/* Read and verify attribute for group or dataset. */
int read_attribute(hid_t obj_id, int this_type, int num)
{
hid_t aid;
hsize_t group_block[2]={1,1}, dset_block[2]={1, 8};
int i, mpi_rank, in_num, in_data[8], out_data[8], vrfy_errors = 0;
char attr_name[32];
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
if(this_type == is_group) {
sprintf(attr_name, "Group Attribute %d", num);
aid = H5Aopen_name(obj_id, attr_name);
if(MAINPROCESS) {
H5Aread(aid, H5T_NATIVE_INT, &in_num);
vrfy_errors = dataset_vrfy(NULL, NULL, NULL, group_block,
&in_num, &num);
}
H5Aclose(aid);
}
else if(this_type == is_dset) {
sprintf(attr_name, "Dataset Attribute %d", num);
for(i=0; i<8; i++)
out_data[i] = i;
aid = H5Aopen_name(obj_id, attr_name);
if(MAINPROCESS) {
H5Aread(aid, H5T_NATIVE_INT, in_data);
vrfy_errors = dataset_vrfy(NULL, NULL, NULL, dset_block, in_data,
out_data);
}
H5Aclose(aid);
}
return vrfy_errors;
}
int AMRreader::
getIntfInfo( hid_t gid )
{
hid_t aid = H5Aopen_name( gid, intf_np_name );
if( aid<0 ) {
nvert_=0;
debug1 << "Failed to find number of interface points.\n";
return -1;
}
else {
H5Aread( aid, H5T_NATIVE_INT, &nvert_ );
H5Aclose(aid);
}
debug2 << "nvert is " << nvert_ << "\n";
aid = H5Aopen_name( gid, intf_ne_name );
if( aid<0 ) {
nrect_=0;
debug1 << "Failed to find number of interface elements.\n";
return -2;
}
else {
H5Aread( aid, H5T_NATIVE_INT, &nrect_ );
H5Aclose(aid);
}
debug2 << "nrect is " << nrect_ << "\n";
return 0;
}
void AbstractHdf5Access::SetUnlimitedDatasetId()
{
// Now deal with the unlimited dimension
// In terms of an Unlimited dimension dataset:
// * Files pre - r16738 (inc. Release 3.1 and earlier) use simply "Time" for "Data"'s unlimited variable.
// * Files generated by r16738 - r18257 used "<DatasetName>_Time" for "<DatasetName>"'s unlimited variable,
// - These are not to be used and there is no backwards compatibility for them, since they weren't in a release.
// * Files post r18257 (inc. Release 3.2 onwards) use "<DatasetName>_Unlimited" for "<DatasetName>"'s
// unlimited variable,
// - a new attribute "Name" has been added to the Unlimited Dataset to allow it to assign
// any name to the unlimited variable. Which can then be easily read by Hdf5DataReader.
// - if this dataset is missing we look for simply "Time" to remain backwards compatible with Releases <= 3.1
if (DoesDatasetExist(mDatasetName + "_Unlimited"))
{
mUnlimitedDatasetId = H5Dopen(mFileId, (mDatasetName + "_Unlimited").c_str());
hid_t name_attribute_id = H5Aopen_name(mUnlimitedDatasetId, "Name");
hid_t unit_attribute_id = H5Aopen_name(mUnlimitedDatasetId, "Unit");
hid_t attribute_type = H5Aget_type(name_attribute_id);
// Read into it.
