Actually get rid of hdf5-file

3 files changed, 0 insertions, 1103 deletions

diff --git a/libcrystfel/CMakeLists.txt b/libcrystfel/CMakeLists.txt
index b3953dbe..efbac466 100644
--- a/libcrystfel/CMakeLists.txt
+++ b/libcrystfel/CMakeLists.txt
@@ -35,7 +35,6 @@ set(LIBCRYSTFEL_SOURCES
     src/cell.c
     src/thread-pool.c
     src/image.c
-    src/hdf5-file.c
     src/geometry.c
     src/peakfinder8.c
     src/symmetry.c
@@ -75,7 +74,6 @@ if (HAVE_FFTW)
 endif (HAVE_FFTW)
 
 set(LIBCRYSTFEL_HEADERS
-    src/hdf5-file.h
     src/reflist.h
     src/symmetry.h
     src/cell.h
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
deleted file mode 100644
index 1b156c54..00000000
--- a/libcrystfel/src/hdf5-file.c
+++ /dev/null
@@ -1,1020 +0,0 @@
-/*
- * hdf5-file.c
- *
- * Read/write HDF5 data files
- *
- * Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
- *                       a research centre of the Helmholtz Association.
- *
- * Authors:
- *   2009-2016 Thomas White <taw@physics.org>
- *   2014      Valerio Mariani
- *
- * 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 <unistd.h>
-
-#include "events.h"
-#include "image.h"
-#include "hdf5-file.h"
-#include "utils.h"
-
-/** \file hdf5-file.h */
-
-struct hdf5_write_location {
-
-	const char      *location;
-	int              n_panels;
-	int             *panel_idxs;
-
-	int              max_ss;
-	int              max_fs;
-
-};
-
-
-struct hdfile {
-
-	const char      *path;  /* Current data path */
-
-	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;
-
-	if ( access( filename, R_OK ) == -1 ) {
-		ERROR("File does not exist or cannot be read: %s\n",
-		      filename);
-		free(f);
-		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;
-	}
-
-	f->data_open = 0;
-	return f;
-}
-
-
-int hdfile_set_image(struct hdfile *f, const char *path)
-{
-	f->dh = H5Dopen2(f->fh, path, H5P_DEFAULT);
-	if ( f->dh < 0 ) {
-		ERROR("Couldn't open dataset\n");
-		return -1;
-	}
-	f->data_open = 1;
-	return 0;
-}
-
-
-static void add_panel_to_location(struct hdf5_write_location *loc,
-                                  struct panel *p, int pi)
-{
-	int *new_panel_idxs;
-
-	new_panel_idxs = realloc(loc->panel_idxs,
-	                         (loc->n_panels+1)*sizeof(int));
-	if ( new_panel_idxs == NULL ) {
-		ERROR("Error while managing write location list.\n");
-		return;
-	}
-	loc->panel_idxs = new_panel_idxs;
-	loc->panel_idxs[loc->n_panels] = pi;
-	loc->n_panels += 1;
-	if ( p->orig_max_fs > loc->max_fs ) {
-		loc->max_fs = p->orig_max_fs;
-	}
-	if ( p->orig_max_ss > loc->max_ss ) {
-		loc->max_ss = p->orig_max_ss;
-	}
-}
-
-
-static void add_panel_location(struct panel *p, const char *p_location, int pi,
-                               struct hdf5_write_location **plocations,
-                               int *pnum_locations)
-{
-	int li;
-	int num_locations = *pnum_locations;
-	struct hdf5_write_location *locations = *plocations;
-	int done = 0;
-
-	/* Does this HDF5 path already exist in the location list?
