Index: trunk/tools/bills/concatsmf
===================================================================
--- trunk/tools/bills/concatsmf	(revision 38746)
+++ trunk/tools/bills/concatsmf	(revision 38746)
@@ -0,0 +1,106 @@
+#!/usr/bin/env perl
+
+# given an smf file create a file with a single fits table containing all of the detections
+# A column giving the imageID (exp_id * 100 + ccdnum) is added for use in matching to
+# PSPS detections and to distingush detections with the same IPP_IDET from different
+# OTAs
+#
+# Optionally just extract from a selected OTA's extension
+
+use strict;
+use warnings;
+
+use File::Basename;
+use File::Temp qw( tempdir  tempfile );
+
+use Getopt::Long qw( GetOptions :config auto_help auto_version gnu_getopt );
+use Pod::Usage qw( pod2usage );
+
+# It wouldn't be too hard to make ota an array and do a list of chips.
+# for now just all or one
+
+my ($ota, $save_temps, $verbose);
+
+GetOptions(
+    "ota|o=s"           =>  \$ota,
+    "vebose|v"          =>  \$verbose,
+    "save-temps"        =>  \$save_temps,
+) or pod2usage( 2 );
+
+die "usage: $0 <smf file> <output> [--ota <ota name>]\n" unless scalar @ARGV == 2;
+
+my $smf = shift;
+my $output = shift;
+
+my $stilts="java -jar $ENV{HOME}/tools/stilts.jar";
+
+my $ofmt = 'fits';
+
+my $infilename = basename($smf);
+my ($exp_name, $exp_id, $cam_id);
+($exp_name, $exp_id, undef, $cam_id) = split '\.', $infilename;
+
+print "$exp_name $exp_id $cam_id\n";
+my $extension = "";
+
+if ($ota) {
+    $ota = uc($ota);
+    if ($ota =~ /^XY/) {
+        $ota = substr $ota, 2, 2;
+    }
+    $extension = sprintf "XY%02d.psf", $ota;
+    extract_chip($smf, $output, $exp_id, $ota, $extension);
+    exit 0;
+}
+
+
+# create temporary directory and temporary list of files for tcat
+my $dir = tempdir( CLEANUP => !$save_temps);
+my ($listfile, $listname) = tempfile( "$dir/filelist.XXXX", UNLINK => !$save_temps);
+
+for (my $y = 0; $y <= 7; $y++) {
+    for (my $x = 0; $x <= 7; $x++) {
+        # skip non existent corner chips.
+        next if (($x == 0 || $x == 7) && ($y == 0 || $y == 7));
+
+        $ota = sprintf "%d%d", $y, $x;
+
+        $extension = sprintf "XY%02d.psf", $ota;
+        my ($ofile, $out) = tempfile ("$dir/$ota.XXXX", SUFFIX => '.cmf', UNLINK => !$save_temps);
+        print $listfile "$out\n";
+        extract_chip($smf, $out, $exp_id, $ota, $extension);
+    }
+}
+
+close $listfile;
+
+# now run stilts tcat to combine the files into one big table
+my $extname = $infilename;
+
+my $cmd = "$stilts tcat in=\@$listname out=$output ofmt=$ofmt ocmd='tablename $extname;'";
+my $rc = system $cmd;
+if ($rc) {
+    my $status = $rc >> 8;
+    die "stilts failed with $status $rc\n";
+}
+
+exit 0;
+
+
+sub extract_chip {
+    my ($in, $out, $frameID, $ota, $extension) = @_;
+
+    my $imageID = $frameID*100 + $ota;
+
+    # Add a column IMAGE_ID which we can match with the imageID in the Detection table.
+    my $cmd = "$stilts tpipe in=$in'#'$extension out=$out ofmt=$ofmt cmd='addcol -after IPP_IDET IMAGE_ID $imageID;' join=1or2";
+
+    print "$cmd\n" if $verbose;
+
+    my $rc = system $cmd;
+    if ($rc) {
+        my $status = $rc >> 8;
+        die "stilts failed with $status $rc\n";
+    }
+}
+
Index: trunk/tools/bills/detectToMeasure
===================================================================
--- trunk/tools/bills/detectToMeasure	(revision 38746)
+++ trunk/tools/bills/detectToMeasure	(revision 38746)
@@ -0,0 +1,226 @@
+#!/usr/bin/env perl
+
+# Given an ra, dec (or CAT_ID), exp_id, class_id, and det_id (IPP_IDET) for a detection,
+# lookup the detection it in the corresponding dvo measures file.
+# output is text unless an output file is specified.
