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setup.sh
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setup.sh
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#!/usr/bin/env bash
#
# Setup ChampKit.
# Download and prepare benchmark datasets.
set -eu
# Get directory of current script.
here="$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}"; )" &> /dev/null && pwd 2> /dev/null; )";
cwd=$(pwd)
if [ "$(realpath $cwd)" != $(realpath "$here") ]; then
echo "[champkit] ERROR: the setup.sh script must be run from $here"
echo "[champkit] Please go to that directory an run this script again."
exit 1
fi
program_exists() {
hash "$1" 2>/dev/null;
}
if ! program_exists "conda"; then
echo "[champkit] ERROR: I cannot find conda."
echo "[champkit] If conda is not installed, please install it from https://github.com/conda-forge/miniforge"
exit 2
fi
# Check if MHIST data is ready to go...
# Check if images.zip exists and prompt user if it does not.
if [[ ! -f data/task6_precancer_vs_benign_polyps/images.zip ]] || [[ ! -f data/task6_precancer_vs_benign_polyps/annotations.csv ]]; then
echo "[champkit] ERROR: cannot find images.zip or annotations.csv for Task 6 (MHIST dataset)."
echo " Please download them from https://bmirds.github.io/MHIST/#accessing-dataset"
echo " and move them to"
echo " $here/data/task6_precancer_vs_benign_polyps/"
echo
echo " Once you have done this, please rerun this script."
exit 3
fi
# https://stackoverflow.com/a/70598193/5666087
conda_env_exists(){
conda env list | grep "${@}" >/dev/null 2>/dev/null
}
if ! conda_env_exists "champkit"; then
echo "[champkit] Creating champkit conda environment..."
conda env create -f environment.yml -n champkit
fi
echo "[champkit] Activating champkit conda environment"
eval "$(conda shell.bash hook)"
set +u
conda activate champkit
set -u
echo "[champkit] IMPORTANT: If this your first time running this, I will download ~75 GB of benchmark data now."
echo "[champkit] This will likely take over two hours."
echo "[champkit] Here we go!"
bash data/task1_tumor_notumor/setup.sh
bash data/task2_tils/setup.sh
bash data/task3_msi_crc_ffpe/setup.sh
bash data/task4_msi_crc_frozen/setup.sh
bash data/task5_msi_stad_ffpe/setup.sh
bash data/task6_precancer_vs_benign_polyps/setup.sh
echo
echo "[champkit] Finished preparing the benchmark datasets."
echo "[champkit] Now you can train and evaluate models on these benchmarks."
echo "[champkit] Enjoy!"