ENH: Add ability to write HDF5 files as part of XdmfVisitor operation.

CMakeLists.txt

@@ -8,9 +8,13 @@ set(BUILD_SHARED_LIBS true)
 find_package(Boost REQUIRED)
 if(Boost_FOUND)
 	include_directories(${Boost_INCLUDE_DIRS})
-	message(${Boost_INCLUDE_DIRS})
 endif(Boost_FOUND)
 
+find_package(HDF5 REQUIRED)
+if(HDF5_FOUND)
+	include_directories(${HDF5_INCLUDE_DIR})
+endif(HDF5_FOUND)
+
 option(XDMF_WRAP_PYTHON ON)
 if(XDMF_WRAP_PYTHON)
 	find_package(PythonLibs REQUIRED)
@@ -37,6 +41,7 @@ set(XdmfSources
 )
 
 add_library(Xdmf ${XdmfSources})
+target_link_libraries(Xdmf ${HDF5_LIBRARIES})
 
 if(XDMF_WRAP_PYTHON)
 	add_library(_Xdmf MODULE XdmfPython)

XdmfAttribute.hpp

@@ -47,9 +47,9 @@ public:
 	void setAttributeType(const XdmfAttributeType& attributeType);
 
 	/**
-	 * Get the name of the AttributeType associated with this Attribute.
+	 * Get the name of the XdmfAttributeType associated with this Attribute.
 	 *
-	 * @return std::string containing name of the AttributeType.
+	 * @return std::string containing name of the XdmfAttributeType.
 	 */
 	std::string getAttributeTypeAsString() const;
 
@@ -70,16 +70,21 @@ public:
 	/**
 	 * Get the name of the XdmfAttributeCenter associated with this Attribute.
 	 *
-	 * @return std::string containing name of the AttributeCenter.
+	 * @return std::string containing name of the XdmfAttributeCenter.
 	 */
 	std::string getAttributeCenterAsString() const;
 
+	/**
+	 * Set the number of values this attribute contains.
+	 *
+	 * @param an int giving the number of values.
+	 */
+	void setNumberValues(int numValues);
+
 	void write(boost::shared_ptr<XdmfVisitor> visitor) const;
 
 	virtual std::string printSelf() const;
 
-	void setNumberValues(int numValues);
-
 protected:
 
 	XdmfAttribute();

XdmfDataItem.cpp

@@ -26,30 +26,93 @@ std::string XdmfDataItem::printSelf() const
 }
 
 template <>
-void XdmfDataItem::setData<int>(int* dataPointer)
+void XdmfDataItem::setValues<char>(char* dataPointer)
+{
+	mDataPointer = dataPointer;
+	mDataType = XdmfDataItemType::Int8();
+}
+
+template <>
+void XdmfDataItem::setValues<unsigned char>(unsigned char* dataPointer)
+{
+	mDataPointer = dataPointer;
+	mDataType = XdmfDataItemType::UInt8();
+}
+
+template <>
+void XdmfDataItem::setValues<short>(short* dataPointer)
+{
+	mDataPointer = dataPointer;
+	mDataType = XdmfDataItemType::Int16();
+}
+
+template <>
+void XdmfDataItem::setValues<unsigned short>(unsigned short* dataPointer)
+{
+	mDataPointer = dataPointer;
+	mDataType = XdmfDataItemType::UInt16();
+}
+
+template <>
+void XdmfDataItem::setValues<int>(int* dataPointer)
 {
 	mDataPointer = dataPointer;
 	mDataType = XdmfDataItemType::Int32();
 }
 
 template <>
-int* XdmfDataItem::getData<int>()
+void XdmfDataItem::setValues<unsigned int>(unsigned int* dataPointer)
 {
-	return mDataPointer;
+	mDataPointer = dataPointer;
+	mDataType = XdmfDataItemType::UInt32();
 }
 
 template <>
-const int* const XdmfDataItem::getData<int>() const
+void XdmfDataItem::setValues<long>(long* dataPointer)
 {
-	return mDataPointer;
+	mDataPointer = dataPointer;
+	mDataType = XdmfDataItemType::Int64();
 }
 
-int XdmfDataItem::getNumberValues() const
+template <>
+void XdmfDataItem::setValues<float>(float* dataPointer)
 {
-	return mNumberValues;
+	mDataPointer = dataPointer;
+	mDataType = XdmfDataItemType::Float32();
+}
+
+template <>
+void XdmfDataItem::setValues<double>(double* dataPointer)
+{
+	mDataPointer = dataPointer;
+	mDataType = XdmfDataItemType::Float64();
 }
 
