mirror of
https://github.com/HDFGroup/hdf5.git
synced 2025-01-24 15:25:00 +08:00
ab5bf9f979
Updated for new array datatypes.
Description:
I missed these tools earlier when I wasn't compiling with HDF4...
Solution:
Updated them (correctly, I hope) to use the new array datatype instead of
compound datatype array fields.
Platforms tested:
FreeBSD 4.1.1 (hawkwind)
825 lines
20 KiB
C
825 lines
20 KiB
C
/*-------------------------------------------------------------------------
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*
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* Copyright (C) 2000 National Center for Supercomputing Applications.
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* All rights reserved.
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*
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*-------------------------------------------------------------------------
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*/
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/******************************************************************************
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Description:
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1. converter
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See HDF4 to HDF5 mapping specification at
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(http://hdf.ncsa.uiuc.edu/HDF5/papers/h4toh5) for the default mapping
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from HDF4 object to HDF5 object.
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The whole converter includes 10 files, h4toh5util.h, h4toh5main.h, h4toh5util.c, h4toh5main.c, h4toh5sds.c, h4toh5image.c,h4toh5vdata.c,h4toh5vgroup.c,h4toh5pal.c and h4toh5anno.c.
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2. this file
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Converting an hdf4 independent vdata object into an hdf5 dataset of compound dataset.
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Author: Kent Yang(ymuqun@ncsa.uiuc.edu)
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*****************************************************************************/
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#include "h4toh5main.h"
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/*-------------------------------------------------------------------------
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* Function: Vdata_h4_to_h5
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*
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* Purpose: translate Vdata object into hdf5 dataset
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*
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* Return: FAIL if failed, SUCCEED if successful.
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*
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* In :
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vdata_id: RI identifier
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group_id: hdf5 group id
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Out:
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Modification:
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*-------------------------------------------------------------------------
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*/
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int Vdata_h4_to_h5(int32 file_id,int32 vdata_id, hid_t group_id) {
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/* define variables for hdf4. */
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int32 istat;
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int32 n_records;
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int32 vdata_ref;
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int32 vdata_tag;
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int32 interlace_mode;
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int32 vdata_size;
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int32 vdatamem_size;
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int32 field_index;
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int32 fieldorder;
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int32 fieldtype;
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int i;
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int32 nfields;
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int num_vd_attrs;
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int num_vd_field_attrs;
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VOIDP vd_data;
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char vdlabel[10];
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char vdata_name[MAX_NC_NAME];
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char fieldname[MAX_NC_NAME];
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char vdata_class[VSNAMELENMAX];
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char field_name_list[VSFIELDMAX*FIELDNAMELENMAX];
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/* define varibles for hdf5. */
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hid_t h5d_sid;
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hid_t h5dset;
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hid_t h5_ctype;
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hid_t h5_cmemtype;
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hid_t* h5memtype = NULL;
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hid_t* h5type = NULL;
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size_t* h4memsize = NULL;
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size_t* h4size = NULL;
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hsize_t h5_vddims[1];
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char* h5cvdata_name;
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int check_vdname;
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/* get absolute path of vdata name. */
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vdata_ref = VSQueryref(vdata_id);
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if (vdata_ref == FAIL) {
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printf("error in getting reference number. \n");
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return FAIL;
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}
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vdata_tag = VSQuerytag(vdata_id);
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if (vdata_tag == FAIL) {
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printf("error in getting object tag number. \n");
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return FAIL;
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}
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/* get the class name */
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if(VSgetclass(vdata_id,vdata_class) == FAIL) {
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printf("error in obtaining class name. \n");
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return FAIL;
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}
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/* get number of record,field_name,Size of a record and
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Name of the vdata*/
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if(VSQueryvsize(vdata_id,&vdata_size)==FAIL) {
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printf("error in getting size of vdata. \n");
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return FAIL;
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}
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if(vdata_size == 0) {/* empty vdata set. */
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return SUCCEED;
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}
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/* obtain number of records, field name list, vdata name. */
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if(VSinquire(vdata_id,&n_records,&interlace_mode,
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field_name_list,&vdata_size,vdata_name) == FAIL) {
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printf("error in inquiring vdata. \n");
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return FAIL;
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}
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vdatamem_size = 0;
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nfields = VFnfields(vdata_id);
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if (nfields == FAIL) {
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printf("error in obtaining number of vdata fields. \n");
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return FAIL;
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}
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h5memtype = calloc(nfields,sizeof(hid_t));
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h5type = calloc(nfields,sizeof(hid_t));
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h4memsize = calloc(nfields,sizeof(size_t));
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h4size = calloc(nfields,sizeof(size_t));
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for (i=0;i<nfields;i++) {
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/* obtain field type. */
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fieldtype = VFfieldtype(vdata_id,i);
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if(fieldtype == FAIL){
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printf("error in obtaining field type. \n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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return FAIL;
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}
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/* obtain field order.*/
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fieldorder = VFfieldorder(vdata_id,i);
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/* printf("fieldorder %d\n",fieldorder);*/
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if(fieldorder == FAIL){
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printf("error in obtaining field order. \n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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return FAIL;
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}
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/* datatype conversion from hdf4 to hdf5.