+# With the option --list-others to output all measures for the given detection's object.
+# if --det_id is omitted, the catalog name and IMAGE_ID for the corresponding exposure is
+# printed to stdout
+
+use strict;
+use warnings;
+
+use IPC::Cmd 0.36 qw( can_run run );
+use Getopt::Long qw( GetOptions :config auto_help auto_version gnu_getopt );
+use Pod::Usage qw( pod2usage );
+
+my ($ra, $dec, $cat_id, $exp_id, $class_id, $det_id);
+
+my ($outputFile, $ofmt, $save_temps, $verbose);
+
+my ($listOthers, $thisImage);
+GetOptions(
+    "ra=s"              =>  \$ra,
+    "dec=s"             =>  \$dec,
+    "cat_id=s"          =>  \$cat_id,
+    "exp_id=s"          =>  \$exp_id,
+    "class_id=s"        =>  \$class_id,
+    "det_id=s"          =>  \$det_id,
+    "list-others"       =>  \$listOthers,
+    "this-image"        =>  \$thisImage,
+    "output|o=s"        =>  \$outputFile,
+    "ofmt=s"            =>  \$ofmt,
+
+    "verbose|v"         =>  \$verbose,
+    "save-temps"        =>  \$save_temps,
+) or pod2usage( 2 );
+
+unless (defined $ra and defined $dec and defined $exp_id and defined $class_id) {
+    print STDERR "usage: $0 --ra <ra> --dec <dec> [--cat_id <cat_id>] --exp_id <exp_id> --class_id <class_id> [--det_id <det_id> --output <output file name>\n";
+    print STDERR "       Other options: --list-others --this-image --ofmt\n";
+    exit 1;
+}
+
+
+my $dvo = can_run('dvo') or die "Can't find dvo";
+my $java = can_run('java') or die "Can't find java";
+my $chiptool = can_run('chiptool') or die "Can't find chiptool";
+
+my $stilts = "$java -jar $ENV{HOME}/ipp/ippToPsps/jars/stilts.jar";
+
+# XXX: make label and catdir options
+my $label = "SAS.20141118";
+my $catdir = '/data/ipp079.0/gpc1/catdirs/SAS/SAS39.V1';
+
+# go find which catalog this detection should belong to
+# in the SkyTable
+my $catalog;
+if ($cat_id) {
+    # We have CAT_ID select using that
+    my $command = "$stilts tpipe ofmt=ascii cmd='addcol CAT_ID INDEX;select CAT_ID==$cat_id;keepcols NAME;'"
+        . " in=$catdir/SkyTable.fits";
+
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+        run(command => $command, verbose => $verbose);
+    unless ($success) {
+        print STDERR "command failed error code: $error_code\nstderr says:\n\t";
+        print STDERR @$stderr_buf;
+
+        my $exit_status = $error_code >> 8;
+        print STDERR "exiting with status $exit_status\n";
+        exit $exit_status;
+    }
+    my $output = join "", @$stdout_buf;
+    my @lines = split "\n", $output;
+    # result is on the second line. split is an easy way to strip off whitespace
+    ($catalog) = split " ", $lines[1];
+} else {
+    # WE only have RA and DEC find the catalog using dvo's gcat command
+    # Note: leaving off the quit in the command causes dvo to exit with an error. Probably because the pipe
+    # unexpectedly went away.
+    my $command = "echo 'gcat $ra $dec;quit' | dvo -D CATDIR $catdir";
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+        run(command => $command, verbose => $verbose);
+    unless ($success) {
+        print STDERR "command failed error code: $error_code\nstderr says:\n\t";
+        print STDERR @$stderr_buf;
+
+        my $exit_status = $error_code >> 8;
+        print STDERR "exiting with status $exit_status\n";
+        exit $exit_status;
+    }
+    # gcat results go to stderr
+    my $output = join "", @$stderr_buf;
+    my @lines = split "\n", $output;
+    my $nlines = scalar @lines;
+    my $lastline = $lines[$nlines-1];
+    # printf "%s\n", $lastline;
+    (undef, $catalog, undef) = split " ", $lastline;
+
+    # XXX: we could go and the find $cat_id if we need it here.
