#!/bin/tcsh -f

HELP:
if ("$1" == '' || "$1" == "-help" || "$1" == "-h") then
   echo "Usage 1: A script to clip regions of a volume"
   echo ""
   echo "   `basename $0` <-input VOL> <-below Zmm> [ [-and/-or] <-above Zmm> ]"
   echo ""
   echo "   Mandatory parameters:"
   echo "      -input VOL: Volume to clip"
   echo "    + At least one of the options below:"
   echo "      -below Zmm: Set to 0 slices below Zmm"
   echo "                  Zmm (and all other coordinates) are in RAI"
   echo "                  as displayed by AFNI on the top left corner"
   echo "                  of the AFNI controller" 
   echo "      -above Zmm: Set to 0 slices above Zmm"
   echo "      -left  Xmm: Set to 0 slices left of Xmm"
   echo "      -right  Xmm: Set to 0 slices right of Xmm"
   echo "      -anterior Ymm: Set to 0 slices anterior to Ymm"
   echo "      -posterior Ymm: Set to 0 slices posterior to Ymm"
   echo ""
   echo "    Optional parameters:"
   echo "      -and (default): Combine with next clipping planes using 'and'"
   echo "      -or           : Combine with next clipping planes using 'or'"
   echo "      -verb         : Verbose, show command"
   echo "      -crop         : Crop the output volume"
   echo "      -prefix PRFX  : Use PRFX for output prefix. Default is the "
   echo "                      input prefix with _clp suffixed to it."
   echo ""    
   echo "Example:"
   echo "@clip_volume -below -30 -above 53 -left 20 -right -13 -anterior -15 \"
   echo "             -posterior 42 -input ABanat+orig. -verb -prefix sample"
   echo ""
   echo "Written by Ziad S. Saad (ziad@nih.gov)"
   echo "                        SSCC/NIMH/NIH/DHHS"
   echo ""
   goto END
endif
  

PARSE:
	echo "Parsing ..."
	set Narg = $#
	
	set cnt = 1
   set crop = 0
   set anat_in = ''
   set prefix = ''
   set sgn = '*'
   set verb = 0
   set neq = 0
   while ($cnt <= $Narg)
		set donext = 1;
      if ($donext && ("$argv[$cnt]" == "-below" || "$argv[$cnt]" == "-inferior") ) then
         set pLoc = $cnt		
		   if ($pLoc == $Narg) then
				echo "Need Zmm after -below"
            goto END
			else
            @ cnt ++
            if ($neq == 0) then 
               set eq = "step(z - ($argv[$cnt]))"
               @ neq ++
            else 
               set eq = "$eq $sgn step(z - ($argv[$cnt]))"
               @ neq ++
            endif
            set donext = 0	
         endif	
      endif
      if ($donext && ("$argv[$cnt]" == "-above" || "$argv[$cnt]" == "-superior") ) then
         set pLoc = $cnt		
		   if ($pLoc == $Narg) then
				echo "Need Zmm after -above"
            goto END
			else
            @ cnt ++
            if ($neq == 0) then 
               set eq = "step(($argv[$cnt]) - z)"
               @ neq ++
            else 
               set eq = "$eq $sgn step(($argv[$cnt]) - z)"
               @ neq ++
            endif
            set donext = 0	
         endif	
      endif
      if ($donext && "$argv[$cnt]" == "-right") then
         set pLoc = $cnt		
		   if ($pLoc == $Narg) then
				echo "Need Xmm after -right"
            goto END
			else
            @ cnt ++
            if ($neq == 0) then 
               set eq = "step(x - ($argv[$cnt]))"
               @ neq ++
            else 
               set eq = "$eq $sgn step(x - ($argv[$cnt]))"
               @ neq ++
            endif
            set donext = 0	
         endif	
      endif
      if ($donext && "$argv[$cnt]" == "-left") then
         set pLoc = $cnt		
		   if ($pLoc == $Narg) then
				echo "Need Xmm after -left"
            goto END
			else
            @ cnt ++
            if ($neq == 0) then 
               set eq = "step(($argv[$cnt]) - x)"
               @ neq ++
            else 
               set eq = "$eq $sgn step(($argv[$cnt]) - x)"
               @ neq ++
            endif
            set donext = 0	
         endif	
      endif
      if ($donext && "$argv[$cnt]" == "-anterior") then
         set pLoc = $cnt		
		   if ($pLoc == $Narg) then
				echo "Need Ymm after -anterior"
            goto END
			else
            @ cnt ++
            if ($neq == 0) then 
               set eq = "step(y - ($argv[$cnt]))"
               @ neq ++
            else 
               set eq = "$eq $sgn step(y - ($argv[$cnt]))"
               @ neq ++
            endif
            set donext = 0	
         endif	
      endif
      if ($donext && "$argv[$cnt]" == "-posterior") then
         set pLoc = $cnt		
		   if ($pLoc == $Narg) then
				echo "Need Ymm after -posterior"
            goto END
			else
            @ cnt ++
            if ($neq == 0) then 
               set eq = "step(($argv[$cnt]) - y)"
               @ neq ++
            else 
               set eq = "$eq $sgn step(($argv[$cnt]) - y)"
               @ neq ++
            endif
            set donext = 0	
         endif	
      endif
      
      if ($donext && "$argv[$cnt]" == "-crop") then
         set crop = 1;		
         set donext = 0		
      endif
      
      if ($donext && "$argv[$cnt]" == "-and") then
         set sgn = '*';		
         set donext = 0		
      endif
      if ($donext && "$argv[$cnt]" == "-or") then
         set sgn = '+';		
         set donext = 0		
      endif
      if ($donext && "$argv[$cnt]" == "-prefix") then
         set pLoc = $cnt		
		   if ($pLoc == $Narg) then
				echo "Need a string after -prefix"
            goto END
			else
            @ cnt ++
            set prefix = "$argv[$cnt]"
            set donext = 0	
         endif	
      endif
      if ($donext && "$argv[$cnt]" == "-input") then
         set pLoc = $cnt		
		   if ($pLoc == $Narg) then
				echo "Need  volume after -input"
            goto END
			else
            @ cnt ++
            set anat_in = "$argv[$cnt]"
            set in_name = `@parse_afni_name $anat_in`
            set donext = 0	
         endif	
      endif
      if ($donext && "$argv[$cnt]" == "-verb") then
         set verb = 1;		
         set donext = 0		
      endif
      if ($donext == 1) then
         echo "Error: Option or parameter '$argv[$cnt]' not understood"
         goto END
      endif
		@ cnt ++
	end
   
   if ($prefix == '') then
      set prefix = $in_name[2]"_clp"
   endif

DOIT:
   echo "Clipping"
   if ($crop == 1) then
      set noglob
      if ($verb) echo "3dcalc -a "$anat_in" -expr "a * $eq" -rai -prefix ___tmp_clp"
      unset noglob
      3dcalc -a "$anat_in" -expr "a * $eq" -rai -prefix ___tmp_clp
      set noglob
      if ($verb) echo "3dAutobox -prefix $prefix -input ___tmp_clp$in_name[3]"
      unset noglob
      3dAutobox -prefix $prefix -input ___tmp_clp$in_name[3]
      rm -f ___tmp_clp$in_name[3].???? >& /dev/null
   else
      set noglob
      if ($verb) echo "3dcalc -a "$anat_in" -expr "a * $eq" -rai -prefix $prefix"
      unset noglob
      3dcalc -a "$anat_in" -expr "a * $eq" -rai -prefix $prefix
   endif
   
END: