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Add RANO Data Preparation MLCube to examples #633

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9a6a4bb
Move rano data prep to examples
aristizabal95 Dec 11, 2024
8f4b995
Write a build script for rano data prep
aristizabal95 Dec 12, 2024
ce44f2f
Fix Dockerfile to point to correct paths
aristizabal95 Dec 12, 2024
620258d
Merge branch 'main' into rano-data-prep-cube
aristizabal95 Dec 12, 2024
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12 changes: 12 additions & 0 deletions examples/RANO/data_preparator/.gitignore
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*.csv
*.txt
*.nii.gz
*.zip
*.mat
*.dcm
*.png
*/mlcube/workspace/*
!requirements.txt
!*/mlcube/workspace/parameters.yaml
models
tmpmodel
35 changes: 35 additions & 0 deletions examples/RANO/data_preparator/Dockerfile
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FROM local/fets_tool AS data_prep

RUN find /Front-End/bin/install/appdir/usr/bin -type f \( -perm -u=x -o -type l \) -exec cp -P {} /usr/bin \;

WORKDIR /

COPY ./project/requirements.txt /project/requirements.txt

RUN pip install --upgrade pip

RUN pip install -r /project/requirements.txt

ENV LANG C.UTF-8

RUN mkdir /project/stages

RUN cp /Front-End/bin/install/appdir/usr/bin/*.py /project/stages/

RUN cp -R /Front-End/bin/install/appdir/usr/bin/data_prep_models /project/stages/data_prep_models

# Hotfix: install more recent version of GaNDLF for metrics generation
RUN pip install git+https://github.com/mlcommons/GaNDLF@616b37bafad8f89d5c816a88f44fa30470601311

# setup a separate env for nnunet
RUN python -m venv /nnunet_env && /nnunet_env/bin/pip install --upgrade pip

RUN /nnunet_env/bin/pip install --default-timeout=1000 torch torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cu118

RUN /nnunet_env/bin/pip install git+https://github.com/MIC-DKFZ/nnUNet.git@nnunetv1

ENV CUDA_VISIBLE_DEVICES="0"

COPY ./project /project

ENTRYPOINT ["python", "/project/mlcube.py"]
10 changes: 10 additions & 0 deletions examples/RANO/data_preparator/build.sh
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#! /bin/bash
mkdir tmp
cd tmp
git clone -b fets_2.0 https://github.com/FeTS-AI/Front-End.git
cd Front-End
git submodule update --init
docker build --target=fets_base -t local/fets_tool .
cd ../../
docker build --platform=linux/amd64 -t mlcommons/rano-data-prep-mlcube:1.0.10 .
rm -rf tmp
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