/****h* H5Rf/H5Rf
* PURPOSE
* This file contains C stubs for H5R Fortran APIs
*
* COPYRIGHT
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*
******
*/
#include "H5f90.h"
#include "H5Eprivate.h"
/****if* H5Rf/h5rcreate_region_c
* NAME
* h5rcreate_region_c
* PURPOSE
* Call H5Rcreate to create a reference to dataset region
* region
* INPUTS
* loc_id - file or group identifier
* name - name of the dataset
* namelen - name length
* space_id - dataset space identifier
* OUTPUTS
* ref - reference to the dataset region
* RETURNS
* 0 on success, -1 on failure
* AUTHOR
* Elena Pourmal
* Wednesday, December 1, 1999
* HISTORY
*
* SOURCE
*/
int_f
h5rcreate_region_c(int_f *ref, hid_t_f *loc_id, _fcd name, int_f *namelen, hid_t_f *space_id)
/******/
{
char *c_name = NULL;
hdset_reg_ref_t ref_c;
int_f ret_value = 0;
/*
* Convert FORTRAN name to C name
*/
if(NULL == (c_name = (char *)HD5f2cstring(name, (size_t)*namelen)))
HGOTO_DONE(FAIL)
/*
* Call H5Rcreate function.
*/
if(H5Rcreate(&ref_c, (hid_t)*loc_id, c_name, H5R_DATASET_REGION, (hid_t)*space_id) < 0)
HGOTO_DONE(FAIL)
/* Copy the reference created */
HDmemcpy(ref, &ref_c, H5R_DSET_REG_REF_BUF_SIZE);
done:
if(c_name)
HDfree(c_name);
return ret_value;
} /* end h5rcreate_region_c() */
/****if* H5Rf/h5rcreate_ptr_c
* NAME
* h5rcreate_ptr_c
* PURPOSE
* Call H5Rcreate to create a reference to dataset region
* INPUTS
* loc_id - file or group identifier
* name - name of the dataset
* namelen - name length
* space_id - dataset space identifier
* OUTPUTS
* ref - reference to the dataset region
* RETURNS
* 0 on success, -1 on failure
* AUTHOR
* M. Scot Breitenfeld
* June 20, 2008
*
* SOURCE
*/
int_f
h5rcreate_ptr_c (void *ref, hid_t_f *loc_id, _fcd name, int_f *namelen, int_f *ref_type, hid_t_f *space_id)
/******/
{
int ret_value = -1;
char *c_name;
/*
* Convert FORTRAN name to C name
*/
c_name = (char *)HD5f2cstring(name, (size_t)*namelen);
if (c_name == NULL) return ret_value;
/*
* Call H5Rcreate function.
*/
if(H5Rcreate(ref, (hid_t)*loc_id, c_name, (H5R_type_t)*ref_type, (hid_t)*space_id) >= 0)
ret_value = 0;
HDfree(c_name);
return ret_value;
}
/****if* H5Rf/h5rdereference_ptr_c
* NAME
* h5rdereference_ptr_c
* PURPOSE
* Call H5Rdereference
* INPUTS
* obj_id - Valid identifier for the file containing the
* referenced object or any object in that file.
* ref_typ - The reference type of ref.
* ref - Object reference
* OUTPUTS
* ref_obj_id - Identifier of referenced object
* RETURNS
* 0 on success, -1 on failure
* AUTHOR
* M. Scot Breitenfeld
* June 20, 2008
* HISTORY
*
* SOURCE
*/
int_f
h5rdereference_ptr_c (hid_t_f *obj_id, int_f *ref_type, void *ref, hid_t_f *ref_obj_id)
/******/
{
int ret_value = -1;
hid_t c_ref_obj_id;
/*
* Call H5Rdereference function.
*/
c_ref_obj_id = H5Rdereference2((hid_t)*obj_id, H5P_DEFAULT, (H5R_type_t)*ref_type, ref);
if(c_ref_obj_id < 0) return ret_value;
*ref_obj_id = (hid_t_f)c_ref_obj_id;
ret_value = 0;
return ret_value;
}
/****if* H5Rf/h5rget_region_region_object_c
* NAME
* h5rget_region_region_object_c
* PURPOSE
* Call H5Rget_region to dereference dataspace region
* INPUTS
* dset_id - dataset identifier
* ref - reference to the dataset region
* OUTPUTS
* space_id - dereferenced dataset dataspace identifier
* RETURNS
* 0 on success, -1 on failure
* AUTHOR
* Elena Pourmal
* Wednesday, December 1, 1999
* HISTORY
*
* SOURCE
*/
int_f
h5rget_region_region_c(hid_t_f *dset_id, int_f *ref, hid_t_f *space_id)
/******/
{
hid_t c_space_id;
hdset_reg_ref_t ref_c;
int_f ret_value = 0;
/* Copy the reference to dereference */
HDmemcpy(&ref_c, ref, H5R_DSET_REG_REF_BUF_SIZE);
/*
* Call H5Rget_region function.
