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/*
* hdf5.c
*
* Read/write HDF5 data files
*
* (c) 2006-2009 Thomas White <thomas.white@desy.de>
*
* pattern_sim - Simulate diffraction patterns from small crystals
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include <hdf5.h>
#include "image.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_TRUNC, 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);
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;
}
H5Gclose(gh);
H5Dclose(dh);
H5Fclose(fh);
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);
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;
}
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