2015 improve explanation of datalist format #2019
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
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]>
DanielNobbe
force-pushed
the
2015-improve-explanation-of-datalist-format
branch
from
1a5afde to
c969d10
Compare
Signed-off-by: Daniël Nobbe <[email protected]>
DanielNobbe
force-pushed
the
2015-improve-explanation-of-datalist-format
branch
from
bc51740 to
5106732
Compare
Signed-off-by: Daniël Nobbe <[email protected]>
DanielNobbe
force-pushed
the
2015-improve-explanation-of-datalist-format
branch
from
6025260 to
4cfa3f6
Compare
Signed-off-by: Daniël Nobbe <[email protected]>
DanielNobbe
force-pushed
the
2015-improve-explanation-of-datalist-format
branch
from
fb53523 to
8f3405a
Compare
Signed-off-by: Daniël Nobbe <[email protected]>
DanielNobbe
force-pushed
the
2015-improve-explanation-of-datalist-format
branch
from
6dd0e48 to
c31841a
Compare
Signed-off-by: Daniël Nobbe <[email protected]>
DanielNobbe
force-pushed
the
2015-improve-explanation-of-datalist-format
branch
2 times, most recently
from
1657278 to
4bd67b7
Compare
7 tasks
Signed-off-by: Daniël Nobbe <[email protected]>
Signed-off-by: Daniël Nobbe <[email protected]>
Signed-off-by: Daniël Nobbe <[email protected]>
DanielNobbe
force-pushed
the
2015-improve-explanation-of-datalist-format
branch
from
5aafac2 to
24493b0
Compare
for more information, see https://pre-commit.ci
KumoLiu
pushed a commit
to Project-MONAI/MONAI
that referenced
this pull request
Aug 22, 2025
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]>
ericspod
reviewed
Sep 5, 2025
| ] | ||
| "training": | ||
| [ | ||
| {"image": "/path/to/image_1.nii.gz", "label": "/path/to/label_1.nii.gz"}, |
There was a problem hiding this comment.
I think this should have the fold value mentioned, the section this replaces was trying to demonstrate how the fold value was set. The "testing" list is also omitted but I think it would be good to include this for illustration.
There was a problem hiding this comment.
Hi Eric, thanks for the feedback!
I'm happy to make the change, but in my understanding this file contains an explanation for running the auto pipeline in the simplest possible way. For me, that would mean that I let the pipeline setup cross-validation automatically, without requiring me to add folds.
I'm not very familiar with the typical expected workflow, however, so if you say we should have the folds there I'll gladly add them back in.
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]>
for more information, see https://pre-commit.ci
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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>