char* string_array = (char *)malloc(sizeof(char)*MAX_STRING_SIZE);
H5Aread( name_attribute_id, attribute_type, string_array);
std::string name_string(&string_array[0]);
mUnlimitedDimensionName = name_string;
H5Aread( unit_attribute_id, attribute_type, string_array);
std::string unit_string(&string_array[0]);
mUnlimitedDimensionUnit = unit_string;
free(string_array);
H5Tclose(attribute_type);
H5Aclose(name_attribute_id);
H5Aclose(unit_attribute_id);
}
else if (DoesDatasetExist("Time"))
{
mUnlimitedDimensionName = "Time";
mUnlimitedDimensionUnit = "msec";
mUnlimitedDatasetId = H5Dopen(mFileId, mUnlimitedDimensionName.c_str());
}
else
{
NEVER_REACHED;
}
mIsUnlimitedDimensionSet = true;
}
static herr_t get_attribute_mem(hid_t obj_id,
const char *attr_name,
hid_t mem_type_id,
void *data)
{
hid_t attr_id;
herr_t status;
attr_id = H5Aopen_name(obj_id, attr_name);
if (attr_id < 0)
return -1;
status = H5Aread(attr_id, mem_type_id, data);
if (status < 0)
{
H5Aclose(attr_id);
return -1;
}
status = H5Aclose(attr_id);
if (status < 0)
return -1;
return 0;
}
static herr_t get_attribute_float(hid_t input, const char *name, float *val)
{
hid_t attr_id;
hid_t type_id;
H5T_class_t type_class;
size_t type_size;
herr_t status;
char *strval;
attr_id = H5Aopen_name(input, name);
type_id = H5Aget_type(attr_id);
type_class = H5Tget_class(type_id);
type_size = H5Tget_size(type_id);
H5Tclose(type_id);
H5Aclose(attr_id);
switch(type_class)
{
case H5T_STRING:
status = get_attribute_str(input, name, &strval);
if (status < 0) return -1;
*val = atof(strval);
free(strval);
return 0;
case H5T_FLOAT:
status = get_attribute(input, name, H5T_NATIVE_FLOAT, val);
if (status < 0) return -1;
return 0;
}
return -1;
}
static herr_t get_attribute_disk(hid_t loc_id,
const char *attr_name,
void *attr_out)
{
hid_t attr_id;
hid_t attr_type;
herr_t status;
attr_id = H5Aopen_name(loc_id, attr_name);
if (attr_id < 0)
return -1;
attr_type = H5Aget_type(attr_id);
if (attr_type < 0)
goto out;
status = H5Aread(attr_id, attr_type, attr_out);
if (status < 0)
goto out;
status = H5Tclose(attr_type);
if (status < 0)
goto out;
status = H5Aclose(attr_id);
if (status < 0)
return -1;
return 0;
out:
H5Tclose(attr_type);
H5Aclose(attr_id);
return -1;
}
bool read_attribute(const char * name, const H5ID & dataset, T & value)
{
H5ID attribute(H5Aopen_name(dataset, name), H5Aclose);
if (!attribute)
return false;
herr_t status = H5Aread(attribute, H5T_NATIVE_FLOAT, &value);
return status >= 0;
}
void
mhdf_getElemTypeName( mhdf_FileHandle file_handle,
const char* elem_handle,
char* buffer, size_t buf_len,
mhdf_Status* status )
{
FileHandle* file_ptr;
hid_t elem_id, type_id, attr_id;
char bytes[16];
herr_t rval;
API_BEGIN;
if (NULL == buffer || buf_len < 2)
{
mhdf_setFail( status, "invalid input" );
return;
}
buffer[0] = '\0';
file_ptr = (FileHandle*)(file_handle);
if (!mhdf_check_valid_file( file_ptr, status ))
return;
elem_id = mhdf_elem_group_from_handle( file_ptr, elem_handle, status );
if (elem_id < 0) return;
attr_id = H5Aopen_name( elem_id, ELEM_TYPE_ATTRIB );
H5Gclose( elem_id );
if (attr_id < 0)
{
mhdf_setFail( status, "Missing element type attribute. Invalid file." );
return;
}
type_id = H5Aget_type( attr_id );
assert( type_id > 0 );
rval = H5Aread( attr_id, type_id, bytes );
H5Aclose( attr_id );
if (rval < 0)
{
H5Tclose( type_id );
mhdf_setFail( status, "Failed to read element type attribute. Invalid file." );
return;
}
