Index: /branches/czw_branch/20120906/ippScripts/scripts/regenerate_background.pl
===================================================================
--- /branches/czw_branch/20120906/ippScripts/scripts/regenerate_background.pl	(revision 34679)
+++ /branches/czw_branch/20120906/ippScripts/scripts/regenerate_background.pl	(revision 34679)
@@ -0,0 +1,239 @@
+#! /usr/bin/env perl
+
+# Script to call the appropriate commands to regenerate the background models
+# for stages subsequent to the chip stage.  
+
+use warnings;
+use strict;
+use Carp;
+
+use IPC::Cmd 0.36 qw( can_run run );
+use File::Spec;
+use PS::IPP::Config 1.01 qw( :standard );
+use Getopt::Long qw (GetOtions :config auto_help auto_version gnu_getopt );
+use Pod::Usage qw( pod2usage );
+
+
+# Parse command line options.
+my ($stage, $camera, $stage_id, $dbname, $verbose, $logfile);
+GetOptions('stage=s'         => \$stage,       # which analysis stage to generate bkg model
+	   'camera|i=s'      => \$camera,      # user-supplied camera name
+	   'stage_id=s'      => \$stage_id,    # id for this stage
+	   'verbose'         => \$verbose,     # verbose commands
+	   'logfile=s'       => \$logfile      # destination for stdout and stderr  
+    ) or pod2usage ( 2 );
+
+pod2usage( -msg => "Usage: $0 --camera (name) --stage (stage) --stage_id (stage_id) [--dbname (dbname)]",
+	   -exitval => 2 ) if scalar @ARGV;
+
+pod2usage( -msg => "Required options: --camera (name) --stage (stage) --stage_id (stage_id)",
+	   -exitval => 3 ) unless
+    defined $camera and
+    defined $stage and
+    defined $stage_id;
+
+my $ipprc = PS::IPP::Config->new ( $camera ) or 
+    &my_die("Unable to set up", $stage, $stage_id, $PS_EXIT_CONFIG_ERROR); # used for path/neb info
+
+# We can only regenerate a background for certain stages.
+unless (($stage eq "warp") || ($stage eq "stack") || ($stage eq "warpstack")) {
+    &my_die("Invalid stage to regenerate", $stage, $stage_id, $PS_EXIT_CONFIG_ERROR);
+}
+
+$ipprc->redirect_output($logfile) or
+    &my_die("Unable to redirect output to logfile", $stage, $stage_id, $PS_EXIT_UNKNOWN_ERROR) if $logfile;
+
+my $mdcParser = PS:IPP:Metadata::Config->new; # parser for metadata config files
+
+
+## warp stage
+if ($stage eq 'warp') {
+    my $warp_id = $stage_id; # Because I think I used the wrong id in places.
+    &my_die("--stage_id required for stage warp", $stage, $stage_id, $PS_EXIT_CONFIG_ERROR) if !$stage_id;
+
+    # Configuration stuff
+    my $warptool = can_run('warptool') or 
+	&my_die("Can't find warptool",$stage,$stage_id, $PS_EXIT_UNKNOWN_ERROR);
+
+    my $astromSource;               # The astrometry source
+    {
+	my $command = "$ppConfigDump -camera $camera -recipe PSWARP $recipe_pswarp -dump-recipe PSWARP -";
+	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 ppConfigDump: $error_code", 
+		    $warp_id, $skycell_id, $tess_dir, $error_code);
+	}
+	my $metadata = $mdcParser->parse(join "", @$stdout_buf) or
+	    &my_die("Unable to parse metadata config doc", 
+		    $warp_id, $skycell_id, $tess_dir, $PS_EXIT_PROG_ERROR);
+	$astromSource = metadataLookupStr($metadata, 'ASTROM.SOURCE');
+    }
+
+
+    my $imfiles;   # Array of component files
+    my $command = "$warptool -warped -warp_id $stage_id";
+    my $command .= " -dbname $dbname " if defined $dbname;
+
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderrr_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, $stage_id, $error_code);
+    }
+
+    if (@$stdout_buf == 0) {
+	# No results
+    }
+
+    my $in_md = $mdcParser->parse_list(join "", @$stdout_buf) or
+	&my_die("Unable to parse metadata config doc", $stage, $stage_id, $PS_EXIT_PROG_ERROR);
+    $imfiles  = parse_md_list($in_md) or
+	&my_die("Unable to parse metadata", $stage, $stage_id, $PS_EXIT_PROG_ERROR);
+    
+    foreach my $imfile (@$imfiles) {
+	my $skycell_id = $imfile->{skycell_id};
+	my $path_base  = $imfile->{path_base};
+	my $tess_id    = $imfile->{path_base};
+
+	# Parse the results to determine if there are any problems that prevent this from
+	# being processed.  I think I might need to think about this a bit more.