+    $cat_id = 'NULL';
+}
+
+my $catalogPrefix = "$catdir/$catalog";
+# print "$catalogPrefix\n";
+
+# Go and find the EXTERN_ID (chip_imfile_id) for this image
+my $extern_id;
+my $image_id;
+{
+    my $command = "$chiptool -processedimfile -exp_id $exp_id -class_id $class_id -label $label | grep chip_imfile_id | awk '{print \$3}'";
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+        run(command => $command, verbose => $verbose);
+    unless ($success) {
+        print STDERR "command failed error code: $error_code\nstderr says:\n\t";
+        print STDERR join "", @$stderr_buf;
+
+        my $exit_status = $error_code >> 8;
+        print STDERR "exiting with status $exit_status\n";
+        exit $exit_status;
+    }
+    my $output = join "", @$stdout_buf;
+    chomp $output;
+    $extern_id = $output;
+}
+
+# go and find the IMAGE_ID for this image in the Images.dat
+{
+    my $command = "$stilts tpipe in=$catdir/Images.dat cmd='select EXTERN_ID==$extern_id;keepcols IMAGE_ID;' ofmt=ascii";
+
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+        run(command => $command, verbose => $verbose);
+    unless ($success) {
+        print STDERR "command failed error code: $error_code\nstderr says:\n\t";
+        print STDERR @$stderr_buf;
+
+        my $exit_status = $error_code >> 8;
+        print STDERR "exiting with status $exit_status\n";
+        exit $exit_status;
+    }
+    my $output = join "", @$stdout_buf;
+    my @lines = split "\n", $output;
+    # result is on the second line. split is an easy way to remove whitespace
+    ($image_id) = split " ", $lines[1];
+}
+
+# Print out what we've found out so far
+print "RA            DEC      NAME     CAT_ID EXTERN_ID IMAGE_ID catalogPrefix\n";
+#      333.71999 -4.47253 s0000/5228.01 NULL 75160686 4620 /data/ipp079.0/gpc1/catdirs/SAS/SAS39.V1/s0000/5228.01
+print "$ra $dec $catalog $cat_id $extern_id $image_id $catalogPrefix\n";
+
+if (!$det_id) {
+    exit 0;
+}
+
+# We have a det_id go find the detection(s) in the catalog
+{
+    my $command = "$stilts tpipe in=$catalogPrefix.cpm cmd='select IMAGE_ID==$image_id&&DET_ID==$det_id;";
+    if ($listOthers) {
+        # just get the OBJ_ID
+        $command .= "keepcols OBJ_ID;' ofmt=ascii";
+    } else {
+        # We only need the specific detection
+        $command .= "'";
+        $command .= " out=$outputFile" if $outputFile;
+        $command .= " ofmt=$ofmt" if $ofmt;
+    }
+
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+        run(command => $command, verbose => $verbose);
+    unless ($success) {
+        print STDERR "command failed error code: $error_code\nstderr says:\n\t";
+        print STDERR @$stderr_buf;
+
+        my $exit_status = $error_code >> 8;
+        print STDERR "exiting with status $exit_status\n";
+        exit $exit_status;
+    }
+    my $output = join "", @$stdout_buf;
+
+    if ($listOthers) {
+        # find the obj_id for our detection
+        my @lines = split "\n", $output;
+        # result is on the second line. split is an easy way to remove whitespace
+        my ($obj_id) = split " ", $lines[1];
+        my $extraSelect = "";
+        if ($thisImage) {
+            # just list detections from this object in this image
+            $extraSelect = "&&IMAGE_ID==$image_id";
+        }
+            
+        my $command = "$stilts tpipe in=$catalogPrefix.cpm cmd='select OBJ_ID==$obj_id$extraSelect;";
+        $command .= "'";
+        $command .= " out=$outputFile" if $outputFile;
+        $command .= " ofmt=$ofmt" if $ofmt;
+        my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+            run(command => $command, verbose => $verbose);
+        unless ($success) {
+            print STDERR "command failed error code: $error_code\nstderr says:\n\t";
+            print STDERR @$stderr_buf;
+
+            my $exit_status = $error_code >> 8;
+            print STDERR "exiting with status $exit_status\n";
+            exit $exit_status;
+        }
+        $output = join "", @$stdout_buf;
+    }
+    if (!$outputFile) {
+        # user did not specify an output file list the results of the commands above
+        print $output;
+    }
+}
+
+exit 0;
+
+
+
+# find the chip_imfile_id of the exposure and ota
+# $extern_id = `chiptool -processedimfile -exp_id $exp_id -class_id $class_id -label SAS.20141118 | grep chip_imfile_id | awk '{print $3}'`
+
+# look up the IMAGE_ID in the Images.Dat
+
+#stilts tpipe in=../Images.dat cmd='select "EXTERN_ID==$extern_id";keepcols IMAGE_ID"'
+
+# Look up the catalog name for the coordinates using dvo's gcat command
+