void write(const hid_attribute_adaptor& attrib, const std::string& value)
{
hid_t attr_type_id = H5CPP_ERR_ON_NEG(H5Aget_type(attrib.id()));
if(H5Tget_class(attr_type_id) != H5T_STRING)
H5CPP_THROW("Attempted to set string value on non-string attribute '"
<< object::get_name(attrib.id()) << '\'');
const char* cstr = value.c_str();
if(H5Tis_variable_str(attr_type_id))
H5CPP_ERR_ON_NEG(H5Awrite(attrib.id(), attr_type_id, &cstr));
else
{
std::size_t attriblen = H5Aget_storage_size(attrib.id());
if(attriblen > value.length())
{
// avoid reading past end of value into unalloc'd mem
std::vector<char> buf(attriblen,'\0');
std::copy(cstr, cstr+value.length(), &buf[0]);
H5CPP_ERR_ON_NEG(H5Awrite(attrib.id(), attr_type_id, &buf[0]));
}
else
H5CPP_ERR_ON_NEG(H5Awrite(attrib.id(), attr_type_id, cstr));
}
}
/* 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);
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5Aget_storage_size
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Aget_1storage_1size
(JNIEnv *env, jclass clss, jlong attr_id)
{
hsize_t retVal = (hsize_t)-1;
retVal = H5Aget_storage_size((hid_t)attr_id);
/* probably returns '0' if fails--don't do an exception */
return (jlong)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Aget_1storage_1size */
herr_t VsH5Attribute::getStringValue(std::string* val) {
hid_t atype = H5Aget_type(getId());
H5T_class_t type = H5Tget_class(atype);
hid_t aspace = H5Aget_space(getId());
size_t rank = H5Sget_simple_extent_ndims(aspace);
if (type != H5T_STRING) {
VsLog::warningLog() <<"VsH5Attribute::getStringValue() - Requested attribute " <<getShortName()
<<" is not a string value." <<std::endl;
val->clear();
return -1;
}
//Yes, this is correct (rank != 0)
if (rank != 0) {
VsLog::warningLog() <<"VsH5Attribute::getStringValue() - Requested attribute " <<getShortName()
<<" is not a string value." <<std::endl;
val->clear();
return -1;
}
size_t len = H5Aget_storage_size(getId());
val->resize(len);
char* v = new char[len];
herr_t err = H5Aread(getId(), atype, v);
// JRC: is this right?
// err = H5Aread(id, H5T_NATIVE_CHAR, v);
for (size_t i = 0; i < len; ++i) {
if (v[i] == 0) {
//This happens when a program (IDL, HdfView) declares a string of length 5
//and uses the 5th character for the null terminator
//In h5dump this shows up as a string "mesh" being declared as 5 characters
//If dumped to a terminal, it prints like so: "mesh^@"
VsLog::warningLog() <<"VsH5Attribute::getStringValue() - Found null char inside string attribute: " <<getFullName() <<std::endl;
val->resize(i);
break;
}
(*val)[i] = v[i];
}
delete [] v;
return err;
}
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;
}
}
/// Return the attribute name of obj, and "" if the attribute does not exist.
