Nektar::LibUtilities::PtsIO Class Reference

#include <PtsIO.h>

Inheritance diagram for Nektar::LibUtilities::PtsIO:

Collaboration diagram for Nektar::LibUtilities::PtsIO:

Public Member Functions
	PtsIO (LibUtilities::CommSharedPtr pComm, bool sharedFilesystem=false)
virtual	~PtsIO ()
void	Import (const string &inFile, PtsFieldSharedPtr &ptsField, FieldMetaDataMap &fieldmetadatamap=NullFieldMetaDataMap)
	Import a pts field from file. More...
void	Write (const string &outFile, const PtsFieldSharedPtr &ptsField, const bool backup=false)
	Save a pts field to a file. More...
void	ImportFieldData (TiXmlDocument docInput, PtsFieldSharedPtr &ptsField)
Public Member Functions inherited from Nektar::LibUtilities::FieldIOXml
	FieldIOXml (LibUtilities::CommSharedPtr pComm, bool sharedFilesystem)
	Default constructor. More...
virtual	~FieldIOXml ()
void	ImportFieldDefs (DataSourceSharedPtr dataSource, std::vector< FieldDefinitionsSharedPtr > &fielddefs, bool expChild)
	Import field definitions from the target file. More...
void	ImportFieldData (DataSourceSharedPtr dataSource, const std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata)
	Import field data from a target file. More...
void	WriteMultiFldFileIDs (const std::string &outfile, const std::vector< std::string > fileNames, std::vector< std::vector< unsigned int > > &elementList, const FieldMetaDataMap &fieldinfomap=NullFieldMetaDataMap)
	Write out a file containing element ID to partition mapping. More...
void	SetUpFieldMetaData (const std::string &outname, const std::vector< FieldDefinitionsSharedPtr > &fielddefs, const FieldMetaDataMap &fieldmetadatamap)
	Set up field meta data map. More...
void	ImportMultiFldFileIDs (const std::string &inFile, std::vector< std::string > &fileNames, std::vector< std::vector< unsigned int > > &elementList, FieldMetaDataMap &fieldmetadatamap)
	Read file containing element ID to partition mapping. More...
void	v_Import (const std::string &infilename, std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata=NullVectorNekDoubleVector, FieldMetaDataMap &fieldinfomap=NullFieldMetaDataMap, const Array< OneD, int > &ElementIDs=NullInt1DArray)
	Import an XML format file. More...
virtual const std::string &	GetClassName () const
	Returns the class name. More...
Public Member Functions inherited from Nektar::LibUtilities::FieldIO
	FieldIO (LibUtilities::CommSharedPtr pComm, bool sharedFilesystem)
	Constructor for FieldIO base class. More...
virtual	~FieldIO ()
void	Write (const std::string &outFile, std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata, const FieldMetaDataMap &fieldinfomap=NullFieldMetaDataMap, const bool backup=false)
	Write out the field information to the file outFile. More...
void	Import (const std::string &infilename, std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata=NullVectorNekDoubleVector, FieldMetaDataMap &fieldinfomap=NullFieldMetaDataMap, const Array< OneD, int > &ElementIDs=NullInt1DArray)
	Read field information from the file infilename. More...
DataSourceSharedPtr	ImportFieldMetaData (const std::string &filename, FieldMetaDataMap &fieldmetadatamap)
	Import the metadata from a field file. More...

Protected Member Functions
void	SetUpFieldMetaData (const std::string outname)
virtual std::string	GetFileEnding () const
	Helper function that determines default file extension. More...
Protected Member Functions inherited from Nektar::LibUtilities::FieldIO
void	AddInfoTag (TagWriterSharedPtr root, const FieldMetaDataMap &fieldmetadatamap)
	Add provenance information to the field metadata map. More...
int	CheckFieldDefinition (const FieldDefinitionsSharedPtr &fielddefs)
	Check field definitions for correctness and return storage size. More...
std::string	SetUpOutput (const std::string outname, bool perRank, bool backup=false)
	Set up the filesystem ready for output. More...

