Changeset 25027 for branches/pap/ippScripts/scripts/chip_imfile.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/chip_imfile.pl (modified) (7 diffs)

branches/pap/ippScripts/scripts/chip_imfile.pl

@@ -20 +20 @@
 use PS::IPP::Metadata::Config;
 use PS::IPP::Config 1.01 qw( :standard );
+use File::Temp qw( tempfile );
 
 use Getopt::Long qw( GetOptions :config auto_help auto_version gnu_getopt );
@@ -39 +40 @@
 # Parse the command-line arguments
 my ( $exp_id, $chip_id, $class_id, $chip_imfile_id, $uri, $camera, $outroot, $dbname, $run_state, $reduction, $threads, $verbose,
-     $no_update, $no_op, $redirect, $magicked, $deburned );
+     $no_update, $save_temps, $no_op, $redirect, $magicked, $deburned );
 GetOptions(
     'exp_id=s'          => \$exp_id,    # Exposure identifier
@@ -52 +53 @@
     'run-state=s'       => \$run_state, # current state of the run (new, update)
     'magicked'          => \$magicked,  # magicked state of input file
-    'deburned=s'        => \$deburned,  # does deburned image exist? 
+    'deburned=s'        => \$deburned,  # does deburned image exist?
     'threads=s'         => \$threads,   # Number of threads to use for ppImage
     'verbose'           => \$verbose,   # Print to stdout
@@ -58 +59 @@
     'no-op'             => \$no_op,     # Don't do any operations?
     'redirect-output'   => \$redirect,
+    'save-temps'        => \$save_temps, # Save temporary files?
     ) or pod2usage( 2 );
 
 pod2usage( -msg => "Unknown option: @ARGV", -exitval => 2 ) if @ARGV;
-pod2usage( -msg => "Required options: --exp_id --chip_id --class_id --uri --camera --outroot --run-state",
+pod2usage( -msg => "Required options: --exp_id --chip_id --chip_imfile_id --class_id --uri --camera --outroot --run-state",
            -exitval => 3) unless
     defined $exp_id and
@@ -142 +144 @@
     my $useDeburnedImage = metadataLookupBool($recipeData, 'USE.DEBURNED.IMAGE');
     if ($useDeburnedImage && $deburned) {
-        $uri =~ s/fits$/burn.fits/;
-        &my_die("Couldn't find deburned input file: $uri\n", $exp_id, $chip_id, $class_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists($uri);
+        $uri =~ s/fits$/burn.fits/;
+        &my_die("Couldn't find deburned input file: $uri\n", $exp_id, $chip_id, $class_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists($uri);
+    }
+
+    # apply the 'tiltystreak' operation, if desired
+    my $tiltystreakApply = metadataLookupBool($recipeData, 'TILTYSTREAK.APPLY');
+    if ($tiltystreakApply) {
+
+        my $tiltystreakByClass = metadataLookupMD($recipeData, 'TILTYSTREAK.BY.CLASS');
+        my $tiltystreakClassApply = metadataLookupBool($tiltystreakByClass, "APPLY.$class_id");
+        if ($tiltystreakClassApply) {
+
+            my $tiltystreakClassOptions = metadataLookupStr($tiltystreakByClass, "OPTIONS.$class_id");
+            if ($tiltystreakClassOptions eq "none") {
+                $tiltystreakClassOptions = "";
+            }
+
+            my ($success, $error_code, $full_buf, $stdout_buf, $stderr_buf);
+
+            # XXX make these optional (must be built by psbuild as well...)
+            my $funpack = can_run('funpack') or &my_die ("Can't find funpack", $exp_id, $chip_id, $class_id, $PS_EXIT_SYS_ERROR);
+            my $tiltystreak = can_run('tiltystreak') or &my_die ("Can't find tiltystreak", $exp_id, $chip_id, $class_id, $PS_EXIT_SYS_ERROR);
+
+            # create an temporary output file:
+            my ($tempFile, $tempName) = tempfile( "/tmp/chip.$exp_id.$class_id.tmp.XXXX", UNLINK => !$save_temps );
+
+            print "uri: $uri\n";
+
+            # get the UNIX version of the (possible) neb: or path: filename
+            my $uriReal = $ipprc->file_resolve( $uri );
+
+            print "uriReal: $uriReal\n";
+
+            # unpack the data (is a NOP if not compressed)
+            $command = "$funpack -S $uriReal > $tempName";
+            ( $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 funpack: $error_code", $exp_id, $chip_id, $class_id, $PS_EXIT_SYS_ERROR);
+            }
+
+            # run tiltystreak
+            $command = "$tiltystreak $tempName $tiltystreakClassOptions";
+            ( $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 tiltystreak: $error_code", $exp_id, $chip_id, $class_id, $PS_EXIT_SYS_ERROR);
+            }
+
+            # supply the output file as the new input file
+            $uri = $tempName;
+        }
     }
 
@@ -201 +253 @@
         }
         chomp $cmdflags;
-        ($quality) = $cmdflags =~ /-quality (\d+)/; # Quality flag
+        if (($camera ne "GPC1") or ($class_id ne "XY27") or ($exp_id < 53171)) {
+            ($quality) = $cmdflags =~ /-quality (\d+)/; # Quality flag
+        } else {
+            # hack to kick ota 27 out of subsequent analysis by setting quality flag to a non-zero value
+            my ($before, $after) = split " -quality ", $cmdflags;
+
+            # get the current value
+            ($quality) = $after =~ /^(\d+)/;
+            $after = substr($after, length($quality));
+
+            # replace it if it is zero
+            $quality = 42 if !$quality;
+
+            # rebuild the cmdflags
+            $cmdflags = $before . " -quality $quality";
+            $cmdflags .= " $after" if $after;
+        }
     }
 
@@ -265 +333 @@
             $command = "$chiptool -addprocessedimfile";
             $command .= " -exp_id $exp_id";
-            $command .= " -uri $outputImage";
+            $command .= " -uri $outputImage" if defined $outputImage;
             $command .= " -path_base $outroot";
             $command .= " -hostname $host" if defined $host;