#!/bin/bash

#########################################

# Demonstrate the comman usage of the

# Multi-Brain Separation (MBS) pipeline

#########################################

# Add niftk installation location to system paths: `PATH` and `LD_LIBRARY_PATH`.

# This will only work if user followed the installation instruction, and installed packages in the recommended location.

# If you installed the packages in other locations, please change the variable `$HOME` to your own installed locations.

# Option 1: if user installed the default niftk package

export PATH=${PATH}:"$HOME/niftk-18.5.4/bin"

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}"$HOME/niftk-18.5.4/bin"

# option 2: if use choose to compile the niftyreg/niftyseg from the source code.

export PATH=${PATH}:"$HOME/nifty_reg/bin"

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}/"$HOME/nifty_reg/lib"

export PATH=${PATH}:"$HOME/nifty_seg/bin"

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:"$HOME/nifty_seg/lib"

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######## prepare demo data #########

####################################

# Ref: https://figshare.com/collections/Tc1_and_WT_data/3258139

# DOI: 10.6084/m9.figshare.c.3258139

# Cohort 1: https://figshare.com/articles/Tc1_and_WT_brains_cohort_1_C1_/3382693

# Cohort 2: https://figshare.com/articles/Tc1_and_WT_brains_cohort_2_C2_/3394786

HOME=$HOME

WORK_DIR=$HOME/Data/TC1

RAW_DIR=$WORK_DIR/RAW_DATA

script=$WORK_DIR/script

mkdir -p $RAW_DIR

mkdir -p $script

# get to the current directory

cd $RAW_DIR

# Get the data if not already existed/downloaded

tc1_269455=$RAW_DIR/'tc1_269455.nii.gz'

tc1_269455=$RAW_DIR/'010913_02.nii.gz'

if [[ ! -e $tc1_269455 ]]; then

    wget --content-disposition -P $RAW_DIR https://ndownloader.figshare.com/files/5275453

    wget --content-disposition -P $RAW_DIR https://ndownloader.figshare.com/files/5303806

fi

####################################

######## start demo script #########

####################################

# Download the main script if not yet done

(cd $script && svn export --force https://github.com/dancebean/multi-atlas-segmentation/trunk/MultiBrainSepsrationHelperFunctions.sh)

(cd $script && svn export --force https://github.com/dancebean/multi-atlas-segmentation/trunk/MASHelperFunctions.sh)

# source the main script (or use the location of your own copy)

source $script/MultiBrainSepsrationHelperFunctions.sh

source $script/MASHelperFunctions.sh > /dev/null 2>&1

# Alternatively, if you want to show the listing of all the available functions, use:

# source ./MASHelperFunctions.sh 

## Three brain separation

## Quickcheck

mas_quickcheck [bg_img] [(optional) overlay_img] [qc_dir] [qc_filename]

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