Clean up old, useless and broken scripts

14 files changed, 2 insertions, 753 deletions

diff --git a/scripts/README b/scripts/README
index 1d117d97..a58cb7ff 100644
--- a/scripts/README
+++ b/scripts/README
@@ -1,3 +1,3 @@
-This director contains useful scripts to enhance the use of CrystFEL.  You are
+This directory contains useful scripts to enhance the use of CrystFEL.  You are
 supposed to copy them to your working directory, edit them and make them
 executable (chmod +x).
diff --git a/scripts/alternate-stream b/scripts/alternate-stream
index 6a711722..1ac2fd3a 100755
--- a/scripts/alternate-stream
+++ b/scripts/alternate-stream
@@ -11,7 +11,7 @@ my $alt = 0;
 
 while ( $line = <FH> ) {
 
-	if ( $line =~ /^Reflections\ from\ indexing/ ) {
+	if ( $line =~ /^-----\ Begin chunk\ -----$/ ) {
 		$alt = 1 - $alt;
 	}
 
diff --git a/scripts/double-hit b/scripts/double-hit
deleted file mode 100755
index 55a95ee1..00000000
--- a/scripts/double-hit
+++ /dev/null
@@ -1,100 +0,0 @@
-#!/usr/bin/perl -w
-
-use strict;
-use File::Basename;
-
-open(FH, $ARGV[0]);
-open(OFH, "> doublehit.dat");
-
-my $line;
-my $filename;
-my $full_filename;
-
-my $hsteps = 128;
-my @hist;
-my $hmin = 0;
-my $hmax = 5;
-my $hstep = ($hmax - $hmin)/$hsteps;
-
-for ( my $i=0; $i<$hsteps; $i++ ) {
-	$hist[$i] = 0;
-}
-
-while ( $line = <FH> ) {
-
-	if ( $line =~ /^Reflections\ from\ indexing\ in\ (.+)$/ ) {
-		$full_filename = $1;
-		$filename = basename($full_filename);
-	}
-
-	if ( $line =~ /^Peak\ statistics:\ (\d+)\ .*\ (\d+)\ .*\ (\d+)\ .*\ (\d+)\ / ) {
-
-		my $foundclose = $1;
-		my $found = $2;
-		my $indclose = $3;
-		my $hits = $3;
-
-		$filename =~ /LCLS_(\d+)_([A-Za-z]+)(\d+)_r\d+_(\d\d)(\d\d)(\d\d)_/;
-		my $year = $1;
-		my $month = $2;
-		my $day = $3;
-		my $hour = $4;
-		my $min = $5;
-		my $sec = $6;
-
-		my $div;
-
-		if ( $foundclose > 0 ) {
-			$div = $found / $foundclose;
-		} else {
-			$div = 0.0;
-		}
-
-		printf(OFH "%s/%s/%s-%s:%s:%s %f\n", $year, $month, $day,
-		                                     $hour, $min, $sec,
-		                                     $div);
-
-		if ( $div > 4.0 ) {
-			printf("Double hit: %s\n", $full_filename);
-		}
-		if ( $div == 1.0 ) {
-			printf("Single hit: %s\n", $full_filename);
-		}
-
-		my $bin = int(($div-$hmin)/$hstep);
-		$hist[$bin]++;
-	}
-
-}
-
-close(FH);
-close(OFH);
-
-open(GP, "| gnuplot");
-
-print(GP "set term postscript enhanced font \"Helvetica,20\"\n");
-print(GP "set output \"doublehit.ps\"\n");
-print(GP "set xtics nomirror out rotate by -60\n");
-print(GP "set xdata time\n");
-print(GP "set timefmt \"%Y/%b/%d-%H:%M:%S\"\n");
-print(GP "set format x \"%d/%b %H:%M\"\n");
-print(GP "unset key\n");
