#! /usr/bin/perl -w

# rendall : creates and runs tksurfer tcl script
#           to render and save rgb's for all w files

use Cwd;

# set defaults
$tclscript = "tempsurf.tcl.$$";
# note: $$ = pid of perl process running script
$name = "unknown";
$indir = cwd;
$outdir = cwd;
$surf = "inflated";
$hemi = "both";
$fthresh = 0.0;
$fslope = 1.5;
$fmid = 1.5;
$fadef = 0.7;
$offset = 0.2;
$cvfact = 1.5;
$truncflag =0;
$smooth = 5;
$scale = 1.0;
$view = "lat";
$cust_rot_x = 0;
$cust_rot_y = 0;
$cust_rot_z = 0;
$polar = 0;
$eccen = 0;
$fieldsign = 0;
$flat = 0;
$angoffset = -1.0;
$angcycles = 0;
$patch = "occip";
$scalebarflag = 0;
$colscalebarflag = 0;
$offscreenflag = 0;

$USAGE = "Usage: rendall name [options]\n".
         "       type rendall -h for help\n";

sub help {
    print <<"HELP"; exit 0;

Usage: rendall <name> [options]
  Required Arguments:
    name       subject name

  Optional Arguments:
    -indir     [.]          input directory
    -outdir    [.]          output directory
    -surf      [inflated]   render surface
    -hemi      [both]       hemisphere (rh, lh, or both)
    -fthresh   [0.0]        stats threshold
    -fslope    [1.5]        stats slope
    -fmid      [1.5]        stats midpoint
    -fadef     [0.7]        fade factor
    -offset    [0.2]        background offset
    -cvfact    [1.5]        curvature contrast factor
    -trunc                  truncate negative values    
    -angoffset              angle offset (polar or eccen only)
               [0 (pol-rh) or 0.5 (pol-lh) or 0.83 (ecc)]
    -cycles                 angle cycles (polar or eccen only)
               [2.2 (pol) or 1 (ecc)]  
    -smooth    [5]          smoothing steps
    -scale     [1.0]        zoom factor
    -view      [lat]        lat,med,ven,pos,dor
    -rotx      [0]          x rotation (done first)
    -roty      [0]          y rotation (done second)
    -rotz      [0]          z rotation (done third)
    -polar                  polar angle complex data
    -eccen                  eccentricity complex data
    -fieldsign              fieldsign data
    -flat                   render on flattened surface
    -patch     [occip]      which flattened patch
    -scalebar               display cm scale bar
    -colscalebar            display color scale bar
    -offscreen              render offscreen
    -h                      prints this message and quits

  This program will render and save an rgb file for each w file in indir
      
HELP
}

# parse arguments
if ($#ARGV < 0) {die "$USAGE";}
for ($i = 0; $i <= $#ARGV; $i++)
{
	if ($ARGV[$i] =~ /^-/) {
		@opt = split (/-/,$ARGV[$i]);	# split the argument into "-" and "opt"
		shift (@opt);                   # get rid of the initial space
      if ($opt[0] eq 'h' || $opt[0] eq 'H') { help; }
      elsif ($opt[0] eq 'indir') {$i++; $indir = $ARGV[$i];}
      elsif ($opt[0] eq 'outdir') {$i++; $outdir = $ARGV[$i];}
      elsif ($opt[0] eq 'surf') {$i++; $surf = $ARGV[$i];}
      elsif ($opt[0] eq 'hemi') {$i++; $hemi = $ARGV[$i];}
      elsif ($opt[0] eq 'fthresh') {$i++; $fthresh = $ARGV[$i];}
      elsif ($opt[0] eq 'fslope') {$i++; $fslope = $ARGV[$i];}
      elsif ($opt[0] eq 'fmid') {$i++; $fmid = $ARGV[$i];}
      elsif ($opt[0] eq 'fadef') {$i++; $fadef = $ARGV[$i];}
      elsif ($opt[0] eq 'offset') {$i++; $offset = $ARGV[$i];}
      elsif ($opt[0] eq 'cvfact') {$i++; $cvfact = $ARGV[$i];}
      elsif ($opt[0] eq 'trunc') {$truncflag = 1;}
      elsif ($opt[0] eq 'angoffset') {$i++; $angoffset = $ARGV[$i];}
      elsif ($opt[0] eq 'cycles') {$i++; $angcycles = $ARGV[$i];}
      elsif ($opt[0] eq 'smooth') {$i++; $smooth = $ARGV[$i];}
      elsif ($opt[0] eq 'scale') {$i++; $scale = $ARGV[$i];}
      elsif ($opt[0] eq 'view') {$i++; $view = $ARGV[$i];}
      elsif ($opt[0] eq 'rotx') {$i++; $cust_rot_x = $ARGV[$i];}
      elsif ($opt[0] eq 'roty') {$i++; $cust_rot_y = $ARGV[$i];}
      elsif ($opt[0] eq 'rotz') {$i++; $cust_rot_z = $ARGV[$i];}
      elsif ($opt[0] eq 'polar') {$polar = 1;}
      elsif ($opt[0] eq 'eccen') {$eccen = 1;}
      elsif ($opt[0] eq 'fieldsign') {$fieldsign = 1;}
      elsif ($opt[0] eq 'flat') {$flat = 1;}
      elsif ($opt[0] eq 'patch') {$i++; $patch = $ARGV[$i];}
      elsif ($opt[0] eq 'scalebar') {$scalebarflag = 1;}
      elsif ($opt[0] eq 'colscalebar') {$colscalebarflag = 1;}
      elsif ($opt[0] eq 'offscreen') {$offscreenflag = 1;}
      else { die "Unknown option -$opt[0]\n";}
  } else {
    if($i==0) {
      $name = $ARGV[$i];
    } else {
      die "Unknown option $ARGV[$i]\n";
    }
  }
}

