#!/usr/bin/perl -w

use strict;
use warnings;

unless ($ARGV[0]){
	print "sm_timecourse.pl version 2.0 (4/30/07) - szymon\@nmr.mgh.harvard.edu\n";
	print "\n";
	print "Takes screenshots of MEG data and arranges them in printable SVG figures\n";
	print "\n";
	print "Usage: sm_timecourse [options]\n";
	print "\n";
	print "Options:\n";
	# Rob, please fill this in based on the arguments below
	print "\n";
	exit;
}

# set defaults here:

my $MEG_DIR=$ENV{MEG_DIR};
my @view=('lat');
my @hemi=('lh', 'rh');
my $sub='meg_normals';
my $comment='';
my $curv='sulc';
my $smooth=5;
my $web='/space/ventzl/15/users/szymon_web/meg_results/';

my $sizex=990;					# width of page in px (use 990 for 8.5x11)
my $sizey=765;					# height of page in px (use 765 for 8.5x11)
my $rowspace=25;				# spacing between rows (px)
my $colspace=10;				# spacing bewteen columns (px)
my $xmin=20;					# left margin width (px)
my $ymin=80;					# top edge of topmost brain (px)


my $width=182;
my $height=124;

# my $width=145;
# my $height=90;

#my $width=116;
#my $height=72;






my $offset=0;
my $dosvg=1;
my $dopng=1;
my $format='png';
my $sub='meg_normals';
my $comment='';
my $suf='';

my(@pre,$analysis,$tmin,$tmax,$tstep,$fthresh,$fmid,$fmax);
my($i,$j,$k,$l);
my @args=@ARGV;

if ($ARGV[0]){
	while($ARGV[0]){
		my $flag=shift;
		if($flag eq '--pre'){
			@pre=();
			while ($ARGV[0]&&$ARGV[0]!~m/^--/){
				$pre[$j++]=shift;
			}
		}elsif($flag eq '--hemi'){
			@hemi=();
			while ($ARGV[0]&&$ARGV[0]!~m/^--/){
				$hemi[$k++]=shift;
			}
		}elsif($flag eq '--view'){
			@view=();
			while ($ARGV[0]&&$ARGV[0]!~m/^--/){
				$view[$l++]=shift;
			}
		}elsif($flag eq '--suf'){
			$suf=shift;
		}elsif($flag eq '--sub'){
			$sub=shift;
		}elsif($flag eq '--analysis'){
			$analysis=shift;
		}elsif($flag eq '--tmin'){
			$tmin=shift;
		}elsif($flag eq '--tmax'){
			$tmax=shift;
		}elsif($flag eq '--tstep'){
			$tstep=shift;
		}elsif($flag eq '--offset'){
			$offset=shift;
		}elsif($flag eq '--fthresh'){
			$fthresh=shift;
		}elsif($flag eq '--fmid'){
			$fmid=shift;
		}elsif($flag eq '--fmax'){
			$fmax=shift;
		}elsif($flag eq '--format'){
			$format=shift;
		}elsif($flag eq '--pngonly'){
			$dopng=1;$dosvg=0;
		}elsif($flag eq '--svgonly'){
			$dopng=0;$dosvg=1;
		}elsif($flag eq '--comment'){
			$comment=(shift);
		}elsif($flag eq '--smooth'){
			$smooth=(shift);
		}else{
			print "\nInvalid Argument: $flag !\n";
			exit 1;
		}
	}
}

my $src="$MEG_DIR/$sub/$analysis/stc/";
my $trg="$src/svg";

if(!-d$trg){
	system("mkdir $trg");
}

my $unique=int(rand 10000000)+1;

my $tmpf="/usr/tmp/png_${unique}.sh";

open (TMP,">$tmpf") or die;

	print TMP "#\!/bin/csh -f\n";
	print TMP "source /space/orsay/8/megdev/megsw/mne/setup/mne/mne_setup_analysis_csh\n";
	
my $tp;
if($dopng==1){
	for(my $n=0;$n<@pre;$n++){
		foreach my $v (@view){
			my $dir="$trg/$pre[$n]-$tmin-$tmax-$v";
			unless(-d$dir){
				system("mkdir $dir");
			}
			print TMP "\n";
			print TMP "mne_make_movie --stcin ${src}/${pre[$n]}${suf}-${hemi[1]}.stc --view $v --subject $sub --curv $curv --fthresh $fthresh --fmid $fmid --fmax $fmax --smooth $smooth --spm --noscalebar --nocomments --$format ${dir}/${pre[$n]} ";
			for($tp=$tmin;$tp<=$tmax;$tp=$tp+$tstep){
				print TMP "--pick $tp ";
			}
			print TMP "\n";
		}
	}
	close (TMP);
	
	chmod(0755, $tmpf);
	system("$tmpf");
	for(my $n=0;$n<@pre;$n++){
		foreach my $v (@view){
			my $dir="$trg/$pre[$n]-$tmin-$tmax-$v";
			system("mogrify -fill \"#fff\" -opaque \"#000\" -trim ${dir}/${pre[$n]}-*-${v}-*h.${format}");
		}
	}
}

