H5::DataSet CompartmentReportHDF5::_openDataset( const H5::H5File& file,
const uint32_t cellID )
{
std::stringstream cellName;
cellName << "a" << cellID;
const std::string datasetName = "/" + cellName.str() + "/" + _reportName +
"/" + dataDatasetName;
H5::DataSet dataset;
H5E_BEGIN_TRY
dataset = file.openDataSet( datasetName );
H5E_END_TRY
if( !dataset.getId() )
{
LBTHROW(
std::runtime_error( "ReportReaderHDF5: "
"Dataset " + datasetName + " not found "
"in file: " + file.getFileName( )));
}
if( dataset.getSpace().getSimpleExtentNdims() != 2 )
{
LBTHROW(
std::runtime_error("Compartment_Report_HDF5_File_Reader: "
"Error, not 2 dimensional array on " +
datasetName));
}
return dataset;
}
H5RandomReader::H5RandomReader(const std::string fileName, const std::string groupPath) throw (InvalidFileException) {
try {
file.openFile(fileName, H5F_ACC_RDONLY);}
catch ( H5::FileIException ) {
throw InvalidFileException("Cannot acces file");}
try {
group = file.openGroup(groupPath);}
catch ( H5::GroupIException ) {
file.close();
throw InvalidFileException("Cannot access group");}
/*
* extract timeline. This is also necessary to get the nbSteps.
*/
try {
timeline = group.openDataSet("timeline");
nSteps = timeline.getSpace().getSimpleExtentNpoints();}
catch ( H5::DataSetIException error ) {
//error.printError();
group.close();
file.close();
throw InvalidFileException("Cannot access timeline dataset");}
if (logging::info)
std::cerr << "Opened group \"" << fileName << groupPath << "\" which has " << nSteps << " steps.\n";
/*
* extract objects names in the xpGroup
*/
std::vector<std::string> names;
H5Literate(group.getId(), H5_INDEX_NAME, H5_ITER_INC, NULL, iterInGroup, &names);
/*
* extract data from object in xpGroup
* these data can be of 3 types: matrix, translate or wrench
* each data are saved in related map
*/
for (unsigned int i=0; i<names.size(); i++){ //TODO: skip timeline
H5::DataSet dSet = group.openDataSet(names[i]);
if (H5Aexists(dSet.getId(), "ArborisViewerType")) {
H5::Attribute att = dSet.openAttribute("ArborisViewerType");
std::string type;
att.read(att.getDataType(), type);
if (type == "matrix"){
H5::DataSpace dSpace = dSet.getSpace();
bool dimension_ok = false;
if (dSpace.getSimpleExtentNdims()==3) {
hsize_t dims[3];
dSpace.getSimpleExtentDims (dims);
if (dims[0] == nSteps && dims[1] == 4 && dims[2] == 4)
dimension_ok = true;}
if (dimension_ok)
matrices[names[i]] = dSet;
else {
if (logging::warning)
std::cerr << "Skipping dataset \"" << names[i] << "\" which has wrong dimensions. I was expecting (" << nSteps << ",4,4).\n";
dSet.close();}}
else if (type == "translate"){
H5::DataSpace dSpace = dSet.getSpace();
bool dimension_ok = false;
if (dSpace.getSimpleExtentNdims()==2) {
hsize_t dims[2];
dSpace.getSimpleExtentDims (dims);
if (dims[0] == nSteps && dims[1] == 3)
dimension_ok = true;}
if (dimension_ok)
translates[names[i]] = dSet;
else {
if (logging::warning)
std::cerr << "Skipping dataset \"" << names[i] << "\" which has wrong dimensions. I was expecting (" << nSteps << ",3).\n";
dSet.close();}}
else if (type == "wrench") {
H5::DataSpace dSpace = dSet.getSpace();
bool dimension_ok = false;
if (dSpace.getSimpleExtentNdims()==2) {
hsize_t dims[2];
dSpace.getSimpleExtentDims (dims);
if (dims[0] == nSteps && dims[1] == 6)
dimension_ok = true;}
if (dimension_ok)
wrenches[names[i]] = dSet;
else {
if (logging::warning)
std::cerr << "Skipping dataset \"" << names[i] << "\" which as wrong dimensions. I was expecting (" << nSteps << ",6).\n";
dSet.close();}}
else {
if (logging::warning)
std::cerr << "Skipping dataset \"" << names[i] << "\" whose ArborisViewerType attribute as unknown value \"" << type << "\".\n";
dSet.close();}
att.close();
}
else {
if (logging::info)
std::cerr << "Skipping dataset \"" << names[i] << "\" which has no ArborisViewerType attribute.\n";
dSet.close();
}
}
};
void ossim_hdf5::printObject( H5::H5File* file,
const std::string& objectName,
const std::string& prefix,
std::ostream& out )
{
#if 0
std::cout << "printObject entered..."
<< "\nobjectName: " << objectName
<< "\nprefix: " << prefix
<< std::endl;
#endif
H5::DataSet dataset = file->openDataSet( objectName );
// Get the class of the datatype that is used by the dataset.
H5T_class_t type_class = dataset.getTypeClass();
out << prefix << ".class_type: "
<< ossim_hdf5::getDatatypeClassType( type_class ) << std::endl;
const ossim_uint32 ATTRS_COUNT = dataset.getNumAttrs();
for ( ossim_uint32 aIdx = 0; aIdx < ATTRS_COUNT; ++aIdx )
{
H5::Attribute attr = dataset.openAttribute( aIdx );
ossim_hdf5::printAttribute( attr, prefix, out );
attr.close();
}
// Extents:
std::vector<ossim_uint32> extents;
ossim_hdf5::getExtents( &dataset, extents );
for ( ossim_uint32 i = 0; i < extents.size(); ++i )
{
ossimString os;
std::string exStr = ".extent";
exStr += os.toString(i).string();
out << prefix << exStr << ": " << extents[i] << std::endl;
}
// ossimScalarType scalar = getScalarType( type_class, dataset.getId() );
ossimScalarType scalar = ossim_hdf5::getScalarType( dataset.getId() );
if ( scalar != OSSIM_SCALAR_UNKNOWN)
{
out << prefix << "." << ossimKeywordNames::SCALAR_TYPE_KW << ": "
<< ossimScalarTypeLut::instance()->getEntryString( scalar ) << std::endl;
if ( ossim::scalarSizeInBytes( scalar ) > 1 )
{
ossimByteOrder byteOrder = ossim_hdf5::getByteOrder( &dataset );
std::string byteOrderString = "little_endian";
if ( byteOrder == OSSIM_BIG_ENDIAN )
{
byteOrderString = "big_endian";
}
out << prefix << "." <<ossimKeywordNames::BYTE_ORDER_KW << ": "
<< byteOrderString << std::endl;
}
}
#if 0
// Attributes:
int numberOfAttrs = dataset.getNumAttrs();
cout << "numberOfAttrs: " << numberOfAttrs << endl;
for ( ossim_int32 attrIdx = 0; attrIdx < numberOfAttrs; ++attrIdx )
{
H5::Attribute attribute = dataset.openAttribute( attrIdx );
cout << "attribute.from class: " << attribute.fromClass() << endl;
}
#endif
dataset.close();
} // End: printObject