#!/bin/bash 
#   Copyright (C) 2012 University of Oxford
#
#   Part of FSL - FMRIB's Software Library
#   http://www.fmrib.ox.ac.uk/fsl
#   fsl@fmrib.ox.ac.uk
#   
#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
#   Imaging of the Brain), Department of Clinical Neurology, Oxford
#   University, Oxford, UK
#   
#   
#   LICENCE
#   
#   FMRIB Software Library, Release 5.0 (c) 2012, The University of
#   Oxford (the "Software")
#   
#   The Software remains the property of the University of Oxford ("the
#   University").
#   
#   The Software is distributed "AS IS" under this Licence solely for
#   non-commercial use in the hope that it will be useful, but in order
#   that the University as a charitable foundation protects its assets for
#   the benefit of its educational and research purposes, the University
#   makes clear that no condition is made or to be implied, nor is any
#   warranty given or to be implied, as to the accuracy of the Software,
#   or that it will be suitable for any particular purpose or for use
#   under any specific conditions. Furthermore, the University disclaims
#   all responsibility for the use which is made of the Software. It
#   further disclaims any liability for the outcomes arising from using
#   the Software.
#   
#   The Licensee agrees to indemnify the University and hold the
#   University harmless from and against any and all claims, damages and
#   liabilities asserted by third parties (including claims for
#   negligence) which arise directly or indirectly from the use of the
#   Software or the sale of any products based on the Software.
#   
#   No part of the Software may be reproduced, modified, transmitted or
#   transferred in any form or by any means, electronic or mechanical,
#   without the express permission of the University. The permission of
#   the University is not required if the said reproduction, modification,
#   transmission or transference is done without financial return, the
#   conditions of this Licence are imposed upon the receiver of the
#   product, and all original and amended source code is included in any
#   transmitted product. You may be held legally responsible for any
#   copyright infringement that is caused or encouraged by your failure to
#   abide by these terms and conditions.
#   
#   You are not permitted under this Licence to use this Software
#   commercially. Use for which any financial return is received shall be
#   defined as commercial use, and includes (1) integration of all or part
#   of the source code or the Software into a product for sale or license
#   by or on behalf of Licensee to third parties or (2) use of the
#   Software or any derivative of it for research with the final aim of
#   developing software products for sale or license to a third party or
#   (3) use of the Software or any derivative of it for research with the
#   final aim of developing non-software products for sale or license to a
#   third party, or (4) use of the Software to provide any service to an
#   external organisation for which payment is received. If you are
#   interested in using the Software commercially, please contact Isis
#   Innovation Limited ("Isis"), the technology transfer company of the
#   University, to negotiate a licence. Contact details are:
#   innovation@isis.ox.ac.uk quoting reference DE/9564.
Usage() {
	function=`basename $0`
	echo Command-line editing of FSL design .\*fsf files 
	echo
	echo $function inputfsffile outputfsffile -option optionparam [-option optionparam] 
	echo $function fsffiles -i fsffiles -option optionparam [-option optionparam]   \*\* Replaces existing files 
	echo
	echo -replace x y - basic global replace x with y \( e.g. Subj10/run2 Subj11/run3 \)
	echo -structural x - sets structural image
	echo -outputdir x \(  level directory only \) 
	echo -outputfulldir x 
	echo -inputdirs x 
	echo -inputfulldir x y - sets input x 
	echo -smooth x - sets spatial smooth levels
	echo -hpfilteron x - set highpass filter on/off \(1/0\)
	echo -hpfilter x - set highpass filter to x
	echo -motion x - add motion parameters to model 
	echo -hilev x  - sets high level analysis to x \(3 - FE,0 - ME OLS 1 - ME FLAME 2 - ME FLAME 1+2 \)  
	echo -outlier x - sets FLAME outlier detection
	echo -nevs_orig x - sets number of original EVs
	echo -nevs_real x - sets number of real EVs
	echo -ncontrasts_orig x - sets number of original contrasts 
	echo -ncontrasts_real x - sets number of real contrasts
	echo -tf x y temporal filtering for ev x on/off \(1/0\) 
	echo -td x y temporal derivative for ev x on/off \(1/0\) \(does not update contrasts\) 
	echo -shape x y set shape of ev x to y 
	echo -evtitle x y set title for EV x to y
	echo -evskip x y skip ev x in web report on/off \(1/0\) 
	echo -contrast_mode x - sets contrast mode real/orig 
	echo -contrast_orig x y z
	echo -contrast_real x y z
	echo -contrast_orig_name x y
	echo -contrast_real_name x y
	echo -contrast_orig_show x y
	echo -contrast_real_show x y
	echo -FNIRT x - sets FNIRT nonlinear reg on/off \(1/0\)
	echo -FNIRTwarpres x
	 