-void XdmfDataItem::write(boost::shared_ptr<XdmfVisitor> visitor) const
+template <typename T>
+void XdmfDataItem::setValues(T* dataPointer)
 {
-	visitor->visit(this);
+	mDataPointer = dataPointer;
+	mDataType = XdmfDataItemType::Unknown();
 }
+
+template <>
+int* XdmfDataItem::getValues<int>()
+{
+	return (int*)mDataPointer;
+}
+
+template <>
+const int* const XdmfDataItem::getValues<int>() const
+{
+	return (int*)mDataPointer;
+}
+
+int XdmfDataItem::getNumberValues() const
+{
+	return mNumberValues;
+}
+
+//void XdmfDataItem::write(boost::shared_ptr<XdmfVisitor> visitor) const
+//{
+//	visitor->visit(this);
+//}

XdmfDataItem.hpp

@@ -16,19 +16,19 @@ class XdmfDataItem : public XdmfItem {
 
 public:
 
-	XdmfNewMacro(XdmfDataItem);
+	//XdmfNewMacro(XdmfDataItem);
 
-	template <typename T> void setData(T * dataPointer);
+	template <typename T> void setValues(T * dataPointer);
 
-	template <typename T> T* getData();
+	template <typename T> T* getValues();
 
-	template <typename T> const T* const getData() const;
+	template <typename T> const T* const getValues() const;
 
 	int getNumberValues() const;
 
 	std::string printSelf() const;
 
-	void write(boost::shared_ptr<XdmfVisitor> visitor) const;
+	void write(boost::shared_ptr<XdmfVisitor> visitor) const = 0;
 
 protected:
 
@@ -42,7 +42,7 @@ private:
 	XdmfDataItem(const XdmfDataItem&);  // Not implemented.
 	void operator=(const XdmfDataItem&);  // Not implemented.
 
-	int* mDataPointer;
+	void* mDataPointer;
 	XdmfDataItemType mDataType;
 };
 

XdmfDataItemType.hpp

@@ -62,6 +62,8 @@ protected:
 
 private:
 
+	static XdmfDataItemType* UnknownPtr;
+
 	std::string mName;
 };
 

XdmfItem.hpp

 /**
- * An XdmfItem replaces the XdmfElement class in the previous version of Xdmf.  An XdmfElement represents and item that can be
- * visited by an XdmfLightDataVisitor and have it's contents added to an XdmfFile.  These include XdmfGrids, XdmfSets,
+ * An XdmfItem replaces the XdmfElement class in the previous version of Xdmf.  An XdmfItem represents an item that can be
+ * visited by an XdmfVisitor and have it's contents added to an xdmf file.  These include XdmfGrids, XdmfSets,
  * XdmfTopologies, etc.
  *
  * This is an abstract base class.

XdmfVisitor.cpp

@@ -13,13 +13,17 @@
 
 XdmfVisitor::XdmfVisitor() :
 	mTabIndex(0),
-	xmlData()
+	xmlData(),
+	mLightDataLimit(0),
+	mHeavyFileName("output.h5"),
+	hdf5Handle(H5Fcreate("output.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT))
 {
 	std::cout << "Created Visitor " << this << std::endl;
 }
 
 XdmfVisitor::~XdmfVisitor()
 {
+	herr_t status = H5Fclose(hdf5Handle);
 	std::cout << "Deleted Visitor " << this << std::endl;
 }
 
@@ -27,25 +31,71 @@ void XdmfVisitor::visit(const XdmfAttribute * const attribute)
 {
 	xmlData << std::setw(mTabIndex) << "" << "<Attribute Name=\"" << attribute->getName() << "\" AttributeType=\"" << attribute->getAttributeTypeAsString() << "\" Center=\"" << attribute->getAttributeCenterAsString() << "\">\n";
 	mTabIndex++;
+	dataHierarchy.push_back(attribute->getName());
 	visit((XdmfDataItem*)attribute);
+	dataHierarchy.pop_back();
 	mTabIndex--;
 	xmlData << std::setw(mTabIndex) << "" << "</Attribute>\n";
 }
 