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the corresponding memory data type is also converted.*/
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if(h4type_to_h5type(fieldtype,&h5memtype[i],&h4memsize[i],
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&h4size[i],&h5type[i])== FAIL){
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printf("error in doing datatype conversion at vdata routine. \n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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return FAIL;
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}
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vdatamem_size +=fieldorder*h4memsize[i];
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}
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vd_data = malloc(vdatamem_size*n_records);
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istat = VSsetfields(vdata_id,field_name_list);
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if(istat == FAIL) {
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printf("error setting fields of vdata.\n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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return FAIL;
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}
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istat = VSread(vdata_id,(uint8*)vd_data,n_records,FULL_INTERLACE);
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if(istat == FAIL) {
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printf("error in obtaining vdata. \n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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return FAIL;
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}
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for (i=0;i<nfields;i++) {
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/* obtain field order.*/
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fieldorder = VFfieldorder(vdata_id,i);
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if(fieldorder == FAIL){
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printf("error in obtaining field order. \n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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return FAIL;
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}
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}
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/* create hdf5 compound datatype for both memory and file.*/
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h5_ctype = H5Tcreate(H5T_COMPOUND, (size_t)vdata_size);
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h5_cmemtype = H5Tcreate(H5T_COMPOUND,(size_t)vdatamem_size);
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if(gen_h5comptype(vdata_id,nfields,h4size,h4memsize,h5type,h5memtype,
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h5_ctype,h5_cmemtype)==FAIL){
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printf("error in generating h5 compound data type.\n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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return FAIL;
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}
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h5_vddims[0] = n_records;
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h5d_sid = H5Screate_simple(1,h5_vddims,NULL);
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if(h5d_sid <0){
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printf("error in obtaining space id.\n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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return FAIL;
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}
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/* choose a number that is not returned from the func.*/
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check_vdname = -3;
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/* obtain hdf5 vdata name. */
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h5cvdata_name = get_name(vdata_ref,estnum_vd,vd_hashtab,&check_vdname);
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if (h5cvdata_name == NULL && check_vdname == 0 ) {
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printf("error,cannot find vdata \n");
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return FAIL;
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}
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if (h5cvdata_name == NULL && check_vdname == -1) {
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printf("error,group name is not defined.\n");
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return FAIL;
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}
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if (h5cvdata_name == NULL && check_vdname == -2 ) {
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printf("cannot allocate memory for vdata.\n");
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return FAIL;
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}