	exit
}

shiftpos() {
	eval "pos=`echo $pos+1 | bc`"
}

[ "$1" = "" ] && Usage

firstchar=`echo $1 | head -c 1`
if [[ $firstchar == '-' ]]
then	shift
	firstchar=`echo $1 | head -c 1`

	while [[ $firstchar != '-' ]] && [[ $firstchar != '' ]] 
		do inputdirs="$inputdirs $1" 
		shift 
		firstchar=`echo $1 | head -c 1`
	done

	outputdirs=$inputdirs

else	inputdirs=$1
	outputdirs=$2
	shift;shift
fi

opts=$@
fsffile=`tmpnam`
cnt=1;

for input in $inputdirs; 
do
	cp $input $fsffile

	outfsffile=`echo $outputdirs | awk '{print $'$cnt'}'`
	cnt=`echo $cnt + 1 | bc`
	tempname=`tmpnam`
	
	pos=1;

	pos2=2;
	pos3=3;
	pos4=4;
	

	in1=$(echo $opts | awk '{ print $'$pos'}')
	in2=$(echo $opts | awk '{ print $'$pos2'}')
	in3=$(echo $opts | awk '{ print $'$pos3'}')
	in4=$(echo $opts | awk '{ print $'$pos4'}')

	while [[ $in1 != '' ]]; do
		
		if [[ $in1 == '-replace' ]]
		then
			# convert "/"  
			old=$(echo $in2 | sed 's/\//\\\//g')
			new=$(echo $in3 | sed 's/\//\\\//g')

			cat $fsffile | sed 's/'$old'/'$new'/g' > $tempname
			cp $tempname $fsffile
			shiftpos; shiftpos; shiftpos
			

		elif [[ $in1 == '-hilev' ]]
		then	cat $fsffile | sed 's/mixed_yn) [0123]/mixed_yn) '$in2'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos

		elif [[ $in1 == '-hilevel' ]]
		then	
			cat $fsffile | sed 's/mixed_yn) [0123]/mixed_yn) '$in2'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos

		elif [[ $in1 == '-FNIRT' ]]
		then	
			cat $fsffile | sed 's/regstandard_nonlinear_yn) [0-9].*/(regstandard_nonlinear_y) '$in2'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos

		elif [[ $in1 == '-FNIRTwarpres' ]]
		then	
			cat $fsffile | sed 's/regstandard_nonlinear_warpres) [0-9].*/(regstandard_nonlinear_warpres) '$in2'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos


		elif [[ $in1 == '-nevs_orig' ]]
		then	
			cat $fsffile | sed 's/evs_orig) [0-9].*/evs_orig) '$in2'/g' > $tempname
			cp $tempname $fsffile
			shiftpos; shiftpos

		elif [[ $in1 == '-nevs_real' ]]
		then
			cat $fsffile | sed 's/evs_real) [0-9].*/evs_real) '$in2'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos

		elif [[ $in1 == '-td' ]]
		then
			cat $fsffile | sed 's/deriv_yn'$in2') [0-9].*/deriv_yn'$in2') '$in3'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos; shiftpos
		
