Пример #1
0
/*-------------------------------------------------------------------------
* Function: diff_datasetid
*
* Purpose: check for comparable datasets and read into a compatible
*  memory type
*
* Return: Number of differences found
*
* Programmer: Pedro Vicente, [email protected]
*
* Date: May 9, 2003
*
* Modifications:
*
*
* October 2006:  Read by hyperslabs for big datasets.
*
*  A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done
*  i.e., if the memory needed to read a dataset is greater than this limit,
*  then hyperslab I/O is done instead of one operation I/O
*  For each dataset, the memory needed is calculated according to
*
*  memory needed = number of elements * size of each element
*
*  if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
*  are done
*
*  H5Dread( input_dataset1 )
*  H5Dread( input_dataset2 )
*
*  with all elements in the datasets selected. If the memory needed is greater than
*  H5TOOLS_MALLOCSIZE, then the following operations are done instead:
*
*  a strip mine is defined for each dimension k (a strip mine is defined as a
*  hyperslab whose size is memory manageable) according to the formula
*
*  (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type)
*
*  where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures
*  that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip
*  mine size k is simply defined as its dimension k, but for larger datasets the
*  hyperslab size is still memory manageable.
*  a cycle is done until the number of elements in the dataset is reached. In each
*  iteration, two parameters are defined for the function H5Sselect_hyperslab,
*  the start and size of each hyperslab, according to
*
*  (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k])
*
*  where hyperslab_offset [k] is initially set to zero, and later incremented in
*  hyperslab_size[k] offsets. The reason for the operation
*
*  dimension[k] - hyperslab_offset[k]
*
*  in (2) is that, when using the strip mine size, it assures that the "remaining" part
*  of the dataset that does not fill an entire strip mine is processed.
*
*-------------------------------------------------------------------------
*/
hsize_t diff_datasetid( hid_t did1,
                        hid_t did2,
                        const char *obj1_name,
                        const char *obj2_name,
                        diff_opt_t *options)
{
    hid_t      sid1=-1;
    hid_t      sid2=-1;
    hid_t      f_tid1=-1;
    hid_t      f_tid2=-1;
    hid_t      m_tid1=-1;
    hid_t      m_tid2=-1;
    size_t     m_size1;
    size_t     m_size2;
    H5T_sign_t sign1;
    H5T_sign_t sign2;
    int        rank1;
    int        rank2;
    hsize_t    nelmts1;
    hsize_t    nelmts2;
    hsize_t    dims1[H5S_MAX_RANK];
    hsize_t    dims2[H5S_MAX_RANK];
    hsize_t    maxdim1[H5S_MAX_RANK];
    hsize_t    maxdim2[H5S_MAX_RANK];
    const char *name1=NULL;            /* relative names */
    const char *name2=NULL;
    hsize_t    storage_size1;
    hsize_t    storage_size2;
    hsize_t    nfound=0;               /* number of differences found */
    int        can_compare=1;          /* do diff or not */
    void       *buf1=NULL;
    void       *buf2=NULL;
    void       *sm_buf1=NULL;
    void       *sm_buf2=NULL;
    hid_t      sm_space;               /*stripmine data space */
    size_t     need;                   /* bytes needed for malloc */
    int        i;
    unsigned int  vl_data = 0;         /*contains VL datatypes */

    /* Get the dataspace handle */
    if ( (sid1 = H5Dget_space(did1)) < 0 )
        goto error;

    /* Get rank */
    if ( (rank1 = H5Sget_simple_extent_ndims(sid1)) < 0 )
        goto error;

    /* Get the dataspace handle */
    if ( (sid2 = H5Dget_space(did2)) < 0 )
        goto error;

    /* Get rank */
    if ( (rank2 = H5Sget_simple_extent_ndims(sid2)) < 0 )
        goto error;

    /* Get dimensions */
    if ( H5Sget_simple_extent_dims(sid1,dims1,maxdim1) < 0 )
        goto error;

