/*-------------------------------------------------------------------------
*
* Copyright (C) 2000 National Center for Supercomputing Applications.
* All rights reserved.
*
*-------------------------------------------------------------------------
*/
/******************************************************************************
Description:
1. converter
See HDF4 to HDF5 mapping specification at
(http://hdf.ncsa.uiuc.edu/HDF5/papers/h4toh5) for the default mapping
from HDF4 object to HDF5 object.
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.
2. this file
Converting an hdf4 independent vdata object into an hdf5 dataset of compound dataset.
Author: Kent Yang(ymuqun@ncsa.uiuc.edu)
*****************************************************************************/
#include "h4toh5main.h"
#include <assert.h>
/*-------------------------------------------------------------------------
* Function: Vdata_h4_to_h5
*
* Purpose: translate Vdata object into hdf5 dataset
*
* Return: FAIL if failed, SUCCEED if successful.
*
* In :
vdata_id: RI identifier
group_id: hdf5 group id
Out:
Modification:
*-------------------------------------------------------------------------
*/
int Vdata_h4_to_h5(int32 file_id,int32 vdata_id, hid_t group_id,int h4_attr) {
/* define variables for hdf4. */
int32 istat;
int32 n_records;
int32 vdata_ref;
int32 vdata_tag;
int32 interlace_mode;
int32 vdata_size;
int32 vdatamem_size;
int32 field_index;
int32 fieldorder;
int32 fieldtype;
int i;
int32 nfields;
int num_vd_attrs;
int num_vd_field_attrs;
VOIDP vd_data;
char vdlabel[LABEL_LENG];
char vdata_name[MAX_NC_NAME];
char fieldname[MAX_NC_NAME];
char vdata_class[VSNAMELENMAX];
char field_name_list[VSFIELDMAX*FIELDNAMELENMAX];
/* define varibles for hdf5. */
hid_t h5d_sid;
hid_t h5dset;
hid_t h5_ctype;
hid_t h5_cmemtype;
hid_t* h5memtype = NULL;
hid_t* h5type = NULL;
size_t* h4memsize = NULL;
size_t* h4size = NULL;
hsize_t h5_vddims[1];
char* h5cvdata_name;
int check_vdname;
/* Zeroing out memory for vdlabel,vdata_class,vdata_name */
h4toh5_ZeroMemory(vdata_name,MAX_NC_NAME);
h4toh5_ZeroMemory(fieldname,MAX_NC_NAME);
h4toh5_ZeroMemory(vdata_class,VSNAMELENMAX);
h4toh5_ZeroMemory(field_name_list,VSFIELDMAX*FIELDNAMELENMAX);
h4toh5_ZeroMemory(vdlabel,10);
/* get absolute path of vdata name. */
vdata_ref = VSQueryref(vdata_id);
if (vdata_ref == FAIL) {
printf("error in getting reference number. \n");
return FAIL;
}
vdata_tag = VSQuerytag(vdata_id);
if (vdata_tag == FAIL) {
printf("error in getting object tag number. \n");
return FAIL;
}
/* get the class name */
if(VSgetclass(vdata_id,vdata_class) == FAIL) {
printf("error in obtaining class name. \n");
return FAIL;
}
/* get number of record,field_name,Size of a record and
Name of the vdata*/
if(VSQueryvsize(vdata_id,&vdata_size)==FAIL) {
printf("error in getting size of vdata. \n");
return FAIL;
}
if(vdata_size == 0) {/* empty vdata set. */
return SUCCEED;
}
/* obtain number of records, field name list, vdata name. */
if(VSinquire(vdata_id,&n_records,&interlace_mode,
field_name_list,&vdata_size,vdata_name) == FAIL) {
printf("error in inquiring vdata. \n");
return FAIL;
}
vdatamem_size = 0;
vdata_size = 0;
nfields = VFnfields(vdata_id);
if (nfields == FAIL) {
printf("error in obtaining number of vdata fields. \n");
return FAIL;
}
assert(nfields>0);
h5memtype = calloc((size_t)nfields,sizeof(hid_t));
h5type = calloc((size_t)nfields,sizeof(hid_t));
h4memsize = calloc((size_t)nfields,sizeof(size_t));
h4size = calloc((size_t)nfields,sizeof(size_t));
for (i=0;i<nfields;i++) {
/* obtain field type. */
fieldtype = VFfieldtype(vdata_id,i);
if(fieldtype == FAIL){
printf("error in obtaining field type. \n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
return FAIL;
}
/* obtain field order.*/
fieldorder = VFfieldorder(vdata_id,i);
/* printf("fieldorder %d\n",fieldorder);*/
if(fieldorder == FAIL){
printf("error in obtaining field order. \n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
return FAIL;
}
/* datatype conversion from hdf4 to hdf5.
