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hdf5/tools/h4toh5/h4toh5sds.c
Quincey Koziol ed663577a5 [svn-r4473] Purpose: 
Code cleanup for better compatibility with C++ compilers
Description:
    C++ compilers are choking on our C code, for various reasons:
        we used our UNUSED macro incorrectly when referring to pointer types
        we used various C++ keywords as variables, etc.
        we incremented enum's with the ++ operator.
Solution:
    Changed variables, etc.to avoid C++ keywords (new, class, typename, typeid,
        template)

    Fixed usage of UNUSED macro from this:
        char UNUSED *c
    to this:
        char * UNUSED c

    Switched the enums from x++ to x=x+1
Platforms tested:
    FreeBSD 4.4 (hawkwind)
2001-09-25 12:46:32 -05:00

2087 lines
57 KiB
C
Raw Blame History

/*-------------------------------------------------------------------------
*
* 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 sds object into an hdf5 dataset.
Author: Kent Yang(ymuqun@ncsa.uiuc.edu)
*****************************************************************************/
#include "h4toh5main.h"
static int convert_zerosdsunlimit(int32 file_id,
int32 sds_id,
hid_t h5_group,
hid_t h5_dimgroup,
int h4_attr);
/*-------------------------------------------------------------------------
* Function: Sds_h4_to_h5
*
* Purpose: translate SDS object into hdf5 dataset
*
* Return: FAIL if failed, SUCCEED if successful.
*
* In :
sds_id: SDS identifier
h5_group: hdf5 group id
h5_dimgroup: hdf5 dimension group id
dim_pathname: dimensional path name
*-------------------------------------------------------------------------
*/
int Sds_h4_to_h5(int32 file_id,int32 sds_id,hid_t h5_group,hid_t h5_dimgroup,int h4_attr){
int32 sds_dtype;
int32 sds_rank;
int32 sds_dimsizes[MAX_VAR_DIMS];
int32* sds_start;
int32* sds_edge;
int32* sds_stride;
int32 count_sdsdata;
int32 sds_ref;
int sds_empty;
int32 istat;
int i;
int32 num_sdsattrs;
void* sds_data;
int check_sdsname;
int check_gloattr;
char sdsname[MAX_NC_NAME];
char sdslabel[MAX_NC_NAME];
size_t h4size;
size_t h4memsize;
HDF_CHUNK_DEF c_def_out;
hsize_t* chunk_dims;
int32 c_flags;
/* for checking compression */
sp_info_block_t info_block;
int16 special_code;
int32 access_id;
uint16 sd_ref;
int gzip_level;
/* define varibles for hdf5. */
hid_t h5dset;
hid_t h5d_sid;
hid_t h5ty_id;
hid_t h5_memtype;
hid_t create_plist;
hid_t write_plist;
hsize_t h5dims[MAX_VAR_DIMS];
hsize_t max_h5dims[MAX_VAR_DIMS];
hsize_t bufsize;
char* h5csds_name;
herr_t ret;
special_code = -1;
/* zeroing out the memory for sdsname and sdslabel.*/
h4toh5_ZeroMemory(sdsname,MAX_NC_NAME);
h4toh5_ZeroMemory(sdslabel,MAX_NC_NAME);
/* check whether the sds is empty. */
if(SDcheckempty(sds_id,&sds_empty)== FAIL) {
printf("error in running SDcheckempty routine. \n");
return FAIL;
}
/*check whether the sds is created with unlimited dimension. */
/*obtain name,rank,dimsizes,datatype and num of attributes of sds */
if (SDgetinfo(sds_id,sdsname,&sds_rank,sds_dimsizes,&sds_dtype,
&num_sdsattrs)==FAIL) {
printf("unable to get information of sds h5dset.\n");
return FAIL;
}
if(sds_empty !=0) {
if(sds_dimsizes[0]==0) {
if(convert_zerosdsunlimit(file_id,sds_id,h5_group,h5_dimgroup,h4_attr)==FAIL){
printf("cannot convert unlimited dimension SDS with 0.\n");
return FAIL;
}
}
else if(convert_sdsfillvalue(file_id,sds_id,h5_group,h5_dimgroup,h4_attr)==FAIL) {
printf("cannot convert fill value successfully.\n");
return FAIL;
}
return SUCCEED;
}
if(SDgetchunkinfo(sds_id,&c_def_out, &c_flags)== FAIL) {
printf("error in getting chunking information. \n");
return FAIL;
}
/* obtain start,edge, stride and number of sds data. */
sds_start = malloc(sizeof(int32)*sds_rank);
if(sds_start == NULL) {
printf("error in allocating memory for sds start.\n");
return FAIL;
}
sds_edge = malloc(sizeof(int32)*sds_rank);
if(sds_edge == NULL) {
printf("error in allocating memory for sds edge.\n");
free(sds_start);
return FAIL;
}
sds_stride = malloc(sizeof(int32)*sds_rank);
if(sds_stride == NULL) {
printf("error in allocating memory for sds stride. \n");
free(sds_start);
free(sds_edge);
return FAIL;
}
count_sdsdata = 1;
for (i=0;i<sds_rank;i++){
sds_stride[i] = 1;
sds_start[i] = 0;
sds_edge[i] = sds_dimsizes[i];
count_sdsdata = count_sdsdata*sds_dimsizes[i];
}
for (i=0;i<sds_rank;i++) {
h5dims[i] = sds_edge[i]-sds_start[i];
max_h5dims[i] = h5dims[i];
}
if(SDisrecord(sds_id)) {
max_h5dims[0] = H5S_UNLIMITED;
}
/* convert hdf4 data type to hdf5 data type. */
if (h4type_to_h5type(sds_dtype,&h5_memtype,&h4memsize,&h4size,
&h5ty_id) == FAIL) {
printf("failed to translate datatype. \n");
free(sds_start);
free(sds_edge);
free(sds_stride);
return FAIL;
}
/* check whether the datatype is string, if we find string format,
we will change them back into integer format.*/
if (h5ty_id == H5T_STRING) {
/* rechange string datatype into numerical datatype.*/
if(h5string_to_int(sds_dtype,&h5_memtype,h4memsize,
&h5ty_id)== FAIL) {
printf("error in translating H5T_STRING to int.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
return FAIL;
}
}
sds_data = malloc(h4memsize*count_sdsdata);
if(sds_data == NULL) {
printf("error in allocating memory. \n");
free(sds_start);
free(sds_edge);
free(sds_stride);
return FAIL;
}
istat = SDreaddata(sds_id, sds_start, sds_stride, sds_edge,
(VOIDP)sds_data);
if (istat == FAIL) {
printf("unable to read data from h5dset. \n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
return FAIL;
}
/* obtaining reference number and name of h5 dataset
corresponding to sds. */
sds_ref = SDidtoref(sds_id);
if(sds_ref == FAIL) {
printf("error in obtaining sds reference number. \n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
return FAIL;
}
h5csds_name = get_name(sds_ref,2*num_sds,sds_hashtab,&check_sdsname);
if (h5csds_name == NULL && check_sdsname == 0 ) {
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
printf("error,cannot find sds name \n");
return FAIL;
}
if (h5csds_name == NULL && check_sdsname == -1) {
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
printf("error,sds name is not defined.\n");
return FAIL;
}
if (h5csds_name == NULL && check_sdsname == -2) {
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
printf("error,not enough memory for allocating sds name.\n");
return FAIL;
}
h5d_sid = H5Screate_simple(sds_rank,h5dims,max_h5dims);
if (h5d_sid < 0) {
printf("failed to create hdf5 data space converted from SDS. \n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
return FAIL;
}
/* create property list. */
create_plist = H5Pcreate(H5P_DATASET_CREATE);
chunk_dims = malloc(sizeof(hsize_t)*sds_rank);
sd_ref = get_SDref(file_id,DFTAG_NDG,sds_ref);
if(sd_ref == 0)
sd_ref = get_SDref(file_id,DFTAG_SDG,sds_ref);
if(sd_ref >0 )
access_id = Hstartread(file_id,DFTAG_SD,sd_ref);
if(sd_ref == 0)
access_id = FAIL;
if(access_id != FAIL) {
istat = Hinquire(access_id,NULL,NULL,NULL,NULL,NULL,NULL,NULL,&special_code);
if(istat == FAIL) {
printf("failed to inquire information \n ");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
return FAIL;
}
if(special_code >0){
if(HDget_special_info(access_id,&info_block)==FAIL){
printf("fail to get special info.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
return FAIL;
}
/* free(info_block.cdims);*/
if(info_block.key == SPECIAL_COMP) {
if(c_flags == HDF_NONE){
/* 1. if the first dimension is unlimited dimension,
we have to provide a chunking size.
