Index: trunk/ippScripts/scripts/skycell_jpeg.pl
===================================================================
--- trunk/ippScripts/scripts/skycell_jpeg.pl	(revision 28375)
+++ trunk/ippScripts/scripts/skycell_jpeg.pl	(revision 28375)
@@ -0,0 +1,360 @@
+#! /usr/bin/env perl
+
+use warnings;
+use strict;
+use Carp;
+use IPC::Cmd 0.36 qw( can_run run);
+use PS::IPP::Metadata::List qw( parse_md_list );
+use PS::IPP::Config 1.01 qw( :standard );
+use Getopt::Long qw( GetOptions :config auto_help auto_version gnu_getopt );
+use Pod::Usage qw( pod2usage );
+use File::Temp qw( tempfile );
+
+my $db;
+
+my ($stage, $stage_id, $outroot, $camera, $dbname, $logfile, $verbose, $save_temps);
+my $missing_tools;
+my ($help,$masks);
+my ($tempFile,$tempName,$maskFile,$maskName);
+my $ppSkycell = can_run('ppSkycell') or (warn "Can't find ppSkycell" and $missing_tools = 1);
+my $warptool  = can_run('warptool') or (warn "Can't find warptool" and $missing_tools = 1);
+my $stacktool = can_run('stacktool') or (warn "Can't find stacktool" and $missing_tools = 1);
+my $difftool  = can_run('difftool') or (warn "Can't find difftool" and $missing_tools = 1);
+GetOptions(
+    'help|h'          => \$help,
+    'stage=s'         => \$stage,
+    'stage_id=s'      => \$stage_id,
+    'outroot=s'       => \$outroot,
+    'dbname=s'        => \$dbname,
+    'camera=s'        => \$camera,
+    'logfile=s'       => \$logfile,
+    'verbose'         => \$verbose,
+    'save_temps'      => \$save_temps,
+    'masks'           => \$masks,
+#    'no-op'           => \$no_op,
+#    'no-update'       => \$no_update,
+    ) or pod2usage ( 2 );
+
+pod2usage( -msg => "Unknown option: @ARGV", -exitval => 2) if @ARGV;
+pod2usage(
+    -msg => "Required options: --stage --stage_id --path_base\nHelpful options: --camera --dbname",
+    -exitval => 3,
+    ) unless
+    defined $stage and defined $stage_id and defined $outroot;
+
+my $ipprc = PS::IPP::Config->new( $camera ) or my_die("Unable to set up", $stage_id, $PS_EXIT_CONFIG_ERROR); # this is used for PATH, NEB filename conversions
+
+my %stages = ('warp' => 1, 'stack' => 1, 'diff' => 1);
+
+unless (exists($stages{$stage})) {
+    my_die("Unknown stage '$stage'",$stage_id,$PS_EXIT_UNKNOWN_ERROR);
+}
+
+my $mdcParser = PS::IPP::Metadata::Config->new; # Parser for metadata config files
+
+if ($stage eq 'warp') {
+    my $imfiles;
+    my $command = "$warptool -warped -warp_id $stage_id";
+    if (defined($dbname)) {
+	$command .= " -dbname $dbname";
+    }
+
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) = run(command => $command, verbose => $verbose);
+    unless ($success) {
+	$error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+	&my_die("unable to perform warptool: $error_code", $stage_id, $error_code);
+    }
+
+    if (@$stdout_buf == 0) {
+	# no results found;
+    }
+    
+    $imfiles = $mdcParser->parse_list(join "", @$stdout_buf) or
+	&my_die("unable to parse metadata config doc", $stage_id, $error_code);
+
+    my %tangents = ();
+    
+    foreach my $imfile (@$imfiles) {
+	my $skycell_id = $imfile->{skycell_id};
+	my $path_base  = $imfile->{path_base};
+	my $quality    = $imfile->{quality};
+	my $state      = $imfile->{data_state};
+	my $projection_cell = $skycell_id;
+	if ($quality == 8007 or $state ne 'full') {
+	    next;
+	}
+
+	$projection_cell =~ s/^(.*)\..*$/$1/;
+	
+	unless (exists($tangents{$projection_cell})) {
