Index: unk/ippScripts/scripts/phase4_diff.pl
===================================================================
--- /trunk/ippScripts/scripts/phase4_diff.pl	(revision 11818)
+++ 	(revision )
@@ -1,233 +1,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-## report the program and machine
-use Sys::Hostname;
-my $host = hostname();
-print "\n\n";
-print "Starting script $0 on $host\n\n";
-
-use vars qw( $VERSION );
-$VERSION = '0.01';
-
-use IPC::Cmd qw( can_run run );
-use PS::IPP::Metadata::Config;
-use PS::IPP::Metadata::Stats;
-use Data::Dumper;
-
-use PS::IPP::Config qw(
-    $PS_EXIT_SUCCESS
-    $PS_EXIT_UNKNOWN_ERROR
-    $PS_EXIT_SYS_ERROR
-    $PS_EXIT_CONFIG_ERROR
-    $PS_EXIT_PROG_ERROR
-    $PS_EXIT_DATA_ERROR
-    $PS_EXIT_TIMEOUT_ERROR
-    );
-my $ipprc = PS::IPP::Config->new(); # IPP configuration
-use File::Spec;
-
-use Getopt::Long qw( GetOptions :config auto_help auto_version gnu_getopt );
-use Pod::Usage qw( pod2usage );
-
-my ($det_id, $iter, $exp_tag, $class_id, $det_type, $detrend,
-        $input_uri, $camera, $mode, $dbname, $workdir, $no_update);
-GetOptions(
-    'det_id|d=s'        => \$det_id,
-    'iteration=s'       => \$iter,
-    'exp_tag|e=s'       => \$exp_tag,
-    'class_id|i=s'      => \$class_id,
-    'det_type|t=s'      => \$det_type,
-    'detrend=s'         => \$detrend,
-    'input_uri|u=s'     => \$input_uri,
-    'camera|c=s'        => \$camera,
-    'mode|m=s'          => \$mode,
-    'dbname|d=s'        => \$dbname, # Database name
-    'workdir|w=s'       => \$workdir,	# Working directory, for output files
-    'no-update'         => \$no_update,
-) or pod2usage( 2 );
-
-pod2usage( -msg => "Unknown option: @ARGV", -exitval => 2 ) if @ARGV;
-pod2usage(
-    -msg => "Required options: --det_id --iteration --exp_tag --class_id --det_type --camera --input_uri --mode --detrend (not for 'verify' mode)",
-    -exitval => 3,
-) unless defined $det_id
-    and defined $iter
-    and defined $exp_tag
-    and defined $class_id
-    and defined $det_type
-    and defined $input_uri
-    and defined $camera
-    and defined $mode
-    and (defined $detrend or lc($mode) eq 'verify');
-
-$ipprc->define_camera($camera);
-
-# Recipes to use, as a function of the detrend type
-use constant RECIPES => {
-    'master' => {		# We're creating a master --- already processed the input
-	'bias' => 'PPIMAGE_B',	# Bias only
-	'dark' => 'PPIMAGE_D',	# Dark only
-	'shutter' => 'PPIMAGE_S',	# Shutter only
-	'flat' => 'PPIMAGE_F',	# Flat-field only
-	'domeflat' => 'PPIMAGE_F',	# Flat-field only
-	'skyflat' => 'PPIMAGE_F',	# Flat-field only
-	'fringe' => 'PPIMAGE_R',	# Fringe only
-    },
-    'verify' => {		# We're checking the master --- input is not already processed
-	'bias' => 'PPIMAGE_OB',	# Bias only
-	'dark' => 'PPIMAGE_OBD',	# Dark only
-	'shutter' => 'PPIMAGE_OBDS',	# Shutter only
-	'flat' => 'PPIMAGE_OBDSF',	# Flat-field only
-	'domeflat' => 'PPIMAGE_OBDSF',	# Flat-field only
-	'skyflat' => 'PPIMAGE_OBDSF',	# Flat-field only
-	'fringe' => 'PPIMAGE_OBDSFR',	# Fringe only
-    },
-};
-
-# Flags to specify the particular detrend to use
-use constant DETRENDS => {
-    'bias' => '-bias',		# Specify the bias frame
-    'dark' => '-dark',		# Specify the dark frame
-    'shutter' => '-shutter',	# Specify the shutter frame
-    'flat' => '-flat',		# Specify the flat frame
-    'domeflat' => '-flat',		# Specify the flat frame
-    'skyflat' => '-flat',		# Specify the flat frame
-    'fringe' => '-fringe',	# Specify the fringe frame
-};
-
-
-use constant DELETE_STATS => 0;	# Delete the statistics file when done?
