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.

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

✨Fully support decathlon datalist #63

Merged
merged 15 commits into from
Mar 14, 2024
Merged

✨Fully support decathlon datalist #63

merged 15 commits into from
Mar 14, 2024

Conversation

dyollb
Copy link
Owner

@dyollb dyollb commented Sep 1, 2023

What do these changes do?

Fully support decathlon datalist

  • add script to create datalists
  • upgrade pre-commit hooks
  • rename dataset to datalist
  • remove image_dir/labels_dir args

Also:

  • refactor cross-validation
  • add MapLabels transform
  • update to support MetaTensor meta information for newer versions of monai

Related issue/s

How to test

Checklist

@codecov
Copy link

codecov bot commented Sep 3, 2023

Codecov Report

Attention: Patch coverage is 72.03390% with 66 lines in your changes are missing coverage. Please review.

Project coverage is 55.47%. Comparing base (9e176d7) to head (ffd9723).

Files Patch % Lines
src/segmantic/seg/monai_unet.py 23.07% 30 Missing ⚠️
src/segmantic/commands/monai_unet_cli.py 25.00% 12 Missing ⚠️
src/segmantic/detect/transforms.py 70.00% 3 Missing and 3 partials ⚠️
src/segmantic/seg/transforms.py 78.57% 6 Missing ⚠️
src/segmantic/image/labels.py 63.63% 4 Missing ⚠️
src/segmantic/utils/file_iterators.py 94.02% 0 Missing and 4 partials ⚠️
src/segmantic/data/transforms.py 81.81% 1 Missing and 1 partial ⚠️
src/segmantic/seg/dataset.py 94.44% 0 Missing and 2 partials ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #63      +/-   ##
==========================================
+ Coverage   53.90%   55.47%   +1.56%     
==========================================
  Files          20       21       +1     
  Lines        1228     1325      +97     
  Branches      218      237      +19     
==========================================
+ Hits          662      735      +73     
- Misses        530      550      +20     
- Partials       36       40       +4     
Flag Coverage Δ
unittests 55.47% <72.03%> (+1.56%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@dyollb dyollb merged commit 288663f into main Mar 14, 2024
8 checks passed
@dyollb dyollb deleted the decathlon_datalist branch March 14, 2024 10:31
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant