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benchmark/tutorial lazy resampling components and workflows #6156

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4 tasks done
wyli opened this issue Mar 16, 2023 · 0 comments
Closed
4 tasks done

benchmark/tutorial lazy resampling components and workflows #6156

wyli opened this issue Mar 16, 2023 · 0 comments
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Lazy resampling (...

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@wyli
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wyli commented Mar 16, 2023 •
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Describe the bug
would be great to provide some measurements about lazy resampling output quality, speed, and memory footprint on cpu/gpu.

please note that the Compose/caching enhancements are still WIP, the logic may need to be tuned accordingly.

cc @yiheng-wang-nv @KumoLiu @Nic-Ma
@wyli wyli added this to MONAI v1.2 Mar 16, 2023
@wyli wyli mentioned this issue Mar 17, 2023
Merged
5 tasks
wyli added a commit to Project-MONAI/tutorials that referenced this issue Mar 19, 2023
@wyli @pre-commit-ci
adds a lazy resampling functional example (#1254)
5608c43 
part of Project-MONAI/MONAI#6156


### 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: Wenqi Li <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@wyli wyli mentioned this issue Apr 3, 2023
Merged
5 tasks
wyli added a commit to Project-MONAI/tutorials that referenced this issue Apr 17, 2023
@wyli @pre-commit-ci
adds a lazy resampling compose tutorial (#1276)
4001c08 
part of Project-MONAI/MONAI#6156


### 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: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@wyli wyli mentioned this issue Apr 19, 2023
Merged
5 tasks
@KumoLiu KumoLiu mentioned this issue Apr 20, 2023
Merged
5 tasks
wyli pushed a commit to Project-MONAI/tutorials that referenced this issue Apr 26, 2023
@KumoLiu @pre-commit-ci
Add lazy-resampling benchmark tutorial (#1322)
97d0af4 
part of Project-MONAI/MONAI#6156

### Description
Show lazy-resampling benchmark results on 3d spleen segmentation. The
results include the following two main parts.
- Time spent on each transform and the total amount of data preparation
in the lazy and non-lazy mode.
- End-to-end time comparison

### 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.
- [ ] Clean up long text outputs from code cells in the notebook.
- [ ] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [ ] 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
- [ ] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`

---------

Signed-off-by: KumoLiu <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@wyli wyli closed this as completed May 5, 2023
boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this issue Apr 21, 2024
@wyli @pre-commit-ci
adds a lazy resampling functional example (Project-MONAI#1254)
88c2488 
part of Project-MONAI/MONAI#6156


### 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: Wenqi Li <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this issue Apr 21, 2024
@wyli @pre-commit-ci
adds a lazy resampling compose tutorial (Project-MONAI#1276)
e293551 
part of Project-MONAI/MONAI#6156


### 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: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this issue Apr 21, 2024
@KumoLiu @pre-commit-ci
Add lazy-resampling benchmark tutorial (Project-MONAI#1322)
852f1fb 
part of Project-MONAI/MONAI#6156

### Description
Show lazy-resampling benchmark results on 3d spleen segmentation. The
results include the following two main parts.
- Time spent on each transform and the total amount of data preparation
in the lazy and non-lazy mode.
- End-to-end time comparison

### 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.
- [ ] Clean up long text outputs from code cells in the notebook.
- [ ] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [ ] 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
- [ ] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`

---------

Signed-off-by: KumoLiu <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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MONAI v1.2
Status: Done
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Lazy resampling (+ cache-based datase...
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