binoculars/hkl-binoculars-hdf5.c

   1 /* This file is part of the hkl library.
   2  *
   3  * The hkl library is free software: you can redistribute it and/or modify
   4  * it under the terms of the GNU General Public License as published by
   5  * the Free Software Foundation, either version 3 of the License, or
   6  * (at your option) any later version.
   7  *
   8  * The hkl library is distributed in the hope that it will be useful,
   9  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  10  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  11  * GNU General Public License for more details.
  12  *
  13  * You should have received a copy of the GNU General Public License
  14  * along with the hkl library.  If not, see <http://www.gnu.org/licenses/>.
  15  *
  16  * Copyright (C) 2003-2023 Synchrotron SOLEIL
  17  *                         L'Orme des Merisiers Saint-Aubin
  18  *                         BP 48 91192 GIF-sur-YVETTE CEDEX
  19  *
  20  * Authors: Picca Frédéric-Emmanuel <picca@synchrotron-soleil.fr>
  21  */
  22 #include <hdf5.h>
  23
  24 #include "hkl/ccan/array_size/array_size.h"
  25 #include "hkl/hkl-macros-private.h"
  26 #include "hkl-binoculars-private.h"
  27
  28 static hid_t create_dataspace_from_axes(const darray_axis *axes)
  29 {
  30         HklBinocularsAxis *axis;
  31         hid_t hid;
  32         darray(hsize_t) dims;
  33
  34         darray_init(dims);
  35         darray_foreach(axis, *axes){
  36                 if(axis_size(axis) > 1)
  37                         darray_append(dims, axis_size(axis));
  38         }
  39
  40         hid = H5Screate_simple(darray_size(dims), &darray_item(dims, 0), NULL);
  41         darray_free(dims);
  42
  43         return hid;
  44 }
  45
  46 static herr_t save_string(hid_t group_id, const char *name, const char* config)
  47 {
  48         hid_t dataset_id;
  49         hid_t dataspace_id;
  50         herr_t status;
  51         hsize_t dims[] = {1};
  52
  53         hid_t filetype = H5Tcopy (H5T_C_S1);
  54         status = H5Tset_size (filetype, strlen(config));
  55         hid_t memtype = H5Tcopy (H5T_C_S1);
  56         status = H5Tset_size (memtype, strlen(config));
  57
  58
  59         dataspace_id = H5Screate_simple(1, dims, NULL);
  60         dataset_id = H5Dcreate (group_id, "config",
  61                                 filetype, dataspace_id,
  62                                 H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
  63         status = H5Dwrite (dataset_id, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, config);
  64
  65         status = H5Dclose(dataset_id);
  66         status = H5Sclose(dataspace_id);
  67         status = H5Tclose(memtype);
  68         status = H5Tclose(filetype);
  69
  70         return status;
  71 }
  72
  73 void hkl_binoculars_cube_save_hdf5(const char *fn,
  74                                    const char *config,
  75                                    const HklBinocularsCube *self)
  76 {
  77         double axis_idx = 0;
  78         hid_t file_id;
  79         hid_t groupe_id;
  80         hid_t groupe_axes_id;
  81         hid_t dataset_id;
  82         hid_t dataspace_id;
  83         herr_t status;
  84         HklBinocularsAxis *axis;
  85
  86         file_id = H5Fcreate(fn, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
  87
  88         groupe_id = H5Gcreate(file_id, "binoculars",
  89                               H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
  90
  91         // config
  92         status = save_string(groupe_id, "config", config);
  93
  94         // axes
  95         groupe_axes_id = H5Gcreate(groupe_id, "axes",
  96                                    H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
  97
  98         darray_foreach(axis, self->axes){
  99                 double *arr;
 100                 hid_t dataspace_id;
 101                 hid_t dataset_id;
 102                 hsize_t dims[] = {6};
 103
 104                 if(axis_size(axis) > 1){
 105                         arr = hkl_binoculars_axis_array(axis);
 106                         /* the arr[0] contains the axis index expected
 107                            by the binoculars gui. This value must
 108                            start from zero, so compute this index
 109                            using an external counter instead of using
 110                            the original index stored in the axis
 111                            array. */
 112                         arr[0] = axis_idx++;
 113                         dataspace_id = H5Screate_simple(ARRAY_SIZE(dims), dims, NULL);
 114                         dataset_id = H5Dcreate(groupe_axes_id, axis->name,
 115                                                H5T_NATIVE_DOUBLE, dataspace_id,
 116                                                H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
 117                         status = H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE,
 118                                           H5S_ALL, H5S_ALL,
 119                                           H5P_DEFAULT, arr);
 120                         status = H5Dclose(dataset_id);
 121                         status = H5Sclose(dataspace_id);
 122                         free(arr);
 123                 }
 124         }
 125
 126         status = H5Gclose(groupe_axes_id);
 127
 128         // create count dataset
 129         dataspace_id = create_dataspace_from_axes(&self->axes);
 130         dataset_id = H5Dcreate(groupe_id, "counts",
 131                                H5T_NATIVE_UINT32, dataspace_id,
 132                                H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
 133         status = H5Dwrite(dataset_id, H5T_NATIVE_UINT32,
 134                           H5S_ALL, H5S_ALL,
 135                           H5P_DEFAULT, self->photons);
 136         status = H5Dclose(dataset_id);
 137         status = H5Sclose(dataspace_id);
 138
 139         // create contributions dataset
 140         dataspace_id = create_dataspace_from_axes(&self->axes);
 141         dataset_id = H5Dcreate(groupe_id, "contributions",
 142                                H5T_NATIVE_UINT32, dataspace_id,
 143                                H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
 144         status = H5Dwrite(dataset_id, H5T_NATIVE_UINT32,
 145                           H5S_ALL, H5S_ALL,
 146                           H5P_DEFAULT, self->contributions);
 147         status = H5Dclose(dataset_id);
 148         status = H5Sclose(dataspace_id);
 149
 150         // terminate access and free identifiers
 151         status = H5Gclose(groupe_id);
 152         status = H5Fclose(file_id);
 153
 154         hkl_assert(status >= 0);
 155 }