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Commit c92bcfad authored by Ken Leiter (Civ's avatar Ken Leiter (Civ
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ENH: Use libxml2 to do construction of xml file rather than using the crude... 

ENH: Use libxml2 to do construction of xml file rather than using the crude stringstream way we were using previously.  XML does not own the data, it is used to make constructing XML files easier and libxml2 will be needed eventually anyway to parse xml files.
parent 436acbe1
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Showing with 83 additions and 45 deletions
CMakeLists.txt
View file @ c92bcfad
......@@ -15,6 +15,11 @@ if(HDF5_FOUND)
include_directories(${HDF5_INCLUDE_DIR})
endif(HDF5_FOUND)
find_package(LibXml2 REQUIRED)
if(LIBXML2_FOUND)
include_directories(${LIBXML2_INCLUDE_DIR})
endif(LIBXML2_FOUND)
option(XDMF_WRAP_PYTHON ON)
if(XDMF_WRAP_PYTHON)
find_package(PythonLibs REQUIRED)
......@@ -41,7 +46,7 @@ set(XdmfSources
)
add_library(Xdmf ${XdmfSources})
target_link_libraries(Xdmf ${HDF5_LIBRARIES})
target_link_libraries(Xdmf ${HDF5_LIBRARIES} ${LIBXML2_LIBRARIES})
if(XDMF_WRAP_PYTHON)
add_library(_Xdmf MODULE XdmfPython)
......
XdmfDataItem.cpp
View file @ c92bcfad
......@@ -125,6 +125,11 @@ int XdmfDataItem::getPrecision() const
return mDataItemType.getPrecision();
}
//std::string getValuesAsString() const
//{
//}
/*
template <typename T>
T* XdmfDataItem::getValues()
......
XdmfVisitor.cpp
View file @ c92bcfad
......@@ -12,46 +12,63 @@
#include <iomanip>
XdmfVisitor::XdmfVisitor() :
mTabIndex(0),
xmlData(),
mLightDataLimit(100),
mHeavyFileName("output.h5"),
hdf5Handle(H5Fcreate("output.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT))
hdf5Handle(H5Fcreate("output.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)),
xmlDocument(xmlNewDoc((xmlChar*)"1.0")),
xmlCurrentNode(xmlNewNode(NULL, (xmlChar*)"Xdmf"))
{
xmlDocSetRootElement(xmlDocument, xmlCurrentNode);
std::cout << "Created Visitor " << this << std::endl;
}
XdmfVisitor::~XdmfVisitor()
{
xmlSaveFormatFile("output.xmf", xmlDocument, 1);
xmlFreeDoc(xmlDocument);
herr_t status = H5Fclose(hdf5Handle);
std::cout << "Deleted Visitor " << this << std::endl;
}
void XdmfVisitor::visit(const XdmfAttribute * const attribute)
{
xmlData << std::setw(mTabIndex) << "" << "<Attribute Name=\"" << attribute->getName() << "\" AttributeType=\"" << attribute->getAttributeTypeAsString() << "\" Center=\"" << attribute->getAttributeCenterAsString() << "\">\n";
mTabIndex++;
xmlNodePtr parentNode = xmlCurrentNode;
xmlCurrentNode = xmlNewChild(xmlCurrentNode, NULL, (xmlChar*)"Attribute", NULL);
xmlNewProp(xmlCurrentNode, (xmlChar*)"Name", (xmlChar*)attribute->getName().c_str());
xmlNewProp(xmlCurrentNode, (xmlChar*)"AttributeType", (xmlChar*)attribute->getAttributeTypeAsString().c_str());
xmlNewProp(xmlCurrentNode, (xmlChar*)"Center", (xmlChar*)attribute->getAttributeCenterAsString().c_str());
dataHierarchy.push_back(attribute->getName());
visit((XdmfDataItem*)attribute);
dataHierarchy.pop_back();
mTabIndex--;