+	    # Make a temp file and fill, but be sure to save 
+	    ($tempFile, $tempName) = tempfile("/tmp/skycell.$projection_cell.XXXX",
+						 UNLINK => !$save_temps);
+	    $tangents{$projection_cell}{FILE} = $tempFile;
+	    $tangents{$projection_cell}{NAME} = $tempName;
+	    if ($masks) {
+		my ($maskFile, $maskName) = tempfile("/tmp/skycell.$projection_cell.masks.XXXX",
+						     UNLINK => !$save_temps);
+		$tangents{$projection_cell}{MFILE} = $maskFile;
+		$tangents{$projection_cell}{MNAME} = $maskName;
+	    }		
+	}
+	print "$skycell_id $projection_cell\n";	
+	my $file = $ipprc->filename("PSWARP.OUTPUT", $path_base, $skycell_id);
+	print "$file $state $quality\n";
+	my $f_fh = $tangents{$projection_cell}{FILE};
+	print $f_fh "$file\n";
+	if ($masks) {
+	    my $mask = $ipprc->filename("PSWARP.OUTPUT.MASK", $path_base, $skycell_id);
+	    print "$mask\n";
+	    my $m_fh = $tangents{$projection_cell}{MFILE};
+	    print $m_fh "$mask\n";
+	}
+    }
+    foreach my $projection_cell (keys %tangents) {
+	$command = "$ppSkycell -images $tangents{$projection_cell}{NAME}";
+	if ($masks) {
+	    $command .= " -masks $tangents{$projection_cell}{MNAME} ";
+	}
+	$command .= " ${outroot}.${projection_cell} ";
+	print "$command\n";
+	( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) = run(command => $command, verbose => $verbose);
+	unless ($success) {
+	    $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+	    &my_die("unable to perform ppSkycell: $error_code", $stage_id, $error_code);
+	}
+	# Update database:
+	$command = "$warptool -addsummary -warp_id $stage_id -projection_cell $projection_cell -path_base $outroot";
+	if (defined($dbname)) {
+	    $command .= " -dbname $dbname";
+	}
+	
+	( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) = run(command => $command, verbose => $verbose);
+	unless ($success) {
+	    $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+	    &my_die("unable to update warp summary: $error_code", $stage_id, $error_code);
+	}
+    }
+    if (scalar (keys %tangents) == 0) {
+	my $projection_cell = 'NULL';
+	$command = "$warptool -addsummary -warp_id $stage_id -projection_cell $projection_cell -path_base $outroot";
+	if (defined($dbname)) {
+	    $command .= " -dbname $dbname";
+	}
+	
+	( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) = run(command => $command, verbose => $verbose);
+	unless ($success) {
+	    $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+	    &my_die("unable to update diff summary: $error_code", $stage_id, $error_code);
+	}
+    }	
+} #end warp stage
+if ($stage eq 'diff') {
+    my $imfiles;
+    my $command = "$difftool -diffskyfile -diff_id $stage_id";
+    if (defined($dbname)) {
+	$command .= " -dbname $dbname";
+    }
+
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) = run(command => $command, verbose => $verbose);
+    unless ($success) {
+	$error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+	&my_die("unable to perform difftool: $error_code", $stage_id, $error_code);
+    }
+
+    if (@$stdout_buf == 0) {
+	# no results found;
+    }
+    
+    $imfiles = $mdcParser->parse_list(join "", @$stdout_buf) or
+	&my_die("unable to parse metadata config doc", $stage_id, $error_code);
+
+    my %tangents = ();
+    
+    foreach my $imfile (@$imfiles) {
+	my $skycell_id = $imfile->{skycell_id};
+	my $path_base  = $imfile->{path_base};
+	my $quality    = $imfile->{quality};
