Index: trunk/ippScripts/scripts/diff_skycell.pl
===================================================================
--- trunk/ippScripts/scripts/diff_skycell.pl	(revision 24166)
+++ trunk/ippScripts/scripts/diff_skycell.pl	(revision 24174)
@@ -35,5 +35,5 @@
 }
 
-my ($diff_id, $dbname, $threads, $outroot, $reduction, $verbose, $no_update, $no_op, $redirect);
+my ($diff_id, $dbname, $threads, $outroot, $reduction, $inverse, $verbose, $no_update, $no_op, $redirect);
 my ($skycell_id, $diff_skyfile_id);
 GetOptions(
@@ -44,4 +44,5 @@
     'threads=s'         => \$threads,   # Number of threads to use
     'outroot=s'         => \$outroot, # Output root name
+    'inverse'           => \$inverse, # Make inverse subtraction?
     'reduction=s'       => \$reduction, # Reduction class
     'verbose'           => \$verbose,   # Print to stdout
@@ -96,5 +97,4 @@
 my $camera;                     # Camera
 my ($inputMagic, $templateMagic); # Are the inputs been magicked?
-my $inverse = 1;                # Generate inverse subtraction if warp-warp
 foreach my $file (@$files) {
     if (defined $file->{template} and $file->{template}) {
@@ -107,5 +107,4 @@
             # template is a stack so it doesn't need to be magicked
             $templateMagic = 1;
-            $inverse = 0;
             ## use an explicit stack name for psphot output objects
         } else {
@@ -123,5 +122,4 @@
             $inputVariance = "PPSTACK.OUTPUT.VARIANCE";
             $inputSources = "PSPHOT.OUT.CMF.MEF";  ## this must be consistent with the value in stack_skycell.pl:161
-            $inverse = 0;
         } else {
             $inputMask = "PSWARP.OUTPUT.MASK";
Index: trunk/ippScripts/scripts/ipp_serial_magic.pl
===================================================================
--- trunk/ippScripts/scripts/ipp_serial_magic.pl	(revision 24174)
+++ trunk/ippScripts/scripts/ipp_serial_magic.pl	(revision 24174)
@@ -0,0 +1,157 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use IPC::Cmd 0.36 qw( can_run run );
+use PS::IPP::Metadata::Config;
+use PS::IPP::Metadata::List qw( parse_md_list );
+use PS::IPP::Config qw( caturi );
+use Data::Dumper;
+
+use Getopt::Long qw( GetOptions :config auto_help auto_version gnu_getopt );
+use Pod::Usage qw( pod2usage );
+
+my ($dbname,                    # Database name to use
+    $identifier,                # Identifier to process
+    $workdir_default,           # Default working directory
+    $verbose,                   # Verbose operations?
+    $no_op,                     # No operations?
+    $no_update,                 # No updating?
+    );
+GetOptions( 'dbname=s' => \$dbname,
+            'magic_id=s' => \$identifier,
+            'workdir=s' => \$workdir_default,
+            'verbose' => \$verbose,
+            'no-op' => \$no_op,
+            'no-update' => \$no_update,
+    ) or pod2usage( 2 );
+
+pod2usage( -msg => "Required options: --dbname --workdir",
+           -exitval => 3,
+           ) unless
+    defined $dbname;
+
+$workdir_default = `pwd` unless defined $workdir_default;
+
+my $mdcParser = PS::IPP::Metadata::Config->new; # Metadata config parser
+my $ipprc = PS::IPP::Config->new; # IPP Configuration
+
+# Look for programs we need
+my $missing_tools;
+my $magictool = can_run('magictool') or (warn "Can't find magictool" and $missing_tools = 1);
+my $magic_tree = can_run('magic_tree.pl') or (warn "Can't find magic_tree.pl" and $missing_tools = 1);
+my $magic_process = can_run('magic_process.pl') or (warn "Can't find magic_process.pl" and $missing_tools = 1);
+die "Can't find required tools.\n" if $missing_tools;
+
+# Tree
+{
+    my @whole;                      # The whole list for processing
+    {
+        my $command = "$magictool -totree -dbname $dbname"; # Command to run
+        $command .= " -magic_id $identifier" if defined $identifier;
+        my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+            run( command => $command, verbose => $verbose );
+        die "Unable to get magic tree list: $error_code\n" if not $success;
+        @whole = split /\n/, join( '', @$stdout_buf );
+    }
+
