ENH: Modift XdmfWriter to utilize new genericized getItemTag and getItemProperties methods

to write out the Xdmf graph.  Modify some random include statements for style.

XdmfArray.cpp

@@ -473,8 +473,12 @@ std::map<std::string, std::string> XdmfArray::getItemProperties() const
 	std::map<std::string, std::string> arrayProperties;
 	arrayProperties["Format"] = "HDF";
 	arrayProperties["DataType"] = this->getType();
-	arrayProperties["Precision"] = this->getPrecision();
-	arrayProperties["Dimensions"] = this->getSize();
+	std::stringstream precision;
+	precision <<  this->getPrecision();
+	arrayProperties["Precision"] = precision.str();
+	std::stringstream size;
+	size <<  this->getSize();
+	arrayProperties["Dimensions"] = size.str();
 	return arrayProperties;
 }
 

XdmfAttribute.cpp

@@ -6,7 +6,6 @@
  */
 
 #include "XdmfAttribute.hpp"
-#include "XdmfVisitor.hpp"
 
 XdmfAttribute::XdmfAttribute() :
 	mName(""),

XdmfAttributeCenter.hpp

@@ -2,6 +2,7 @@
 #define XDMFATTRIBUTECENTER_HPP_
 
 // Includes
+#include <string>
 #include "XdmfItemProperty.hpp"
 
 /**

XdmfAttributeType.hpp

@@ -2,6 +2,7 @@
 #define XDMFATTRIBUTETYPE_HPP_
 
 // Includes
+#include <string>
 #include "XdmfItemProperty.hpp"
 
 /**

XdmfDomain.cpp

@@ -7,7 +7,6 @@
 
 #include "XdmfDomain.hpp"
 #include "XdmfGrid.hpp"
-#include "XdmfVisitor.hpp"
 
 XdmfDomain::XdmfDomain()
 {

XdmfDomain.hpp

@@ -5,8 +5,8 @@
 class XdmfGrid;
 
 // Includes
-#include "XdmfItem.hpp"
 #include <vector>
+#include "XdmfItem.hpp"
 
 /**
  * @brief The root XdmfItem that contains XdmfGrids.

XdmfGeometry.cpp

@@ -6,7 +6,6 @@
  */
 
 #include "XdmfGeometry.hpp"
-#include "XdmfVisitor.hpp"
 
 XdmfGeometry::XdmfGeometry() :
 	mGeometryType(XdmfGeometryType::NoGeometryType()),

XdmfGeometryType.cpp

@@ -5,6 +5,7 @@
  *      Author: kleiter
  */
 
+#include <map>
 #include "XdmfGeometryType.hpp"
 
 // Supported XdmfGeometryTypes

XdmfGeometryType.hpp

@@ -2,6 +2,7 @@
 #define XDMFGEOMETRYTYPE_HPP_
 
 // Includes
+#include <string>
 #include "XdmfItemProperty.hpp"
 
 /**

XdmfGrid.cpp

@@ -9,8 +9,6 @@
 #include "XdmfGrid.hpp"
 #include "XdmfGeometry.hpp"
 #include "XdmfTopology.hpp"
-#include "XdmfVisitor.hpp"
-#include <sstream>
 
 XdmfGrid::XdmfGrid() :
 	mGeometry(XdmfGeometry::New()),

XdmfItem.cpp

 #include "XdmfItem.hpp"
-#include "XdmfVisitor.hpp"
 
 XdmfItem::XdmfItem()
 {

XdmfItemProperty.hpp

@@ -2,7 +2,6 @@
 #define XDMFITEMPROPERTY_HPP_
 
 // Includes
-#include <string>
 #include <map>
 #include "XdmfObject.hpp"
 

XdmfObject.hpp

@@ -4,7 +4,6 @@
 // Includes
 #include <boost/shared_ptr.hpp>
 
-
 #define XdmfNewMacro(type) \
 template <typename T> friend void boost::checked_delete(T * x); \
 static boost::shared_ptr<type> New() \

XdmfTopology.cpp

@@ -5,9 +5,9 @@
  *      Author: kleiter
  */
 
+#include <sstream>
 #include "XdmfArray.hpp"
 #include "XdmfTopology.hpp"
-#include "XdmfVisitor.hpp"
 
 XdmfTopology::XdmfTopology() :
 	mTopologyType(XdmfTopologyType::NoTopologyType()),
@@ -30,6 +30,9 @@ std::map<std::string, std::string> XdmfTopology::getItemProperties() const
 {
 	std::map<std::string, std::string> topologyProperties;
 	mTopologyType.getProperties(topologyProperties);
+	std::stringstream numElements;
+	numElements << this->getNumberElements();
+	topologyProperties["Dimensions"] = numElements.str();
 	return topologyProperties;
 }
 