-	 * If so, add the new panel to it (with a unique index, we hope) */
-	for ( li=0; li<num_locations; li++ ) {
-		if ( strcmp(p_location, locations[li].location) == 0 ) {
-			add_panel_to_location(&locations[li], p, pi);
-			done = 1;
-		}
-	}
-
-	/* If not, add a new location to ths list */
-	if ( !done ) {
-
-		struct hdf5_write_location *new_locations;
-		size_t nsz;
-
-		nsz = (num_locations+1)*sizeof(struct hdf5_write_location);
-		new_locations = realloc(locations, nsz);
-		if ( new_locations == NULL ) {
-			ERROR("Failed to grow location list.\n");
-			return;
-		}
-		locations = new_locations;
-
-		locations[num_locations].max_ss = p->orig_max_ss;
-		locations[num_locations].max_fs = p->orig_max_fs;
-		locations[num_locations].location = p_location;
-		locations[num_locations].panel_idxs = malloc(sizeof(int));
-		if ( locations[num_locations].panel_idxs == NULL ) {
-			ERROR("Failed to allocate single idx (!)\n");
-			return;
-		}
-		locations[num_locations].panel_idxs[0] = pi;
-		locations[num_locations].n_panels = 1;
-
-		num_locations += 1;
-
-	}
-
-	*plocations = locations;
-	*pnum_locations = num_locations;
-}
-
-
-static struct hdf5_write_location *make_location_list(struct detector *det,
-                                                      const char *def_location,
-                                                      int *pnum_locations)
-{
-	int pi;
-	struct hdf5_write_location *locations = NULL;
-	int num_locations = 0;
-
-	for ( pi=0; pi<det->n_panels; pi++ ) {
-
-		struct panel *p;
-		const char *p_location;
-
-		p = &det->panels[pi];
-
-		if ( p->data == NULL ) {
-			p_location = def_location;
-		} else {
-			p_location = p->data;
-		}
-
-		add_panel_location(p, p_location, pi,
-		                   &locations, &num_locations);
-
-	}
-
-	*pnum_locations = num_locations;
-	return locations;
-}
-
-
-static void write_location(hid_t fh, struct detector *det, float **dp,
-                           struct hdf5_write_location *loc)
-{
-	hid_t sh, dh, ph;
-	hid_t dh_dataspace;
-	hsize_t size[2];
-	int pi;
-
-	/* Note the "swap" here, according to section 3.2.5,
-	 * "C versus Fortran Dataspaces", of the HDF5 user's guide. */
-	size[0] = loc->max_ss+1;
-	size[1] = loc->max_fs+1;
-	sh = H5Screate_simple(2, size, NULL);
-
-	ph = H5Pcreate(H5P_LINK_CREATE);
-	H5Pset_create_intermediate_group(ph, 1);
-
-	dh = H5Dcreate2(fh, loc->location, H5T_NATIVE_FLOAT, sh,
-	                ph, H5P_DEFAULT, H5P_DEFAULT);
-	if ( dh < 0 ) {
-		ERROR("Couldn't create dataset\n");
-		H5Fclose(fh);
-		return;
-	}
-
-	H5Sget_simple_extent_dims(sh, size, NULL);
-
-	for ( pi=0; pi<loc->n_panels; pi++ ) {
-
-		hsize_t f_offset[2], f_count[2], dims[2];
-		hid_t memspace;
-		struct panel p;
-		int r;
-
-		p = det->panels[loc->panel_idxs[pi]];
-
-		f_offset[0] = p.orig_min_ss;
-		f_offset[1] = p.orig_min_fs;
-		f_count[0] = p.orig_max_ss - p.orig_min_ss +1;
-		f_count[1] = p.orig_max_fs - p.orig_min_fs +1;
-
-		dh_dataspace = H5Dget_space(dh);
-		r = H5Sselect_hyperslab(dh_dataspace, H5S_SELECT_SET,
-		                        f_offset, NULL, f_count, NULL);
-		if ( r < 0 ) {
-			ERROR("Error selecting file dataspace "
-			      "for panel %s\n", p.name);
-			H5Pclose(ph);
-			H5Dclose(dh);
-			H5Sclose(dh_dataspace);
-			H5Sclose(sh);
-			H5Fclose(fh);
