// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void VoxelDataContainerWriter::execute()
{
int err = 0;
std::stringstream ss;
setErrorCondition(err);
VoxelDataContainer* m = getVoxelDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The Voxel DataContainer Object was NULL", -999);
return;
}
setErrorCondition(0);
dataCheck(false, 1, 1, 1);
hid_t dcGid = -1;
// Create the HDF5 Group for the Data Container
err = H5Utilities::createGroupsFromPath(DREAM3D::HDF5::VoxelDataContainerName.c_str(), m_HdfFileId);
if (err < 0)
{
ss.str("");
ss << "Error creating HDF Group " << DREAM3D::HDF5::VoxelDataContainerName << std::endl;
setErrorCondition(-60);
notifyErrorMessage( ss.str(), err);
return;
}
dcGid = H5Gopen(m_HdfFileId, DREAM3D::HDF5::VoxelDataContainerName.c_str(), H5P_DEFAULT );
if (dcGid < 0)
{
ss.str("");
ss << "Error opening Group " << DREAM3D::HDF5::VoxelDataContainerName << std::endl;
setErrorCondition(-61);
notifyErrorMessage( ss.str(), err);
return;
}
// This just writes the header information
int64_t volDims[3] =
{ m->getXPoints(), m->getYPoints(), m->getZPoints() };
float spacing[3] =
{ m->getXRes(), m->getYRes(), m->getZRes() };
float origin[3] =
{ 0.0f, 0.0f, 0.0f };
m->getOrigin(origin);
err = writeMetaInfo(DREAM3D::HDF5::VoxelDataContainerName, volDims, spacing, origin);
if (err < 0)
{
ss.str("");
ss << ":Error Writing header information to output file" << std::endl;
setErrorCondition(-62);
notifyErrorMessage( ss.str(), err);
H5Gclose(dcGid); // Close the Data Container Group
return;
}
err = writeVertexData(dcGid);
if (err < 0)
{
H5Gclose(dcGid); // Close the Data Container Group
return;
}
err = writeEdgeData(dcGid);
if (err < 0)
{
H5Gclose(dcGid); // Close the Data Container Group
return;
}
err = writeFaceData(dcGid);
if (err < 0)
{
H5Gclose(dcGid); // Close the Data Container Group
return;
}
err = writeCellData(dcGid);
if (err < 0)
{
H5Gclose(dcGid); // Close the Data Container Group
return;
}
err = writeFieldData(dcGid);
if (err < 0)
{
H5Gclose(dcGid); // Close the Data Container Group
return;
}
err = writeEnsembleData(dcGid);
if (err < 0)
{
H5Gclose(dcGid); // Close the Data Container Group
return;
}
// Now finally close the group and the HDf5 File
H5Gclose(dcGid); // Close the Data Container Group
notifyStatusMessage("Complete");
}
/*!
* Writes data only in VTK file
*/
void VTK::writeData( ){
std::fstream str ;
std::fstream::pos_type position_insert, position_eof ;
int length;
char* buffer ;
str.open( fh.getPath( ), std::ios::in | std::ios::out ) ;
{ // Write Ascii
position_insert = str.tellg();
VTKField temp ;
//Writing first point data then cell data
for( auto &field : data ){
if( field->getCodification() == VTKFormat::ASCII && field->getLocation() == VTKLocation::POINT ) {
str.seekg( position_insert);
readDataArray( str, *field ) ;
str.seekg( field->getPosition() ) ;
genericIO::copyUntilEOFInString( str, buffer, length );
writeFieldData( str, *field) ;
position_insert = str.tellg();
str << std::endl ;
genericIO::flushBINARY( str, buffer, length) ;
delete [] buffer ;
};
};
for( auto &field : data ){
if( field->getCodification() == VTKFormat::ASCII && field->getLocation() == VTKLocation::CELL ) {
str.seekg( position_insert);
readDataArray( str, *field ) ;
str.seekg( field->getPosition() ) ;
genericIO::copyUntilEOFInString( str, buffer, length );
writeFieldData( str, *field) ;
position_insert = str.tellg();
str << std::endl ;
genericIO::flushBINARY( str, buffer, length) ;
delete [] buffer ;
};
};
for( auto &field : geometry ){
if( field->getCodification() == VTKFormat::ASCII ) {
str.seekg( position_insert);
readDataArray( str, *field ) ;
str.seekg( field->getPosition() ) ;
genericIO::copyUntilEOFInString( str, buffer, length );
writeFieldData( str, *field) ;
//flushData( str, VTKFormat::ASCII, field.getName() ) ;
position_insert = str.tellg();
str << std::endl ;
genericIO::flushBINARY( str, buffer, length) ;
delete [] buffer ;
};
};
str.seekg( temp.getPosition() ) ;
}
{ // Write Appended
char c_;
std::string line ;
