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-rw-r--r--tools/h5repack/h5repack_copy.c83
-rw-r--r--tools/h5repack/h5repack_refs.c211
2 files changed, 149 insertions, 145 deletions
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index c14d1f0..bdde91c 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -239,10 +239,8 @@ int do_copy_objects(hid_t fidin,
* in a second traversal of the output file
*-------------------------------------------------------------------------
*/
-
- if ( H5Tget_class(mtype_id) != H5T_REFERENCE )
+ if ( (H5T_REFERENCE!=H5Tget_class(mtype_id)))
{
-
/* the information about the object to be filtered/"layouted" */
pack_info_t obj;
init_packobject(&obj);
@@ -254,64 +252,64 @@ int do_copy_objects(hid_t fidin,
* read to memory
*-------------------------------------------------------------------------
*/
-
- buf=(void *) HDmalloc((unsigned)(nelmts*msize));
- if ( buf==NULL){
- printf( "cannot read into memory\n" );
- goto error;
- }
- if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * apply the layout; check first if the object is to be modified.
- * if the layout could not be applied, continue
- *-------------------------------------------------------------------------
- */
- if (layout_this(dcpl_id,travt->objs[i].name,options,&obj))
+ if (nelmts)
{
- if (apply_layout(dcpl_id,&obj)<0)
- continue;
- }
-
+ buf=(void *) HDmalloc((unsigned)(nelmts*msize));
+ if ( buf==NULL){
+ printf( "cannot read into memory\n" );
+ goto error;
+ }
+ if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * apply the layout; check first if the object is to be modified.
+ * if the layout could not be applied, continue
+ *-------------------------------------------------------------------------
+ */
+ if (layout_this(dcpl_id,travt->objs[i].name,options,&obj))
+ {
+ if (apply_layout(dcpl_id,&obj)<0)
+ continue;
+ }
/*-------------------------------------------------------------------------
* apply the filter; check first if the object is to be filtered.
* if the filter could not be applied, continue
*-------------------------------------------------------------------------
*/
- if (filter_this(travt->objs[i].name,options,&obj))
- {
- if (rank)
+ if (filter_this(travt->objs[i].name,options,&obj))
{
- /* filters require CHUNK layout; if we do not have one define a default */
- if (obj.chunk.rank<=0)
+ if (rank)
{
- obj.chunk.rank=rank;
- for (j=0; j<rank; j++)
- obj.chunk.chunk_lengths[j] = dims[j];
+ /* filters require CHUNK layout; if we do not have one define a default */
+ if (obj.chunk.rank<=0)
+ {
+ obj.chunk.rank=rank;
+ for (j=0; j<rank; j++)
+ obj.chunk.chunk_lengths[j] = dims[j];
+ }
+ if (apply_filters(dcpl_id,H5Tget_size(mtype_id),options,&obj)<0)
+ continue;
}
- if (apply_filters(dcpl_id,H5Tget_size(mtype_id),options,&obj)<0)
- continue;
- }
- else
- {
- if (options->verbose)
- printf("Warning: Filter could not be applied to <%s>\n",
+ else
+ {
+ if (options->verbose)
+ printf("Warning: Filter could not be applied to <%s>\n",
travt->objs[i].name);
+ }
}
- }
+ }/*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
- if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,ftype_id,space_id,dcpl_id))<0)
+ if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0)
goto error;
- if (dsize_in) {
+ if (dsize_in && nelmts) {
if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
goto error;
}
-
/*-------------------------------------------------------------------------
* copy attrs
*-------------------------------------------------------------------------
@@ -332,16 +330,13 @@ int do_copy_objects(hid_t fidin,
if (buf)
free(buf);
-
}/*H5T_STD_REF_OBJ*/
-
