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/*
* hdf5.c
*
* Read/write HDF5 data files
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#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"
#include "utils.h"
struct hdfile {
const char *path; /* Current data path */
size_t nx; /* Image width */
size_t ny; /* Image height */
hid_t fh; /* HDF file handle */
hid_t dh; /* Dataset handle */
int data_open; /* True if dh is initialised */
};
struct hdfile *hdfile_open(const char *filename)
{
struct hdfile *f;
f = malloc(sizeof(struct hdfile));
if ( f == NULL ) return NULL;
/* Please stop spamming my terminal */
H5Eset_auto(H5E_DEFAULT, NULL, 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;
}
f->data_open = 0;
return f;
}
int hdfile_set_image(struct hdfile *f, const char *path)
{
hsize_t size[2];
hsize_t max_size[2];
hid_t sh;
f->dh = H5Dopen(f->fh, path, H5P_DEFAULT);
if ( f->dh < 0 ) {
ERROR("Couldn't open dataset\n");
return -1;
}
f->data_open = 1;
sh = H5Dget_space(f->dh);
if ( H5Sget_simple_extent_ndims(sh) != 2 ) {
ERROR("Dataset is not two-dimensional\n");
return -1;
}
H5Sget_simple_extent_dims(sh, size, max_size);
H5Sclose(sh);
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;
}
int get_peaks(struct image *image, struct hdfile *f)
{
hid_t dh, sh;
hsize_t size[2];
hsize_t max_size[2];
int i;
float *buf;
herr_t r;
dh = H5Dopen(f->fh, "/processing/hitfinder/peakinfo", H5P_DEFAULT);
if ( dh < 0 ) {
ERROR("No peak list found!\n");
return 1;
}
sh = H5Dget_space(dh);
if ( sh < 0 ) {
H5Dclose(dh);
ERROR("Couldn't get dataspace for peak list.\n");
return 1;
}
if ( H5Sget_simple_extent_ndims(sh) != 2 ) {
ERROR("Peak list has the wrong dimensionality (%i).\n",
H5Sget_simple_extent_ndims(sh));
H5Sclose(sh);
H5Dclose(dh);
return 1;
}
H5Sget_simple_extent_dims(sh, size, max_size);
if ( size[1] != 3 ) {
H5Sclose(sh);
H5Dclose(dh);
ERROR("Peak list has the wrong dimensions.\n");
return 1;
}
buf = malloc(sizeof(float)*size[0]*size[1]);
if ( buf == NULL ) {
H5Sclose(sh);
H5Dclose(dh);
ERROR("Couldn't reserve memory for the peak list.\n");
return 1;
}
r = H5Dread(dh, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
if ( r < 0 ) {
ERROR("Couldn't read peak list.\n");
free(buf);
return 1;
}
for ( i=0; i<size[0]; i++ ) {
unsigned int x, y;
float val;
x = buf[3*i+0];
y = buf[3*i+1];
val = buf[3*i+2];
STATUS("%i %i %f\n", x, y, val);
image_add_feature(image->features, x, y, image, val, NULL);
}
STATUS("Got %i peaks from peak list.\n", (int)size[0]);
free(buf);
H5Sclose(sh);
H5Dclose(dh);
return 0;
}
static void cleanup(hid_t fh)
{
int n_ids, i;
hid_t ids[256];
n_ids = H5Fget_obj_ids(fh, H5F_OBJ_ALL, 256, ids);
for ( i=0; i<n_ids; i++ ) {
hid_t id;
H5I_type_t type;
id = ids[i];
type = H5Iget_type(id);
if ( type == H5I_GROUP ) H5Gclose(id);
if ( type == H5I_DATASET ) H5Dclose(id);
if ( type == H5I_DATATYPE ) H5Tclose(id);
if ( type == H5I_DATASPACE ) H5Sclose(id);
if ( type == H5I_ATTR ) H5Aclose(id);
}
}
void hdfile_close(struct hdfile *f)
{
if ( f->data_open ) {
H5Dclose(f->dh);
}
cleanup(f->fh);
H5Fclose(f->fh);
free(f);
}
int hdf5_write(const char *filename, const void *data,
int width, int height, int type)
{
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", type, 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, type, 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;
}
static double get_wavelength(struct hdfile *f)
{
herr_t r;
hid_t dh;
double lambda;
dh = H5Dopen(f->fh, "/LCLS/photon_wavelength_nm", H5P_DEFAULT);
if ( dh < 0 ) return -1.0;
r = H5Dread(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
H5P_DEFAULT, &lambda);
H5Dclose(dh);
if ( r < 0 ) return -1.0;
/* Convert nm -> m */
return lambda / 1.0e9;
}
static double get_f0(struct hdfile *f)
{
herr_t r;
hid_t dh;
double f0;
