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Add the missing content file (#310)
* Add the missing content file Signed-off-by: mmelqin <mingmelvinq@nvidia.com> * Minor editorial change Signed-off-by: mmelqin <mingmelvinq@nvidia.com>
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# 6) Creating a Segmentation app consuming a MONAI Bundle
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## Setup
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```bash
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# Create a virtual environment with Python 3.7.
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# Skip if you are already in a virtual environment.
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# (JupyterLab dropped its support for Python 3.6 since 2021-12-23.
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# See https://github.com/jupyterlab/jupyterlab/pull/11740)
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conda create -n monai python=3.7 pytorch torchvision jupyterlab cudatoolkit=11.1 -c pytorch -c conda-forge
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conda activate monai
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# Launch JupyterLab if you want to work on Jupyter Notebook
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jupyter-lab
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```
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## Executing from Jupyter Notebook
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```{toctree}
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:maxdepth: 4
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../../notebooks/tutorials/06_monai_bundle_app.ipynb
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```
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```{raw} html
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<p style="text-align: center;">
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<a class="sphinx-bs btn text-wrap btn-outline-primary col-md-6 reference external" href="../../_static/notebooks/tutorials/06_monai_bundle_app.ipynb">
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<span>Download 06_monai_bundle_app.ipynb</span>
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</a>
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</p>
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```
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## Executing from Shell
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```bash
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# Clone the github project (the latest version of main branch only)
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git clone --branch main --depth 1 https://github.com/Project-MONAI/monai-deploy-app-sdk.git
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cd monai-deploy-app-sdk
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# Install monai-deploy-app-sdk package
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pip install monai-deploy-app-sdk
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# Download/Extract ai_spleen_bundle_data zip file from https://drive.google.com/file/d/1cJq0iQh_yzYIxVElSlVa141aEmHZADJh/view?usp=sharing
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# Download ai_spleen_bundle_data.zip
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pip install gdown
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gdown https://drive.google.com/uc?id=1cJq0iQh_yzYIxVElSlVa141aEmHZADJh
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# After downloading ai_spleen_bundle_data.zip from the web browser or using gdown,
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unzip -o ai_spleen_bundle_data.zip
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# Install necessary packages from the app; note that numpy-stl and trimesh are only
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# needed if the application uses the STL Conversion Operator
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pip install monai pydicom SimpleITK Pillow nibabel scikit-image numpy-stl trimesh
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# Local execution of the app directly or using MONAI Deploy CLI
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python examples/apps/ai_spleen_seg_app/app.py -i dcm/ -o output -m model.ts
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# or alternatively,
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monai-deploy exec ../examples/apps/ai_spleen_seg_app/app.py -i dcm/ -o output -m model.ts
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# Package app (creating MAP docker image) using `-l DEBUG` option to see progress.
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# This assumes that nvidia docker is installed in the local machine.
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# Please see https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html#docker to install nvidia-docker2.
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monai-deploy package examples/apps/ai_spleen_seg_app --tag seg_app:latest --model model.ts -l DEBUG
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# Run the app with docker image and input file locally
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monai-deploy run seg_app:latest dcm/ output
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```

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