Write an HDF5 file

configure.ac

@@ -18,4 +18,6 @@ AC_FUNC_MALLOC
 AC_TYPE_SIGNAL
 AC_CHECK_FUNCS([strdup])
 
+LIBS="$LIBS -lhdf5"
+
 AC_OUTPUT(Makefile src/Makefile)

src/Makefile.am

 bin_PROGRAMS = template_index simulate_patterns
 
-template_index_SOURCES = main.c relrod.c utils.c image.c cell.c
+template_index_SOURCES = main.c relrod.c utils.c image.c cell.c hdf5-file.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
+simulate_patterns_SOURCES = sim-main.c relrod.c utils.c image.c cell.c \
+                            hdf5-file.c
 simulate_patterns_LDADD = @LIBS@ -lm -lgsl -lgslcblas

src/hdf5-file.c

+/*
+ * hdf5.c
+ *
+ * Read/write HDF5 data files
+ *
+ * (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
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <hdf5.h>
+
+
+int hdf5_write(const char *filename, const uint16_t *data,
+               int width, int height)
+{
+	hid_t fh, gh, sh, dh;	/* File, group, dataspace and data handles */
+	herr_t r;
+	hsize_t size[2];
+	hsize_t max_size[2];
+
+	fh = H5Fcreate(filename, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
+	if ( fh < 0 ) {
+		fprintf(stderr, "Couldn't create file: %s\n", filename);
+		return 1;
+	}
+
+	gh = H5Gcreate(fh, "data", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+	if ( gh < 0 ) {
+		fprintf(stderr, "Couldn't create group\n");
+		H5Fclose(fh);
+		return 1;
+	}
+
+	size[0] = width;
+	size[1] = height;
+	max_size[0] = width;
+	max_size[1] = height;
+	sh = H5Screate_simple(2, size, max_size);
+
+	dh = H5Dcreate(gh, "data", H5T_NATIVE_UINT16, sh,
+	               H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+	if ( dh < 0 ) {
+		fprintf(stderr, "Couldn't create dataset\n");
+		H5Fclose(fh);
+		return 1;
+	}
+
+	/* Muppet check */
+	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]);
+
+	r = H5Dwrite(dh, H5T_NATIVE_UINT16, H5S_ALL,
+	             H5S_ALL, H5P_DEFAULT, data);
+	if ( r < 0 ) {
+		fprintf(stderr, "Couldn't write data\n");
+		H5Dclose(dh);
+		H5Fclose(fh);
+		return 1;
+	}
+
+	H5Fclose(fh);
+
+	return 0;
+}

src/hdf5-file.h

+/*
+ * hdf5.h
+ *
+ * Read/write HDF5 data files
+ *
+ * (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 HDF5_H
+#define HDF5_H
+
+#include <stdint.h>
+
+extern int hdf5_write(const char *filename, const uint16_t *data,
+                      int width, int height);
+
+#endif	/* HDF5_H */

src/image.c

@@ -145,3 +145,20 @@ struct imagefeature *image_feature_closest(ImageFeatureList *flist,
 	*d = +INFINITY;
 	return NULL;
 }
+
+
+int image_feature_count(ImageFeatureList *flist)
+{
+	if ( flist == NULL ) return 0;
+	return flist->n_features;
+}
+
+
+struct imagefeature *image_get_feature(ImageFeatureList *flist, int idx)
+{
+	/* Sanity check */
+	if ( flist == NULL ) return NULL;
+	if ( idx > flist->n_features ) return NULL;
+
+	return &flist->features[idx];
+}

src/image.h

@@ -100,5 +100,7 @@ extern struct imagefeature *image_feature_closest(ImageFeatureList *flist,
                                                   double x, double y, double *d,
                                                   int *idx);
 
+extern int image_feature_count(ImageFeatureList *flist);
+extern struct imagefeature *image_get_feature(ImageFeatureList *flist, int idx);
 
 #endif	/* IMAGE_H */

src/sim-main.c

@@ -24,6 +24,7 @@
 #include "relrod.h"
 #include "cell.h"
 #include "utils.h"
+#include "hdf5-file.h"
 
 
 static void main_show_help(const char *s)
@@ -36,10 +37,11 @@ static void main_show_help(const char *s)
 
 int main(int argc, char *argv[])
 {
-	int c;
+	int c, i;
 	ImageList *list;
 	UnitCell *cell;
 	struct image image;
+	int nrefl;
 
 	while ((c = getopt(argc, argv, "h")) != -1) {
 
@@ -69,14 +71,27 @@ int main(int argc, char *argv[])
 	image.data = malloc(512*512*2);
 	image_add(list, &image);
 
-	cell = cell_new_from_parameters(28.10e-9,
-	                                28.10e-9,
-	                                16.52e-9,
-	                                deg2rad(90.0),
-	                                deg2rad(90.0),
-	                                deg2rad(120.0));
-
+	/* Calculate reflections */
 	get_reflections(&image, cell);
 
+	/* Construct the image */
+	nrefl = image_feature_count(image.rflist);
+	for ( i=0; i<nrefl; i++ ) {
+
+		struct imagefeature *f;
+		int x, y;
+
+		f = image_get_feature(image.rflist, i);
+
+		x = f->x;
+		y = f->y;	/* Discards digits after the decimal point */
+
+		image.data[y*image.width+x] = 1;
+
+	}
+
+	/* Write the output file */
+	hdf5_write("simulated.h5", image.data, image.width, image.height);
+
 	return 0;
 }