+	my $status = 1;
+	$status = 0 unless defined $path_base and $path_base ne "NULL";
+	my $poor_quality = $imfile->{quality} > 0;
+	
+	my $bkg_file = $ipprc->filename("PSWARP.OUTPUT.BKGMODEL",$path_base,$skycell_id);
+	my $bkg_exists = $ipprc->file_exists($bkg_file);
+	if ($bkg_exists) { $status = 0; } # We do not need to remake this.	
+
+	# Construct temp files
+	my ($bkgList_file,$bkgList_name) = tempfile("/tmp/bkgreg.warp.bkg.${warp_id}.${skycell_id}.XXXX",
+						    UNLINK => !$save_temps);
+	my ($astromList_file,$astroList_name) = tempfile("/tmp/bkgreg.warp.astrom.${warp_id}.${skycell_id}.XXXX",
+							 UNLINK => !$save_temps);
+	my $chipFiles;
+	{
+	    my $inputs_command = "$warptool -scmap -warp_id $warp_id ";
+	    $inputs_command   .= " -skycell_id $skycell_id ";
+	    $inputs_command   .= " -dbname $dbname " if defined $dbname;
+	    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+		run (command => $inputs_command, verbose => $verbose);
+	    unless ($success) {
+		$error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+		&my_die("Unable to perform warptool -scmap: $error_code", 
+			$skycell_id,$warp_id,$PS_EXIT_SYS_ERROR);
+	    }
+	    my $md = $mdcParser->parse(join "", @$stdout_buf) or
+		&my_die("Unable to parse warptool -scmap: $error_code", 
+			$skycell_id,$warp_id,$PS_EXIT_SYS_ERROR);
+	    $chipFiles = parse_md_list($md) or
+		&my_die("Unable to parse warptool -scmap: $error_code", 
+			$skycell_id,$warp_id,$PS_EXIT_SYS_ERROR);
+	}
+	my $wrote_astrom = 0;
+	foreach my $chipFile (@$chipFiles) {
+	    my $bkgModel = $ipprc->filename("PSPHOT.BACKMDL",
+					    $chipFile->{chip_path_base},
+					    $chipFile->{class_id});
+	    my $astrom   = $ipprc->filename($astromSource,$chipFile->{cam_path_base});
+	    print $bkgList_file "$bkgModel\n";
+	    if (!$wrote_astrom) {
+		print $astromList_file "$astrom\n";
+		$wrote_astrom = 1;
+	    }
+	}
+	close ($bkgList_file);
+	close ($astromList_file);
+
+	# Construct skyfile if needed
+	my $skyCell_name = $ipprc->filename("SKYCELL.TEMPLATE",$path_base,$skycell_id);
+	my $skyCell_exists = $ipprc->file_exists($skyCell_name);
+	if (!$skyCell_exists) { # Generate it
+	    my $skyFile = prepare_output("SKYCELL.TEMPLATE", $path_base, $skycell_id, 1);
+	    $ipprc->skycell_file( $tess_dir, $skycell_id, $skyFile, $verbose ) or
+		&my_die("Unable to generate template skycell",$skycell_id,$warp_id,$PS_EXIT_SYS_ERROR);
+	}
+
+
+	# Construct pswarp command
+	my $pswarp_command = "$pswarp ";
+	$pswarp_command .= " -list $bkgList_name -astromlist $astromList_name -bkglist $bkgList_name ";
+	$pswarp_command .= " $skyCell_name ";