Additional Inherited Members
Static Public Member Functions inherited from Nektar::LibUtilities::FieldIOXml
static FieldIOSharedPtr	create (LibUtilities::CommSharedPtr pComm, bool sharedFilesystem)
	Creates an instance of this class. More...
Static Public Member Functions inherited from Nektar::LibUtilities::FieldIO
static const std::string	GetFileType (const std::string &filename, CommSharedPtr comm)
	Determine file type of given input file. More...
static boost::shared_ptr< FieldIO >	CreateDefault (const LibUtilities::SessionReaderSharedPtr session)
	Returns an object for the default FieldIO method. More...
static boost::shared_ptr< FieldIO >	CreateForFile (const LibUtilities::SessionReaderSharedPtr session, const std::string &filename)
	Construct a FieldIO object for a given input filename. More...
Static Public Attributes inherited from Nektar::LibUtilities::FieldIOXml
static std::string	className
	Name of class. More...
Protected Attributes inherited from Nektar::LibUtilities::FieldIO
LibUtilities::CommSharedPtr	m_comm
	Communicator to use when writing parallel format. More...
bool	m_sharedFilesystem
	Boolean dictating whether we are on a shared filesystem. More...

Detailed Description

Definition at line 64 of file PtsIO.h.

Constructor & Destructor Documentation

Nektar::LibUtilities::PtsIO::PtsIO	(	LibUtilities::CommSharedPtr	pComm,
		bool	sharedFilesystem = false
	)

Definition at line 58 of file PtsIO.cpp.

    : FieldIOXml(pComm, sharedFilesystem)
{
}

virtual Nektar::LibUtilities::PtsIO::~PtsIO ( )

inlinevirtual

Definition at line 70 of file PtsIO.h.

    {
    }

Member Function Documentation

virtual std::string Nektar::LibUtilities::PtsIO::GetFileEnding ( ) const

inlineprotectedvirtual

Helper function that determines default file extension.

Reimplemented from Nektar::LibUtilities::FieldIO.

Definition at line 89 of file PtsIO.h.

Referenced by Import(), and SetUpFieldMetaData().

    {
        return "pts";
    };

void Nektar::LibUtilities::PtsIO::Import	(	const string &	inFile,
		PtsFieldSharedPtr &	ptsField,
		FieldMetaDataMap &	fieldmetadatamap = NullFieldMetaDataMap
	)

Import a pts field from file.

Parameters

inFile	filename of the file to read
ptsField	the resulting pts field.

Definition at line 69 of file PtsIO.cpp.

References ASSERTL0, CellMLToNektar.pycml::format, GetFileEnding(), ImportFieldData(), Nektar::LibUtilities::FieldIO::ImportFieldMetaData(), Nektar::LibUtilities::FieldIOXml::ImportMultiFldFileIDs(), Nektar::LibUtilities::FieldIO::m_comm, and Nektar::LibUtilities::PortablePath().

Referenced by Nektar::SolverUtils::EquationSystem::LoadPts().

{
    std::string infile = inFile;

    fs::path pinfilename(infile);

    // check to see that infile is a directory
    if (fs::is_directory(pinfilename))
    {
        fs::path infofile("Info.xml");
        fs::path fullpath = pinfilename / infofile;
        infile = PortablePath(fullpath);

        std::vector<std::string> filenames;
        std::vector<std::vector<unsigned int> > elementIDs_OnPartitions;

        ImportMultiFldFileIDs(
            infile, filenames, elementIDs_OnPartitions, fieldmetadatamap);

        // Load metadata
        ImportFieldMetaData(infile, fieldmetadatamap);

        if (filenames.size() == m_comm->GetSize())
        {
        // only load the file that matches this rank
            filenames.clear();
            boost::format pad("P%1$07d.%2$s");
            pad % m_comm->GetRank() % GetFileEnding();
            filenames.push_back(pad.str());
        }

        for (int i = 0; i < filenames.size(); ++i)
        {
            fs::path pfilename(filenames[i]);
            fullpath = pinfilename / pfilename;
            string fname = PortablePath(fullpath);

