#!/bin/bash

# multi-scan-script

#

# @brief: Run qDESS, Cubequant, and Cones analysis on super folder (absolute path) specified as an argument

#

# @folder structure:

#   |subject_scans

#       |patient01

#           |qdess

#           |cubequant

#           |cones

#       |patient02

#           |qdess

#           |cubequant

#           |cones

#       |patient03

#           |qdess

#           |cubequant

#           |cones

#       ...

#

# @usage (from terminal/command line):

#   ./multi-scan-script PATH_TO_SUPER_FOLDER

#   eg: "./multi-scan-script Users/john/Documents/subject_scans/"

#

# @initialization protocol:

#   1. run "chmod +x multi-scan-script" from the command line

#   2. Update `WEIGHTS_DIRECTORY` field below

#

# @notes:

#   - If data already exists for subject, then script does not recalculate - delete `data` folder and rerun script to redo analysis

#

# @author: Arjun Desai, Stanford University

#          (c) Stanford University, 2018

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

    if [ ! -e $TARGET_SCAN ]; then

        dosma --d $i --s $SAVE_DIRNAME qdess --fc segment --rms --weights_dir $WEIGHTS_DIRECTORY

        dosma --l $SAVE_DIRNAME qdess --fc t2

    fi

    # interregister cubequant with qdess

    if [ ! -e $CUBEQUANT_INTERREGISTERED_DATA ]; then

        echo $CUBEQUANT_INTERREGISTERED_DATA

        dosma --d $CUBEQUANT_DIRNAME --s $SAVE_DIRNAME cubequant interregister --ts $TARGET_SCAN --tm $MASK

    fi

    # cubequant 3D t1rho map

    if [ ! -e $CUEQUANT_T1RHO ]; then

        dosma --l $SAVE_DIRNAME cubequant t1_rho

    fi

    # interregister cones with qdess

    if [ ! -e $CONES_INTERREGISTERED_DATA ]; then

        dosma --d $CONES_DIRNAME --s $SAVE_DIRNAME cones interregister --ts $TARGET_SCAN --tm $MASK

    fi

    # cones 3D t2_star map

    if [ ! -e $CONES_T2STAR ]; then

        dosma --l $SAVE_DIRNAME cones t2_star

    fi

    # analyze femoral cartilage

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

done