rval = H5Tenum_nameof( type_id, bytes, buffer, buf_len );
H5Tclose( type_id );
if (rval < 0)
{
mhdf_setFail( status, "Invalid datatype for element type attribute. Invalid file." );
return;
}
mhdf_setOkay( status );
API_END;
return ;
}
/* fetch num_cols and the col for a particular trackname */
void get_cols(chromosome_t *chromosome, char *trackname, hsize_t *num_cols,
hsize_t *col) {
hid_t attr, root, dataspace, datatype;
hsize_t data_size, cell_size, num_cells;
char *attr_data;
/* Tracknames are stored in the attributes of the root group of each file */
root = H5Gopen(chromosome->h5group, "/", H5P_DEFAULT);
assert(root >= 0);
attr = H5Aopen_name(root, "tracknames");
assert(attr >= 0);
dataspace = H5Aget_space(attr);
assert(dataspace >= 0);
assert(H5Sget_simple_extent_dims(dataspace, num_cols, NULL) == 1);
assert(H5Sclose(dataspace) >= 0);
if (trackname && col) {
datatype = H5Aget_type(attr);
assert(datatype >= 0);
assert(H5Tget_class(datatype) == H5T_STRING);
cell_size = H5Tget_size(datatype);
assert(cell_size > 0);
data_size = H5Aget_storage_size(attr);
assert(data_size > 0);
num_cells = data_size / cell_size;
/* allocate room for tracknames */
attr_data = xmalloc(data_size);
assert(attr_data);
assert(H5Aread(attr, datatype, attr_data) >= 0);
*col = 0;
for (*col = 0; *col <= num_cells; (*col)++) {
if (*col == num_cells) {
fprintf(stderr, "can't find trackname: %s\n", trackname);
free(attr_data);
exit(EXIT_FAILURE);
} else {
if (!strncmp(attr_data + (*col * cell_size), trackname, cell_size)) {
break;
}
}
}
/* clean up read tracknames */
free(attr_data);
}
assert(H5Aclose(attr) >= 0);
}
void get_attr(hid_t loc, const char *name, hid_t mem_type_id, void *buf) {
hid_t attr;
attr = H5Aopen_name(loc, name);
assert(attr >= 0);
assert(H5Aread(attr, mem_type_id, buf) >= 0);
assert(H5Aclose(attr) >= 0);
}
/*
* check if the dataset is an image
*/
void H5Dataset_check_image(H5Dataset *d, hid_t did)
{
hid_t aid=-1;
char *buf;
if (!d)
return;
aid = H5Aopen_name(did, "CLASS");
if (aid > 0) {
buf = (char *) H5Dataset_read_attr_value(aid);
if (buf) {
if(strncmp(buf, "IMAGE", 5)==0)
d->time |= H5D_IMAGE_FLAG;
free(buf);
}
H5Aclose(aid);
}
aid = H5Aopen_name(did, "IMAGE_SUBCLASS");
if (aid > 0) {
buf = (char *) H5Dataset_read_attr_value(aid);
if (buf) {
if(strncmp(buf, "IMAGE_TRUECOLOR", 15)==0)
d->time |= H5D_IMAGE_TRUECOLOR_FLAG;
free(buf);
}
H5Aclose(aid);
}
aid = H5Aopen_name(did, "INTERLACE_MODE");
if (aid > 0) {
buf = (char *) H5Dataset_read_attr_value(aid);
if (buf) {
if(strncmp(buf, "INTERLACE_PIXEL", 15)==0)
d->time |= H5D_IMAGE_INTERLACE_PIXEL_FLAG;
else if(strncmp(buf, "INTERLACE_PLANE", 15)==0)
d->time |= H5D_IMAGE_INTERLACE_PLANE_FLAG;
free(buf);
}
H5Aclose(aid);
}
}
static herr_t get_attribute_str(hid_t obj_id,
const char *attr_name,
char **data)
{
hid_t attr_id;
hid_t attr_type;
size_t type_size;
herr_t status;
*data = NULL;
attr_id = H5Aopen_name(obj_id, attr_name);
if (attr_id < 0)
return -1;
attr_type = H5Aget_type(attr_id);
if (attr_type < 0)
goto out;
/* Get the size */
type_size = H5Tget_size(attr_type);
if (type_size < 0)
goto out;
/* malloc enough space for the string, plus 1 for trailing '\0' */
*data = (char *)malloc(type_size + 1);
status = H5Aread(attr_id, attr_type, *data);
if (status < 0)
goto out;
/* Set the last character to '\0' in case we are dealing with
* null padded or space padded strings
*/
(*data)[type_size] = '\0';
status = H5Tclose(attr_type);
if (status < 0)
goto out;