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
-
if (H5Tclose(ftype_id)<0)
goto error;
if (H5Tclose(mtype_id)<0)
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index 8b07624..baa4019 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -19,9 +19,6 @@
#include "H5private.h"
#include "h5repack.h"
-
-
-
static const char* MapIdToName(hid_t refobj_id,
trav_table_t *travt);
@@ -32,7 +29,6 @@ static int copy_refs_attr(hid_t loc_in,
hid_t fidout /* for saving references */
);
-
/*-------------------------------------------------------------------------
* Function: do_copy_refobjs
*
@@ -145,8 +141,8 @@ int do_copy_refobjs(hid_t fidin,
{
H5G_obj_t obj_type;
hid_t refobj_id;
- hobj_ref_t *refbuf; /* buffer for object references */
- hobj_ref_t *buf;
+ hobj_ref_t *refbuf=NULL; /* buffer for object references */
+ hobj_ref_t *buf=NULL;
const char* refname;
unsigned u;
@@ -154,55 +150,62 @@ int do_copy_refobjs(hid_t fidin,
* read to memory
*-------------------------------------------------------------------------
*/
-
- buf=(void *) HDmalloc((unsigned)(nelmts*msize));
- if ( buf==NULL){
- printf( "cannot read into memory\n" );
- goto error;
- }
- if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
- goto error;
- if ((obj_type = H5Rget_obj_type(dset_in,H5R_OBJECT,buf))<0)
- goto error;
- refbuf=HDmalloc((unsigned)nelmts*msize);
- if ( refbuf==NULL){
- printf( "cannot allocate memory\n" );
- goto error;
- }
- for ( u=0; u<nelmts; u++)
+ if (nelmts)
{
- H5E_BEGIN_TRY {
- if ((refobj_id = H5Rdereference(dset_in,H5R_OBJECT,&buf[u]))<0)
- continue;
- } H5E_END_TRY;
- /* get the name. a valid name could only occur in the
- second traversal of the file */
- if ((refname=MapIdToName(refobj_id,travt))!=NULL)
- {
- /* create the reference, -1 parameter for objects */
- if (H5Rcreate(&refbuf[u],fidout,refname,H5R_OBJECT,-1)<0)
- goto error;
-
- if (options->verbose)
- printf("object <%s> object reference created to <%s>\n",
- travt->objs[i].name,
- refname);
+ buf=(void *) HDmalloc((unsigned)(nelmts*msize));
+ if ( buf==NULL){
+ printf( "cannot read into memory\n" );
+ goto error;
}
- close_obj(obj_type,refobj_id);
- }/* j */
-
+ if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
+ goto error;
+
+ if ((obj_type = H5Rget_obj_type(dset_in,H5R_OBJECT,buf))<0)
+ goto error;
+ refbuf=HDmalloc((unsigned)nelmts*msize);
+ if ( refbuf==NULL){
+ printf( "cannot allocate memory\n" );
+ goto error;
+ }
+ for ( u=0; u<nelmts; u++)
+ {
+ H5E_BEGIN_TRY {
+ if ((refobj_id = H5Rdereference(dset_in,H5R_OBJECT,&buf[u]))<0)
+ continue;
+ } H5E_END_TRY;
+ /* get the name. a valid name could only occur in the
+ second traversal of the file */
+ if ((refname=MapIdToName(refobj_id,travt))!=NULL)
+ {
+ /* create the reference, -1 parameter for objects */
+ if (H5Rcreate(&refbuf[u],fidout,refname,H5R_OBJECT,-1)<0)
+ goto error;
+
+ if (options->verbose)
+ printf("object <%s> object reference created to <%s>\n",
+ travt->objs[i].name,
+ refname);
+ close_obj(obj_type,refobj_id);
+ }/*refname*/
+ }/* u */
+ }/*nelmts*/
+
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
- if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,ftype_id,space_id,dcpl_id))<0)
- goto error;
- if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
+ if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0)
goto error;
+ if (nelmts) {
+ if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
+ goto error;
+ }
- free(buf);
- free(refbuf);
+ if (buf)
+ free(buf);
+ if (refbuf)
+ free(refbuf);
}/*H5T_STD_REF_OBJ*/
@@ -214,8 +217,8 @@ int do_copy_refobjs(hid_t fidin,
{
H5G_obj_t obj_type;
hid_t refobj_id;
- hdset_reg_ref_t *refbuf; /* input buffer for region references */