+    my @single = ();
+
+    while ( scalar @whole > 0 ) {
+        my $value = shift @whole;
+        push @single, $value;
+        if ($value =~ /^\s*END\s*$/) {
+            push @single, "\n";
+
+            my $list = parse_md_list( $mdcParser->parse( join( "\n", @single ) ) ) or
+                die "Unable to parse output from magictool.\n";
+
+            foreach my $item (@$list) {
+                my $magic_id = $item->{magic_id};
+                my $exp_id = $item->{exp_id};
+                my $camera = $item->{camera};
+                my $tess_id = $item->{tess_id};
+                my $ra = $item->{ra};
+                my $dec = $item->{decl};
+                my $workdir = $item->{workdir};
+                $workdir = $workdir_default unless (defined $workdir or $workdir ne "NULL");
+
+                my $outroot = caturi( $workdir, $exp_id, "$exp_id.mgc.$magic_id" );
+                $ipprc->outroot_prepare( $outroot );
+
+                my $command = "$magic_tree --magic_id $magic_id --camera $camera --tess_id $tess_id --outroot $outroot --ra $ra --dec $dec --dbname $dbname";
+                $command .= " --verbose" if defined $verbose;
+                $command .= " --no-op" if defined $no_op;
+                $command .= " --no-update" if defined $no_update;
+                my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+                    run( command => $command, verbose => $verbose );
+                die "Unable to do magic tree on $magic_id: $error_code\n" if not $success;
+            }
+
+            @single = ();
+        }
+    }
+}
+
+# Process leaf
+{
+    my @whole;                      # The whole list for processing
+    {
+        my $command = "$magictool -toprocess -dbname $dbname"; # Command to run
+        $command .= " -magic_id $identifier" if defined $identifier;
+        my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+            run( command => $command, verbose => $verbose );
+        die "Unable to get magic tree list: $error_code\n" if not $success;
+        @whole = split /\n/, join( '', @$stdout_buf );
+    }
+
+    my @single = ();
+
+    while ( scalar @whole > 0 ) {
+        my $value = shift @whole;
+        push @single, $value;
+        if ($value =~ /^\s*END\s*$/) {
+            push @single, "\n";
+
+            my $list = parse_md_list( $mdcParser->parse( join( "\n", @single ) ) ) or
+                die "Unable to parse output from magictool.\n";
+
+            foreach my $item (@$list) {
+                my $magic_id = $item->{magic_id};
+                my $exp_id = $item->{exp_id};
+                my $camera = $item->{camera};
+                my $node = $item->{node};
+                my $workdir = $item->{workdir};
+                $workdir = $workdir_default unless (defined $workdir or $workdir ne "NULL");
+
+                my $outroot = caturi( $workdir, $exp_id, "$exp_id.mgc.$magic_id.$node" );
+                $ipprc->outroot_prepare( $outroot );
+
+                my $command = "$magic_process --magic_id $magic_id --camera $camera --node $node --outroot $outroot --dbname $dbname";
+                $command .= " --verbose" if defined $verbose;
+                $command .= " --no-op" if defined $no_op;
+                $command .= " --no-update" if defined $no_update;
+                my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+                    run( command => $command, verbose => $verbose );
+                die "Unable to do magic process on $magic_id $node: $error_code\n" if not $success;
+            }
+
+            @single = ();
+        }
+    }
+}
+
+
+
+END {
+    my $status = $?;
+    system("sync") == 0
+        or die "failed to execute sync: $!" ;
+    $? = $status;
+}
+
+
+__END__
+
+
Index: trunk/ippScripts/scripts/magic_definerun.pl
===================================================================
--- trunk/ippScripts/scripts/magic_definerun.pl	(revision 24166)
+++ trunk/ippScripts/scripts/magic_definerun.pl	(revision 24174)
@@ -164,4 +164,7 @@
 &my_die("failed to retrieve new magic run information", $PS_EXIT_CONFIG_ERROR) if !$magic_id;
 