XdmfTopology.hpp

@@ -8,7 +8,7 @@
 /**
  * @brief Handles the connectivity information in an XdmfGrid.
  *
- * XdmfTopology is a required part of an XdmfGrid.  It stores the connectivty information
+ * XdmfTopology is a required part of an XdmfGrid.  It stores the connectivity information
  * between all points contained in an XdmfGrid.  XdmfTopology contains an XdmfTopologyType property
  * which should be set that specifies the element type stored.
  */

XdmfTopologyType.hpp

@@ -2,6 +2,7 @@
 #define XDMFTOPOLOGYTYPE_HPP_
 
 // Includes
+#include <string>
 #include "XdmfItemProperty.hpp"
 /**
  * @brief Property describing the types of elements stored in an XdmfTopology.

XdmfWriter.cpp

 // Kenneth Leiter
 // Xdmf Smart Pointer Test
 
+#include <sstream>
 #include "XdmfArray.hpp"
-#include "XdmfAttribute.hpp"
-#include "XdmfDomain.hpp"
-#include "XdmfGeometry.hpp"
-#include "XdmfGrid.hpp"
-#include "XdmfTopology.hpp"
+#include "XdmfItem.hpp"
 #include "XdmfWriter.hpp"
 
-//#include <iomanip>
-
 XdmfWriter::XdmfWriter() :
 	mLightDataLimit(100),
 	mHeavyFileName("output.h5"),
-	hdf5Handle(H5Fcreate("output.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)),
-	xmlDocument(xmlNewDoc((xmlChar*)"1.0")),
-	xmlCurrentNode(xmlNewNode(NULL, (xmlChar*)"Xdmf"))
+	mHDF5Handle(H5Fcreate("output.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)),
+	mXMLDocument(xmlNewDoc((xmlChar*)"1.0")),
+	mXMLCurrentNode(xmlNewNode(NULL, (xmlChar*)"Xdmf"))
 {
-	xmlDocSetRootElement(xmlDocument, xmlCurrentNode);
+	xmlDocSetRootElement(mXMLDocument, mXMLCurrentNode);
 	std::cout << "Created visitor " << this << std::endl;
 }
 
 XdmfWriter::~XdmfWriter()
 {
-	xmlSaveFormatFile("output.xmf", xmlDocument, 1);
-	xmlFreeDoc(xmlDocument);
+	xmlSaveFormatFile("output.xmf", mXMLDocument, 1);
+	xmlFreeDoc(mXMLDocument);
 	xmlCleanupParser();
-	herr_t status = H5Fclose(hdf5Handle);
+	herr_t status = H5Fclose(mHDF5Handle);
 	std::cout << "Deleted visitor " << this << std::endl;
 }
 
-void XdmfWriter::visit(XdmfAttribute & attribute, boost::shared_ptr<Loki::BaseVisitor> visitor)
+std::string XdmfWriter::createHDF5Group(std::stringstream & groupPath, int index)
 {
-	std::cout << "Writing Attribute" << std::endl;
-	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.getAttributeType().getName().c_str());
-	xmlNewProp(xmlCurrentNode, (xmlChar*)"Center", (xmlChar*)attribute.getAttributeCenter().getName().c_str());
-
-	dataHierarchy.push_back(attribute.getName());
-	attribute.traverse(visitor);
-	dataHierarchy.pop_back();
-
-	xmlCurrentNode = parentNode;
+	groupPath << "/" << mDataHierarchy[index];
+	hid_t handle = H5Gopen(mHDF5Handle, groupPath.str().c_str(), H5P_DEFAULT);
+	if(handle < 0)
+	{
+		// Open failed, create a new group
+		handle = H5Gcreate(mHDF5Handle, groupPath.str().c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+	}
+	H5Gclose(handle);
+
+	// + 2 because we ignore last value in mDataHierarchy (== dataset name)
+	if(index + 2 < mDataHierarchy.size())
+	{
+		return createHDF5Group(groupPath, index + 1);
+
+	}
+	return groupPath.str().c_str();
 }
 
