XdmfWriter Class Reference

#include <xdmfwriter.h>

Collaboration diagram for XdmfWriter:

[legend]

List of all members.

Classes
struct	comp
Public Member Functions
	XdmfWriter ()
void	writeXdmf (std::string hdf5FileName)
	~XdmfWriter ()
Protected Types
typedef std::map< std::string, StringList, comp >	TimexDataSets
typedef __gnu_cxx::hash_map < std::string, TimexDataSets, StringHashFun, struct eqstr >	MeshxTimexDataSets
Protected Member Functions
void	printData ()
void	write_grid (std::ofstream &out, std::string tria)
void	write_grid_info (xmlwriter &out, std::string tria)
void	write_grid_reference (xmlwriter &out, std::string gridName, unsigned infoNumber)
void	write_temporal_grid_collection (xmlwriter &out, std::string tria)
void	write_dataset (xmlwriter &out, std::string dataset, std::string datasetName)
void	write_time_list (xmlwriter &out, StringList times)
void	write_time (xmlwriter &xml, std::string times)
Protected Attributes
MeshxTimexDataSets	m_map
Private Attributes
HDF5Reader	h5Reader

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Detailed Description

Definition at line 12 of file xdmfwriter.h.

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Member Typedef Documentation

typedef __gnu_cxx::hash_map<std::string,TimexDataSets,StringHashFun,struct eqstr> XdmfWriter::MeshxTimexDataSets [protected]

Definition at line 33 of file xdmfwriter.h.

typedef std::map<std::string,StringList,comp> XdmfWriter::TimexDataSets [protected]

Definition at line 30 of file xdmfwriter.h.

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Constructor & Destructor Documentation

XdmfWriter::XdmfWriter

(

)

Definition at line 6 of file xdmfwriter.cpp.

{
  
}

XdmfWriter::~XdmfWriter

(

)

[inline]

Definition at line 49 of file xdmfwriter.h.

{}

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Member Function Documentation

void XdmfWriter::printData

(

)

[protected]

Definition at line 95 of file xdmfwriter.cpp.

{
  for (MeshxTimexDataSets::iterator it= m_map.begin();it!=m_map.end();it++)
  {
    for (TimexDataSets::iterator it2=it->second.begin();it2!=it->second.end();it2++)
      for (StringList::iterator it3=it2->second.begin();it3!=it2->second.end();it3++)
        std::cout << it->first << "  " << it2->first << "  " << *it3 << std::endl;
  }
}

void XdmfWriter::write_dataset	(	xmlwriter &	out,
		std::string	dataset,
		std::string	datasetName
	)			[protected]

Definition at line 210 of file xdmfwriter.cpp.

{
   VecIndex datasetDims=h5Reader.getDataSetDim(dataset);
   assert(datasetDims.size() == 1);
   xml.AddAttributes("Name",datasetName);
   xml.AddAttributes("Center","Node");
   xml.CreateTag("Attribute");
   
   xml.AddAttributes("Format","HDF");
   xml.AddAttributes("DataType","Float");
   xml.AddAttributes("Precision","8");
   xml.AddAttributes("Dimensions",to_string(datasetDims[0]));
   xml.CreateChild("DataItem",h5Reader.getFileName()+":" +dataset);
   xml.CloseTag("Attribute");
}

void XdmfWriter::write_grid	(	std::ofstream &	out,
		std::string	tria
	)			[protected]

Definition at line 106 of file xdmfwriter.cpp.