+### This is left over from when diffs were composed of a single skycell
+### When we're not too busy, it should be deleted in favour of:
+### magicRun JOIN diffSkyfile USING(diff_id) WHERE diffSkyfile.fault = 0 AND diffSkyfile.quality = 0
 foreach my $diff_skyfile (@$inputs) {
     my $skycell_id = $diff_skyfile->{skycell_id};
@@ -171,6 +174,7 @@
     }
     my $diff_id = $diff_skyfile->{diff_id};
-    my $command = "$magictool -addinputskyfile -magic_id $magic_id -diff_id $diff_id";
-    $command .= "  -node $skycell_id";
+    my $command = "$magictool -addinputskyfile";
+    $command .= " -magic_id $magic_id";
+    $command .= " -node $skycell_id";
     $command .= " -dbname $dbname" if $dbname;
 
Index: trunk/ippScripts/scripts/magic_destreak.pl
===================================================================
--- trunk/ippScripts/scripts/magic_destreak.pl	(revision 24166)
+++ trunk/ippScripts/scripts/magic_destreak.pl	(revision 24174)
@@ -35,5 +35,5 @@
 
 # Parse the command-line arguments
-my ($magic_ds_id, $camera, $streaks, $stage, $stage_id, $component, $uri, $path_base, $cam_path_base);
+my ($magic_ds_id, $camera, $streaks, $stage, $stage_id, $component, $uri, $path_base, $inverse, $cam_path_base);
 my ($outroot, $recoveryroot);
 my ($replace, $remove, $release);
@@ -49,4 +49,5 @@
            'uri=s'          => \$uri,        # uri of the input image
            'path_base=s'    => \$path_base,  # path_base of the input
+           'inverse'        => \$inverse,    # Inverse subtraction?
            'cam_path_base=s'=> \$cam_path_base,  # path_base of the associated camera run
            'outroot=s'      => \$outroot,     # "directory" for temporary images (may be nebulous)
@@ -183,7 +184,8 @@
 my $image = $uri;
 
-my ($mask, $ch_mask, $weight, $astrom);
+my ($image, $mask, $ch_mask, $weight, $astrom);
 
 if ($stage eq "raw") {
+    $image = $uri;
     $astrom = $ipprc->filename("PSASTRO.OUTPUT", $cam_path_base);
     $mask   = $ipprc->filename("PSASTRO.OUTPUT.MASK", $cam_path_base, $class_id) if $release ;
@@ -191,4 +193,5 @@
     # we use the mask output from the camera stage for input and replace
     # the output of the chip stage with that mask as well.
+    $image  = $ipprc->filename("PPIMAGE.CHIP", $path_base, $class_id);
     $mask   = $ipprc->filename("PSASTRO.OUTPUT.MASK", $cam_path_base, $class_id);
     $ch_mask= $ipprc->filename("PPIMAGE.CHIP.MASK", $path_base, $class_id);
@@ -196,9 +199,12 @@
     $astrom = $ipprc->filename("PSASTRO.OUTPUT", $cam_path_base);
 } elsif ($stage eq "warp") {
+    $image  = $ipprc->filename("PSWARP.OUTPUT", $path_base);
     $mask   = $ipprc->filename("PSWARP.OUTPUT.MASK", $path_base);
     $weight = $ipprc->filename("PSWARP.OUTPUT.VARIANCE", $path_base);
 } elsif ($stage eq "diff") {
-    $mask   = $ipprc->filename("PPSUB.OUTPUT.MASK", $path_base);
-    $weight = $ipprc->filename("PPSUB.OUTPUT.VARIANCE", $path_base);
+    my $name = $inverse ? "PPSUB.INVERSE" : "PPSUB.OUTPUT"; # Base name for images
+    $image  = $ipprc->filename($name, $path_base);
+    $mask   = $ipprc->filename("$name.MASK", $path_base);
+    $weight = $ipprc->filename("$name.VARIANCE", $path_base);
 }
 