 void XdmfVisitor::visit(const XdmfDataItem * const dataItem)
 {
-	xmlData << std::setw(mTabIndex) << "" << "<DataItem Format=\"XML\" DataType=\"Int\" Precision=\"4\" Dimensions=\"" << dataItem->getNumberValues() << "\">";
-	const int* const intPointer = dataItem->getData<int>();
+	std::string format = "XML";
+	if(dataItem->getNumberValues() > mLightDataLimit)
+	{
+		format = "HDF";
+	}
+	xmlData << std::setw(mTabIndex) << "" << "<DataItem Format=\"" << format << "\" DataType=\"Int\" Precision=\"4\" Dimensions=\"" << dataItem->getNumberValues() << "\">";
+
+	const int* const intPointer = dataItem->getValues<int>();
 	mTabIndex++;
-	for (unsigned int i=0; i<dataItem->getNumberValues(); ++i)
+	if(dataItem->getNumberValues() > mLightDataLimit)
 	{
-		if (i % 10 == 0)
+		std::cout << hdf5Handle << std::endl;
+		herr_t status;
+		hsize_t size = dataItem->getNumberValues();
+		hid_t dataspace = H5Screate_simple(1, &size, NULL);
+		hid_t handle = hdf5Handle;
+		std::string groupName = getHDF5GroupName();
+		// Need to make sure this group exists before we add to it.
+		if(dataHierarchy.size() > 1)
 		{
-			xmlData << "\n" << std::setw(mTabIndex) << "" << intPointer[i] << " ";
+			/* Save old error handler */
+			H5E_auto_t old_func;
+			void* old_client_data;
+			H5Eget_auto(0, &old_func, &old_client_data);
+
+			/* Turn off error handling */
+			H5Eset_auto2(0, NULL, NULL);
+
+			/* Probe. May fail, but that's okay */
+			handle = H5Gopen(hdf5Handle, groupName.c_str(), H5P_DEFAULT);
+
+			/* Restore previous error handler */
+			H5Eset_auto2(0, old_func, old_client_data);
+			if(handle < 0)
+			{
+				handle = H5Gcreate(hdf5Handle, groupName.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+			}
 		}
-		else
+		hid_t dataset = H5Dcreate(handle, dataHierarchy.back().c_str(), H5T_NATIVE_INT, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+		xmlData << "\n" << std::setw(mTabIndex) << "" << mHeavyFileName << ":" << groupName << "/" << dataHierarchy.back();
+		status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, dataItem->getValues<int>());
+		status = H5Dclose(dataset);
+		status = H5Sclose(dataspace);
+	}
+	else
+	{
+		for (unsigned int i=0; i<dataItem->getNumberValues(); ++i)
 		{
-			xmlData << intPointer[i] << " ";
+			if (i % 10 == 0)
+			{
+				xmlData << "\n" << std::setw(mTabIndex) << "" << intPointer[i] << " ";
+			}
+			else
+			{
+				xmlData << intPointer[i] << " ";
+			}
 		}
 	}
 	mTabIndex--;
@@ -68,7 +118,9 @@ void XdmfVisitor::visit(const XdmfGeometry * const geometry)
 {
 	xmlData << std::setw(mTabIndex) << "" << "<Geometry GeometryType=\"" << geometry->getGeometryTypeAsString() << "\">\n";
 	mTabIndex++;
+	dataHierarchy.push_back("XYZ");
 	visit((XdmfDataItem*)geometry);
+	dataHierarchy.pop_back();
 	mTabIndex--;
 	xmlData << std::setw(mTabIndex) << "" << "</Geometry>\n";
 }
@@ -77,12 +129,14 @@ void XdmfVisitor::visit(const XdmfGrid * const grid)
 {
 	xmlData << std::setw(mTabIndex) << "" << "<Grid Name=\"" << grid->getName() <<"\">\n";
 	mTabIndex++;
+	dataHierarchy.push_back(grid->getName());
 	visit(grid->getGeometry().get());
 	visit(grid->getTopology().get());
-	for(unsigned int i=0; i<grid->getNumberOfAttributes(); i++)
+	for(unsigned int i=0; i<grid->getNumberOfAttributes(); ++i)
 	{
 		visit(grid->getAttribute(i).get());
 	}
+	dataHierarchy.pop_back();
 	mTabIndex--;
 	xmlData << std::setw(mTabIndex) << "" << "</Grid>\n";
 }
@@ -91,7 +145,9 @@ void XdmfVisitor::visit(const XdmfTopology * const topology)
 {
 	xmlData << std::setw(mTabIndex) << "" << "<Topology TopologyType=\"" << topology->getTopologyTypeAsString() << "\" NumberOfElements=\"" << topology->getNumberElements() << "\">\n";
 	mTabIndex++;
+	dataHierarchy.push_back("Connectivity");
 	visit((XdmfDataItem*)topology);
+	dataHierarchy.pop_back();
 	mTabIndex--;
 	xmlData << std::setw(mTabIndex) << "" << "</Topology>\n";
 }
@@ -100,3 +156,14 @@ std::string XdmfVisitor::printSelf() const
 {
 	return "XdmfVisitor:\n" + xmlData.str();
 }
+
+std::string XdmfVisitor::getHDF5GroupName()
+{
+	std::stringstream datasetName;
+	for(unsigned int i=0; i<dataHierarchy.size() - 1; ++i)
+	{
+		datasetName << "/" << dataHierarchy[i];
+	}
+	std::cout << datasetName.str() << std::endl;
+	return datasetName.str();
+}

