// Read string attribute <attr_name> given by address <path>
char AH5_read_str_attr(hid_t loc_id, const char *path, char *attr_name, char **rdata)
{
hid_t attr_id, filetype, memtype;
size_t sdim;
char success = AH5_FALSE;
if (AH5_path_valid(loc_id, path) || strcmp(path, ".") == 0)
if (H5Aexists_by_name(loc_id, path, attr_name, H5P_DEFAULT) > 0)
{
attr_id = H5Aopen_by_name(loc_id, path, attr_name, H5P_DEFAULT, H5P_DEFAULT);
filetype = H5Aget_type(attr_id);
sdim = H5Tget_size(filetype);
sdim++; // make a space for null terminator
*rdata = (char *) malloc(sdim * sizeof(char));
memtype = H5Tcopy(H5T_C_S1);
H5Tset_size(memtype, sdim);
if (H5Aread(attr_id, memtype, *rdata) >= 0)
success = AH5_TRUE;
else
free(*rdata);
H5Tclose(memtype);
H5Tclose(filetype);
H5Aclose(attr_id);
}
if (!success)
*rdata = NULL;
return success;
}
static int readIntAttribute_v1(int _iDatasetId, const char *_pstName)
{
hid_t iAttributeId;
herr_t status;
hsize_t n = 0;
int iVal = -1;
if (H5Aiterate(_iDatasetId, H5_INDEX_NAME, H5_ITER_NATIVE, &n, find_attr_by_name_v1, (void *)_pstName) > 0)
{
iAttributeId = H5Aopen_by_name(_iDatasetId, ".", _pstName, H5P_DEFAULT, H5P_DEFAULT);
if (iAttributeId < 0)
{
return -1;
}
status = H5Aread(iAttributeId, H5T_NATIVE_INT, &iVal);
if (status < 0)
{
return -1;
}
status = H5Aclose(iAttributeId);
if (status < 0)
{
return -1;
}
}
return iVal;
}
// read a complex float attribute
float_complex read_complex_attribute(hid_t loc_id, const char* path,
const char* name)
{
float_complex value;
float *buf;
hid_t attr_id, real_type_id;
;
hsize_t *dims;
herr_t status;
status = H5Aexists_by_name(loc_id, path, name, H5P_DEFAULT);
if (status < 0)
{
printf("attribut %s does not exist \n", name);
}
real_type_id = create_real_type_id();
attr_id = H5Aopen_by_name(loc_id, path, name, H5P_DEFAULT, H5P_DEFAULT);
status = H5Aread(attr_id, real_type_id, buf);
if (status < 0)
{
printf("Can't read attribute : %s\n", name);
}
value.re = buf[0]; value.im=buf[1];
return value;
}
attribute get_attribute(handle const& loc,
const char* obj_name,
const char* attr_name)
{
hid_t id = H5Aopen_by_name(loc.getId(), obj_name, attr_name,
H5P_DEFAULT, H5P_DEFAULT);
if (id < 0) throw std::runtime_error("H5Aopen_by_name failed");
return attribute(std::move(id));
}
med_err _MEDattributeStringRdByName(med_idt pid,
const char * const path,
const char * const attname,
const med_size attsize,
char * const val)
{
med_err _ret=-1;
med_idt _attid=0;
int type_hdf=0;
if ( (type_hdf = H5Tcopy(H5T_C_S1)) < 0) {
MED_ERR_(_ret,MED_ERR_CREATE,MED_ERR_HDFTYPE, MED_ERR_NAME_MSG );
SSCRUTE("H5T_C_S1"); goto ERROR;
}
if ( H5Tset_size(type_hdf,attsize+1) < 0) {
MED_ERR_(_ret,MED_ERR_CREATE,MED_ERR_HDFTYPE, MED_ERR_NAME_MSG );
SSCRUTE("H5T_C_S1"); goto ERROR;
}
if ( (_attid=H5Aopen_by_name( pid, path, attname, H5P_DEFAULT, H5P_DEFAULT )) < 0 ) {
MED_ERR_(_ret,MED_ERR_OPEN,MED_ERR_ATTRIBUTE, MED_ERR_NAME_MSG );
SSCRUTE(attname); SSCRUTE(path);goto ERROR;
}
if ( H5Aread(_attid,type_hdf,val) < 0 ) {
MED_ERR_(_ret,MED_ERR_READ,MED_ERR_ATTRIBUTE, MED_ERR_NAME_MSG );
SSCRUTE(attname); SSCRUTE(path);goto ERROR;
}
_ret=0;
ERROR:
if (type_hdf >0) if ( H5Tclose(type_hdf) < 0) {
MED_ERR_(_ret,MED_ERR_CLOSE,MED_ERR_HDFTYPE, MED_ERR_ID_MSG );
ISCRUTE_int(type_hdf);
}
if (_attid >0) if ( H5Aclose(_attid) < 0) {
MED_ERR_(_ret,MED_ERR_CLOSE,MED_ERR_ATTRIBUTE, MED_ERR_ID_MSG );
ISCRUTE_id(_attid);
}
return _ret;
}
/*
* Class: hdf_hdf5lib_H5
* Method: _H5Aopen_by_name