Index: trunk/ippScripts/scripts/magic_mask.pl
===================================================================
--- trunk/ippScripts/scripts/magic_mask.pl	(revision 24166)
+++ 	(revision )
@@ -1,168 +1,0 @@
-#!/usr/bin/env perl
-
-use Carp;
-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 0.36 qw( can_run run );
-use PS::IPP::Metadata::Config;
-use PS::IPP::Metadata::List qw( parse_md_list );
-
-use Astro::FITS::CFITSIO qw( :constants );
-Astro::FITS::CFITSIO::PerlyUnpacking(1);
-
-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 $magictool = can_run('magictool') or (warn "Can't find magictool" and $missing_tools = 1);
-my $streaksremove = can_run('streaksremove') or (warn "Can't find streaksremove" and $missing_tools = 1);
-if ($missing_tools) {
-    warn("Can't find required tools.");
-    exit($PS_EXIT_CONFIG_ERROR);
-}
-
-# Parse the command-line arguments
-my ($magic_id, $camera, $dbname, $outroot, $save_temps, $verbose, $no_update, $no_op, $logfile);
-GetOptions(
-           'magic_id=s'      => \$magic_id,   # Magic identifier
-           'camera=s'        => \$camera,     # Camera name
-           'dbname=s'        => \$dbname,     # Database name
-           'outroot=s'       => \$outroot,    # Output root name
-           'save-temps'      => \$save_temps, # Save temporary files?
-           'verbose'         => \$verbose,    # Print stuff?
-           'no-update'       => \$no_update,  # Don't update the database?
-           'no-op'           => \$no_op,      # Don't do any operations?
-           'logfile=s'       => \$logfile,   # Redirect output?
-           ) or pod2usage( 2 );
-
-pod2usage( -msg => "Unknown option: @ARGV", -exitval => 2 ) if @ARGV;
-pod2usage( -msg => "Required options: --magic_id --camera --outroot",
-           -exitval => 3) unless
-    defined $magic_id and
-    defined $camera and
-    defined $outroot;
-
-my $ipprc = PS::IPP::Config->new( $camera ) or my_die( "Unable to set up", $magic_id, $PS_EXIT_CONFIG_ERROR ); # IPP configuration
-$ipprc->redirect_output($logfile) or my_die( "Unable to redirect output", $magic_id, $PS_EXIT_SYS_ERROR ) if $logfile;
-
-my $mdcParser = PS::IPP::Metadata::Config->new; # Parser for metadata config files
-
-### Get a list of inputs
-my $inputs;                     # List of inputs
-{
-    my $command = "$magictool -inputs -magic_id $magic_id -node root"; # Command to run
-    $command .= " -dbname $dbname" if defined $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 magictool -inputs: $error_code", $magic_id, $error_code);
-    }
-
-    my $metadata = $mdcParser->parse(join "", @$stdout_buf) or
-        &my_die("Unable to parse metadata config doc", $magic_id, $PS_EXIT_PROG_ERROR);
-
-    $inputs = parse_md_list($metadata) or
-        &my_die("Unable to parse metadata list", $magic_id, $PS_EXIT_PROG_ERROR);
-}
-
-### Do the heavy lifting
-{
-    my $command = "$streaksremove --streaks"; # Command to execute
-    my @basenames;              # List of base names
-
-    # Concatenate the names
-    foreach my $node (@$inputs) {
-        push @basenames, $ipprc->file_resolve( $node->{path_base} );
-    }
-    $command .= ' ' . join(' ', @basenames);
-
-    unless ($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 RemoveStreaks: $error_code", $magic_id, $error_code);
-        }
-
-        foreach my $basename (@basenames) {
-            file_check( $basename . '.mask' );
-        }
-    } else {
-        print "Skipping command: $command\n";
-    }
-}
-
-
-
-### Input mask into database
-{
-    my $command = "$magictool -addmask";
-    $command   .= " -magic_id $magic_id";
-    $command   .= " -uri $outroot";
-    $command   .= " -dbname $dbname" if defined $dbname;
-
-    # Add the processed file to the database
-    unless ($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_die("Unable to perform magictool -addmask: $error_code", $magic_id, $error_code);
-        }
-    } else {
-        print "Skipping command: $command\n";
-    }
-}
-
-
-
-### Pau.
-
-sub file_check
-{
-    my $file = shift;           # Name of file
-    &my_die("Unable to find output file: $file", $magic_id, $PS_EXIT_SYS_ERROR) unless
-        $ipprc->file_exists($file);
-}
-
-sub my_die
-{
-    my $msg = shift;            # Warning message on die
-    my $magic_id = shift;       # Magic identifier
-    my $exit_code = shift;      # Exit code to add
-
-    $exit_code = $PS_EXIT_PROG_ERROR unless defined $exit_code;
-
-    carp($msg);
-    if (defined $magic_id and not $no_update) {
-        my $command = "$magictool -addmask";
-        $command .= " -magic_id $magic_id";
-        $command .= " -fault $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__
Index: trunk/ippScripts/scripts/magic_process.pl
===================================================================
--- trunk/ippScripts/scripts/magic_process.pl	(revision 24166)
+++ trunk/ippScripts/scripts/magic_process.pl	(revision 24174)
@@ -37,5 +37,5 @@
 