void h5_read_attribute(hid_t id, std::string const &name, std::string & s) {
s = "";
// if the attribute is not present, return 0
if (H5LTfind_attribute(id, name.c_str()) == 0) return; // not present
attribute attr = H5Aopen(id, name.c_str(), H5P_DEFAULT);
if (!attr.is_valid()) TRIQS_RUNTIME_ERROR << "Cannot open the attribute " << name;
dataspace space = H5Aget_space(attr);
int rank = H5Sget_simple_extent_ndims(space);
if (rank != 0) TRIQS_RUNTIME_ERROR << "Reading a string attribute and got rank !=0";
datatype strdatatype = H5Aget_type(attr);
std::vector<char> buf(H5Aget_storage_size(attr) + 1, 0x00);
auto err = H5Aread(attr, strdatatype, (void *)(&buf[0]));
if (err < 0) TRIQS_RUNTIME_ERROR << "Cannot read the attribute " << name;
s.append(&(buf.front()));
}
int
NC4_write_ncproperties(NC_FILE_INFO_T* h5)
{
int retval = NC_NOERR;
hid_t hdf5grpid = -1;
hid_t attid = -1;
hid_t aspace = -1;
hid_t atype = -1;
char* text = NULL;
size_t len = 0;
LOG((3, "%s", __func__));
/* If the file is read-only, return an error. */
if (h5->no_write)
{retval = NC_EPERM; goto done;}
hdf5grpid = ((NC_HDF5_GRP_INFO_T *)(h5->root_grp->format_grp_info))->hdf_grpid;
if(H5Aexists(hdf5grpid,NCPROPS) > 0) /* Already exists, no overwrite */
goto done;
/* Build the attribute string */
if((retval = NC4_buildpropinfo(&h5->provenance->propattr,&text)))
goto done;
/* Build the HDF5 string type */
if ((atype = H5Tcopy(H5T_C_S1)) < 0)
{retval = NC_EHDFERR; goto done;}
if (H5Tset_strpad(atype, H5T_STR_NULLTERM) < 0)
{retval = NC_EHDFERR; goto done;}
if(H5Tset_cset(atype, H5T_CSET_ASCII) < 0)
{retval = NC_EHDFERR; goto done;}
len = strlen(text);
if(H5Tset_size(atype, len) < 0)
{retval = NC_EFILEMETA; goto done;}
/* Create NCPROPS attribute */
if((aspace = H5Screate(H5S_SCALAR)) < 0)
{retval = NC_EFILEMETA; goto done;}
if ((attid = H5Acreate(hdf5grpid, NCPROPS, atype, aspace, H5P_DEFAULT)) < 0)
{retval = NC_EFILEMETA; goto done;}
if (H5Awrite(attid, atype, text) < 0)
{retval = NC_EFILEMETA; goto done;}
/* Verify */
#if 0
{
hid_t spacev, typev;
hsize_t dsize, tsize;
typev = H5Aget_type(attid);
spacev = H5Aget_space(attid);
dsize = H5Aget_storage_size(attid);
tsize = H5Tget_size(typev);
fprintf(stderr,"dsize=%lu tsize=%lu\n",(unsigned long)dsize,(unsigned long)tsize);
}
#endif
done:
if(text != NULL) free(text);
/* Close out the HDF5 objects */
if(attid > 0 && H5Aclose(attid) < 0) retval = NC_EHDFERR;
if(aspace > 0 && H5Sclose(aspace) < 0) retval = NC_EHDFERR;
if(atype > 0 && H5Tclose(atype) < 0) retval = NC_EHDFERR;
/* For certain errors, actually fail, else log that attribute was invalid and ignore */
switch (retval) {
case NC_ENOMEM:
case NC_EHDFERR:
case NC_EPERM:
case NC_EFILEMETA:
case NC_NOERR:
break;
default:
LOG((0,"Invalid _NCProperties attribute"));
retval = NC_NOERR;
break;
}
return retval;
}
std::string fast5_get_string_attribute(fast5_file& fh, const std::string& group_name, const std::string& attribute_name)
{
hid_t group, attribute, attribute_type, native_type;
std::string out;
// according to http://hdf-forum.184993.n3.nabble.com/check-if-dataset-exists-td194725.html
// we should use H5Lexists to check for the existence of a group/dataset using an arbitrary path
// HDF5 1.8 returns 0 on the root group, so we explicitly check for it
int ret = group_name == "/" ? 1 : H5Lexists(fh.hdf5_file, group_name.c_str(), H5P_DEFAULT);
if(ret <= 0) {
return "";
}
// Open the group containing the attribute we want
group = H5Gopen(fh.hdf5_file, group_name.c_str(), H5P_DEFAULT);
if(group < 0) {
#ifdef DEBUG_FAST5_IO
fprintf(stderr, "could not open group %s\n", group_name.c_str());
#endif
goto close_group;
}
// Ensure attribute exists