* Signature: (JLjava/lang/String;Ljava/lang/String;JJ)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Aopen_1by_1name
(JNIEnv *env, jclass clss, jlong loc_id, jstring obj_name, jstring attr_name, jlong aapl_id, jlong lapl_id)
{
hid_t status = -1;
const char *aName;
const char *oName;
PIN_JAVA_STRING_TWO(obj_name, oName, attr_name, aName);
if (oName != NULL && aName != NULL) {
status = H5Aopen_by_name((hid_t)loc_id, oName, aName, (hid_t)aapl_id, (hid_t)lapl_id);
UNPIN_JAVA_STRING_TWO(obj_name, oName, attr_name, aName);
if (status < 0)
h5libraryError(env);
}
return (jlong)status;
} /* end Java_hdf_hdf5lib_H5__1H5Aopen_1by_1name */
// Read complex attribute <attr_name> given by address <path>
char AH5_read_cpx_attr(hid_t loc_id, const char* path, char* attr_name, AH5_complex_t *rdata)
{
hid_t attr_id, type_id;
float buf[2];
char success = AH5_FALSE;
if (AH5_path_valid(loc_id, path))
if (H5Aexists_by_name(loc_id, path, attr_name, H5P_DEFAULT) > 0)
{
attr_id = H5Aopen_by_name(loc_id, path, attr_name, H5P_DEFAULT, H5P_DEFAULT);
type_id = AH5_H5Tcreate_cpx_memtype();
if (H5Aread(attr_id, type_id, buf) >= 0)
{
*rdata = AH5_set_complex(buf[0], buf[1]);
success = AH5_TRUE;
}
H5Tclose(type_id);
H5Aclose(attr_id);
}
if (!success)
*rdata = AH5_set_complex(0, 0);
return success;
}
/*
** WARNING : this function returns an allocated value that must be freed.
*/
static char* readAttribute_v1(int _iDatasetId, const char *_pstName)
{
hid_t iAttributeId;
hid_t iFileType, memtype, iSpace;
herr_t status;
hsize_t dims[1];
hsize_t n = 0;
size_t iDim;
char *pstValue = NULL;
if (H5Aiterate(_iDatasetId, H5_INDEX_NAME, H5_ITER_NATIVE, &n, find_attr_by_name_v1, (void *)_pstName) > 0)
{
iAttributeId = H5Aopen_by_name(_iDatasetId, ".", _pstName, H5P_DEFAULT, H5P_DEFAULT);
if (iAttributeId < 0)
{
return NULL;
}
/*
* Get the datatype and its size.
*/
iFileType = H5Aget_type(iAttributeId);
iDim = H5Tget_size(iFileType);
iDim++; /* Make room for null terminator */
/*
* Get dataspace and allocate memory for read buffer. This is a
* two dimensional attribute so the dynamic allocation must be done
* in steps.
*/
iSpace = H5Aget_space(iAttributeId);
if (iSpace < 0)
{
return NULL;
}
status = H5Sget_simple_extent_dims(iSpace, dims, NULL);
if (status < 0)
{
return NULL;
}
/*
* Allocate space for string data.
*/
pstValue = (char *)MALLOC((size_t) ((dims[0] * iDim + 1) * sizeof(char)));
/*
* Create the memory datatype.
*/
memtype = H5Tcopy(H5T_C_S1);
status = H5Tset_size(memtype, iDim);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
/*
* Read the data.
*/
status = H5Aread(iAttributeId, memtype, pstValue);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
status = H5Tclose(memtype);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
status = H5Sclose(iSpace);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
status = H5Tclose(iFileType);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
status = H5Aclose(iAttributeId);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
}
return pstValue;
}
/*-------------------------------------------------------------------------
* Function: read_records
*
* Purpose: For a given dataset, checks to make sure that the stated
* and actual sizes are the same. If they are not, then
* we have an inconsistent dataset due to a SWMR error.
*
* Parameters: const char *filename
* The SWMR test file's name.
*
* unsigned verbose
* Whether verbose console output is desired.
*
* unsigned long nrecords
* The total number of records to read.
*
* unsigned poll_time
* The amount of time to sleep (s).