 # Parse the command-line arguments
-my ($magic_id, $node, $camera, $dbname, $outroot, $template_uri, $save_temps, $verbose, $no_update, $no_op, $logfile);
+my ($magic_id, $node, $camera, $dbname, $outroot, $save_temps, $verbose, $no_update, $no_op, $logfile);
 
 GetOptions(
@@ -45,5 +45,4 @@
            'dbname=s'        => \$dbname,     # Database name
            'outroot=s'       => \$outroot,    # Output root name
-           'template_uri=s'  => \$template_uri,# uri of diff template
            'save-temps'      => \$save_temps, # Save temporary files?
            'verbose'         => \$verbose,    # Print stuff?
@@ -59,6 +58,5 @@
     defined $node and
     defined $camera and
-    defined $outroot and
-    defined $template_uri;
+    defined $outroot;
 
 my $ipprc = PS::IPP::Config->new( $camera ) or my_die( "Unable to set up", $magic_id, $node, $PS_EXIT_CONFIG_ERROR ); # IPP configuration
@@ -138,7 +136,7 @@
         }
 
-        my $template = $ipprc->file_resolve($template_uri);
-        &my_die("failed to resolve template_uri: $template_uri", $magic_id, $node, $PS_EXIT_DATA_ERROR)
-            if !($template);
+        my $template = resolve_template($innode);
+        &my_die("failed to resolve template", $magic_id, $node, $PS_EXIT_DATA_ERROR)
+            unless defined $template;
 
         $command .= " --detect --image $image --mask $mask --weight $weight -k $template";
@@ -189,13 +187,13 @@
             foreach my $innode (@$inputs) {
                 # root for inputs from previous stage
-                my $in_uri = $innode->{uri};
-                print $sfh "$in_uri\n";
-
-                cat_list_to_list($in_fh, $in_uri, "input.list");
+                my $in_path_base = $innode->{magic_path_base};
+                print $sfh "$in_path_base\n";
+
+                cat_list_to_list($in_fh, $in_path_base, "input.list");
                 # build input lists by combining the lists from
                 # previous stages
-                cat_list_to_list($ifh, $in_uri, "image.list");
-                cat_list_to_list($mfh, $in_uri, "mask.list");
-                cat_list_to_list($wfh, $in_uri, "weight.list");
+                cat_list_to_list($ifh, $in_path_base, "image.list");
+                cat_list_to_list($mfh, $in_path_base, "mask.list");
+                cat_list_to_list($wfh, $in_path_base, "weight.list");
             }
             close $in_fh;
@@ -243,5 +241,5 @@
     $command   .= " -magic_id $magic_id";
     $command   .= " -node $node";
-    $command   .= " -uri $outroot";
+    $command   .= " -path_base $outroot";
     $command   .= " -dbname $dbname" if defined $dbname;
 
