Index: trunk/ippScripts/scripts/skycalibration.pl
===================================================================
--- trunk/ippScripts/scripts/skycalibration.pl	(revision 32959)
+++ trunk/ippScripts/scripts/skycalibration.pl	(revision 32959)
@@ -0,0 +1,273 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+## report the program and machine
+use Sys::Hostname;
+my $host = hostname();
+my $date = `date`;
+print "\n\n";
+print "Starting script $0 on $host at $date\n\n";
+
+use DateTime;
+my $mjd_start = DateTime->now->mjd;   # MJD of starting script
+
+use vars qw( $VERSION );
+$VERSION = '0.01';
+
+use IPC::Cmd 0.36 qw( can_run run );
+use PS::IPP::Metadata::Config;
+use PS::IPP::Metadata::List qw( parse_md_list );
+use Data::Dumper;
+use File::Temp qw( tempfile );
+use File::Basename;
+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 );
+
+# Look for programs we need
+my $missing_tools;
+my $staticskytool = can_run('staticskytool') or (warn "Can't find staticskytool" and $missing_tools = 1);
+my $psastro = can_run('psastro') or (warn "Can't find psastro" and $missing_tools = 1);
+my $fhead = can_run('fhead') or (warn "Can't find fhead" and $missing_tools = 1);
+my $ppStatsFromMetadata = can_run('ppStatsFromMetadata') or (warn "Can't find ppStatsFromMetadata" and $missing_tools = 1);
+my $ppConfigDump = can_run('ppConfigDump') or (warn "Can't find ppConfigDump" and $missing_tools = 1);
+if ($missing_tools) {
+    warn("Can't find required tools.");
+    exit($PS_EXIT_CONFIG_ERROR);
+}
+
+sub HelpMessage {
+    print "USAGE: skycalibration.pl --skycal_id (skycal_id) --outroot (root) --camera (camera) [options]\n";
+    print "  --skycal_id (skycal_id) : run identifier\n";
+    print "  --camera (camera)       : Camera name\n";
+    print "  --dbname (dbname)       : Database name\n";
+    print "  --threads (N)           : Number of threads to use\n";
+    print "  --outroot (root)        : Output root name\n";
+    print "  --path_base (path_base) : path_base of input\n";
+    print "  --reduction (class)     : Reduction class\n";
+    print "  --verbose               : Be extra verbose\n";
+    print "  --no-update             : Don't update the database?\n";
+    print "  --no-op                 : Don't do any operations?\n";
+    print "  --redirect-output       : send output to the log file,\n";
+    print "  --save-temps            : Save temporary files?\n";
+    print "  --help                  : show this message\n";
+    exit 2;
+}
+
+my ($skycal_id, $stack_id, $camera, $dbname, $threads, $outroot, $path_base, $filter, $reduction, $verbose, $no_update, $no_op, $redirect, $save_temps);
+GetOptions(
+    'skycal_id=s'       => \$skycal_id, # sky calibration run id
+    'stack_id=s'        => \$stack_id,    # static sky run id
+    'camera|c=s'        => \$camera,    # Camera name
+    'dbname|d=s'        => \$dbname,    # Database name
+    'threads=s'         => \$threads,   # Number of threads to use
+    'outroot=s'         => \$outroot,   # Output root name
+    'path_base=s'       => \$path_base, # path_base of input
+    'filter=s'          => \$filter,    # filter for input stack
+    'reduction=s'       => \$reduction, # Reduction class
+    'verbose'           => \$verbose,   # Print to stdout
+    'no-update'         => \$no_update, # Don't update the database?
+    'no-op'             => \$no_op, # Don't do any operations?
+    'redirect-output'   => \$redirect,
+    'save-temps'        => \$save_temps, # Save temporary files?