*
* unsigned reopen_count
*
*
* Return: Success: 0
* Failure: -1
*
*-------------------------------------------------------------------------
*/
static int
read_records(const char *filename, unsigned verbose, unsigned long nrecords,
unsigned poll_time, unsigned reopen_count)
{
hid_t fid; /* File ID */
hid_t aid; /* Attribute ID */
time_t start_time; /* Starting time */
hid_t mem_sid; /* Memory dataspace ID */
symbol_t record; /* The record to add to the dataset */
unsigned seed; /* Seed for random number generator */
unsigned iter_to_reopen = reopen_count; /* # of iterations until reopen */
unsigned long u; /* Local index variable */
hid_t fapl;
HDassert(filename);
HDassert(poll_time != 0);
/* Create file access property list */
if((fapl = h5_fileaccess()) < 0)
return -1;
H5Pset_fclose_degree(fapl, H5F_CLOSE_SEMI);
/* Emit informational message */
if(verbose)
HDfprintf(stderr, "Opening file: %s\n", filename);
/* Open the file */
if((fid = H5Fopen(filename, H5F_ACC_RDONLY | H5F_ACC_SWMR_READ, fapl)) < 0)
return -1;
/* Seed the random number generator with the attribute in the file */
if((aid = H5Aopen(fid, "seed", H5P_DEFAULT)) < 0)
return -1;
if(H5Aread(aid, H5T_NATIVE_UINT, &seed) < 0)
return -1;
if(H5Aclose(aid) < 0)
return -1;
HDsrandom(seed);
/* Reset the record */
/* (record's 'info' field might need to change for each record written, also) */
HDmemset(&record, 0, sizeof(record));
/* Create a dataspace for the record to read */
if((mem_sid = H5Screate(H5S_SCALAR)) < 0)
return -1;
/* Emit informational message */
if(verbose)
HDfprintf(stderr, "Reading records\n");
/* Get the starting time */
start_time = HDtime(NULL);
/* Read records */
for(u = 0; u < nrecords; u++) {
symbol_info_t *symbol = NULL; /* Symbol (dataset) */
htri_t attr_exists; /* Whether the sequence number attribute exists */
unsigned long file_u; /* Attribute sequence number (writer's "u") */
/* Get a random dataset, according to the symbol distribution */
symbol = choose_dataset();
/* Fill in "nrecords" field. Note that this depends on the writer
* using the same algorithm and "nrecords" */
symbol->nrecords = nrecords / 5;
/* Wait until we can read the dataset */
do {
/* Check if sequence attribute exists */
if((attr_exists = H5Aexists_by_name(fid, symbol->name, "seq", H5P_DEFAULT)) < 0)
return -1;
if(attr_exists) {
/* Read sequence number attribute */
if((aid = H5Aopen_by_name(fid, symbol->name, "seq", H5P_DEFAULT, H5P_DEFAULT)) < 0)
return -1;
if(H5Aread(aid, H5T_NATIVE_ULONG, &file_u) < 0)
return -1;
if(H5Aclose(aid) < 0)
return -1;
/* Check if sequence number is at least u - if so, this should
* guarantee that this record has been written */
if(file_u >= u)
break;
} /* end if */
/* Check for timeout */
if(HDtime(NULL) >= (time_t)(start_time + (time_t)TIMEOUT)) {
HDfprintf(stderr, "Reader timed out\n");
return -1;
} /* end if */
/* Pause */
HDsleep(poll_time);
/* Retrieve and print the collection of metadata read retries */
if(print_metadata_retries_info(fid) < 0)
HDfprintf(stderr, "Warning: could not obtain metadata retries info\n");
/* Reopen the file */
if(H5Fclose(fid) < 0)
return -1;
if((fid = H5Fopen(filename, H5F_ACC_RDONLY | H5F_ACC_SWMR_READ, fapl)) < 0)
return -1;
iter_to_reopen = reopen_count;
} while(1);
/* Emit informational message */
if(verbose)
HDfprintf(stderr, "Checking dataset %lu\n", u);
/* Check dataset */
if(check_dataset(fid, verbose, symbol, &record, mem_sid) < 0)
