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-rw-r--r--src/Makefile.am2
-rw-r--r--src/dirax.c99
-rw-r--r--src/displaywindow.c35
-rw-r--r--src/hdf5-file.c22
-rw-r--r--src/hdf5-file.h1
-rw-r--r--src/indexamajig.c4
-rw-r--r--src/render.c27
-rw-r--r--src/utils.h4
8 files changed, 174 insertions, 20 deletions
diff --git a/src/Makefile.am b/src/Makefile.am
index 64567c2c..839f7450 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -20,7 +20,7 @@ indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c dirax.c cell.c
indexamajig_LDADD = @LIBS@
if HAVE_GTK
-hdfsee_SOURCES = hdfsee.c displaywindow.c render.c hdf5-file.c utils.c
+hdfsee_SOURCES = hdfsee.c displaywindow.c render.c hdf5-file.c utils.c image.c
hdfsee_LDADD = @LIBS@
endif
diff --git a/src/dirax.c b/src/dirax.c
index c9c5f010..c1794764 100644
--- a/src/dirax.c
+++ b/src/dirax.c
@@ -32,6 +32,7 @@
#include "image.h"
#include "dirax.h"
+#include "utils.h"
typedef enum {
@@ -371,10 +372,13 @@ static int map_position(struct image *image, double x, double y,
}
+#define PEAK_WINDOW_SIZE (10)
+
static void search_peaks(struct image *image)
{
FILE *fh;
- int x, y;
+ int x, y, width;
+ int16_t *data;
fh = fopen("xfel.drx", "w");
if ( !fh ) {
@@ -383,23 +387,96 @@ static void search_peaks(struct image *image)
}
fprintf(fh, "%f\n", 0.5); /* Lie about the wavelength. */
- for ( x=0; x<image->width; x++ ) {
- for ( y=0; y<image->height; y++ ) {
+ data = image->data;
+ width = image->width;
+
+ 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;
+
+ /* 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;
- int val;
+ if ( grad < 2000000 ) continue;
- val = image->data[y+image->height*(image->width-1-x)];
+ mask_x = x;
+ mask_y = y;
- if ( val > 1000 ) {
+ while ( (did_something)
+ && (distance(mask_x, mask_y, x, y)<50) ) {
- double rx, ry, rz;
+ 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, image->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;
+ }
+
+ }
+ }
- /* Map and record reflection */
- map_position(image, x, 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);
+
+ if ( distance(mask_x, mask_y, x, y) > 50.0 ) continue;
+
+ /* Check for a feature at exactly the
+ * same coordinates */
+ //image_feature_closest(flist, 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 */
+ printf("%i %i\n", x, y);
+ map_position(image, x, y, &rx, &ry, &rz);
+ fprintf(fh, "%10f %10f %10f %8f\n",
+ rx/1e10, ry/1e10, rz/1e10, 1.0);
+ //}
+
+ }
+
+
}
}
diff --git a/src/displaywindow.c b/src/displaywindow.c
index 84f89347..9a65fb16 100644
--- a/src/displaywindow.c
+++ b/src/displaywindow.c
@@ -26,6 +26,7 @@
#include "render.h"
#include "hdf5-file.h"
#include "hdfsee.h"
+#include "utils.h"
#define INITIAL_BINNING 2
@@ -399,6 +400,37 @@ static gint displaywindow_set_boostint(GtkWidget *widget, DisplayWindow *dw)
}
+static void load_features_from_file(struct image *image, const char *filename)
+{
+ FILE *fh;
+ char *rval;
+
+ fh = fopen(filename, "r");
+ if ( fh == NULL ) return;
+
+ if ( image->features != NULL ) {
+ image_feature_list_free(image->features);
+ }
+ image->features = image_feature_list_new();
+
+ do {
+ char line[1024];
+ int x, y;
+ int r;
+
+ rval = fgets(line, 1023, fh);
+ if ( rval == NULL ) continue;
+ chomp(line);
+
+ r = sscanf(line, "%i %i", &x, &y);
+ if ( r != 2 ) continue;
+
+ image_add_feature(image->features, x, y, image, 1.0);
+
+ } while ( rval != NULL );
+}
+
+
static gint displaywindow_peaklist_response(GtkWidget *d, gint response,
DisplayWindow *dw)
{
@@ -408,7 +440,8 @@ static gint displaywindow_peaklist_response(GtkWidget *d, gint response,
filename = gtk_file_chooser_get_filename(GTK_FILE_CHOOSER(d));
- load_features_from_file(dw->image);
