HDF5 documents and links Introduction to HDF5 HDF5 Reference Manual HDF5 User's Guide for Release 1.6 | And in this document, the HDF5 User's Guide from Release 1.4.5: Files Datasets Datatypes Dataspaces Groups References Attributes Property Lists Error Handling Filters Caching Chunking Mounting Files Performance Debugging Environment DDL

# The Reference Interface (H5R) and
the Identifier Interface (H5I)

## 1. Introduction

This document discusses the kinds of references implemented (and planned) in HDF5 and the functions implemented (and planned) to support them.

## 2. References

This section contains an overview of the kinds of references implemented, or planned for implementation, in HDF5.

Object reference
  Reference to an entire object in the current HDF5 file.

  An object reference points to an entire object in the current HDF5 file by storing the relative file address (OID) of the object header for the object pointed to. The relative file address of an object header is constant for the life of the object. An object reference is of a fixed size in the file.

Dataset region reference
  Reference to a specific dataset region.

  A dataset region reference points to a region of a dataset in the current HDF5 file by storing the OID of the dataset and the global heap offset of the region referenced. The region referenced is located by retrieving the coordinates of the areas in the region from the global heap. A dataset region reference is of a variable size in the file.

Note: All references are treated as soft links for the purposes of reference counting. The library does not keep track of reference links and they may dangle if the object they refer to is deleted, moved, or not yet available.

## 3. Reference Types

Valid HDF5 reference types for use in the H5R functions are as follows:

Reference Type | Value | Description
--- | --- | ---
`H5R_OBJECT` | `0` | Object reference
`H5R_DATASET_REGION` | `1` | Dataset region reference

## 4. Functions

Five functions, four in the H5R interface and one in the H5I interface, have been implemented to support references. The H5I function is also useful outside the context of references.

herr_t `H5Rcreate(`void *`reference,` hid_t `loc_id,` const char *`name,` H5R_type_t `type,` hid_t `space_id)`
  `H5Rcreate` creates an object which is a particular type of reference (specified with the `type` parameter) to some file object and/or location specified with the `space_id` parameter. For dataset region references, the selection specified in the dataspace is the portion of the dataset which will be referred to.

hid_t `H5Rdereference(`hid_t `dset,` H5R_type_t `rtype,` void *`reference)`
  `H5Rdereference` opens the object referenced and returns an identifier for that object. The parameter `reference` specifies a reference of type `rtype` that is stored in the dataset `dset`.

int `H5Rget_object_type(`hid_t `obj_id,` void *`reference)`
  `H5Rget_object_type` retrieves the type of object that an object reference points to. The parameter `obj_id` specifies the dataset containing the reference object or the location identifier of the object that the dataset is located within. The parameter `reference` specifies the reference being queried.

H5S_t `H5Rget_region(`H5D_t `dataset,` H5R_type_t `type,` void *`reference)`
  `H5Rget_region` creates a copy of dataspace of the dataset that is pointed to and defines a selection in the copy which is the location (or region) pointed to. The parameter `ref` specifies a reference of type `rtype` that is stored in the dataset `dset`.

H5I_type_t `H5Iget_type(`hid_t `id)`
  Returns the type of object referred to by the identifier `id`. Valid return values appear in the following list:

  `H5I_FILE` | File objects
  `H5I_GROUP` | Group objects
  `H5I_DATATYPE` | Datatype objects
  `H5I_DATASPACE` | Dataspace objects
  `H5I_DATASET` | Dataset objects
  `H5I_ATTR` | Attribute objects

  This function was inspired by the need of users to figure out which type of object closing function (`H5Dclose`, `H5Gclose`, etc.) to call after a call to `H5Rdereference`, but it is also of general use.

## 5. Examples

Object Reference Writing Example
Create a dataset which has links to other datasets as part of its raw data and write the dataset to the file.

    {
        hid_t file1;
        hid_t dataset1;
        hid_t datatype, dataspace;
        char buf[128];
        hobj_ref_t link;
        hobj_ref_t data[10][10];
        int rank;
        size_t dimsf[2];
        int i, j;

        /* Open the file */
        file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);

        /* Describe the size of the array and create the data space */
        rank=2;
        dimsf[0] = 10;
        dimsf[1] = 10;
        dataspace = H5Screate_simple(rank, dimsf, NULL);

        /* Define datatype */
        datatype = H5Tcopy(H5T_STD_REF_OBJ);

        /* Create a dataset */
        dataset1=H5Dcreate(file1,"Dataset One",datatype,dataspace,H5P_DEFAULT);

        /* Construct array of OIDs for other datasets in the file */
        /* somewhat hokey and artificial, but demonstrates the point */
        for(i=0; i<10; i++)
            for(j=0; j<10; j++)
              {
                sprintf(buf,"/Group/Linked Set %d-%d",i,j);
                if(H5Rcreate(&link,file1,buf,H5R_OBJECT,-1)>0)
                    data[i][j]=link;
              } /* end for */

        /* Write the data to the dataset using default transfer properties.  */
        H5Dwrite(dataset, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);

        /* Close everything */
        H5Sclose(dataspace);
        H5Tclose(datatype);
        H5Dclose(dataset1);
        H5Fclose(file1);
    }

Object Reference Reading Example
Open a dataset which has links to other datasets as part of its raw data and read in those links.

