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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"
#include "hdf5-file.h"
struct hdfile {
const char *path; /* Current data path */
struct image *image;
size_t nx; /* Image width */
size_t ny; /* Image height */
hid_t fh; /* HDF file handle */
hid_t dh; /* Dataset handle */
hid_t sh; /* Dataspace handle */
};
struct hdfile *hdfile_open(const char *filename)
{
struct hdfile *f;
f = malloc(sizeof(struct hdfile));
if ( f == NULL ) return NULL;
f->fh = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
if ( f->fh < 0 ) {
ERROR("Couldn't open file: %s\n", filename);
free(f);
return NULL;
}
return f;
}
int hdfile_set_image(struct hdfile *f, const char *path)
{
hsize_t size[2];
hsize_t max_size[2];
f->dh = H5Dopen(f->fh, path, H5P_DEFAULT);
if ( f->dh < 0 ) {
ERROR("Couldn't open dataset\n");
return -1;
}
f->sh = H5Dget_space(f->dh);
if ( H5Sget_simple_extent_ndims(f->sh) != 2 ) {
ERROR("Dataset is not two-dimensional\n");
return -1;
}
H5Sget_simple_extent_dims(f->sh, size, max_size);
f->nx = size[0];
f->ny = size[1];
return 0;
}
int hdfile_get_width(struct hdfile *f)
{
return f->nx;
}
int hdfile_get_height(struct hdfile *f)
{
return f->ny;
}
void hdfile_close(struct hdfile *f)
{
H5Fclose(f->fh);
free(f->image);
free(f);
}
static void *hdfile_bin(uint16_t *in, int inw, int inh,
int binning, uint16_t *maxp)
{
uint16_t *data;
int x, y;
int w, h;
uint16_t max;
w = inw / binning;
h = inh / binning; /* Some pixels might get discarded */
data = malloc(w*h*sizeof(uint16_t));
max = 0;
for ( x=0; x<w; x++ ) {
for ( y=0; y<h; y++ ) {
/* Big enough to hold large values */
unsigned long long int total;
size_t xb, yb;
total = 0;
for ( xb=0; xb<binning; xb++ ) {
for ( yb=0; yb<binning; yb++ ) {
total += in[inh*(binning*x+xb)+binning*y+yb];
}
}
data[y+h*(w-1-x)] = total / (binning * binning);
if ( data[y+h*(w-1-x)] > max ) max = data[y+h*(w-1-x)];
}
}
*maxp = max;
return data;
}
uint16_t *hdfile_get_image_binned(struct hdfile *f, int binning, uint16_t *max)
{
struct image *image;
uint16_t *data;
image = malloc(sizeof(struct image));
if ( image == NULL ) return NULL;
hdf5_read(f, image);
f->image = image;
data = hdfile_bin(image->data, f->nx, f->ny, binning, max);
return data;
}
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 ) {
ERROR("Couldn't create file: %s\n", filename);
return 1;
}
gh = H5Gcreate(fh, "data", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if ( gh < 0 ) {
ERROR("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 ) {
ERROR("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 ) {
ERROR("Couldn't write data\n");
H5Dclose(dh);
H5Fclose(fh);
return 1;
}
H5Gclose(gh);
H5Dclose(dh);
H5Fclose(fh);
return 0;
}
int hdf5_read(struct hdfile *f, struct image *image)
{
herr_t r;
uint16_t *buf;
buf = malloc(sizeof(float)*f->nx*f->ny);
r = H5Dread(f->dh, H5T_NATIVE_UINT16, H5S_ALL, H5S_ALL,
H5P_DEFAULT, buf);
if ( r < 0 ) {
ERROR("Couldn't read data\n");
H5Dclose(f->dh);
return 1;
}
image->data = buf;
image->height = f->nx;
image->width = f->ny;
image->x_centre = image->width/2;
image->y_centre = image->height/2;
return 0;
}
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