Adding HDF group files

Most of this will vanish when all examples are ported to C++.

Update #318

examples/hdfgroup/H5D/CMakeLists.txt

@@ -9,4 +9,7 @@ add_executable(h5ex_d_chunk h5ex_d_chunk.cpp)
 target_link_libraries(h5ex_d_chunk h5cpp)
 
 add_executable(h5ex_d_compact h5ex_d_compact.cpp)
-target_link_libraries(h5ex_d_compact h5cpp)
+target_link_libraries(h5ex_d_compact h5cpp)
+
+add_executable(h5ex_d_fillval h5ex_d_fillval.cpp)
+target_link_libraries(h5ex_d_fillval h5cpp)

examples/hdfgroup/H5D/C_sourcefiles.cmake

@@ -0,0 +1,25 @@
+#-----------------------------------------------------------------------------
+# Define Sources, one file per application
+#-----------------------------------------------------------------------------
+set (examples
+    h5ex_d_alloc.c
+    h5ex_d_checksum.c
+    h5ex_d_chunk.c
+    h5ex_d_compact.c
+    h5ex_d_extern.c
+    h5ex_d_fillval.c
+    h5ex_d_gzip.c
+    h5ex_d_hyper.c
+    h5ex_d_nbit.c
+    h5ex_d_rdwr.c
+    h5ex_d_soint.c
+    h5ex_d_transform.c
+    h5ex_d_unlimmod.c
+    h5ex_d_shuffle.c
+    h5ex_d_sofloat.c
+    h5ex_d_unlimadd.c
+    h5ex_d_unlimgzip.c
+)
+if (HDF5_ENABLE_SZIP_SUPPORT)
+  set (examples ${examples} h5ex_d_szip.c)
+endif ()

examples/hdfgroup/H5D/h5ex_d_alloc.c

@@ -0,0 +1,141 @@
+/************************************************************
+
+  This example shows how to set the space allocation time
+  for a dataset.  The program first creates two datasets,
+  one with the default allocation time (late) and one with
+  early allocation time, and displays whether each has been
+  allocated and their allocation size.  Next, it writes data
+  to the datasets, and again displays whether each has been
+  allocated and their allocation size.
+
+  This file is intended for use with HDF5 Library version 1.8
+
+ ************************************************************/
+
+#include "hdf5.h"
+#include <stdio.h>
+#include <stdlib.h>
+
+#define FILE            "h5ex_d_alloc.h5"
+#define DATASET1        "DS1"
+#define DATASET2        "DS2"
+#define DIM0            4
+#define DIM1            7
+#define FILLVAL         99
+
+int
+main (void)
+{
+    hid_t                   file, space, dset1, dset2, dcpl;
+                                                    /* Handles */
+    herr_t                  status;
+    H5D_space_status_t      space_status;
+    hsize_t                 dims[2] = {DIM0, DIM1},
+                            storage_size;
+    int                     wdata[DIM0][DIM1],      /* Write buffer */
+                            i, j;
+
+    /*
+     * Initialize data.
+     */
+    for (i=0; i<DIM0; i++)
+        for (j=0; j<DIM1; j++)
+            wdata[i][j] = i * j - j;
+
+    /*
+     * Create a new file using the default properties.
+     */
+    file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+    /*
+     * Create dataspace.  Setting maximum size to NULL sets the maximum
+     * size to be the current size.
+     */
+    space = H5Screate_simple (2, dims, NULL);
+
+    /*
+     * Create the dataset creation property list, and set the chunk
+     * size.
