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-rw-r--r--Makefile.am3
-rw-r--r--src/Makefile.am5
-rw-r--r--src/hdf5-file.c58
-rw-r--r--src/hdf5-file.h2
-rw-r--r--src/main.c49
-rw-r--r--src/templates.c140
-rw-r--r--src/templates.h29
7 files changed, 282 insertions, 4 deletions
diff --git a/Makefile.am b/Makefile.am
index c4402796..03aa63dd 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,2 +1,3 @@
-EXTRA_DIST = configure src/reflist.h src/statistics.h
+EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h src/relrod.h \
+ src/templates.h src/utils.h
SUBDIRS = src
diff --git a/src/Makefile.am b/src/Makefile.am
index ccb4527d..40a39194 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,9 +1,10 @@
bin_PROGRAMS = template_index simulate_patterns
-template_index_SOURCES = main.c relrod.c utils.c image.c cell.c hdf5-file.c
+template_index_SOURCES = main.c relrod.c utils.c image.c cell.c hdf5-file.c \
+ templates.c
template_index_LDADD = @LIBS@ -lm -lgsl -lgslcblas
AM_CFLAGS = -Wall -g
simulate_patterns_SOURCES = sim-main.c relrod.c utils.c image.c cell.c \
- hdf5-file.c
+ hdf5-file.c templates.c
simulate_patterns_LDADD = @LIBS@ -lm -lgsl -lgslcblas
diff --git a/src/hdf5-file.c b/src/hdf5-file.c
index 9ece8ada..8a7ffbab 100644
--- a/src/hdf5-file.c
+++ b/src/hdf5-file.c
@@ -19,6 +19,8 @@
#include <stdint.h>
#include <hdf5.h>
+#include "image.h"
+
int hdf5_write(const char *filename, const uint16_t *data,
int width, int height)
@@ -74,3 +76,59 @@ int hdf5_write(const char *filename, const uint16_t *data,
return 0;
}
+
+
+int hdf5_read(struct image *image, const char *filename)
+{
+ hid_t fh, sh, dh; /* File, dataspace and data handles */
+ herr_t r;
+ hsize_t size[2];
+ hsize_t max_size[2];
+ uint16_t *buf;
+
+ fh = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
+ if ( fh < 0 ) {
+ /* TODO: Try other formats here. */
+ fprintf(stderr, "Couldn't open file: %s\n", filename);
+ return 1;
+ }
+
+ dh = H5Dopen(fh, "/data/data", H5P_DEFAULT);
+ if ( dh < 0 ) {
+ fprintf(stderr, "Couldn't open dataset\n");
+ H5Fclose(fh);
+ return 1;
+ }
+
+ sh = H5Dget_space(dh);
+ if ( H5Sget_simple_extent_ndims(sh) != 2 ) {
+ fprintf(stderr, "Dataset is not two-dimensional\n");
+ H5Fclose(fh);
+ return 1;
+ }
+
+ H5Sget_simple_extent_dims(sh, size, max_size);
+ printf("Data dimensions %i %i (max %i %i)\n",
+ (int)size[1], (int)size[0],
+ (int)max_size[1], (int)max_size[0]);
+
+ buf = malloc(sizeof(float)*size[0]*size[1]);
+
+ r = H5Dread(dh, H5T_NATIVE_UINT16, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+ if ( r < 0 ) {
+ fprintf(stderr, "Couldn't read data\n");
+ H5Dclose(dh);
+ H5Fclose(fh);
+ return 1;
+ }
+
+ image->data = buf;
+ image->height = size[0];
+ image->width = size[1];
+ image->x_centre = image->width/2;
+ image->y_centre = image->height/2;
+
+ H5Fclose(fh);
+
+ return 0;
+}
diff --git a/src/hdf5-file.h b/src/hdf5-file.h
index fa0de15f..c288d4cd 100644
--- a/src/hdf5-file.h
+++ b/src/hdf5-file.h
@@ -21,4 +21,6 @@
extern int hdf5_write(const char *filename, const uint16_t *data,
int width, int height);
+extern int hdf5_read(struct image *image, const char *filename);
+
#endif /* HDF5_H */
diff --git a/src/main.c b/src/main.c
index 79dff45a..257a1169 100644
--- a/src/main.c
+++ b/src/main.c
@@ -20,6 +20,12 @@
#include <string.h>
#include <unistd.h>
+#include "cell.h"
+#include "image.h"
+#include "utils.h"
+#include "hdf5-file.h"
+#include "templates.h"
+
static void main_show_help(const char *s)
{
@@ -35,6 +41,9 @@ int main(int argc, char *argv[])
char **in_files;
size_t nin;
size_t i;
+ UnitCell *cell;
+ TemplateList *templates;
+ struct image template_parameters;
while ((c = getopt(argc, argv, "h")) != -1) {
@@ -60,11 +69,49 @@ int main(int argc, char *argv[])
return 1;
}
- printf("Generating templates...\n");
+ /* Define unit cell */
+ cell = cell_new_from_parameters(28.10e-9,
+ 28.10e-9,
+ 16.52e-9,
+ deg2rad(90.0),
+ deg2rad(90.0),
+ deg2rad(120.0));
+
+ /* Generate templates */
+ template_parameters.width = 512;
+ template_parameters.height = 512;
+ template_parameters.fmode = FORMULATION_CLEN;
+ template_parameters.x_centre = 255.5;
+ template_parameters.y_centre = 255.5;
+ template_parameters.camera_len = 0.2; /* 20 cm */