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h5dset = H5Dcreate(group_id,h5cvdata_name,h5_ctype,h5d_sid,H5P_DEFAULT);
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if(h5dset <0) {
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printf("error in obtaining dataset.\n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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free(h5cvdata_name);
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return FAIL;
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}
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free(h5cvdata_name);
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if(H5Dwrite(h5dset,h5_cmemtype,H5S_ALL,H5S_ALL,H5P_DEFAULT,vd_data)<0){
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printf("error in writing dataset converted from vdata.\n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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return FAIL;
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}
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/* handle vdata attributes and vdata field attributes. */
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num_vd_attrs = VSfnattrs(vdata_id,_HDF_VDATA);
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if (num_vd_attrs == FAIL) {
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printf("error in obtaining attributes of vdata.\n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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return FAIL;
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}
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/* when field_index = -1, only transfer vdata attribute.*/
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field_index = -1;
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if(vdata_transattrs(vdata_id,h5dset,num_vd_attrs,field_index,NULL)==FAIL){
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printf("error in translating vdata attibutes.\n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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return FAIL;
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}
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for (i =0;i< nfields;i++) {
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if(VFfieldname(vdata_id,i)== NULL) {
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printf("error in obtaining field name. \n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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return FAIL;
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}
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strcpy(fieldname,VFfieldname(vdata_id,i));
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num_vd_field_attrs = VSfnattrs(vdata_id,i);
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if(num_vd_field_attrs == FAIL){
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printf("error in number of vd field attribute \n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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return FAIL;
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}
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if(vdata_transattrs(vdata_id,h5dset,num_vd_field_attrs,i,fieldname)
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==FAIL){
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printf("error in transfering vdata attributes.\n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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return FAIL;
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}
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}
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/* converting annotations of vdata into corresponding hdf5 attribute.*/
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if( Annoobj_h4_to_h5(file_id,vdata_ref,vdata_tag,h5dset)== FAIL){
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printf("fail to convert HDF4 VDATA annotation into hdf5 attributes.\n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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return FAIL;
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}
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/* converting predefined attributes. */
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strcpy(vdlabel,VDATALABEL);
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if(h4_transpredattrs(h5dset,HDF4_OBJECT_TYPE,vdlabel)==FAIL){
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printf("error in transfering vdata attributes.\n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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return FAIL;
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}
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if(vdata_name != NULL) {
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if(h4_transpredattrs(h5dset,HDF4_OBJECT_NAME,vdata_name)==FAIL){
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printf("error in transfering vdata attributes.\n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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return FAIL;