2. the current HDF5 will not handle compression case itself,
in order that the converted HDF5 is compressed, we have to
provide a chunking size. currently it is set to h5dim[i].*/
for(i=0;i<sds_rank;i++){
chunk_dims[i] = (hsize_t)(h5dims[i]);
}
if(H5Pset_chunk(create_plist, sds_rank, chunk_dims)<0) {
printf("failed to set up chunking information for ");
printf("property list.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
return FAIL;
}
if(H5Pset_deflate(create_plist,GZIP_COMLEVEL)<0){
/* if(H5Pset_deflate(create_plist,2)<0){*/
printf("fail to set compression method for HDF5 file.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
}
}
}
else if(c_flags == HDF_NONE && SDisrecord(sds_id))
{
for(i=0;i<sds_rank;i++){
chunk_dims[i] = (hsize_t)(sds_dimsizes[i]);
}
if(H5Pset_chunk(create_plist, sds_rank, chunk_dims)<0) {
printf("failed to set up chunking information for ");
printf("property list.\n");
free(chunk_dims);
H5Pclose(create_plist);
return FAIL;
}
}
}
}
/* HDF4 can support various compression methods including simple RLE, NBIT, Skip Huffman, gzip,Jpeg , HDF5 currently only supports gzip compression.
By default, we will compress HDF5 dataset by using gzip compression if HDF5 file is compressed. */
if(c_flags == HDF_CHUNK || c_flags == (HDF_CHUNK | HDF_COMP)
|| c_flags == (HDF_CHUNK | HDF_NBIT) ){
if(c_def_out.comp.comp_type == COMP_CODE_RLE || c_def_out.comp.comp_type == COMP_CODE_NBIT || c_def_out.comp.comp_type == COMP_CODE_SKPHUFF || c_def_out.comp.comp_type == COMP_CODE_DEFLATE || c_def_out.comp.comp_type == COMP_CODE_JPEG) {
for(i=0;i<sds_rank;i++)
chunk_dims[i] = (hsize_t)c_def_out.chunk_lengths[i];
if(H5Pset_chunk(create_plist, sds_rank, chunk_dims)<0) {
printf("failed to set up chunking information for ");
printf("property list.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
return FAIL;
}
if(c_def_out.comp.comp_type == COMP_CODE_DEFLATE)
gzip_level = c_def_out.comp.cinfo.deflate.level;
else gzip_level = GZIP_COMLEVEL;
if(H5Pset_deflate(create_plist,gzip_level)<0){
printf("fail to set compression method for HDF5 file.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
}
}
}
if(access_id == FAIL && c_flags != HDF_CHUNK && c_flags != (HDF_CHUNK | HDF_COMP)
&& c_flags != (HDF_CHUNK | HDF_NBIT)) {
for(i=0;i<sds_rank;i++)
chunk_dims[i] = h5dims[i];
if(H5Pset_chunk(create_plist, sds_rank, chunk_dims)<0) {
printf("failed to set up chunking information for ");
printf("property list.\n");
free(chunk_dims);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
return FAIL;
}
}
h5dset = H5Dcreate(h5_group,h5csds_name,h5ty_id,h5d_sid,create_plist);
if (h5dset < 0) {
printf("failed to create hdf5 dataset converted from SDS. \n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
return FAIL;
}
/* comment this out.
write_plist = H5Pcreate(H5P_DATASET_XFER);
write_plist = H5Pcreate_list(H5P_DATASET_XFER_NEW);
bufsize = h4memsize;
for(i=1;i<sds_rank;i++)
bufsize *= h5dims[i];
if(H5Pset_buffer(write_plist,bufsize,NULL,NULL)<0) {
printf("fail to create data transfer property list.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
H5Pclose_list(write_plist);
return FAIL;
}
if (H5Dwrite(h5dset,h5_memtype,h5d_sid,h5d_sid,write_plist,
(void *)sds_data)<0) {
*/
if (H5Dwrite(h5dset,h5_memtype,h5d_sid,h5d_sid,H5P_DEFAULT,
(void *)sds_data)<0) {
printf("failed to write data into hdf5 dataset");
printf(" converted from SDS.\n");
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
return FAIL;
}
/* convert sds annotation into attribute of sds dataset.
Since there is no routines to find the exact tag of sds object,
we will check three possible object tags of sds objects, that is:
DFTAG_SD,DFTAG_SDG,DFTAG_NDG. If the object tag of sds object is
falling out of this scope, we will not convert annotations into
hdf5 attributes; it is user's responsibility to make sure object tags
for sds objects are only one of the above three tags.*/
if(Annoobj_h4_to_h5(file_id,sds_ref,DFTAG_SD,h5dset)== FAIL){
printf("failed to convert sds annotation into hdf5 attribute.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
return FAIL;
}
if(Annoobj_h4_to_h5(file_id,sds_ref,DFTAG_SDG,h5dset)== FAIL){
printf("failed to convert sds annotation into hdf5 attribute.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
return FAIL;
}
if(Annoobj_h4_to_h5(file_id,sds_ref,DFTAG_NDG,h5dset)== FAIL){
printf("failed to convert sds annotation into hdf5 attribute.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
return FAIL;
}
/* convert sds dimensional scale dataset into hdf5 dataset. */
if(sdsdim_to_h5dataset(sds_id,sds_rank,h5dset,h5_dimgroup,sds_dimsizes[0]) == FAIL) {
printf("failed to convert dimensional scale to hdf5 dataset. \n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
return FAIL;
}
check_gloattr = 0;
if (sds_transattrs(sds_id,h5dset,num_sdsattrs,check_gloattr)==FAIL) {
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
printf(" Error in obtaining sds attributes. \n");
return FAIL;
}
/********************************************/
/* handle extra attributes of sds : sds label, object type
and reference num */
if(h4_attr !=0) {
strcpy(sdslabel,SDSLABEL);
if(h4_transpredattrs(h5dset,HDF4_OBJECT_TYPE,sdslabel)==FAIL) {
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
printf("unable to transfer sds label to HDF4 OBJECT TYPE.\n");
return FAIL;
}
if(sdsname[0] != '\0') {
if(h4_transpredattrs(h5dset,HDF4_OBJECT_NAME,sdsname)==FAIL){
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
printf("unable to transfer sds name to HDF5 dataset attribute.\n");
return FAIL;
}
}
if(h4_transnumattr(h5dset,HDF4_REF_NUM,sds_ref)==FAIL){
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
printf("unable to transfer sds ref. to HDF5 dataset attribute.\n");
return FAIL;
}
}
istat = SDendaccess(sds_id);
ret = H5Pclose(create_plist);
ret = H5Sclose(h5d_sid);
ret = H5Dclose(h5dset);
free(sds_data);
free(sds_start);
free(sds_edge);
free(sds_stride);
free(chunk_dims);
return SUCCEED;
}
/*-------------------------------------------------------------------------
* Function: sds_transattrs
*
* Purpose: translate attribute of HDF4 SDS object into
hdf5 dataset attribute
*
* Return: FAIL if failed, SUCCEED if successful.
