Merge branch 'develop' into feature/coding_standardsfeature/coding_standards

1 files changed, 252 insertions, 0 deletions

diff --git a/doxygen/examples/H5D_examples.c b/doxygen/examples/H5D_examples.c
new file mode 100644
index 0000000..4e54c1d
--- /dev/null
+++ b/doxygen/examples/H5D_examples.c
@@ -0,0 +1,252 @@
+/* -*- c-file-style: "stroustrup" -*- */
+
+#include "hdf5.h"
+
+#include <stdio.h>
+#include <stdlib.h>
+
+//! <!-- [H5Dchunk_iter_cb] -->
+int
+chunk_cb(const hsize_t *offset, uint32_t filter_mask, haddr_t addr, uint32_t nbytes, void *op_data)
+{
+    // only print the allocated chunk size only
+    printf("%d\n", nbytes);
+    return EXIT_SUCCESS;
+}
+//! <!-- [H5Dchunk_iter_cb] -->
+
+//! <!-- [H5Ovisit_cb] -->
+herr_t
+H5Ovisit_cb(hid_t obj, const char *name, const H5O_info2_t *info, void *op_data)
+{
+    herr_t retval    = 0;
+    char * base_path = (char *)op_data;
+
+    if (info->type == H5O_TYPE_DATASET) // current object is a dataset
+    {
+        hid_t dset, dcpl;
+        if ((dset = H5Dopen(obj, name, H5P_DEFAULT)) == H5I_INVALID_HID) {
+            retval = -1;
+            goto func_leave;
+        }
+        if ((dcpl = H5Dget_create_plist(dset)) == H5I_INVALID_HID) {
+            retval = -1;
+            goto fail_dcpl;
+        }
+        if (H5Pget_layout(dcpl) == H5D_CHUNKED) // dataset is chunked
+        {
+            __label__ fail_dtype, fail_dspace, fail_shape;
+            hid_t   dspace, dtype;
+            size_t  size, i;
+            int     rank;
+            hsize_t cdims[H5S_MAX_RANK];
+
+            // get resources
+            if ((dtype = H5Dget_type(dset)) < 0) {
+                retval = -1;
+                goto fail_dtype;
+            }
+            if ((dspace = H5Dget_space(dset)) < 0) {
+                retval = -1;
+                goto fail_dspace;
+            }
+            // get the shape
+            if ((size = H5Tget_size(dtype)) == 0 || (rank = H5Sget_simple_extent_ndims(dspace)) < 0 ||
+                H5Pget_chunk(dcpl, H5S_MAX_RANK, cdims) < 0) {
+                retval = -1;
+                goto fail_shape;
+            }
+            // calculate the nominal chunk size
+            size = 1;
+            for (i = 0; i < (size_t)rank; ++i)
+                size *= cdims[i];
+            // print dataset info
+            printf("%s%s : nominal chunk size %lu [B] \n", base_path, name, size);
+            // get the allocated chunk sizes
+            if (H5Dchunk_iter(dset, H5P_DEFAULT, &chunk_cb, NULL) < 0) {
+                retval = -1;
+                goto fail_fig;
+            }
+
+fail_shape:
+            H5Sclose(dspace);
+fail_dspace:
+            H5Tclose(dtype);
+fail_dtype:;
+        }
+
+        H5Pclose(dcpl);
+fail_dcpl:
+        H5Dclose(dset);
+    }
+
+func_leave:
+    return retval;
+}
+//! <!-- [H5Ovisit_cb] -->
+
+int
+main(void)
+{
+    int ret_val = EXIT_SUCCESS;
+
+    //! <!-- [create] -->
+    {
+        __label__ fail_lcpl, fail_dset, fail_file;
+        hid_t file, lcpl, fspace, dset;
+
+        unsigned mode        = H5F_ACC_TRUNC;
+        char     file_name[] = "d1.h5";
+        // link names can be arbitrary Unicode strings
+        char dset_name[] = "σύνολο/δεδομένων";
+
+        if ((file = H5Fcreate(file_name, mode, H5P_DEFAULT, H5P_DEFAULT)) == H5I_INVALID_HID) {
+            ret_val = EXIT_FAILURE;
+            goto fail_file;
+        }
+        if ((lcpl = H5Pcreate(H5P_LINK_CREATE)) == H5I_INVALID_HID) {
+            ret_val = EXIT_FAILURE;
+            goto fail_lcpl;
+        }
+        // use UTF-8 encoding for link names
+        if (H5Pset_char_encoding(lcpl, H5T_CSET_UTF8) < 0) {
+            ret_val = EXIT_FAILURE;
+            goto fail_fspace;
+        }
+        // create intermediate groups as needed
+        if (H5Pset_create_intermediate_group(lcpl, 1) < 0) {
+            ret_val = EXIT_FAILURE;
+            goto fail_fspace;
+        }
+        // create a 1D dataspace
+        if ((fspace = H5Screate_simple(1, (hsize_t[]){10}, NULL)) == H5I_INVALID_HID) {
