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-rw-r--r--Makefile.am2
-rw-r--r--src/Makefile.am2
-rw-r--r--src/dirax.c139
-rw-r--r--src/peaks.c138
-rw-r--r--src/peaks.h24
5 files changed, 181 insertions, 124 deletions
diff --git a/Makefile.am b/Makefile.am
index f6fa5efe..0406c2f4 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -2,5 +2,5 @@ EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h src/relrod.h \
src/utils.h src/diffraction.h src/detector.h src/ewald.h \
src/sfac.h src/intensities.h src/reflections.h src/list_tmp.h \
src/statistics.h src/displaywindow.h src/render.h src/hdfsee.h \
- data/displaywindow.ui src/dirax.h
+ data/displaywindow.ui src/dirax.h src/peaks.h
SUBDIRS = src data
diff --git a/src/Makefile.am b/src/Makefile.am
index 9010373c..948d2fbf 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -17,7 +17,7 @@ process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
process_hkl_LDADD = @LIBS@
indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c dirax.c cell.c image.c \
- intensities.c ewald.c
+ intensities.c ewald.c peaks.c
indexamajig_LDADD = @LIBS@
if HAVE_GTK
diff --git a/src/dirax.c b/src/dirax.c
index 070e714d..9930ca03 100644
--- a/src/dirax.c
+++ b/src/dirax.c
@@ -34,6 +34,7 @@
#include "dirax.h"
#include "utils.h"
#include "sfac.h"
+#include "peaks.h"
typedef enum {
@@ -377,13 +378,15 @@ static int map_position(struct image *image, double x, double y,
}
-#define PEAK_WINDOW_SIZE (10)
-
-static void search_peaks(struct image *image, int dump_peaks)
+void index_pattern(struct image *image, int no_index, int dump_peaks)
{
+ unsigned int opts;
+ int saved_stderr;
FILE *fh;
- int x, y, width, height;
- int16_t *data;
+ int i;
+
+ /* Do peak search and splurge out 'xfel.drx' */
+ search_peaks(image, dump_peaks);
fh = fopen("xfel.drx", "w");
if ( !fh ) {
@@ -392,128 +395,20 @@ static void search_peaks(struct image *image, int dump_peaks)
}
fprintf(fh, "%f\n", 0.5); /* Lie about the wavelength. */
- data = image->data;
- width = image->width;
- height = image->height;
-
- if ( image->features != NULL ) {
- image_feature_list_free(image->features);
- }
- image->features = image_feature_list_new();
-
- for ( x=1; x<image->width-1; x++ ) {
- for ( y=1; y<image->height-1; y++ ) {
-
- double dx1, dx2, dy1, dy2;
- double dxs, dys;
- double grad;
- int mask_x, mask_y;
- int sx, sy;
- double max;
- unsigned int did_something = 1;
-
- /* Overall threshold */
- if ( data[x+width*y] < 800 ) continue;
-
- /* Ignore streak */
- if ( abs(x-image->x_centre) < 15 ) continue;
+ for ( i=0; i<image_feature_count(image->features); i++ ) {
- /* Get gradients */
- dx1 = data[x+width*y] - data[(x+1)+width*y];
- dx2 = data[(x-1)+width*y] - data[x+width*y];
- dy1 = data[x+width*y] - data[(x+1)+width*(y+1)];
- dy2 = data[x+width*(y-1)] - data[x+width*y];
+ struct imagefeature *f;
+ double rx = 0.0;
+ double ry = 0.0;
+ double rz = 0.0;
- /* Average gradient measurements from both sides */
- dxs = ((dx1*dx1) + (dx2*dx2)) / 2;
- dys = ((dy1*dy1) + (dy2*dy2)) / 2;
-
- /* Calculate overall gradient */
- grad = dxs + dys;
-
- if ( grad < 2000000 ) continue;
-
- mask_x = x;
- mask_y = y;
-
- while ( (did_something)
- && (distance(mask_x, mask_y, x, y)<50) ) {
-
- max = data[mask_x+width*mask_y];
- did_something = 0;
-
- for ( sy=biggest(mask_y-PEAK_WINDOW_SIZE/2, 0);
- sy<smallest(mask_y+PEAK_WINDOW_SIZE/2, height);
- sy++ ) {
- for ( sx=biggest(mask_x-PEAK_WINDOW_SIZE/2, 0);
- sx<smallest(mask_x+PEAK_WINDOW_SIZE/2, width);
- sx++ ) {
-
- if ( data[sx+width*sy] > max ) {
- max = data[sx+width*sy];
- mask_x = sx;
- mask_y = sy;
- did_something = 1;
- }
-
- }
- }
-
- }
+ f = image_get_feature(image->features, i);
+ map_position(image, f->x, f->y, &rx, &ry, &rz);
+ fprintf(fh, "%10f %10f %10f %8f\n",
+ rx/1e10, ry/1e10, rz/1e10, 1.0);
- if ( !did_something ) {
-
- double d;
- int idx;
-
- assert(mask_x<image->width);
- assert(mask_y<image->height);
- assert(mask_x>=0);
- assert(mask_y>=0);
-