{
  std::string path="/Triangulations/" + tria;
  std::string connections=path+"/connections";
  std::string vertices=path+"/vertices";
  VecIndex conDims=h5Reader.getDataSetDim(connections);
  VecIndex vertDims=h5Reader.getDataSetDim(vertices);

  assert(conDims[1] == 8);
  assert(vertDims[1] == 3);

  char str[10000];

  
  
  sprintf(str,"\
<Topology TopologyType=\"Tetrahedron\"  Order=\"0 1 3 2 4 5 7 6\" NumberOfElements=\"%d\">\n\
   <DataItem ItemType=\"Uniform\"   Format=\"HDF\"   NumberType=\"Int\"   Dimensions=\"%d 8\">\n\
   %s\n\
   </DataItem>\n\
</Topology>\n\
<Geometry GeometryType=\"XYZ\">\n\
  <DataItem ItemType=\"Uniform\"   Format=\"HDF\"   NumberType=\"Float\"  Precision=\"8\"  Dimensions=\"%d 3\">\n\
    %s\n\
  </DataItem>\n\
</Geometry>\n",conDims[0],conDims[0],connections.c_str(),vertDims[0],vertices.c_str()); 
  out << str;   

  
}

void XdmfWriter::write_grid_info	(	xmlwriter &	out,
		std::string	tria
	)			[protected]

Definition at line 138 of file xdmfwriter.cpp.

{
  std::string path="/Triangulations/" + tria;
  std::string connections=path+"/connections";
  std::string vertices=path+"/vertices";
  VecIndex conDims=h5Reader.getDataSetDim(connections);
  VecIndex vertDims=h5Reader.getDataSetDim(vertices);

  assert(conDims[1] == 8);
  assert(vertDims[1] == 3);


  xml.AddAttributes("TopologyType","Hexahedron");
  xml.AddAttributes("Order","0 1 3 2 4 5 7 6");
  xml.AddAttributes("NumberType","Int");
  xml.AddAttributes("NumberOfElements",to_string(conDims[0]));
  xml.CreateTag("Topology");

  xml.AddAttributes("ItemType","Uniform");
  xml.AddAttributes("Format","HDF");
  xml.AddAttributes("NumberType","Int");
  xml.AddAttributes("Dimensions",to_string(conDims[0],8));
  xml.CreateTag("DataItem");
  xml.AddString(h5Reader.getFileName()+":"+connections);
  xml.CloseTag("DataItem");
  xml.CloseTag("Topology");
  
  xml.AddAttributes("GeometryType","XYZ");
  xml.CreateTag("Geometry");

  xml.AddAttributes("ItemType","Uniform");
  xml.AddAttributes("Format","HDF");
  xml.AddAttributes("NumberType","Float");
  xml.AddAttributes("Precision","8");
  xml.AddAttributes("Dimensions",to_string(vertDims[0],3));
  xml.CreateTag("DataItem");
  xml.AddString(h5Reader.getFileName()+":"+vertices);
  xml.CloseTag("DataItem");
  xml.CloseTag("Geometry");




}

void XdmfWriter::write_grid_reference	(	xmlwriter &	out,
		std::string	gridName,
		unsigned	infoNumber
	)			[protected]

Definition at line 195 of file xdmfwriter.cpp.

{
  out.AddAttributes("Name",gridName);
  out.AddAttributes("GridType","Uniform");
  out.CreateTag("Grid");
  out.AddAttributes("Reference","/Xdmf/Domain/Topology[" + to_string(infoNumber) + "]");
  out.CreateEmptyElement("Topology");
  out.AddAttributes("Reference","/Xdmf/Domain/Geometry[" + to_string(infoNumber) + "]");
  out.CreateEmptyElement("Geometry");


}

void XdmfWriter::write_temporal_grid_collection	(	xmlwriter &	out,
		std::string	tria
	)			[protected]

Definition at line 184 of file xdmfwriter.cpp.

{

  xml.AddAttributes("Name","TimeSeries_"+tria);
  xml.AddAttributes("GridType","Collection");
  xml.AddAttributes("CollectionType","Temporal");
  xml.CreateTag("Grid");

}

void XdmfWriter::write_time	(	xmlwriter &	xml,
		std::string	times
	)			[protected]

Definition at line 243 of file xdmfwriter.cpp.

