SHA
    f2f4f43 View commit details
    Browse the repository at this point in the history

  8. add Readme

    @naga-karthik
    naga-karthik committed Feb 5, 2024
    Configuration menu
    Copy the full SHA
    b7f920e View commit details
    Browse the repository at this point in the history

Commits on Feb 12, 2024

  1. rename perform_everything_on_device nnUNetPredictor arg

    @naga-karthik
    naga-karthik committed Feb 12, 2024
    Configuration menu
    Copy the full SHA
    cb4c9de View commit details
    Browse the repository at this point in the history

  2. add unified qc generation script

    @naga-karthik
    naga-karthik committed Feb 12, 2024
    Configuration menu
    Copy the full SHA
    d3b0f75 View commit details
    Browse the repository at this point in the history

Commits on Feb 17, 2024

  1. add einops requirement for swinunetr

    @naga-karthik
    naga-karthik committed Feb 17, 2024
    Configuration menu
    Copy the full SHA
    ff85f67 View commit details
    Browse the repository at this point in the history

  2. add qc generation script for epi data

    @naga-karthik
    naga-karthik committed Feb 17, 2024
    Configuration menu
    Copy the full SHA
    aaa3971 View commit details
    Browse the repository at this point in the history

Commits on Feb 21, 2024

  1. add script for comparing preds across thresholds

    @naga-karthik
    naga-karthik committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    d1fe4c3 View commit details
    Browse the repository at this point in the history

Commits on Feb 22, 2024

  1. add unified script to generate csa plots across methods and thresholds

    @naga-karthik
    naga-karthik committed Feb 22, 2024
    Configuration menu
    Copy the full SHA
    e04c7e4 View commit details
    Browse the repository at this point in the history

  2. update docstring

    @naga-karthik
    naga-karthik committed Feb 22, 2024
    Configuration menu
    Copy the full SHA
    953e6f0 View commit details
    Browse the repository at this point in the history

  3. remove old analyse_csa script

    @naga-karthik
    naga-karthik committed Feb 22, 2024
    Configuration menu
    Copy the full SHA
    5a6eafb View commit details
    Browse the repository at this point in the history

Commits on Feb 23, 2024

  1. add v2 inference

    @naga-karthik
    naga-karthik committed Feb 23, 2024
    Configuration menu
    Copy the full SHA
    aecb98f View commit details
    Browse the repository at this point in the history

  2. fix issue with lambda for abs_csa_error plot

    @naga-karthik
    naga-karthik committed Feb 23, 2024
    9 Configuration menu
    Copy the full SHA
    c30ca03 View commit details
    Browse the repository at this point in the history

Commits on Mar 5, 2024

  1. add script for csa comparison across old & new models

    @naga-karthik
    naga-karthik committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    1b63685 View commit details
    Browse the repository at this point in the history

  2. add script for csa comparison across resolutions for old & new models

    @naga-karthik
    naga-karthik committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    eb90326 View commit details
    Browse the repository at this point in the history

  3. update by adding support for analyzing csa across resolutions

    @naga-karthik
    naga-karthik committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    2dc4cd3 View commit details
    Browse the repository at this point in the history

  4. add feature for training swinunetr & mednext models

    @naga-karthik
    naga-karthik committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    5425989 View commit details
    Browse the repository at this point in the history

  5. add support for running inference with new models

    @naga-karthik
    naga-karthik committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    47edbbd View commit details
    Browse the repository at this point in the history

  6. add arg to output soft/hard sc seg masks

    @naga-karthik
    naga-karthik committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    8cafaab View commit details
    Browse the repository at this point in the history

  7. add --pred-type soft input in segment_sc_MONAI function

    @naga-karthik
    naga-karthik committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    8911c97 View commit details
    Browse the repository at this point in the history

  8. add keys for mednext and swinunetr models in training yaml

    @naga-karthik
    naga-karthik committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    d96c3a4 View commit details
    Browse the repository at this point in the history

Commits on Mar 7, 2024

  1. add keep_largest_object postprocessing util

    @naga-karthik
    naga-karthik committed Mar 7, 2024
    Configuration menu
    Copy the full SHA
    dadb666 View commit details
    Browse the repository at this point in the history

  2. update script to generate qc for all models

    @naga-karthik
    naga-karthik committed Mar 7, 2024
    Configuration menu
    Copy the full SHA
    894db9c View commit details
    Browse the repository at this point in the history

  3. update usage examples in docstring

    @naga-karthik
    naga-karthik committed Mar 7, 2024
    Configuration menu
    Copy the full SHA
    041ba27 View commit details
    Browse the repository at this point in the history

  4. incorporate suggestions

    @naga-karthik
    naga-karthik committed Mar 7, 2024
    Configuration menu
    Copy the full SHA
    d37f255 View commit details
    Browse the repository at this point in the history

  5. update docstring usage example

    @naga-karthik
    naga-karthik committed Mar 7, 2024
    Configuration menu
    Copy the full SHA
    b728ee7 View commit details
    Browse the repository at this point in the history

  6. Merge branch 'main' into nk/improve-training-procedure

    @naga-karthik
    naga-karthik authored Mar 7, 2024
    Configuration menu
    Copy the full SHA
    907d927 View commit details
    Browse the repository at this point in the history

  7. fix minor bug in --model args

    @naga-karthik
    naga-karthik committed Mar 7, 2024
    Configuration menu
    Copy the full SHA
    c1c4e80 View commit details
    Browse the repository at this point in the history