*/
if((c_space_id = H5Rget_region((hid_t)*dset_id, H5R_DATASET_REGION, &ref_c)) < 0)
HGOTO_DONE(FAIL)
/* Copy the dataspace ID */
*space_id = (hid_t_f)c_space_id;
done:
return ret_value;
} /* end h5rget_region_region_c() */
/****if* H5Rf/h5rget_region_ptr_c
* NAME
* h5rget_region_ptr_c
* PURPOSE
* Call H5Rget_region to dereference dataspace region
* INPUTS
* dset_id - dataset identifier
* ref - reference to the dataset region
* OUTPUTS
* space_id - dereferenced dataset dataspace identifier
* RETURNS
* 0 on success, -1 on failure
* AUTHOR
* M. Scot Breitenfeld
* August 4, 2012
* HISTORY
*
* SOURCE
*/
int_f
h5rget_region_ptr_c(hid_t_f *dset_id, void *ref, hid_t_f *space_id)
/******/
{
hid_t c_space_id;
int_f ret_value = 0;
/*
* Call H5Rget_region function.
*/
if((c_space_id = H5Rget_region((hid_t)*dset_id, H5R_DATASET_REGION, ref)) < 0)
HGOTO_DONE(FAIL)
/* Copy the dataspace ID */
*space_id = (hid_t_f)c_space_id;
done:
return ret_value;
} /* end h5rget_region_ptr_c() */
/****if* H5Rf/h5rget_object_type_obj_c
* NAME
* h5rget_object_type_obj_c
* PURPOSE
* Call H5Rget_object_type to retrieve the type of the object reference points
* to
* INPUTS
* dset_id - dataset identifier
* ref - reference to the dataset region
* OUTPUTS
* obj_type - type of dereferenced object
* RETURNS
* 0 on success, -1 on failure
* AUTHOR
* Elena Pourmal
* Wednesday, December 1, 1999
* HISTORY
*
* SOURCE
*/
int_f
h5rget_object_type_obj_c(hid_t_f *dset_id, haddr_t_f *ref, int_f *obj_type)
/******/
{
H5O_type_t c_obj_type;
hobj_ref_t ref_c = (hobj_ref_t)*ref;
int_f ret_value = 0;
/*
* Call H5Rget_object_type function.
*/
if(H5Rget_obj_type2((hid_t)*dset_id, H5R_OBJECT, &ref_c, &c_obj_type) < 0)
HGOTO_DONE(FAIL)
/* Copy the object type */
*obj_type = (int_f)c_obj_type;
done:
return ret_value;
} /* end h5rget_object_type_obj_c() */
/****if* H5Rf/h5rget_name_ptr_c
* NAME
* h5rget_name_ptr_c
* PURPOSE
* Call H5Rget_name
* INPUTS
*
* loc_id - Identifier for the dataset containing the reference or for the group that dataset is in.
* ref_type - Type of reference.
* ref - An object or dataset region reference.
*
* OUTPUTS
* name - A name associated with the referenced object or dataset region.
* size - The size of the name buffer.
*
* RETURNS
* 0 on success, -1 on failure
* AUTHOR
* M. Scot Breitenfeld
* June 20, 2008
* HISTORY
*
* SOURCE
*/
int_f
h5rget_name_ptr_c (hid_t_f *loc_id, int_f *ref_type, void *ref, _fcd name, size_t_f *name_len, size_t_f *size_default)
/******/
{
int_f ret_value = -1;
ssize_t c_size;
size_t c_bufsize;
char *c_buf= NULL; /* Buffer to hold C string */
c_bufsize = (size_t)*name_len+1;
/*
* Allocate buffer to hold name of an attribute
*/
if ((c_buf = (char *)HDmalloc(c_bufsize)) == NULL)
return ret_value;
/*
* Call H5Rget_name function.