-
-# Look for programs we need
-my $missing_tools;
-my $dettool = can_run('dettool') or (warn "Can't find dettool" and $missing_tools = 1);
-my $ppImage = can_run('ppImage') or (warn "Can't find ppImage" and $missing_tools = 1);
-if ($missing_tools) { 
-    warn("Can't find required tools.");
-    exit($PS_EXIT_CONFIG_ERROR); 
-}
-$ppImage .= " -dbname $dbname" if defined $dbname;
-
-# Recipe to use in processing
-&my_die("Unrecognised mode: $mode", $det_id, $iter, $exp_tag, $class_id, $PS_EXIT_PROG_ERROR) unless defined RECIPES->{$mode};
-my $recipe = RECIPES->{$mode}->{lc($det_type)};
-&my_die("Unrecognised detrend type: $det_type", $det_id, $iter, $exp_tag, $class_id, $PS_EXIT_PROG_ERROR) unless defined $recipe;
-
-### Output file names --- must match camera configuration!
-if (defined $workdir) {
-    $workdir = $ipprc->convert_filename_absolute( $workdir );
-} else {
-    my ($vol, $dir, $file) = File::Spec->splitpath( $input_uri );
-    $workdir = $dir;
-}
-
-my $outputFile = "$exp_tag.detresid.$det_id.$iter"; # Root name
-my $outputRoot = File::Spec->catfile( $workdir, $exp_tag, $outputFile );
-
-my $outputName = $ipprc->filename("PPIMAGE.OUTPUT", $outputRoot, $class_id);
-my $bin1Name =  $ipprc->filename("PPIMAGE.BIN1", $outputRoot, $class_id);
-my $bin2Name =  $ipprc->filename("PPIMAGE.BIN2", $outputRoot, $class_id);
-
-my $outputStats = $outputRoot . '.' . $class_id . '.stats';
-
-$detrend = $ipprc->convert_filename_absolute( $detrend ) if defined $detrend;
-$input_uri = $ipprc->convert_filename_absolute( $input_uri );
-
-# Run ppImage
-{
-    my $command = "$ppImage -file $input_uri $outputRoot -recipe PPIMAGE $recipe" .
-	" -stat $outputStats "; # Command to run ppImage
-
-    # Detrend to use in processing
-    if (lc($mode) ne 'verify') {
-	my $detFlag = DETRENDS->{lc($det_type)};
-	&my_die("Unrecognised detrend type: $det_type", $det_id, $iter, $exp_tag, $class_id, $PS_EXIT_PROG_ERROR) unless defined $detFlag;
-	$command .= "$detFlag $detrend";
-    }
-
-    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
-	run(command => $command, verbose => 1);
-    unless ($success) {
-	$error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
-	&my_die("Unable to perform ppImage: $error_code", $det_id, $iter, $exp_tag, $class_id, $error_code);
-    }
-    &my_die("Couldn't find expected output file: $outputName", $det_id, $iter, $exp_tag, $class_id, $PS_EXIT_SYS_ERROR) unless -f $outputName;
-    &my_die("Couldn't find expected output file: $outputStats", $det_id, $iter, $exp_tag, $class_id, $PS_EXIT_SYS_ERROR) unless -f $outputStats;
-    &my_die("Couldn't find expected output file: $bin1Name", $det_id, $iter, $exp_tag, $class_id, $PS_EXIT_SYS_ERROR) unless -f $bin1Name;
-    &my_die("Couldn't find expected output file: $bin2Name", $det_id, $iter, $exp_tag, $class_id, $PS_EXIT_SYS_ERROR) unless -f $bin2Name;
-}
-
-# Get the statistics on the residual image
-my $stats;			# Statistics from ppImage
-{
-    my $statsFile;		# File handle
-    open $statsFile, $outputStats or &my_die("Can't open statistics file $outputStats: $!", $det_id, $iter, $exp_tag, $class_id, $PS_EXIT_SYS_ERROR);
-    my @contents = <$statsFile>; # Contents of file
-    close $statsFile;
-    my $mdcParser = PS::IPP::Metadata::Config->new;	# Parser for metadata config files