+     */
+    dcpl = H5Pcreate (H5P_DATASET_CREATE);
+
+    /*
+     * Set the allocation time to "early".  This way we can be sure
+     * that reading from the dataset immediately after creation will
+     * return the fill value.
+     */
+    status = H5Pset_alloc_time (dcpl, H5D_ALLOC_TIME_EARLY);
+
+    printf ("Creating datasets...\n");
+    printf ("%s has allocation time H5D_ALLOC_TIME_LATE\n", DATASET1);
+    printf ("%s has allocation time H5D_ALLOC_TIME_EARLY\n\n", DATASET2);
+
+    /*
+     * Create the dataset using the dataset creation property list.
+     */
+    dset1 = H5Dcreate (file, DATASET1, H5T_STD_I32LE, space, H5P_DEFAULT,
+                H5P_DEFAULT, H5P_DEFAULT);
+    dset2 = H5Dcreate (file, DATASET2, H5T_STD_I32LE, space, H5P_DEFAULT, dcpl,
+                H5P_DEFAULT);
+
+    /*
+     * Retrieve and print space status and storage size for dset1.
+     */
+    status = H5Dget_space_status (dset1, &space_status);
+    storage_size = H5Dget_storage_size (dset1);
+    printf ("Space for %s has%sbeen allocated.\n", DATASET1,
+                space_status == H5D_SPACE_STATUS_ALLOCATED ? " " : " not ");
+    printf ("Storage size for %s is: %ld bytes.\n", DATASET1,
+                (long) storage_size);
+
+    /*
+     * Retrieve and print space status and storage size for dset2.
+     */
+    status = H5Dget_space_status (dset2, &space_status);
+    storage_size = H5Dget_storage_size (dset2);
+    printf ("Space for %s has%sbeen allocated.\n", DATASET2,
+                space_status == H5D_SPACE_STATUS_ALLOCATED ? " " : " not ");
+    printf ("Storage size for %s is: %ld bytes.\n", DATASET2,
+                (long) storage_size);
+
+    printf ("\nWriting data...\n\n");
+
+    /*
+     * Write the data to the datasets.
+     */
+    status = H5Dwrite (dset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+                wdata[0]);
+    status = H5Dwrite (dset2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+                wdata[0]);
+
+    /*
+     * Retrieve and print space status and storage size for dset1.
+     */
+    status = H5Dget_space_status (dset1, &space_status);
+    storage_size = H5Dget_storage_size (dset1);
+    printf ("Space for %s has%sbeen allocated.\n", DATASET1,
+                space_status == H5D_SPACE_STATUS_ALLOCATED ? " " : " not ");
+    printf ("Storage size for %s is: %ld bytes.\n", DATASET1,
+                (long) storage_size);
+
+    /*
+     * Retrieve and print space status and storage size for dset2.
+     */
+    status = H5Dget_space_status (dset2, &space_status);
+    storage_size = H5Dget_storage_size (dset2);
+    printf ("Space for %s has%sbeen allocated.\n", DATASET2,
+                space_status == H5D_SPACE_STATUS_ALLOCATED ? " " : " not ");
+    printf ("Storage size for %s is: %ld bytes.\n", DATASET2,
+                (long) storage_size);
+
+    /*
+     * Close and release resources.
+     */
+    status = H5Pclose (dcpl);
+    status = H5Dclose (dset1);
+    status = H5Dclose (dset2);
+    status = H5Sclose (space);
+    status = H5Fclose (file);
+
+    return 0;
+}