+    'help'              => sub { HelpMessage() },
+) or pod2usage( 2 );
+
+pod2usage( -msg => "Unknown option: @ARGV", -exitval => 2 ) if @ARGV;
+
+pod2usage(
+    -msg => "Required options: --skycal_id --stack_id --outroot --camera --path_base",
+    -exitval => 3,
+          ) unless 
+    defined $skycal_id and
+    defined $stack_id and
+    defined $path_base and
+    defined $outroot and
+    defined $camera;
+
+my $ipprc = PS::IPP::Config->new( $camera ) or my_die( "Unable to set up", $skycal_id, $PS_EXIT_CONFIG_ERROR ); # IPP configuration
+
+my $logDest = $ipprc->filename("LOG.EXP", $outroot);
+$ipprc->redirect_to_logfile($logDest) or my_die( "Unable to redirect output", $skycal_id, $PS_EXIT_SYS_ERROR ) if $redirect;
+
+my $traceDest  = $ipprc->filename("TRACE.EXP", $outroot);
+my $stats      = $ipprc->filename("PSASTRO.STATS", $outroot);
+
+my $outbase = basename($outroot);
+
+# Get list of input images to stack photometry
+my $mdcParser = PS::IPP::Metadata::Config->new; # Parser for metadata config files
+my $files;
+
+# Recipes to use based on reduction class
+$reduction = 'DEFAULT' unless defined $reduction;
+
+# generate the input 
+my $cmdflags = "";
+
+my $recipe_psastro  = $ipprc->reduction($reduction, 'STATICSKY_CALIBRATION'); # Recipe to use for psastro
+unless ($recipe_psastro) {
+    # XXX: ADD to reduction: hard code recipe for now
+    $recipe_psastro = 'STATICSKY_CAL';
+#            &my_die("Couldn't find selected reduction for STACKPHOT: $reduction\n", $skycal_id, $PS_EXIT_CONFIG_ERROR);
+}
+
+print "reduction:      $reduction\n";
+print "recipe_psastro: $recipe_psastro\n";
+
+my $configuration = $ipprc->filename("PSASTRO.CONFIG", $outroot);
+
+# find input file
+# First check the expected file name where the stack_id is the FILE_ID
+my $file  = $ipprc->filename('PSPHOT.STACK.OUTPUT', $path_base, $stack_id);
+if (! $ipprc->file_resolve($file)) {
+    # XXX: Beginning of section that can go eventually
+
+    # no file with the expected name found
+    # assume that the input is from an early staticsky run that did not use stack_id as the FILE_ID
+    # but instead used FILE_ID = [0 .. num_filters-1]
+    print "\nfailed to resolve $file\n";
+    if (!$filter) {
+        &my_die("filter not supplied unable to identify appropriate staticsky input.", $skycal_id, $PS_EXIT_SYS_ERROR);
+    }
+    print "Trying old FILE_ID\n";
+    my $max_filters = 5;
+    for (my $i=0; $i < $max_filters; $i++) {
+        my $file_id = sprintf "%03d", $i;
+        $file  = $ipprc->filename('PSPHOT.STACK.OUTPUT', $path_base, $file_id);
+        my $resolved = $ipprc->file_resolve($file);
+        if (!$resolved) {
+            # we fail here assumming that if file_id N doesn't exist, neither to N+1
+            print "\nfailed to resolve $file\n\n";
+            &my_die("unable to identify appropriate staticsky input.", $skycal_id, $PS_EXIT_SYS_ERROR);
+        }
+        # Check the filter id for this file
+        my $command = "$fhead $resolved | grep FILTERID";
+        my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+            run(command => $command, verbose => 0);
+        unless ($success) {
+            $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+            &my_die("Unable to perform $command: $error_code", $skycal_id, $PS_EXIT_SYS_ERROR);
+        }
+        # Expected output: HIERARCH FPA.FILTERID = 'r.00000 ' / Filter used (parsed, abstract name)
+        my ($undef, undef, undef, $filt) = split " ", join("", @$stdout_buf);
+        my $this_filter = substr $filt, 1, 7;
+
+        # if it matches we're done