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}
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}
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if(h4_transnumattr(h5dset,HDF4_REF_NUM,vdata_ref)==FAIL){
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printf("error in transfering vdata attributes.\n");
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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return FAIL;
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}
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H5Sclose(h5d_sid);
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H5Dclose(h5dset);
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VSdetach(vdata_id);
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free(h5memtype);
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free(h5type);
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free(h4memsize);
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free(h4size);
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free(vd_data);
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return SUCCEED;
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}
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/*-------------------------------------------------------------------------
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* Function: vdata_transattrs
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*
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* Purpose: translate Vdata attributes into attributes of the
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corresponding hdf5 dataset
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*
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* Return: FAIL if failed, SUCCEED if successful.
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*
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* In :
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vdata_id: vdata identifier
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h5dset: hdf5 dataset
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snum_vdattrs: number of vd attributes
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field_index: index of vdata fields
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attr_name: vdata(or vdata field) attribute name
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Out:
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Modifications:
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*-------------------------------------------------------------------------
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*/
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int vdata_transattrs(int32 vdata_id,hid_t h5dset,int snum_vdattrs,
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int field_index,char* attr_name){
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char svdattr_name[2*MAX_NC_NAME];
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char* svdrepattr_name;
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char refstr[MAXREF_LENGTH];
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int32 count_svdadata;
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int32 svd_atype;
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size_t sh4_amemsize;
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size_t sh4_asize;
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hid_t sh5a_sid;
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hid_t sh5a_id;
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hid_t sh5_atype;
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hid_t sh5_amemtype;
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hid_t sh5str_type;
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hid_t sh5str_memtype;
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hsize_t sh5dims[1];
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void* svd_adata;
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herr_t sret;
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int i;
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/* separate vdata attribute from vdata field attributes. */
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if (field_index < -1) {
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printf("error: check_field should be either -1(vdata) or ");
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printf(">=0(vdata field).\n");
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return FAIL;
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}
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for (i = 0;i < snum_vdattrs; i++) {
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/* if the field_index is 0, no field attribute exists, only
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VDATA attributes are converted.*/
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if (VSattrinfo(vdata_id,field_index,i,svdattr_name,&svd_atype,
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&count_svdadata,NULL)== FAIL){