ret = H5Aexists(group, attribute_name.c_str());
if(ret <= 0) {
goto close_group;
}
// Open the attribute
attribute = H5Aopen(group, attribute_name.c_str(), H5P_DEFAULT);
if(attribute < 0) {
#ifdef DEBUG_FAST5_IO
fprintf(stderr, "could not open attribute: %s\n", attribute_name.c_str());
#endif
goto close_attr;
}
// Get data type and check it is a fixed-length string
attribute_type = H5Aget_type(attribute);
if(attribute_type < 0) {
#ifdef DEBUG_FAST5_IO
fprintf(stderr, "failed to get attribute type %s\n", attribute_name.c_str());
#endif
goto close_type;
}
if(H5Tget_class(attribute_type) != H5T_STRING) {
#ifdef DEBUG_FAST5_IO
fprintf(stderr, "attribute %s is not a string\n", attribute_name.c_str());
#endif
goto close_type;
}
native_type = H5Tget_native_type(attribute_type, H5T_DIR_ASCEND);
if(native_type < 0) {
#ifdef DEBUG_FAST5_IO
fprintf(stderr, "failed to get native type for %s\n", attribute_name.c_str());
#endif
goto close_native_type;
}
if(H5Tis_variable_str(attribute_type) > 0) {
// variable length string
char* buffer;
ret = H5Aread(attribute, native_type, &buffer);
if(ret < 0) {
fprintf(stderr, "error reading attribute %s\n", attribute_name.c_str());
exit(EXIT_FAILURE);
}
out = buffer;
free(buffer);
buffer = NULL;
} else {
// fixed length string
size_t storage_size;
char* buffer;
// Get the storage size and allocate
storage_size = H5Aget_storage_size(attribute);
buffer = (char*)calloc(storage_size + 1, sizeof(char));
// finally read the attribute
ret = H5Aread(attribute, attribute_type, buffer);
if(ret >= 0) {
out = buffer;
}
// clean up
free(buffer);
}
close_native_type:
H5Tclose(native_type);
close_type:
H5Tclose(attribute_type);
close_attr:
H5Aclose(attribute);
close_group:
H5Gclose(group);
return out;
}
herr_t HDF5AttrIterate( hid_t hH5ObjID,
const char *AttrName,
void *pDS )
{
hid_t hAttrID;
hid_t hAttrTypeID;
hid_t hAttrNativeType;
hid_t hAttrSpace;
char *szData = NULL;
hsize_t nSize[64];
unsigned int nAttrElmts;
hsize_t nAttrSize;
hsize_t i;
void *buf = NULL;
unsigned int nAttrDims;
HDF5Dataset *poDS;
char *szTemp = (char*) CPLMalloc( 8192 );
char *szValue = NULL;
poDS = (HDF5Dataset *) pDS;
sprintf( szTemp, "%s:%s", poDS->poH5CurrentObject->pszName,
AttrName );
hAttrID = H5Aopen_name( hH5ObjID, AttrName );
hAttrTypeID = H5Aget_type( hAttrID );
hAttrNativeType = H5Tget_native_type( hAttrTypeID, H5T_DIR_DEFAULT );
hAttrSpace = H5Aget_space( hAttrID );
nAttrDims = H5Sget_simple_extent_dims( hAttrSpace, nSize, NULL );
if( H5Tget_class( hAttrNativeType ) == H5T_STRING ) {
nAttrSize = H5Aget_storage_size( hAttrID );
szData = (char*) CPLMalloc((size_t) (nAttrSize+1));
szValue = (char*) CPLMalloc((size_t) (nAttrSize+1));
H5Aread( hAttrID, hAttrNativeType, szData );
szData[nAttrSize]='\0';
sprintf( szValue, "%s", szData );
}
else {
nAttrElmts = 1;
for( i=0; i < nAttrDims; i++ ) {
nAttrElmts *= (int) nSize[i];
}
if( nAttrElmts > 0 ){
buf = (void *) CPLMalloc( nAttrElmts*
H5Tget_size( hAttrNativeType ));
szData = (char*) CPLMalloc( 8192 );
szValue = (char*) CPLMalloc( MAX_METADATA_LEN );
szData[0]='\0';
szValue[0] ='\0';
H5Aread( hAttrID, hAttrNativeType, buf );
}
if( H5Tequal( H5T_NATIVE_CHAR, hAttrNativeType ) ){
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%c ", ((char *) buf)[i]);
if( CPLStrlcat(szValue,szData,MAX_METADATA_LEN) >= MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_UCHAR, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%c", ((char *) buf)[i] );
if( CPLStrlcat(szValue,szData,MAX_METADATA_LEN) >= MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_SHORT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%d ", ((short *) buf)[i] );