+ load_features_from_file(hdfile_get_image(dw->hdfile), filename);
+ displaywindow_update(dw);
g_free(filename);
diff --git a/src/hdf5-file.c b/src/hdf5-file.c
index 0e9453cf..509147a0 100644
--- a/src/hdf5-file.c
+++ b/src/hdf5-file.c
@@ -45,6 +45,7 @@ struct hdfile *hdfile_open(const char *filename)
f = malloc(sizeof(struct hdfile));
if ( f == NULL ) return NULL;
+ f->image = NULL;
f->fh = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
if ( f->fh < 0 ) {
@@ -149,18 +150,29 @@ int16_t *hdfile_get_image_binned(struct hdfile *f, int binning, int16_t *max)
struct image *image;
int16_t *data;
- image = malloc(sizeof(struct image));
- if ( image == NULL ) return NULL;
+ if ( f->image == NULL ) {
- hdf5_read(f, image);
- f->image = image;
+ image = malloc(sizeof(struct image));
+ if ( image == NULL ) return NULL;
+ image->features = NULL;
- data = hdfile_bin(image->data, f->nx, f->ny, binning, max);
+ hdf5_read(f, image);
+ f->image = image;
+
+ }
+
+ data = hdfile_bin(f->image->data, f->nx, f->ny, binning, max);
return data;
}
+struct image *hdfile_get_image(struct hdfile *f)
+{
+ return f->image;
+}
+
+
int hdfile_get_unbinned_value(struct hdfile *f, int x, int y, int16_t *val)
{
if ( (x>=f->image->width) || (y>=f->image->height) ) {
diff --git a/src/hdf5-file.h b/src/hdf5-file.h
index a212f677..f0954fbd 100644
--- a/src/hdf5-file.h
+++ b/src/hdf5-file.h
@@ -42,5 +42,6 @@ extern int hdfile_set_first_image(struct hdfile *f, const char *group);
extern void hdfile_close(struct hdfile *f);
extern char *hdfile_get_string_value(struct hdfile *f, const char *name);
+extern struct image *hdfile_get_image(struct hdfile *f);
#endif /* HDF5_H */
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 952433dd..6f09df30 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -176,7 +176,7 @@ static int image_fom(struct image *image)
n_valid = 0;
for ( i=0; i<n_peaks; i++ ) {
if ( peaks[i].invalid ) continue;
- printf("%i %i\n", peaks[i].x, peaks[i].y);
+ //printf("%i %i\n", peaks[i].x, peaks[i].y);
n_valid++;
}
@@ -267,7 +267,7 @@ int main(int argc, char *argv[])
printf("%6i %i\n", n_images, fom);
if ( fom > 0 ) {
- STATUS("Hit: %s\n", line);
+ printf("%s\n", line);
index_pattern(&image);
diff --git a/src/render.c b/src/render.c
index 4de441f3..ce44610c 100644
--- a/src/render.c
+++ b/src/render.c
@@ -89,6 +89,31 @@ static void render_free_data(guchar *data, gpointer p)
free(data);
}
+
+static void show_marked_features(struct image *image, guchar *data,
+ int w, int h, int binning)
+{
+ int i;
+
+ if ( image->features == NULL ) return;
+
+ for ( i=0; i<image_feature_count(image->features); i++ ) {
+
+ struct imagefeature *f;
+ int x, y;
+
+ f = image_get_feature(image->features, i);
+
+ x = f->x; y = f->y;
+
+ x /= binning;
+ y /= binning;
+
+ data[3*( x+w*(h-1-y) )+0] = 255;
+ }
+}
+
+
/* Return a pixbuf containing a rendered version of the image after binning.
* This pixbuf might be scaled later - hopefully mostly in a downward
* direction. */
@@ -144,6 +169,8 @@ GdkPixbuf *render_get_image(struct hdfile *hdfile, int binning, int boostint,
}
}
+ show_marked_features(hdfile_get_image(hdfile), data, w, h, binning);
+
/* Finished with this */
free(hdr);
diff --git a/src/utils.h b/src/utils.h
index 4f1dc86c..9aa07c8c 100644
--- a/src/utils.h
+++ b/src/utils.h
@@ -110,6 +110,10 @@ static inline double distance3d(double x1, double y1, double z1,
#define is_odd(a) ((a)%2==1)
+#define biggest(a,b) ((a>b) ? (a) : (b))
+#define smallest(a,b) ((a<b) ? (a) : (b))
+
+
/* Photon energy (J) to wavelength (m) */
#define ph_en_to_lambda(a) ((PLANCK*C_VACUO)/(a))
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-10 03:20:10 +0000