		elif [[ $in1 == '-tf' ]]
		then
			cat $fsffile | sed 's/tempfilt_yn'$in2') [0-9].*/tempfilt_yn'$in2') '$in3'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos; shiftpos
			
		elif [[ $in1 == '-evskip' ]]
		then
			cat $fsffile | sed 's/skip'$in2') [0-9].*/skip'$in2') '$in3'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos; shiftpos
			
		elif [[ $in1 == '-shape' ]]
		then
			cat $fsffile | sed 's/shape'$in2') [0-9].*/shape'$in2') '$in3'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos; shiftpos
		
		elif [[ $in1 == '-evtitle' ]]
		then
			cat $fsffile | sed 's/evtitle'$in2') ".*"/evtitle'$in2') "'$in3'"/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos; shiftpos

		elif [[ $in1 == '-custom' ]]
		then
			newdir=$(echo $in3 | sed 's/\//\\\//g')
			cat $fsffile | sed 's/custom'$in2') ".*"/custom'$in2') "'$newdir'"/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos; shiftpos

		elif [[ $in1 == '-contrast_mode' ]]
		then	
			cat $fsffile | sed 's/con_mode) [a-z].*/con_mode) '$in2'/g' | sed 's/con_mode_old) [a-z].*/con_mode_old) '$in2'/g' > $tempname
			cp $tempname $fsffile
			shiftpos; shiftpos

		elif [[ $in1 == '-contrast_orig' ]]
		then
			cat $fsffile | sed 's/conpic_orig\.'$in2'.'$in3') [0-9].*/conpic_orig\.'$in2'\.'$in3') '$in4'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos; shiftpos; shiftpos
			
		elif [[ $in1 == '-contrast_real' ]]
		then
			cat $fsffile | sed 's/conpic_real\.'$in2'.'$in3') [0-9].*/conpic_real\.'$in2'\.'$in3') '$in4'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos; shiftpos; shiftpos

		elif [[ $in1 == '-contrast_orig_show' ]]
		then
			cat $fsffile | sed 's/conpic_orig\.'$in2') [0-9].*/conpic_orig\.'$in2') '$in3'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos; shiftpos
		
		elif [[ $in1 == '-contrast_orig_title' ]]
		then
			cat $fsffile | sed 's/conname_orig\.'$in2') ".*"/conname_orig\.'$in2') "'$in3'"/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos; shiftpos

		elif [[ $in1 == '-contrast_real_show' ]]
		then
			cat $fsffile | sed 's/conpic_real\.'$in2') [0-9].*/conpic_real\.'$in2') '$in3'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos; shiftpos
		
		elif [[ $in1 == '-contrast_real_title' ]]
		then
			cat $fsffile | sed 's/conname_real\.'$in2') ".*"/conname_real\.'$in2') "'$in3'"/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos; shiftpos

		elif [[ $in1 == '-smooth' ]]
		then	
			cat $fsffile | sed 's/smooth) [0-9].*/smooth) '$in2'/g' > $tempname
			cp $tempname $fsffile
			shiftpos; shiftpos

		elif [[ $in1 == '-hpfilteron' ]]
		then	
			cat $fsffile | sed 's/temphp_yn) [0-9].*/temphp_yn) '$in2'/g' > $tempname
			cp $tempname $fsffile
			shiftpos; shiftpos

		elif [[ $in1 == '-hpfilter' ]]
		then	
			cat $fsffile | sed 's/paradigm_hp) [0-9].*/paradigm_hp) '$in2'/g' > $tempname
			cp $tempname $fsffile
			shiftpos; shiftpos


		elif [[ $in1 == '-motion' ]]
		then	
			cat $fsffile | sed 's/motionevs) [0-9].*/motionevs) '$in2'/g' > $tempname
			cp $tempname $fsffile
			shiftpos; shiftpos

		elif [[ $in1 == '-outlier ' ]]
		then	
			cat $fsffile | sed 's/robust_yn) [01].*/robust_yn) '$in2'/g' > $tempname
			cp $tempname $fsffile
			shiftpos; shiftpos


