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|
/*
* hdf5-file.c
*
* Read/write HDF5 data files
*
* Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2009-2012 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
* CrystFEL is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* CrystFEL is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include <hdf5.h>
#include <assert.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_auto2(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 = H5Dopen2(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 get_peaks(struct image *image, struct hdfile *f, const char *p)
{
hid_t dh, sh;
hsize_t size[2];
hsize_t max_size[2];
int i;
float *buf;
herr_t r;
int tw;
dh = H5Dopen2(f->fh, p, H5P_DEFAULT);
if ( dh < 0 ) {
ERROR("Peak list (%s) not found.\n", p);
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);
tw = size[1];
if ( (tw != 3) && (tw != 4) ) {
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;
}
if ( image->features != NULL ) {
image_feature_list_free(image->features);
}
image->features = image_feature_list_new();
for ( i=0; i<size[0]; i++ ) {
float fs, ss, val;
struct panel *p;
fs = buf[tw*i+0];
ss = buf[tw*i+1];
val = buf[tw*i+2];
p = find_panel(image->det, fs, ss);
if ( p == NULL ) continue;
if ( p->no_index ) continue;
image_add_feature(image->features, fs, ss, image, val, NULL);
}
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);
}
/* Deprecated */
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 */
hid_t ph; /* Property list */
herr_t r;
hsize_t 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 = H5Gcreate2(fh, "data", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if ( gh < 0 ) {
ERROR("Couldn't create group\n");
H5Fclose(fh);
return 1;
}
/* Note the "swap" here, according to section 3.2.5,
* "C versus Fortran Dataspaces", of the HDF5 user's guide. */
size[0] = height;
size[1] = width;
sh = H5Screate_simple(2, size, NULL);
/* Set compression */
ph = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(ph, 2, size);
H5Pset_deflate(ph, 3);
dh = H5Dcreate2(gh, "data", type, sh,
H5P_DEFAULT, ph, H5P_DEFAULT);
if ( dh < 0 ) {
ERROR("Couldn't create dataset\n");
H5Fclose(fh);
return 1;
}
/* Muppet check */
H5Sget_simple_extent_dims(sh, size, NULL);
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;
}
H5Dclose(dh);
H5Gclose(gh);
H5Pclose(ph);
H5Fclose(fh);
return 0;
}
int hdf5_write_image(const char *filename, struct image *image)
{
hid_t fh, gh, sh, dh; /* File, group, dataspace and data handles */
hid_t ph; /* Property list */
herr_t r;
hsize_t size[2];
double lambda, eV;
fh = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
if ( fh < 0 ) {
ERROR("Couldn't create file: %s\n", filename);
return 1;
}
gh = H5Gcreate2(fh, "data", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if ( gh < 0 ) {
ERROR("Couldn't create group\n");
H5Fclose(fh);
return 1;
}
/* Note the "swap" here, according to section 3.2.5,
* "C versus Fortran Dataspaces", of the HDF5 user's guide. */
size[0] = image->height;
size[1] = image->width;
sh = H5Screate_simple(2, size, NULL);
/* Set compression */
ph = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(ph, 2, size);
H5Pset_deflate(ph, 3);
dh = H5Dcreate2(gh, "data", H5T_NATIVE_FLOAT, sh,
H5P_DEFAULT, ph, H5P_DEFAULT);
if ( dh < 0 ) {
ERROR("Couldn't create dataset\n");
H5Fclose(fh);
return 1;
}
/* Muppet check */
H5Sget_simple_extent_dims(sh, size, NULL);
r = H5Dwrite(dh, H5T_NATIVE_FLOAT, H5S_ALL,
H5S_ALL, H5P_DEFAULT, image->data);
if ( r < 0 ) {
ERROR("Couldn't write data\n");
H5Dclose(dh);
H5Fclose(fh);
return 1;
}
H5Dclose(dh);
H5Gclose(gh);
gh = H5Gcreate2(fh, "LCLS", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if ( gh < 0 ) {
printf("Couldn't create group\n");
H5Fclose(fh);
return 1;
}
size[0] = 1;
sh = H5Screate_simple(1, size, NULL);
dh = H5Dcreate2(gh, "photon_energy_eV", H5T_NATIVE_DOUBLE, sh,
H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
if ( dh < 0 ) {
H5Fclose(fh);
return 1;
}
eV = ph_lambda_to_eV(image->lambda);
r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
H5S_ALL, H5P_DEFAULT, &eV);
if ( r < 0 ) {
H5Dclose(dh);
H5Fclose(fh);
return 1;
}
H5Dclose(dh);
dh = H5Dcreate2(fh, "/LCLS/photon_wavelength_A", H5T_NATIVE_DOUBLE, sh,
H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
if ( dh < 0 ) {
H5Fclose(fh);
return 1;
}
lambda = image->lambda * 1e10;
r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
H5S_ALL, H5P_DEFAULT, &lambda);
if ( r < 0 ) {
H5Dclose(dh);
H5Fclose(fh);
return 1;
}
H5Dclose(dh);
H5Gclose(gh);
H5Pclose(ph);
H5Fclose(fh);
return 0;
}
static double get_wavelength(struct hdfile *f)
{
herr_t r;
hid_t dh;
double lambda;
int nm = 1;
dh = H5Dopen2(f->fh, "/LCLS/photon_wavelength_nm", H5P_DEFAULT);
if ( dh < 0 ) {
dh = H5Dopen2(f->fh, "/LCLS/photon_wavelength_A", H5P_DEFAULT);
if ( dh < 0 ) {
ERROR("Couldn't get wavelength from HDF5 file.\n");
return -1.0;