*
* In :
ssds_id: SDS identifier
sh5_dset: hdf5 dataset
snum_sdsattrs: number of sds attribute
check_gloflag: a flag that check whether the attribute is
a file attribute or a sds id or a dimensional scale id.
*-------------------------------------------------------------------------
*/
int sds_transattrs(int32 ssds_id, hid_t sh5_dset,int snum_sdsattrs,
int check_gloflag) {
char ssdsatrr_name[2*MAX_NC_NAME];
char sdsglo[MAX_NC_NAME];
char* sdsrepattr_name;
int32 count_ssdsadata;
int32 ssds_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[MAX_VAR_DIMS];
void* ssds_adata;
herr_t sret;
int i;
for (i = 0;i < snum_sdsattrs; i++) {
if (SDattrinfo(ssds_id,i,ssdsatrr_name,&ssds_atype,
&count_ssdsadata)==FAIL){
printf("unable to obtain SDS attribute information. \n");
return FAIL;
}
/* make a table for the attribute type, to do the corresponding type. */
if(h4type_to_h5type(ssds_atype,&sh5_amemtype,&sh4_amemsize,
&sh4_asize,&sh5_atype)== FAIL) {
printf("fail to translate sds attribute data type from H4 to H5. \n");
return FAIL;
}
ssds_adata = malloc(sh4_amemsize * count_ssdsadata);
if(ssds_adata == NULL) {
printf("error, cannot allocate memory for sds attribute data. \n");
return FAIL;
}
if(SDreadattr(ssds_id,i,(VOIDP)ssds_adata)== FAIL) {
printf("error in reading attributes of sds object. \n");
free(ssds_adata);
return FAIL;
}
/* if attribute doesn't have name, a default name is set. */
if(ssdsatrr_name[0] == '\0') {
sdsrepattr_name = trans_obj_name(DFTAG_NDG,i);
strcpy(ssdsatrr_name,sdsrepattr_name);
free(sdsrepattr_name);
}
/* if the sds attribute is a file attribute. */
if(check_gloflag == 1){
strcpy(sdsglo,GLOSDS);
strcat(ssdsatrr_name,"_");
strcat(ssdsatrr_name,sdsglo);
}
/* now do attribute-transferring.
1. deal with string data type
2. set attribute space.
3. get attribute name, set property list. */
if (sh5_atype == H5T_STRING) {
sh5a_sid = H5Screate(H5S_SCALAR);
if (sh5a_sid < 0) {
printf("failed to create attribute space for");
printf(" HDF4_OBJECT_TYPE SDS. \n");
free(ssds_adata);
return FAIL;
}
if ((sh5str_type = mkstr(count_ssdsadata,
H5T_STR_SPACEPAD))<0) {
printf("error in making string. \n");
H5Sclose(sh5a_sid);
free(ssds_adata);
return FAIL;
}
/* check this line later. */
if ((sh5str_memtype = mkstr(count_ssdsadata*sh4_amemsize,
H5T_STR_SPACEPAD))<0) {
printf("error in making memory string. \n");
H5Sclose(sh5a_sid);
free(ssds_adata);
return FAIL;
}
sh5a_id = H5Acreate(sh5_dset,ssdsatrr_name,sh5str_type,
sh5a_sid,H5P_DEFAULT);
if (sh5a_id <0) {
printf("failed to obtain attribute id for");
printf(" HDF4_OBJECT_TYPE SDS. \n");
H5Sclose(sh5a_sid);
free(ssds_adata);
return FAIL;
}
sret = H5Awrite(sh5a_id,sh5str_memtype,(void *)ssds_adata);
if (sret <0) {
printf("failed to write attribute data for");
printf(" HDF4_OBJECT_TYPE SDS. \n");
H5Sclose(sh5a_sid);
H5Aclose(sh5a_id);
free(ssds_adata);
return FAIL;
}
sret = H5Sclose(sh5a_sid);
sret = H5Aclose(sh5a_id);
}
else {
if(count_ssdsadata == 1) {
sh5a_sid = H5Screate(H5S_SCALAR);
if (sh5a_sid < 0) {
printf("failed to create space id. \n");
free(ssds_adata);
return FAIL;
}
}
else {
sh5dims[0] = count_ssdsadata;
sh5a_sid = H5Screate_simple(1,sh5dims,NULL);
if (sh5a_sid < 0) {
printf("failed to create attribute space. \n");
free(ssds_adata);
return FAIL;
}
}
sh5a_id = H5Acreate(sh5_dset,ssdsatrr_name,sh5_atype,
sh5a_sid,H5P_DEFAULT);
if(sh5a_id <0) {
printf("failed to obtain attribute id. \n");
H5Sclose(sh5a_sid);
free(ssds_adata);
return FAIL;
}
sret = H5Awrite(sh5a_id,sh5_amemtype,(void *)ssds_adata);
if(sret <0) {
printf("failed to write attribute data.\n ");
H5Sclose(sh5a_sid);
H5Aclose(sh5a_id);
free(ssds_adata);
return FAIL;
}
sret = H5Sclose(sh5a_sid);
sret = H5Aclose(sh5a_id);
}
free(ssds_adata);
}
return SUCCEED;
}
/****************sdsdim_to_h5dataset*******************
* Purpose: translate dimensional scale dataset into
hdf5 dataset
*
* Return: FAIL if failed, SUCCEED if successful.