-			return;
-		}
-
-		dims[0] = p.h;
-		dims[1] = p.w;
-		memspace = H5Screate_simple(2, dims, NULL);
-
-		r = H5Dwrite(dh, H5T_NATIVE_FLOAT, memspace, dh_dataspace,
-		             H5P_DEFAULT, dp[loc->panel_idxs[pi]]);
-		if ( r < 0 ) {
-			ERROR("Couldn't write data\n");
-			H5Pclose(ph);
-			H5Dclose(dh);
-			H5Sclose(dh_dataspace);
-			H5Sclose(memspace);
-			H5Sclose(sh);
-			H5Fclose(fh);
-			return;
-		}
-
-		H5Sclose(dh_dataspace);
-		H5Sclose(memspace);
-	}
-	H5Pclose(ph);
-	H5Sclose(sh);
-	H5Dclose(dh);
-}
-
-
-static void write_photon_energy(hid_t fh, double eV, const char *ph_en_loc)
-{
-	hid_t ph, sh, dh;
-	hsize_t size1d[1];
-	int r;
-
-	ph = H5Pcreate(H5P_LINK_CREATE);
-	H5Pset_create_intermediate_group(ph, 1);
-
-	size1d[0] = 1;
-	sh = H5Screate_simple(1, size1d, NULL);
-
-	dh = H5Dcreate2(fh, ph_en_loc, H5T_NATIVE_DOUBLE, sh,
-	                ph, H5S_ALL, H5P_DEFAULT);
-	if ( dh < 0 ) {
-		ERROR("Couldn't create dataset for photon energy.\n");
-		return;
-	}
-	r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &eV);
-	if ( r < 0 ) {
-		ERROR("Couldn't write photon energy.\n");
-		/* carry on */
-	}
-
-	H5Pclose(ph);
-	H5Dclose(dh);
-}
-
-
-static void write_spectrum(hid_t fh, Spectrum *s)
-{
-	herr_t r;
-	double *arr;
-	int i;
-	hid_t sh, dh, ph;
-	double kmin, kmax, step;
-	const hsize_t n = 1024;
-
-	ph = H5Pcreate(H5P_LINK_CREATE);
-	H5Pset_create_intermediate_group(ph, 1);
-
-	arr = malloc(n*sizeof(double));
-	if ( arr == NULL ) {
-		ERROR("Failed to allocate memory for spectrum.\n");
-		return;
-	}
-
-	/* Save the wavelength values */
-	spectrum_get_range(s, &kmin, &kmax);
-	step = (kmax-kmin)/n;
-	for ( i=0; i<n; i++ ) {
-		arr[i] = 1.0e10/(kmin+i*step);
-	}
-
-	sh = H5Screate_simple(1, &n, NULL);
-
-	dh = H5Dcreate2(fh, "/spectrum/wavelengths_A", H5T_NATIVE_DOUBLE,
-	                sh, ph, H5S_ALL, H5P_DEFAULT);
-	if ( dh < 0 ) {
-		ERROR("Failed to create dataset for spectrum wavelengths.\n");
-		return;
-	}
-	r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
-		     H5S_ALL, H5P_DEFAULT, arr);
-	if ( r < 0 ) {
-		ERROR("Failed to write spectrum wavelengths.\n");
-		return;
-	}
-	H5Dclose(dh);
-
-	/* Save the probability density values */
-	for ( i=0; i<n; i++ ) {
-		arr[i] = spectrum_get_density_at_k(s, kmin+i*step);
-	}
-
-	dh = H5Dcreate2(fh, "/spectrum/pdf", H5T_NATIVE_DOUBLE, sh,
-		        H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
-	if ( dh < 0 ) {
-		ERROR("Failed to create dataset for spectrum p.d.f.\n");
-		return;
-	}
-	r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
-		     H5S_ALL, H5P_DEFAULT, arr);
-	if ( r < 0 ) {
-		ERROR("Failed to write spectrum p.d.f.\n");
-		return;
-	}
-
-	H5Dclose(dh);
-	H5Pclose(ph);
-	free(arr);
-}
-
-
-int hdf5_write_image(const char *filename, const struct image *image,
-                     char *element)
-{
-	hid_t fh;
-	int li;
-	char *default_location;
-	struct hdf5_write_location *locations;
-	int num_locations;
-	const char *ph_en_loc;
-
-	if ( image->det == NULL ) {
-		ERROR("Geometry not available\n");
-		return 1;
-	}
-
-	fh = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
-	if ( fh < 0 ) {
-		ERROR("Couldn't create file: %s\n", filename);
-		return 1;
-	}
-
-	if ( element != NULL ) {
-		default_location = strdup(element);
