#!/bin/bash

echo "This file is currently deprecated - if needed, please make an issue on the corresponding Github repository"

exit 125

WEIGHTS_DIRECTORY="/Users/arjundesai/Documents/stanford/research/msk_pipeline_raw/weights"

if [ -z "$WEIGHTS_DIRECTORY" ]; then

    echo "Please define WEIGHTS_DIRECTORY in script. Use the absolute path"

    exit 125

fi

if [ $# -eq 1 ]

then

SERIES="qdess"

else

SERIES=$2

fi

# find relevant dicom files

FILES=$(find $1 -type d -name $SERIES)

cd ..

for i in $FILES; do

    DIRNAME=$(dirname $i)

    SAVE_DIRNAME="$DIRNAME/data"

    CUBEQUANT_DIRNAME="$DIRNAME/cubequant"

    CONES_DIRNAME="$DIRNAME/cones"

    TARGET_SCAN="$SAVE_DIRNAME/qdess_data/echo1.nii.gz"

    MASK="$SAVE_DIRNAME/fc/fc.nii.gz"

    CUBEQUANT_INTERREGISTERED_DATA="$SAVE_DIRNAME/cubequant_data/interregistered"

    CUEQUANT_T1RHO="$SAVE_DIRNAME/cubequant_data/t1_rho.nii.gz"

    CONES_INTERREGISTERED_DATA="$SAVE_DIRNAME/cones_data/interregistered"

    CONES_T2STAR="$SAVE_DIRNAME/cones_data/t2_star.nii.gz"

    echo ""

    echo "----------Analyzing $DIRNAME---------"

    # use qDESS to get femoral cartilage segmentation + 3D t2 maps

    echo "qDESS T2map time:"

    python -m pipeline -d $i -s $SAVE_DIRNAME qdess -fc -t2

    echo "segmentation time:"

    python -m pipeline -l $SAVE_DIRNAME -s $SAVE_DIRNAME qdess -fc segment -rms --weights_dir $WEIGHTS_DIRECTORY

    echo "cubequant registration time:"

    echo $CUBEQUANT_INTERREGISTERED_DATA

    python -m pipeline -d $CUBEQUANT_DIRNAME -s $SAVE_DIRNAME cq interregister -ts $TARGET_SCAN

    echo "cubequant T2map time:"

    python -m pipeline -l $SAVE_DIRNAME cq -t1rho -fm $MASK

    echo "cones registration time:"

    python -m pipeline -d $CONES_DIRNAME -s $SAVE_DIRNAME cones interregister -ts $TARGET_SCAN

    echo "cones t2star time:"

    python -m pipeline -l $SAVE_DIRNAME cones -t2star -fm $MASK

    echo "analysis time"

    python -m pipeline -l $SAVE_DIRNAME knee -fc -t2 -t1_rho -t2_star

done