*
* In :
sds_id: SDS identifier
sds_rank: number of sds dimensions
Out:
Modification:
*-------------------------------------------------------------------------
*/
int sdsdim_to_h5dataset(int32 sds_id,int32 sds_rank,hid_t sh5dset,
hid_t sh5_dimgroup,int32 firstdimsize) {
int32 sdsdim_id;
int32 sdsdim_type = 0;
int32 sds_dimscasize[1];
int32 istat;
int i,k;
int count_h5objref;/* this counter updates the number of h5 object reference. */
int count_h5attrname;/*this counter updates the number of h5 dimensional name attribute.*/
int check_gloattr;
int32 num_sdsdimattrs;
int check_sdsdim;
void* dim_scadata;
char sdsdim_name[MAX_NC_NAME+1];
char* cor_sdsdimname;
size_t h4dim_memsize;
size_t h4dim_size;
HDF_CHUNK_DEF c_def_out;
int32 c_flags;
int32* sdsdimempty;
/* define varibles for hdf5. */
hid_t h5dim_dset;
hid_t h5dim_sid;
hid_t h5dim_tid;
hid_t h5dim_memtype;
hid_t h5dim_nameaid;
hid_t h5dim_namesid;
hid_t h5str_dimntype;
hid_t attr_refSpace;
hid_t attr_refType;
hid_t attribID;
hid_t create_plist;
int dim_index;
hsize_t h5dimscas[1];
hsize_t max_h5dimscas[1];
hsize_t h5dim_dims[1];
hsize_t h5dimname_dims[1];
hsize_t attr_refDims[1];
hsize_t h5dim_chunkdim[1];
hobj_ref_t dim_refdat;
hobj_ref_t* alldim_refdat;
char* h5sdsdim_name;
/* char *h5sdsdim_allname[MAX_VAR_DIMS];
char *h5newsdsdim_name; */
char h5sdsdim_allname[MAX_VAR_DIMS*MAX_DIM_NAME];
char h5newsdsdim_name[MAX_DIM_NAME];
char h5dimpath_name[MAX_DIM_NAME];
herr_t ret;
sdsdimempty = malloc(sds_rank *sizeof(int32));
for(i=0;i<sds_rank;i++)
sdsdimempty[i] = 0;
/*zero out memory for h5sdsdim_allname and h5dimpath_name */
/*** the following line should be erased for variable length HDF5 string.**/
h4toh5_ZeroMemory(h5sdsdim_allname,(MAX_VAR_DIMS*MAX_DIM_NAME)*sizeof(char));
h4toh5_ZeroMemory(h5dimpath_name,MAX_DIM_NAME*sizeof(char));
/*check whether the sds is created with unlimited dimension. */
if(firstdimsize !=0) {
if(SDgetchunkinfo(sds_id,&c_def_out, &c_flags)== FAIL) {
printf("error in getting chunking information. \n");
return FAIL;
}
}
/* initialize the dimensional number of sds dimensions, h5dim_dims
is used for grabbing hdf5 dimensional name list and object reference
list. */
h5dim_dims[0] = (hsize_t)sds_rank;
count_h5objref = 0;
count_h5attrname = 0;
for (i = 0; i<sds_rank;i++) {
sdsdim_id = SDgetdimid(sds_id,i);
if(sdsdim_id == FAIL) {
printf("error in obtaining sds dimension id. \n");
return FAIL;
}
istat = SDdiminfo(sdsdim_id,sdsdim_name,sds_dimscasize,
&sdsdim_type,&num_sdsdimattrs);
if (istat == FAIL) {
printf("sds get dim. information failed. \n");
SDendaccess(sdsdim_id);
return FAIL;
}
/* Here we have very messy cases for dimensional scale when
sdsdim_type is 0(or not set).
When sdsdim_type is 0, it means no SDS dimensional scale
data for this dimensions. However, users may define SDS dimensional
scale name. We want to keep this information.
If user doesn't specific the name we will skip this dimension */
if(sdsdim_type == 0) {
if(strncmp(sdsdim_name,fakeDim,strlen(fakeDim))==0){
SDendaccess(sdsdim_id);
continue;
}
}
/* for unlimited SDS dimension, grab the current dimensional size. */
if(sds_dimscasize[0] == 0) sds_dimscasize[0] = firstdimsize;
/* check whether this dimensional scale dataset is looked up. */
check_sdsdim = lookup_name(sdsdim_name,DIM_HASHSIZE,dim_hashtab);
strcpy(h5dimpath_name,HDF4_DIMG);
/* checking whether sds dimension scale name contains ORI_SLASH, changing into CHA_SLASH.*/
cor_sdsdimname = correct_name(sdsdim_name);
if(cor_sdsdimname == NULL) {
printf("error in generating corrected sds dimensional scale name.\n");
SDendaccess(sdsdim_id);
return FAIL;
}
/* generating hdf5 dimensional scale name. */
h5sdsdim_name = get_obj_aboname(cor_sdsdimname,NULL,h5dimpath_name,NULL);
if (h5sdsdim_name == NULL) {
printf("error in getting hdf5 sds dimension name.\n");
SDendaccess(sdsdim_id);
free(cor_sdsdimname);
return FAIL;
}
free(cor_sdsdimname);
strncpy(&h5sdsdim_allname[count_h5attrname*MAX_DIM_NAME],h5sdsdim_name,MAX_DIM_NAME);
/*h5sdsdim_allname[count_h5attrname]=HDstrdup(h5sdsdim_name);
should be added for variable length HDF5 string. 6/11/2001. */
/* here we should add some comments for fakedim0--name. It seems that
hdf4(netcdf) will use unique fake dimension name, fakedim + unique
number, so check_sdsdim will never be 1 if the dimension name is fake
name. Under this case, count_h5objref and count_h5attrname
will not increase if this dimension doesnot
have dimensional scale data. That assures the object reference of sds is
correct. */
/*if this dimension is not touched, get name of the dimensional scale data. */
if (check_sdsdim == 1){/* the dimension is touched, skip this one.*/
free(h5sdsdim_name);
SDendaccess(sdsdim_id);
/* here we have to check a special case when the dimension type is 0.
We should ignore counting object reference.*/
if(sdsdim_type == 0) {
count_h5attrname++;
continue;
}
count_h5objref = count_h5objref + 1;
count_h5attrname = count_h5attrname + 1;
continue;
}
if (check_sdsdim != 0) {
printf("error in checking sds dimensions.\n");
SDendaccess(sdsdim_id);
free(h5sdsdim_name);
return FAIL;
}
/* here we want to keep the dimensional scale name without
making the object reference. */
if(sdsdim_type == 0) {
count_h5attrname = count_h5attrname + 1;
sdsdimempty[i] = 1;
continue;
}
/* get h5 dimensional scale data type. */
if(h4type_to_h5type(sdsdim_type,&h5dim_memtype,&h4dim_memsize,
&h4dim_size,&h5dim_tid)== FAIL) {
printf("error in transferring sds dimension data type.\n");
SDendaccess(sdsdim_id);
free(h5sdsdim_name);
return FAIL;
}
/* dimensional scale dataset cannot be H5T_STRING data type.