    {
        hid_t file1;
        hid_t dataset1, tmp_dset;
        href_t data[10][10];
        int i, j;

        /* Open the file */
        file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);

        /* Open the dataset */
        dataset1=H5Dopen(file1,"Dataset One",H5P_DEFAULT);

        /*
         * Read the data to the dataset using default transfer properties.
         * (we are assuming the dataset is the same and not querying the
         *  dimensions, etc.)
         */
        H5Dread(dataset, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);

        /* Analyze array of OIDs of linked datasets in the file */
        /* somewhat hokey and artificial, but demonstrates the point */
        for(i=0; i<10; i++)
            for(j=0; j<10; i++)
              {
                if((tmp_dset=H5Rdereference(dataset, H5T_STD_REF_OBJ, data[i][j]))>0)
                  {

                  } /* end if */
                H5Dclose(tmp_dset);
              } /* end for */

        /* Close everything */
        H5Dclose(dataset1);
        H5Fclose(file1);
    }

Dataset Region Reference Writing Example
Create a dataset which has links to other dataset regions (single elements in this case) as part of its raw data and write the dataset to the file.

    {
        hid_t file1;
        hid_t dataset1, dataset2;
        hid_t datatype, dataspace1, dataspace2;
        char buf[128];
        href_t link;
        href_t data[10][10];     /* HDF5 reference type */
        int rank;
        size_t dimsf[2];
        hsize_t start[3],count[3];
        int i, j;

        /* Open the file */
        file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);

        /* Describe the size of the array and create the data space */
        rank=2;
        dimsf[0] = 10;
        dimsf[1] = 10;
        dataspace1 = H5Screate_simple(rank, dimsf, NULL);

        /* Define Dataset Region Reference datatype */
        datatype = H5Tcopy(H5T_STD_REF_DATAREG);

        /* Create a dataset */
        dataset1=H5Dcreate(file1,"Dataset One",datatype,dataspace1,H5P_DEFAULT);

        /* Construct array of OIDs for other datasets in the file */
        /* (somewhat artificial, but demonstrates the point) */
        for(i=0; i<10; i++)
            for(j=0; j<10; i++)
              {
                sprintf(buf,"/Group/Linked Set %d-%d",i,j);

                /* Get the dataspace for the object to point to */
                dataset2=H5Dopen(file1,buf,H5P_DEFAULT);
                dataspace2=H5Dget_space(dataspace2);

                /* Select the region to point to */
                /* (could be different region for each pointer) */
                start[0]=5; start[1]=4; start[2]=3;
                count[0]=2; count[1]=4; count[2]=1;
                H5Sselect_hyperslab(dataspace2,H5S_SELECT_SET,start,NULL,count,NULL);

                if(H5Rcreate(&link,file1,buf,H5R_REF_DATAREG,dataspace2)>0)
                    /* Store the reference */
                    data[i][j]=link;

                H5Sclose(dataspace2);
                H5Dclose(dataspace2);
              } /* end for */

        /* Write the data to the dataset using default transfer properties.  */
        H5Dwrite(dataset, H5T_STD_REF_DATAREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);

        /* Close everything */
        H5Sclose(dataspace);
        H5Tclose(datatype);
        H5Dclose(dataset1);
        H5Fclose(file1);
    }

Dataset Region Reference Reading Example
Open a dataset which has links to other datasets regions (single elements in this case) as part of its raw data and read in those links.

    {
        hid_t file1;
        hid_t dataset1, tmp_dset;
        hid_t dataspace;
        href_t data[10][10];     /* HDF5 reference type */
        int i, j;

        /* Open the file */
        file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);

        /* Open the dataset */
        dataset1=H5Dopen(file1,"Dataset One",H5P_DEFAULT);

        /*
         * Read the data to the dataset using default transfer properties.
         * (we are assuming the dataset is the same and not querying the
         *  dimensions, etc.)
         */
        H5Dread(dataset, H5T_STD_REF_DATAREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);

        /* Analyze array of OIDs of linked datasets in the file */
        /* (somewhat artificial, but demonstrates the point) */
        for(i=0; i<10; i++)
            for(j=0; j<10; i++)
              {
                if((tmp_dset=H5Rdereference(dataset, H5D_STD_REF_DATAREG,data[i][j]))>0)
                  {
                      /* Get the dataspace with the pointed to region selected */
                      dataspace=H5Rget_space(data[i][j]);

                      H5Sclose(dataspace);
                  } /* end if */
                H5Dclose(tmp_dset);
              } /* end for */

        /* Close everything */
        H5Dclose(dataset1);
        H5Fclose(file1);
    }

HDF5 documents and links Introduction to HDF5 HDF5 Reference Manual HDF5 User's Guide for Release 1.6 | And in this document, the HDF5 User's Guide from Release 1.4.5: Files Datasets Datatypes Dataspaces Groups References Attributes Property Lists Error Handling Filters Caching Chunking Mounting Files Performance Debugging Environment DDL

Last modified: 2 August 2004