examples/hdfgroup/H5D/h5ex_d_checksum.c

@@ -0,0 +1,197 @@
+/************************************************************
+
+  This example shows how to read and write data to a dataset
+  using the Fletcher32 checksum filter.  The program first
+  checks if the Fletcher32 filter is available, then if it
+  is it writes integers to a dataset using Fletcher32, then
+  closes the file.  Next, it reopens the file, reads back
+  the data, checks if the filter detected an error and
+  outputs the type of filter and the maximum value in the
+  dataset to the screen.
+
+  This file is intended for use with HDF5 Library version 1.8
+
+ ************************************************************/
+
+#include "hdf5.h"
+#include <stdio.h>
+#include <stdlib.h>
+
+#define FILE            "h5ex_d_checksum.h5"
+#define DATASET         "DS1"
+#define DIM0            32
+#define DIM1            64
+#define CHUNK0          4
+#define CHUNK1          8
+
+int
+main (void)
+{
+    hid_t           file, space, dset, dcpl;
+                                                /* Handles */
+    herr_t          status;
+    htri_t          avail;
+    H5Z_filter_t    filter_type;
+    hsize_t         dims[2] = {DIM0, DIM1},
+                    chunk[2] = {CHUNK0, CHUNK1};
+    size_t          nelmts;
+    unsigned int    flags,
+                    filter_info;
+    int             wdata[DIM0][DIM1],          /* Write buffer */
+                    rdata[DIM0][DIM1],          /* Read buffer */
+                    max,
+                    i, j;
+
+    /*
+     * Check if the Fletcher32 filter is available and can be used for
+     * both encoding and decoding.  Normally we do not perform error
+     * checking in these examples for the sake of clarity, but in this
+     * case we will make an exception because this filter is an
+     * optional part of the hdf5 library.
+     */
+    avail = H5Zfilter_avail(H5Z_FILTER_FLETCHER32);
+    if (!avail) {
+        printf ("Fletcher32 filter not available.\n");
+        return 1;
+    }
+    status = H5Zget_filter_info (H5Z_FILTER_FLETCHER32, &filter_info);
+    if ( !(filter_info & H5Z_FILTER_CONFIG_ENCODE_ENABLED) ||
+                !(filter_info & H5Z_FILTER_CONFIG_DECODE_ENABLED) ) {
+        printf ("Fletcher32 filter not available for encoding and decoding.\n");
+        return 1;
+    }
+
+    /*
+     * Initialize data.
+     */
+    for (i=0; i<DIM0; i++)
+        for (j=0; j<DIM1; j++)
+            wdata[i][j] = i * j - j;
+
+    /*
+     * Create a new file using the default properties.
+     */
+    file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+    /*
+     * Create dataspace.  Setting maximum size to NULL sets the maximum
+     * size to be the current size.
+     */
+    space = H5Screate_simple (2, dims, NULL);
+
+    /*
+     * Create the dataset creation property list, add the Fletcher32 filter
+     * and set the chunk size.
+     */
+    dcpl = H5Pcreate (H5P_DATASET_CREATE);
+    status = H5Pset_fletcher32 (dcpl);
+    status = H5Pset_chunk (dcpl, 2, chunk);
+
+    /*
+     * Create the dataset.
+     */
+    dset = H5Dcreate (file, DATASET, H5T_STD_I32LE, space, H5P_DEFAULT, dcpl,
+                H5P_DEFAULT);
+
+    /*
+     * Write the data to the dataset.
+     */
+    status = H5Dwrite (dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+                wdata[0]);
+
+    /*
+     * Close and release resources.
+     */
+    status = H5Pclose (dcpl);
+    status = H5Dclose (dset);
+    status = H5Sclose (space);
+    status = H5Fclose (file);
+
+
+    /*
+     * Now we begin the read section of this example.
+     */
+
+    /*
+     * Open file and dataset using the default properties.
+     */
+    file = H5Fopen (FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
+    dset = H5Dopen (file, DATASET, H5P_DEFAULT);
+
+    /*
+     * Retrieve dataset creation property list.
+     */
+    dcpl = H5Dget_create_plist (dset);
+
+    /*
+     * Retrieve and print the filter type.  Here we only retrieve the
+     * first filter because we know that we only added one filter.
+     */
+    nelmts = 0;
+    filter_type = H5Pget_filter (dcpl, 0, &flags, &nelmts, NULL, 0, NULL,
+                &filter_info);
+    printf ("Filter type is: ");
+    switch (filter_type) {
+        case H5Z_FILTER_DEFLATE:
+            printf ("H5Z_FILTER_DEFLATE\n");
+            break;
+        case H5Z_FILTER_SHUFFLE:
+            printf ("H5Z_FILTER_SHUFFLE\n");
+            break;
+        case H5Z_FILTER_FLETCHER32:
+            printf ("H5Z_FILTER_FLETCHER32\n");
+            break;
+        case H5Z_FILTER_SZIP:
+            printf ("H5Z_FILTER_SZIP\n");
+            break;
+        case H5Z_FILTER_NBIT:
+            printf ("H5Z_FILTER_NBIT\n");
+            break;
+        case H5Z_FILTER_SCALEOFFSET:
+            printf ("H5Z_FILTER_SCALEOFFSET\n");
+    }
+
+    /*
+     * Read the data using the default properties.
+     */
+    status = H5Dread (dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+                rdata[0]);
+
+    /*
+     * Check if the read was successful.  Normally we do not perform
+     * error checking in these examples for the sake of clarity, but in
+     * this case we will make an exception because this is how the
+     * fletcher32 checksum filter reports data errors.
+     */
+    if (status<0) {
+        fprintf (stderr, "Dataset read failed!\n");
+        status = H5Pclose (dcpl);
+        status = H5Dclose (dset);
+        status = H5Fclose (file);
+        return 2;
+    }
+
+    /*
+     * Find the maximum value in the dataset, to verify that it was
+     * read correctly.
+     */
+    max = rdata[0][0];
+    for (i=0; i<DIM0; i++)
+        for (j=0; j<DIM1; j++)
+            if (max < rdata[i][j])
+                max = rdata[i][j];
+
+    /*
+     * Print the maximum value.
+     */
+    printf ("Maximum value in %s is: %d\n", DATASET, max);
+
+    /*
+     * Close and release resources.
+     */
+    status = H5Pclose (dcpl);
+    status = H5Dclose (dset);
+    status = H5Fclose (file);
+
+    return 0;
+}