std::fstream::pos_type position_appended ;
//Go to the initial position of the appended section
while( getline(str, line) && (! bitpit::utils::keywordInString( line, "<AppendedData")) ){} ;
str >> c_;
while( c_ != '_') str >> c_;
position_insert = str.tellg();
genericIO::copyUntilEOFInString( str, buffer, length );
str.close();
str.clear();
//Reopening in binary mode
str.open( fh.getPath( ), std::ios::out | std::ios::in | std::ios::binary);
str.seekg( position_insert) ;
//str.open( "data.dat", std::ios::out | std::ios::binary);
//Writing first point data then cell data
for( auto &field : data ){
if( field->getCodification() == VTKFormat::APPENDED && field->getLocation() == VTKLocation::POINT ) {
if( getHeaderType() == "UInt32"){
uint32_t nbytes = field->getNbytes() ;
genericIO::flushBINARY(str, nbytes) ;
}
else{
uint64_t nbytes = field->getNbytes() ;
genericIO::flushBINARY(str, nbytes) ;
};
writeFieldData( str, *field) ;
};
}
for( auto &field : data ){
if( field->getCodification() == VTKFormat::APPENDED && field->getLocation() == VTKLocation::CELL ) {
if( getHeaderType() == "UInt32"){
uint32_t nbytes = field->getNbytes() ;
genericIO::flushBINARY(str, nbytes) ;
}
else{
uint64_t nbytes = field->getNbytes() ;
genericIO::flushBINARY(str, nbytes) ;
};
writeFieldData( str, *field) ;
};
}
//Writing Geometry Data
for( auto &field : geometry ){
if( field->getCodification() == VTKFormat::APPENDED ) {
if( getHeaderType() == "UInt32"){
uint32_t nbytes = field->getNbytes() ;
genericIO::flushBINARY(str, nbytes) ;
}
else{
uint64_t nbytes = field->getNbytes() ;
genericIO::flushBINARY(str, nbytes) ;
};
writeFieldData( str, *field) ;
};
};
//{
//std::fstream str2 ;
//str2.open( "test2.dat", std::ios::out | std::ios::binary);
//genericIO::flushBINARY( str2, buffer, length) ;
//str2.close();
//}
genericIO::flushBINARY( str, buffer, length) ;
delete [] buffer ;
};
// Closing Appended Secyion
str.close();
return ;
};
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SurfaceMeshDataContainerWriter::execute()
{
int err = 0;
std::stringstream ss;
setErrorCondition(err);
SurfaceMeshDataContainer* sm = getSurfaceMeshDataContainer();
if(NULL == sm)
{
setErrorCondition(-999);
notifyErrorMessage("The Surfacemesh DataContainer Object was NULL", -999);
return;
}
setErrorCondition(0);
// Create the HDF5 Group for the Data Container
err = H5Utilities::createGroupsFromPath(DREAM3D::HDF5::SurfaceMeshDataContainerName.c_str(), m_HdfFileId);
if (err < 0)
{
ss.str("");
ss << "Error creating HDF Group " << DREAM3D::HDF5::SurfaceMeshDataContainerName << std::endl;
setErrorCondition(-60);
addErrorMessage(getHumanLabel(), ss.str(), err);
return;
}
hid_t dcGid = H5Gopen(m_HdfFileId, DREAM3D::HDF5::SurfaceMeshDataContainerName.c_str(), H5P_DEFAULT );
if (dcGid < 0)
{
ss.str("");
ss << "Error opening Group " << DREAM3D::HDF5::SurfaceMeshDataContainerName << std::endl;
setErrorCondition(-61);
addErrorMessage(getHumanLabel(), ss.str(), err);
return;
}
// Add some VTK hints into the group
err = createVtkObjectGroup(DREAM3D::HDF5::SurfaceMeshDataContainerName, H5_VTK_POLYDATA);
if (err < 0) {
return;
}
writeXdmfGridHeader();
H5GroupAutoCloser dcGidAutoCloser(&dcGid);
err = writeVertices(dcGid);
if (err < 0)
{
return;
}
err = writeMeshVertLinks(dcGid);
if (err < 0)
{
return;
}
err = writeVertexAttributeData(dcGid);
if (err < 0)
{
return;
}
err = writeFaces(dcGid);
if (err < 0)
{
return;
}
err = writeMeshFaceNeighborLists(dcGid);
if (err < 0)
{
return;
}
err = writeFaceAttributeData(dcGid);
if (err < 0)
{
return;
}
err = writeEdges(dcGid);
if (err < 0)
{
return;
}
err = writeEdgeAttributeData(dcGid);
if (err < 0)
{
return;
}
err = writeFieldData(dcGid);
if (err < 0)
{
H5Gclose(dcGid); // Close the Data Container Group
return;
}
err = writeEnsembleData(dcGid);
if (err < 0)
{
H5Gclose(dcGid); // Close the Data Container Group
return;
}
// Now finally close the group and the HDf5 File
H5Gclose(dcGid); // Close the Data Container Group
dcGid = -1;
writeXdmfGridFooter();
notifyStatusMessage("Complete");
}
