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-rwxr-xr-xscripts/frequency165
-rw-r--r--src/process_hkl.c104
2 files changed, 114 insertions, 155 deletions
diff --git a/scripts/frequency b/scripts/frequency
index 26e29bb4..d6caf72c 100755
--- a/scripts/frequency
+++ b/scripts/frequency
@@ -2,168 +2,37 @@
use strict;
-my $bins = 200;
my $nplots = 32;
+my $sym = "6/mmm";
-open(FH, $ARGV[0]);
+my $stream = $ARGV[0];
-my $line;
-my %counts;
-
-# --- Step 1: Count reflections and find the most popular ones
-
-while ( $line = <FH> ) {
-
- my $h;
- my $k;
- my $l;
-
- chomp($line);
-
- if ( $line =~ /^\s+(\d+)\s+(\d+)\s+(\d+)/ ) {
-
- my $key;
-
- $h = $1;
- $k = $2;
- $l = $3;
-
- $key = $h.",".$k.",".$l;
- $counts{$key}++;
-
- }
-
-}
-
-my $ref;
-my $i;
-$i = 0;
-foreach $ref ( sort {-($counts{$a} <=> $counts{$b})} keys %counts )
-{
- $i++;
- if ( $i > $nplots ) {
- delete($counts{$ref});
- } else {
- printf("%s %i\n", $ref, $counts{$ref});
- }
-}
-
-
-# --- Step 2: Work out histogram bins for each reflection
-
-seek(FH, 0, 0);
-
-my %mins;
-my %maxs;
+#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> ) {
- my $key;
- my $intensity;
-
- chomp($line);
-
- if ( $line =~ /^\s+(\d+)\s+(\d+)\s+(\d+)\s+([\d\.]+)/ ) {
-
- my $h;
- my $k;
- my $l;
+ chomp $line;
- $h = $1;
- $k = $2;
- $l = $3;
- $intensity = $4;
-
- $key = $h.",".$k.",".$l;
-
- next unless exists($counts{$key});
-
- unless ( exists($mins{$key}) ) {
- $mins{$key} = $intensity;
- }
- unless ( exists($maxs{$key}) ) {
- $maxs{$key} = $intensity;
- }
- if ( $intensity < $mins{$key} ) {
- $mins{$key} = $intensity;
- }
- if ( $intensity > $maxs{$key} ) {
- $maxs{$key} = $intensity;
- }
-
- }
-
-}
-
-# --- Step 3: Bin the counts and plot
-
-open(GP, "| gnuplot");
-printf(GP "set term postscript enhanced font \"Helvetica,20\"\n");
-printf(GP "set output \"histo.ps\"\n");
-printf(GP "set xtics nomirror out rotate by -60\n");
-#printf(GP "set logscale x\n");
-foreach $ref ( sort {-($counts{$a} <=> $counts{$b})} keys %counts )
-{
- my $max = $maxs{$ref};
- my $min = $mins{$ref};
- my $binsize = ($max+1-$min)/$bins;
- my @hist;
-
- printf("%s %f -> %f\n", $ref, $mins{$ref}, $maxs{$ref});
-
- for ( $i=0; $i<$bins; $i++ ) {
- $hist[$i] = 0;
- }
-
- seek(FH, 0, 0);
- while ( $line = <FH> ) {
-
- my $bin;
- my $h;
- my $k;
- my $l;
- my $intensity;
-
- chomp($line);
-
- if ( $line =~ /^\s+(\d+)\s+(\d+)\s+(\d+)\s+([\d\.]+)/ ) {
-
- my $key;
+ if ( $line =~ /\s+(\d+)$/ ) {