@@ -262,12 +260,15 @@
     my $resolved = $ipprc->file_resolve($streaks_file);
 
-    my $fh;
-    open $fh, "<$resolved" or
-        &my_die("failed to open streaks file $streaks_file", $magic_id, $node, $PS_EXIT_UNKNOWN_ERROR);
-    # the first line in the streaks file contains the number of streaks found
-    my $num_streaks = <$fh>;
-    chomp $num_streaks;
-    close $fh;
-    print "$num_streaks streaks found on magicRun $magic_id\n" if $verbose;
+    my $num_streaks = -1;
+    unless ($no_op) {
+        my $fh;
+        open $fh, "<$resolved" or
+            &my_die("failed to open streaks file $streaks_file", $magic_id, $node, $PS_EXIT_UNKNOWN_ERROR);
+        # the first line in the streaks file contains the number of streaks found
+        $num_streaks = <$fh>;
+        chomp $num_streaks;
+        close $fh;
+        print "$num_streaks streaks found on magicRun $magic_id\n" if $verbose;
+    }
 
     my $command = "$magictool -addmask";
@@ -309,8 +310,8 @@
 sub cat_list_to_list   {
     my $out = shift;        # output file handle
-    my $uri = shift;        # uri to append ...
+    my $path_base = shift;  # path_base to append ...
     my $extension = shift;  # ... the extension to
 
-    my $filename = "$uri.$extension";
+    my $filename = "$path_base.$extension";
 
     my $in;
@@ -321,14 +322,46 @@
 }
 
-sub resolve_inputs {
-
+sub resolve_inputs
+{
     my $node = shift;
-    my $input_base = $node->{path_base};
-
-    my $image = $ipprc->file_resolve($ipprc->filename("PPSUB.OUTPUT", $input_base));
-    my $mask = $ipprc->file_resolve($ipprc->filename("PPSUB.OUTPUT.MASK", $input_base));
-    my $weight= $ipprc->file_resolve($ipprc->filename("PPSUB.OUTPUT.VARIANCE", $input_base));
-
-    return ($image, $mask, $weight);
+    my $input_base = $node->{diff_path_base};
+
+    my ($image, $mask, $variance); # Names to return
+    if ($node->{inverse}) {
+        $image = "PPSUB.INVERSE";
+        $mask = "PPSUB.INVERSE.MASK";
+        $variance = "PPSUB.INVERSE.VARIANCE";
+    } else {
+        $image = "PPSUB.OUTPUT";
+        $mask = "PPSUB.OUTPUT.MASK";
+        $variance = "PPSUB.OUTPUT.VARIANCE";
+    }
+
+    $image = $ipprc->file_resolve($ipprc->filename($image, $input_base));
+    $mask = $ipprc->file_resolve($ipprc->filename($mask, $input_base));
+    $variance= $ipprc->file_resolve($ipprc->filename($variance, $input_base));
+
+    return ($image, $mask, $variance);
+}
+
+sub resolve_template
+{
+    my $node = shift;
+
+    my $image;                  # Name of template to return
+    my $path_base;              # Base name for name
+    if (defined $node->{warp_path_base} and $node->{warp_path_base} ne "NULL") {
+        $path_base = $node->{warp_path_base};
+        $image = "PSWARP.OUTPUT";
+    } elsif (defined $node->{stack_path_base} and $node->{stack_path_base} ne "NULL") {
+        $path_base = $node->{stack_path_base};
+        $image = "PPSTACK.OUTPUT";
+    } else {
+        return undef;
+    }
+
+    $image = $ipprc->file_resolve($ipprc->filename($image, $path_base));
+
+    return $image
 }
 
Index: trunk/ippScripts/scripts/magic_tree.pl
===================================================================
--- trunk/ippScripts/scripts/magic_tree.pl	(revision 24166)
+++ trunk/ippScripts/scripts/magic_tree.pl	(revision 24174)
@@ -73,31 +73,4 @@
 my $mdcParser = PS::IPP::Metadata::Config->new; # Parser for metadata config files
 
