#!/bin/sh

#{{{ copyright and script setup

#   featquery - apply masking etc to get out stats from FEAT runs
#
#   Stephen Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 2002-2008 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.
#   
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#   University harmless from and against any and all claims, damages and
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#   
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#   
#   You are not permitted under this Licence to use this Software
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#   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.

# the next line restarts using wish \
exec $FSLTCLSH "$0" "$@"

set INGUI 0

global n_atlases atlasmenu atlasname atlasimage atlaslabelcount atlaslabelid atlaslabelname

source $env(FSLDIR)/tcl/fslstart.tcl

proc fq_exit { errmsg } {
    global logout
    fsl:echo $logout $errmsg
    puts $errmsg
    exit 0
}

#}}}
#{{{ process options

if { [ lindex $argv 0 ] == "" } {
    puts "\nUsage: featquery <N_featdirs> <featdir1> ... <N_stats> <stats1> ... <outputrootname> \[-a <atlas>\] \[-p\] \[-t <thresh>\] \[-i <interp_thresh>\] \[-s\] \[-w\] \[-b\] <mask> \[-vox <X> <Y> <Z>\]

-a : use selected atlas to generate label (etc.) information
-p : convert PE / COPE values into %
-t : threshold stats images
-i : affect size of resampled masks by changing post-interpolation thresholding (default 0.5)
-s : create time-series plots
-w : do not binarise mask (allow weighting)
-b : popup results in browser when finished
<mask> is necessary even if using co-ordinates, because a co-ordinate frame is needed to refer the co-ordinates to; if it is a relative filename (ie doesn't start with \"/\") it will be looked for inside each FEAT directory
-vox can be replaced with -mm\n\n"
    exit 1
}

set featquery(multiple) [ lindex $argv 0 ]
set featquery(nstats)   [ lindex $argv [ expr $featquery(multiple) + 1 ] ]
set featquery(output)   [ lindex $argv [ expr $featquery(multiple) + $featquery(nstats) + 2 ] ]

set pm [ expr $featquery(multiple) + $featquery(nstats) + 3 ]

set atlas ""
if { [ string compare [ lindex $argv $pm ] -a ] == 0 } {
    incr pm 1
    set atlas [ lindex $argv $pm ]
    parseatlases
    incr pm 1
}

set percent 0
if { [ string compare [ lindex $argv $pm ] -p ] == 0 } {
    set percent 1
    incr pm 1
}

set threshstat ""
if { [ string compare [ lindex $argv $pm ] -t ] == 0 } {
    incr pm 1
    set threshstat [ lindex $argv $pm ]
    incr pm 1
}

set interpthresh 0.5
if { [ string compare [ lindex $argv $pm ] -i ] == 0 } {
    incr pm 1
    set interpthresh [ lindex $argv $pm ]
    incr pm 1
}

set tsplot 0
if { [ string compare [ lindex $argv $pm ] -s ] == 0 } {
    set tsplot 1
    incr pm 1
}

set maskweight 0
if { [ string compare [ lindex $argv $pm ] -w ] == 0 } {
    set maskweight 1
    incr pm 1
}

set fqpopup 0
if { [ string compare [ lindex $argv $pm ] -b ] == 0 } {
    set fqpopup 1
    incr pm 1
}

set origmask [ lindex $argv $pm ]
set maskname ""
if { [ file exists ${origmask}.name ] } {
    set maskname [ exec sh -c "cat ${origmask}.name" ]
}

#}}}

for { set f 1 } { $f <= $featquery(multiple) } { incr f 1 } {

    #{{{ setup output dir and logging etc.

set mask $origmask

cd [ lindex $argv $f ]
set featdir [ pwd ]

set higherlevel 0
if { [ file exists design.lev ] } {
    set higherlevel 1
}

set fqroot ${featdir}/[ new_filename $featquery(output) ]
exec sh -c "mkdir $fqroot"

set fq ${fqroot}/report.html
set fqtxt ${fqroot}/report.txt
set logout ${fqroot}/report.log

fsl:echo $fq "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\"../.files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY>
<STYLE TYPE=\"text/css\">BODY { font-size: small }</STYLE>
<STYLE TYPE=\"text/css\">TABLE { font-size: x-small }</STYLE>
<CENTER><br><br><H2>Featquery output</H2><p>${fqroot}<hr>
"