+	$pswarp_command .= " -F PSPHOT.PSF.SAVE PSPHOT.PSF.SKY.SAVE -F PSPHOT.OUTPUT PSPHOT.OUT.CMF.MEF ";
+	$pswarp_command .= " -F PSPHOT.BACKMDL PSPHOT.BACKMDL.MEF ";
+	$pswarp_command .= " -F SOURCE.PLOT.MOMENTS SOURCE.PLOT.SKY.MOMENTS ";
+	$pswarp_command .= " -F SOURCE.PLOT.PSFMODEL SOURCE.PLOT.SKY.PSFMODEL ";
+	$pswarp_command .= " -F SOURCE.PLOT.APRESID SOURCE.PLOT.SKY.APRESID ";
+	$pswarp_command .= " -recipe PSWARP WARP -Db PSF FALSE -Db BACKGROUND.MODEL TRUE ";
+	$pswarp_command .= " -Db SOURCES FALSE ";
+	$pswarp_command .= " -log $bkgOut_log -threads 1 ";
+	$pswarp_command .= " -dbname $dbname " if defined $dbname;
+
+	# Execute
+	my ( $success, $error_code, $full_buf, $stdout_buf, $stderrr_buf ) = 
+	    run(command => $pswarp_command, verbose => $verbose);
+	unless ($success) {
+	    $error_code = (($error_code >> 8)  or $PS_EXIT_PROG_ERROR);
+	    &my_die("Unable to perform warptool: $error_code", $stage, $stage_id, $error_code);
+	}
+	
+
+    }
+}
+## stack stage
+elsif ($stage eq 'stack') {
+    
+
+    my $ppStack_command = "$ppStackMedian -input $inputMDC_name $path_base ";
+    $ppStack_command   .= " -recipe PPSTACK STACK -recipe PPSUB STACK -recipe PSPHOT STACK ";
+    $ppStack_command   .= " -recipe PPSTATS STACKSTATS -stack-type DEEP_STACK ";
+    $ppStack_command   .= " -F PSPHOT.PSF.SAVE PSPHOT.PSF.SKY.SAVE ";
+    $ppStack_command   .= " -F PSPHOT.OUTPUT PSPHOT.OUT.CMF.MEF -F PSPHOT.BACKMDL PSPHOT.BACKMDL.MEF ";
+    $ppStack_command   .= " -F SOURCE.PLOT.MOMENTS SOURCE.PLOT.SKY.MOMENTS ";
+    $ppStack_command   .= " -F SOURCE.PLOT.PSFMODEL SOURCE.PLOT.SKY.PSFMODEL ";
+    $ppStack_command   .= " -F SOURCE.PLOT.APRESID SOURCE.PLOT.SKY.APRESID ";
+    $ppStack_command   .= " -Db PHOTOMETRY F -Db VARIANCE F -Db CONVOLVE F ";
+    $ppStack_command   .= " -Df DEFAULT.EXPTIME $expTime ";
+    $ppStack_command   .= " -threads $threads -log $bkgOut_log ";
+    $ppStack_command   .= " -dbname $dbname " if defined $dbname;
+
+}
+## do both warp and stack
+elsif ($stage eq 'warpstack') {
+
+}
+
+sub prepare_output
+{
+    my $filerule = shift;
+    my $outroot  = shift;
+    my $skycell_id = shift;
+    my $delete = shift;
+    $delete = 0 if !defined $delete;
+
+    my $error;
+    my $output = $ipprc->prepare_output($filerule, $outroot, $skycell_id, $delete, \$error)
+	or &my_die("failed to prepare output file for: $filerule", $skycell_id, $warp_id, $error);
+    return $output;
+}
+
+
+sub my_die {
+    my $msg = shift;       # Warning message on die
+    my $stage = shift;     # stage name
+    my $stage_id = shift;  # identifier
+    my $exit_code = shift; # exit code
+
+    carp($msg);
+    exit $exit_code;
+}
+
+
+
+
+	
+    
+
+
+