diff options
| -rw-r--r-- | tools/h5repack/h5repack_copy.c | 83 | ||||
| -rw-r--r-- | tools/h5repack/h5repack_refs.c | 211 |
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 */ |