if( CPLStrlcat(szValue,szData,MAX_METADATA_LEN) >= MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_USHORT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ud ", ((unsigned short *) buf)[i] );
if( CPLStrlcat(szValue,szData,MAX_METADATA_LEN) >= MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_INT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%d ", ((int *) buf)[i] );
if( CPLStrlcat(szValue,szData,MAX_METADATA_LEN) >= MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_UINT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ud ", ((unsigned int *) buf)[i] );
if( CPLStrlcat(szValue,szData,MAX_METADATA_LEN) >= MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_LONG, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ld ", ((long *)buf)[i] );
if( CPLStrlcat(szValue,szData,MAX_METADATA_LEN) >= MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_ULONG, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ld ", ((unsigned long *)buf)[i] );
if( CPLStrlcat(szValue,szData,MAX_METADATA_LEN) >= MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_FLOAT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%f ", ((float *)buf)[i] );
if( CPLStrlcat(szValue,szData,MAX_METADATA_LEN) >= MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_DOUBLE, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%g ", ((double *)buf)[i] );
if( CPLStrlcat(szValue,szData,MAX_METADATA_LEN) >= MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
CPLFree( buf );
}
H5Sclose(hAttrSpace);
H5Tclose(hAttrNativeType);
H5Tclose(hAttrTypeID);
H5Aclose( hAttrID );
//printf( "%s = %s\n",szTemp, szValue );
poDS->papszMetadata =
CSLSetNameValue( poDS->papszMetadata, szTemp,
CPLSPrintf( "%s", szValue ) );
CPLFree( szTemp );
CPLFree( szData );
CPLFree( szValue );
return 0;
}
static herr_t HDF5AttrIterate( hid_t hH5ObjID,
const char *pszAttrName,
// TODO(schwehr): void * -> HDF5Dataset *
void *pDS )
{
char **papszTokens = nullptr;
CPLString osKey;
HDF5Dataset *const poDS = static_cast<HDF5Dataset *>(pDS);
// Convert "/" into "_" for the path component
const char *pszPath = poDS->poH5CurrentObject->pszUnderscorePath;
if(pszPath != nullptr && strlen(pszPath) > 0)
{
papszTokens = CSLTokenizeString2(pszPath, "/", CSLT_HONOURSTRINGS);
for( hsize_t i = 0; papszTokens != nullptr && papszTokens[i] != nullptr; ++i )
{
if( i != 0)
osKey += '_';
osKey += papszTokens[i];
}
CSLDestroy(papszTokens);
}
// Convert whitespaces into "_" for the attribute name component
papszTokens = CSLTokenizeString2(
pszAttrName, " ", CSLT_STRIPLEADSPACES | CSLT_STRIPENDSPACES);
for( hsize_t i = 0; papszTokens != nullptr && papszTokens[i] != nullptr; ++i )
{
if(!osKey.empty())
osKey += '_';
osKey += papszTokens[i];
}
CSLDestroy(papszTokens);
const hid_t hAttrID = H5Aopen_name(hH5ObjID, pszAttrName);
const hid_t hAttrTypeID = H5Aget_type(hAttrID);
const hid_t hAttrNativeType =
H5Tget_native_type(hAttrTypeID, H5T_DIR_DEFAULT);
const hid_t hAttrSpace = H5Aget_space(hAttrID);
if( H5Tget_class(hAttrNativeType) == H5T_VLEN )
return 0;
hsize_t nSize[64] = {};
const unsigned int nAttrDims =
H5Sget_simple_extent_dims(hAttrSpace, nSize, nullptr);
unsigned int nAttrElmts = 1;
for( hsize_t i = 0; i < nAttrDims; i++ )
{
nAttrElmts *= static_cast<int>(nSize[i]);
}
char *szData = nullptr;
hsize_t nAttrSize = 0;
char *szValue = nullptr;
if( H5Tget_class(hAttrNativeType) == H5T_STRING )
{
if ( H5Tis_variable_str(hAttrNativeType) )
{
char **papszStrings =
static_cast<char **>(CPLMalloc(nAttrElmts * sizeof(char *)));
// Read the values.
H5Aread(hAttrID, hAttrNativeType, papszStrings);
// Concatenate all values as one string separated by a space.