#}}}
    #{{{ process co-ordinates - produce dummy mask

set coords 0

if { [ lindex $argv [ expr $pm + 1 ] ] != "" } {

    set coords 1
	
    set cX [ lindex $argv [ expr $pm + 2 ] ]
    set cY [ lindex $argv [ expr $pm + 3 ] ]
    set cZ [ lindex $argv [ expr $pm + 4 ] ]

    if { [ string compare [ lindex $argv [ expr $pm + 1 ] ] -mm ] == 0 } {
	catch { exec sh -c "echo $cX $cY $cZ | $FSLDIR/bin/std2imgcoord -img $mask -std $mask -vox - | tail -n 1" } thevals
	set cX [ lindex $thevals 0 ]
	set cY [ lindex $thevals 1 ]
	set cZ [ lindex $thevals 2 ]
    }

    fsl:echo $fq "Using co-ordinates $cX $cY $cZ. "

    fsl:exec "${FSLDIR}/bin/fslmaths $mask -mul 0 -add 100 -roi $cX 1 $cY 1 $cZ 1 0 1 ${fqroot}/mask -odt float"
    
    set mask ${fqroot}/mask
}

#}}}
    #{{{ work out what space the mask is in

if { ! [ imtest $mask ] } {
    fq_exit "Error - mask file $mask doesn't exist"
}

set maskdimx [ exec sh -c "$FSLDIR/bin/fslval $mask dim1" ]
set maskdimy [ exec sh -c "$FSLDIR/bin/fslval $mask dim2" ]
set maskdimz [ exec sh -c "$FSLDIR/bin/fslval $mask dim3" ]

set spaces ""

if { ! $higherlevel && [ file exists reg ] } {
    foreach possiblespaces { example_func highres standard } {
	if { [ imtest reg/$possiblespaces ] &&
	     $maskdimx == [ exec sh -c "$FSLDIR/bin/fslval reg/$possiblespaces dim1" ] &&
	     $maskdimy == [ exec sh -c "$FSLDIR/bin/fslval reg/$possiblespaces dim2" ] &&
	     $maskdimz == [ exec sh -c "$FSLDIR/bin/fslval reg/$possiblespaces dim3" ] } {
	    set spaces $possiblespaces
	}
    }
} else {
    if { [ imtest example_func ] &&
	 $maskdimx == [ exec sh -c "$FSLDIR/bin/fslval example_func dim1" ] &&
	 $maskdimy == [ exec sh -c "$FSLDIR/bin/fslval example_func dim2" ] &&
	 $maskdimz == [ exec sh -c "$FSLDIR/bin/fslval example_func dim3" ] } {
	set spaces example_func
    }
}

if { $spaces == "" } {
    fq_exit "Error - mask size doesn't match any of the images in the FEAT directory"
}

set themaskname $origmask
if { $maskname != "" } {
    set themaskname $maskname
}
fsl:echo $fq "Mask <em>${themaskname}</em> is in space of $spaces.<br>Image of mask in native space:<br><IMG SRC=\"mask.png\">"

#}}}
    #{{{ make mask

if { [ string compare $spaces example_func ] != 0 } {

    if { ! [ file exists reg/${spaces}2example_func.mat ] } {
	fq_exit "Error - transform to take mask into space of example_func does not exist in the FEAT directory - run FEAT registration"
    }

    if { $coords == 1 } {
	fsl:exec "${FSLDIR}/bin/fslmaths $mask -s 5 ${fqroot}/mask -odt float"
    }

    if { [ string compare $spaces standard ] == 0 && [ imtest reg/highres2standard_warp ] } {
	fsl:exec "${FSLDIR}/bin/invfeatreg $featdir"
	fsl:exec "${FSLDIR}/bin/fslmaths $mask ${fqroot}/mask -odt float"
	fsl:exec "${FSLDIR}/bin/applywarp --ref=example_func --in=${fqroot}/mask --out=${fqroot}/mask --warp=reg/highres2standard_warp_inv --postmat=reg/highres2example_func.mat"
    } else {
	fsl:exec "${FSLDIR}/bin/flirt -in $mask -ref example_func -out ${fqroot}/mask -applyxfm -init reg/${spaces}2example_func.mat -datatype float"
    }

    set mask ${fqroot}/mask

    if { $coords == 1 } {
	catch { exec sh -c "${FSLDIR}/bin/fslstats $mask -x" } themax
	fsl:exec "${FSLDIR}/bin/fslmaths $mask -roi [ lindex $themax 0 ] 1 [ lindex $themax 1 ] 1 [ lindex $themax 2 ] 1 0 1 -bin $mask"
    } else {
	if { ! $maskweight } {
	    fsl:exec "${FSLDIR}/bin/fslmaths $mask -thr $interpthresh $mask"
	}
    }