-	} else {
-		default_location = strdup("/data/data");
-	}
-
-	locations = make_location_list(image->det, default_location,
-	                               &num_locations);
-
-	for ( li=0; li<num_locations; li++ ) {
-		write_location(fh, image->det, image->dp, &locations[li]);
-	}
-
-	if ( image->beam == NULL
-	 || (image->beam != NULL && image->beam->photon_energy_from == NULL) ) {
-		ph_en_loc = "photon_energy_eV";
-	} else {
-		ph_en_loc = image->beam->photon_energy_from;
-	}
-
-	write_photon_energy(fh, ph_lambda_to_eV(image->lambda), ph_en_loc);
-
-	if ( image->spectrum != NULL ) {
-		write_spectrum(fh, image->spectrum);
-	}
-
-	H5Fclose(fh);
-	free(default_location);
-	for ( li=0; li<num_locations; li ++ ) {
-		free(locations[li].panel_idxs);
-	}
-	free(locations);
-	return 0;
-}
-
-
-int hdfile_get_value(struct hdfile *f, const char *name, struct event *ev,
-                     void *val, hid_t memtype)
-{
-	hid_t dh;
-	hid_t type;
-	hid_t class;
-	hid_t sh;
-	hid_t ms;
-	hsize_t *f_offset = NULL;
-	hsize_t *f_count = NULL;
-	hsize_t m_offset[1];
-	hsize_t m_count[1];
-	hsize_t msdims[1];
-	hsize_t size[64];
-	herr_t r;
-	herr_t check;
-	int check_pe;
-	int dim_flag;
-	int ndims;
-	int i;
-	char *subst_name = NULL;
-
-	if ( (ev != NULL) && (ev->path_length != 0) ) {
-		subst_name = retrieve_full_path(ev, name);
-	} else {
-		subst_name = strdup(name);
-	}
-
-	check_pe = check_path_existence(f->fh, subst_name);
-	if ( check_pe == 0 ) {
-		ERROR("No such event-based float field '%s'\n", subst_name);
-		return 1;
-	}
-
-	dh = H5Dopen2(f->fh, subst_name, H5P_DEFAULT);
-	type = H5Dget_type(dh);
-	class = H5Tget_class(type);
-
-	if ( (class != H5T_FLOAT) && (class != H5T_INTEGER) ) {
-		ERROR("Not a floating point or integer value.\n");
-		H5Tclose(type);
-		H5Dclose(dh);
-		return 1;
-	}
-
-	/* Get the dimensionality.  We have to cope with scalars expressed as
-	 * arrays with all dimensions 1, as well as zero-d arrays. */
-	sh = H5Dget_space(dh);
-	ndims = H5Sget_simple_extent_ndims(sh);
-	if ( ndims > 64 ) {
-		ERROR("Too many dimensions for hdfile_get_value\n");
-		H5Tclose(type);
-		H5Dclose(dh);
-		return 1;
-	}
-	H5Sget_simple_extent_dims(sh, size, NULL);
-
-	m_offset[0] = 0;
-	m_count[0] = 1;
-	msdims[0] = 1;
-	ms = H5Screate_simple(1,msdims,NULL);
-
-	/* Check that the size in all dimensions is 1
-	 * or that one of the dimensions has the same
-	 * size as the hyperplane events */
-
-	dim_flag = 0;
-
-	for ( i=0; i<ndims; i++ ) {
-		if ( size[i] == 1 ) continue;
-		if ( ( i==0 ) && (ev != NULL) && (ev->dim_length > 0)
-		  && (size[i] > ev->dim_entries[0]) )
-		{
-			dim_flag = 1;
-		} else {
-			H5Tclose(type);
-			H5Dclose(dh);
-			return 1;
-		}
-	}
-
-	if ( dim_flag == 0 ) {
-
-		if ( H5Dread(dh, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, val) < 0 ) {
-			ERROR("Couldn't read value.\n");
-			H5Tclose(type);
-			H5Dclose(dh);
-			return 1;
-		}
-
-	} else {
-
-		f_offset = malloc(ndims*sizeof(hsize_t));
-		f_count = malloc(ndims*sizeof(hsize_t));
-
-		for ( i=0; i<ndims; i++ ) {
-
-			if ( i == 0 ) {
-				f_offset[i] = ev->dim_entries[0];
-				f_count[i] = 1;
-			} else {
-				f_offset[i] = 0;
-				f_count[i] = 0;
-			}
-
-		}
-
-		check = H5Sselect_hyperslab(sh, H5S_SELECT_SET,
-		                            f_offset, NULL, f_count, NULL);