CPLString osVal = papszStrings[0];
for( hsize_t i = 1; i < nAttrElmts; i++ )
{
osVal += " ";
osVal += papszStrings[i];
}
szValue = static_cast<char *>(CPLMalloc(osVal.length() + 1));
strcpy(szValue, osVal.c_str());
H5Dvlen_reclaim(hAttrNativeType, hAttrSpace, H5P_DEFAULT,
papszStrings);
CPLFree(papszStrings);
}
else
{
nAttrSize = H5Aget_storage_size(hAttrID);
szValue = static_cast<char *>(CPLMalloc((size_t)(nAttrSize + 1)));
H5Aread(hAttrID, hAttrNativeType, szValue);
szValue[nAttrSize] = '\0';
}
}
else
{
const size_t nDataLen = 8192;
void *buf = nullptr;
if( nAttrElmts > 0 )
{
buf = CPLMalloc(nAttrElmts * H5Tget_size(hAttrNativeType));
szData = static_cast<char *>(CPLMalloc(nDataLen));
szValue = static_cast<char *>(CPLMalloc(MAX_METADATA_LEN));
szData[0] = '\0';
szValue[0] = '\0';
H5Aread(hAttrID, hAttrNativeType, buf);
}
if( H5Tequal(H5T_NATIVE_CHAR, hAttrNativeType ) ||
H5Tequal(H5T_NATIVE_SCHAR, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
snprintf(szData, nDataLen, "%c ", static_cast<char *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_UCHAR, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
snprintf(szData, nDataLen, "%c", static_cast<char *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_SHORT, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
snprintf(szData, nDataLen, "%d ", static_cast<short *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_USHORT, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
snprintf(szData, nDataLen, "%ud ",
static_cast<unsigned short *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_INT, hAttrNativeType) )
{
for( hsize_t i=0; i < nAttrElmts; i++ )
{
snprintf(szData, nDataLen, "%d ", static_cast<int *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_UINT, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
snprintf(szData, nDataLen, "%ud ",
static_cast<unsigned int *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_LONG, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
snprintf(szData, nDataLen, "%ld ", static_cast<long *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_ULONG, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ ) {
snprintf(szData, nDataLen, "%lu ",
static_cast<unsigned long *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_FLOAT, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
CPLsnprintf(szData, nDataLen, "%.8g ",
static_cast<float *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_DOUBLE, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
CPLsnprintf(szData, nDataLen, "%.15g ",
static_cast<double *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
CPLFree(buf);
}
H5Sclose(hAttrSpace);
H5Tclose(hAttrNativeType);
H5Tclose(hAttrTypeID);
H5Aclose(hAttrID);
poDS->papszMetadata = CSLSetNameValue(poDS->papszMetadata, osKey, szValue);
CPLFree(szData);
CPLFree(szValue);
return 0;
}
herr_t H5IMis_palette( hid_t loc_id,
const char *dset_name )
{
hid_t did;
int has_class;
hid_t atid;
hid_t aid = -1;
char* attr_data; /* Name of attribute */
hsize_t storage_size; /* Size of storage for attribute */
herr_t ret;
/* check the arguments */
if (dset_name == NULL)
return -1;
/* Assume initially fail condition */
ret = -1;
/* Open the dataset. */
if((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
return -1;
/* Try to find the attribute "CLASS" on the dataset */
has_class = H5LT_find_attribute(did, "CLASS");
if(has_class == 0)
{
H5Dclose( did );
return 0;
}
else if(has_class == 1)
{
if((aid = H5Aopen(did, "CLASS", H5P_DEFAULT)) < 0)
goto out;
if((atid = H5Aget_type(aid)) < 0)
goto out;
/* check to make sure attribute is a string */
if(H5T_STRING != H5Tget_class(atid))
goto out;
/* check to make sure string is null-terminated */
if(H5T_STR_NULLTERM != H5Tget_strpad(atid))
goto out;
/* allocate buffer large enough to hold string */
if((storage_size = H5Aget_storage_size(aid)) == 0)
goto out;
attr_data = (char*)HDmalloc( (size_t)storage_size * sizeof(char) + 1);
if(attr_data == NULL)
goto out;
if(H5Aread(aid, atid, attr_data) < 0)
goto out;
if(HDstrncmp(attr_data, PALETTE_CLASS, MIN(HDstrlen(PALETTE_CLASS),HDstrlen(attr_data))) == 0)
ret = 1;
else
ret = 0;
HDfree(attr_data);
if ( H5Tclose( atid ) < 0)
goto out;
if ( H5Aclose( aid ) < 0)
goto out;
}
/* Close the dataset. */
if ( H5Dclose( did ) < 0)
return -1;