# check args
if ($name eq "unknown") {print "Must supply subject name ... quitting\n"; exit;}
opendir(DIR, "$outdir") || die "Cannot open outdir $outdir: $!";
closedir(DIR);
if ("$hemi" eq "rh") {
  @hemilist = ("rh");
} elsif ("$hemi" eq "lh") {
  @hemilist = ("lh")
} elsif ("$hemi" eq "both") {
  @hemilist = ("rh","lh")
} else {
  print "hemi must be rh, lh, or both\n";
  exit;
}

if ($angcycles == 0) {
  if ($polar == 1) {
    $angcycles = 2.2;
  } else {
    $angcycles = 1;
  }
}

foreach $hemi (@hemilist) {
  opendir(DIR, "$indir") || die "Cannot open indir $indir: $!";
  if ($fieldsign == 1) {
    @wfiles = grep /$hemi/, (grep !/^\.\.?$/, readdir DIR);
    @iwfiles = grep /$hemi.fm$/, @wfiles;
    @wfiles = grep /$hemi.fs$/, @wfiles;
#    print "wfiles = @wfiles\n";
#    print "iwfiles = @iwfiles\n";
    if ($#wfiles != $#iwfiles) {
      die "Unequal numbers of fieldsign and mask files ... quitting\n";
    }
  } elsif ($polar == 1 || $eccen == 1) {
    @wfiles = grep /$hemi.w$/, (grep !/^\.\.?$/, readdir DIR);
    @iwfiles = grep /_i-$hemi.w/, @wfiles;
    @wfiles = grep /_r-$hemi.w/, @wfiles;
    if ($#wfiles != $#iwfiles) {
      die "Unequal numbers of real and imaginary files ... quitting\n";
    }
  } else {
    @wfiles = grep /\-$hemi.w$/, (grep !/^\.\.?$/, readdir DIR);
#    print "wfiles = @wfiles\n";
  }
  if ($#wfiles < 0) {
    if ($fieldsign == 1) {
      print "No $hemi fieldsign files found in $indir/\n";
    } else {
      print "No $hemi w files found in $indir/\n";
    }
    next;
  }
  closedir(DIR);

  # strip off endings
  if ($fieldsign == 1) {
    @filestems = @wfiles;
    grep s/-$hemi.fs//, @filestems;
#    print "filestems = @filestems\n";
  } elsif ($polar == 1 || $eccen == 1) {
    @filestems = @wfiles;
    grep s/_r-$hemi.w//, @filestems;
  } else {
    @filestems = @wfiles;
    grep s/-$hemi.w//, @filestems;
#    print "filestems = @filestems\n";
  }

  open(OUTFILE, ">$tclscript") || die "Cannot create temporary tcl script: $!";
  print(OUTFILE
    "set overlayflag 1\n".
    "set surfcolor 1\n".
    "set avgflag 1\n".
    "set fthresh $fthresh\n".
    "set fslope $fslope\n".
    "set fmid $fmid\n".
    "set fadef $fadef\n".
    "set offset $offset\n".
    "set cvfact $cvfact\n".
    "set truncphaseflag $truncflag\n".
    "set flatzrot 0\n".
    "set flatscale 1.0\n".
    "set smoothsteps $smooth\n".
    "set scalebarflag $scalebarflag\n".
    "set colscalebarflag $colscalebarflag\n"
  );

  if ($fieldsign == 1) {
    print(OUTFILE
      "set complexvalflag 0\n".
      "set autoscaleflag 1\n".
      "set colscale 9\n".
      "set angle_offset 0.0\n".
      "set angle_cycles 1.0\n"
    );
  } elsif ($polar == 1) {
    print(OUTFILE
      "set complexvalflag 1\n".
      "set colscale 0\n".
      "set angle_cycles $angcycles\n"
    );
    if ($hemi eq "rh") {
      if ($angoffset == -1) {
        print(OUTFILE "set angle_offset 0.0\n");
      } else {
        print(OUTFILE "set angle_offset $angoffset\n");
      }
      print(OUTFILE "set revphaseflag 0\n");
    } else {
      if ($angoffset == -1) {
        print(OUTFILE "set angle_offset 0.5\n");
      } else {
        print(OUTFILE "set angle_offset $angoffset\n");
      }
      print(OUTFILE "set revphaseflag 1\n");
    }
  } elsif ($eccen == 1) {
    print(OUTFILE
      "set complexvalflag 1\n".
      "set colscale 0\n".
      "set angle_cycles $angcycles\n"
    );
    if ($angoffset == -1) {
      print(OUTFILE "set angle_offset 0.83\n");
    } else {
      print(OUTFILE "set angle_offset $angoffset\n");
    }
    print(OUTFILE "set revphaseflag 0\n");
  } else {
    print(OUTFILE
      "set complexvalflag 0\n".
      "set colscale 6\n".
      "set angle_offset 0.0\n".
      "set angle_cycles 1.0\n"
    );
  }