status = H5Aclose(attr_id);
if (status < 0)
return -1;
return 0;
out:
H5Tclose(attr_type);
H5Aclose(attr_id);
if (*data)
free(*data);
return -1;
}
static herr_t get_attribute_info(hid_t obj_id,
const char *attr_name,
hsize_t *dims,
H5T_class_t *type_class,
size_t *type_size,
hid_t *type_id)
{
hid_t attr_id;
hid_t space_id;
herr_t status;
int rank;
/* Open the attribute. */
attr_id = H5Aopen_name(obj_id, attr_name);
if (attr_id < 0)
return -1;
/* Get an identifier for the datatype. */
*type_id = H5Aget_type(attr_id);
/* Get the class. */
*type_class = H5Tget_class(*type_id);
/* Get the size. */
*type_size = H5Tget_size(*type_id);
/* Get the dataspace handle */
space_id = H5Aget_space(attr_id);
if (space_id < 0)
goto out;
/* Get dimensions */
rank = H5Sget_simple_extent_dims(space_id, dims, NULL);
if (rank < 0)
goto out;
/* Terminate access to the dataspace */
status = H5Sclose(space_id);
if (status < 0)
goto out;
/* End access to the attribute */
status = H5Aclose(attr_id);
if (status < 0)
goto out;
return 0;
out:
H5Tclose(*type_id);
H5Aclose(attr_id);
return -1;
}
static herr_t get_max_id( hid_t group_id,
const char* subgroup,
const char* datatable,
unsigned long* data )
{
unsigned long id;
hid_t elem_id, conn_id, attr_id, space_id;
herr_t rval;
int rank;
hsize_t dims[2];
#if defined(H5Gopen_vers) && H5Gopen_vers > 1
elem_id = H5Gopen2( group_id, subgroup, H5P_DEFAULT );
#else
elem_id = H5Gopen( group_id, subgroup );
#endif
if (elem_id < 0) return (herr_t)-1;
#if defined(H5Dopen_vers) && H5Dopen_vers > 1
conn_id = H5Dopen2( elem_id, datatable, H5P_DEFAULT );
#else
conn_id = H5Dopen( elem_id, datatable );
#endif
H5Gclose( elem_id );
if (conn_id < 0) return (herr_t)-1;
space_id = H5Dget_space( conn_id );
if (space_id < 0) { H5Dclose( conn_id ); return -1; }
rank = H5Sget_simple_extent_ndims( space_id );
if (rank <= 0 || rank > 2) { H5Dclose(conn_id); H5Sclose(space_id); return -1; }
rval = H5Sget_simple_extent_dims( space_id, dims, NULL );
H5Sclose( space_id );
if (rval < 0) { H5Dclose( conn_id ); return -1; }
attr_id = H5Aopen_name( conn_id, START_ID_ATTRIB );
H5Dclose( conn_id );
if (attr_id < 0) return (herr_t)-1;
rval = H5Aread( attr_id, H5T_NATIVE_ULONG, &id );
H5Aclose( attr_id );
if (rval < 0) return rval;
id += dims[0];
if (id > *data)
*data = id;
return 0;
}
bool GH5_FetchAttribute( hid_t loc_id, const char *pszAttrName,
CPLString &osResult, bool bReportError )
{
bool retVal = false;
hid_t hAttr = H5Aopen_name( loc_id, pszAttrName );
osResult.clear();
if( hAttr < 0 )
{
if( bReportError )
CPLError( CE_Failure, CPLE_AppDefined,
"Attempt to read attribute %s failed, not found.",
pszAttrName );
return false;
}
hid_t hAttrTypeID = H5Aget_type( hAttr );
hid_t hAttrNativeType = H5Tget_native_type( hAttrTypeID, H5T_DIR_DEFAULT );
if( H5Tget_class( hAttrNativeType ) == H5T_STRING )
{
int nAttrSize = H5Tget_size( hAttrTypeID );
char *pachBuffer = (char *) CPLCalloc(nAttrSize+1,1);
H5Aread( hAttr, hAttrNativeType, pachBuffer );
osResult = pachBuffer;
CPLFree( pachBuffer );
retVal = true;
}
else
{
if( bReportError )
CPLError( CE_Failure, CPLE_AppDefined,
"Attribute %s of unsupported type for conversion to string.",
pszAttrName );
retVal = false;
}
H5Tclose( hAttrNativeType );
H5Tclose( hAttrTypeID );
H5Aclose( hAttr );
return retVal;
}
/* reads the references of palettes into an array
* Each reference requires eight bytes storage. Therefore, the array length
* is 8*numberOfPalettes.