return ret;
out:
H5Dclose( did );
return -1;
}
herr_t HDF5AttrIterate( hid_t hH5ObjID,
const char *pszAttrName,
void *pDS )
{
hid_t hAttrID;
hid_t hAttrTypeID;
hid_t hAttrNativeType;
hid_t hAttrSpace;
char *szData = NULL;
hsize_t nSize[64];
unsigned int nAttrElmts;
hsize_t nAttrSize;
hsize_t i;
void *buf = NULL;
unsigned int nAttrDims;
char **papszTokens;
HDF5Dataset *poDS;
CPLString osKey;
char *szValue = NULL;
poDS = (HDF5Dataset *) pDS;
// Convert "/" into "_" for the path component
const char* pszPath = poDS->poH5CurrentObject->pszUnderscorePath;
if(pszPath != NULL && strlen(pszPath) > 0)
{
papszTokens = CSLTokenizeString2( pszPath, "/", CSLT_HONOURSTRINGS );
for( i = 0; papszTokens != NULL && papszTokens[i] != NULL; ++i )
{
if( i != 0)
osKey += '_';
osKey += papszTokens[i];
}
CSLDestroy( papszTokens );
}
// Convert whitespaces into "_" for the attribute name component
papszTokens = CSLTokenizeString2( pszAttrName, " ",
CSLT_STRIPLEADSPACES | CSLT_STRIPENDSPACES );
for( i = 0; papszTokens != NULL && papszTokens[i] != NULL; ++i )
{
if(!osKey.empty())
osKey += '_';
osKey += papszTokens[i];
}
CSLDestroy( papszTokens );
hAttrID = H5Aopen_name( hH5ObjID, pszAttrName );
hAttrTypeID = H5Aget_type( hAttrID );
hAttrNativeType = H5Tget_native_type( hAttrTypeID, H5T_DIR_DEFAULT );
hAttrSpace = H5Aget_space( hAttrID );
nAttrDims = H5Sget_simple_extent_dims( hAttrSpace, nSize, NULL );
nAttrElmts = 1;
for( i=0; i < nAttrDims; i++ ) {
nAttrElmts *= (int) nSize[i];
}
if( H5Tget_class( hAttrNativeType ) == H5T_STRING )
{
if ( H5Tis_variable_str(hAttrNativeType) )
{
char** papszStrings;
papszStrings = (char**) CPLMalloc( nAttrElmts * sizeof(char*) );
// Read the values
H5Aread( hAttrID, hAttrNativeType, papszStrings );
// Concatenate all values as one string (separated by a space)
CPLString osVal = papszStrings[0];
for( i=1; i < nAttrElmts; i++ ) {
osVal += " ";
osVal += papszStrings[i];
}
szValue = (char*) CPLMalloc(osVal.length() + 1);
strcpy( szValue, osVal.c_str() );
H5Dvlen_reclaim( hAttrNativeType, hAttrSpace, H5P_DEFAULT,
papszStrings );
CPLFree( papszStrings );
}
else
{
nAttrSize = H5Aget_storage_size( hAttrID );
szValue = (char*) CPLMalloc((size_t) (nAttrSize+1));
H5Aread( hAttrID, hAttrNativeType, szValue );
szValue[nAttrSize] = '\0';
}
}
else {
if( nAttrElmts > 0 ) {
buf = (void *) CPLMalloc( nAttrElmts*
H5Tget_size( hAttrNativeType ));
szData = (char*) CPLMalloc( 8192 );
szValue = (char*) CPLMalloc( MAX_METADATA_LEN );
szData[0] = '\0';
szValue[0] ='\0';
H5Aread( hAttrID, hAttrNativeType, buf );
}
if( H5Tequal( H5T_NATIVE_CHAR, hAttrNativeType )
|| H5Tequal( H5T_NATIVE_SCHAR, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%c ", ((char *) buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_UCHAR, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%c", ((char *) buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_SHORT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%d ", ((short *) buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_USHORT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ud ", ((unsigned short *) buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_INT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%d ", ((int *) buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_UINT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ud ", ((unsigned int *) buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_LONG, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ld ", ((long *)buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_ULONG, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ld ", ((unsigned long *)buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_FLOAT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
CPLsprintf( szData, "%.8g ", ((float *)buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_DOUBLE, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
CPLsprintf( szData, "%.15g ", ((double *)buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
CPLFree( buf );
}
H5Sclose(hAttrSpace);
H5Tclose(hAttrNativeType);
H5Tclose(hAttrTypeID);
H5Aclose( hAttrID );
poDS->papszMetadata = CSLSetNameValue( poDS->papszMetadata, osKey, szValue);
CPLFree( szData );
CPLFree( szValue );
return 0;
}
// JRC: This fat interface may not scale? What about
// scalar attributes?