xmlData << std::setw(mTabIndex) << "" << "</Attribute>\n";
xmlCurrentNode = parentNode;
}
void XdmfVisitor::visit(const XdmfDataItem * const dataItem)
{
xmlNodePtr parentNode = xmlCurrentNode;
xmlCurrentNode = xmlNewChild(xmlCurrentNode, NULL, (xmlChar*)"DataItem", NULL);
std::string format = "XML";
if(dataItem->getNumberValues() > mLightDataLimit)
{
format = "HDF";
}
xmlData << std::setw(mTabIndex) << "" << "<DataItem Format=\"" << format << "\" DataType=\"" << dataItem->getName() << "\" Precision=\"" << dataItem->getPrecision() << "\" Dimensions=\"" << dataItem->getNumberValues() << "\">";
xmlNewProp(xmlCurrentNode, (xmlChar*)"Format", (xmlChar*)format.c_str());
xmlNewProp(xmlCurrentNode, (xmlChar*)"DataType", (xmlChar*)dataItem->getName().c_str());
std::stringstream precisionString;
precisionString << dataItem->getPrecision();
xmlNewProp(xmlCurrentNode, (xmlChar*)"Precision", (xmlChar*)precisionString.str().c_str());
std::stringstream dimensionString;
dimensionString << dataItem->getNumberValues();
xmlNewProp(xmlCurrentNode, (xmlChar*)"Dimensions", (xmlChar*)dimensionString.str().c_str());
const void* const pointer = dataItem->getValues();
mTabIndex++;
std::stringstream xmlTextValues;
if(dataItem->getNumberValues() > mLightDataLimit)
{
std::cout << hdf5Handle << std::endl;
herr_t status;
hsize_t size = dataItem->getNumberValues();
hid_t dataspace = H5Screate_simple(1, &size, NULL);
......@@ -79,56 +96,62 @@ void XdmfVisitor::visit(const XdmfDataItem * const dataItem)
}
}
hid_t dataset = H5Dcreate(handle, dataHierarchy.back().c_str(), dataItem->getHDF5DataType(), dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
xmlData << "\n" << std::setw(mTabIndex) << "" << mHeavyFileName << ":" << groupName << "/" << dataHierarchy.back();
xmlTextValues << mHeavyFileName << ":" << groupName << "/" << dataHierarchy.back();
status = H5Dwrite(dataset, dataItem->getHDF5DataType(), H5S_ALL, H5S_ALL, H5P_DEFAULT, dataItem->getValues());
status = H5Dclose(dataset);
status = H5Sclose(dataspace);
}
else
{
//for (unsigned int i=0; i<dataItem->getNumberValues(); ++i)
//{
// if (i % 10 == 0)
// {
// xmlData << "\n" << std::setw(mTabIndex) << "" << pointer[i] << " ";
// }
// else
// {
// xmlData << pointer[i] << " ";
// }
//}
for (unsigned int i=0; i<dataItem->getNumberValues(); ++i)
{
if (i % 10 == 9)
{
xmlTextValues << ((int*)pointer)[i] << "\n";
}
else
{
xmlTextValues << ((int*)pointer)[i] << " ";
}
}
}
mTabIndex--;
xmlData << "\n" << std::setw(mTabIndex) << "" << "</DataItem>\n";
xmlAddChild(xmlCurrentNode, xmlNewText((xmlChar*)xmlTextValues.str().c_str()));
xmlCurrentNode = parentNode;
}
void XdmfVisitor::visit(const XdmfDomain * const domain)
{
xmlData << std::setw(mTabIndex) << "" << "<Domain>\n";
mTabIndex++;
xmlNodePtr parentNode = xmlCurrentNode;
xmlCurrentNode = xmlNewChild(xmlCurrentNode, NULL, (xmlChar*)"Domain", NULL);
for(unsigned int i=0; i<domain->getNumberOfGrids(); ++i)
{
visit(domain->getGrid(i).get());
}
mTabIndex--;
xmlData << std::setw(mTabIndex) << "" << "</Domain>\n";
xmlCurrentNode = parentNode;
}
