#!/bin/bash

#--------------------------------
# Sample Batch Processing File
# Jimmy Dias (dias@biac.duke.edu)
#
# CVS ID and Authorship
# $Id: batch_sample,v 1.4 2004/02/17 17:17:35 dias Exp $
#--------------------------------

# For more help on Bash scripting, see
#  http://www.tldp.org/LDP/abs/html/

# Set variables here. Make sure there is no space before or after the
# "=' sign. 
# For example, RUNGLOB = run* would NOT work but RUNGLOB=run* would.
RUNGLOB=run004*
ANATGLOB=series002
# This is the debug level for all scripts being run. The higher the number
# the more verbose the output. Numbers 1-10 are generally used.
DEBUG=5
# EXPID=BIRN.02
# Added 02/17/04
USERNAME=anderson

ANATDIR=~/net/nernst/data1/BIRN.02/Data/Anat/20040120_42710_jd
FUNCDIR=~/net/nernst/data1/BIRN.02/Data/Func/20040120_42710_jd
CONFFILE=~/BIRN.02/birn.conf
# If you would like to use the default global configuration file, uncomment
# the following line and comment out the above line
#CONFFILE=/etc/SPM99_procd.conf

# Check if directory exists and is writable
if [ ! -d "/data/users/$USERNAME" ]
then
    echo "/data/users/$USERNAME does not exist.";
    echo "Please contact Jimmy Dias to set up a temporary data directory.";
fi

# Use Process ID number as temporary directory
TEMPDIR=/data/users/$USERNAME/tmp$$
echo "creating $TEMPDIR"
if ! mkdir $TEMPDIR
then
    echo "make directory failed. You do not have permission for $TEMPDIR"
    exit $?
fi

echo "copying directories to local"
time dircopy -D $DEBUG "$ANATDIR/$ANATGLOB" $TEMPDIR
time dircopy -D $DEBUG "$FUNCDIR/$RUNGLOB" $TEMPDIR

echo "changing to local directory"
cd $TEMPDIR

echo "running tralign"
time tralign -D $DEBUG -c $CONFFILE -s -r "$RUNGLOB"

echo "copying tralign results back"
time dircopy -D $DEBUG "a$RUNGLOB" $FUNCDIR

echo "running motioncorrect"
time motioncorrect -D $DEBUG -c $CONFFILE -s -r "a$RUNGLOB"

echo "copying motion correction results back"
time dircopy -D $DEBUG "ra$RUNGLOB" $FUNCDIR

echo "running coreg_normalize"
time coreg_normalize -D $DEBUG -c $CONFFILE -s -r "ra$RUNGLOB" -a "$ANATGLOB"

echo "copying coreg_normalize results back"
time dircopy -D $DEBUG "ncra$RUNGLOB" $FUNCDIR
time dircopy -D $DEBUG "nc$ANATGLOB" $ANATDIR

echo "running smooth"
time smooth -D $DEBUG -c $CONFFILE -s -r "ncra$RUNGLOB"

echo "copying smooth results back"
time dircopy -D $DEBUG "sncra$RUNGLOB" $FUNCDIR

echo "cleaning and removing temporary directory"
rm -rf $TEMPDIR

echo "processing script done"
exit $?

#
# $Log: batch_sample,v $
# Revision 1.4  2004/02/17 17:17:35  dias
# removed use of EXPID for temporary directory and used username instead
#
# Revision 1.3  2004/01/30 15:28:40  dias
# added some useful documentation
#
# Revision 1.2  2004/01/29 20:06:38  dias
# added tmp to temp and check for mkdir
#
# Revision 1.1  2004/01/29 18:36:44  dias
# imported source
#
# TODO:
# 1) use epoch time for temporary directory to ensure uniqueness