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Add notebook for pythonic bundle access#1501

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wyli merged 16 commits into
Project-MONAI:mainfrom
KumoLiu:pythonic-bundle
Sep 6, 2023
Merged

Add notebook for pythonic bundle access#1501
wyli merged 16 commits into
Project-MONAI:mainfrom
KumoLiu:pythonic-bundle

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@KumoLiu

@KumoLiu KumoLiu commented Sep 1, 2023

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Fixes #1502 .

Description

In this PR, we'll explore how to access a bundle in Python and use it in your own application which cover the following topics:

  1. Downloading the Bundle
  2. Creating a BundleWorkflow
  3. Getting Properties from the Bundle
  4. Using Pretrained Weights from the Bundle
  5. Updating Properties
  6. Using Components in Your Own Pipeline

Checks

  • 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 <yunl@nvidia.com>
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pre-commit-ci Bot and others added 9 commits September 1, 2023 08:47
`ConfigParser` and `BundleWorkflow`

Signed-off-by: KumoLiu <yunl@nvidia.com>
Signed-off-by: KumoLiu <yunl@nvidia.com>
Signed-off-by: KumoLiu <yunl@nvidia.com>
…into pythonic-bundle

Signed-off-by: KumoLiu <yunl@nvidia.com>
@KumoLiu KumoLiu marked this pull request as ready for review September 6, 2023 06:10
Signed-off-by: KumoLiu <yunl@nvidia.com>
@KumoLiu KumoLiu marked this pull request as draft September 6, 2023 06:24
Signed-off-by: KumoLiu <yunl@nvidia.com>
Signed-off-by: KumoLiu <yunl@nvidia.com>
@KumoLiu KumoLiu marked this pull request as ready for review September 6, 2023 07:10
@KumoLiu KumoLiu requested review from Nic-Ma, ericspod and wyli September 6, 2023 07:14
Signed-off-by: KumoLiu <yunl@nvidia.com>
Comment thread bundle/pythonic_usage_guidance/pythonic_bundle_access.ipynb
Comment thread bundle/pythonic_usage_guidance/pythonic_bundle_access.ipynb
KumoLiu and others added 2 commits September 6, 2023 17:31
Signed-off-by: KumoLiu <yunl@nvidia.com>

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Thanks, it looks good to me.

@wyli wyli merged commit 799f40b into Project-MONAI:main Sep 6, 2023
@KumoLiu KumoLiu deleted the pythonic-bundle branch September 6, 2023 13:19
boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this pull request Apr 21, 2024
Fixes Project-MONAI#1502 .

### Description
In this PR, we'll explore how to access a bundle in Python and use it in
your own application which cover the following topics:
1. Downloading the Bundle
2. Creating a `BundleWorkflow`
3. Getting Properties from the Bundle
4. Using Pretrained Weights from the Bundle
5. Updating Properties
6. Using Components in Your Own Pipeline

### 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: KumoLiu <yunl@nvidia.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Guide for pythonic bundle access

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