+        last if $this_filter eq $filter;
+
+        # nope loop around to try the next one
+        print "Input file for $filter is not $file ($this_filter)\n";
+        $file = undef;
+    }
+    print "\nInput file for $stack_id filter: $filter: $file\n";
+
+    # XXX: End of section that can go eventually
+}
+
+# Perform psastro analysis
+my $output_sources_filerule =  'PSASTRO.OUTPUT.CMF';
+{
+    my $command = "$psastro $outroot";
+    $command .= " -file $file";
+    $command .= " -threads $threads" if defined $threads;
+    $command .= " -recipe PSASTRO  $recipe_psastro";
+    $command .= " -F PSASTRO.OUTPUT $output_sources_filerule";
+    $command .= " -stats $stats";
+    $command .= " -recipe PPSTATS CAMSTATS";
+    $command .= " -dumpconfig $configuration" if $configuration;
+    $command .= " -tracedest $traceDest";
+
+    unless ($no_op) {
+        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 psastro: $error_code", $skycal_id, $error_code);
+        }
+
+        &my_die("Couldn't find stats file: $stats", $skycal_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists($stats);
+
+        {
+            my $command = "$ppStatsFromMetadata $stats - STATICSKY_CAL";
+            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 psastro: $error_code", $skycal_id, $error_code);
+            }
+            $cmdflags = join "", @$stdout_buf;
+            chomp $cmdflags;
+        }
+
+        my $quality;
+        ($quality) =  $cmdflags =~ /-quality (\d+)/;
+        if (!$quality) {
+            my $outputSources  = $ipprc->filename($output_sources_filerule, $outroot);
+            &my_die("Couldn't find expected output file: $outputSources", $skycal_id, $PS_EXIT_SYS_ERROR)
+                unless $ipprc->file_exists($outputSources);
+
+            &my_die("Couldn't find expected output file: $configuration", $skycal_id, $PS_EXIT_SYS_ERROR) 
+                unless $ipprc->file_exists($configuration);
+        }
+    } else {
+        print "Not executing: $command\n";
+    }
+}
+
+
+# Add the result to the database
+{
+    my $command = "$staticskytool -skycal_id $skycal_id";
+    $command .= " -addskycalresult -path_base $outroot";
+    $command .= " $cmdflags";
+    $command .= (" -dtime_script " . ((DateTime->now->mjd - $mjd_start) * 86400));
+    $command .= " -hostname $host" if defined $host;
+    $command .= " -dbname $dbname" if defined $dbname;
+
+    unless($no_update) {
+        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 $err_message = "Unable to perform staticskytool -addresult";
+	    warn($err_message);
+	    exit $error_code;
+        }
+    } else {
+        print "skipping $command\n";
+    }
+}
+
+exit 0;
+
+
+sub my_die
+{
+    my $msg = shift;            # Warning message on die
+    my $skycal_id = shift;        # Diff identifier
+    my $exit_code = shift;      # Exit code to add
+
+    $exit_code = $PS_EXIT_PROG_ERROR unless defined $exit_code;
+
+    warn($msg);
+    if (defined $skycal_id and not $no_update) {
+        my $command = "$staticskytool -skycal_id $skycal_id -fault $exit_code";
+	$command .= " -addskycalresult";
+	$command .= (" -dtime_script " . ((DateTime->now->mjd - $mjd_start) * 86400));
+	$command .= " -hostname $host" if defined $host;
+	$command .= " -path_base $outroot" if defined $outroot;
+	$command .= " -dbname $dbname" if defined $dbname;
+        run(command => $command, verbose => $verbose);
+    }
+    exit $exit_code;
+}
+
+END {
+    my $exit = $?;
+    system("sync") == 0 or die "failed to execute sync: $!";
+    $? = $exit;
+}
+
+__END__