}

set maskbin "-bin"
if { $maskweight } {
    catch { exec sh -c "${FSLDIR}/bin/fslstats $mask -M" } maskmean
    set maskbin "-div $maskmean"
}

fsl:exec "${FSLDIR}/bin/fslmaths $mask $maskbin ${fqroot}/mask"

#}}}
    #{{{ setup percent

if { $percent } {
    if { ! [ imtest mean_func ] } {
	fsl:exec "${FSLDIR}/bin/fslmaths filtered_func_data -Tmean mean_func"
    }
    fsl:echo $fq "<p>PE/COPE values converted into % (VARCOPE into %<sup>2</sup>)."
}

#}}}
    #{{{ run tsplot

if { [ imtest filtered_func_data ] } {
    fsl:exec "${FSLDIR}/bin/fslmaths filtered_func_data -mul ${fqroot}/mask ${fqroot}/tmpts"
    fsl:exec "${FSLDIR}/bin/fslmeants -i ${fqroot}/tmpts -o ${fqroot}/mean_mask_ts.txt -m ${fqroot}/mask"
    imrm ${fqroot}/tmpts
    fsl:echo $fq "<p><a href=\"mean_mask_ts.txt\">Mean time series (masked/weighted)</a>. &nbsp;&nbsp;&nbsp;"

    if { $tsplot } {
	fsl:exec "mkdir ${fqroot}/tsplot"
	fsl:exec "${FSLDIR}/bin/tsplot ${featdir} -m ${fqroot}/mask -o ${fqroot}/tsplot"
	fsl:echo $fq "<a href=\"tsplot/tsplot_index.html\">Masked time series plots.</a><br>
"
    }
}

#}}}
    #{{{ setup html table

if { $atlas > 0 } {
    fsl:echo $fq "<p>Using atlas:  $atlasname($atlas)"
}

fsl:echo $fq "<p><table border=1 cellspacing=3>
<tr><th>stats image<th> # voxels <th colspan=7> image statistics <th colspan=7> position of max </tr>
<tr><th><th><th> min <th> 10% <th> mean <th> median <th> 90% <th> max <th> stddev <th colspan=3> vox (FMRI space) <th colspan=3> mm (standard space) <th>max voxel atlas results</tr>
"

#}}}

    for { set s 0 } { $s < $featquery(nstats) } { incr s 1 } {
	set statsimage [ lindex $argv [ expr $featquery(multiple) + 2 + $s ] ]
	#{{{ estimate PE/COPE as a % change

set percentcommand ""
if { $percent } {

    set thename   [ string trimright [ file tail $statsimage ] "0123456789" ]

    if { $thename == "cope" || $thename == "pe" || $thename == "varcope" } {

	set height_file design.mat
	if { $thename == "cope" || $thename == "varcope" } {
	    set height_file design.con
	}
    
	# get pe or cope number
	set thenumber [ expr 1 + [ string trimleft  [ file tail $statsimage ] "varcope" ] ]

	# get higher-level contrast height if it exists (this is the mean of lower-level contrast heights)
	set higherheight 1
	if { [ file exists design.lcon ] } {
	    set higherheight [ exec sh -c "cat design.lcon" ]
	}

	# get regressor scaling value from design.mat or design.con file
	# set to 100 if scaling not set (ie FEAT directory was created by old version of FEAT)
	set theheight [ exec sh -c "grep PPheights $height_file | awk '{ print \$$thenumber }'" ]
	if { $theheight != "" && $theheight != 0 } {
	    set theheight [ expr 100.0 *  $theheight * $higherheight ]
	} else {
	    set theheight 100
	}

	# begin scaling command
	set percentcommand "-mul $theheight"

	# divide by mean image unless is a higher-level analysis
	if { [ imtest mean_func ] } {
	    set percentcommand "$percentcommand -div mean_func"
	}

	# square it all for varcopes
	if { $thename == "varcope" } {
	    set percentcommand "$percentcommand $percentcommand"
	}