-		if ( check <0 ) {
-			ERROR("Error selecting dataspace for float value");
-			free(f_offset);
-			free(f_count);
-			return 1;
-		}
-
-		ms = H5Screate_simple(1,msdims,NULL);
-		check = H5Sselect_hyperslab(ms, H5S_SELECT_SET,
-		                            m_offset, NULL, m_count, NULL);
-		if ( check < 0 ) {
-			ERROR("Error selecting memory dataspace for float value");
-			free(f_offset);
-			free(f_count);
-			return 1;
-		}
-
-		r = H5Dread(dh, memtype, ms, sh, H5P_DEFAULT, val);
-		if ( r < 0 )  {
-			ERROR("Couldn't read value.\n");
-			H5Tclose(type);
-			H5Dclose(dh);
-			return 1;
-		}
-
-	}
-
-	free(subst_name);
-
-	return 0;
-}
-
-
-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)
-{
-	int i;
-
-	/* Already on the list?   Don't re-add if so. */
-	for ( i=0; i<copyme->n_fields; i++ ) {
-		if ( strcmp(copyme->fields[i], name) == 0 ) return;
-	}
-
-	/* 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, struct event *ev)
-{
-	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, ev);
-
-		if ( field[0] == '/' ) {
-			fprintf(fh, "hdf5%s = %s\n", field, val);
-		} else {
-			fprintf(fh, "hdf5/%s = %s\n", field, val);
-		}
-
-		free(val);
-
-	}
-}
-
-
-static int make_dataspaces(hid_t dh, struct event *ev, hid_t *memspace,
-                           hid_t *filespace)
-{
-	hsize_t *f_offset, *f_count;
-	hsize_t *m_offset, *m_count;
-	hid_t sh, mh;
-	int ndims;
-	int i;
-
-	if ( ev == NULL ) {
-		ERROR("Can't make dataspaces: no event ID\n");
-		return 1;
-	}
-
-	/* Check that there are at least as many dim entries as dimensions */
-	sh = H5Dget_space(dh);
-	ndims = H5Sget_simple_extent_ndims(sh);
-	if ( ndims > ev->dim_length ) {
-		return 1;
-	}
-
-	/* Now set up arrays of offsets and counts in files and memory */
-	f_offset = malloc(sizeof(hsize_t)*ndims);
-	f_count = malloc(sizeof(hsize_t)*ndims);
-	m_offset = malloc(sizeof(hsize_t)*ndims);
-	m_count = malloc(sizeof(hsize_t)*ndims);
-	if ( (f_offset == NULL) || (f_count == NULL)
-	  || (m_offset == NULL) || (m_count == NULL) ) return 1;
-
-	for ( i=0; i<ev->dim_length; i++ ) {
-		f_offset[i] = ev->dim_entries[i];
-		f_count[i] = 1;
-		m_offset[i] = 0;
-		m_count[i] = 1;
-	}
-
-	if ( H5Sselect_hyperslab(sh, H5S_SELECT_SET,
-	                         f_offset, NULL, f_count, NULL) ) return 1;
-
-	free(f_offset);
-	free(f_count);
-
-	mh = H5Screate_simple(ndims, m_count, NULL);
-	if ( H5Sselect_hyperslab(mh, H5S_SELECT_SET,
-	                         m_offset, NULL, m_count, NULL) ) return 1;
-	free(m_offset);
-	free(m_count);
-
-	*memspace = mh;
-	*filespace = sh;
-
-	return 0;
-}
-
-
-static char *read_vlen_string(hid_t dh, struct event *ev)
-{
-	hid_t memspace, filespace;
-	herr_t r;
-	char *tmp;
-	hid_t type;
-
-	if ( make_dataspaces(dh, ev, &memspace, &filespace) ) {
-		return strdup("[couldn't make dataspaces - variable len]");
-	}
-
-	type = H5Dget_type(dh);
-	r = H5Dread(dh, type, memspace, filespace, H5P_DEFAULT, &tmp);
-	H5Tclose(type);
-	if ( r < 0 ) {
-		return strdup("[couldn't read vlen string]");
-	}
-
-	H5Sclose(memspace);
-	H5Sclose(filespace);
-
-	/* Variable strings are 0-terminated */
-	chomp(tmp);
-	return tmp;
-}
-
-
-static char *read_fixed_string(hid_t dh, struct event *ev)
-{
-	hid_t memspace, filespace;
-	herr_t r;