the corresponding memory data type is also converted.*/
if(h4type_to_h5type(fieldtype,&h5memtype[i],&h4memsize[i],
&h4size[i],&h5type[i])== FAIL){
printf("error in doing datatype conversion at vdata routine. \n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
return FAIL;
}
vdatamem_size +=fieldorder*h4memsize[i];
vdata_size +=fieldorder*h4size[i];
}
vd_data = malloc((size_t)(vdatamem_size*n_records));
istat = VSsetfields(vdata_id,field_name_list);
if(istat == FAIL) {
printf("error setting fields of vdata.\n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
return FAIL;
}
istat = VSread(vdata_id,(uint8*)vd_data,n_records,FULL_INTERLACE);
if(istat == FAIL) {
printf("error in obtaining vdata. \n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
return FAIL;
}
for (i=0;i<nfields;i++) {
/* obtain field order.*/
fieldorder = VFfieldorder(vdata_id,i);
if(fieldorder == FAIL){
printf("error in obtaining field order. \n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
return FAIL;
}
}
/* create hdf5 compound datatype for both memory and file.*/
h5_ctype = H5Tcreate(H5T_COMPOUND, (size_t)vdata_size);
h5_cmemtype = H5Tcreate(H5T_COMPOUND,(size_t)vdatamem_size);
if(gen_h5comptype(vdata_id,nfields,h4size,h4memsize,h5type,h5memtype,
h5_ctype,h5_cmemtype)==FAIL){
printf("error in generating h5 compound data type.\n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
return FAIL;
}
h5_vddims[0] = n_records;
h5d_sid = H5Screate_simple(1,h5_vddims,NULL);
if(h5d_sid <0){
printf("error in obtaining space id.\n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
return FAIL;
}
/* choose a number that is not returned from the func.*/
check_vdname = -3;
/* obtain hdf5 vdata name. */
h5cvdata_name = get_name(vdata_ref,estnum_vd,vd_hashtab,&check_vdname);
if (h5cvdata_name == NULL && check_vdname == 0 ) {
printf("error,cannot find vdata \n");
return FAIL;
}
if (h5cvdata_name == NULL && check_vdname == -1) {
printf("error,group name is not defined.\n");
return FAIL;
}
if (h5cvdata_name == NULL && check_vdname == -2 ) {
printf("cannot allocate memory for vdata.\n");
return FAIL;
}
h5dset = H5Dcreate(group_id,h5cvdata_name,h5_ctype,h5d_sid,H5P_DEFAULT);
if(h5dset <0) {
printf("error in obtaining dataset.\n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
free(h5cvdata_name);
return FAIL;
}
free(h5cvdata_name);
if(H5Dwrite(h5dset,h5_cmemtype,H5S_ALL,H5S_ALL,H5P_DEFAULT,vd_data)<0){
printf("error in writing dataset converted from vdata.\n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
return FAIL;
}
/* handle vdata attributes and vdata field attributes. */
num_vd_attrs = VSfnattrs(vdata_id,_HDF_VDATA);
if (num_vd_attrs == FAIL) {
printf("error in obtaining attributes of vdata.\n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
return FAIL;
}
/* when field_index = -1, only transfer vdata attribute.*/
field_index = -1;
if(vdata_transattrs(vdata_id,h5dset,num_vd_attrs,field_index,NULL)==FAIL){
printf("error in translating vdata attibutes.\n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
return FAIL;
}
for (i =0;i< nfields;i++) {
if(VFfieldname(vdata_id,i)== NULL) {
printf("error in obtaining field name. \n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
return FAIL;
}
strcpy(fieldname,VFfieldname(vdata_id,i));
num_vd_field_attrs = VSfnattrs(vdata_id,i);
if(num_vd_field_attrs == FAIL){
printf("error in number of vd field attribute \n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
return FAIL;
}
if(vdata_transattrs(vdata_id,h5dset,num_vd_field_attrs,i,fieldname)
==FAIL){
printf("error in transfering vdata attributes.\n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
return FAIL;
}
}
/* converting annotations of vdata into corresponding hdf5 attribute.*/
if( Annoobj_h4_to_h5(file_id,vdata_ref,vdata_tag,h5dset)== FAIL){
printf("fail to convert HDF4 VDATA annotation into hdf5 attributes.\n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
return FAIL;
