Index: trunk/ippScripts/scripts/detrend_reject.pl
===================================================================
--- trunk/ippScripts/scripts/detrend_reject.pl	(revision 8507)
+++ 	(revision )
@@ -1,146 +1,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use IPC::Cmd qw( can_run run );
-use PS::IPP::Metadata::Config;
-use Data::Dumper;
-
-use constant RECIPE => "PPSTATS_REJECT"; # Recipe to use on residuals
-use constant CLIP => 3;		# Rejection limit for sigma clipping
-
-if (scalar @ARGV == 0) {
-    die "Output rejected images from a stack, based on their statistics.\n\n" .
-	"Usage: $0 FILE_1.fits FILE_2.fits FILE_3.fits ...\n\n";
-}
-
-# look for commands we need
-my $missing_tools;
-my $ppStats = can_run('ppStats')
-    or (warn "can't find ppStats" and $missing_tools = 1);
-die "Can't find required tools.\n" if $missing_tools;
-
-my @filenames = @ARGV;		# Input files
-my %stats;			# Statistics for each file
-
-my $mdcParser = PS::IPP::Metadata::Config->new;	# Parser for metadata config files
-
-foreach my $fileName (@filenames) {
-    my $command = "$ppStats $fileName -robust-median -robust-stdev"; # Command to run
-    print "Executing: $command\n";
-    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
-	run(command => $command, verbose => 0);
-    die "Unable to perform ppStats on $fileName: $error_code\n" if not $success;
-    my $parsed = $mdcParser->parse(join "", @$stdout_buf); # Parsed metadata
-    $stats{$fileName} = assembleStats($parsed);
-}
-
-my $rejectList = rejectFiles(\%stats); # List of files to reject
-
-foreach my $fileName (keys %$rejectList) {
-    print "$fileName\n";
-}
-
-### Pau.
-
-
-# Assemble the statistics into a Perl-ish data structure: a hash of hashes of hashes of hashes.
-sub assembleStats
-{
-    my $parsed = shift;		# Parsed metadata config file containing the stats
-
-    my %fpaStats;		# Container for statistics for fpa
-    foreach my $fpaItem (@$parsed) {
-	if ($fpaItem->{class} eq "metadata") {
-	    my $chipName = $fpaItem->{name}; # Name of chip
-	    my $chipData = $fpaItem->{value};
-	    my %chipStats;	# Container for statistics for chip
-	    foreach my $chipItem (@$chipData) {
-		if ($chipItem->{class} eq "metadata") {
-		    my $cellName = $chipItem->{name}; # Name of cell
-		    my $cellData = $chipItem->{value};
-		    my %cellStats; # Container for statistics for cell
-		    foreach my $cellItem (@$cellData) {
-			if ($cellItem->{name} =~ /^(SAMPLE|ROBUST|FITTED|CLIPPED)/) {
-			    # It's a statistic of some sort
-			    if ($cellItem->{name} =~ /STDEV$/) {
-				$cellStats{'stdev'} = $cellItem->{value};
-			    } else {
-				$cellStats{'value'} = $cellItem->{value};
-			    }
-			}
-		    }
-		    $chipStats{$cellName} = \%cellStats;
-		}
-	    }
-	    $fpaStats{$chipName} = \%chipStats;
-	}
-    }
-    return \%fpaStats;
-}
-
-# Reject files on the basis of the statistics
-sub rejectFiles
-{
-    my $stats = shift;		# The statistics structure
-
-    my %reject;			# List of files to reject
-
-    # Measure the mean
-    my $sum = 0;		# Sum of the values
-    my $num = 0;		# Number of values
-    foreach my $file (keys %$stats) {
-	my $fileData = $stats->{$file}; # Data for the file
-	foreach my $chipName (keys %$fileData) {
-	    my $chipData = $fileData->{$chipName}; # Data for the chip
-	    foreach my $cellName (keys %$chipData) {
-		my $cellData = $chipData->{$cellName}; # Data for the cell
-		if (defined $cellData->{'value'}) {
-		    $sum += $cellData->{'value'};
-		    $num++;
-		}
-	    }
-	}
-    }
-    die "Unable to measure mean\n" if $num == 0;
-    my $mean = $sum / $num;	# Mean of the values
-
-    # Measure the standard deviation
-    $sum = 0;
-    $num = 0;
-    foreach my $fileName (keys %$stats) {
-	my $fileData = $stats->{$fileName}; # Data for the file
-	foreach my $chipName (keys %$fileData) {
-	    my $chipData = $fileData->{$chipName}; # Data for the chip
-	    foreach my $cellName (keys %$chipData) {
-		my $cellData = $chipData->{$cellName}; # Data for the cell
-		if (defined $cellData->{'value'}) {
-		    $sum += ($cellData->{'value'} - $mean)**2;
-		    $num++;
-		}
-	    }
-	}
-    }
-    die "Unable to measure stadard deviation\n" if $num == 1;
-    my $stdev = sqrt($sum/($num-1)); # Standard deviation of the values
-
-    # Identify values exceeding the tolerance
-  FILE:    foreach my $fileName (keys %$stats) {
-      my $fileData = $stats->{$fileName}; # Data for the file
-      foreach my $chipName (keys %$fileData) {
-	  my $chipData = $fileData->{$chipName}; # Data for the chip
-	  foreach my $cellName (keys %$chipData) {
-	      my $cellData = $chipData->{$cellName}; # Data for the cell
-	      if (defined $cellData->{'value'}) {
-		  my $residual = abs($cellData->{'value'} - $mean) / $stdev;
-		  if ($residual > CLIP) {
-		      $reject{$fileName} = 1;
-		      next FILE;
-		  }
-	      }
-	  }
-      }
-  }
-    return \%reject;
-}