-	hid_t sh, type;
-	size_t size;
-	char *tmp;
-
-	type = H5Dget_type(dh);
-	size = H5Tget_size(type);
-	tmp = malloc(size+1);
-	if ( tmp == NULL ) {
-		H5Tclose(type);
-		return strdup("[couldn't allocate string]");
-	}
-
-	if ( ev == NULL ) {
-
-		/* Try a simple fixed-length string */
-		sh = H5Dget_space(dh);
-		if ( H5Sget_simple_extent_ndims(sh) ) {
-			H5Tclose(type);
-			return strdup("[non-scalar string]");
-		}
-
-		sh = H5Screate(H5S_SCALAR);
-		r = H5Dread(dh, type, sh, H5S_ALL, H5P_DEFAULT, tmp);
-		H5Sclose(sh);
-		if ( r < 0 ) {
-			free(tmp);
-			H5Tclose(type);
-			return strdup("[couldn't read scalar string]");
-		} else {
-			H5Tclose(type);
-			tmp[size] = '\0';
-			chomp(tmp);
-			return tmp;
-		}
-	}
-
-	if ( make_dataspaces(dh, ev, &memspace, &filespace) ) {
-		H5Tclose(type);
-		return strdup("[couldn't make dataspaces - fixed len]");
-	}
-
-	r = H5Dread(dh, type, memspace, filespace, H5P_DEFAULT, tmp);
-	if ( r < 0 ) {
-		H5Tclose(type);
-		return strdup("[couldn't read string]");
-	}
-
-	H5Tclose(type);
-	H5Sclose(memspace);
-	H5Sclose(filespace);
-
-	tmp[size] = '\0';
-	chomp(tmp);
-	return tmp;
-}
-
-
-static char *read_general_string(hid_t dh, struct event *ev)
-{
-	htri_t v;
-	hid_t type;
-
-	type = H5Dget_type(dh);
-	v = H5Tis_variable_str(type);
-	H5Tclose(type);
-
-	if ( v < 0 ) {
-		return strdup("[unrecognised string type]");
-
-	} else if ( v > 0 ) {
-		/* Variable length string */
-		return read_vlen_string(dh, ev);
-
-	} else {
-		/* Fixed-length string */
-		return read_fixed_string(dh, ev);
-
-	}
-}
-
-
-char *hdfile_get_string_value(struct hdfile *f, const char *name,
-                              struct event *ev)
-{
-	hid_t dh;
-	hid_t type;
-	hid_t class;
-	int buf_i;
-	double buf_f;
-	char *tmp = NULL;
-	char *subst_name = NULL;
-
-	if ( (ev != NULL) && (ev->path_length != 0) ) {
-		subst_name = retrieve_full_path(ev, name);
-	} else {
-		subst_name = strdup(name);
-	}
-
-	dh = H5Dopen2(f->fh, subst_name, H5P_DEFAULT);
-	if ( dh < 0 ) {
-		free(subst_name);
-		return strdup("[couldn't read string]");
-	}
-
-	type = H5Dget_type(dh);
-	class = H5Tget_class(type);
-	H5Tclose(type);
-
-	if ( class == H5T_STRING ) {
-
-		free(subst_name);
-		tmp = read_general_string(dh, ev);
-		H5Dclose(dh);
-		return tmp;
-
-	} else {
-
-		int r;
-
-		H5Dclose(dh);
-
-		switch ( class ) {
-
-			case H5T_FLOAT :
-			r = hdfile_get_value(f, subst_name, ev, &buf_f,
-			                     H5T_NATIVE_DOUBLE);
-			free(subst_name);
-			if ( r == 0 ) {
-				tmp = malloc(256);
-				if ( tmp == NULL ) {
-					ERROR("Failed to allocate float\n");
-					return NULL;
-				}
-				snprintf(tmp, 255, "%f", buf_f);
-				return tmp;
-			} else {
-				return NULL;
-			}
-			break;
-
-			case H5T_INTEGER :
-			r = hdfile_get_value(f, subst_name, ev, &buf_i,
-			                     H5T_NATIVE_INT);
-			free(subst_name);
-			if ( r == 0 ) {
-				tmp = malloc(256);
-				if ( tmp == NULL ) {
-					ERROR("Failed to allocate int buf!\n");
-					return NULL;
-				}
-				snprintf(tmp, 255, "%d", buf_i);
-				return tmp;
-
-			} else {
-				return NULL;
-			}
-			break;
-
-			default :
-			ERROR("Unrecognised type: %s\n", subst_name);
-			free(subst_name);
-			return NULL;
-		}
-
-	}
-}
-
-
-int check_path_existence(hid_t fh, const char *path)