return -1;
HDmemset(&record, 0, sizeof(record));
/* Check for reopen */
iter_to_reopen--;
if(iter_to_reopen == 0) {
/* Emit informational message */
if(verbose)
HDfprintf(stderr, "Reopening file: %s\n", filename);
/* Retrieve and print the collection of metadata read retries */
if(print_metadata_retries_info(fid) < 0)
HDfprintf(stderr, "Warning: could not obtain metadata retries info\n");
/* Reopen the file */
if(H5Fclose(fid) < 0)
return -1;
if((fid = H5Fopen(filename, H5F_ACC_RDONLY | H5F_ACC_SWMR_READ, fapl)) < 0)
return -1;
iter_to_reopen = reopen_count;
} /* end if */
} /* end while */
/* Retrieve and print the collection of metadata read retries */
if(print_metadata_retries_info(fid) < 0)
HDfprintf(stderr, "Warning: could not obtain metadata retries info\n");
/* Close file */
if(H5Fclose(fid) < 0)
return -1;
/* Close the memory dataspace */
if(H5Sclose(mem_sid) < 0)
return -1;
return 0;
} /* end read_records() */
med_err _MEDattributeStringWrByName(med_idt pid,
const char * const path,
const char * const attname,
const med_size attsize,
const char * const val)
{
med_access_mode MED_ACCESS_MODE;
med_idt _attid=0,aid=0;
med_err _ret=-1;
int type_hdf=0;
med_bool _attmustbecreated= MED_FALSE;
hsize_t _attsize=0;
med_size _valsize=0;
if ( (MED_ACCESS_MODE = _MEDmodeAcces(pid) ) == MED_ACC_UNDEF ) {
MED_ERR_(_ret,MED_ERR_INVALID,MED_ERR_ACCESSMODE, "MED_ACC_UNDEF" );
SSCRUTE(attname); SSCRUTE(path);goto ERROR;
}
_valsize=strlen(val);
if (_valsize > attsize) {
MED_ERR_(_ret,MED_ERR_INVALID,MED_ERR_ATTRIBUTE, attname );
ISCRUTE_size(_valsize);ISCRUTE_size(attsize);goto ERROR;
}
if ((aid = H5Screate(H5S_SCALAR)) < 0){
MED_ERR_(_ret,MED_ERR_CREATE,MED_ERR_DATASPACE, attname );
ISCRUTE_id(aid);
}
if ( (type_hdf = H5Tcopy(H5T_C_S1)) < 0) {
MED_ERR_(_ret,MED_ERR_CREATE,MED_ERR_HDFTYPE, MED_ERR_NAME_MSG );
SSCRUTE("H5T_C_S1"); goto ERROR;
}
if ( H5Tset_size(type_hdf,_valsize+1) < 0) {
MED_ERR_(_ret,MED_ERR_CREATE,MED_ERR_HDFTYPE, MED_ERR_NAME_MSG );
SSCRUTE("H5T_C_S1"); goto ERROR;
}
if ( (_attid=H5Aopen_by_name( pid, path, attname, H5P_DEFAULT, H5P_DEFAULT )) >= 0 )
if ( MED_ACCESS_MODE == MED_ACC_RDEXT ) {
MED_ERR_(_ret,MED_ERR_INVALID,MED_ERR_ACCESSMODE, "MED_ACC_RDEXT" );
SSCRUTE(attname); SSCRUTE(path);goto ERROR;
}
if ( _attid > 0 ) {
if ( (_attsize=H5Aget_storage_size(_attid) ) < 0 ) goto ERROR;
if ( (_valsize+1) > _attsize ) {
if (H5Aclose(_attid) < 0) {
MED_ERR_(_ret,MED_ERR_CLOSE,MED_ERR_ATTRIBUTE,"");
ISCRUTE_id(_attid);
goto ERROR;
}
if ( H5Adelete_by_name(pid,path,attname,H5P_DEFAULT) < 0 ) goto ERROR;
_attmustbecreated=MED_TRUE;
}
}
if ( (_attid < 0) || _attmustbecreated )
if ( (_attid=H5Acreate_by_name( pid, path, attname, type_hdf, aid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT )) < 0 ) {
MED_ERR_(_ret,MED_ERR_CREATE,MED_ERR_ATTRIBUTE, attname );
SSCRUTE(path);goto ERROR;
}
if ( H5Awrite(_attid,type_hdf,val) < 0) {
MED_ERR_(_ret,MED_ERR_WRITE,MED_ERR_ATTRIBUTE, attname );
SSCRUTE(path);goto ERROR;
}
_ret=0;
ERROR:
if (type_hdf > 0 ) if ( H5Tclose(type_hdf) < 0) {
MED_ERR_(_ret,MED_ERR_CLOSE,MED_ERR_HDFTYPE, MED_ERR_ID_MSG );
ISCRUTE_int(type_hdf);
}
if (aid > 0 ) if ( H5Sclose(aid) < 0) {
MED_ERR_(_ret,MED_ERR_CLOSE,MED_ERR_DATASPACE, MED_ERR_ID_MSG );
ISCRUTE_id(aid);
}
if (_attid >0) if ( H5Aclose(_attid) < 0) {
MED_ERR_(_ret,MED_ERR_CLOSE,MED_ERR_ATTRIBUTE, MED_ERR_ID_MSG );
ISCRUTE_id(_attid);
}
return _ret;
}