    /* Get dimensions */
    if ( H5Sget_simple_extent_dims(sid2,dims2,maxdim2) < 0 )
    {
        goto error;
    }

    /*-------------------------------------------------------------------------
    * get the file data type
    *-------------------------------------------------------------------------
    */

    /* Get the data type */
    if ( (f_tid1 = H5Dget_type(did1)) < 0 )
        goto error;

    /* Get the data type */
    if ( (f_tid2 = H5Dget_type(did2)) < 0 )
    {
        goto error;
    }

    /*-------------------------------------------------------------------------
    * check for empty datasets
    *-------------------------------------------------------------------------
    */

    storage_size1=H5Dget_storage_size(did1);
    storage_size2=H5Dget_storage_size(did2);

    if (storage_size1==0 || storage_size2==0)
    {
        if ( (options->m_verbose||options->m_list_not_cmp) && obj1_name && obj2_name)
            parallel_print("Not comparable: <%s> or <%s> is an empty dataset\n", obj1_name, obj2_name);
        can_compare=0;
        options->not_cmp=1;
    }

    /*-------------------------------------------------------------------------
    * check for comparable TYPE and SPACE
    *-------------------------------------------------------------------------
    */

    if (diff_can_type(f_tid1,
        f_tid2,
        rank1,
        rank2,
        dims1,
        dims2,
        maxdim1,
        maxdim2,
        obj1_name,
        obj2_name,
        options,
        0)!=1)
    {
        can_compare=0;
    }

    /*-------------------------------------------------------------------------
    * memory type and sizes
    *-------------------------------------------------------------------------
    */
    if ((m_tid1=h5tools_get_native_type(f_tid1)) < 0)
        goto error;

    if ((m_tid2=h5tools_get_native_type(f_tid2)) < 0)
        goto error;

    m_size1 = H5Tget_size( m_tid1 );
    m_size2 = H5Tget_size( m_tid2 );

    /*-------------------------------------------------------------------------
    * check for different signed/unsigned types
    *-------------------------------------------------------------------------
    */
    if (can_compare)
    {
        sign1=H5Tget_sign(m_tid1);
        sign2=H5Tget_sign(m_tid2);
        if ( sign1 != sign2 )
        {
            if ((options->m_verbose||options->m_list_not_cmp) && obj1_name && obj2_name)
            {
                parallel_print("Not comparable: <%s> has sign %s ", obj1_name, get_sign(sign1));
                parallel_print("and <%s> has sign %s\n", obj2_name, get_sign(sign2));
            }
    
            can_compare=0;
            options->not_cmp=1;
        }
    }

    /* Check if type is either VLEN-data or VLEN-string to reclaim any
     * VLEN memory buffer later */
    if( TRUE == h5tools_detect_vlen(m_tid1) )
        vl_data = TRUE;

    /*------------------------------------------------------------------------
    * only attempt to compare if possible
    *-------------------------------------------------------------------------
    */
    if(can_compare) /* it is possible to compare */
    {

        /*-----------------------------------------------------------------
        * get number of elements
        *------------------------------------------------------------------
        */
        nelmts1 = 1;
        for(i = 0; i < rank1; i++)
            nelmts1 *= dims1[i];

        nelmts2 = 1;
        for(i = 0; i < rank2; i++)
            nelmts2 *= dims2[i];

        HDassert(nelmts1 == nelmts2);

        /*-----------------------------------------------------------------
        * "upgrade" the smaller memory size
        *------------------------------------------------------------------
        */

        if (FAIL == match_up_memsize (f_tid1, f_tid2,
                                      &m_tid1, &m_tid2, 
                                      &m_size1, &m_size2))
            goto error;

        /* print names */
        if(obj1_name)
            name1 = diff_basename(obj1_name);
        if(obj2_name)
            name2 = diff_basename(obj2_name);