-### Get a list of warpSkyfiles
-### This is a workaround to allow processing with older diffSkyfiles that don't have
-### a wcs. If warp_id is provided, we get the wcs from there
-my %warpSkyfiles;                   # hash of warps
-if ($warp_id) {
-    my $command = "$warptool -warped -warp_id $warp_id"; # Command to run
-    $command .= " -dbname $dbname" if defined $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 -warped: $error_code", $magic_id, $error_code);
-    }
-
-    my $metadata = $mdcParser->parse(join "", @$stdout_buf) or
-        &my_die("Unable to parse metadata config doc", $magic_id, $PS_EXIT_PROG_ERROR);
-
-    my $warps = parse_md_list($metadata) or
-        &my_die("Unable to parse metadata list", $magic_id, $PS_EXIT_PROG_ERROR);
-
-    # make a hash indexed by skycell_id
-    foreach my $warp ( @$warps ) {
-        my $skycell_id = $warp->{skycell_id};
-        die "failed to lookup skycell_id from warp" if !$skycell_id;
-        $warpSkyfiles{$skycell_id} = $warp;
-    }
-}
 ### Get a list of skycells
 my @skycells;                   # List of skycells
@@ -126,29 +99,9 @@
 my @fields;
 foreach my $input ( @skycells ) {
-    # the filename method doesn't add the $skycell_id
-
-    # my $skyfile = $ipprc->filename("SKYCELL.TEMPLATE", $outroot, $skycell_id );
-    #my $skyfile = $ipprc->filename("SKYCELL.TEMPLATE", $outroot, $skycell_id );
-
-#    my $skycellBase = "$outroot/$skycell_id";
-#    my $skyfile = $ipprc->filename("SKYCELL.TEMPLATE", $skycellBase);
-#    $ipprc->skycell_file($tess_id, $skycell_id, $skyfile, $verbose) or &my_die("Unable to generate skycells $skycell_id", $magic_id, $PS_EXIT_PROG_ERROR);
-
-    my $skyfile;
-    my $skycell_id = $input->{node};
-    if ($warp_id) {
-        # Applying the workaround
-        my $warp = $warpSkyfiles{$skycell_id};
-        die "warpSkyfile for $skycell_id not found" if !$warp;
-        my $skyfileBase = $warp->{path_base};
-        $skyfile = $ipprc->filename("SKYCELL.TEMPLATE", $skyfileBase);
-    } else {
-        # using the diffSkyfile
-        $skyfile = $input->{uri};
-    }
-    my $skyfileResolved = $ipprc->file_resolve( $skyfile );
-
-#    my ($header, $status) = Astro::FITS::CFITSIO::fits_read_header( $skyfileResolved );
-#    &my_die("Unable to read skycell header: $status", $magic_id, $PS_EXIT_SYS_ERROR) if $status;
+    # We use the WCS in the diff image
+    my $name = "PPSUB.OUTPUT"; # Name of file
+    my $skycell_id = $input->{node}; # Name of skycell
+    my $skyfile = $ipprc->filename($name, $input->{path_base}, $skycell_id); # Filename for diff
+    my $skyfileResolved = $ipprc->file_resolve( $skyfile ); # Resolved filename
 