-print(GP "plot [] [0:5] \"doublehit.dat\" u 1:2 w points\n");
-
-open(OFH, "> doublehit-hist.dat");
-for ( my $i=0; $i<$hsteps; $i++ ) {
-	printf(OFH "%f %f\n", $hmin+$hstep*$i+($hstep/2), $hist[$i]);
-}
-close(OFH);
-
-print(GP "set xtics nomirror out rotate by 0\n");
-print(GP "unset xdata\n");
-print(GP "set format x \"% g\"\n");
-print(GP "unset key\n");
-print(GP "plot [] [0:1000] \"doublehit-hist.dat\" u 1:2 w histeps\n");
-
-close(GP);
-
-system("ps2pdf doublehit.ps");
-unlink("doublehit.dat");
-unlink("doublehit.ps");
diff --git a/scripts/facetron-partiality.gp b/scripts/facetron-partiality.gp
deleted file mode 100644
index 914a7478..00000000
--- a/scripts/facetron-partiality.gp
+++ /dev/null
@@ -1,7 +0,0 @@
-set xlabel "Calculated partiality"
-set ylabel "Observed Partiality"
-set xrange [0:1]
-set yrange [0:1]
-unset key
-set size square
-plot "p-iteration-1.dat" using 7:8 w p ps 1 pt 7 lc -1
diff --git a/scripts/facetron-patterns.gp b/scripts/facetron-patterns.gp
deleted file mode 100644
index 3fdb6b80..00000000
--- a/scripts/facetron-patterns.gp
+++ /dev/null
@@ -1,4 +0,0 @@
-set xlabel "Pattern number"
-set ylabel "Mean intensity deviation"
-unset key
-plot "g-iteration-1.dat" using 1:2 w impulses lw 1 lc -1
diff --git a/scripts/frequency b/scripts/frequency
deleted file mode 100755
index d6caf72c..00000000
--- a/scripts/frequency
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/usr/bin/perl -w
-
-use strict;
-
-my $nplots = 32;
-my $sym = "6/mmm";
-
-my $stream = $ARGV[0];
-
-#system("~/crystfel/src/process_hkl -i ".$stream." -o test.hkl -y ".$sym);
-
-open(FH, "test.hkl");
-my $max = 0;
-my $h;
-my $k;
-my $l;
-my $line;
-while ( $line = <FH> ) {
-
-	chomp $line;
-
-	if ( $line =~ /\s+(\d+)$/ ) {
-
-		my $n = $1;
-		if ( $n > $max ) {
-			$line =~ /^\s+(\d+)\s+(\d+)\s+(\d+)\s+/;
-			$h = $1;
-			$k = $2;
-			$l = $3;
-			$max = $n;
-		}
-
-	}
-}
-
-printf("%i %i %i = %i\n", $h, $k, $l, $max);
-
-exit 0;
diff --git a/scripts/i0-analysis b/scripts/i0-analysis
deleted file mode 100755
index b29892a9..00000000
--- a/scripts/i0-analysis
+++ /dev/null
@@ -1,110 +0,0 @@
-#!/usr/bin/perl -w
-
-use strict;
-use File::Basename;
-use POSIX;
-
-open(FH, $ARGV[0]);
-
-my $line;
-my $filename;
-my $full_filename;
-
-my $hsteps = 128;
-my @hist;
-
-open(GP, "| gnuplot");
-print(GP "set term postscript enhanced font \"Helvetica,20\"\n");
-print(GP "set output \"i0.ps\"\n");
-print(GP "unset key\n");
-print(GP "set xtics nomirror out rotate by 0\n");
-print(GP "unset xdata\n");
-print(GP "set format x \"% g\"\n");
-print(GP "unset key\n");
-
-
-# First graph: distribution of scaling factors
-my $hmin = -0.1;
-my $hmax = 1.5;
-my $hstep = ($hmax - $hmin)/$hsteps;
-for ( my $i=0; $i<$hsteps; $i++ ) {
