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authorThomas White <taw@bitwiz.org.uk>2009-10-14 18:30:49 +0200
committerThomas White <taw@bitwiz.org.uk>2009-10-14 18:30:49 +0200
commit69b33e88a4ebecc5bc6e2dae8b35643f26cdb22d (patch)
tree4ca274d0990c827486dc2ebfc99ab5723dd382ef /src
parent4e1e2ef4472e28a146e6c83d053f1fc4d2419f88 (diff)
Write an HDF5 file
Diffstat (limited to 'src')
-rw-r--r--src/Makefile.am5
-rw-r--r--src/hdf5-file.c76
-rw-r--r--src/hdf5-file.h24
-rw-r--r--src/image.c17
-rw-r--r--src/image.h2
-rw-r--r--src/sim-main.c31
6 files changed, 145 insertions, 10 deletions
diff --git a/src/Makefile.am b/src/Makefile.am
index 46a5e9d9..ccb4527d 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,8 +1,9 @@
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
diff --git a/src/hdf5-file.c b/src/hdf5-file.c
new file mode 100644
index 00000000..2992357d
--- /dev/null
+++ b/src/hdf5-file.c
@@ -0,0 +1,76 @@
+/*
+ * 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;
+}
diff --git a/src/hdf5-file.h b/src/hdf5-file.h
new file mode 100644
index 00000000..fa0de15f
--- /dev/null
+++ b/src/hdf5-file.h
@@ -0,0 +1,24 @@
+/*
+ * 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 */
diff --git a/src/image.c b/src/image.c
index d3e65685..b7cf4c31 100644
--- a/src/image.c
+++ b/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];
+}
diff --git a/src/image.h b/src/image.h
index fc8a1f2f..41e6e2b6 100644
--- a/src/image.h
+++ b/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 */
diff --git a/src/sim-main.c b/src/sim-main.c
index 23ba3e99..af7f57bd 100644
--- a/src/sim-main.c
+++ b/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;
}