}
nm = 0;
}
r = H5Dread(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
H5P_DEFAULT, &lambda);
H5Dclose(dh);
if ( r < 0 ) return -1.0;
if ( isnan(lambda) ) return -1.0;
/* Convert nm -> m */
if ( nm ) return lambda / 1.0e9;
return lambda / 1.0e10;
}
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 = H5Dopen2(f->fh, "/processing/hitfinder/peakinfo_saturated",
H5P_DEFAULT);
if ( dh < 0 ) {
/* This isn't an error */
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 ) {
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;
}
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;
/* Note the "swap" here, according to section 3.2.5,
* "C versus Fortran Dataspaces", of the HDF5 user's guide. */
image->width = f->ny;
image->height = f->nx;
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");
free(buf);
return 1;
}
image->data = buf;
if ( (image->det != NULL) && (image->det->mask != NULL) ) {
mask_dh = H5Dopen2(f->fh, image->det->mask, 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");
free(flags);
image->flags = NULL;
} else {
image->flags = flags;
}
H5Dclose(mask_dh);
}
}
/* Read wavelength from file */
image->lambda = get_wavelength(f);
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;
}
double get_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;
herr_t r;
double buf;
dh = H5Dopen2(f->fh, name, H5P_DEFAULT);
if ( dh < 0 ) {
return 0.0;
}
type = H5Dget_type(dh);
class = H5Tget_class(type);
if ( class != H5T_FLOAT ) {
ERROR("Not a floating point value.\n");
H5Tclose(type);
H5Dclose(dh);
return 0.0;
}
sh = H5Dget_space(dh);
if ( H5Sget_simple_extent_ndims(sh) != 1 ) {
ERROR("Not a scalar value.\n");
H5Tclose(type);
H5Dclose(dh);
return 0.0;
}
H5Sget_simple_extent_dims(sh, &size, &max_size);
if ( size != 1 ) {
ERROR("Not a scalar value.\n");
H5Tclose(type);
H5Dclose(dh);
return 0.0;
}
r = H5Dread(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
H5P_DEFAULT, &buf);
if ( r < 0 ) {
ERROR("Couldn't read value.\n");
H5Tclose(type);
H5Dclose(dh);
return 0.0;
}
return buf;
}
struct copy_hdf5_field
{
char **fields;
int n_fields;
int max_fields;
};
struct copy_hdf5_field *new_copy_hdf5_field_list()
{
struct copy_hdf5_field *n;
n = calloc(1, sizeof(struct copy_hdf5_field));
if ( n == NULL ) return NULL;
n->max_fields = 32;
n->fields = malloc(n->max_fields*sizeof(char *));
if ( n->fields == NULL ) {
free(n);
return NULL;
}
return n;
}
void free_copy_hdf5_field_list(struct copy_hdf5_field *n)
{
int i;
for ( i=0; i<n->n_fields; i++ ) {
free(n->fields[i]);
}
free(n->fields);
free(n);
}
void add_copy_hdf5_field(struct copy_hdf5_field *copyme,
const char *name)
{
/* Need more space? */
if ( copyme->n_fields == copyme->max_fields ) {
char **nfields;
int nmax = copyme->max_fields + 32;
nfields = realloc(copyme->fields, nmax*sizeof(char *));
if ( nfields == NULL ) {
ERROR("Failed to allocate space for new HDF5 field.\n");
return;
}
copyme->max_fields = nmax;
copyme->fields = nfields;
}
copyme->fields[copyme->n_fields] = strdup(name);
if ( copyme->fields[copyme->n_fields] == NULL ) {
ERROR("Failed to add field for copying '%s'\n", name);
return;
}
copyme->n_fields++;
}
void copy_hdf5_fields(struct hdfile *f, const struct copy_hdf5_field *copyme,
FILE *fh)
{
int i;
if ( copyme == NULL ) return;
for ( i=0; i<copyme->n_fields; i++ ) {
char *val;
char *field;
field = copyme->fields[i];
val = hdfile_get_string_value(f, field);
if ( field[0] == '/' ) {
fprintf(fh, "hdf5%s = %s\n", field, val);
} else {
fprintf(fh, "hdf5/%s = %s\n", field, val);
}
free(val);
}
}
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;
herr_t r;
int buf_i;
double buf_f;
char *tmp;
dh = H5Dopen2(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 :
r = H5Dread(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
H5P_DEFAULT, &buf_f);
if ( r < 0 ) goto fail;
tmp = malloc(256);
snprintf(tmp, 255, "%f", buf_f);
return tmp;
case H5T_INTEGER :
r = H5Dread(dh, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, &buf_i);
if ( r < 0 ) goto fail;
tmp = malloc(256);
snprintf(tmp, 255, "%d", buf_i);
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;
H5G_info_t ginfo;
gh = H5Gopen2(f->fh, parent, H5P_DEFAULT);
if ( gh < 0 ) {
*n = 0;
return NULL;
}
if ( H5Gget_info(gh, &ginfo) < 0 ) {
/* Whoopsie */
*n = 0;
return NULL;
}
num = ginfo.nlinks;
*n = num;
if ( num == 0 ) return NULL;
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];
hid_t dh;
H5I_type_t type;
H5Lget_name_by_idx(gh, ".", H5_INDEX_NAME, H5_ITER_NATIVE,
i, buf, 255, H5P_DEFAULT);
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 */
is_image[i] = 0;
is_group[i] = 0;
dh = H5Oopen(gh, buf, H5P_DEFAULT);
if ( dh < 0 ) continue;
type = H5Iget_type(dh);
if ( type == H5I_GROUP ) {
is_group[i] = 1;
} else if ( type == H5I_DATASET ) {
is_image[i] = looks_like_image(dh);
}
H5Oclose(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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