        /*----------------------------------------------------------------
        * read/compare
        *-----------------------------------------------------------------
        */
        need = (size_t)(nelmts1 * m_size1);  /* bytes needed */
        if(need < H5TOOLS_MALLOCSIZE) {
            buf1 = HDmalloc(need);
            buf2 = HDmalloc(need);
        } /* end if */

        if(buf1 != NULL && buf2 != NULL) {
            if(H5Dread(did1, m_tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf1) < 0)
                goto error;
            if(H5Dread(did2, m_tid2, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf2) < 0)
                goto error;

            /* array diff */
            nfound = diff_array(buf1, buf2, nelmts1, (hsize_t)0, rank1, dims1,
                options, name1, name2, m_tid1, did1, did2);

            /* reclaim any VL memory, if necessary */
            if(vl_data) {
                H5Dvlen_reclaim(m_tid1, sid1, H5P_DEFAULT, buf1);
                H5Dvlen_reclaim(m_tid2, sid2, H5P_DEFAULT, buf2);
            } /* end if */
        } /* end if */
        else /* possibly not enough memory, read/compare by hyperslabs */
        {
            size_t        p_type_nbytes = m_size1; /*size of memory type */
            hsize_t       p_nelmts = nelmts1;      /*total selected elmts */
            hsize_t       elmtno;                  /*counter  */
            int           carry;                   /*counter carry value */

            /* stripmine info */
            hsize_t       sm_size[H5S_MAX_RANK];   /*stripmine size */
            hsize_t       sm_nbytes;               /*bytes per stripmine */
            hsize_t       sm_nelmts;               /*elements per stripmine*/

            /* hyperslab info */
            hsize_t       hs_offset[H5S_MAX_RANK]; /*starting offset */
            hsize_t       hs_size[H5S_MAX_RANK];   /*size this pass */
            hsize_t       hs_nelmts;               /*elements in request */
            hsize_t       zero[8];                 /*vector of zeros */

            /*
             * determine the strip mine size and allocate a buffer. The strip mine is
             * a hyperslab whose size is manageable.
             */
            sm_nbytes = p_type_nbytes;

            for(i = rank1; i > 0; --i) {
                hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;

                if(size == 0) /* datum size > H5TOOLS_BUFSIZE */
                    size = 1;
                sm_size[i - 1] = MIN(dims1[i - 1], size);
                sm_nbytes *= sm_size[i - 1];
                HDassert(sm_nbytes > 0);
            } /* end for */

            /* malloc return code should be verified.
             * If fail, need to handle the error.
             * This else branch should be recoded as a separate function.
             * Note that there are many "goto error" within this branch
             * that fails to address freeing other objects created here.
             * E.g., sm_space.
             */
            sm_buf1 = HDmalloc((size_t)sm_nbytes);
            HDassert(sm_buf1);
            sm_buf2 = HDmalloc((size_t)sm_nbytes);
            HDassert(sm_buf2);

            sm_nelmts = sm_nbytes / p_type_nbytes;
            sm_space = H5Screate_simple(1, &sm_nelmts, NULL);

            /* the stripmine loop */
            HDmemset(hs_offset, 0, sizeof hs_offset);
            HDmemset(zero, 0, sizeof zero);

            for(elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) {
                /* calculate the hyperslab size */
                if(rank1 > 0) {
                    for(i = 0, hs_nelmts = 1; i < rank1; i++) {
                        hs_size[i] = MIN(dims1[i] - hs_offset[i], sm_size[i]);
                        hs_nelmts *= hs_size[i];
                    } /* end for */
                    if(H5Sselect_hyperslab(sid1, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0)
                        goto error;
                    if(H5Sselect_hyperslab(sid2, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0)
                        goto error;
                    if(H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) < 0)
                        goto error;
                } /* end if */
                else
                    hs_nelmts = 1;

                if(H5Dread(did1,m_tid1,sm_space,sid1,H5P_DEFAULT,sm_buf1) < 0)
                    goto error;
                if(H5Dread(did2,m_tid2,sm_space,sid2,H5P_DEFAULT,sm_buf2) < 0)
                    goto error;