    }
}

#}}}
	#{{{ apply mask, run fslstats and convert max vox coords to standard space

fsl:exec "${FSLDIR}/bin/fslmaths $statsimage $percentcommand ${fqroot}/tmp"

if { $threshstat == "" } {
    fsl:exec "${FSLDIR}/bin/imcp ${fqroot}/mask ${fqroot}/tmpmask"
} else {
    fsl:exec "${FSLDIR}/bin/fslmaths $statsimage -thr $threshstat -bin -mul ${fqroot}/mask ${fqroot}/tmpmask"
}

catch { exec sh -c "${FSLDIR}/bin/fslstats ${fqroot}/tmp -k ${fqroot}/tmpmask -m -R -V -p 10 -p 50 -p 90 -x -s" } thevals

set themean  [ format %.4g [ lindex $thevals 0 ] ]
set themin   [ format %.4g [ lindex $thevals 1 ] ]
set themax   [ format %.4g [ lindex $thevals 2 ] ]
set thecount [ lindex $thevals 3 ]
set perc10   [ format %.4g [ lindex $thevals 5 ] ]
set perc50   [ format %.4g [ lindex $thevals 6 ] ]
set perc90   [ format %.4g [ lindex $thevals 7 ] ]
set thestd   [ format %.4g [ lindex $thevals 11 ] ]
set maxx     [ lindex $thevals 8 ]
set maxy     [ lindex $thevals 9 ]
set maxz     [ lindex $thevals 10 ]

set SSmaxx ""
set SSmaxy ""
set SSmaxz ""
set atlasstring ""
if { $higherlevel || ( [ imtest reg/standard ] && [ file exists reg/example_func2standard.mat ] ) && $maxx != 0  && $maxy != 0  && $maxz != 0 } {
    if { $higherlevel } {
	set SSmax [ fsl:exec "echo $maxx $maxy $maxz | ${FSLDIR}/bin/img2stdcoord -img example_func -std example_func -vox -" ]	    
    } else {
	set stdxfm "-xfm reg/example_func2standard.mat"
	if { [ imtest reg/highres2standard_warp ] } {
	    set stdxfm "-premat reg/example_func2highres.mat -warp reg/highres2standard_warp"
	}
	set SSmax [ fsl:exec "echo $maxx $maxy $maxz | ${FSLDIR}/bin/img2stdcoord -img example_func -std reg/standard $stdxfm -vox -" ]
    }
    set SSmaxx [ format %.1f [ lindex $SSmax 0 ] ]
    set SSmaxy [ format %.1f [ lindex $SSmax 1 ] ]
    set SSmaxz [ format %.1f [ lindex $SSmax 2 ] ]
    
    if { $atlas > 0 } {
	set atlasstring [ fsl:exec "export DYLD_LIBRARY_PATH=/Applications/fslview.app/Contents/Frameworks; ${FSLDIR}/bin/atlasquery -a \"$atlasname($atlas)\" -c ${SSmaxx},${SSmaxy},${SSmaxz} | awk -F \"<br>\" '{print \$2}' " -n ]
    }
}

#}}}
	#{{{ save max-vox, masked-mean and weighted-mask-mean timeseries text files to file

set txtfiletxt "$statsimage"

if { [ imtest filtered_func_data ] } {
    regsub -all "stats/" $statsimage "" statsname
    fsl:exec "${FSLDIR}/bin/fslmeants -i filtered_func_data -o ${fqroot}/max_${statsname}_ts.txt -c $maxx $maxy $maxz"
    set txtfiletxt "<a href=\"max_${statsname}_ts.txt\">${statsimage}</a>"
}

#}}}
	#{{{ main stats text outputs to html and raw text files

fsl:echo $fq "<tr><td> $txtfiletxt <td> $thecount <td> $themin <td> $perc10 <td> $themean <td> $perc50 <td> $perc90 <td> $themax <td> $thestd <td> $maxx <td> $maxy <td> $maxz <td> $SSmaxx <td> $SSmaxy <td> $SSmaxz <td width=\"40%\"> $atlasstring</tr>"

fsl:echo $fqtxt "$f $statsimage $thecount $themin $perc10 $themean $perc50 $perc90 $themax $thestd $maxx $maxy $maxz $SSmaxx $SSmaxy $SSmaxz"

#}}}
    }

    #{{{ finish up

fsl:exec "/bin/rm ${fqroot}/tmp*"

fsl:exec "${FSLDIR}/bin/slicesmask mean_func ${fqroot}/mask ${fqroot}/mask.png"

fsl:echo $fq "</table></BODY></HTML>"

if { $fqpopup } {
	FmribWebHelp file: $fq
}

#}}}
}