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printf("unable to obtain attribute information. \n");
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return FAIL;
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}
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if(svdattr_name[0] == '\0') {
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svdrepattr_name = trans_obj_name(DFTAG_VG,i);
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strcpy(svdattr_name,svdrepattr_name);
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free(svdrepattr_name);
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}
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if (field_index == -1);
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else if (field_index != -1 && attr_name != NULL) {
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strcat(svdattr_name,":");
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strcat(svdattr_name,attr_name);
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}
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else {
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strcat(svdattr_name,":");
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strcat(svdattr_name,"HDF4_VDATA_ATTR_");
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if(conv_int_str(field_index,refstr)==FAIL) {
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printf("error in converting vdata field index to string.\n");
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return FAIL;
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}
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strcat(svdattr_name,refstr);
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}
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/* converting attribute data type into the corresponding hdf5 data type */
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if(h4type_to_h5type(svd_atype,&sh5_amemtype,&sh4_amemsize,
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&sh4_asize,&sh5_atype)==FAIL){
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printf("fail to translate vdata attribute datatype from H4 to H5.\n");
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return FAIL;
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}
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svd_adata = malloc(sh4_amemsize * count_svdadata);
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if(svd_adata == NULL) {
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printf("fail to allocate memory for vdata attribute data.\n");
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return FAIL;
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}
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if(VSgetattr(vdata_id,field_index,i,(VOIDP)svd_adata)==FAIL){
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printf("error in getting attributes of vdata. \n");
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free(svd_adata);
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return FAIL;
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|
}
|
|
|
|
/* now do attribute-transferring:
|
|
1. deal with string data type
|
|
2. set attribute space
|
|
3. get attribute name */
|
|
|
|
if (sh5_atype == H5T_STRING) {
|
|
|
|
if ((sh5str_type = mkstr(count_svdadata,
|
|
H5T_STR_SPACEPAD))<0) {
|
|
printf("error in making string for vdata attribute. \n");
|
|
free(svd_adata);
|
|
return FAIL;
|
|
}
|
|
|
|
if ((sh5str_memtype = mkstr(count_svdadata*sh4_amemsize,
|
|
H5T_STR_SPACEPAD))<0) {
|
|
printf("error in making memory string for vdata attribute. \n");
|
|
free(svd_adata);
|
|
return FAIL;
|
|
}
|
|
|
|
sh5a_sid = H5Screate(H5S_SCALAR);
|
|
|
|
if (sh5a_sid < 0) {
|
|
printf("failed to create attribute space for ");
|
|
printf("HDF4_OBJECT_TYPE VDATA. \n");
|
|
free(svd_adata);
|
|
return FAIL;
|
|
}
|
|
|
|
|
|
sh5a_id = H5Acreate(h5dset,svdattr_name,sh5str_type,
|
|
sh5a_sid,H5P_DEFAULT);
|
|
|
|
if (sh5a_id <0) {
|
|
printf("failed to obtain attribute id for");
|
|
printf(" HDF4_OBJECT_TYPE VDATA. \n");
|
|
H5Sclose(sh5a_sid);
|
|
free(svd_adata);
|
|
return FAIL;
|
|
}
|
|
|
|
sret = H5Awrite(sh5a_id,sh5str_memtype,(void *)svd_adata);
|
|
|
|
if (sret <0) {
|
|
printf("fail to write vdata attr into hdf5 dataset attr\n ");
|
|
H5Sclose(sh5a_sid);
|
|
H5Aclose(sh5a_id);
|
|
free(svd_adata);
|
|
return FAIL;
|
|
}
|
|
|
|
free(svd_adata);
|
|
sret = H5Sclose(sh5a_sid);
|
|
sret = H5Aclose(sh5a_id);
|
|
}
|
|
|
|
else {
|
|
|
|
if(count_svdadata == 1) {
|
|
sh5a_sid = H5Screate(H5S_SCALAR);
|
|
|
|
if (sh5a_sid < 0) {
|
|
printf("failed to create scalar space id for hdf5 attribute ");
|
|
printf("of dataset converted from attribute of VDATA.\n");
|
|
free(svd_adata);
|
|
return FAIL;
|
|
}
|
|
}
|
|
else {
|
|
sh5dims[0] = count_svdadata;
|
|
sh5a_sid = H5Screate_simple(1,sh5dims,NULL);
|
|
|
|
if (sh5a_sid < 0) {
|
|
printf("failed to create simple space id for hdf5 attribute ");
|
|
printf("of dataset converted from attribute of VDATA.\n");
|
|
free(svd_adata);
|
|
return FAIL;
|
|
}
|
|
}
|
|
|
|