*/
hobj_ref_t* H5Dataset_get_paletteRef(hid_t did)
{
hid_t aid=-1;
hobj_ref_t *ref_buf=NULL;
aid = H5Aopen_name(did, "PALETTE");
if (aid > 0) {
ref_buf = (hobj_ref_t *) H5Dataset_read_attr_value(aid);
H5Aclose(aid);
}
return ref_buf;
}
int _GetValue(hid_t loc_id, const char *attr_name, void *strname)
{
int iQualityIndex;
hid_t hAttributeID;
if(strcmp(attr_name,(char *)strname)==0)
{
hAttributeID = H5Aopen_name(loc_id, attr_name);
H5Aread(hAttributeID, H5T_NATIVE_INT, &iQualityIndex);
H5Aclose(hAttributeID);
return iQualityIndex;
}
else
return 0;
}
void read_header_attributes_in_hdf5(char *fname)
{
hid_t hdf5_file, hdf5_headergrp, hdf5_attribute;
hdf5_file = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT);
hdf5_headergrp = H5Gopen(hdf5_file, "/Header");
hdf5_attribute = H5Aopen_name(hdf5_headergrp, "NumPart_ThisFile");
H5Aread(hdf5_attribute, H5T_NATIVE_INT, header.npart);
H5Aclose(hdf5_attribute);
hdf5_attribute = H5Aopen_name(hdf5_headergrp, "NumPart_Total");
H5Aread(hdf5_attribute, H5T_NATIVE_UINT, header.npartTotal);
H5Aclose(hdf5_attribute);
hdf5_attribute = H5Aopen_name(hdf5_headergrp, "NumPart_Total_HighWord");
H5Aread(hdf5_attribute, H5T_NATIVE_UINT, header.npartTotalHighWord);
H5Aclose(hdf5_attribute);
hdf5_attribute = H5Aopen_name(hdf5_headergrp, "MassTable");
H5Aread(hdf5_attribute, H5T_NATIVE_DOUBLE, header.mass);
H5Aclose(hdf5_attribute);
hdf5_attribute = H5Aopen_name(hdf5_headergrp, "Time");
H5Aread(hdf5_attribute, H5T_NATIVE_DOUBLE, &header.time);
H5Aclose(hdf5_attribute);
#ifdef LT_STELLAREVOLUTION
hdf5_attribute = H5Aopen_name(hdf5_headergrp, "BoxSize");
H5Aread(hdf5_attribute, H5T_NATIVE_DOUBLE, &header.BoxSize);
H5Aclose(hdf5_attribute);
#endif
hdf5_attribute = H5Aopen_name(hdf5_headergrp, "NumFilesPerSnapshot");
H5Aread(hdf5_attribute, H5T_NATIVE_INT, &header.num_files);
H5Aclose(hdf5_attribute);
hdf5_attribute = H5Aopen_name(hdf5_headergrp, "Flag_IC_Info");
H5Aread(hdf5_attribute, H5T_NATIVE_INT, &header.flag_ic_info);
H5Aclose(hdf5_attribute);
H5Gclose(hdf5_headergrp);
H5Fclose(hdf5_file);
}
static int
NC4_get_propattr(NC_HDF5_FILE_INFO_T* h5)
{
int ncstat = NC_NOERR;
size_t size;
H5T_class_t t_class;
hid_t grp = -1;
hid_t attid = -1;
hid_t aspace = -1;
hid_t atype = -1;
hid_t ntype = -1;
herr_t herr = 0;
char* text = NULL;
/* Get root group */
grp = h5->root_grp->hdf_grpid; /* get root group */
/* Try to extract the NCPROPS attribute */
if(H5Aexists(grp,NCPROPS) > 0) { /* Does exist */
attid = H5Aopen_name(grp, NCPROPS);
herr = -1;
aspace = H5Aget_space(attid); /* dimensions of attribute data */
atype = H5Aget_type(attid);
/* Verify that atype and size */
t_class = H5Tget_class(atype);
if(t_class != H5T_STRING) {ncstat = NC_EATTMETA; goto done;}
size = H5Tget_size(atype);
if(size == 0) goto done;
text = (char*)malloc(size+1);
if(text == NULL)
{ncstat = NC_ENOMEM; goto done;}
HCHECK((ntype = H5Tget_native_type(atype, H5T_DIR_ASCEND)));
HCHECK((H5Aread(attid, ntype, text)));
/* Make sure its null terminated */
text[size] = '\0';
/* Try to parse text */
ncstat = NC4_properties_parse(&h5->fileinfo->propattr,text);
herr = 0;
}
done:
if(attid >= 0) HCHECK((H5Aclose(attid)));
if(aspace >= 0) HCHECK((H5Sclose(aspace)));
if(ntype >= 0) HCHECK((H5Tclose(ntype)));
if(atype >= 0) HCHECK((H5Tclose(atype)));
if(text != NULL) free(text);
return ncstat;
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5Aopen_name
* Signature: (JLjava/lang/String;)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Aopen_1name
(JNIEnv *env, jclass clss, jlong loc_id, jstring name)
{
hid_t attr_id = -1;
const char *aName;
PIN_JAVA_STRING(name, aName);
if (aName != NULL) {
attr_id = H5Aopen_name((hid_t)loc_id, aName);
UNPIN_JAVA_STRING(name,aName);
if (attr_id < 0)
h5libraryError(env);
}
return (jlong)attr_id;
} /* end Java_hdf_hdf5lib_H5__1H5Aopen_1name */
static int
NC4_get_propattr(NC_HDF5_FILE_INFO_T* h5)
{
int ncstat = NC_NOERR;
size_t size;
H5T_class_t t_class;
char text[NCPROPS_LENGTH+1];
hid_t grp = -1;
hid_t attid = -1;
hid_t aspace = -1;
hid_t atype = -1;
hid_t ntype = -1;
herr_t herr = 0;
/* Get root group */
grp = h5->root_grp->hdf_grpid; /* get root group */
/* Try to extract the NCPROPS attribute */
attid = H5Aopen_name(grp, NCPROPS);
if(attid >= 0) {
herr = -1;
aspace = H5Aget_space(attid); /* dimensions of attribute data */
atype = H5Aget_type(attid);
/* Verify that atype and size */
t_class = H5Tget_class(atype);
if(t_class != H5T_STRING) {ncstat = NC_EATTMETA; goto done;}
size = H5Tget_size(atype);
if(size != NCPROPS_LENGTH) {ncstat = NC_EATTMETA; goto done;}
HCHECK((ntype = H5Tget_native_type(atype, H5T_DIR_ASCEND)));
HCHECK((H5Aread(attid, ntype, text)));
/* Try to parse text */
strncpy(h5->fileinfo->propattr.text,text,NCPROPS_LENGTH);
h5->fileinfo->propattr.text[NCPROPS_LENGTH-1] = '\0';
ncstat = NC4_properties_parse(&h5->fileinfo->propattr);
herr = 0;
}
done:
if(attid >= 0) HCHECK((H5Aclose(attid)));
if(aspace >= 0) HCHECK((H5Sclose(aspace)));
if(ntype >= 0) HCHECK((H5Tclose(ntype)));
if(atype >= 0) HCHECK((H5Tclose(atype)));
return ncstat;
}
/*
* - Nom de la fonction : _MEDattrStringLire
* - Description : lecture d'un attribut chaine de caracteres
* - Parametres :
* - pere (IN) : l'ID de l'objet HDF pere ou placer l'attribut
* - nom (IN) : le nom de l'attribut
* - longueur (IN) : strlen(val)
* - val (OUT) : la valeur de l'attribut
* - Resultat : 0 en cas de succes, -1 sinon
*/
med_err _MEDattrStringLire(med_idt pere,char *nom,int longueur,char *val)
{
med_idt attid,datatype;
med_err ret;
if ((datatype = H5Tcopy(H5T_C_S1)) < 0)
return -1;
if ((ret = H5Tset_size(datatype,longueur+1)) < 0)
return -1;
if ((attid = H5Aopen_name(pere,nom)) < 0)
return -1;
if ((ret = H5Aread(attid,datatype,val)) < 0)
return -1;
if ((ret = H5Tclose(datatype)) < 0)
return -1;
if ((ret = H5Aclose(attid)) < 0)
return -1;
return 0;
}
int VsFilter::visitAttrib(hid_t dId, const char* name,
const H5A_info_t* ai, void* opdata) {
RECURSION_DATA* data = static_cast< RECURSION_DATA* >(opdata);
VsObject* parent = data->parent;
VsLog::debugLog() << "VsFilter::visitAttrib(...): getting attribute '" <<
name << "'." << std::endl;
if (!parent) {
VsLog::errorLog() <<"VsFilter::visitAttrib(): Parent is NULL?" <<std::endl;
return 0;
}