+            ret_val = EXIT_FAILURE;
+            goto fail_fspace;
+        }
+        // create a 32-bit integer dataset
+        if ((dset = H5Dcreate2(file, dset_name, H5T_STD_I32LE, fspace, lcpl, H5P_DEFAULT, H5P_DEFAULT)) ==
+            H5I_INVALID_HID) {
+            ret_val = EXIT_FAILURE;
+            goto fail_dset;
+        }
+
+        H5Dclose(dset);
+fail_dset:
+        H5Sclose(fspace);
+fail_fspace:
+        H5Pclose(lcpl);
+fail_lcpl:
+        H5Fclose(file);
+fail_file:;
+    }
+    //! <!-- [create] -->
+
+    //! <!-- [read] -->
+    {
+        __label__ fail_dset, fail_file;
+        hid_t file, dset;
+
+        unsigned mode        = H5F_ACC_RDONLY;
+        char     file_name[] = "d1.h5";
+        // assume a priori knowledge of dataset name and size
+        char dset_name[] = "σύνολο/δεδομένων";
+        int  elts[10];
+
+        if ((file = H5Fopen(file_name, mode, H5P_DEFAULT)) == H5I_INVALID_HID) {
+            ret_val = EXIT_FAILURE;
+            goto fail_file;
+        }
+        if ((dset = H5Dopen2(file, dset_name, H5P_DEFAULT)) == H5I_INVALID_HID) {
+            ret_val = EXIT_FAILURE;
+            goto fail_dset;
+        }
+        // read all dataset elements
+        if (H5Dread(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, elts) < 0)
+            ret_val = EXIT_FAILURE;
+
+        // do something w/ the dataset elements
+
+        H5Dclose(dset);
+fail_dset:
+        H5Fclose(file);
+fail_file:;
+    }
+    //! <!-- [read] -->
+
+    //! <!-- [update] -->
+    {
+        __label__ fail_update, fail_fspace, fail_dset, fail_file;
+        hid_t file, dset, fspace;
+
+        unsigned mode           = H5F_ACC_RDWR;
+        char     file_name[]    = "d1.h5";
+        char     dset_name[]    = "σύνολο/δεδομένων";
+        int      new_elts[6][2] = {{-1, 1}, {-2, 2}, {-3, 3}, {-4, 4}, {-5, 5}, {-6, 6}};
+
+        if ((file = H5Fopen(file_name, mode, H5P_DEFAULT)) == H5I_INVALID_HID) {
+            ret_val = EXIT_FAILURE;
+            goto fail_file;
+        }
+        if ((dset = H5Dopen2(file, dset_name, H5P_DEFAULT)) == H5I_INVALID_HID) {
+            ret_val = EXIT_FAILURE;
+            goto fail_dset;
+        }
+        // get the dataset's dataspace
+        if ((fspace = H5Dget_space(dset)) == H5I_INVALID_HID) {
+            ret_val = EXIT_FAILURE;
+            goto fail_fspace;
+        }
+        // select the first 5 elements in odd positions
+        if (H5Sselect_hyperslab(fspace, H5S_SELECT_SET, (hsize_t[]){1}, (hsize_t[]){2}, (hsize_t[]){5},
+                                NULL) < 0) {
+            ret_val = EXIT_FAILURE;
+            goto fail_update;
+        }
+
+        // (implicitly) select and write the first 5 elements of the second column of NEW_ELTS
+        if (H5Dwrite(dset, H5T_NATIVE_INT, H5S_ALL, fspace, H5P_DEFAULT, new_elts) < 0)
+            ret_val = EXIT_FAILURE;
+
+fail_update:
+        H5Sclose(fspace);
+fail_fspace:
+        H5Dclose(dset);
+fail_dset:
+        H5Fclose(file);
+fail_file:;
+    }
+    //! <!-- [update] -->
+
+    //! <!-- [delete] -->
+    {
+        __label__ fail_delete, fail_file;
+        hid_t file;
+
+        unsigned mode         = H5F_ACC_RDWR;
+        char     file_name[]  = "d1.h5";
+        char     group_name[] = "σύνολο";
+        char     dset_name[]  = "σύνολο/δεδομένων";
+
+        if ((file = H5Fopen(file_name, mode, H5P_DEFAULT)) == H5I_INVALID_HID) {
+            ret_val = EXIT_FAILURE;
+            goto fail_file;
+        }
+        // delete (unlink) the dataset
+        if (H5Ldelete(file, dset_name, H5P_DEFAULT) < 0) {
+            ret_val = EXIT_FAILURE;
+            goto fail_delete;
+        }
+        // the previous call deletes (unlinks) only the dataset
+        if (H5Ldelete(file, group_name, H5P_DEFAULT) < 0) {
+            ret_val = EXIT_FAILURE;
+            goto fail_delete;
+        }
+
+fail_delete:
+        H5Fclose(file);
+fail_file:;
+    }
+    //! <!-- [delete] -->
+
+    return ret_val;
+}