		elif [[ $in1 == '-ncontrasts_orig' ]]
		then
			cat $fsffile | sed 's/ncon_orig) [0-9].*/ncon_orig) '$in2'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos

		elif [[ $in1 == '-ncontrasts_real' ]]
		then
			cat $fsffile | sed 's/ncon_real) [0-9].*/ncon_real) '$in2'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos

		elif [[ $in1 == '-outputfulldir' ]]
		then
			newdir=$(echo $in2 | sed 's/\//\\\//g')
			cat $fsffile | sed 's/\([^"]*outputdir) "\)\([^"]*\)"/\1'$newdir'"/g'  > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos

		elif [[ $in1 == '-outputdir' ]]
		then
			dir=`cat "$fsffile" | grep outputdir | sed 's/[^"]*"\([^"]*\)"/\1/g'`

			firstchar=`echo $dir | head -c 1`
			lastchar=`echo $dir | tail -c 1`

			if [[ $dir == '' ]]
			then newdir=$in2
			elif 	[[ $lastchar == / ]]
			then 	newdir=$dir/$in2
			else	newdir=`dirname $dir`/$in2
				newdir=`echo $newdir | sed 's/^.\///g'`
			fi

			newdir=$(echo $newdir | sed 's/\//\\\//g')
			cat $fsffile | sed 's/\([^\"]*outputdir) "\)\([^\"]*\)\"/\1'$newdir'\"/g' > $tempname
			cp $tempname $fsffile
			shiftpos; shiftpos

		elif [[ $in1 == '-inputdirs' ]]
		then
			dir=`cat "$fsffile" | grep feat_files\(1\) | sed 's/[^"]*"\([^"]*\)"/\1/g'`

			firstchar=`echo $dir | head -c 1`
			lastchar=`echo $dir | tail -c 1`
			if [[ $dir == '' ]]
			then newdir=$in2
			elif 	[[ $lastchar == / ]]
			then 	newdir=$dir/$in2
			else	newdir=`dirname $dir`/$in2
				newdir=$(echo $newdir | sed 's/^.\///g')
			fi

			newdir=$(echo $newdir | sed 's/\//\\\//g')
			cat $fsffile | sed 's/\([^\"]*feat_files(.) "\)\([^\"]*\)\"/\1'$newdir'\"/g' > $tempname
			cp $tempname $fsffile
			shiftpos; shiftpos

		elif [[ $in1 == '-inputfulldir' ]]
		then
			newdir=$(echo $in3 | sed 's/\//\\\//g')
			cat $fsffile | sed 's/\([^"]*feat_files('$in2') "\)\([^"]*\)"/\1'$newdir'"/g'  > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos; shiftpos

		elif [[ $in1 == '-ncopeinputs' ]]
		then
			cat $fsffile | sed 's/ncopeinputs) [0-9].*/ncopeinputs) '$in2'/g' > $tempname
		
			cp $tempname $fsffile
			shiftpos; shiftpos

		elif [[ $in1 == '-structural' ]]
		then
			newdir=$(echo $in2 | sed 's/\//\\\//g')
			cat $fsffile | sed 's/\([^"]*highres_files(.) "\)\([^"]*\)"/\1'$newdir'"/g'  > $tempname
		
			cp $tempname $fsffile
			shift; shift


		else
			echo Error: no option $in1
			exit
		fi

	pos2=$(echo $pos+1 | bc)
	pos3=$(echo $pos+2 | bc)
	pos4=$(echo $pos+3 | bc)

	in1=$(echo $opts | awk '{ print $'$pos' }')
	in2=$(echo $opts | awk '{ print $'$pos2' }')
	in3=$(echo $opts | awk '{ print $'$pos3' }')
	in4=$(echo $opts | awk '{ print $'$pos4' }')

	done

	cp $fsffile $outfsffile
	rm $fsffile
	rm $tempname

done