So transferring back to int8 */
if (h5dim_tid == H5T_STRING) {
if(h5string_to_int(sdsdim_type,&h5dim_memtype,h4dim_memsize,
&h5dim_tid)==FAIL){
printf("error in translating from string to int. \n");
SDendaccess(sdsdim_id);
free(h5sdsdim_name);
return FAIL;
}
}
/* get the dimensional scale data. */
dim_scadata = malloc(h4dim_memsize*sds_dimscasize[0]);
istat = SDgetdimscale(sdsdim_id,(VOIDP)dim_scadata);
if (istat == FAIL) {
printf("sds get dim. scale failed. \n");
SDendaccess(sdsdim_id);
free(h5sdsdim_name);
free(dim_scadata);
return FAIL;
}
/* set dimensional scale size properly. */
h5dimscas[0] = sds_dimscasize[0];
/* only set for the first dimension if SDS is unlimited dimension. */
if(SDisrecord(sds_id) && i == 0)
max_h5dimscas[0] = H5S_UNLIMITED;
else
max_h5dimscas[0] = h5dimscas[0];
h5dim_sid = H5Screate_simple(1,h5dimscas,max_h5dimscas);
if(h5dim_sid <0) {
printf("error in creating space. \n");
SDendaccess(sdsdim_id);
free(h5sdsdim_name);
free(dim_scadata);
return FAIL;
}
/* create property list, for chunked sds or unlimited dimension cases */
create_plist = H5Pcreate(H5P_DATASET_CREATE);
if(create_plist == -1) {
printf("failed to create property list. \n");
SDendaccess(sdsdim_id);
free(h5sdsdim_name);
free(dim_scadata);
H5Sclose(h5dim_sid);
}
if(c_flags == HDF_NONE && SDisrecord(sds_id) && i == 0)
{
h5dim_chunkdim[0] = (hsize_t)(h5dimscas[0]/2);
if(H5Pset_chunk(create_plist,1, h5dim_chunkdim)<0) {
printf("failed to set up chunking information for ");
printf("dimensional scale property list.\n");
SDendaccess(sdsdim_id);
free(h5sdsdim_name);
free(dim_scadata);
H5Sclose(h5dim_sid);
H5Pclose(create_plist);
return FAIL;
}
}
if(c_flags == HDF_CHUNK || c_flags == (HDF_CHUNK | HDF_COMP)
|| c_flags == (HDF_CHUNK | HDF_NBIT) ){
h5dim_chunkdim[0] = (hsize_t)c_def_out.chunk_lengths[0];
if(H5Pset_chunk(create_plist,1, h5dim_chunkdim)<0) {
printf("failed to set up chunking information for ");
printf("property list.\n");
SDendaccess(sdsdim_id);
free(h5sdsdim_name);
free(dim_scadata);
H5Sclose(h5dim_sid);
H5Pclose(create_plist);
return FAIL;
}
}
/* create h5 dataset under group HDF4_DIMG*/
h5dim_dset = H5Dcreate(sh5_dimgroup,h5sdsdim_name,h5dim_tid,
h5dim_sid,create_plist);
if(h5dim_dset <0) {
printf("error in creating dataset. \n");
free(h5sdsdim_name);
free(dim_scadata);
SDendaccess(sdsdim_id);
H5Sclose(h5dim_sid);
H5Pclose(create_plist);
return FAIL;
}
if (H5Dwrite(h5dim_dset,h5dim_memtype,h5dim_sid,h5dim_sid,
H5P_DEFAULT,(void *)dim_scadata)<0) {
printf("error writing dimensional scale data\n");
free(h5sdsdim_name);
free(dim_scadata);
SDendaccess(sdsdim_id);
H5Sclose(h5dim_sid);
H5Pclose(create_plist);
H5Dclose(h5dim_dset);
return FAIL;
}
check_gloattr = 0;
if(sds_transattrs(sdsdim_id,h5dim_dset,num_sdsdimattrs,check_gloattr)
== FAIL){
printf("error in transferring attributes. \n");
free(h5sdsdim_name);
free(dim_scadata);
SDendaccess(sdsdim_id);
H5Sclose(h5dim_sid);
H5Dclose(h5dim_dset);
H5Pclose(create_plist);
return FAIL;
}
SDendaccess(sdsdim_id);
free(dim_scadata);
free(h5sdsdim_name);
ret = H5Sclose(h5dim_sid);
ret = H5Dclose(h5dim_dset);
ret = H5Pclose(create_plist);
count_h5objref = count_h5objref + 1;
count_h5attrname =count_h5attrname + 1;
}
/*1. create object reference number to dimensional scale dataset.
2. store absolute name of dimensional name into
dimensional list. */
if ( count_h5objref != 0) {
h5dim_dims[0] = count_h5objref;
attr_refDims[0] = count_h5objref;
attr_refSpace = H5Screate_simple(1,attr_refDims,NULL);
attr_refType = H5Tcopy(H5T_STD_REF_OBJ);
alldim_refdat = calloc((size_t)count_h5objref,sizeof(hobj_ref_t));
if(alldim_refdat == NULL) {
printf("error in allocating memory. \n");
H5Sclose(attr_refSpace);
H5Tclose(attr_refType);
return FAIL;
}
k =0;
for(i=0;i<count_h5objref;i++){
if(sdsdimempty[i])
k = k +1;
h4toh5_ZeroMemory(h5newsdsdim_name,MAX_DIM_NAME);
strcpy(h5newsdsdim_name,&h5sdsdim_allname[k*MAX_DIM_NAME]);
/*h5newsdsdim_name = HDstrdup(h5sdsdim_allname[k]);
for variable length HDF5 string. 6/11/2001; Kent*/
ret = H5Rcreate(&dim_refdat,sh5_dimgroup,h5newsdsdim_name,
H5R_OBJECT,-1);
if(ret <0) {
free(alldim_refdat);
H5Sclose(attr_refSpace);
H5Tclose(attr_refType);
printf("error in generating H5 reference. \n");
return FAIL;
}
alldim_refdat[i] = dim_refdat;
k = k +1;
/*free(h5newsdsdim_name); for variable length HDF5 string 6/11/2001.*/
}
attribID = H5Acreate(sh5dset,DIMSCALE,attr_refType,attr_refSpace,
H5P_DEFAULT);
if(attribID < 0) {
free(alldim_refdat);
H5Sclose(attr_refSpace);
H5Tclose(attr_refType);
H5Aclose(attribID);
printf("error in generating H5 attribute ID. \n");
return FAIL;
}
ret = H5Awrite(attribID,attr_refType,(void *)alldim_refdat);
H5Sclose(attr_refSpace);
H5Tclose(attr_refType);
H5Aclose(attribID);
free(alldim_refdat);
}
if(count_h5attrname!= 0) {
h5dimname_dims[0] = count_h5attrname;
h5dim_namesid = H5Screate_simple(1,h5dimname_dims,NULL);
if(h5dim_namesid <0) {
printf("error in creating sds dimensionlist space.\n");
return FAIL;
}
/*h5str_dimntype = mkstr(MAX_DIM_NAME,H5T_STR_SPACEPAD); */
h5str_dimntype = mkstr(MAX_DIM_NAME,H5T_STR_NULLTERM);
if(h5str_dimntype < 0) {
H5Sclose(h5dim_namesid);
printf("error in generating H5T_STRING type.\n");
return FAIL;
}
/*using variable length, h5dump and h5view do not
support this, this will be supported later.
h5str_dimntype = H5Tcopy(H5T_C_S1);
ret = H5Tset_size(h5str_dimntype,H5T_VARIABLE);
6/11/2001, Kent Yang
*/
h5dim_nameaid = H5Acreate(sh5dset,HDF4_DIMENSION_LIST,h5str_dimntype,
h5dim_namesid,H5P_DEFAULT);
if(h5dim_nameaid <0) {
H5Sclose(h5dim_namesid);
printf("error in creating sds dimensionlist id.\n");
return FAIL;
}
ret = H5Awrite(h5dim_nameaid,h5str_dimntype,h5sdsdim_allname);
if(ret < 0) {
H5Sclose(h5dim_namesid);
H5Aclose(h5dim_nameaid);
printf("error in writing sds dimensionlist. \n");
return FAIL;
}
ret = H5Sclose(h5dim_namesid);
ret = H5Aclose(h5dim_nameaid);
/*used for variable length HDF5 string.
for(dim_index = 0; dim_index <count_h5attrname;dim_index++)
free(h5sdsdim_allname[dim_index]);
6/11/2001, kent
since variable length has not been supported in h5dump yet and
that will cause testing failed so we use NULL TERM instead.