- hdset_reg_ref_t *buf; /* output buffer */
+ hdset_reg_ref_t *refbuf=NULL; /* input buffer for region references */
+ hdset_reg_ref_t *buf=NULL; /* output buffer */
const char* refname;
unsigned u;
@@ -223,69 +226,75 @@ int do_copy_refobjs(hid_t fidin,
* read input to memory
*-------------------------------------------------------------------------
*/
-
- buf=(void *) HDmalloc((unsigned)(nelmts*msize));
- if ( buf==NULL){
- printf( "cannot read into memory\n" );
- goto error;
- }
- if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
- goto error;
- if ((obj_type = H5Rget_obj_type(dset_in,H5R_DATASET_REGION,buf))<0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * create output
- *-------------------------------------------------------------------------
- */
-
- refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
- if ( refbuf==NULL){
- printf( "cannot allocate memory\n" );
- goto error;
- }
- for ( u=0; u<nelmts; u++)
+ if (nelmts)
{
- H5E_BEGIN_TRY {
- if ((refobj_id = H5Rdereference(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
- continue;
- } H5E_END_TRY;
-
- /* get the name. a valid name could only occur in the
- second traversal of the file */
- if ((refname=MapIdToName(refobj_id,travt))!=NULL)
+ buf=(void *) HDmalloc((unsigned)(nelmts*msize));
+ if ( buf==NULL){
+ printf( "cannot read into memory\n" );
+ goto error;
+ }
+ if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
+ goto error;
+ if ((obj_type = H5Rget_obj_type(dset_in,H5R_DATASET_REGION,buf))<0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * create output
+ *-------------------------------------------------------------------------
+ */
+
+ refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
+ if ( refbuf==NULL){
+ printf( "cannot allocate memory\n" );
+ goto error;
+ }
+ for ( u=0; u<nelmts; u++)
{
- hid_t region_id; /* region id of the referenced dataset */
+ H5E_BEGIN_TRY {
+ if ((refobj_id = H5Rdereference(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
+ continue;
+ } H5E_END_TRY;
- if ((region_id = H5Rget_region(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
- goto error;
-
- /* create the reference, we need the space_id */
- if (H5Rcreate(&refbuf[u],fidout,refname,H5R_DATASET_REGION,region_id)<0)
- goto error;
-
- if (H5Sclose(region_id)<0)
- goto error;
-
- if (options->verbose)
- printf("object <%s> region reference created to <%s>\n",
- travt->objs[i].name,
- refname);
- }
- close_obj(obj_type,refobj_id);
- }/* u */
+ /* get the name. a valid name could only occur in the
+ second traversal of the file */
+ if ((refname=MapIdToName(refobj_id,travt))!=NULL)
+ {
+ hid_t region_id; /* region id of the referenced dataset */
+
+ if ((region_id = H5Rget_region(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
+ goto error;
+
+ /* create the reference, we need the space_id */
+ if (H5Rcreate(&refbuf[u],fidout,refname,H5R_DATASET_REGION,region_id)<0)
+ goto error;
+
+ if (H5Sclose(region_id)<0)
+ goto error;
+
+ if (options->verbose)
+ printf("object <%s> region reference created to <%s>\n",
+ travt->objs[i].name,
+ refname);
+ close_obj(obj_type,refobj_id);
+ }/*refname*/
+ }/* u */
+ }/*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
- if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,ftype_id,space_id,dcpl_id))<0)
- goto error;
- if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
+ if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0)
goto error;
+ if (nelmts) {
+ if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
+ goto error;
+ }
- free(buf);
- free(refbuf);
+ if (buf)
+ free(buf);
+ if (refbuf)
+ free(refbuf);
} /* H5T_STD_REF_DSETREG */