-    my $metadata = $mdcParser->parse(join "", @contents) or
-	&my_die("Unable to parse metadata config doc", $det_id, $iter, $exp_tag, $class_id, $PS_EXIT_PROG_ERROR);
-    $stats = PS::IPP::Metadata::Stats->new(); # Stats parser
-    $stats->parse($metadata) or &my_die("Unable to find all values in statistics output.", $det_id, $iter, $exp_tag, $class_id, $PS_EXIT_PROG_ERROR);
-}
-
-# Add the processed file to the database
-$outputName = $ipprc->convert_filename_relative( $outputName );
-$bin1Name = $ipprc->convert_filename_relative( $bin1Name );
-$bin2Name = $ipprc->convert_filename_relative( $bin2Name );
-unless ($no_update) {
-    my $command = "$dettool -addresidimfile -det_id $det_id -iteration $iter -exp_tag $exp_tag " .
-	"-class_id $class_id -recip $recipe -uri $outputName -b1_uri $outputRoot"; # Command to run dettool
-    $command .= " -bg " . $stats->bg_mean();
-    $command .= " -dbname $dbname" if defined $dbname;
-
-    if (defined($stats->bg_mean_stdev())) {
-	$command .= " -bg_mean_stdev " . $stats->bg_mean_stdev();
-    } else {
-	# May be undefined if there is only a single imfile
-	$command .= ' -bg_stdev 0';
-    }
-
-    $command .= " -bg_stdev " . $stats->bg_stdev();
-
-    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
-	run(command => $command, verbose => 1);
-    unless ($success) {
-	$error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
-	warn("Unable to perform dettool -addresidimfile: $error_code\n");
-	exit($error_code);
-    }
-
-    unlink $outputStats;    
-}
-
-
-
-sub my_die
-{
-    my $msg = shift; # Warning message on die
-    my $det_id = shift;		# Detrend identifier
-    my $iter = shift;		# Iteration
-    my $exp_tag = shift; # Exposure tag
-    my $class_id = shift; # Class identifier
-    my $exit_code = shift; # Exit code to add
-
-    warn($msg);
-    if ($det_id and $iter and $exp_tag) {
-	my $command = "$dettool -addresidimfile -det_id $det_id -iteration $iter -exp_tag $exp_tag -class_id $class_id -code $exit_code";
-	$command .= " -dbname $dbname" if defined $dbname;
-        system ($command);
-    }
-    exit $exit_code;
-}
-
-END {
-    my $exit = $?;
-    system("sync") == 0 or die "failed to execute sync: $!";
-    $? = $exit;
-}
-
-__END__
Index: unk/ippScripts/scripts/phase4_stack.pl
===================================================================
--- /trunk/ippScripts/scripts/phase4_stack.pl	(revision 11818)
+++ 	(revision )
@@ -1,201 +1,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-## report the program and machine
-use Sys::Hostname;
-my $host = hostname();
-print "\n\n";
-print "Starting script $0 on $host\n\n";
-
-use vars qw( $VERSION );
-$VERSION = '0.01';
-
-use IPC::Cmd qw( can_run run );
-use PS::IPP::Metadata::Config;
-use PS::IPP::Metadata::List qw( parse_md_list );
-use PS::IPP::Metadata::Stats;
-
-use PS::IPP::Config qw(
-    $PS_EXIT_SUCCESS
-    $PS_EXIT_UNKNOWN_ERROR
-    $PS_EXIT_SYS_ERROR
-    $PS_EXIT_CONFIG_ERROR
-    $PS_EXIT_PROG_ERROR
-    $PS_EXIT_DATA_ERROR
-    $PS_EXIT_TIMEOUT_ERROR
-    );
-my $ipprc = PS::IPP::Config->new(); # IPP configuration
-use File::Spec;
-
-use Getopt::Long qw( GetOptions :config auto_help auto_version gnu_getopt );
-use Pod::Usage qw( pod2usage );