}
/* converting predefined attributes. */
if(h4_attr != 0) {
istat = VSisattr(vdata_id);
if (istat == FAIL) {
printf("error in checking vdata attribute. \n");
VSdetach(vdata_id);
return FAIL;
}
if(istat) strcpy(vdlabel,VDATTRLAB);
else strcpy(vdlabel,VDATALABEL);
if(h4_transpredattrs(h5dset,HDF4_OBJECT_TYPE,vdlabel)==FAIL){
printf("error in transfering vdata attributes.\n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
return FAIL;
}
if(vdata_name[0] != '\0') {
if(h4_transpredattrs(h5dset,HDF4_OBJECT_NAME,vdata_name)==FAIL){
printf("error in transfering vdata attributes.\n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
return FAIL;
}
}
if(h4_transnumattr(h5dset,HDF4_REF_NUM,vdata_ref)==FAIL){
printf("error in transfering vdata attributes.\n");
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
return FAIL;
}
}
H5Sclose(h5d_sid);
H5Dclose(h5dset);
VSdetach(vdata_id);
free(h5memtype);
free(h5type);
free(h4memsize);
free(h4size);
free(vd_data);
return SUCCEED;
}
/*-------------------------------------------------------------------------
* Function: vdata_transattrs
*
* Purpose: translate Vdata attributes into attributes of the
corresponding hdf5 dataset
*
* Return: FAIL if failed, SUCCEED if successful.
*
* In :
vdata_id: vdata identifier
h5dset: hdf5 dataset
snum_vdattrs: number of vd attributes
field_index: index of vdata fields
attr_name: vdata(or vdata field) attribute name
Out:
Modifications:
*-------------------------------------------------------------------------
*/
int vdata_transattrs(int32 vdata_id,hid_t h5dset,int snum_vdattrs,
int field_index,char* attr_name){
char svdattr_name[2*MAX_NC_NAME];
char* svdrepattr_name;
char refstr[MAXREF_LENGTH];
int32 count_svdadata;
int32 svd_atype;
size_t sh4_amemsize;
size_t sh4_asize;
hid_t sh5a_sid;
hid_t sh5a_id;
hid_t sh5_atype;
hid_t sh5_amemtype;
hid_t sh5str_type;
hid_t sh5str_memtype;
hsize_t sh5dims[1];
void* svd_adata;
herr_t sret;
int i;
/* zeroing out memory for svdattr_name and refstr */
h4toh5_ZeroMemory(svdattr_name,2*MAX_NC_NAME);
h4toh5_ZeroMemory(refstr,MAXREF_LENGTH);
/* separate vdata attribute from vdata field attributes. */
if (field_index < -1) {
printf("error: check_field should be either -1(vdata) or ");
printf(">=0(vdata field).\n");
return FAIL;
}
for (i = 0;i < snum_vdattrs; i++) {
/* if the field_index is 0, no field attribute exists, only
VDATA attributes are converted.*/
if (VSattrinfo(vdata_id,field_index,i,svdattr_name,&svd_atype,
&count_svdadata,NULL)== FAIL){
printf("unable to obtain attribute information. \n");
return FAIL;
}
if(svdattr_name[0] == '\0') {
svdrepattr_name = trans_obj_name(DFTAG_VG,i);
strcpy(svdattr_name,svdrepattr_name);
free(svdrepattr_name);
}
if (field_index == -1);
else if (field_index != -1 && attr_name != NULL) {
strcat(svdattr_name,":");
strcat(svdattr_name,attr_name);
}
else {
strcat(svdattr_name,":");
strcat(svdattr_name,"HDF4_VDATA_ATTR_");
if(conv_int_str(field_index,refstr)==FAIL) {
printf("error in converting vdata field index to string.\n");
return FAIL;
}
strcat(svdattr_name,refstr);
}
/* converting attribute data type into the corresponding hdf5 data type */
if(h4type_to_h5type(svd_atype,&sh5_amemtype,&sh4_amemsize,
&sh4_asize,&sh5_atype)==FAIL){
printf("fail to translate vdata attribute datatype from H4 to H5.\n");
return FAIL;
}
svd_adata = malloc(sh4_amemsize * count_svdadata);
if(svd_adata == NULL) {
printf("fail to allocate memory for vdata attribute data.\n");
return FAIL;
}
if(VSgetattr(vdata_id,field_index,i,(VOIDP)svd_adata)==FAIL){
printf("error in getting attributes of vdata. \n");
free(svd_adata);
return FAIL;
}
/* 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;
size_t fil_offset;
size_t mem_offset;
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;
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;
}
/* 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,mem_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;
}