-	$hist[$i] = 0;
-}
-while ( $line = <FH> ) {
-	if ( $line =~ /^([\d\.]+)\ ([\d\.]+)$/ ) {
-		my $scale = $1;
-		my $i0 = $2;
-		my $bin = floor(($scale-$hmin)/$hstep);
-		$hist[$bin]++;
-	}
-}
-close(FH);
-open(OFH, "> i0-scale-hist.dat");
-for ( my $i=0; $i<$hsteps; $i++ ) {
-	printf(OFH "%f %f\n", $hmin+$hstep*$i+($hstep/2), $hist[$i]);
-}
-close(OFH);
-print(GP "set title \"Distribution of Scaling Factors\"\n");
-print(GP "plot [] [] \"i0-scale-hist.dat\" u 1:2 w histeps\n");
-
-
-# Second graph: distribution of gas detector values
-$hmin = -0.5;
-$hmax = 3.0;
-$hstep = ($hmax - $hmin)/$hsteps;
-open(FH, $ARGV[0]);
-for ( my $i=0; $i<$hsteps; $i++ ) {
-	$hist[$i] = 0;
-}
-while ( $line = <FH> ) {
-	if ( $line =~ /^([\d\.]+)\ ([\d\.]+)$/ ) {
-		my $scale = $1;
-		my $i0 = $2;
-		my $bin = floor(($i0-$hmin)/$hstep);
-		$hist[$bin]++;
-	}
-}
-close(FH);
-open(OFH, "> i0-hist.dat");
-for ( my $i=0; $i<$hsteps; $i++ ) {
-	printf(OFH "%f %f\n", $hmin+$hstep*$i+($hstep/2), $hist[$i]);
-}
-close(OFH);
-print(GP "set title \"Distribution of Gas Detector Values\"\n");
-print(GP "plot [] [] \"i0-hist.dat\" u 1:2 w histeps\n");
-
-
-# Third graph: distribution of scale factors after scaling i0=1
-$hmin = -0.1;
-$hmax = 1.5;
-$hstep = ($hmax - $hmin)/$hsteps;
-open(FH, $ARGV[0]);
-for ( my $i=0; $i<$hsteps; $i++ ) {
-	$hist[$i] = 0;
-}
-while ( $line = <FH> ) {
-	if ( $line =~ /^([\d\.]+)\ ([\d\.]+)$/ ) {
-		my $scale = $1;
-		my $i0 = $2;
-		my $bin = floor((($scale/$i0)-$hmin)/$hstep);
-		$hist[$bin]++;
-	}
-}
-close(FH);
-open(OFH, "> i0-prior-hist.dat");
-for ( my $i=0; $i<$hsteps; $i++ ) {
-	printf(OFH "%f %f\n", $hmin+$hstep*$i+($hstep/2), $hist[$i]);
-}
-close(OFH);
-print(GP "set title \"Distribution of Scaling Factors with I0=1\"\n");
-print(GP "plot [] [] \"i0-prior-hist.dat\" u 1:2 w histeps\n");
-
-
-close(GP);
-
-system("ps2pdf i0.ps");
-unlink("i0.dat");
-unlink("i0.ps");
-unlink("i0-hist.dat");
-unlink("i0-prior-hist.dat");
-unlink("i0-scale-hist.dat");
diff --git a/scripts/indexing-rate b/scripts/indexing-rate
deleted file mode 100755
index 6dc61f36..00000000
--- a/scripts/indexing-rate
+++ /dev/null
@@ -1,93 +0,0 @@
-#!/usr/bin/perl -w
-
-use strict;
-use File::Basename;
-
-open(FH, $ARGV[0]);
-open(HITRATE, "> hitrate.dat");
-
-my $line;
-my $year;
-my $month;
-my $day;
-my $hour;
-my $min = -1;
-my $sec = -1;
-my $nh = 0;
-
-while ( $line = <FH> ) {
-
-	chomp($line);
-
-	unless ( $line =~ /^Reflections\ from\ indexing\ in\ (.+)$/ ) {
-		next;
-	}
-
-	my $filename = basename($1);
-
-	if ( $filename ) {
-
-		unless ( $filename =~
-		   /LCLS_(\d+)_([A-Za-z]+)(\d+)_r\d\d\d\d_(\d\d)(\d\d)(\d\d)_/ ) {
-			printf(STDERR "Wrong filename format '%s'!\n",