//TODO - actually load & cache string attribute values here
hid_t attId = H5Aopen_name(dId, name);
parent->addAttribute(name, attId);
return 0;
}
int pioReadAttributeString(PIOObject pioObject,
const char* attr_name, char** attr_value)
{
hid_t attr;
size_t storage;
if (pioHasAttribute(pioObject, attr_name))
{
attr = H5Aopen_name(pioObject.identifier, attr_name);
storage = H5Aget_storage_size(attr);
H5Aclose(attr);
*attr_value = (char*)malloc( storage + sizeof(char));
H5LTget_attribute_string(pioObject.identifier, ".",
attr_name, *attr_value);
return 1;
}
else {
return -1;
}
}
static int find_attr(hid_t attr_id, const char *name, void *op_data)
{
hid_t obj, type;
int status;
h5item *parent = (h5item *)op_data;
h5item *item = (h5item *)malloc(sizeof(h5item));
h5item *itm;
item->item_type = -1;
item->name=strcpy(malloc(strlen(name)+1),name);
item->child = 0;
item->brother = 0;
item->parent = parent;
item->obj = 0;
item->attribute = 0;
if(parent) {
if (parent->attribute == NULL)
{
parent->attribute = item;
}
else
{
for (itm = parent->attribute; itm->brother; itm = itm->brother);
itm->brother = item;
}
}
if ((obj = H5Aopen_name(attr_id,name)) >= 0) {
int size;
char dtype;
int htype = 42;
int is_signed;
hsize_t ds_dims[64];
hid_t space = H5Aget_space(obj);
int n_ds_dims = H5Sget_simple_extent_dims(space,ds_dims,0);
size_t precision;
H5Sclose(space);
item->obj = obj;
}
return 0;
}
/*
* - Nom de la fonction : _MEDattrNumLire
* - Description : lecture d'un attribut entier
* - Parametres :
* - pere (IN) : l'ID de l'objet HDF pere ou placer l'attribut
* - type (IN) : le type du champ {MED_FLOAT64,MED_INT}
* - nom (IN) : le nom de l'attribut
* - val (OUT) : la valeur de l'attribut
* - Resultat : 0 en cas de succes, -1 sinon
*/
med_err _MEDattrNumLire(med_idt pere,med_field_type type,char *nom,unsigned char *val)
{
med_idt attid;
med_err ret;
hid_t type_hdf;
/* ISCRUTE(sizeof(med_int)); */
/* ISCRUTE_id(pere); */
/* SSCRUTE(nom); */
if ((attid = H5Aopen_name(pere,nom)) < 0)
return -1;
switch(type)
{
case MED_FLOAT64 :
type_hdf = H5T_NATIVE_DOUBLE;
break;
case MED_INT :
#if defined(HAVE_F77INT64)
type_hdf = H5T_NATIVE_LONG;
#else
type_hdf = H5T_NATIVE_INT;
#endif
break;
default :
return -1;
}
if ((ret = H5Aread(attid,type_hdf, val)) < 0)
return -1;
if ((ret = H5Aclose(attid)) < 0)
return -1;
return 0;
}
/*----------------------------------------------------------------------------
* Name: h5aopen_name _c
* Purpose: Call H5Aopen_name to open an attribute
* Inputs: obj_id - object identifier
* name - name of the attribute
* namelen - name length
* Outputs: attr_id - dataset identifier
* Returns: 0 on success, -1 on failure
* Programmer: Elena Pourmal
* Thursday, August 12, 1999
* Modifications:
*---------------------------------------------------------------------------*/
int_f
nh5aopen_name_c (hid_t_f *obj_id, _fcd name, size_t_f *namelen, hid_t_f *attr_id)
{
char *c_name=NULL; /* Buffer to hold C string */
int_f ret_value=0; /* Return value */
/*
* Convert FORTRAN name to C name
*/
if ((c_name = HD5f2cstring(name, (size_t)*namelen)) == NULL)
HGOTO_DONE(FAIL);
/*
* Call H5Aopen function.
