#!/bin/bash

# 1. Separate dicom files from bilateral dess knee scan into left dicoms and right dicoms

# 2. Run qDESS analysis on left and right knees

#

# @usage (from terminal/command line):

# ./bilateral-knee-dess PATH_TO_DICOM_FOLDER PATIENT_ID

# eg: "./bilateral-knee-dess /Users/data/Patient07/005 07"

#

# @initialization protocol:

#   1. run "chmod +x bilateral-knee-dess" from the command line

#   2. Update `WEIGHTS_DIRECTORY` field below to point to the appropriate weights

#   3. Update 'TISSUES' field if additional tissues desired

#      e.g. '--fc --tc' for femoral cartilage and tibial cartilage

#

# @assumptions:

#   - Scan volumes are acquired in sagittal direction from patient left to patient right

#     (i.e. left knee, then right knee)

#   - Volume slices (1...N) - Left knee slices (1...N/2), right knee slices (N/2 + 1, ... N)

#   - Left knee - lateral --> medial

#   - Right knee - medial --> lateral

#

# @author: Arjun Desai, Stanford University

#          (c) Stanford University, 2018

SCRIPTS_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"

DOSMA_DIR="$( cd "$( dirname "${SCRIPTS_DIR}" )" >/dev/null 2>&1 && pwd )"

WEIGHTS_DIRECTORY=$DOSMA_DIR/"../weights"

TISSUES='--fc'

if [[ -z "$WEIGHTS_DIRECTORY" ]]; then

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

    exit 125

fi

if [[ $# -lt 1 ]]; then

    echo "Please provide path to dicom folder and patient id"

    exit 125

fi

if [[ $# -lt 2 ]]; then

    echo "Please provide patient id"

    exit 125

fi

DICOM_PATH=$1

PID=$2

echo "dicom path: $DICOM_PATH"

echo "patient id: $PID"

# get list of dicoms in this folder

dicom_list_str=$(find $DICOM_PATH -type f -name "*.dcm" -maxdepth 1 | sort)

dicom_array=()

for filepath in $dicom_list_str

do

    dicom_array+=($filepath)

done

echo "Number of dicoms: ${#dicom_array[@]}"

# halfpoint in dicom list to split 

half_point=$((${#dicom_array[@]} / 2))

# Assume directories exist, if they don't set this to false

DIRS_EXIST=1

LEFT_DIR="$DICOM_PATH/LEFT/"

if [[ ! -d "$LEFT_DIR" ]]; then

    mkdir $LEFT_DIR

    DIRS_EXIST=0

fi

RIGHT_DIR="$DICOM_PATH/RIGHT/"

if [[ ! -d "$RIGHT_DIR" ]]; then

    mkdir $RIGHT_DIR

    DIRS_EXIST=0

fi

# if the directories already exist, assume the data has already been separated into different folders

if [[ $DIRS_EXIST -eq 0 ]]; then

    counter=1

    for filepath in ${dicom_array[@]}

    do

        filename=$(basename $filepath)

        if [[ $counter -gt $half_point ]]; then

            # store in right directory

            cp $filepath $RIGHT_DIR

        else

            cp $filepath $LEFT_DIR

        fi

        counter=$(expr $counter + 1)

    done

fi

cd ..

base_dicom_path=$(dirname $DICOM_PATH)

base_filename=$(basename $DICOM_PATH)

DATA_DIR="$base_dicom_path/data/$base_filename"

echo "Save path: $DATA_DIR"

# 2. run analysis on the qdess files

#    if data directory already exist, skip analysis

DATA_DIR_LEFT="$DATA_DIR/LEFT"

dosma --d $LEFT_DIR --s $DATA_DIR_LEFT qdess $TISSUES segment --rms --weights_dir $WEIGHTS_DIRECTORY

dosma --l $DATA_DIR_LEFT qdess $TISSUES t2

dosma --l $DATA_DIR_LEFT knee --pid $PID $TISSUES

DATA_DIR_RIGHT="$DATA_DIR/RIGHT"

dosma --d $RIGHT_DIR --s $DATA_DIR_RIGHT qdess $TISSUES segment --rms --weights_dir $WEIGHTS_DIRECTORY

dosma --l $DATA_DIR_RIGHT qdess $TISSUES t2

dosma --l $DATA_DIR_RIGHT knee --ml --pid $PID $TISSUES