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kvtttpre-commit-ci[bot]ebrahimebrahim
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1587 add regularizer demo (#1589)
Fixes #1587. ### Description As mentioned in #1587, the notebook should contain - [x] Formula for bending energy and diffusion, - [x] Demonstration that bending energy is not scale invariant while diffusion is not scale invariant in some cases (maybe display examples of these cases), and - [x] How both losses are made invariant by specifying `normalize=True`. ### 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. - [ ] 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: kaibo <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Ebrahim Ebrahim <[email protected]>
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README.md

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@@ -237,6 +237,8 @@ Tutorial that demonstrates how monai `SlidingWindowInferer` can be used when a 3
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This tutorial uses the MedNIST hand CT scan dataset to demonstrate MONAI's autoencoder class. The autoencoder is used with an identity encode/decode (i.e., what you put in is what you should get back), as well as demonstrating its usage for de-blurring and de-noising.
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##### [batch_output_transform](./modules/batch_output_transform.ipynb)
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Tutorial to explain and show how to set `batch_transform` and `output_transform` of handlers to work with MONAI engines.
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##### [bending_energy_diffusion_loss_notes](./modules/bending_energy_diffusion_loss_notes.ipynb)
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This notebook demonstrates when and how to compute normalized bending energy and diffusion loss.
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##### [compute_metric](./modules/compute_metric.py)
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Example shows how to compute metrics from saved predictions and labels with PyTorch multi-processing support.
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##### [csv_datasets](./modules/csv_datasets.ipynb)

modules/bending_energy_diffusion_loss_notes.ipynb

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runner.sh

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@@ -76,6 +76,7 @@ doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" 01_bundle_intro.ipy
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doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" 02_mednist_classification.ipynb)
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doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" 03_mednist_classification_v2.ipynb)
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doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" 04_integrating_code.ipynb)
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doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" bending_energy_diffusion_loss_notes.ipynb)
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# Execution of the notebook in these folders / with the filename cannot be automated
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skip_run_papermill=()

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