dh = H5Dopen(f->fh, "/LCLS/f_11_ENRC", H5P_DEFAULT);
if ( dh < 0 ) return -1.0;
r = H5Dread(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
H5P_DEFAULT, &f0);
H5Dclose(dh);
if ( r < 0 ) return -1.0;
return f0;
}
static void debodge_saturation(struct hdfile *f, struct image *image)
{
hid_t dh, sh;
hsize_t size[2];
hsize_t max_size[2];
int i;
float *buf;
herr_t r;
dh = H5Dopen(f->fh, "/processing/hitfinder/peakinfo_saturated",
H5P_DEFAULT);
if ( dh < 0 ) {
/* This isn't an error */
STATUS("No saturation table found.\n");
return;
}
sh = H5Dget_space(dh);
if ( sh < 0 ) {
H5Dclose(dh);
ERROR("Couldn't get dataspace for saturation table.\n");
return;
}
if ( H5Sget_simple_extent_ndims(sh) != 2 ) {
ERROR("Saturation table has the wrong dimensionality (%i).\n",
H5Sget_simple_extent_ndims(sh));
H5Sclose(sh);
H5Dclose(dh);
return;
}
H5Sget_simple_extent_dims(sh, size, max_size);
if ( size[1] != 3 ) {
H5Sclose(sh);
H5Dclose(dh);
ERROR("Saturation table has the wrong dimensions.\n");
return;
}
buf = malloc(sizeof(float)*size[0]*size[1]);
if ( buf == NULL ) {
H5Sclose(sh);
H5Dclose(dh);
ERROR("Couldn't reserve memory for saturation table.\n");
return;
}
r = H5Dread(dh, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
if ( r < 0 ) {
ERROR("Couldn't read saturation table.\n");
free(buf);
return;
}
for ( i=0; i<size[0]; i++ ) {
unsigned int x, y;
float val;
x = buf[3*i+0];
y = buf[3*i+1];
val = buf[3*i+2];
image->data[x+image->width*y] = val / 5.0;
image->data[x+1+image->width*y] = val / 5.0;
image->data[x-1+image->width*y] = val / 5.0;
image->data[x+image->width*(y+1)] = val / 5.0;
image->data[x+image->width*(y-1)] = val / 5.0;
}
STATUS("Corrected %i saturation values\n", (int)size[0]);
free(buf);
H5Sclose(sh);
H5Dclose(dh);
}
int hdf5_read(struct hdfile *f, struct image *image, int satcorr)
{
herr_t r;
float *buf;
uint16_t *flags;
hid_t mask_dh;
image->height = f->nx;
image->width = f->ny;
buf = malloc(sizeof(float)*f->nx*f->ny);
r = H5Dread(f->dh, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, buf);
if ( r < 0 ) {
ERROR("Couldn't read data\n");
return 1;
}
image->data = buf;
mask_dh = H5Dopen(f->fh, "/processing/hitfinder/masks", H5P_DEFAULT);
if ( mask_dh <= 0 ) {
ERROR("Couldn't open flags\n");
image->flags = NULL;
} else {
flags = malloc(sizeof(uint16_t)*f->nx*f->ny);
r = H5Dread(mask_dh, H5T_NATIVE_UINT16, H5S_ALL, H5S_ALL,
H5P_DEFAULT, flags);
if ( r < 0 ) {
ERROR("Couldn't read flags\n");
image->flags = NULL;
} else {
image->flags = flags;
}
H5Dclose(mask_dh);
}
/* Read wavelength from file */
image->lambda = get_wavelength(f);
if ( image->lambda < 0.0 ) {
ERROR("Couldn't read wavelength - using 2 keV.\n");
image->lambda = ph_en_to_lambda(eV_to_J(2000.0));
}
image->f0 = get_f0(f);
if ( image->f0 < 0.0 ) {
ERROR("Couldn't read incident intensity - using 1.0.\n");
image->f0 = 1.0;
image->f0_available = 0;
} else {
image->f0_available = 1;
}
if ( satcorr ) debodge_saturation(f, image);
return 0;
}
static int looks_like_image(hid_t h)
{
hid_t sh;
hsize_t size[2];
hsize_t max_size[2];
sh = H5Dget_space(h);
if ( sh < 0 ) return 0;
if ( H5Sget_simple_extent_ndims(sh) != 2 ) {
return 0;
}
H5Sget_simple_extent_dims(sh, size, max_size);
if ( ( size[0] > 64 ) && ( size[1] > 64 ) ) return 1;
return 0;
}
char *hdfile_get_string_value(struct hdfile *f, const char *name)
{
hid_t dh;
hid_t sh;
hsize_t size;
hsize_t max_size;
hid_t type;
hid_t class;
dh = H5Dopen(f->fh, name, H5P_DEFAULT);
if ( dh < 0 ) return NULL;
type = H5Dget_type(dh);
class = H5Tget_class(type);
if ( class == H5T_STRING ) {
herr_t r;
char *tmp;
hid_t sh;
size = H5Tget_size(type);
tmp = malloc(size+1);
sh = H5Screate(H5S_SCALAR);
r = H5Dread(dh, type, sh, sh, H5P_DEFAULT, tmp);
if ( r < 0 ) goto fail;
/* Two possibilities:
* String is already zero-terminated
* String is not terminated.