*/
if((c_size=H5Rget_name((hid_t)*loc_id, (H5R_type_t)*ref_type, ref, c_buf, c_bufsize)) < 0){
if(c_buf) HDfree(c_buf);
return ret_value;
}
/*
* Convert C name to FORTRAN and place it in the given buffer
*/
HD5packFstring(c_buf, _fcdtocp(name), c_bufsize-1);
*size_default = (size_t_f)c_size;
ret_value = 0;
if(c_buf) HDfree(c_buf);
return ret_value;
}
/****if* H5Rf/h5rget_obj_type_c
* NAME
* h5rget_obj_type_c
* PURPOSE
* Call H5Rget_obj_type
* INPUTS
* loc_id - Identifier for the dataset containing the reference or
* for the group that dataset is in.
* ref_type - Type of reference to query.
* ref - Reference to query.
*
* OUTPUTS
* obj_type - Type of referenced object. These are defined in H5Opublic.h,
* enum H5O_type_t
*
* RETURNS
* 0 on success, -1 on failure
* AUTHOR
* M. Scot Breitenfeld
* December 17, 2008
*
* SOURCE
*/
int_f
h5rget_obj_type_c (hid_t_f *loc_id, int_f *ref_type, void *ref, int_f *obj_type)
/******/
{
int_f ret_value = -1;
H5O_type_t obj_type_c;
/*
* Call H5Rget_obj_type function.
*/
if((H5Rget_obj_type2((hid_t)*loc_id, (H5R_type_t)*ref_type, ref, &obj_type_c)) < 0)
return ret_value;
*obj_type = (int_f)obj_type_c;
ret_value = 0;
return ret_value;
}
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/************************************************************
This example illustrates the concept of the virtual dataset.
Percival use case. Every fifth 10x10 plane in VDS is stored in
the corresponding 3D unlimited dataset.
There are 4 source datasets total.
This file is intended for use with HDF5 Library version 1.10
************************************************************/
/* EIP Add link to the picture */
#include "hdf5.h"
#include <stdio.h>
#include <stdlib.h>
#define VFILE "vds-percival-unlim.h5"
#define DATASET "VDS-Percival-unlim"
#define VDSDIM0 H5S_UNLIMITED
#define VDSDIM1 10
#define VDSDIM2 10
#define DIM0 H5S_UNLIMITED
#define DIM0_1 10 /* Initial size of the datasets */
#define DIM1 10
#define DIM2 10
#define RANK 3
#define PLANE_STRIDE 4
const char *SRC_FILE[] = {
"a.h5",
"b.h5",
"c.h5",
"d.h5"
};
const char *SRC_DATASET[] = {
"A",
"B",
"C",
"D"
};
int
main (void)
{
hid_t vfile, file, src_space, mem_space, vspace,
vdset, dset; /* Handles */
hid_t dcpl;
herr_t status;
hsize_t vdsdims[3] = {4*DIM0_1, VDSDIM1, VDSDIM2},
vdsdims_max[3] = {VDSDIM0, VDSDIM1, VDSDIM2},
dims[3] = {DIM0_1, DIM1, DIM2},
extdims[3] = {2*DIM0_1, DIM1, DIM2},
chunk_dims[3] = {DIM0_1, DIM1, DIM2},
dims_max[3] = {DIM0, DIM1, DIM2},
vdsdims_out[3],
vdsdims_max_out[3],
start[3], /* Hyperslab parameters */
stride[3],
count[3],
src_count[3],
block[3];
hsize_t start_out[3], /* Hyperslab parameter out */
stride_out[3],
count_out[3],
block_out[3];
int i, j, k;
H5D_layout_t layout; /* Storage layout */
size_t num_map; /* Number of mappings */
ssize_t len; /* Length of the string; also a return value */
char *filename;
char *dsetname;
int wdata[DIM0_1*DIM1*DIM2];
int rdata[80][10][10];
int a_rdata[20][10][10];
/*
* Create source files and datasets. This step is optional.
*/
for (i=0; i < PLANE_STRIDE; i++) {
/*
* Initialize data for i-th source dataset.
*/
for (j = 0; j < DIM0_1*DIM1*DIM2; j++) wdata[j] = i+1;
/*
* Create the source files and datasets. Write data to each dataset and
* close all resources.