+ template_parameters.resolution = 5120; /* 512 pixels in 10 cm */
+ template_parameters.lambda = 0.2e-9; /* LCLS wavelength */
+ templates = generate_templates(cell, template_parameters);
printf("Input files (%i):\n", nin);
for ( i=0; i<nin; i++ ) {
+
+ struct image image;
+
printf("%6i: %s\n", i+1, in_files[i]);
+
+ image.width = 512;
+ image.height = 512;
+ image.fmode = FORMULATION_CLEN;
+ image.x_centre = 255.5;
+ image.y_centre = 255.5;
+ image.camera_len = 0.2; /* 20 cm */
+ image.resolution = 5120; /* 512 pixels in 10 cm */
+ image.lambda = 0.2e-9; /* LCLS wavelength */
+
+ if ( hdf5_read(&image, in_files[i]) ) {
+ fprintf(stderr, "Couldn't read file '%s'\n",
+ in_files[i]);
+ continue;
+ }
+
+ try_templates(&image, templates);
+
}
return 0;
diff --git a/src/templates.c b/src/templates.c
new file mode 100644
index 00000000..33dc1720
--- /dev/null
+++ b/src/templates.c
@@ -0,0 +1,140 @@
+/*
+ * templates.c
+ *
+ * Handle templates
+ *
+ * (c) 2006-2009 Thomas White <thomas.white@desy.de>
+ *
+ * template_index - Indexing diffraction patterns by template matching
+ *
+ */
+
+
+#define _GNU_SOURCE 1
+#include <stdlib.h>
+#include <assert.h>
+#include <math.h>
+#include <stdio.h>
+
+#include "templates.h"
+#include "cell.h"
+#include "image.h"
+#include "utils.h"
+#include "relrod.h"
+
+
+struct _templatelist
+{
+ int n_templates;
+ struct template *templates;
+};
+
+
+struct template_feature
+{
+ float x;
+ float y;
+ struct template_feature *next;
+};
+
+
+struct template
+{
+ float omega;
+ float tilt;
+ struct template_feature *features;
+};
+
+
+static int template_add(TemplateList *list, struct template *template)
+{
+ if ( list->templates ) {
+ list->templates = realloc(list->templates,
+ (list->n_templates+1)*sizeof(struct template));
+ } else {
+ assert(list->n_templates == 0);
+ list->templates = malloc(sizeof(struct template));
+ }
+
+ /* Copy the data */
+ list->templates[list->n_templates] = *template;
+
+ list->n_templates++;
+
+ return list->n_templates - 1;
+}
+
+
+static TemplateList *template_list_new()
+{
+ TemplateList *list;
+
+ list = malloc(sizeof(TemplateList));
+
+ list->n_templates = 0;
+ list->templates = NULL;
+
+ return list;
+}
+
+
+TemplateList *generate_templates(UnitCell *cell, struct image params)
+{
+ TemplateList *list;
+ double omega, tilt;
+
+ list = template_list_new();
+
+ omega = deg2rad(40.0);
+
+ //for ( omega=deg2rad(-180); omega<deg2rad(180); omega+=deg2rad(1) ) {
+
+ params.omega = omega;
+
+ for ( tilt=0; tilt<deg2rad(180); tilt+=deg2rad(1) ) {
+
+ struct template t;
+ struct template_feature *tfc;
+ int nrefl, i;
+
+ t.omega = omega;
+ t.tilt = tilt;
+ t.features = malloc(sizeof(struct template_feature));
+ t.features->next = NULL;
+ tfc = t.features;
+
+ params.tilt = tilt;
+ get_reflections(&params, cell, 0.01e9);
+
+ nrefl = image_feature_count(params.rflist);
+ for ( i=0; i<nrefl; i++ ) {
+
+ struct imagefeature *f;
+
+ f = image_get_feature(params.rflist, i);
+
+ tfc->x = f->x;
+ tfc->y = f->y;
+ tfc->next = malloc(sizeof(struct template_feature));
+ tfc = tfc->next;
+
+ }
+
+ template_add(list, &t);
+
+ image_feature_list_free(params.rflist);
+
+ printf("Generating templates... %+5.2f %+5.2f\r",
+ rad2deg(omega), rad2deg(tilt));
+
+ }
+ //}
+
+ return list;
+}
+
+
+int try_templates(struct image *image, TemplateList *list)
+{
+ return 0;
+}
diff --git a/src/templates.h b/src/templates.h
new file mode 100644
index 00000000..c4b66171
--- /dev/null
+++ b/src/templates.h
@@ -0,0 +1,29 @@
+/*
+ * templates.h
+ *
+ * Handle templates
+ *
+ * (c) 2006-2009 Thomas White <thomas.white@desy.de>
+ *
+ * template_index - Indexing diffraction patterns by template matching
+ *
+ */
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#ifndef TEMPLATES_H
+#define TEMPLATES_H
+
+#include "cell.h"
+#include "image.h"
+
+/* An opaque type representing a list of templates */
+typedef struct _templatelist TemplateList;
+
+extern TemplateList *generate_templates(UnitCell *cell, struct image params);
+extern int try_templates(struct image *image, TemplateList *list);
+
+#endif /* TEMPLAETS_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-12 13:48:13 +0000