            TiXmlDocument doc1(fname);
            bool loadOkay1 = doc1.LoadFile();

            std::stringstream errstr;
            errstr << "Unable to load file: " << fname << std::endl;
            errstr << "Reason: " << doc1.ErrorDesc() << std::endl;
            errstr << "Position: Line " << doc1.ErrorRow() << ", Column "
                   << doc1.ErrorCol() << std::endl;
            ASSERTL0(loadOkay1, errstr.str());

            if (i == 0)
            {
                ImportFieldData(doc1, ptsField);
            }
            else
            {
                LibUtilities::PtsFieldSharedPtr newPtsField;
                ImportFieldData(doc1, newPtsField);
                Array<OneD, Array<OneD, NekDouble> > pts;
                newPtsField->GetPts(pts);
                ptsField->AddPoints(pts);
            }

        }
    }
    else
    {
        TiXmlDocument doc(infile);
        bool loadOkay = doc.LoadFile();

        std::stringstream errstr;
        errstr << "Unable to load file: " << infile << std::endl;
        errstr << "Reason: " << doc.ErrorDesc() << std::endl;
        errstr << "Position: Line " << doc.ErrorRow() << ", Column "
               << doc.ErrorCol() << std::endl;
        ASSERTL0(loadOkay, errstr.str());

        ImportFieldData(doc, ptsField);
    }
}

void Nektar::LibUtilities::PtsIO::ImportFieldData	(	TiXmlDocument	docInput,
		PtsFieldSharedPtr &	ptsField
	)

Definition at line 232 of file PtsIO.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, Nektar::LibUtilities::eIsEquiSpacedData, Nektar::LibUtilities::ePtsPerElmtEdge, Nektar::ParseUtils::GenerateOrderedStringVector(), npts, and Nektar::LibUtilities::NullPtsInfoMap.

Referenced by Import().

{
    TiXmlElement *nektar = docInput.FirstChildElement("NEKTAR");
    TiXmlElement *points = nektar->FirstChildElement("POINTS");
    int dim;
    int err = points->QueryIntAttribute("DIM", &dim);

    ASSERTL0(err == TIXML_SUCCESS, "Unable to read attribute DIM.");

    std::string fields = points->Attribute("FIELDS");

    vector<string> fieldNames;
    if (!fields.empty())
    {
        bool valid =
            ParseUtils::GenerateOrderedStringVector(fields.c_str(), fieldNames);
        ASSERTL0(
            valid,
            "Unable to process list of field variable in  FIELDS attribute:  " +
                fields);
    }

    map<PtsInfo,int>  ptsInfo = NullPtsInfoMap;

    const char *ptinfo = points->Attribute("PTSINFO");
    if(ptinfo&&boost::iequals(ptinfo,"EquiSpaced"))
    {
        ptsInfo[eIsEquiSpacedData] = 1;
    }

    int np;
    err = points->QueryIntAttribute("PTSPERELMTEDGE",&np);
    if(err == TIXML_SUCCESS)
    {
        ptsInfo[ePtsPerElmtEdge] = np; 
    }

    int nfields = fieldNames.size();
    int totvars = dim + nfields;

    TiXmlNode *pointsBody = points->FirstChild();

    std::istringstream pointsDataStrm(pointsBody->ToText()->Value());

    vector<NekDouble> ptsSerial;
    Array<OneD, Array<OneD, NekDouble> > pts(totvars);

    try
    {
        NekDouble ptsStream;
        while (!pointsDataStrm.fail())
        {
            pointsDataStrm >> ptsStream;

            ptsSerial.push_back(ptsStream);
        }
    }
    catch (...)
    {
        ASSERTL0(false, "Unable to read Points data.");
    }

    int npts = ptsSerial.size() / totvars;

    for (int i = 0; i < totvars; ++i)
    {
        pts[i] = Array<OneD, NekDouble>(npts);
    }

    for (int i = 0; i < npts; ++i)
    {
        for (int j = 0; j < totvars; ++j)
        {
            pts[j][i] = ptsSerial[i * totvars + j];
        }
    }

    ptsField = MemoryManager<PtsField>::AllocateSharedPtr(dim, fieldNames, pts, ptsInfo);
}

void Nektar::LibUtilities::PtsIO::SetUpFieldMetaData ( const std::string  outname )

protected

Definition at line 312 of file PtsIO.cpp.

References ASSERTL0, CellMLToNektar.pycml::format, GetFileEnding(), Nektar::LibUtilities::FieldIO::m_comm, Nektar::LibUtilities::PortablePath(), and Nektar::LibUtilities::FieldIOXml::WriteMultiFldFileIDs().