8/9/2001 kent */
}
free(sdsdimempty);
return SUCCEED;
}
int convert_sdsfillvalue(int32 file_id,int32 sds_id,hid_t h5_group,hid_t h5_dimgroup,int h4_attr){
int32 sds_dtype;
int32 sds_rank;
int32 sds_dimsizes[MAX_VAR_DIMS];
int32* sds_start;
int32* sds_edge;
int32* sds_stride;
int32 count_sdsdata;
int32 sds_ref;
int32 istat;
int i;
int32 num_sdsattrs;
void* fill_value;
int check_sdsname;
int check_gloattr;
char sdsname[MAX_NC_NAME];
char sdslabel[MAX_NC_NAME];
size_t h4size;
size_t h4memsize;
HDF_CHUNK_DEF c_def_out;
hsize_t* chunk_dims;
int32 c_flags;
/* define varibles for hdf5. */
hid_t h5dset;
hid_t h5d_sid;
hid_t h5ty_id;
hid_t h5_memtype;
hid_t create_plist;
hid_t write_plist;
hsize_t h5dims[MAX_VAR_DIMS];
hsize_t max_h5dims[MAX_VAR_DIMS];
hsize_t bufsize;
char* h5csds_name;
if (SDgetinfo(sds_id,sdsname,&sds_rank,sds_dimsizes,&sds_dtype,
&num_sdsattrs)==FAIL) {
printf("unable to get information of sds h5dset.\n");
return FAIL;
}
/* obtain start,edge, stride and number of sds data. */
sds_start = malloc(sizeof(int32)*sds_rank);
if(sds_start == NULL) {
printf("error in allocating memory for sds start.\n");
return FAIL;
}
sds_edge = malloc(sizeof(int32)*sds_rank);
if(sds_edge == NULL) {
printf("error in allocating memory for sds edge.\n");
free(sds_start);
return FAIL;
}
sds_stride = malloc(sizeof(int32)*sds_rank);
if(sds_stride == NULL) {
printf("error in allocating memory for sds stride. \n");
free(sds_start);
free(sds_edge);
return FAIL;
}
count_sdsdata = 1;
for (i=0;i<sds_rank;i++){
sds_stride[i] = 1;
sds_start[i] = 0;
sds_edge[i] = sds_dimsizes[i];
count_sdsdata = count_sdsdata*sds_dimsizes[i];
}
for (i=0;i<sds_rank;i++) {
h5dims[i] = sds_edge[i]-sds_start[i];
max_h5dims[i] = h5dims[i];
}
if(SDisrecord(sds_id)) {
max_h5dims[0] = H5S_UNLIMITED;
}
/* convert hdf4 data type to hdf5 data type. */
if (h4type_to_h5type(sds_dtype,&h5_memtype,&h4memsize,&h4size,
&h5ty_id) == FAIL) {
printf("failed to translate datatype. \n");
free(sds_start);
free(sds_edge);
free(sds_stride);
return FAIL;
}
/* check whether the datatype is string, if we find string format,
we will change them back into integer format.*/
if (h5ty_id == H5T_STRING) {
/* rechange string datatype into numerical datatype.*/
if(h5string_to_int(sds_dtype,&h5_memtype,h4memsize,
&h5ty_id)== FAIL) {
printf("error in translating H5T_STRING to int.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
return FAIL;
}
}
/* Since we know this SDS dataset fills with fill value, so currently
we will comment this out. */
/*
sds_data = malloc(h4memsize*count_sdsdata);
if(sds_data == NULL) {
printf("error in allocating memory. \n");
free(sds_start);
free(sds_edge);
free(sds_stride);
return FAIL;
}
istat = SDreaddata(sds_id, sds_start, sds_stride, sds_edge,
(VOIDP)sds_data);
if (istat == FAIL) {
printf("unable to read data from h5dset. \n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(sds_data);
return FAIL;
}
*/
fill_value = malloc(h4memsize);
h4toh5_ZeroMemory(fill_value,h4memsize*sizeof(char));
if(num_sdsattrs != 0)
if(SDgetfillvalue(sds_id,fill_value)==FAIL)
printf("unable to get fill value, fill value will be set to zero \n");
sds_ref = SDidtoref(sds_id);
if(sds_ref == FAIL) {
printf("error in obtaining sds reference number. \n");
free(sds_start);
free(sds_edge);
free(sds_stride);
return FAIL;
}
h5csds_name = get_name(sds_ref,2*num_sds,sds_hashtab,&check_sdsname);
if (h5csds_name == NULL && check_sdsname == 0 ) {
free(sds_start);
free(sds_edge);
free(sds_stride);
printf("error,cannot find sds name \n");
return FAIL;
}
if (h5csds_name == NULL && check_sdsname == -1) {
free(sds_start);
free(sds_edge);
free(sds_stride);
printf("error,sds name is not defined.\n");
return FAIL;
}
if (h5csds_name == NULL && check_sdsname == -2) {
free(sds_start);
free(sds_edge);
free(sds_stride);
printf("error,not enough memory for allocating sds name.\n");
return FAIL;
}
h5d_sid = H5Screate_simple(sds_rank,h5dims,max_h5dims);
if (h5d_sid < 0) {
printf("failed to create hdf5 data space converted from SDS. \n");
free(sds_start);
free(sds_edge);
free(sds_stride);
return FAIL;
}
/* set creation property list. */
create_plist = H5Pcreate(H5P_DATASET_CREATE);
if(create_plist <0) {
printf("failed to create hdf5 creation list.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
return FAIL;
}
chunk_dims = malloc(sizeof(hsize_t)*sds_rank);
if(chunk_dims == NULL) {
H5Pclose(H5P_DATASET_CREATE);
free(sds_start);
free(sds_edge);
free(sds_stride);
printf("unable to allocate memory for chunk_dims\n");
return FAIL;
}
if(SDisrecord(sds_id)){
for(i=0;i<sds_rank;i++){
chunk_dims[i] = (hsize_t)(sds_dimsizes[i]/2);
}
if(H5Pset_chunk(create_plist, sds_rank, chunk_dims)<0) {
printf("cannot set chunking size properly.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(chunk_dims);
H5Pclose(create_plist);
return FAIL;
}
}
if(H5Pset_fill_value(create_plist,h5ty_id,fill_value)<0){
printf("failed to set property list fill value.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
return FAIL;
}
h5dset = H5Dcreate(h5_group,h5csds_name,h5ty_id,h5d_sid,create_plist);
if (h5dset < 0) {
printf("failed to create hdf5 dataset converted from SDS. \n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
return FAIL;
}
/* Before HDF5 library make the optimzation of dealing with fill value
data, leave this alone. */
/* write_plist = H5Pcreate_list(H5P_DATASET_XFER_NEW);
bufsize = h4memsize;
for(i=1;i<sds_rank;i++)
bufsize *= h5dims[i];
if(H5Pset_buffer(write_plist,bufsize,NULL,NULL)<0) {
printf("fail to create data transfer property list.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
H5Pclose_list(write_plist);
return FAIL;
}
if (H5Dwrite(h5dset,h5_memtype,h5d_sid,h5d_sid,write_plist,
(void *)sds_data)<0) {
printf("failed to write data into hdf5 dataset");
printf(" converted from SDS.\n");
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
H5Pclose_list(write_plist);
free(sds_start);
free(sds_edge);
free(sds_stride);
free(chunk_dims);
return FAIL;
}
*/
/* convert sds annotation into attribute of sds dataset.
