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-rw-r--r--tools/h5repack/h5repack_copy.c99
1 files changed, 52 insertions, 47 deletions
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 6c47cfb..5153cc4 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -13,11 +13,7 @@
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
#include "h5repack.h"
-#include "H5private.h"
#include "h5tools.h"
#include "h5tools_utils.h"
@@ -543,22 +539,23 @@ int do_copy_objects(hid_t fidin,
trav_table_t *travt,
pack_opt_t *options) /* repack options */
{
- hid_t grp_in=-1; /* group ID */
- hid_t grp_out=-1; /* group ID */
- hid_t dset_in=-1; /* read dataset ID */
- hid_t dset_out=-1; /* write dataset ID */
- hid_t gcpl_in=-1; /* group creation property list */
- hid_t gcpl_out=-1; /* group creation property list */
- hid_t type_in=-1; /* named type ID */
- hid_t type_out=-1; /* named type ID */
- hid_t dcpl_id=-1; /* dataset creation property list ID */
- hid_t dcpl_out=-1; /* dataset creation property list ID */
- hid_t f_space_id=-1; /* file space ID */
- hid_t ftype_id=-1; /* file type ID */
- hid_t wtype_id=-1; /* read/write type ID */
- named_dt_t *named_dt_head=NULL; /* Pointer to the stack of named datatypes copied */
+ hid_t grp_in = -1; /* group ID */
+ hid_t grp_out = -1; /* group ID */
+ hid_t dset_in = -1; /* read dataset ID */
+ hid_t dset_out = -1; /* write dataset ID */
+ hid_t gcpl_in = -1; /* group creation property list */
+ hid_t gcpl_out = -1; /* group creation property list */
+ hid_t type_in = -1; /* named type ID */
+ hid_t type_out = -1; /* named type ID */
+ hid_t dcpl_id = -1; /* dataset creation property list ID */
+ hid_t dcpl_out = -1; /* dataset creation property list ID */
+ hid_t f_space_id = -1; /* file space ID */
+ hid_t ftype_id = -1; /* file type ID */
+ hid_t wtype_id = -1; /* read/write type ID */
+ named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
size_t msize; /* size of type */
hsize_t nelmts; /* number of elements in dataset */
+ H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */
int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
hsize_t dsize_in; /* input dataset size before filter */
@@ -688,7 +685,7 @@ int do_copy_objects(hid_t fidin,
/* check if filters were requested for individual objects */
for (u = 0; u < options->op_tbl->nelems; u++) {
- if (strcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) {
+ if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) {
if (options->op_tbl->objs[u].filter->filtn > 0) {
req_filter = 1;
}
@@ -746,11 +743,13 @@ int do_copy_objects(hid_t fidin,
HDmemset(dims, 0, sizeof dims);
if(H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
goto error;
+
+ if(H5Dget_space_status(dset_in, &space_status) < 0)
+ goto error;
+
nelmts = 1;
- for ( j = 0; j < rank; j++)
- {
+ for(j = 0; j < rank; j++)
nelmts *= dims[j];
- }
/* wtype_id will have already been set if using a named dtype */
if(!is_named) {
@@ -834,20 +833,26 @@ int do_copy_objects(hid_t fidin,
* read/write
*-------------------------------------------------------------------------
*/
- if (nelmts)
+ if(nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED)
{
- size_t need = (size_t)(nelmts*msize); /* bytes needed */
- if ( need < H5TOOLS_MALLOCSIZE )
+ size_t need = (size_t)(nelmts * msize); /* bytes needed */
+
+ /* have to read the whole dataset if there is only one element in the dataset */
+ if(need < H5TOOLS_MALLOCSIZE)
buf = HDmalloc(need);
- if (buf != NULL )
- {
- if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf) < 0)
+ if(buf != NULL) {
+ if(H5Dread(dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
- if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf) < 0)
+ if(H5Dwrite(dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
- }
+ /* Check if we have VL data in the dataset's
+ * datatype that must be reclaimed */
+ if(TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
+ if(H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0)
+ goto error;
+ }
else /* possibly not enough memory, read/write by hyperslabs */
{
size_t p_type_nbytes = msize; /*size of memory type */
@@ -949,7 +954,7 @@ int do_copy_objects(hid_t fidin,
sm_buf=NULL;
}
} /* hyperslab read */
- }/*nelmts*/
+ } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
/*-------------------------------------------------------------------------
* amount of compression used
@@ -1212,7 +1217,7 @@ static void print_dataset_info(hid_t dcpl_id,
int i;
- strcpy(strfilter,"\0");
+ HDstrcpy(strfilter,"\0");
/* get information about input filters */
if((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
@@ -1229,51 +1234,51 @@ static void print_dataset_info(hid_t dcpl_id,
break;
case H5Z_FILTER_DEFLATE:
- strcat(strfilter,"GZIP ");
+ HDstrcat(strfilter,"GZIP ");
#if defined (PRINT_DEBUG)
{
unsigned level=cd_values[0];
sprintf(temp,"(%d)",level);
- strcat(strfilter,temp);
+ HDstrcat(strfilter,temp);
}
#endif
break;
case H5Z_FILTER_SZIP:
- strcat(strfilter,"SZIP ");
+ HDstrcat(strfilter,"SZIP ");
#if defined (PRINT_DEBUG)
{
unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
unsigned ppb=cd_values[1];
sprintf(temp,"(%d,",ppb);
- strcat(strfilter,temp);
+ HDstrcat(strfilter,temp);
if (options_mask & H5_SZIP_EC_OPTION_MASK)
- strcpy(temp,"EC) ");
+ HDstrcpy(temp,"EC) ");
else if (options_mask & H5_SZIP_NN_OPTION_MASK)
- strcpy(temp,"NN) ");
+ HDstrcpy(temp,"NN) ");
}
- strcat(strfilter,temp);
+ HDstrcat(strfilter,temp);
#endif
break;
case H5Z_FILTER_SHUFFLE:
- strcat(strfilter,"SHUF ");
+ HDstrcat(strfilter,"SHUF ");
break;
case H5Z_FILTER_FLETCHER32:
- strcat(strfilter,"FLET ");
+ HDstrcat(strfilter,"FLET ");
break;
case H5Z_FILTER_NBIT:
- strcat(strfilter,"NBIT ");
+ HDstrcat(strfilter,"NBIT ");
break;
case H5Z_FILTER_SCALEOFFSET:
- strcat(strfilter,"SCALEOFFSET ");
+ HDstrcat(strfilter,"SCALEOFFSET ");
break;
} /* switch */
}/*i*/
@@ -1283,10 +1288,10 @@ static void print_dataset_info(hid_t dcpl_id,
else
{
char str[255], temp[20];
- strcpy(str,"dset ");
- strcat(str,strfilter);
+ HDstrcpy(str,"dset ");
+ HDstrcat(str,strfilter);
sprintf(temp," (%.3f:1)",ratio);
- strcat(str,temp);
+ HDstrcat(str,temp);
printf(FORMAT_OBJ,str,objname);
}
}
@@ -1364,7 +1369,7 @@ copy_user_block(const char *infile, const char *outfile, hsize_t size)
} /* end while */
/* Update size of userblock left to transfer */
- size -= nread;
+ size = size - (hsize_t)nread;
} /* end while */
done:
generated by cgit v0.12 at 2024-07-21 00:14:08 (GMT)