Changeset 25027 for branches/pap/ippScripts/scripts/magic_process.pl

Timestamp:

Aug 7, 2009, 4:08:25 PM (17 years ago)

Author:

Paul Price

Message:

Merging trunk (r25026) to get up-to-date on old branch.

Location:

branches/pap

Files:

• . (modified) (1 prop)
• ippScripts/scripts/magic_process.pl (modified) (7 diffs)

branches/pap/ippScripts/scripts/magic_process.pl

@@ -136 +136 @@
         }
 
-        $command .= " --detect --image $image --mask $mask --weight $weight";
-
-        # set threshold to 4 sigma
-        $command .= ' -t 4';
-
-        # add -S
+        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";
+
+        # XXX: get all of these parameters from a recipe
+
+        # set threshold to 2.3 sigma (Default specified by Paul Sydney)
+        $command .= ' -t 2.3';
+
+        # set threshold to 2.75 sigma (Test by EAM : uncorrelated noise is typically ~20% higher than expected)
+        # XXX we have fixed the output variance to address this
+        # $command .= ' -t 2.75';
+
+        # set threshold to 4 sigma (for testing)
+        # $command .= ' -t 4';
+
+        # set Minimum percent visible required between pixels clusters in a valid streak [0.0 - 1.0]
+        # default is 0.2
+        $command .= ' -P 0.2';
+
+        #$command .= ' -t 4' . ' -P 0.25';
+
+        # add -S "Number of pixels to shift for determining maximum differences in mean images default:8"
         $command .= ' -S';
+
+        # add 3 x 3 binning
+        $command .= ' -b 3';
 
         # create the list of inputs used at this stage. At higher levels the
@@ -183 +205 @@
             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;
@@ -202 +224 @@
             $command .= " --images $image_list --masks $mask_list --weights $weight_list" ;
             $command .= " --inputstreaks $streaks_list";
+            # new option to "merge duplicate streaks into unique streaks"
+            $command .= " --duplicates";
         };
         if ($@) {
@@ -235 +259 @@
     $command   .= " -magic_id $magic_id";
     $command   .= " -node $node";
-    $command   .= " -uri $outroot";
+    $command   .= " -path_base $outroot";
     $command   .= " -dbname $dbname" if defined $dbname;
 
@@ -254 +278 @@
     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";
@@ -301 +328 @@
 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;
@@ -313 +340 @@
 }
 
-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 $path_base = $node->{diff_path_base}; # Base name for name
+    my $image = $node->{inverse} ? "PPSUB.INPUT.CONV" : "PPSUB.REF.CONV"; # File rule of interest
+
+    $image = $ipprc->file_resolve($ipprc->filename($image, $path_base));
+
+    return $image
 }