- /* Too far from foot point? */
- if ( distance(mask_x, mask_y, x, y) > 50.0 ) continue;
-
- /* Check for a feature at exactly the
- * same coordinates */
- image_feature_closest(image->features, mask_x, mask_y,
- &d, &idx);
-
- if ( d > 1.0 ) {
-
- double rx = 0.0;
- double ry = 0.0;
- double rz = 0.0;
-
- /* Map and record reflection */
- if ( dump_peaks ) {
- printf("%i %i\n", x, y);
- }
-
- image_add_feature(image->features,
- mask_x, mask_y, image, 1.0);
- map_position(image, x, y, &rx, &ry, &rz);
- fprintf(fh, "%10f %10f %10f %8f\n",
- rx/1e10, ry/1e10, rz/1e10, 1.0);
- }
-
- }
-
-
- }
}
-
fclose(fh);
-}
-
-
-void index_pattern(struct image *image, int no_index, int dump_peaks)
-{
- unsigned int opts;
- int saved_stderr;
-
- /* Do peak search and splurge out 'xfel.drx' */
- search_peaks(image, dump_peaks);
if ( no_index ) return;
diff --git a/src/peaks.c b/src/peaks.c
new file mode 100644
index 00000000..afc05401
--- /dev/null
+++ b/src/peaks.c
@@ -0,0 +1,138 @@
+/*
+ * peaks.c
+ *
+ * Peak search and other image analysis
+ *
+ * (c) 2006-2009 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+#include <string.h>
+#include <assert.h>
+
+#include "image.h"
+#include "utils.h"
+
+
+#define PEAK_WINDOW_SIZE (10)
+
+void search_peaks(struct image *image, int dump_peaks)
+{
+ int x, y, width, height;
+ int16_t *data;
+
+ data = image->data;
+ width = image->width;
+ height = image->height;
+
+ if ( image->features != NULL ) {
+ image_feature_list_free(image->features);
+ }
+ image->features = image_feature_list_new();
+
+ for ( x=1; x<image->width-1; x++ ) {
+ for ( y=1; y<image->height-1; y++ ) {
+
+ double dx1, dx2, dy1, dy2;
+ double dxs, dys;
+ double grad;
+ int mask_x, mask_y;
+ int sx, sy;
+ double max;
+ unsigned int did_something = 1;
+
+ /* Overall threshold */
+ if ( data[x+width*y] < 800 ) continue;
+
+ /* Ignore streak */
+ if ( abs(x-image->x_centre) < 15 ) continue;
+
+ /* Get gradients */
+ dx1 = data[x+width*y] - data[(x+1)+width*y];
+ dx2 = data[(x-1)+width*y] - data[x+width*y];
+ dy1 = data[x+width*y] - data[(x+1)+width*(y+1)];
+ dy2 = data[x+width*(y-1)] - data[x+width*y];
+
+ /* Average gradient measurements from both sides */
+ dxs = ((dx1*dx1) + (dx2*dx2)) / 2;
+ dys = ((dy1*dy1) + (dy2*dy2)) / 2;
+
+ /* Calculate overall gradient */
+ grad = dxs + dys;
+
+ if ( grad < 2000000 ) continue;
+
+ mask_x = x;
+ mask_y = y;
+
+ while ( (did_something)
+ && (distance(mask_x, mask_y, x, y)<50) ) {
+
+ max = data[mask_x+width*mask_y];
+ did_something = 0;
+
+ for ( sy=biggest(mask_y-PEAK_WINDOW_SIZE/2, 0);
+ sy<smallest(mask_y+PEAK_WINDOW_SIZE/2, height);
+ sy++ ) {
+ for ( sx=biggest(mask_x-PEAK_WINDOW_SIZE/2, 0);
+ sx<smallest(mask_x+PEAK_WINDOW_SIZE/2, width);
+ sx++ ) {
+
+ if ( data[sx+width*sy] > max ) {
+ max = data[sx+width*sy];
+ mask_x = sx;
+ mask_y = sy;
+ did_something = 1;
+ }
+
+ }
+ }
+
+ }
+
+ if ( !did_something ) {
+
+ double d;
+ int idx;
+
+ assert(mask_x<image->width);
+ assert(mask_y<image->height);
+ assert(mask_x>=0);
+ assert(mask_y>=0);
+
+ /* Too far from foot point? */
+ if ( distance(mask_x, mask_y, x, y) > 50.0 ) continue;
+
+ /* Check for a feature at exactly the
+ * same coordinates */
+ image_feature_closest(image->features, mask_x, mask_y,
+ &d, &idx);
+
+ if ( d > 1.0 ) {
+
+ /* Map and record reflection */
+ if ( dump_peaks ) {
+ printf("%i %i\n", x, y);
+ }
+
+ image_add_feature(image->features,
+ mask_x, mask_y, image, 1.0);
+
+ }
+
+ }
+
+
+ }
+ }
+}
diff --git a/src/peaks.h b/src/peaks.h
new file mode 100644
index 00000000..d7bbca4d
--- /dev/null
+++ b/src/peaks.h
@@ -0,0 +1,24 @@
+/*
+ * peaks.h
+ *
+ * Peak search and other image analysis
+ *
+ * (c) 2006-2009 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+
+#ifndef PEAKS_H
+#define PEAKS_H
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+extern void search_peaks(struct image *image, int dump_peaks);
+
+
+#endif /* PEAKS_H */
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