                /* get array differences. in the case of hyperslab read, increment the number of differences
                found in each hyperslab and pass the position at the beggining for printing */
                nfound += diff_array(sm_buf1, sm_buf2, hs_nelmts, elmtno, rank1,
                    dims1, options, name1, name2, m_tid1, did1, did2);

                /* reclaim any VL memory, if necessary */
                if(vl_data) {
                    H5Dvlen_reclaim(m_tid1, sm_space, H5P_DEFAULT, sm_buf1);
                    H5Dvlen_reclaim(m_tid1, sm_space, H5P_DEFAULT, sm_buf2);
                } /* end if */

                /* calculate the next hyperslab offset */
                for(i = rank1, carry = 1; i > 0 && carry; --i) {
                    hs_offset[i - 1] += hs_size[i - 1];
                    if(hs_offset[i - 1] == dims1[i - 1])
                        hs_offset[i - 1] = 0;
                    else
                        carry = 0;
                } /* i */
            } /* elmtno */

            H5Sclose(sm_space);
        } /* hyperslab read */
    } /*can_compare*/


    /*-------------------------------------------------------------------------
     * close
     *-------------------------------------------------------------------------
     */

    /* free */
    if(buf1 != NULL) {
        HDfree(buf1);
        buf1 = NULL;
    } /* end if */
    if(buf2 != NULL) {
        HDfree(buf2);
        buf2 = NULL;
    } /* end if */
    if(sm_buf1 != NULL) {
        HDfree(sm_buf1);
        sm_buf1 = NULL;
    } /* end if */
    if(sm_buf2 != NULL) {
        HDfree(sm_buf2);
        sm_buf2 = NULL;
    } /* end if */

    H5E_BEGIN_TRY {
        H5Sclose(sid1);
        H5Sclose(sid2);
        H5Tclose(f_tid1);
        H5Tclose(f_tid2);
        H5Tclose(m_tid1);
        H5Tclose(m_tid2);
    } H5E_END_TRY;

    return nfound;

error:
    options->err_stat=1;

    /* free */
    if (buf1!=NULL)
    {
        /* reclaim any VL memory, if necessary */
        if(vl_data)
            H5Dvlen_reclaim(m_tid1, sid1, H5P_DEFAULT, buf1);
        HDfree(buf1);
        buf1=NULL;
    }
    if (buf2!=NULL)
    {
        /* reclaim any VL memory, if necessary */
        if(vl_data)
            H5Dvlen_reclaim(m_tid2, sid2, H5P_DEFAULT, buf2);
        HDfree(buf2);
        buf2=NULL;
    }
    if (sm_buf1!=NULL)
    {
        /* reclaim any VL memory, if necessary */
        if(vl_data)
            H5Dvlen_reclaim(m_tid1, sm_space, H5P_DEFAULT, sm_buf1);
        HDfree(sm_buf1);
        sm_buf1=NULL;
    }
    if (sm_buf2!=NULL)
    {
        /* reclaim any VL memory, if necessary */
        if(vl_data)
            H5Dvlen_reclaim(m_tid1, sm_space, H5P_DEFAULT, sm_buf2);
        HDfree(sm_buf2);
        sm_buf2=NULL;
    }

    /* disable error reporting */
    H5E_BEGIN_TRY {
        H5Sclose(sid1);
        H5Sclose(sid2);
        H5Tclose(f_tid1);
        H5Tclose(f_tid2);
        H5Tclose(m_tid1);
        H5Tclose(m_tid2);
        /* enable error reporting */
    } H5E_END_TRY;