{
  xml.AddAttributes("Value",time);
  xml.CreateEmptyElement("Time");
}

void XdmfWriter::write_time_list	(	xmlwriter &	out,
		StringList	times
	)			[protected]

Definition at line 227 of file xdmfwriter.cpp.

{
  xml.AddAttributes("TimeType","List");
  xml.CreateTag("Time");

  xml.AddAttributes("Format","XML");
  xml.AddAttributes("DataType","Float");
  xml.AddAttributes("Precision","4");
  xml.AddAttributes("Dimensions",to_string(times.size()));
  xml.CreateChild("DataItem",to_string(times));
  xml.CloseTag("Time");  
    
    
}

void XdmfWriter::writeXdmf

(

std::string

hdf5FileName

)

Definition at line 12 of file xdmfwriter.cpp.

{

  h5Reader.open(hdf5FileName);
  //Get all the triangulations names
  StringList trias = h5Reader.ls("/Triangulations");
  //Get All DataSets fields
  StringList fieldvs= h5Reader.ls("/DataSets");
  //For all fields
  for (unsigned i=0;i<fieldvs.size();i++)
  {
    //Get the list of each data of this field
    fieldvs[i]="/DataSets/"+fieldvs[i];
    StringList vInst=h5Reader.ls(fieldvs[i]);
    //For each data of each field
    for (unsigned j=0;j<vInst.size();j++)
    {
          vInst[j]=fieldvs[i]+"/"+vInst[j];
          std::string triaName=h5Reader.getDataSetTriangulation(vInst[j]);
          std::string time=h5Reader.readAtt(vInst[j],"Time",false);
          m_map[triaName][time].push_back(vInst[j]);
    }
  }

  std::string xdmfFileName = StringFunctions::get_prefix_file(StringFunctions::get_file_name(hdf5FileName));
  xdmfFileName+=".xdmf";


  xmlwriter xml(xdmfFileName);


  
  xml.CreateTag("Xdmf");
  xml.CreateTag("Domain");
  //for each mesh
  for (MeshxTimexDataSets::iterator it= m_map.begin();it!=m_map.end();it++)
  {
    //Write the geometry and topology info
    write_grid_info(xml,it->first);
  }

  std::string dataName;
  //Run through the meshes again
  unsigned gridRef=1;
  for (MeshxTimexDataSets::iterator it= m_map.begin();it!=m_map.end();it++)
  {
    StringList times;
    
    write_temporal_grid_collection(xml,it->first);

    //Write Time attribute, first get all time values
    for (TimexDataSets::iterator txd=it->second.begin();txd!=it->second.end();txd++)
    {
       times.push_back(txd->first);
    }
    //write_time_list(xml,times);
    
    //Now get the TimexDataSet list
    for (TimexDataSets::iterator txd=it->second.begin();txd!=it->second.end();txd++)
    {
      write_grid_reference(xml,it->first+"_"+txd->first,gridRef); 
      //for each data set
      write_time(xml,txd->first);
      StringList &strLst=txd->second;
      for (StringList::iterator dataIt=strLst.begin();dataIt!=strLst.end();dataIt++)
      {
        dataName=StringFunctions::get_file_name(*dataIt);
        dataName=StringFunctions::strip_from_end(dataName,'_'); 
        write_dataset(xml,*dataIt,dataName);
      }
      xml.CloseTag("Grid");
    }
    gridRef++;
    xml.CloseTag("Grid");
  }
  xml.CloseTag("Domain");
  xml.CloseTag("Xdmf");
  
}

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Member Data Documentation

HDF5Reader XdmfWriter::h5Reader [private]

Definition at line 25 of file xdmfwriter.h.

MeshxTimexDataSets XdmfWriter::m_map [protected]

Definition at line 35 of file xdmfwriter.h.

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The documentation for this class was generated from the following files:

• xdmfwriter.h
• xdmfwriter.cpp