*/
if ((*attr_id = (hid_t_f)H5Aopen_name((hid_t)*obj_id, c_name)) < 0)
HGOTO_DONE(FAIL);
done:
if(c_name) HDfree(c_name);
return ret_value;
}
med_err _MED21attrNumLire(med_idt pere,med_type_champ type,char *nom,
unsigned char *val,hid_t hdf_file)
{
med_idt attid;
med_err ret;
int type_hdf;
if ((attid = H5Aopen_name(pere,nom)) < 0)
return -1;
switch(type)
{
case MED_FLOAT64 :
if (H5Tequal(hdf_file,H5T_IEEE_F64BE))
type_hdf = H5T_IEEE_F64LE;
if (H5Tequal(hdf_file,H5T_IEEE_F64LE))
type_hdf = H5T_IEEE_F64BE;
break;
case MED_INT :
#if defined(HAVE_F77INT64)
type_hdf = H5T_NATIVE_LONG;
#else
type_hdf = H5T_NATIVE_INT;
#endif
break;
default :
return -1;
}
if ((ret = H5Aread(attid,type_hdf,val)) < 0)
return -1;
if ((ret = H5Aclose(attid)) < 0)
return -1;
return 0;
}
void read_header_attributes_in_hdf5(char *fname)
{
hid_t hdf5_file, hdf5_headergrp, hdf5_attribute;
hdf5_file = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT);
hdf5_headergrp = H5Gopen(hdf5_file, "/Header");
hdf5_attribute = H5Aopen_name(hdf5_headergrp, "NumPart_ThisFile");
H5Aread(hdf5_attribute, H5T_NATIVE_INT, header.npart);
H5Aclose(hdf5_attribute);
hdf5_attribute = H5Aopen_name(hdf5_headergrp, "NumPart_Total");
H5Aread(hdf5_attribute, H5T_NATIVE_UINT, header.npartTotal);
H5Aclose(hdf5_attribute);
hdf5_attribute = H5Aopen_name(hdf5_headergrp, "NumPart_Total_HighWord");
H5Aread(hdf5_attribute, H5T_NATIVE_UINT, header.npartTotalHighWord);
H5Aclose(hdf5_attribute);
hdf5_attribute = H5Aopen_name(hdf5_headergrp, "MassTable");
H5Aread(hdf5_attribute, H5T_NATIVE_DOUBLE, header.mass);
H5Aclose(hdf5_attribute);
hdf5_attribute = H5Aopen_name(hdf5_headergrp, "Time");
H5Aread(hdf5_attribute, H5T_NATIVE_DOUBLE, &header.time);
H5Aclose(hdf5_attribute);
hdf5_attribute = H5Aopen_name(hdf5_headergrp, "NumFilesPerSnapshot");
H5Aread(hdf5_attribute, H5T_NATIVE_INT, &header.num_files);
H5Aclose(hdf5_attribute);
hdf5_attribute = H5Aopen_name(hdf5_headergrp, "Flag_Entropy_ICs");
H5Aread(hdf5_attribute, H5T_NATIVE_INT, &header.flag_entropy_instead_u);
H5Aclose(hdf5_attribute);
H5Gclose(hdf5_headergrp);
H5Fclose(hdf5_file);
}
int
NC4_put_propattr(NC_HDF5_FILE_INFO_T* h5)
{
int ncstat = NC_NOERR;
char text[NCPROPS_LENGTH+1];
H5T_class_t t_class;
size_t size;
hid_t grp = -1;
hid_t exists = -1;
hid_t attid = -1;
hid_t aspace = -1;
hid_t atype = -1;
herr_t herr = 0;
/* Get root group */
grp = h5->root_grp->hdf_grpid; /* get root group */
/* See if the NCPROPS attribute exists */
exists = H5Aopen_name(grp, NCPROPS);
if(exists < 0) {/* Does not exist */
herr = -1;
/* Create a datatype to refer to. */
HCHECK((atype = H5Tcopy(H5T_C_S1)));
HCHECK((H5Tset_cset(atype, H5T_CSET_UTF8)));
HCHECK((H5Tset_size(atype, NCPROPS_LENGTH)));
HCHECK((aspace = H5Screate(H5S_SCALAR)));
HCHECK((attid = H5Acreate(grp, NCPROPS, atype, aspace, H5P_DEFAULT)));
HCHECK((H5Awrite(attid, atype, h5->fileinfo->propattr.text)));
herr = 0;
}
done:
if(exists >= 0) HCHECK((H5Aclose(exists)));
if(attid >= 0) HCHECK((H5Aclose(attid)));
if(aspace >= 0) HCHECK((H5Sclose(aspace)));
if(atype >= 0) HCHECK((H5Tclose(atype)));
return ncstat;
}