+ my $n = $1;
+ if ( $n > $max ) {
+ $line =~ /^\s+(\d+)\s+(\d+)\s+(\d+)\s+/;
$h = $1;
$k = $2;
$l = $3;
- $intensity = $4;
-
- $key = $h.",".$k.",".$l;
-
- next unless ( $ref eq $key );
-
- $bin = int(($intensity-$min)/$binsize);
- $hist[$bin]++;
-
+ $max = $n;
}
}
-
- open(OFH, "> ".$ref.".dat");
- for ( $i=0; $i<$bins; $i++ ) {
- printf(OFH "%f\t%i\n", $min+(($i+0.5)*$binsize), $hist[$i]);
- }
- close(OFH);
-
- my $nref = $ref;
- $nref =~ s/\,/\ /g;
- my $title = "t \"".$nref." reflection\"";
- printf(GP "plot [] [0:20]\"".$ref.".dat\" u 1:2 w histeps ".$title."\n");
-
}
-close(FH);
-close(GP);
+printf("%i %i %i = %i\n", $h, $k, $l, $max);
-foreach $ref ( sort {-($counts{$a} <=> $counts{$b})} keys %counts ) {
- unlink($ref.".dat");
-}
-system("ps2pdf histo.ps");
-unlink("histo.ps");
+exit 0;
diff --git a/src/process_hkl.c b/src/process_hkl.c
index ec23e1cd..05c71985 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -29,8 +29,8 @@
#include "symmetry.h"
-/* Number of divisions for R vs |q| graphs */
-#define RVQDV (20)
+/* Number of divisions for intensity histograms */
+#define NBINS (200)
static void show_help(const char *s)
@@ -56,6 +56,8 @@ static void show_help(const char *s)
" --stop-after=<n> Stop after processing n patterns. Zero means\n"
" keep going until the end of the input, and is\n"
" the default.\n"
+" -g, --histogram=<h,k,l> Calculate the histogram of measurements for this\n"
+" reflection.\n"
"\n"
" --scale Scale each pattern for best fit with the current\n"
" model.\n"
@@ -64,6 +66,47 @@ static void show_help(const char *s)
}
+static void plot_histogram(double *vals, int n)
+{
+ int i;
+ double max = -INFINITY;
+ double min = +INFINITY;
+ double step;
+ int histo[NBINS];
+ FILE *fh;
+
+ fh = fopen("histogram.dat", "w");
+ if ( fh == NULL ) {
+ ERROR("Couldn't open 'histogram.dat'\n");
+ return;
+ }
+
+ for ( i=0; i<n; i++ ) {
+ if ( vals[i] > max ) max = vals[i];
+ if ( vals[i] < min ) min = vals[i];
+ }
+ STATUS("%f %f\n", min, max);
+
+ for ( i=0; i<NBINS; i++ ) {
+ histo[i] = 0;
+ }
+
+ step = (max-min)/NBINS;
+
+ for ( i=0; i<n; i++ ) {
+ int bin;
+ bin = (vals[i]-min)/step;
+ histo[bin]++;
+ }
+
+ for ( i=0; i<NBINS; i++ ) {
+ fprintf(fh, "%f %i\n", min+step*i, histo[i]);
+ }
+
+ fclose(fh);
+}
+
+
/* Note "holo" needn't actually be a holohedral point group, if you want to try
* something strange like resolving from a low-symmetry group into an even
* lower symmetry one.