*/
file = H5Fcreate (SRC_FILE[i], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
src_space = H5Screate_simple (RANK, dims, dims_max);
dcpl = H5Pcreate(H5P_DATASET_CREATE);
status = H5Pset_chunk (dcpl, RANK, chunk_dims);
dset = H5Dcreate2 (file, SRC_DATASET[i], H5T_NATIVE_INT, src_space, H5P_DEFAULT,
dcpl, H5P_DEFAULT);
status = H5Dwrite (dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
wdata);
status = H5Sclose (src_space);
status = H5Pclose (dcpl);
status = H5Dclose (dset);
status = H5Fclose (file);
}
vfile = H5Fcreate (VFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* Create VDS dataspace. */
vspace = H5Screate_simple (RANK, vdsdims, vdsdims_max);
/* Create dataspaces for the source dataset. */
src_space = H5Screate_simple (RANK, dims, dims_max);
/* Create VDS creation property */
dcpl = H5Pcreate (H5P_DATASET_CREATE);
/* Initialize hyperslab values */
start[0] = 0;
start[1] = 0;
start[2] = 0;
stride[0] = PLANE_STRIDE; /* we will select every fifth plane in VDS */
stride[1] = 1;
stride[2] = 1;
count[0] = H5S_UNLIMITED;
count[1] = 1;
count[2] = 1;
src_count[0] = H5S_UNLIMITED;
src_count[1] = 1;
src_count[2] = 1;
block[0] = 1;
block[1] = DIM1;
block[2] = DIM2;
/*
* Build the mappings
*
*/
status = H5Sselect_hyperslab (src_space, H5S_SELECT_SET, start, NULL, src_count, block);
for (i=0; i < PLANE_STRIDE; i++) {
status = H5Sselect_hyperslab (vspace, H5S_SELECT_SET, start, stride, count, block);
status = H5Pset_virtual (dcpl, vspace, SRC_FILE[i], SRC_DATASET[i], src_space);
start[0]++;
}
H5Sselect_none(vspace);
/* Create a virtual dataset */
vdset = H5Dcreate2 (vfile, DATASET, H5T_NATIVE_INT, vspace, H5P_DEFAULT,
dcpl, H5P_DEFAULT);
status = H5Sclose (vspace);
status = H5Sclose (src_space);
status = H5Pclose (dcpl);
/* Let's get space of the VDS and its dimension; we should get 40x10x10 */
vspace = H5Dget_space (vdset);
H5Sget_simple_extent_dims (vspace, vdsdims_out, vdsdims_max_out);
printf ("VDS dimensions first time \n");
printf (" Current: ");
for (i=0; i<RANK; i++)
printf (" %d ", (int)vdsdims_out[i]);
printf ("\n");
/* Let's add data to the source datasets and check new dimensions for VDS */
for (i=0; i < PLANE_STRIDE; i++) {
/*
* Initialize data for i-th source dataset.
*/
for (j = 0; j < DIM0_1*DIM1*DIM2; j++) wdata[j] = 10*(i+1);
/*
* Create the source files and datasets. Write data to each dataset and
* close all resources.
*/
file = H5Fopen (SRC_FILE[i], H5F_ACC_RDWR, H5P_DEFAULT);
dset = H5Dopen2 (file, SRC_DATASET[i], H5P_DEFAULT);
status = H5Dset_extent (dset, extdims);
src_space = H5Dget_space (dset);
start[0] = DIM0_1;
start[1] = 0;
start[2] = 0;
count[0] = 1;
count[1] = 1;
count[2] = 1;
block[0] = DIM0_1;
block[1] = DIM1;
block[2] = DIM2;
mem_space = H5Screate_simple(RANK, dims, NULL);
status = H5Sselect_hyperslab (src_space, H5S_SELECT_SET, start, NULL, count, block);
status = H5Dwrite (dset, H5T_NATIVE_INT, mem_space, src_space, H5P_DEFAULT,
wdata);
status = H5Sclose (src_space);
status = H5Dclose (dset);
status = H5Fclose (file);
}
status = H5Dclose (vdset);
status = H5Fclose (vfile);
/*
* Now we begin the read section of this example.
*/
/*
* Open file and dataset using the default properties.
*/
vfile = H5Fopen (VFILE, H5F_ACC_RDONLY, H5P_DEFAULT);
vdset = H5Dopen2 (vfile, DATASET, H5P_DEFAULT);
/*
* Get creation property list and mapping properties.
*/
dcpl = H5Dget_create_plist (vdset);
/*
* Get storage layout.
*/
layout = H5Pget_layout (dcpl);
if (H5D_VIRTUAL == layout)
printf(" Dataset has a virtual layout \n");
else
printf(" Wrong layout found \n");
/*
* Find number of mappings.
*/
status = H5Pget_virtual_count (dcpl, &num_map);
printf(" Number of mappings is %lu\n", (unsigned long)num_map);
/*
* Get mapping parameters for each mapping.