Since there is no routines to find the exact tag of sds object,
we will check three possible object tags of sds objects, that is:
DFTAG_SD,DFTAG_SDG,DFTAG_NDG. If the object tag of sds object is
falling out of this scope, we will not convert annotations into
hdf5 attributes; it is user's responsibility to make sure object tags
for sds objects are only one of the above three tags.*/
if(Annoobj_h4_to_h5(file_id,sds_ref,DFTAG_SD,h5dset)== FAIL){
printf("failed to convert sds annotation into hdf5 attribute.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
return FAIL;
}
if(Annoobj_h4_to_h5(file_id,sds_ref,DFTAG_SDG,h5dset)== FAIL){
printf("failed to convert sds annotation into hdf5 attribute.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
return FAIL;
}
if(Annoobj_h4_to_h5(file_id,sds_ref,DFTAG_NDG,h5dset)== FAIL){
printf("failed to convert sds annotation into hdf5 attribute.\n");
free(sds_start);
free(sds_edge);
free(sds_stride);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
return FAIL;
}
check_gloattr = 0;
if (sds_transattrs(sds_id,h5dset,num_sdsattrs,check_gloattr)==FAIL) {
free(sds_start);
free(sds_edge);
free(sds_stride);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
printf(" Error in obtaining sds attributes. \n");
return FAIL;
}
/********************************************/
/* handle extra attributes of sds : sds label, object type
and reference num */
if(h4_attr !=0) {
strcpy(sdslabel,SDSLABEL);
if(h4_transpredattrs(h5dset,HDF4_OBJECT_TYPE,sdslabel)==FAIL) {
free(sds_start);
free(sds_edge);
free(sds_stride);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
printf("unable to transfer sds label to HDF4 OBJECT TYPE.\n");
return FAIL;
}
if(sdsname[0] != '\0') {
if(h4_transpredattrs(h5dset,HDF4_OBJECT_NAME,sdsname)==FAIL){
free(sds_start);
free(sds_edge);
free(sds_stride);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
printf("unable to transfer sds name to HDF5 dataset attribute.\n");
return FAIL;
}
}
if(h4_transnumattr(h5dset,HDF4_REF_NUM,sds_ref)==FAIL){
free(sds_start);
free(sds_edge);
free(sds_stride);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
printf("unable to transfer sds ref. to HDF5 dataset attribute.\n");
return FAIL;
}
}
free(sds_start);
free(sds_edge);
free(sds_stride);
free(chunk_dims);
free(fill_value);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
/* H5Pclose_list(write_plist); */
return SUCCEED;
}
uint16 get_SDref(int32 file_id,uint16 tag,int32 sds_ref){
DFdi di;
int32 found,GroupID;
int sd_ref = 0;
if((GroupID = DFdiread(file_id,tag,(uint16)sds_ref))<0){
/* for some cases, although sd_ref cannot be found, the current
SDS object is still legal(unlimited dimension with the current
size set to 0. so comment this the following warning printfs out. */
/* printf("cannot find sd_ref\n");*/
return sd_ref;
}
found = 0;
di.tag = DFTAG_NULL;
di.ref = 0;
while((found == 0) &&(DFdiget(GroupID,&di.tag,&di.ref)==0)){
if(di.tag == DFTAG_SD)
found = 1;
}
sd_ref = di.ref;
if(!found) ;
/* printf("cannot find sd_ref\n");*/
DFdifree(GroupID);
return sd_ref;
}
static int convert_zerosdsunlimit(int32 file_id,
int32 sds_id,
hid_t h5_group,
hid_t h5_dimgroup,
int h4_attr) {
int32 sds_dtype;
int32 sds_rank;
int32 sds_dimsizes[MAX_VAR_DIMS];
int32* sds_start;
int32* sds_edge;
int32* sds_stride;
int32 count_sdsdata;
int32 sds_ref;
int32 istat;
int i;
int32 num_sdsattrs;
void* fill_value;
int check_sdsname;
int check_gloattr;
char sdsname[MAX_NC_NAME];
char sdslabel[MAX_NC_NAME];
size_t h4size;
size_t h4memsize;
HDF_CHUNK_DEF c_def_out;
hsize_t* chunk_dims;
int32 c_flags;
/* for checking compression */
sp_info_block_t info_block;
int16 special_code;
int32 access_id;
uint16 sd_ref;
int gzip_level;
/* define varibles for hdf5. */
hid_t h5dset;
hid_t h5d_sid;
hid_t h5ty_id;
hid_t h5_memtype;
hid_t create_plist;
hid_t write_plist;
hsize_t h5dims[MAX_VAR_DIMS];
hsize_t max_h5dims[MAX_VAR_DIMS];
hsize_t bufsize;
char* h5csds_name;
if (SDgetinfo(sds_id,sdsname,&sds_rank,sds_dimsizes,&sds_dtype,
&num_sdsattrs)==FAIL) {
printf("unable to get information of sds h5dset.\n");
return FAIL;
}
for (i=0;i<sds_rank;i++) {
h5dims[i] = sds_dimsizes[i];
max_h5dims[i] = h5dims[i];
}
if(SDisrecord(sds_id)){
max_h5dims[0] = H5S_UNLIMITED;
h5dims[0] = H5S_UNLIMITED;
}
/* convert hdf4 data type to hdf5 data type. */
if (h4type_to_h5type(sds_dtype,&h5_memtype,&h4memsize,&h4size,
&h5ty_id) == FAIL) {
printf("failed to translate datatype. \n");
return FAIL;
}
/* check whether the datatype is string, if we find string format,
we will change them back into integer format.*/
if (h5ty_id == H5T_STRING) {
/* rechange string datatype into numerical datatype.*/
if(h5string_to_int(sds_dtype,&h5_memtype,h4memsize,
&h5ty_id)== FAIL) {
printf("error in translating H5T_STRING to int.\n");
return FAIL;
}
}
sds_ref = SDidtoref(sds_id);
if(sds_ref == FAIL) {
printf("error in obtaining sds reference number. \n");
return FAIL;
}
h5csds_name = get_name(sds_ref,2*num_sds,sds_hashtab,&check_sdsname);
if (h5csds_name == NULL && check_sdsname == 0 ) {
printf("error,cannot find sds name \n");
return FAIL;
}
if (h5csds_name == NULL && check_sdsname == -1) {
printf("error,sds name is not defined.\n");
return FAIL;
}
if (h5csds_name == NULL && check_sdsname == -2) {
printf("error,not enough memory for allocating sds name.\n");
return FAIL;
}
h5d_sid = H5Screate_simple(sds_rank,h5dims,max_h5dims);
if (h5d_sid < 0) {
printf("failed to create hdf5 data space converted from SDS. \n");
return FAIL;
}
/* create property list. */
create_plist = H5Pcreate(H5P_DATASET_CREATE);
chunk_dims = malloc(sizeof(hsize_t)*sds_rank);
sd_ref = get_SDref(file_id,DFTAG_NDG,sds_ref);
if(sd_ref == 0)
sd_ref = get_SDref(file_id,DFTAG_SDG,sds_ref);
if(sd_ref >0 )
access_id = Hstartread(file_id,DFTAG_SD,sd_ref);
if(sd_ref == 0)
access_id = FAIL;
if(access_id != FAIL) {
istat = Hinquire(access_id,NULL,NULL,NULL,NULL,NULL,NULL,NULL,&special_code);
if(istat == FAIL) {
printf("failed to inquire information \n ");
free(chunk_dims);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
free(h5csds_name);
return FAIL;
}
if(special_code >0){
if(HDget_special_info(access_id,&info_block)==FAIL){
printf("fail to get special info.\n");
free(chunk_dims);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
free(h5csds_name);
return FAIL;
}
/* free(info_block.cdims);*/
if(info_block.key == SPECIAL_COMP) {
if(c_flags == HDF_NONE){
/* 1. if the first dimension is unlimited dimension,
we have to provide a chunking size.