    return nfound;
}
Пример #2
0
hsize_t diff_attr(hid_t loc1_id,
                  hid_t loc2_id,
                  const char *path1,
                  const char *path2,
                  diff_opt_t *options)
{
    hid_t      attr1_id=-1;     /* attr ID */
    hid_t      attr2_id=-1;     /* attr ID */
    hid_t      space1_id=-1;    /* space ID */
    hid_t      space2_id=-1;    /* space ID */
    hid_t      ftype1_id=-1;    /* file data type ID */
    hid_t      ftype2_id=-1;    /* file data type ID */
    int	       vstrtype1=0;     /* ftype1 is a variable string */
    int	       vstrtype2=0;     /* ftype2 is a variable string */
    hid_t      mtype1_id=-1;    /* memory data type ID */
    hid_t      mtype2_id=-1;    /* memory data type ID */
    size_t     msize1;          /* memory size of memory type */
    size_t     msize2;          /* memory size of memory type */
    void       *buf1=NULL;      /* data buffer */
    void       *buf2=NULL;      /* data buffer */
    int	       buf1hasdata=0;	/* buffer has data */
    int	       buf2hasdata=0;	/* buffer has data */
    hsize_t    nelmts1;         /* number of elements in dataset */
    int        rank1;           /* rank of dataset */
    int        rank2;           /* rank of dataset */
    hsize_t    dims1[H5S_MAX_RANK];/* dimensions of dataset */
    hsize_t    dims2[H5S_MAX_RANK];/* dimensions of dataset */
    char       *name1;
    char       *name2;
    char       np1[512];
    char       np2[512];
    unsigned   u;                  /* Local index variable */
    hsize_t    nfound = 0;
    hsize_t    nfound_total = 0;
    int       j;

    table_attrs_t * match_list_attrs = NULL;
    if( build_match_list_attrs(loc1_id, loc2_id, &match_list_attrs, options) < 0)
        goto error;

    /* if detect any unique extra attr */
    if(match_list_attrs->nattrs_only1 || match_list_attrs->nattrs_only2)
    {
        /* exit will be 1 */
        options->contents = 0;
    }

    for(u = 0; u < (unsigned)match_list_attrs->nattrs; u++)
    {
        if( (match_list_attrs->attrs[u].exist[0]) && (match_list_attrs->attrs[u].exist[1]) )
        {
        name1 = name2 = match_list_attrs->attrs[u].name;

       /*--------------
        * attribute 1 */
        if((attr1_id = H5Aopen(loc1_id, name1, H5P_DEFAULT)) < 0)
            goto error;

       /*--------------
        * attribute 2 */
        if((attr2_id = H5Aopen(loc2_id, name2, H5P_DEFAULT)) < 0)
            goto error;

        /* get the datatypes  */
        if((ftype1_id = H5Aget_type(attr1_id)) < 0)
            goto error;
	vstrtype1 = H5Tis_variable_str(ftype1_id);
        if((ftype2_id = H5Aget_type(attr2_id)) < 0)
            goto error;
	vstrtype2 = H5Tis_variable_str(ftype2_id);
	/* no compare if either one but not both are variable string type */
	if (vstrtype1 != vstrtype2){
	    if ((options->m_verbose||options->m_list_not_cmp))
		parallel_print("Not comparable: one of attribute <%s/%s> or <%s/%s> is of variable length type\n",
		    path1, name1, path2, name2);
	    options->not_cmp = 1;
	    return 0;
	}

        if((mtype1_id = h5tools_get_native_type(ftype1_id))<0)
            goto error;
        if((mtype2_id = h5tools_get_native_type(ftype2_id))<0)
            goto error;
        if((msize1 = H5Tget_size(mtype1_id))==0)
            goto error;
        if((msize2 = H5Tget_size(mtype2_id))==0)
            goto error;

        /* get the dataspace   */
        if((space1_id = H5Aget_space(attr1_id)) < 0)
            goto error;
        if((space2_id = H5Aget_space(attr2_id)) < 0)
            goto error;

        /* get dimensions  */
        if((rank1 = H5Sget_simple_extent_dims(space1_id, dims1, NULL)) < 0)
            goto error;
        if((rank2 = H5Sget_simple_extent_dims(space2_id, dims2, NULL)) < 0)
            goto error;


       /*----------------------------------------------------------------------
        * check for comparable TYPE and SPACE
        *----------------------------------------------------------------------
        */