*/
for (i = 0; i < (int)num_map; i++) {
printf(" Mapping %d \n", i);
printf(" Selection in the virtual dataset \n");
/* Get selection in the virttual dataset */
vspace = H5Pget_virtual_vspace (dcpl, (size_t)i);
if (H5Sget_select_type(vspace) == H5S_SEL_HYPERSLABS) {
if (H5Sis_regular_hyperslab(vspace)) {
status = H5Sget_regular_hyperslab (vspace, start_out, stride_out, count_out, block_out);
printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], (unsigned long long)start_out[1], (unsigned long long)start_out[2]);
printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]);
printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], (unsigned long long)count_out[1], (unsigned long long)count_out[2]);
printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], (unsigned long long)block_out[1], (unsigned long long)block_out[2]);
}
}
/* Get source file name */
len = H5Pget_virtual_filename (dcpl, (size_t)i, NULL, 0);
filename = (char *)malloc((size_t)len*sizeof(char)+1);
H5Pget_virtual_filename (dcpl, (size_t)i, filename, len+1);
printf(" Source filename %s\n", filename);
/* Get source dataset name */
len = H5Pget_virtual_dsetname (dcpl, (size_t)i, NULL, 0);
dsetname = (char *)malloc((size_t)len*sizeof(char)+1);
H5Pget_virtual_dsetname (dcpl, (size_t)i, dsetname, len+1);
printf(" Source dataset name %s\n", dsetname);
/* Get selection in the source dataset */
printf(" Selection in the source dataset \n");
src_space = H5Pget_virtual_srcspace (dcpl, (size_t)i);
if (H5Sget_select_type(src_space) == H5S_SEL_HYPERSLABS) {
if (H5Sis_regular_hyperslab(src_space)) {
status = H5Sget_regular_hyperslab (src_space, start_out, stride_out, count_out, block_out);
printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], (unsigned long long)start_out[1], (unsigned long long)start_out[2]);
printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]);
printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], (unsigned long long)count_out[1], (unsigned long long)count_out[2]);
printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], (unsigned long long)block_out[1], (unsigned long long)block_out[2]);
}
}
H5Sclose(vspace);
H5Sclose(src_space);
free(filename);
free(dsetname);
}
/*
* Read data from VDS.
*/
vspace = H5Dget_space (vdset);
H5Sget_simple_extent_dims (vspace, vdsdims_out, vdsdims_max_out);
printf ("VDS dimensions second time \n");
printf (" Current: ");
for (i=0; i<RANK; i++)
printf (" %d ", (int)vdsdims_out[i]);
printf ("\n");
/* Read all VDS data */
/* EIP We should be able to do it by using H5S_ALL instead of making selection
* or using H5Sselect_all from vspace.
*/
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = 1;
count[1] = 1;
count[2] = 1;
block[0] = vdsdims_out[0];
block[1] = vdsdims_out[1];
block[2] = vdsdims_out[2];
status = H5Sselect_hyperslab (vspace, H5S_SELECT_SET, start, NULL, count, block);
mem_space = H5Screate_simple(RANK, vdsdims_out, NULL);
status = H5Dread (vdset, H5T_NATIVE_INT, mem_space, vspace, H5P_DEFAULT,
rdata);
printf (" All data: \n");
for (i=0; i < (int)vdsdims_out[0]; i++) {
for (j=0; j < (int)vdsdims_out[1]; j++) {
printf ("(%d, %d, 0)", i, j);
for (k=0; k < (int)vdsdims_out[2]; k++)
printf (" %d ", rdata[i][j][k]);
printf ("\n");
}
}
/* Read VDS, but only data mapeed to dataset a.h5 */
start[0] = 0;
start[1] = 0;
start[2] = 0;
stride[0] = PLANE_STRIDE;
stride[1] = 1;
stride[2] = 1;
count[0] = 2*DIM0_1;
count[1] = 1;
count[2] = 1;
block[0] = 1;
block[1] = vdsdims_out[1];
block[2] = vdsdims_out[2];
dims[0] = 2*DIM0_1;
status = H5Sselect_hyperslab (vspace, H5S_SELECT_SET, start, stride, count, block);
mem_space = H5Screate_simple(RANK, dims, NULL);
status = H5Dread (vdset, H5T_NATIVE_INT, mem_space, vspace, H5P_DEFAULT,
a_rdata);
printf (" All data: \n");
for (i=0; i < 2*DIM0_1; i++) {
for (j=0; j < (int)vdsdims_out[1]; j++) {
printf ("(%d, %d, 0)", i, j);
for (k=0; k < (int)vdsdims_out[2]; k++)
printf (" %d ", a_rdata[i][j][k]);
printf ("\n");
}
}
/*
* Close and release resources.
*/
status = H5Sclose(mem_space);
status = H5Pclose (dcpl);
status = H5Dclose (vdset);
status = H5Fclose (vfile);
return 0;
}
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