+	my $state      = $imfile->{data_state};
+	my $projection_cell = $skycell_id;
+	if ($quality == 8007 or $quality = 1010 or $state ne 'full') {
+	    next;
+	}
+
+	$projection_cell =~ s/^(.*)\..*$/$1/;
+	
+	unless (exists($tangents{$projection_cell})) {
+	    # Make a temp file and fill, but be sure to save 
+	    ($tempFile, $tempName) = tempfile("/tmp/skycell.$projection_cell.XXXX",
+						 UNLINK => !$save_temps);
+	    $tangents{$projection_cell}{FILE} = $tempFile;
+	    $tangents{$projection_cell}{NAME} = $tempName;
+	    if ($masks) {
+		my ($maskFile, $maskName) = tempfile("/tmp/skycell.$projection_cell.masks.XXXX",
+						     UNLINK => !$save_temps);
+		$tangents{$projection_cell}{MFILE} = $maskFile;
+		$tangents{$projection_cell}{MNAME} = $maskName;
+	    }		
+	}
+	print "$skycell_id $projection_cell\n";	
+	my $file = $ipprc->filename("PPSUB.OUTPUT", $path_base, $skycell_id);
+	print "$file $state $quality\n";
+	my $f_fh = $tangents{$projection_cell}{FILE};
+	print $f_fh "$file\n";
+	if ($masks) {
+	    my $mask = $ipprc->filename("PPSUB.OUTPUT.MASK", $path_base, $skycell_id);
+	    print "$mask\n";
+	    my $m_fh = $tangents{$projection_cell}{MFILE};
+	    print $m_fh "$mask\n";
+	}
+    }
+    foreach my $projection_cell (keys %tangents) {
+	$command = "$ppSkycell -images $tangents{$projection_cell}{NAME}";
+	if ($masks) {
+	    $command .= " -masks $tangents{$projection_cell}{MNAME} ";
+	}
+	$command .= " ${outroot}.${projection_cell} ";
+	print "$command\n";
+	( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) = run(command => $command, verbose => $verbose);
+	unless ($success) {
+	    $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+	    &my_die("unable to perform ppSkycell: $error_code", $stage_id, $error_code);
+	}
+	# Update database:
+	$command = "$difftool -addsummary -diff_id $stage_id -projection_cell $projection_cell -path_base $outroot";
+	if (defined($dbname)) {
+	    $command .= " -dbname $dbname";
+	}
+	
+	( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) = run(command => $command, verbose => $verbose);
+	unless ($success) {
+	    $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+	    &my_die("unable to update diff summary: $error_code", $stage_id, $error_code);
+	}
+    }
+    if (scalar (keys %tangents) == 0) {
+	my $projection_cell = 'NULL';
+	$command = "$difftool -addsummary -diff_id $stage_id -projection_cell $projection_cell -path_base $outroot";
+	if (defined($dbname)) {
+	    $command .= " -dbname $dbname";
+	}
+	
+	( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) = run(command => $command, verbose => $verbose);
+	unless ($success) {
+	    $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+	    &my_die("unable to update diff summary: $error_code", $stage_id, $error_code);
+	}
+    }	
+} #end diff stage
+if ($stage eq 'stack') {
+    my $imfiles;
+    my $command = "$stacktool -sassskyfile -sass_id $stage_id";
+    if (defined($dbname)) {
+	$command .= " -dbname $dbname";
+    }
+
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) = run(command => $command, verbose => $verbose);
+    unless ($success) {
+	$error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+	&my_die("unable to perform stacktool: $error_code", $stage_id, $error_code);
+    }
+
+    if (@$stdout_buf == 0) {
+	# no results found;
+    }
+    
+    $imfiles = $mdcParser->parse_list(join "", @$stdout_buf) or