2. the current HDF5 will not handle compression case itself,
in order that the converted HDF5 is compressed, we have to
provide a chunking size. currently it is set to h5dim[i].*/
for(i=0;i<sds_rank;i++){
chunk_dims[i] = (hsize_t)(h5dims[i]);
}
if(H5Pset_chunk(create_plist, sds_rank, chunk_dims)<0) {
printf("failed to set up chunking information for ");
printf("property list.\n");
free(chunk_dims);
free(h5csds_name);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
return FAIL;
}
if(H5Pset_deflate(create_plist,GZIP_COMLEVEL)<0){
/* if(H5Pset_deflate(create_plist,2)<0){*/
printf("fail to set compression method for HDF5 file.\n");
free(chunk_dims);
free(h5csds_name);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
}
}
}
else if(c_flags == HDF_NONE && SDisrecord(sds_id))
{
for(i=0;i<sds_rank;i++){
chunk_dims[i] = (hsize_t)(sds_dimsizes[i]);
if(sds_dimsizes[0] == 0)
chunk_dims[0] = (hsize_t)DEF_CHUNKSIZE;
}
if(H5Pset_chunk(create_plist, sds_rank, chunk_dims)<0) {
printf("failed to set up chunking information for ");
printf("property list.\n");
free(h5csds_name);
free(chunk_dims);
H5Pclose(create_plist);
return FAIL;
}
}
}
}
/* HDF4 can support various compression methods including simple RLE, NBIT, Skip Huffman, gzip,Jpeg , HDF5 currently only supports gzip compression.
By default, we will compress HDF5 dataset by using gzip compression if HDF5 file is compressed. */
if(c_flags == HDF_CHUNK || c_flags == (HDF_CHUNK | HDF_COMP)
|| c_flags == (HDF_CHUNK | HDF_NBIT) ){
if(c_def_out.comp.comp_type == COMP_CODE_RLE || c_def_out.comp.comp_type == COMP_CODE_NBIT || c_def_out.comp.comp_type == COMP_CODE_SKPHUFF || c_def_out.comp.comp_type == COMP_CODE_DEFLATE || c_def_out.comp.comp_type == COMP_CODE_JPEG) {
for(i=0;i<sds_rank;i++)
chunk_dims[i] = (hsize_t)c_def_out.chunk_lengths[i];
if(H5Pset_chunk(create_plist, sds_rank, chunk_dims)<0) {
printf("failed to set up chunking information for ");
printf("property list.\n");
free(chunk_dims);
free(h5csds_name);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
return FAIL;
}
if(c_def_out.comp.comp_type == COMP_CODE_DEFLATE)
gzip_level = c_def_out.comp.cinfo.deflate.level;
else gzip_level = GZIP_COMLEVEL;
if(H5Pset_deflate(create_plist,gzip_level)<0){
printf("fail to set compression method for HDF5 file.\n");
free(chunk_dims);
free(h5csds_name);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
}
}
}
if(access_id == FAIL) {
chunk_dims[0] = (hsize_t)DEF_CHUNKSIZE;
for(i=1;i<sds_rank;i++)
chunk_dims[i] = h5dims[i];
if(H5Pset_chunk(create_plist, sds_rank, chunk_dims)<0) {
printf("failed to set up chunking information for ");
printf("property list.\n");
free(chunk_dims);
free(h5csds_name);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
return FAIL;
}
}
h5dset = H5Dcreate(h5_group,h5csds_name,h5ty_id,h5d_sid,create_plist);
if (h5dset < 0) {
printf("failed to create hdf5 dataset converted from SDS. \n");
free(chunk_dims);
free(h5csds_name);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
return FAIL;
}
if(sdsdim_to_h5dataset(sds_id,sds_rank,h5dset,h5_dimgroup,sds_dimsizes[0])<0){
printf("failed to convert SDS dimensional scale dataset correctly \n"); free(h5csds_name);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Pclose(create_plist);
return FAIL;
}
/* convert sds annotation into attribute of sds dataset.
Since there is no routines to find the exact tag of sds object,
we will check three possible object tags of sds objects, that is:
DFTAG_SD,DFTAG_SDG,DFTAG_NDG. If the object tag of sds object is
falling out of this scope, we will not convert annotations into
hdf5 attributes; it is user's responsibility to make sure object tags
for sds objects are only one of the above three tags.*/
if(Annoobj_h4_to_h5(file_id,sds_ref,DFTAG_SD,h5dset)== FAIL){
printf("failed to convert sds annotation into hdf5 attribute.\n");
free(h5csds_name);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
return FAIL;
}
if(Annoobj_h4_to_h5(file_id,sds_ref,DFTAG_SDG,h5dset)== FAIL){
printf("failed to convert sds annotation into hdf5 attribute.\n");
free(h5csds_name);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
return FAIL;
}
if(Annoobj_h4_to_h5(file_id,sds_ref,DFTAG_NDG,h5dset)== FAIL){
printf("failed to convert sds annotation into hdf5 attribute.\n");
free(h5csds_name);
free(chunk_dims);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
return FAIL;
}
check_gloattr = 0;
if (sds_transattrs(sds_id,h5dset,num_sdsattrs,check_gloattr)==FAIL) {
free(chunk_dims);
free(h5csds_name);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
printf(" Error in obtaining sds attributes. \n");
return FAIL;
}
/********************************************/
/* handle extra attributes of sds : sds label, object type
and reference num */
if(h4_attr !=0) {
strcpy(sdslabel,SDSLABEL);
if(h4_transpredattrs(h5dset,HDF4_OBJECT_TYPE,sdslabel)==FAIL) {
free(chunk_dims);
free(h5csds_name);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
printf("unable to transfer sds label to HDF4 OBJECT TYPE.\n");
return FAIL;
}
if(sdsname[0] != '\0') {
if(h4_transpredattrs(h5dset,HDF4_OBJECT_NAME,sdsname)==FAIL){
free(chunk_dims);
free(h5csds_name);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
printf("unable to transfer sds name to HDF5 dataset attribute.\n");
return FAIL;
}
}
if(h4_transnumattr(h5dset,HDF4_REF_NUM,sds_ref)==FAIL){
free(chunk_dims);
free(h5csds_name);
H5Sclose(h5d_sid);
H5Dclose(h5dset);
H5Pclose(create_plist);
printf("unable to transfer sds ref. to HDF5 dataset attribute.\n");
return FAIL;
}
}
H5Sclose(h5d_sid);
free(h5csds_name);
free(chunk_dims);
H5Dclose(h5dset);
H5Pclose(create_plist);
return SUCCEED;
}
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