* Make sure things are done properly... */
tmp[size] = '\0';
chomp(tmp);
return tmp;
}
sh = H5Dget_space(dh);
if ( H5Sget_simple_extent_ndims(sh) != 1 ) goto fail;
H5Sget_simple_extent_dims(sh, &size, &max_size);
if ( size != 1 ) {
H5Dclose(dh);
goto fail;
}
switch ( class ) {
case H5T_FLOAT : {
herr_t r;
double buf;
char *tmp;
r = H5Dread(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
H5P_DEFAULT, &buf);
if ( r < 0 ) goto fail;
tmp = malloc(256);
snprintf(tmp, 255, "%f", buf);
return tmp;
}
case H5T_INTEGER : {
herr_t r;
int buf;
char *tmp;
r = H5Dread(dh, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, &buf);
if ( r < 0 ) goto fail;
tmp = malloc(256);
snprintf(tmp, 255, "%d", buf);
return tmp;
}
default : {
goto fail;
}
}
fail:
H5Tclose(type);
H5Dclose(dh);
return NULL;
}
char **hdfile_read_group(struct hdfile *f, int *n, const char *parent,
int **p_is_group, int **p_is_image)
{
hid_t gh;
hsize_t num;
char **res;
int i;
int *is_group;
int *is_image;
gh = H5Gopen(f->fh, parent, H5P_DEFAULT);
if ( gh < 0 ) {
*n = 0;
return NULL;
}
if ( H5Gget_num_objs(gh, &num) < 0 ) {
/* Whoopsie */
*n = 0;
return NULL;
}
*n = num;
if ( num == 0 ) return NULL; /* Bail out now */
res = malloc(num*sizeof(char *));
is_image = malloc(num*sizeof(int));
is_group = malloc(num*sizeof(int));
*p_is_image = is_image;
*p_is_group = is_group;
for ( i=0; i<num; i++ ) {
char buf[256];
int type;
H5Gget_objname_by_idx(gh, i, buf, 255);
res[i] = malloc(256);
if ( strlen(parent) > 1 ) {
snprintf(res[i], 255, "%s/%s", parent, buf);
} else {
snprintf(res[i], 255, "%s%s", parent, buf);
} /* ick */
type = H5Gget_objtype_by_idx(gh, i);
is_image[i] = 0;
is_group[i] = 0;
if ( type == H5G_GROUP ) {
is_group[i] = 1;
} else if ( type == H5G_DATASET ) {
hid_t dh;
dh = H5Dopen(gh, res[i], H5P_DEFAULT);
is_image[i] = looks_like_image(dh);
H5Dclose(dh);
}
}
return res;
}
int hdfile_set_first_image(struct hdfile *f, const char *group)
{
char **names;
int *is_group;
int *is_image;
int n, i, j;
names = hdfile_read_group(f, &n, group, &is_group, &is_image);
if ( n == 0 ) return 1;
for ( i=0; i<n; i++ ) {
if ( is_image[i] ) {
hdfile_set_image(f, names[i]);
for ( j=0; j<n; j++ ) free(names[j]);
free(is_image);
free(is_group);
free(names);
return 0;
} else if ( is_group[i] ) {
if ( !hdfile_set_first_image(f, names[i]) ) {
for ( j=0; j<n; j++ ) free(names[j]);
free(is_image);
free(is_group);
free(names);
return 0;
}
}
}
for ( j=0; j<n; j++ ) free(names[j]);
free(is_image);
free(is_group);
free(names);
return 1;
}
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