        /* pass dims1 and dims2 for maxdims as well since attribute's maxdims
         * are always same */
        if( diff_can_type(ftype1_id, ftype2_id, rank1, rank2, dims1, dims2,
                          dims1, dims2, name1, name2, options, 0) != 1 )
        {
            if(H5Tclose(ftype1_id) < 0)
                goto error;
            if(H5Tclose(ftype2_id) < 0)
                goto error;
            if(H5Sclose(space1_id) < 0)
                goto error;
            if(H5Sclose(space2_id) < 0)
                goto error;
            if(H5Aclose(attr1_id) < 0)
                goto error;
            if(H5Aclose(attr2_id) < 0)
                goto error;
            if(H5Tclose(mtype1_id) < 0)
                goto error;
            if(H5Tclose(mtype2_id) < 0)
                goto error;

            continue;
        }

       /*-----------------------------------------------------------------
        * "upgrade" the smaller memory size
        *------------------------------------------------------------------
        */
        if (FAIL == match_up_memsize (ftype1_id, ftype2_id,
                                      &mtype1_id, &mtype2_id, 
                                      &msize1, &msize2))
            goto error;

        /*---------------------------------------------------------------------
        * read
        *----------------------------------------------------------------------
        */
        nelmts1 = 1;
        for(j = 0; j < rank1; j++)
            nelmts1 *= dims1[j];

        buf1 = (void *)HDmalloc((size_t)(nelmts1 * msize1));
        buf2 = (void *)HDmalloc((size_t)(nelmts1 * msize2));
        if(buf1 == NULL || buf2 == NULL){
            parallel_print( "cannot read into memory\n" );
            goto error;
        }
        if(H5Aread(attr1_id,mtype1_id,buf1) < 0){
	    parallel_print("Failed reading attribute1 %s/%s\n", path1, name1);
	    goto error;
	}else
	    buf1hasdata = 1;
        if(H5Aread(attr2_id,mtype2_id,buf2) < 0){
	    parallel_print("Failed reading attribute2 %s/%s\n", path2, name2);
	    goto error;
	}else
	    buf2hasdata = 1;

        /* format output string */
        HDsnprintf(np1, sizeof(np1), "%s of <%s>", name1, path1);
        HDsnprintf(np2, sizeof(np1), "%s of <%s>", name2, path2);

        /*---------------------------------------------------------------------
        * array compare
        *----------------------------------------------------------------------
        */

        /* always print name */
        /* verbose (-v) and report (-r) mode */
        if(options->m_verbose || options->m_report) {
            do_print_attrname("attribute", np1, np2);

            nfound = diff_array(buf1, buf2, nelmts1, (hsize_t)0, rank1, dims1,
                options, np1, np2, mtype1_id, attr1_id, attr2_id);
            print_found(nfound);
        }
        /* quiet mode (-q), just count differences */
        else if(options->m_quiet) {
            nfound = diff_array(buf1, buf2, nelmts1, (hsize_t)0, rank1, dims1,
                options, np1, np2, mtype1_id, attr1_id, attr2_id);
        }
        /* the rest (-c, none, ...) */
        else {
            nfound = diff_array(buf1, buf2, nelmts1, (hsize_t)0, rank1, dims1,
                options, np1, np2, mtype1_id, attr1_id, attr2_id);

                /* print info if compatible and difference found */
                if(nfound) {
                    do_print_attrname("attribute", np1, np2);
                    print_found(nfound);
                } /* end if */
        } /* end else */


       /*----------------------------------------------------------------------
        * close
        *----------------------------------------------------------------------
        */

