#!/bin/bash

#############################################################
## This script is used to download and install patches        
## to the freesurfer installation for running the             
## freesurfer tutorials.                                      
##                                                            
## See the following link for information in the tutorials:   
##                                                            
##  http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial       
##                                                            
## rsync command explained:
## -z         = compress file data during the transfer
## -t         = preserve time stamp (so fsfast wont rerun)
## -b         = make backups
## -r         = recursive
## -l         = copy symlinks as symlinks
## -v         = increase verbosity
## --progress = show progress during transfer
## --suffix   = suffix used for backups
############################################################# 

show_usage() { 
echo " Usage:"
echo  
echo " Update \$FREESURFER_HOME:"
echo "   $> fs_update" 
echo
echo " Update only certain files (directories copied recusrsively):"
echo "   $> fs_update bin/mri_convert subjects/fsaverge"
echo
echo " Show help:"
echo "   $> fs_update -h, -help, --help"
echo 
} 
 
if [ "$#" -eq 1 ]; then
  if [ $1 = "-h" ] || [ $1 = "-help" ] || [ $1 = "--help" ]; then 
    show_usage
    exit 0
  fi
fi

if [ -z "$FREESURFER_HOME" ]; then
    echo " ERROR: Environment variable FREESURFER_HOME needs to be set."
    exit 1
fi

if [ ! -e $FREESURFER_HOME/build-stamp.txt ]; then
    echo " ERROR: File $FREESURFER_HOME/build-stamp.txt does not exist."
    exit 1
fi

build=`cat $FREESURFER_HOME/build-stamp.txt`
rsync_cmd="rsync -zbrlv --progress --suffix=.`date +%s`_bak rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/${build}"
echo    " Build is ${build}"
echo  
echo    "   Running this will update some of your freesurfer binaries."
echo 
read -p " Shall I proceed? [y/n/Abort]: "
echo
if [[ $REPLY =~ ^[Yy]$ ]]; then
    if [ "$#" -eq 0 ]; then
      rsync_cmd+="/* $FREESURFER_HOME"
      echo "$rsync_cmd"
      $rsync_cmd
    else
      for update_file in "$@"; do
        rsync_cmd+="/${update_file} $FREESURFER_HOME/${update_file}"
        echo "$rsync_cmd"
        $rsync_cmd
      done
    fi
    if [ "$?" -eq 0 ]; then
      echo "Done."
      exit 0
    else
      exit 1
    fi
fi