     my ($header, $status) = (undef, 0);
@@ -162,5 +115,4 @@
 
     # Get the useful header keywords
-#    my $naxis1 = $$header{'NAXIS1'} or &my_die("Can't find NAXIS1", $magic_id, $PS_EXIT_SYS_ERROR);
     my $naxis1 = $$header{'NAXIS1'};
     my $naxis2;
@@ -181,16 +133,16 @@
         $naxis2 = $$header{'ZNAXIS2'} or &my_die("Can't find ZNAXIS2", $magic_id, $PS_EXIT_SYS_ERROR);
     }
-    my $ctype1 = $$header{'CTYPE1'} or &my_die("Can't find CTYPE1", $magic_id, $PS_EXIT_SYS_ERROR);
-    my $ctype2 = $$header{'CTYPE2'} or &my_die("Can't find CTYPE2", $magic_id, $PS_EXIT_SYS_ERROR);
-    my $cdelt1 = $$header{'CDELT1'} or &my_die("Can't find CDELT1", $magic_id, $PS_EXIT_SYS_ERROR);
-    my $cdelt2 = $$header{'CDELT2'} or &my_die("Can't find CDELT2", $magic_id, $PS_EXIT_SYS_ERROR);
-    my $crval1 = $$header{'CRVAL1'} or &my_die("Can't find CRVAL1", $magic_id, $PS_EXIT_SYS_ERROR);
-    my $crval2 = $$header{'CRVAL2'} or &my_die("Can't find CRVAL2", $magic_id, $PS_EXIT_SYS_ERROR);
-    my $crpix1 = $$header{'CRPIX1'} or &my_die("Can't find CRPIX1", $magic_id, $PS_EXIT_SYS_ERROR);
-    my $crpix2 = $$header{'CRPIX2'} or &my_die("Can't find CRPIX2", $magic_id, $PS_EXIT_SYS_ERROR);
-    my $pc11 = $$header{'PC001001'} or &my_die("Can't find PC001001", $magic_id, $PS_EXIT_SYS_ERROR);
-    my $pc12 = $$header{'PC001002'} or &my_die("Can't find PC001002", $magic_id, $PS_EXIT_SYS_ERROR);
-    my $pc21 = $$header{'PC002001'} or &my_die("Can't find PC002001", $magic_id, $PS_EXIT_SYS_ERROR);
-    my $pc22 = $$header{'PC002002'} or &my_die("Can't find PC002002", $magic_id, $PS_EXIT_SYS_ERROR);
+    my $ctype1 = $$header{'CTYPE1'} or &my_die("Can't find CTYPE1 in $skyfile", $magic_id, $PS_EXIT_SYS_ERROR);
+    my $ctype2 = $$header{'CTYPE2'} or &my_die("Can't find CTYPE2 in $skyfile", $magic_id, $PS_EXIT_SYS_ERROR);
+    my $cdelt1 = $$header{'CDELT1'} or &my_die("Can't find CDELT1 in $skyfile", $magic_id, $PS_EXIT_SYS_ERROR);
+    my $cdelt2 = $$header{'CDELT2'} or &my_die("Can't find CDELT2 in $skyfile", $magic_id, $PS_EXIT_SYS_ERROR);
+    my $crval1 = $$header{'CRVAL1'} or &my_die("Can't find CRVAL1 in $skyfile", $magic_id, $PS_EXIT_SYS_ERROR);
+    my $crval2 = $$header{'CRVAL2'} or &my_die("Can't find CRVAL2 in $skyfile", $magic_id, $PS_EXIT_SYS_ERROR);
+    my $crpix1 = $$header{'CRPIX1'} or &my_die("Can't find CRPIX1 in $skyfile", $magic_id, $PS_EXIT_SYS_ERROR);
+    my $crpix2 = $$header{'CRPIX2'} or &my_die("Can't find CRPIX2 in $skyfile", $magic_id, $PS_EXIT_SYS_ERROR);
+    my $pc11 = $$header{'PC001001'} or &my_die("Can't find PC001001 in $skyfile", $magic_id, $PS_EXIT_SYS_ERROR);
+    my $pc12 = $$header{'PC001002'} or &my_die("Can't find PC001002 in $skyfile", $magic_id, $PS_EXIT_SYS_ERROR);
+    my $pc21 = $$header{'PC002001'} or &my_die("Can't find PC002001 in $skyfile", $magic_id, $PS_EXIT_SYS_ERROR);
+    my $pc22 = $$header{'PC002002'} or &my_die("Can't find PC002002 in $skyfile", $magic_id, $PS_EXIT_SYS_ERROR);
     my $crota1 = $$header{'CROTA1'};
     my $crota2 = $$header{'CROTA2'};