XdmfVisitor.hpp

@@ -13,7 +13,9 @@ class XdmfGrid;
 class XdmfTopology;
 
 // Includes
+#include <hdf5.h>
 #include <sstream>
+#include <vector>
 #include "XdmfObject.hpp"
 
 class XdmfVisitor : public XdmfObject {
@@ -24,7 +26,7 @@ public:
 
 	virtual void visit(const XdmfAttribute * const attribute);
 
-	virtual void visit(const XdmfDataItem * const geometry);
+	virtual void visit(const XdmfDataItem * const dataItem);
 
 	virtual void visit(const XdmfDomain * const domain);
 
@@ -46,8 +48,15 @@ private:
 	XdmfVisitor(const XdmfVisitor&);  // Not implemented.
 	void operator=(const XdmfVisitor&);  // Not implemented.
 
+	std::string getHDF5GroupName();
+
 	int mTabIndex;
 	std::stringstream xmlData;
+	hid_t hdf5Handle;
+	std::vector<std::string> dataHierarchy;
+	int mLightDataLimit;
+	std::string mHeavyFileName;
+
 };
 
 #endif /* XDMFVISITOR_HPP_ */

tests/TestXdmfDataItem.cpp

@@ -2,7 +2,7 @@
 
 int main(int argc, char* argv[])
 {
-	boost::shared_ptr<XdmfDataItem> dataItem = XdmfDataItem::New();
-	int intArray[10] = {1,2,3,4,5,6,7,8,9,10};
-	dataItem->setData(intArray);
+	//boost::shared_ptr<XdmfDataItem> dataItem = XdmfDataItem::New();
+	//int intArray[10] = {1,2,3,4,5,6,7,8,9,10};
+	//dataItem->setValues(intArray);
 }

tests/TestXdmfVisitor.cpp

@@ -18,13 +18,13 @@ int main(int argc, char* argv[])
 			0, 0, -1, 1, 0, -1, 3, 0, -2, 0, 1, -1, 1, 1, -1, 3, 2, -2};
 	grid->getGeometry()->setNumberPoints(12);
 	grid->getGeometry()->setGeometryType(XdmfGeometryType::XYZ());
-	grid->getGeometry()->setData(points);
+	grid->getGeometry()->setValues(points);
 
 	// Set Topology
 	int connectivity[] = {0, 1, 7, 6, 3, 4, 10, 9, 1, 2, 8, 7, 4, 5, 11, 10};
 	grid->getTopology()->setNumberElements(2);
 	grid->getTopology()->setTopologyType(XdmfTopologyType::Hexahedron());
-	grid->getTopology()->setData(connectivity);
+	grid->getTopology()->setValues(connectivity);
 
 	// Add Node Attribute
 	boost::shared_ptr<XdmfAttribute> nodalAttribute = XdmfAttribute::New();
@@ -33,7 +33,7 @@ int main(int argc, char* argv[])
 	nodalAttribute->setNumberValues(12);
 	nodalAttribute->setAttributeType(XdmfAttributeType::Scalar());
 	nodalAttribute->setAttributeCenter(XdmfAttributeCenter::Node());
-	nodalAttribute->setData(nodeValues);
+	nodalAttribute->setValues(nodeValues);
 
 	// Add Cell Attribute
 	boost::shared_ptr<XdmfAttribute> cellAttribute = XdmfAttribute::New();
@@ -42,7 +42,7 @@ int main(int argc, char* argv[])
 	cellAttribute->setNumberValues(2);
 	cellAttribute->setAttributeType(XdmfAttributeType::Scalar());
 	cellAttribute->setAttributeCenter(XdmfAttributeCenter::Cell());
-	cellAttribute->setData(cellValues);
+	cellAttribute->setValues(cellValues);
 
 	grid->insert(nodalAttribute);
 	grid->insert(cellAttribute);