+	&my_die("unable to parse metadata config doc", $stage_id, $error_code);
+
+    my %tangents = ();
+    
+    foreach my $imfile (@$imfiles) {
+	my $skycell_id = $imfile->{skycell_id};
+	my $path_base  = $imfile->{path_base};
+	my $quality    = $imfile->{quality};
+	my $state      = $imfile->{state};
+	my $fault      = $imfile->{fault};
+	my $projection_cell = $skycell_id;
+	if ($quality == 8007 or $state ne 'full') {
+	    next;
+	}
+
+	$projection_cell =~ s/^(.*)\..*$/$1/;
+	
+	unless (exists($tangents{$projection_cell})) {
+	    # Make a temp file and fill, but be sure to save 
+	    ($tempFile, $tempName) = tempfile("/tmp/skycell.$projection_cell.XXXX",
+						 UNLINK => !$save_temps);
+	    $tangents{$projection_cell}{FILE} = $tempFile;
+	    $tangents{$projection_cell}{NAME} = $tempName;
+	    if ($masks) {
+		my ($maskFile, $maskName) = tempfile("/tmp/skycell.$projection_cell.masks.XXXX",
+						     UNLINK => !$save_temps);
+		$tangents{$projection_cell}{MFILE} = $maskFile;
+		$tangents{$projection_cell}{MNAME} = $maskName;
+	    }		
+	}
+	print "$skycell_id $projection_cell\n";	
+	my $file = $ipprc->filename("PPSTACK.OUTPUT", $path_base, $skycell_id);
+	print "$file $state $quality\n";
+	my $f_fh = $tangents{$projection_cell}{FILE};
+	print $f_fh "$file\n";
+	if ($masks) {
+	    my $mask = $ipprc->filename("PPSTACK.OUTPUT.MASK", $path_base, $skycell_id);
+	    print "$mask\n";
+	    my $m_fh = $tangents{$projection_cell}{MFILE};
+	    print $m_fh "$mask\n";
+	}
+    }
+    foreach my $projection_cell (keys %tangents) {
+	$command = "$ppSkycell -images $tangents{$projection_cell}{NAME}";
+	if ($masks) {
+	    $command .= " -masks $tangents{$projection_cell}{MNAME} ";
+	}
+	$command .= " ${outroot}.${projection_cell} ";
+	print "$command\n";
+	( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) = run(command => $command, verbose => $verbose);
+	unless ($success) {
+	    $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+	    &my_die("unable to perform ppSkycell: $error_code", $stage_id, $error_code);
+	}
+	# Update database:
+	$command = "$stacktool -addsummary -sass_id $stage_id -projection_cell $projection_cell -path_base $outroot";
+	if (defined($dbname)) {
+	    $command .= " -dbname $dbname";
+	}
+	
+	( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) = run(command => $command, verbose => $verbose);
+	unless ($success) {
+	    $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+	    &my_die("unable to update stack summary: $error_code", $stage_id, $error_code);
+	}
+    }
+    if (scalar (keys %tangents) == 0) {
+	my $projection_cell = 'NULL';
+	$command = "$stacktool -addsummary -sass_id $stage_id -projection_cell $projection_cell -path_base $outroot";
+	if (defined($dbname)) {
+	    $command .= " -dbname $dbname";
+	}
+#	print "$command\n";
+	( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) = run(command => $command, verbose => $verbose);
+	unless ($success) {
+	    $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+	    &my_die("unable to update stack summary: $error_code", $stage_id, $error_code);
+	}
+    }	
+
+} #end stack stage
+
+
+sub my_die
+{
+    my $msg = shift; # Warning message on die
+    my $stage = shift; # stage name
+    my $stage_id = shift; #  identifier
+    my $exit_code = shift; # Exit code
+    # outputImage and path_base are globals
+
+    carp($msg);
+    exit $exit_code;
+}