-
-my ($p4_id, $class_id, $det_type, $camera, $dbname, $workdir, $no_update);
-GetOptions(
-    'det_id|d=s'        => \$det_id,
-    'iteration=s'       => \$iter,
-    'class_id|i=s'      => \$class_id,
-    'det_type|t=s'      => \$det_type,
-    'camera|c=s'        => \$camera,
-    'dbname|d=s'        => \$dbname, # Database name
-    'workdir|w=s'       => \$workdir,	# Working directory, for output files
-    'no-update'         => \$no_update
-) or pod2usage( 2 );
-
-pod2usage( -msg => "Unknown option: @ARGV", -exitval => 2 ) if @ARGV;
-pod2usage(
-    -msg => "Required options: --det_id --iteration --class_id --det_type --camera",
-    -exitval => 3,
-) unless defined $det_id
-    and defined $iter
-    and defined $class_id
-    and defined $det_type
-    and defined $camera;
-
-# Recipes to use as a function of detrend type
-use constant RECIPES => {
-    'bias' => 'PPMERGE_BIAS',
-    'dark' => 'PPMERGE_DARK',
-    'shutter' => 'PPMERGE_SHUTTER',
-    'flat' => 'PPMERGE_FLAT',
-    'domeflat' => 'PPMERGE_FLAT',
-    'skyflat' => 'PPMERGE_FLAT',
-    'fringe' => 'PPMERGE_FRINGE',
-    };
-
-# Look for programs we need
-my $missing_tools;
-my $dettool = can_run('dettool') or (warn "Can't find dettool" and $missing_tools = 1);
-my $ppMerge = can_run('ppMerge') or (warn "Can't find ppMerge" and $missing_tools = 1);
-if ($missing_tools) { 
-    warn("Can't find required tools.");
-    exit($PS_EXIT_CONFIG_ERROR); 
-}
-
-my $recipe = RECIPES()->{lc($det_type)}; # Recipe to use in stacking
-&my_die("Unrecognised detrend type: $det_type", $det_id, $iter, $class_id, $PS_EXIT_PROG_ERROR) unless defined $recipe;
-
-my $mdcParser = PS::IPP::Metadata::Config->new;	# Parser for metadata config files
-
-# Get list of files to stack
-my $files;			# Array of files to be stacked
-{
-    my $command = "$dettool -processedimfile -det_id $det_id -class_id $class_id -included"; # Command to run
-    $command .= " -dbname $dbname" if defined $dbname;
-    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
-	run(command => $command, verbose => 1);
-    unless ($success) {
-	$error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
-	&my_die("Unable to perform dettool -processedimfile: $error_code", $det_id, $iter, $class_id, $error_code);
-    }
-    my $metadata = $mdcParser->parse(join "", @$stdout_buf) or
-	&my_die("Unable to parse metadata config doc", $det_id, $iter, $class_id, $PS_EXIT_PROG_ERROR);
-    $files = parse_md_list($metadata) or 
-	&my_die("Unable to parse metadata list", $det_id, $iter, $class_id, $PS_EXIT_PROG_ERROR);
-}
-
-if (defined $workdir) {
-    $workdir = $ipprc->convert_filename_absolute( $workdir );
-} else {
-    my $example = ${$files}[0]->{uri}; # Example file
-    my ($vol, $dir, $file) = File::Spec->splitpath( $example );
-    $workdir = $dir;
-}
-
-# Stack the files
-my $outputFile = "$camera.$det_type.$det_id.$iter.$class_id"; # Root name
-my $outputSubD = "$camera.$det_type.$det_id";
-my $outputRoot = File::Spec->catfile( $workdir, $outputSubD, $outputFile );
-my $outputStack = $outputRoot . '.fits'; # Output name
-my $outputStats = $outputRoot . '.stats'; # Statistics name
-
-{
-    my $command = "$ppMerge $outputStack"; # Command to run
-    foreach my $file (@$files) {
