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run_all.sh
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!/bin/bash
CIMMYT_TAR_FILE_NAME=paper_data_cimmyt.tar.gz
TERRAREF_TAR_FILE_NAME=paper_data_terraref.tar.gz
echo "Processing CIMMYT data"
echo "Creating working folder"
mkdir -p cimmyt
pushd cimmyt
if [ ! -f $CIMMYT_TAR_FILE_NAME ]; then
echo "Downloading image files. This may take a while..."
wget https://data.cyverse.org/dav-anon/iplant/home/schnaufer/paper_data/CIMMYT/paper_data_cimmyt.tar.gz
else
echo "Found tar file \"$CIMMYT_TAR_FILE_NAME\" and skipping download"
echo "Run \"rm $PWD/$CIMMYT_TAR_FILE_NAME\" to remove the file so it's downloaded again"
fi
echo "Extracting images"
tar -xzf paper_data_cimmyt.tar.gz
echo "Downloading script file"
wget -O run_all_cimmyt.sh https://raw.githubusercontent.com/AgPipeline/Paper-data/main/run_all_cimmyt.sh
chmod 555 run_all_cimmyt.sh
echo "Generating canopy cover"
./run_all_cimmyt.sh
echo "Copying CSV file with results"
cp canopycover.csv ../canopycover_cimmyt.csv
echo "Cleaning up"
rm $CIMMYT_TAR_FILE_NAME
./run_all_cimmyt.sh --clean
popd
rmdir cimmyt
echo "Processing TAMU Corn data"
echo "Creating working folder"
mkdir -p tamu_corn
pushd tamu_corn
echo "Downloading script file"
wget -O run_all_tamu_corn.sh https://raw.githubusercontent.com/AgPipeline/Paper-data/main/run_all_tamu_corn.sh
chmod 555 run_all_tamu_corn.sh
echo "Generating canopy cover"
./run_all_tamu_corn.sh
echo "Copying CSV file with results"
cp canopycover.csv ../canopycover_tamu_corn.csv
echo "Cleaning up"
./run_all_tamu_corn.sh --clean
popd
rmdir tamu_corn
echo "Processing YCEDA data"
echo "Creating working folder"
mkdir -p yceda
pushd yceda
echo "Downloading script file"
wget -O run_all_yceda.sh https://raw.githubusercontent.com/AgPipeline/Paper-data/main/run_all_yceda.sh
chmod 555 run_all_yceda.sh
echo "Generating canopy cover"
./run_all_yceda.sh
echo "Copying CSV file with results"
cp canopycover.csv ../canopycover_yceda.csv
echo "Cleaning up"
./run_all_yceda.sh --clean
popd
rmdir yceda
echo "Processing TERRAREF data"
echo "Creating working folder"
mkdir -p terraref
pushd terraref
if [ ! -f $TERRAREF_TAR_FILE_NAME ]; then
echo "Downloading image files. This may take a while..."
wget -O paper_data_terraref.tar.gz https://data.cyverse.org/dav-anon/iplant/home/schnaufer/paper_data/terraref/paper_data_terraref.tar.gz
else
echo "Found tar file \"$TERRAREF_TAR_FILE_NAME\" and skipping download"
echo "Run \"rm $PWD/$TERRAREF_TAR_FILE_NAME\" to remove the file so it's downloaded again"
fi
echo "Extracting images"
tar -xzf paper_data_terraref.tar.gz
echo "Downloading script file"
wget -O run_all_terraref.sh https://raw.githubusercontent.com/AgPipeline/Paper-data/main/run_all_terraref.sh
chmod 555 run_all_terraref.sh
echo "Generating canopy cover"
./run_all_terraref.sh
echo "Copying CSV file with results"
cp canopycover.csv ../canopycover_terraref.csv
echo "Cleaning up"
rm $TERRAREF_TAR_FILE_NAME
./run_all_terraref.sh --clean
popd
rmdir terraref