-			       $filename);
-			exit(1);
-		}
-
-		my $new_year = $1;
-		my $new_month = $2;
-		my $new_day = $3;
-		my $new_hour = $4;
-		my $new_min = $5;
-		my $new_sec = $6;
-
-		if ( $new_min != $min ) {
-
-			# Not the first time
-			if ( $sec != -1 ) {
-				printf(HITRATE "%s/%s/%s-%s:%s:%s %i\n",
-				               $year, $month, $day,
-				               $hour, $min, $sec, $nh);
-			}
-
-			$year = $new_year;
-			$month = $new_month;
-			$day = $new_day;
-			$hour = $new_hour;
-			$min = $new_min;
-			$sec = $new_sec;
-			$nh = 0;
-
-		} else {
-
-			$nh++;
-
-		}
-
-	}
-
-}
-
-close(FH);
-close(HITRATE);
-
-#system("head -n 67 hitrate.dat > hitrate2.dat");
-system("tail -n 105 hitrate.dat > hitrate2.dat");
-
-open(GP, "| gnuplot");
-
-print(GP "set term postscript enhanced font \"Helvetica,20\"\n");
-print(GP "set output \"hitrate.ps\"\n");
-print(GP "set title \"Hit rate\"\n");
-print(GP "set xtics nomirror rotate by -60\n");
-print(GP "set xdata time\n");
-print(GP "set timefmt \"%Y/%b/%d-%H:%M:%S\"\n");
-print(GP "set format x \"%d/%b %H:%M\"\n");
-print(GP "set rmargin 6\n");
-print(GP "unset key\n");
-print(GP "plot [] [] \"hitrate2.dat\" u 1:2 w histeps lw 3 lc 3\n");
-close(GP);
-
-system("ps2pdf hitrate.ps");
-#unlink("hitrate.dat");
-unlink("hitrate.ps");
diff --git a/scripts/observed-peak-rate b/scripts/observed-peak-rate
deleted file mode 100755
index 00e0ba4d..00000000
--- a/scripts/observed-peak-rate
+++ /dev/null
@@ -1,122 +0,0 @@
-#!/usr/bin/perl -w
-
-use strict;
-use File::Basename;
-
-open(FH, $ARGV[0]);
-open(HITRATE, "> hitrate.dat");
-open(NPEAKS, "> npeaks.dat");
-
-my $line;
-my $filename = "";
-my $full_filename;
-my $np;
-my $year;
-my $month;
-my $day;
-my $hour;
-my $min;
-my $sec = -1;
-my $nh = 0;
-my $ns = 0;
-
-while ( $line = <FH> ) {
-
-	chomp($line);
-
-	if ( $line =~ /^\s+[0-9\.]+\s+[0-9\.]+\s+[0-9\.]+\s+[0-9\.]+$/ ) {
-		$np++;
-	}
-
-	unless ( $line =~ /^Peaks\ from\ peak\ search\ in\ (.+)$/ ) {
-		next;
-	}
-
-	$full_filename = $1;
-
-	# Process last image
-	if ( $filename ) {
-
-		unless ( $filename =~
-		   /LCLS_(\d+)_([A-Za-z]+)(\d+)_(\d\d)(\d\d)(\d\d)_/ ) {
-			printf(STDERR "Wrong filename format '%s'!\n",
-			       $filename);
-			exit(1);
-		}
-
-		my $new_year = $1;
-		my $new_month = $2;
-		my $new_day = $3;
-		my $new_hour = $4;
-		my $new_min = $5;
-		my $new_sec = $6;
-
-		if ( $new_sec != $sec ) {
-
-			if ( $ns > 0 ) {
-
-				printf(HITRATE "%s/%s/%s-%s:%s:%s %f\n",
-				               $year, $month, $day,
-			                       $hour, $min, $sec,
-			                       $nh);
-
-			}
-
-			$year = $new_year;
-			$month = $new_month;
-			$day = $new_day;
-			$hour = $new_hour;
-			$min = $new_min;
