2015 improve explanation of datalist format #2019
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I, Daniël Nobbe <[email protected]>, hereby add my Signed-off-by to this commit: afce136 I, Daniël Nobbe <[email protected]>, hereby add my Signed-off-by to this commit: ffb501d I, Daniël Nobbe <[email protected]>, hereby add my Signed-off-by to this commit: 5bf0ed6 I, Daniël Nobbe <[email protected]>, hereby add my Signed-off-by to this commit: 9e3d557 I, Daniël Nobbe <[email protected]>, hereby add my Signed-off-by to this commit: 79484f7 Signed-off-by: Daniël Nobbe <[email protected]>
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Fixes #8525 . ### Description I found the description of the Medical Segmentation Decathlon datalist format (short: decathlon datalist) lacking, although some parts of the framework depend on it, specifically the Auto3DSeg AutoRunner. I've added a comprehensive description of the format under `monai.data.decathlon_datalist.load_decathlon_datalist`, and some small notes elsewhere. There's a corresponding PR for the tutorials [here](Project-MONAI/tutorials#2019). Please let me know if anything is incorrect, the codebase is quite big and I haven't been working with it for very long. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Daniël Nobbe <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Kerfoot <[email protected]>
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grammar correction Co-authored-by: Eric Kerfoot <[email protected]> Signed-off-by: Daniël Nobbe <[email protected]>
Add "testing" set to datalist description Signed-off-by: Daniël Nobbe <[email protected]>
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Fixes #2015 .
Description
Added explanation of datalist format for easier quick-start for new users interested in using the Auto3DSeg AutoRunner. Also simplified the datalist explanation in
run_with_minimal_input.md, and specified that themsd_datalist_generator.ipynbnotebook is only used to generate a datalist with cross-validation folds from an existing MSD dataset (and renamed it accordingly tomsd_crossval_datalist_generator.ipynb).New users landing on the main README of the Auto3DSeg tutorial will now directly see how to create a datalist for their own data, and can easily find where further steps are described.
I also removed a paragraph on epoch/iteration numbers from the
auto_runner.ipynbthat is no longer relevant since MONAI v1.1.There is a corresponding PR here that contains improvements to the MONAI library with regards to the datalist format.
Checks
./figurefolder./runner.sh -t <path to .ipynb file>