-	my $uri = $file->{uri};	# URI for input file
-	$uri = $ipprc->convert_filename_absolute($uri);
-	$command .= ' ' . $uri;
-    }
-    $command .= " -recipe PPMERGE $recipe";
-    $command .= ' -type ' . uc($det_type); # Type of stacking to perform
-    $command .= " -stats $outputStats";	# Statistics output filename
-
-    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
-	run(command => $command, verbose => 1);
-    unless ($success) {
-	$error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
-	&my_die("Unable to perform ppMerge: $error_code", $det_id, $iter, $class_id, $error_code);
-    }
-    &my_die("Unable to find expected output file: $outputStack\n", $det_id, $iter, $class_id, $PS_EXIT_SYS_ERROR) unless -f $outputStack;
-    &my_die("Unable to find expected output file: $outputStats\n", $det_id, $iter, $class_id, $PS_EXIT_SYS_ERROR) unless -f $outputStats;
-}
-
-# Get the statistics on the stacked image
-my $stats;			# Statistics from ppMerge
-{
-    open(my $statsFile, "$outputStats") or
-	&my_die("Can't open statistics file $outputStats: $!", $det_id, $iter, $class_id, $PS_EXIT_SYS_ERROR);
-    my $contents = do { local $/; <$statsFile> }; # Contents of file
-    close($statsFile);
-
-    my $mdcParser = PS::IPP::Metadata::Config->new;	# Parser for metadata config files
-    my $metadata = $mdcParser->parse($contents) or
-	&my_die("Unable to parse metadata config doc", $det_id, $iter, $class_id, $PS_EXIT_SYS_ERROR);
-    $stats = PS::IPP::Metadata::Stats->new(); # Stats parser
-    $stats->parse($metadata)  or
-	&my_die("Unable to find all values in statistics output.", $det_id, $iter, $class_id, $PS_EXIT_SYS_ERROR);
-}
-
-# Add the resultant into the database
-$outputStack = $ipprc->convert_filename_relative($outputStack);
-unless ($no_update) {
-    my $command = "$dettool -addstacked -det_id $det_id -iteration $iter -class_id $class_id" .
-	" -uri $outputStack -recip $recipe"; # Command to run
-    $command .= ' -bg ' . $stats->bg_mean();
-    if (defined($stats->bg_stdev())) {
-    $command .= ' -bg_stdev ' . $stats->bg_stdev();
-    } else {
-	# May be undefined if there is only a single imfile
-	$command .= ' -bg_stdev 0';
-    }
-    $command .= ' -bg_mean_stdev ' . $stats->bg_mean_stdev();
-    $command .= " -dbname $dbname" if defined $dbname;
-    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
-	run(command => $command, verbose => 1);
-    unless ($success) {
-	$error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
-	warn("Unable to perform dettool -addstacked: $error_code\n");
-	exit($error_code);
-    }
-
-    unlink $outputStats;
-}
-
-
-sub my_die
-{
-    my $msg = shift; # Warning message on die
-    my $det_id = shift;		# Detrend identifier
-    my $iter = shift;		# Iteration
-    my $class_id = shift; # Class identifier
-    my $exit_code = shift; # Exit code to add
-
-    warn($msg);
-    if ($det_id and $iter and $class_id) {
-	my $command = "$dettool -addstacked -det_id $det_id -iteration $iter -class_id $class_id -code $exit_code";
-	$command .= " -dbname $dbname" if defined $dbname;
-        system ($command);
-    }
-    exit $exit_code;
-}
-
-END {
-    my $status = $?;
-    system("sync") == 0
-        or die "failed to execute sync: $!" ;
-    $? = $status;
-}
-
-__END__