-			$sec = $new_sec;
-
-			$nh = 0;
-			$ns = 0;
-
-		}
-
-		printf(NPEAKS "%s/%s/%s-%s:%s:%s %f\n",
-		              $year, $month, $day, $hour, $min, $sec, $np);
-
-		printf("%s: %i peaks\n", $filename, $np);
-		if ( $np > 10 ) {
-			$nh++;
-		}
-		$ns++;
-
-	}
-
-	$filename = basename($full_filename);
-	$np = 0;
-
-}
-
-close(FH);
-close(HITRATE);
-close(NPEAKS);
-
-open(GP, "| gnuplot");
-
-print(GP "set term postscript enhanced font \"Helvetica,20\"\n");
-print(GP "set output \"hitrate.ps\"\n");
-print(GP "set title \"Hit rate\"\n");
-print(GP "set xtics nomirror rotate by -60\n");
-print(GP "set xdata time\n");
-print(GP "set timefmt \"%Y/%b/%d-%H:%M:%S\"\n");
-print(GP "set format x \"%d/%b %H:%M\"\n");
-print(GP "set rmargin 6\n");
-print(GP "unset key\n");
-print(GP "plot [] [] \"hitrate.dat\" u 1:2 w points\n");
-
-print(GP "set xtics nomirror rotate by -60\n");
-print(GP "set title \"Number of Peaks per Image\"\n");
-print(GP "set xdata time\n");
-print(GP "set timefmt \"%Y/%b/%d-%H:%M:%S\"\n");
-print(GP "set format x \"%d/%b %H:%M\"\n");
-print(GP "unset key\n");
-print(GP "plot [] [] \"npeaks.dat\" u 1:2 w points\n");
-
-close(GP);
-
-system("ps2pdf hitrate.ps");
-unlink("hitrate.dat");
-unlink("hitrate.ps");
diff --git a/scripts/sk_to_crystfel.pl b/scripts/sk_to_crystfel.pl
deleted file mode 100755
index d0dd0f4f..00000000
--- a/scripts/sk_to_crystfel.pl
+++ /dev/null
@@ -1,139 +0,0 @@
-#!/usr/bin/perl -w
-
-use strict;
-
-open(ROT, "< rotations.lst");
-open(COORD, "< coords.dat");
-open(OUT, "> cspad-feb2011.geom");
-
-my $quadrant = 0;
-printf(OUT "n_panels = 64\n\n");
-my $x = 0;
-my $y = 0;
-my $p = 0;
-
-my $global_x = 0.0;
-my $global_y = 0.0;
-
-while ( my $coord = <COORD> ) {
-
-	my $rot = <ROT>;
-	my $cx = 0.0;
-	my $cy = 0.0;
-	my $minx = $x*194;
-	my $miny = $y*185;
-	my $sc1;
-	my $sc2;
-
-	chomp $coord;
-	chomp $rot;
-
-	if ( $coord =~ /\(([0-9\.\-]+),\s([0-9\.\-]+)\)/ ) {
-		$sc1 = $1;
-		$sc2 = $2;
-		printf("%f %f\n", $sc1, $sc2);
-
-	} else {
-		printf("!!!\n");
-	}
-
-	my $a = 388.0; # Fast scan
-	my $b = 185.0; # Slow scan
-
-	# FIXME: Remove the $b for versions of Stephan's code after 20th Feb
-	$sc1 -= (1308.696-$b);
-	$sc2 -= (980.3862-$b);
-
-	my $sx = -$sc2;
-	my $sy = -$sc1;
-
-	printf(OUT "; Quadrant %i, asic %i\n", $quadrant, ($x%2)+2*$y);
-	printf(OUT "%i/min_fs = %i\n", $p, $minx);
-	printf(OUT "%i/min_ss = %i\n", $p, $miny);
-	printf(OUT "%i/max_fs = %i\n", $p, ($x+1)*194-1);
-	printf(OUT "%i/max_ss = %i\n", $p, ($y+1)*185-1);
-	printf(OUT "%i/badrow_direction = -\n", $p);
-	printf(OUT "%i/res = 9090.91\n", $p);
-	printf(OUT "%i/peak_sep = 6.0\n", $p);
-	printf(OUT "%i/clen = 77.0e-3\n", $p);
-	if ( $rot == "0" ) {
