#!/bin/sh

#   convert cluster text output to html
#
#   Mark Jenkinson and Matthew Webster, FMRIB Image Analysis Group
#
#   Copyright (C) 1999-2009 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
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#   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.
export LC_ALL=C

Usage() {
    echo "Usage: cluster2html <featdir> <inroot> [-std]"
    echo "<inroot> should not contain the _std extension"
    exit 1
}

[ "$1" = "" ] || [ "$2" = "" ] && Usage

cd $1
shift

if [ "$2" = "" ] ; then
    echo "<HTML><TITLE>Cluster List</TITLE><BODY BACKGROUND=\"file:$FSLDIR/doc/images/fsl-bg.jpg\">" > $1.html
    echo "<CENTER><hr>Co-ordinate information for $1 - <A HREF=\"$1_std.html\">Standard-space version</A> (if present) - <A HREF=\"report.html\">back</A> to main FEAT report<hr>" >> $1.html

    echo "<H1>Cluster List</H1>" >> $1.html
    echo "<table border=3 cellspacing=3>" >> $1.html
    cat $1.txt | sed "s/	/<td>/g" \
	       | sed "s/^\(.*\)$/<tr><td>\1<\/tr>/" \
               | sed "1s/<td>/<th>/g" >> $1.html
    echo "</TABLE>" >> $1.html

    lmaxname=`echo $1 | sed "s/cluster/lmax/g"`.txt
    if [ -f $lmaxname ] ; then
	echo "<br><br><H1>Local Maxima</H1>" >> $1.html
	echo "<table border=3 cellspacing=3>" >> $1.html
	cat $lmaxname | sed "s/	/<td>/g" \
		      | sed "s/^\(.*\)$/<tr><td>\1<\/tr>/" \
                      | sed "1s/<td>/<th>/g" >> $1.html
	echo "</TABLE>" >> $1.html
    fi

    echo "</BODY></HTML>" >> $1.html
else
    echo "<HTML><TITLE>Standard-Space Cluster List</TITLE><BODY BACKGROUND=\"file:$FSLDIR/doc/images/fsl-bg.jpg\">" > $1_std.html
    echo "<CENTER><hr>Co-ordinate information for $1 - " >> $1_std.html
    if [ -f $1.html ] ; then
	echo "<A HREF=\"$1.html\">voxel-space version</A> - " >> $1_std.html
    fi
    echo "<A HREF=\"report.html\">back</A> to main FEAT report<hr>" >> $1_std.html

    echo "<H1>Cluster List</H1>" >> $1_std.html
    echo "<table border=3 cellspacing=3>" >> $1_std.html
    cat $1_std.txt | sed "s/	/<td>/g" \
	           | sed "s/^\(.*\)$/<tr><td>\1<\/tr>/" \
                   | sed "1s/<td>/<th>/g" >> $1_std.html
    echo "</TABLE>" >> $1_std.html

    lmaxname=`echo $1 | sed "s/cluster/lmax/g"`_std.txt
    if [ -f $lmaxname ] ; then
	echo "<br><br><H1>Local Maxima</H1>" >> $1_std.html
	echo "<table border=3 cellspacing=3>" >> $1_std.html
	cat $lmaxname | sed "s/	/<td>/g" \
		      | sed "s/^\(.*\)$/<tr><td>\1<\/tr>/" \
                      | sed "1s/<td>/<th>/g" >> $1_std.html
	echo "</TABLE>" >> $1_std.html
    fi

    echo "</BODY></HTML>" >> $1_std.html
fi