        /* Free buf1 and buf2, check both VLEN-data VLEN-string to reclaim any 
         * VLEN memory first */
        if(TRUE == h5tools_detect_vlen(mtype1_id))
            H5Dvlen_reclaim(mtype1_id, space1_id, H5P_DEFAULT, buf1);
        HDfree(buf1);
        buf1 = NULL;

        if(TRUE == h5tools_detect_vlen(mtype2_id))
            H5Dvlen_reclaim(mtype2_id, space2_id, H5P_DEFAULT, buf2);
        HDfree(buf2);
        buf2 = NULL;

        if(H5Tclose(ftype1_id) < 0)
            goto error;
        if(H5Tclose(ftype2_id) < 0)
            goto error;
        if(H5Sclose(space1_id) < 0)
            goto error;
        if(H5Sclose(space2_id) < 0)
            goto error;
        if(H5Aclose(attr1_id) < 0)
            goto error;
        if(H5Aclose(attr2_id) < 0)
            goto error;
        if(H5Tclose(mtype1_id) < 0)
            goto error;
        if(H5Tclose(mtype2_id) < 0)
            goto error;

        nfound_total += nfound;
        }
    } /* u */

    table_attrs_free(match_list_attrs);

    return nfound_total;

error:
    H5E_BEGIN_TRY {
        if(buf1) {
            if(buf1hasdata && TRUE == h5tools_detect_vlen(mtype1_id))
                H5Dvlen_reclaim(mtype1_id, space1_id, H5P_DEFAULT, buf1);
            HDfree(buf1);
        } /* end if */
        if(buf2) {
            if(buf2hasdata && TRUE == h5tools_detect_vlen(mtype2_id))
                H5Dvlen_reclaim(mtype2_id, space2_id, H5P_DEFAULT, buf2);
            HDfree(buf2);
        } /* end if */

        table_attrs_free(match_list_attrs);

        H5Tclose(ftype1_id);
        H5Tclose(ftype2_id);
        H5Tclose(mtype1_id);
        H5Tclose(mtype2_id);
        H5Sclose(space1_id);
        H5Sclose(space2_id);
        H5Aclose(attr1_id);
        H5Aclose(attr2_id);
    } H5E_END_TRY;

    options->err_stat = 1;
    return nfound_total;
}
Пример #3
0
/*-------------------------------------------------------------------------
 * Function: copy_attr
 *
 * Purpose: copy attributes located in LOC_IN, which is obtained either from
 * loc_id = H5Gopen2( fid, name);
 * loc_id = H5Dopen2( fid, name);
 * loc_id = H5Topen2( fid, name);
 *
 * Return: 0, ok, -1 no
 *-------------------------------------------------------------------------
 */
int
copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
        trav_table_t *travt, pack_opt_t *options)
{
    int         ret_value = 0;
    hid_t       attr_id = -1;  /* attr ID */
    hid_t       attr_out = -1; /* attr ID */
    hid_t       space_id = -1; /* space ID */
    hid_t       ftype_id = -1; /* file type ID */
    hid_t       wtype_id = -1; /* read/write type ID */
    size_t      msize;         /* size of type */
    void       *buf = NULL;    /* data buffer */
    hsize_t     nelmts;        /* number of elements in dataset */
    int         rank;          /* rank of dataset */
    htri_t      is_named;      /* Whether the datatype is named */
    hsize_t     dims[H5S_MAX_RANK];/* dimensions of dataset */
    char        name[255];
    H5O_info_t  oinfo;         /* object info */
    int         j;
    unsigned    u;
    hbool_t     is_ref = 0;
    H5T_class_t type_class = -1;

    if (H5Oget_info(loc_in, &oinfo) < 0)
        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed");

    /*-------------------------------------------------------------------------
     * copy all attributes
     *-------------------------------------------------------------------------
     */
    for (u = 0; u < (unsigned) oinfo.num_attrs; u++) {
        /* open attribute */
        if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed");

        /* get name */
        if (H5Aget_name(attr_id, (size_t) 255, name) < 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");

        /* get the file datatype  */
        if ((ftype_id = H5Aget_type(attr_id)) < 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_type failed");

        /* Check if the datatype is committed */
        if ((is_named = H5Tcommitted(ftype_id)) < 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommitted failed");
        if (is_named && travt) {
            hid_t fidout = -1;

            /* Create out file id */
            if ((fidout = H5Iget_file_id(loc_out)) < 0)
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Iget_file_id failed");