sh5a_id = H5Acreate(h5dset,svdattr_name,sh5_atype,
|
|
sh5a_sid,H5P_DEFAULT);
|
|
|
|
if(sh5a_id <0) {
|
|
printf("failed to create attribute id for hdf5 attribute ");
|
|
printf("of dataset converted from attribute of VDATA.\n");
|
|
H5Sclose(sh5a_sid);
|
|
free(svd_adata);
|
|
return FAIL;
|
|
}
|
|
|
|
sret = H5Awrite(sh5a_id,sh5_amemtype,(void *)svd_adata);
|
|
|
|
if(sret <0) {
|
|
printf("failed to write attribute data for hdf5 attribute ");
|
|
printf("of dataset converted from attribute of VDATA.\n");
|
|
H5Sclose(sh5a_sid);
|
|
H5Aclose(sh5a_id);
|
|
free(svd_adata);
|
|
return FAIL;
|
|
}
|
|
|
|
sret = H5Aclose(sh5a_id);
|
|
sret = H5Sclose(sh5a_sid);
|
|
free(svd_adata);
|
|
}
|
|
}
|
|
return SUCCEED;
|
|
}
|
|
/*-------------------------------------------------------------------------
|
|
* Function: gen_h5comptype
|
|
*
|
|
* Purpose: generate hdf5 compound data type
|
|
|
|
*
|
|
* Return: FAIL if failed, SUCCEED if successful.
|
|
*
|
|
* In :
|
|
vdata_id: vdata identifier
|
|
nfields: number of fields
|
|
sh4size: pointer to datatype size in memory
|
|
sh4memsize: pointer to datatype size in memory
|
|
sh5type: pointer to hdf5 datatype
|
|
sh5memtype: pointer to actual hdf5 datatype in memory
|
|
h5_ctype: hdf5 compound datatype
|
|
h5_cmemtype: hdf5 compound datatype in memory
|
|
Out:
|
|
Modifications:
|
|
|
|
*-------------------------------------------------------------------------
|
|
*/
|
|
|
|
int gen_h5comptype(int32 vdata_id,int32 nfields,
|
|
size_t* sh4size,size_t* sh4memsize,
|
|
hid_t* sh5type,hid_t* sh5memtype,
|
|
hid_t h5_ctype,hid_t h5_cmemtype) {
|
|
|
|
char* fieldname;
|
|
int32 fieldorder;
|
|
int32 fieldsize;
|
|
size_t fil_offset;
|
|
size_t mem_offset;
|
|
size_t fieldsizef;
|
|
hsize_t fielddim[1];
|
|
hid_t h5str_type;
|
|
int check_ifstr;/* flag to check if the h5 type is string.*/
|
|
int i;
|
|
|
|
|
|
check_ifstr = 0;
|
|
fil_offset = 0;
|
|
mem_offset = 0;
|
|
fieldsizef = 0;
|
|
|
|
|
|
for (i =0;i< nfields;i++) {
|
|
|
|
fieldname = NULL;
|
|
fieldorder = VFfieldorder(vdata_id,i);
|
|
|
|
if(fieldorder == FAIL){
|
|
printf("error in obtaining fieldorder.\n");
|
|
return FAIL;
|
|
}
|
|
|
|
fieldname = VFfieldname(vdata_id,i);
|
|
if(fieldname == NULL){
|
|
printf("fail to obtain Vdata field name. \n");
|
|
return FAIL;
|
|
}
|
|
|
|
fieldsize = VFfieldesize(vdata_id,i);
|
|
if(fieldsize == FAIL) {
|
|
printf("error in obtaining fieldsize of vdata field.\n");
|
|
return FAIL;
|
|
}
|
|
|
|
/* when vdata is a character array, we will write the whole
|
|
array as one hdf5 type string. */
|
|
|
|
if(sh5type[i] == H5T_STRING) {
|
|
|
|
if ((h5str_type = mkstr(sh4size[i]*fieldorder,H5T_STR_SPACEPAD))<0) {
|
|
printf("error in making string of hdf5 string. \n");
|
|
return FAIL;
|
|
}
|
|
sh5type[i] = h5str_type;
|
|
check_ifstr = 1;
|
|
}
|
|
|
|
if (sh5memtype[i] == H5T_STRING) {
|
|
|
|
if((h5str_type = mkstr(sh4memsize[i]*fieldorder,H5T_STR_SPACEPAD))<0){
|
|
printf("error in making string for VDATA in memory. \n");
|
|
return FAIL;
|
|
}
|
|
sh5memtype[i] = h5str_type;
|
|
|
|
}
|
|
|
|
fielddim[0] = fieldorder;
|
|
|
|
/* if field type is an array, use H5Tinsert_array.
|
|
When the data type is H5T_STRING,
|
|
we will treat the the vdata as a HDF5 scalar type.*/
|
|
|
|
if (fielddim[0] == 1 || check_ifstr == 1) {
|
|
|
|
if(H5Tinsert(h5_ctype,fieldname,fil_offset,sh5type[i])<0) {
|
|
printf("error inserting hdf5 compound datatype while ");
|
|
printf("converting vdata.\n");
|
|
return FAIL;
|
|
}
|
|
|
|
if(H5Tinsert(h5_cmemtype,fieldname,mem_offset,sh5memtype[i])<0){
|
|
printf("error inserting hdf5 compound datatype of memory");
|
|
printf(" while converting vdata.\n");
|
|
return FAIL;
|
|
}
|
|
}
|
|
|
|
else {
|
|
hid_t arr_type; /* Array datatype for inserting fields */
|
|
|
|
/* Create array datatype */
|
|
if((arr_type=H5Tarray_create(sh5type[i],1,fielddim,NULL))<0) {
|
|
printf("error creating array datatype.\n");
|
|
return FAIL;
|
|
}
|
|
|
|
if(H5Tinsert(h5_ctype,fieldname,fil_offset,arr_type)<0) {
|
|
printf("error inserting array into hdf5 compound datatype. \n");
|
|
return FAIL;
|
|
}
|
|
|
|
/* Close array datatype */
|
|
if(H5Tclose(arr_type)<0) {
|
|
printf("error closing array datatype.\n");
|
|
return FAIL;
|
|
}
|
|
|
|
/* Create array datatype */
|
|
if((arr_type=H5Tarray_create(sh5memtype[i],1,fielddim,NULL))<0) {
|
|
printf("error creating array datatype.\n");
|
|
return FAIL;
|
|
}
|
|
|
|
if(H5Tinsert(h5_cmemtype,fieldname,fil_offset,arr_type)<0) {
|
|
printf("error inserting array into hdf5 compound datatype for memory. \n");
|
|
return FAIL;
|
|
}
|
|
|
|
/* Close array datatype */
|
|
if(H5Tclose(arr_type)<0) {
|
|
printf("error closing array datatype.\n");
|
|
return FAIL;
|
|
}
|
|
|
|
|
|
}
|
|
|
|
if( check_ifstr == 1) {
|
|
fil_offset = fil_offset + sh4size[i]*fieldorder;
|
|
mem_offset = mem_offset + sh4memsize[i]*fieldorder;
|
|
check_ifstr = 0;
|
|
}
|
|
else {
|
|
|
|
fil_offset = fil_offset + sh4size[i]*fieldorder;
|
|
mem_offset = mem_offset + sh4memsize[i]*fieldorder;
|
|
}
|
|
|
|
}
|
|
|
|
return SUCCEED;
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|