Referenced by Write().

{
    ASSERTL0(!outname.empty(), "Empty path given to SetUpFieldMetaData()");

    int nprocs = m_comm->GetSize();
    int rank = m_comm->GetRank();

    fs::path specPath(outname);

    // Collate per-process element lists on root process to generate
    // the info file.
    if (rank == 0)
    {
        // Set up output names
        std::vector<std::string> filenames;
        std::vector<std::vector<unsigned int> > ElementIDs;
        for (int i = 0; i < nprocs; ++i)
        {
            boost::format pad("P%1$07d.%2$s");
            pad % i % GetFileEnding();
            filenames.push_back(pad.str());

            std::vector<unsigned int> tmp;
            tmp.push_back(0);
            ElementIDs.push_back(tmp);
        }

        // Write the Info.xml file
        string infofile =
            LibUtilities::PortablePath(specPath / fs::path("Info.xml"));

        cout << "Writing: " << specPath << endl;

        const FieldMetaDataMap fieldmetadatamap;
        WriteMultiFldFileIDs(infofile, filenames, ElementIDs, fieldmetadatamap);
    }
}

void Nektar::LibUtilities::PtsIO::Write	(	const string &	outFile,
		const PtsFieldSharedPtr &	ptsField,
		const bool	backup = false
	)

Save a pts field to a file.

Parameters

outFile	filename of the file
ptsField	the pts field

Definition at line 155 of file PtsIO.cpp.

References SetUpFieldMetaData(), and Nektar::LibUtilities::FieldIO::SetUpOutput().

Referenced by Nektar::FieldUtils::OutputPts::Process().

{
    int nTotvars = ptsField->GetNFields() + ptsField->GetDim();
    int np = ptsField->GetNpoints();

    std::string filename = SetUpOutput(outFile, true, backup);
    SetUpFieldMetaData(outFile);

    // until tinyxml gains support for line break, write the xml manually
    std::ofstream ptsFile;
    ptsFile.open(filename.c_str());

    ptsFile << "<?xml version=\"1.0\" encoding=\"utf-8\" ?>" << endl;
    ptsFile << "<NEKTAR>" << endl;
    ptsFile << "  <POINTS ";
    ptsFile << "DIM=\"" << ptsField->GetDim() << "\" ";
    string fn = boost::algorithm::join(ptsField->GetFieldNames(), ",");
    ptsFile << "FIELDS=\"" << fn << "\" ";
    ptsFile << ">" << endl;

    Array<OneD, Array<OneD, NekDouble> > pts;
    ptsField->GetPts(pts);
    for (int i = 0; i < np; ++i)
    {
        ptsFile << "    ";
        ptsFile << pts[0][i];
        for (int j = 1; j < nTotvars; ++j)
        {
            ptsFile << " " << pts[j][i];
        }
        ptsFile << endl;
    }
    ptsFile << "  </POINTS>" << endl;
    ptsFile << "</NEKTAR>" << endl;

    ptsFile.close();

    // this is what the above cpart would read if tinyxml
    // supported line breaks
    /*
    // Create the file (partition)
    TiXmlDocument doc;
    TiXmlDeclaration *decl = new TiXmlDeclaration("1.0", "utf-8", "");
    doc.LinkEndChild(decl);

    TiXmlElement *root = new TiXmlElement("NEKTAR");
    doc.LinkEndChild(root);

    TiXmlElement *pointsTag = new TiXmlElement("POINTS");
    root->LinkEndChild(pointsTag);

    pointsTag->SetAttribute("DIM", ptsField->GetDim());

    string fn = boost::algorithm::join(ptsField->GetFieldNames(), ",");
    pointsTag->SetAttribute("FIELDS", fn);

    Array <OneD, Array <OneD, NekDouble > > pts;
    ptsField->GetPts(pts);
    ostringstream os;
    for (int i = 0; i < np; ++i)
    {
        os << pts[0][i];
        for (int j = 1; j < nTotvars; ++j)
        {
            os << " " << pts[j][i];
        }
        os << " ";
    }

    pointsTag->LinkEndChild(new TiXmlText(os.str()));

    doc.SaveFile(filename);
    */
}