-		printf(OUT "%i/fs = -x\n", $p);
-		printf(OUT "%i/ss = -y\n", $p);
-		$cx = $sx;
-		$cy = $sy;
-	} elsif ( $rot == "90" ) {
-		printf(OUT "%i/fs = +y\n", $p);
-		printf(OUT "%i/ss = -x\n", $p);
-		$cx = $sx;
-		$cy = $sy - $a - 5.0;
-	} elsif ( $rot == "180" ) {
-		printf(OUT "%i/fs = +x\n", $p);
-		printf(OUT "%i/ss = +y\n", $p);
-		$cx = $sx - $a - 5.0;
-		$cy = $sy - $b;
-	} elsif ( $rot == "270" ) {
-		printf(OUT "%i/fs = -y\n", $p);
-		printf(OUT "%i/ss = +x\n", $p);
-		$cx = $sx - $b;
-		$cy = $sy;
-	}
-	printf(OUT "%i/corner_x = %5.2f\n", $p, $cx+$global_x);
-	printf(OUT "%i/corner_y = %5.2f\n", $p, $cy+$global_y);
-	printf(OUT "%i/no_index = 0\n", $p);
-	printf(OUT "\n");
-	#if ( ($y < 20) &&  ($x < 1) ) {
-		printf(STDERR "%f %f %f %f\n", $cx, $cy, $sc1, $sc2);
-	#}
-	$x++;
-	$p++;
-
-	printf(OUT "; Quadrant %i, asic %i\n", $quadrant, ($x%2)+2*$y);
-	printf(OUT "%i/min_fs = %i\n", $p, $x*194);
-	printf(OUT "%i/min_ss = %i\n", $p, $y*185);
-	printf(OUT "%i/max_fs = %i\n", $p, ($x+1)*194-1);
-	printf(OUT "%i/max_ss = %i\n", $p, ($y+1)*185-1);
-	printf(OUT "%i/badrow_direction = -\n", $p);
-	printf(OUT "%i/res = 9090.91\n", $p);
-	printf(OUT "%i/peak_sep = 6.0\n", $p);
-	printf(OUT "%i/clen = 77.0e-3\n", $p);
-	if ( $rot == "0" ) {
-		printf(OUT "%i/fs = -x\n", $p);
-		printf(OUT "%i/ss = -y\n", $p);
-		$cx = $sx - $a/2.0 - 5.0;
-		$cy = $sy;
-	} elsif ( $rot == "90" ) {
-		printf(OUT "%i/fs = +y\n", $p);
-		printf(OUT "%i/ss = -x\n", $p);
-		$cx = $sx;
-		$cy = $sy - $a/2.0;
-	} elsif ( $rot == "180" ) {
-		printf(OUT "%i/fs = +x\n", $p);
-		printf(OUT "%i/ss = +y\n", $p);
-		$cx = $sx - $a/2.0;
-		$cy = $sy - $b;
-	} elsif ( $rot == "270" ) {
-		printf(OUT "%i/fs = -y\n", $p);
-		printf(OUT "%i/ss = +x\n", $p);
-		$cx = $sx - $b;
-		$cy = $sy - $a/2.0 - 5.0;
-	}
-	printf(OUT "%i/corner_x = %5.2f\n", $p, $cx+$global_x);
-	printf(OUT "%i/corner_y = %5.2f\n", $p, $cy+$global_y);
-	printf(OUT "%i/no_index = 0\n", $p);
-	printf(OUT "\n");
-	#if ( ($y < 20) &&  ($x < 1) ) {
-		printf(STDERR "%f %f %f %f\n", $cx, $cy, $sc1, $sc2);
-	#}
-	$x++;
-	$p++;
-
-	if ( $x == 8 ) {
-		$x = 0;
-		$y++;
-	}
-
-	$quadrant++;
-	if ( $quadrant == 4 ) {
-		$quadrant = 0;
-	}
-}
diff --git a/scripts/stream-split b/scripts/stream-split
deleted file mode 100755
index 739b341b..00000000
--- a/scripts/stream-split
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/perl -w
-
-use strict;
-
-open(FH, $ARGV[0]);
-open(OFH_IND, "> ".$ARGV[1]);
-open(OFH_PEAKS, "> ".$ARGV[2]);
-
-my $line;
-my $mode = 0;
-
-while ( $line = <FH> ) {
-
-	if ( $line =~ /^Reflections\ from\ indexing/ ) {
-		$mode = 1;
-	}
-
-	if ( $line =~ /^Peaks\ from\ peak\ search/ ) {
-		$mode = 2;
-	}
-
-	if ( $mode == 1 ) {