@@ -160,7 +203,9 @@ static void merge_pattern(double *model, ReflItemList *observed,
const double *new, ReflItemList *items,
unsigned int *model_counts, int mo,
ReflItemList *twins,
- const char *holo, const char *mero)
+ const char *holo, const char *mero, double *hist_vals,
+ signed int hist_h, signed int hist_k,
+ signed int hist_l, int *hist_n)
{
int i;
int twin;
@@ -216,6 +261,14 @@ static void merge_pattern(double *model, ReflItemList *observed,
/* Increase count count */
integrate_count(model_counts, h, k, l, 1);
+ if ( hist_vals != NULL ) {
+ int p = *hist_n;
+ if ( (h==hist_h) && (k==hist_k) && (l==hist_l) ) {
+ hist_vals[p] = intensity;
+ *hist_n = p+1;
+ }
+ }
+
}
/* Dump the reflections in this pattern into the overall list */
@@ -230,7 +283,9 @@ static void merge_all(FILE *fh, double **pmodel, ReflItemList **pobserved,
int config_maxonly, int config_scale, int config_sum,
int config_stopafter,
ReflItemList *twins, const char *holo, const char *mero,
- int n_total_patterns)
+ int n_total_patterns, double *hist_vals,
+ signed int hist_h, signed int hist_k, signed int hist_l,
+ int *hist_i)
{
char *rval;
float f0;
@@ -277,7 +332,9 @@ static void merge_all(FILE *fh, double **pmodel, ReflItemList **pobserved,
/* Start of second or later pattern */
merge_pattern(model, observed, new_pattern, items,
counts, config_maxonly,
- twins, holo, mero);
+ twins, holo, mero,
+ hist_vals, hist_h, hist_k, hist_l,
+ hist_i);
if ( n_patterns == config_stopafter ) break;
@@ -380,6 +437,10 @@ int main(int argc, char *argv[])
ReflItemList *observed;
int i;
const char *holo = NULL;
+ char *histo = NULL;
+ signed int hist_h, hist_k, hist_l;
+ double *hist_vals = NULL;
+ int hist_i;
/* Long options */
const struct option longopts[] = {
@@ -393,11 +454,12 @@ int main(int argc, char *argv[])
{"scale", 0, &config_scale, 1},
{"symmetry", 1, NULL, 'y'},
{"pdb", 1, NULL, 'p'},
+ {"histogram", 1, NULL, 'g'},
{0, 0, NULL, 0}
};
/* Short options */
- while ((c = getopt_long(argc, argv, "hi:e:ro:p:y:",
+ while ((c = getopt_long(argc, argv, "hi:e:ro:p:y:g:",
longopts, NULL)) != -1) {
switch (c) {
@@ -425,6 +487,10 @@ int main(int argc, char *argv[])
sym = strdup(optarg);
break;
+ case 'g' :
+ histo = strdup(optarg);
+ break;
+
case 0 :
break;
@@ -475,6 +541,22 @@ int main(int argc, char *argv[])
holo = strdup("1");
}
+ if ( histo != NULL ) {
+ int r;
+ r = sscanf(histo, "%i,%i,%i", &hist_h, &hist_k, &hist_l);
+ if ( r != 3 ) {
+ ERROR("Invalid indices for '--histogram'\n");
+ return 1;
+ }
+ hist_vals = malloc(10*1024*sizeof(double));
+ free(histo);
+ STATUS("Histogramming %i %i %i -> ", hist_h, hist_k, hist_l);
+ /* Put into the asymmetric cell for the target group */
+ get_asymm(hist_h, hist_k, hist_l,
+ &hist_h, &hist_k, &hist_l, sym);
+ STATUS("%i %i %i\n", hist_h, hist_k, hist_l);
+ }
+
/* Open the data stream */
if ( strcmp(filename, "-") == 0 ) {
fh = stdin;
@@ -492,13 +574,21 @@ int main(int argc, char *argv[])
STATUS("There are %i patterns to process\n", n_total_patterns);
rewind(fh);
+ hist_i = 0;
merge_all(fh, &model, &observed, &counts,
config_maxonly, config_scale, config_sum, config_stopafter,
- twins, holo, sym, n_total_patterns);
+ twins, holo, sym, n_total_patterns,
+ hist_vals, hist_h, hist_k, hist_l, &hist_i);
rewind(fh);
fclose(fh);
+ if ( hist_vals != NULL ) {
+ STATUS("%i %i %i was seen %i times.\n", hist_h, hist_k, hist_l,
+ hist_i);
+ plot_histogram(hist_vals, hist_i);
+ }
+
if ( output != NULL ) {
write_reflections(output, observed, model, NULL, counts, cell);
}