my $hy=$ymin-50;				# vertical position of header (px)
my $tymin=$ymin-5;				# vertical position of timepoint (offset) labels relative to brains
my $txmin=$xmin+$width/2;			# horizontal position of timepoint (offset) labels relative to brains

if($dosvg==1){
for(my $n=0;$n<@pre;$n++){
foreach my $v (@view){
	my $dir="$trg/$pre[$n]-$tmin-$tmax-$v";
	foreach my $h (@hemi){
		my @outputs;
	
		my $x=$xmin;
		my $y=$ymin;
		my $tx=$txmin;
		my $ty=$tymin;
		my $tstart;
	
		for($tp=$tmin;$tp<=$tmax;$tp=$tp+$tstep){
			my $timepoint=$tp+($offset);
			if($y==$ymin && $x==$xmin){
				
				my $svgf="$dir/$pre[$n]-$tp-$tmax-$v-$h.svg";
				$tstart=$tp;

				open (SVG,">$svgf") or die;
				print SVG "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n";
				print SVG "<!-- Created with sm_figure.pl (szymon\@nmr.mgh.harvard.edu) -->\n";
				print SVG "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\" \n";
				print SVG "\"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n";
				print SVG "<svg width=\"$sizex\" height=\"$sizey\" version=\"1.1\"\n";
				print SVG "xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n";
				print SVG "\n";
				
				print SVG "<comment cmd=\"$0 @args\" />\n";

				print SVG "<text\n";
				print SVG "xml:space=\"preserve\"\n";
				print SVG "style=\"font-size:16px;font-style:normal;font-variant:normal;font-weight:bold;font-stretch:normal;text-align:start;line-height:100%;writing-mode:lr-tb;text-anchor:start;fill:black;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;font-family:Bitstream Vera Sans\"\n";
				print SVG "x=\"$xmin\"\n";
				print SVG "y=\"$hy\"\n";
				print SVG "id=\"title\">\n";
				print SVG "<tspan\n";
				print SVG "id=\"title\"\n";
				print SVG "x=\"$xmin\"\n";
				print SVG "y=\"$hy\">$analysis    $pre[$n]    $h    ($fthresh;$fmid;$fmax)     $comment </tspan></text>\n";
			}
			
			print SVG "<image\n";
			print SVG "id=\"$tp\"\n";
			print SVG "height=\"$height\"\n";
			print SVG "width=\"$width\"\n";
			print SVG "y=\"$y\"\n";
			print SVG "x=\"$x\"\n";
			printf SVG "xlink:href=\"${pre[$n]}-%07.1f-$v-$h.png\" />\n",$tp;
			print SVG "\n";

			print SVG "<text\n";
			print SVG "xml:space=\"preserve\"\n";
			print SVG "style=\"font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;text-align:start;line-height:100%;writing-mode:lr-tb;text-anchor:middle;fill:black;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;font-family:Bitstream Vera Sans\"\n";
			print SVG "x=\"$tx\"\n";
			print SVG "y=\"$ty\"\n";
			print SVG "id=\"text$tp\">\n";
			print SVG "<tspan\n";
			print SVG "id=\"tspan$tp\"\n";
			print SVG "x=\"$tx\"\n";
			print SVG "y=\"$ty\">$timepoint</tspan></text>\n";

			$x=$x+$width;
			$tx=$tx+$width;

			if($x+$width>$sizex-$xmin){
				$y=$y+$height+$rowspace;
				$ty=$ty+$height+$rowspace;
				$x=$xmin;
				$tx=$txmin;
			}

			if($y+$height>$sizey-$xmin && $tp!=$tmax){
				$y=$ymin;
				$ty=$tymin;
				print SVG "</svg>\n";
				close (SVG);
				system("mv $dir/${pre[$n]}-$tstart-$tmax-$v-$h.svg $dir/${pre[$n]}-$tstart-$tp-$v-$h.svg");
				
				push(@outputs,"${pre[$n]}-$tstart-$tp-$v-$h");
			}
			if($tp==$tmax){
				print SVG "</svg>\n";
				close (SVG);
				
				push(@outputs,"${pre[$n]}-$tstart-$tp-$v-$h");
			}
		}
		
		unless (-d"$web/$analysis/$v/$h"){
			system("mkdir -p $web/$analysis/$v/$h");
			open (IDX,">>$web/index.html") or die;
				print IDX "<a href=\"$analysis/$v/$h\">$analysis : $v : $h</a><br />\n";
			close (IDX);
		} 
		
		foreach my $op (@outputs){
			system("inkscape -e $web/$analysis/$v/$h/$op.png -b #ffffff $dir/$op.svg");
		}
		
		open (WWW,">$web/$analysis/$v/$h/${pre[$n]}-$tmin-$tmax-$v-$h.html") or die;
		print WWW "<html><body>\n";
		foreach my $op (@outputs){
			print WWW "<img src=\"$op.png\"\n";
		}
		print WWW "</body></html>\n";
		close (WWW);
		open (IDX,">>$web/$analysis/$v/$h/index.html") or die;
			print IDX "<a href=\"${pre[$n]}-$tmin-$tmax-$v-$h.html\">${pre[$n]}-$tmin-$tmax-$v-$h</a><br />\n";
		close (IDX);
	}
}
}
}