-		printf(OFH_IND $line);
-	} elsif ( $mode == 2 ) {
-		printf(OFH_PEAKS $line);
-	} else {
-		printf($line);
-	}
-
-}
diff --git a/scripts/test-facetron b/scripts/test-facetron
deleted file mode 100755
index 63efc811..00000000
--- a/scripts/test-facetron
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/sh
-
-echo $1 | ~/crystfel/src/indexamajig --indexing=dirax -i - \
-                      -g ~/crystfel/examples/lcls-dec.geom \
-                      -p ~/lcls/1JB0.pdb \
-                      --near-bragg \
-        | ~/crystfel/src/facetron -g ~/crystfel/examples/lcls-dec.geom
diff --git a/scripts/update-geometry b/scripts/update-geometry
deleted file mode 100755
index 82f961ba..00000000
--- a/scripts/update-geometry
+++ /dev/null
@@ -1,76 +0,0 @@
-#!/usr/bin/perl -w
-
-use strict;
-
-open(FH, $ARGV[0]);
-
-my $done = 0;
-my $cx = 0.0;
-my $cy = 0.0;
-my $pan = 10000000;
-my $min_x;
-my $min_y;
-
-while ( my $line = <FH> ) {
-
-	chomp $line;
-
-	if ( $line =~ /^([0-9]+)\/min_x\ =\ ([0-9,\.\-e]+)$/ ) {
-
-		$pan = $1;
-		$min_x = $2;
-		printf("%i/min_fs = %i\n", $pan, $min_x);
-
-	} elsif ( $line =~ /^([0-9]+)\/min_y\ =\ ([0-9,\.\-e]+)$/ ) {
-
-		if ( $1 != $pan ) {
-			printf(STDERR "Error!\n");
-			exit(1);
-		}
-		$min_y = $2;
-		printf("%i/min_ss = %i\n", $pan, $min_y);
-
-	} elsif ( $line =~ /^([0-9]+)\/max_x\ =\ ([0-9,\.\-e]+)$/ ) {
-
-		if ( $1 != $pan ) {
-			printf(STDERR "Error!\n");
-			exit(1);
-		}
-		printf("%i/max_fs = %i\n", $pan, $2);
-
-	} elsif ( $line =~ /^([0-9]+)\/max_y\ =\ ([0-9,\.\-e]+)$/ ) {
-
-		if ( $1 != $pan ) {
-			printf(STDERR "Error!\n");
-			exit(1);
-		}
-		printf("%i/max_ss = %i\n", $pan, $2);
-
-	} elsif ( $line =~ /^([0-9]+)\/cx\ =\ ([0-9,\.\-e]+)$/ ) {
-
-		$cx = $2;
-		if ( $1 != $pan ) {
-			printf(STDERR "Error!\n");
-			exit(1);
-		}
-
-	} elsif ( $line =~ /^([0-9]+)\/cy\ =\ ([0-9,\.\-e]+)$/ ) {
-
-		$cy = $2;
-		if ( $1 != $pan ) {
-			printf(STDERR "Error!\n");
-			exit(1);
-		}
-
-		printf("%i/corner_x = %5.2f\n", $pan, $min_x - $cx);
-		printf("%i/corner_y = %5.2f\n", $pan, $min_y - $cy);
-		printf("%i/fs = x\n", $pan);
-		printf("%i/ss = y\n", $pan);
-
-	} else {
-		printf("%s\n", $line);
-	}
-
-}
-
-exit($done);
diff --git a/scripts/zone-axis b/scripts/zone-axis
deleted file mode 100755
index a9e77dda..00000000
--- a/scripts/zone-axis
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/perl -w
-
-use strict;
-
-open(FH, $ARGV[0]);
-
-my $line;
-
-while ( $line = <FH> ) {
-
-	if ( $line =~ /^([\d\-]+)\s+([\d\-]+)\s+([\d\-]+)\s+([\d\.\-]+)\s+/ ) {
-
-		my $h = $1;
-		my $k = $2;
-		my $l = $3;
-		my $intensity = $4;
-
-		if ( $l == 0 ) {
-			printf("%3i %3i %3i %f\n", $h, $k, $l, $intensity);
-		}
-
-
-	}
-
-}