void XdmfVisitor::visit(const XdmfGeometry * const geometry)
{
xmlData << std::setw(mTabIndex) << "" << "<Geometry GeometryType=\"" << geometry->getGeometryTypeAsString() << "\">\n";
mTabIndex++;
xmlNodePtr parentNode = xmlCurrentNode;
xmlCurrentNode = xmlNewChild(xmlCurrentNode, NULL, (xmlChar*)"Geometry", NULL);
xmlNewProp(xmlCurrentNode, (xmlChar*)"GeometryType", (xmlChar*)geometry->getGeometryTypeAsString().c_str());
dataHierarchy.push_back("XYZ");
visit((XdmfDataItem*)geometry);
dataHierarchy.pop_back();
mTabIndex--;
xmlData << std::setw(mTabIndex) << "" << "</Geometry>\n";
xmlCurrentNode = parentNode;
}
void XdmfVisitor::visit(const XdmfGrid * const grid)
{
xmlData << std::setw(mTabIndex) << "" << "<Grid Name=\"" << grid->getName() <<"\">\n";
mTabIndex++;
xmlNodePtr parentNode = xmlCurrentNode;
xmlCurrentNode = xmlNewChild(xmlCurrentNode, NULL, (xmlChar*)"Grid", NULL);
xmlNewProp(xmlCurrentNode, (xmlChar*)"Name", (xmlChar*)grid->getName().c_str());
dataHierarchy.push_back(grid->getName());
visit(grid->getGeometry().get());
visit(grid->getTopology().get());
......@@ -137,24 +160,29 @@ void XdmfVisitor::visit(const XdmfGrid * const grid)
visit(grid->getAttribute(i).get());
}
dataHierarchy.pop_back();
mTabIndex--;
xmlData << std::setw(mTabIndex) << "" << "</Grid>\n";
xmlCurrentNode = parentNode;
}
void XdmfVisitor::visit(const XdmfTopology * const topology)
{
xmlData << std::setw(mTabIndex) << "" << "<Topology TopologyType=\"" << topology->getTopologyTypeAsString() << "\" NumberOfElements=\"" << topology->getNumberElements() << "\">\n";
mTabIndex++;
xmlNodePtr parentNode = xmlCurrentNode;
xmlCurrentNode = xmlNewChild(xmlCurrentNode, NULL, (xmlChar*)"Topology", NULL);
xmlNewProp(xmlCurrentNode, (xmlChar*)"TopologyType", (xmlChar*)topology->getTopologyTypeAsString().c_str());
std::stringstream numberElementsString;
numberElementsString << topology->getNumberElements();
xmlNewProp(xmlCurrentNode, (xmlChar*)"NumberOfElements", (xmlChar*)numberElementsString.str().c_str());
dataHierarchy.push_back("Connectivity");
visit((XdmfDataItem*)topology);
dataHierarchy.pop_back();
mTabIndex--;
xmlData << std::setw(mTabIndex) << "" << "</Topology>\n";
xmlCurrentNode = parentNode;
}
std::string XdmfVisitor::printSelf() const
{
return "XdmfVisitor:\n" + xmlData.str();
return "XdmfVisitor";
}
int XdmfVisitor::getLightDataLimit() const
......@@ -174,6 +202,5 @@ std::string XdmfVisitor::getHDF5GroupName()
{
datasetName << "/" << dataHierarchy[i];
}
std::cout << datasetName.str() << std::endl;
return datasetName.str();
}
XdmfVisitor.hpp
View file @ c92bcfad
......@@ -14,6 +14,7 @@ class XdmfTopology;
// Includes
#include <hdf5.h>
#include <libxml/tree.h>
#include <sstream>
#include <vector>
#include "XdmfObject.hpp"
......@@ -64,12 +65,12 @@ private:
std::string getHDF5GroupName();
int mTabIndex;
std::stringstream xmlData;
hid_t hdf5Handle;
std::vector<std::string> dataHierarchy;
std::string mHeavyFileName;
int mLightDataLimit;
xmlDocPtr xmlDocument;
xmlNodePtr xmlCurrentNode;
};
......
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