  if ($flat == 1) {
    print(OUTFILE
      "setfile patch $hemi.$patch.patch.flat\n".
      "read_binary_patch\n"
    );
  } else {
    if ($view eq "lat") {
      $rot_x = 0;
      $rot_y = 0;
      $rot_z = 0;
    } elsif ($view eq "med") {
      $rot_x = 0;
      $rot_y = 180;
      $rot_z = 0;
    } elsif ($view eq "ven") {
      $rot_x = 90;
      $rot_y = 0;
      $rot_z = 0;
    } elsif ($view eq "pos") {
      $rot_x = 0;
      if ($hemi eq "rh") {
        $rot_y = 270;
      } else {
        $rot_y = 90;
      }
      $rot_z = 0;
    } elsif ($view eq "dor") {
      $rot_x = 270;
      if ($hemi eq "rh") {
        $rot_z = 90;
      } else {
        $rot_z = 270;
      }
      $rot_y = 0;
    }
  }
  print(OUTFILE "read_binary_curv\n");
  if ($offscreenflag) {
    print(OUTFILE "set renderoffscreen 1\n");
  }
  print(OUTFILE
    "do_lighting_model -1 -1 -1 -1 \$offset\n".
    "open_window\n"
  );
  if ($flat == 0) {
    print(OUTFILE "make_lateral_view\n");
    if ($rot_x != 0) {
      print(OUTFILE "rotate_brain_x $rot_x\n");
    }  
    if ($rot_y != 0) {
      print(OUTFILE "rotate_brain_y $rot_y\n");
    }
    if ($rot_z != 0) {
      print(OUTFILE "rotate_brain_z $rot_z\n");
    }  
    if ($cust_rot_x != 0) {
      print(OUTFILE "rotate_brain_x $cust_rot_x\n");
      $view = "cus";
    }  
    if ($cust_rot_y != 0) {
      print(OUTFILE "rotate_brain_y $cust_rot_y\n");
      $view = "cus";
    }
    if ($cust_rot_z != 0) {
      print(OUTFILE "rotate_brain_z $cust_rot_z\n");
      $view = "cus";
    }  
  } else {
    print(OUTFILE "restore\n");
    if ($cust_rot_z != 0) {
      print(OUTFILE "rotate_brain_z $cust_rot_z\n");
    }  
  }

  print(OUTFILE "scale_brain $scale\n");

  foreach $filestem (@filestems) {
    if ($fieldsign == 1) {
      $fsfile = "$filestem-$hemi.fs";
      $fmfile = "$filestem-$hemi.fm";

#      print "indir = $indir\n";
#      print "fsfile = $fsfile\n";
#      print "fmfile = $fmfile\n";
      
      print(OUTFILE
        "setfile fs $indir/$fsfile\n".
        "setfile fm $indir/$fmfile\n".
        "read_fieldsign\n".
        "read_fsmask\n".
        "set complexvalflag 0\n"
      );
    } elsif ($polar == 1 || $eccen == 1) {
      $realfile = "$filestem"."_r-$hemi.w";
      $imagfile = "$filestem"."_i-$hemi.w";
      print(OUTFILE
        "setfile val $indir/$imagfile\n".
        "read_binary_values\n"
      );
      if ($smooth != 0) {
        print(OUTFILE "smooth_val $smooth\n");
      }
      print(OUTFILE
        "shift_values\n".
        "setfile val $indir/$realfile\n".
        "read_binary_values\n"
      );
      if ($smooth != 0) {
        print(OUTFILE "smooth_val $smooth\n");
      }
    } else {
      $realfile = "$filestem-$hemi.w";
      print(OUTFILE
        "setfile val $indir/$realfile\n".
        "read_binary_values\n"
      );
      if ($smooth != 0) {
        print(OUTFILE "smooth_val $smooth\n");
      }
    }
    if ($flat == 1) {
      $rgbname = "$outdir/$filestem-$hemi-$patch.patch.flat.rgb";
    } else {
      $rgbname = "$outdir/$filestem-$hemi-$surf-$view.rgb";
    }
    print(OUTFILE
      "redraw\n".
      "set rgb $rgbname\n".
      "save_rgb\n"
    );
  }
  print(OUTFILE "exit\n");
  close(OUTFILE);
  system("tksurfer -$name $hemi $surf -tcl $tclscript");
}

exit;