ALADIN/run.sh at main · fastlib/ALADIN · GitHub

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#!/usr/bin/env bash
set -ex

# This is the master script for the capsule. When you click "Reproducible Run", the code in this file will execute.
python3.10 --version
pip3.10 --version

cd src
pip3.10 install .
cd ..
cd nnUNet
pip3.10 install .
cd ..

unzip -o /data/ALADIN-weights.zip -d "/data/models"
unzip -o /data/STANFORD.zip -d "/data"
unzip -o /data/RDB.zip -d "/data"
mkdir /data/VALIDATION
unzip -o /data/VALIDATION.zip -d "/data/VALIDATION"

#Set environment variables
export aladin_models=/data/models
export benchmark_results=/results
export benchmark_data=/data

#Run demo
python3.10 demo.py --case STANFORD1
python3.10 demo.py --case STANFORD2
python3.10 demo.py --case A01986
python3.10 demo.py --case A08391

#Install SoTA models for delineation
git clone https://github.com/guillermo-jimenez/DelineatorSwitchAndCompose.git
cd DelineatorSwitchAndCompose
git clone https://github.com/guillermo-jimenez/sak.git
cd sak
pip3.10 install . --no-deps
cd ..
cd ..
pip3.10 install -r requirements.txt

mkdir DelineatorSwitchAndCompose/TrainedModels
unzip -o /data/TrainedModels.zip -d "/code/DelineatorSwitchAndCompose/TrainedModels"

#Benchmark delineation
chmod 777 benchmark_delineation.sh
./benchmark_delineation.sh

#Benchmark diagnosis on iRhythm dataset
chmod 777 benchmark_diagnosis_STANFORD.sh
./benchmark_diagnosis_STANFORD.sh

python3.10 paper/boxplot-stanford.py

#Benchmark diagnosis on AliveCor
cd /data/CINC
chmod 777 download.sh
./download.sh
cd ..
cd ..

chmod 777 benchmark_diagnosis_CINC.sh
./benchmark_diagnosis_CINC.sh

python3.10 paper/boxplot-cinc.py