            /* Copy named dt */
            if ((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p, travt, options)) < 0) {
                H5Fclose(fidout);
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");
            } /* end if */

            if (H5Fclose(fidout) < 0)
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed");
        } /* end if */
        else {
            if (options->use_native == 1)
                wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT);
            else
                wtype_id = H5Tcopy(ftype_id);
        } /* end else */

        /* get the dataspace handle  */
        if ((space_id = H5Aget_space(attr_id)) < 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_space failed");

        /* get dimensions  */
        if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");

        nelmts = 1;
        for (j = 0; j < rank; j++)
            nelmts *= dims[j];

        if ((msize = H5Tget_size(wtype_id)) == 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");

        /*-------------------------------------------------------------------------
         * object references are a special case. We cannot just copy the buffers,
         * but instead we recreate the reference.
         * This is done on a second sweep of the file that just copies the referenced
         * objects at copy_refs_attr()
         *-------------------------------------------------------------------------
         */
        type_class = H5Tget_class(wtype_id);
        is_ref = (type_class == H5T_REFERENCE);
        if (type_class == H5T_VLEN || type_class == H5T_ARRAY) {
            hid_t base_type = -1;

            base_type = H5Tget_super(ftype_id);
            is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE));
            if (H5Tclose(base_type) < 0)
                H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose base_type failed");
        }

        if (type_class == H5T_COMPOUND) {
            int nmembers = H5Tget_nmembers(wtype_id);

            for (j = 0; j < nmembers; j++) {
                hid_t mtid = H5Tget_member_type(wtype_id, (unsigned)j);
                H5T_class_t mtclass = H5Tget_class(mtid);
                if (H5Tclose(mtid) < 0)
                    H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose mtid failed");

                if (mtclass == H5T_REFERENCE) {
                    is_ref = 1;
                    break;
                }
            } /* for (j=0; i<nmembers; j++) */
        } /* if (type_class == H5T_COMPOUND) */

        if (!is_ref) {
            /*-------------------------------------------------------------------------
             * read to memory
             *-------------------------------------------------------------------------
             */

            buf = (void *)HDmalloc((size_t)(nelmts * msize));
            if (buf == NULL) {
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
            } /* end if */
            if (H5Aread(attr_id, wtype_id, buf) < 0)
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");

            /*-------------------------------------------------------------------------
             * copy
             *-------------------------------------------------------------------------
             */

            if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Acreate2 failed on ,%s>", name);
            if (H5Awrite(attr_out, wtype_id, buf) < 0)
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed");

            /*close*/
            if (H5Aclose(attr_out) < 0)
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");

            /* Check if we have VL data and string in the attribute's  datatype that must
             * be reclaimed */
            if (TRUE == h5tools_detect_vlen(wtype_id))
                H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
            HDfree(buf);
            buf = NULL;
        } /*H5T_REFERENCE*/

        if (options->verbose)
            printf(FORMAT_OBJ_ATTR, "attr", name);

        /*-------------------------------------------------------------------------
         * close
         *-------------------------------------------------------------------------
         */
        if (H5Sclose(space_id) < 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
        space_id = -1;
        if (H5Tclose(wtype_id) < 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
        wtype_id = -1;
        if (H5Tclose(ftype_id) < 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
        ftype_id = -1;
        if (H5Aclose(attr_id) < 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
        attr_id = -1;
    } /* for u */

done:
    H5E_BEGIN_TRY {
        if (buf) {
            /* Check if we have VL data and string in the attribute's  datatype that must
            * be reclaimed */
            if (TRUE == h5tools_detect_vlen(wtype_id))
                H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);

            /* Free buf */
            HDfree(buf);
        } /* end if */

        H5Aclose(attr_out);
        H5Sclose(space_id);
        H5Tclose(wtype_id);
        H5Tclose(ftype_id);
        H5Aclose(attr_id);
    } H5E_END_TRY;

    return ret_value;
} /* end copy_attr() */