herr_t getAttributeHelper(const hid_t id, std::string* sval, std::vector<int>* ivals,
std::vector<float>* fvals) {
herr_t err = 0;
size_t npoints;
hid_t atype = H5Aget_type(id);
H5T_class_t type = H5Tget_class(atype);
hid_t aspace = H5Aget_space(id);
size_t rank = H5Sget_simple_extent_ndims(aspace);
/*
hsize_t sdim[rank];
ret = H5Sget_simple_extent_dims(aspace, sdim, NULL);
dims->resize(rank);
for (size_t i = 0; i < rank; ++i)
(*dims)[i] = sdim[i];
*/
if (type == H5T_INTEGER) {
if (rank == 0) {
ivals->resize(1);
int v;
// err = H5Aread(id, atype, &v);
err = H5Aread(id, H5T_NATIVE_INT, &v);
(*ivals)[0] = v;
return err;
}
// rank>0
npoints = H5Sget_simple_extent_npoints(aspace);
int* v = new int[npoints];
err = H5Aread(id, H5T_NATIVE_INT, v);
ivals->resize(npoints);
for (size_t i = 0; i<npoints; ++i) {
(*ivals)[i] = v[i];
}
delete v;
return err;
}
if (type == H5T_FLOAT) {
if (rank == 0) {
fvals->resize(1);
float v;
err = H5Aread(id, H5T_NATIVE_FLOAT, &v);
(*fvals)[0] = v;
return err;
}
// rank>0
npoints = H5Sget_simple_extent_npoints(aspace);
float* v = new float[npoints];
err = H5Aread(id, H5T_NATIVE_FLOAT, v);
fvals->resize(npoints);
for (size_t i = 0; i<npoints; ++i) {
(*fvals)[i] = v[i];
}
delete v;
return err;
}
if (type == H5T_STRING) {
if (rank != 0) {
return -1;
}
size_t len = H5Aget_storage_size(id);
sval->resize(len);
char* v = new char[len];
err = H5Aread(id, atype, v);
// JRC: is this right?
// err = H5Aread(id, H5T_NATIVE_CHAR, v);
for (size_t i = 0; i < len; ++i) {
(*sval)[i] = v[i];
}
delete [] v;
return err;
}
return err;
}
med_err _MEDattributeStringWr(med_idt pid,
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); 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( pid, attname,H5P_DEFAULT )) >= 0 )
if ( MED_ACCESS_MODE == MED_ACC_RDEXT ) {
MED_ERR_(_ret,MED_ERR_INVALID,MED_ERR_ACCESSMODE, "MED_ACC_RDEXT" );
SSCRUTE(attname); 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(pid,attname) < 0 ) goto ERROR;
_attmustbecreated=MED_TRUE;
}
}
if ( (_attid < 0) || _attmustbecreated )
if ( (_attid=H5Acreate( pid, attname, type_hdf, aid, H5P_DEFAULT )) < 0 ) {
MED_ERR_(_ret,MED_ERR_CREATE,MED_ERR_ATTRIBUTE, attname );
goto ERROR;
}
if ( H5Awrite(_attid,type_hdf,val) < 0) {
MED_ERR_(_ret,MED_ERR_WRITE,MED_ERR_ATTRIBUTE, attname );
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;
}
