Add zarr merger notebook section #1433
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Signed-off-by: Behrooz <[email protected]>
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Fixes #6006 ### Description This PR implements `ZarrAvgMerger` which can be used for patch inference. Also a use case is demonstrated [here](Project-MONAI/tutorials#1433). ### 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). - [x] New tests added to cover the changes. - [x] 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: Behrooz <[email protected]>
Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Behrooz <[email protected]>
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Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Behrooz <[email protected]>
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View / edit / reply to this conversation on ReviewNB KumoLiu commented on 2023-06-30T02:19:35Z Line #4. import zarr Seems zarr didn't install successfully. https://github.com/Project-MONAI/tutorials/actions/runs/5413785783/jobs/9839865836?pr=1433#step:5:663 |
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View / edit / reply to this conversation on ReviewNB KumoLiu commented on 2023-06-30T02:19:36Z I just noticed that this one maybe "effect of adding patch filtering" to be consistent with the above cells. What do you think? |
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View / edit / reply to this conversation on ReviewNB KumoLiu commented on 2023-06-30T02:19:37Z I'm a little confused here, maybe add some explanation or put some official zarr links to help users understand. What do you think? |
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Thanks for the update, overall looks good to me. Just leave a few comments inline. |
Signed-off-by: Behrooz <[email protected]>
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Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Behrooz <[email protected]>
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Hi @KumoLiu, please take another look. Thanks |
This PR add an example for `ZarrAvgMerger` to be plugged into `PatchInferer` along with `WSISlidingWindowSplitter`. Note: Project-MONAI/MONAI#6633 in MONAI core should be merged before this one. ### Checks <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Avoid including large-size files in the PR. - [x] Clean up long text outputs from code cells in the notebook. - [x] For security purposes, please check the contents and remove any sensitive info such as user names and private key. - [x] Ensure (1) hyperlinks and markdown anchors are working (2) use relative paths for tutorial repo files (3) put figure and graphs in the `./figure` folder - [x] Notebook runs automatically `./runner.sh -t <path to .ipynb file>` --------- Signed-off-by: Behrooz <[email protected]>
This PR add an example for
ZarrAvgMergerto be plugged intoPatchInfereralong withWSISlidingWindowSplitter.Note: Project-MONAI/MONAI#6633 in MONAI core should be merged before this one.
Checks
./figurefolder./runner.sh -t <path to .ipynb file>