-{
-
-	char buffer[256];
-	char buffer_full_path[2048];
-	herr_t herrt;
-	struct H5O_info_t ob_info;
-	char *path_copy = strdup(path);
-	char *start = path_copy;
-	char *sep = NULL;
-
-	buffer[0] = '\0';
-	buffer_full_path[0] = '\0';
-
-	if ( strcmp(path_copy, "/" ) == 0 ) {
-		return 1;
-	}
-
-	do {
-
-		int check;
-
-		sep = strstr(start, "/");
-		if ( sep != NULL && strlen(sep) == 1 ) {
-			ERROR("Error: Data path ends with a / symbol\n");
-			free(path_copy);
-			return 1;
-		}
-
-		if ( sep != NULL ) {
-
-			if ( sep == start ) {
-				start = sep+1;
-				strcat(buffer_full_path, "/");
-				continue;
-			}
-
-			strncpy(buffer, start, sep-start);
-			buffer[sep-start] = '\0';
-			strcat(buffer_full_path, buffer);
-
-			check = H5Lexists(fh, buffer_full_path, H5P_DEFAULT);
-			if ( check == 0 ) {
-				return 0;
-			} else {
-				herrt = H5Oget_info_by_name(fh, buffer_full_path,
-				                            &ob_info,
-				                            H5P_DEFAULT);
-				if ( herrt < 0 ) {
-					return -1;
-				}
-				if ( ob_info.type != H5O_TYPE_GROUP ) {
-					return 0;
-				}
-
-				start = sep+1;
-				strcat(buffer_full_path, "/");
-
-			}
-
-		} else {
-
-			strcpy(buffer, start);
-			strcat(buffer_full_path, buffer);
-
-			check = H5Lexists(fh, buffer_full_path, H5P_DEFAULT);
-			if ( check == 0 ) {
-				return 0;
-			}
-
-		}
-	} while (sep);
-
-	free(path_copy);
-	return 1;
-
-}
diff --git a/libcrystfel/src/hdf5-file.h b/libcrystfel/src/hdf5-file.h
deleted file mode 100644
index eab7b55d..00000000
--- a/libcrystfel/src/hdf5-file.h
+++ /dev/null
@@ -1,81 +0,0 @@
-/*
- * hdf5-file.h
- *
- * Read/write HDF5 data files
- *
- * Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
- *                       a research centre of the Helmholtz Association.
- *
- * Authors:
- *   2009-2017 Thomas White <taw@physics.org>
- *   2014      Valerio Mariani
-
- *
- * 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
-
-#ifndef HDF5_H
-#define HDF5_H
-
-struct event_list;
-
-#include <stdint.h>
-#include <hdf5.h>
-#include "image.h"
-#include "events.h"
-
-struct copy_hdf5_field;
-
-#include "image.h"
-#include "events.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/**
- * \file hdf5-file.h
- * HDF5 utility functions
- */
-
-extern int hdf5_write_image(const char *filename, const struct image *image,
-                            char *element);
-
-extern int check_path_existence(hid_t fh, const char *path);
-
-extern struct copy_hdf5_field *new_copy_hdf5_field_list(void);
-extern void free_copy_hdf5_field_list(struct copy_hdf5_field *f);
-extern void copy_hdf5_fields(struct hdfile *f,
-                             const struct copy_hdf5_field *copyme,
-                             FILE *fh, struct event *ev);
-extern void add_copy_hdf5_field(struct copy_hdf5_field *copyme,
-                                const char *name);
-extern int hdfile_get_value(struct hdfile *f, const char *name,
-                            struct event *ev, void *val, hid_t memtype);
-extern int hdfile_is_scalar(struct hdfile *f, const char *name, int verbose);
-extern char *hdfile_get_string_value(struct hdfile *f, const char *name,
-                                     struct event *ev);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif	/* HDF5_H */