-void XdmfWriter::visit(XdmfArray & array, boost::shared_ptr<Loki::BaseVisitor> visitor)
+std::string XdmfWriter::getHDF5GroupHandle()
 {
-	std::cout << "Writing Array" << std::endl;
-	xmlNodePtr parentNode = xmlCurrentNode;
-	xmlCurrentNode = xmlNewChild(xmlCurrentNode, NULL, (xmlChar*)"DataItem", NULL);
-
-	std::string format = "XML";
-	if(array.getSize() > mLightDataLimit)
+	if(mDataHierarchy.size() > 1)
 	{
-		format = "HDF";
+		// Save old error handler and turn off error handling for now
+		H5E_auto_t old_func;
+		void* old_client_data;
+		H5Eget_auto(0, &old_func, &old_client_data);
+		H5Eset_auto2(0, NULL, NULL);
+
+		std::stringstream emptyPath;
+		std::string handle = createHDF5Group(emptyPath);
+
+		// Restore previous error handler
+		H5Eset_auto2(0, old_func, old_client_data);
+
+		return handle;
 	}
+	return "";
+}
 
-	xmlNewProp(xmlCurrentNode, (xmlChar*)"Format", (xmlChar*)format.c_str());
-	xmlNewProp(xmlCurrentNode, (xmlChar*)"DataType", (xmlChar*)array.getType().c_str());
-	std::stringstream precisionString;
-	precisionString << array.getPrecision();
-	xmlNewProp(xmlCurrentNode, (xmlChar*)"Precision", (xmlChar*)precisionString.str().c_str());
-	std::stringstream dimensionString;
-	dimensionString << array.getSize();
-	xmlNewProp(xmlCurrentNode, (xmlChar*)"Dimensions", (xmlChar*)dimensionString.str().c_str());
+unsigned int XdmfWriter::getLightDataLimit() const
+{
+	return mLightDataLimit;
+}
+
+void XdmfWriter::setLightDataLimit(unsigned int numValues)
+{
+	mLightDataLimit = numValues;
+}
+
+void XdmfWriter::visit(XdmfArray & array, boost::shared_ptr<Loki::BaseVisitor> visitor)
+{
+	this->visit(dynamic_cast<XdmfItem &>(array), visitor);
+
+	xmlNodePtr parentNode = mXMLCurrentNode;
+	mXMLCurrentNode = mXMLCurrentNode->children;
 
 	std::stringstream xmlTextValues;
 	if(array.getSize() > mLightDataLimit)
@@ -74,32 +90,19 @@ void XdmfWriter::visit(XdmfArray & array, boost::shared_ptr<Loki::BaseVisitor> v
 		herr_t status;
 		hsize_t size = array.getSize();
 		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)
+		hid_t handle = mHDF5Handle;
+		std::string groupName = getHDF5GroupHandle();
+		if(groupName.compare("") != 0)
 		{
-			// 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);
-			}
+			handle = H5Gopen(mHDF5Handle, groupName.c_str(), H5P_DEFAULT);
 		}
-		hid_t dataset = H5Dcreate(handle, dataHierarchy.back().c_str(), array.getHDF5Type(), dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
-		xmlTextValues << mHeavyFileName << ":" << groupName << "/" << dataHierarchy.back();
+		hid_t dataset = H5Dcreate(handle, mDataHierarchy.back().c_str(), array.getHDF5Type(), dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+		xmlTextValues << mHeavyFileName << ":" << groupName << "/" << mDataHierarchy.back();
 		status = H5Dwrite(dataset, array.getHDF5Type(), H5S_ALL, H5S_ALL, H5P_DEFAULT, array.getValuesPointer());
+		if(groupName.compare("") != 0)
+		{
+			H5Gclose(handle);
+		}
 		status = H5Dclose(dataset);
 		status = H5Sclose(dataspace);
 	}
@@ -108,82 +111,31 @@ void XdmfWriter::visit(XdmfArray & array, boost::shared_ptr<Loki::BaseVisitor> v
 		xmlTextValues << array.getValuesString();
 	}
 
-	xmlAddChild(xmlCurrentNode, xmlNewText((xmlChar*)xmlTextValues.str().c_str()));
-	xmlCurrentNode = parentNode;
-}
-
-void XdmfWriter::visit(XdmfDomain & domain, boost::shared_ptr<Loki::BaseVisitor> visitor)
-{
-	std::cout << "Writing Domain" << std::endl;
-	xmlNodePtr parentNode = xmlCurrentNode;
-	xmlCurrentNode = xmlNewChild(xmlCurrentNode, NULL, (xmlChar*)"Domain", NULL);
-
-	domain.traverse(visitor);
-
-	xmlCurrentNode = parentNode;
-}
-
-void XdmfWriter::visit(XdmfGeometry & geometry, boost::shared_ptr<Loki::BaseVisitor> visitor)
-{
-	std::cout << "Writing Geometry" << std::endl;
-	xmlNodePtr parentNode = xmlCurrentNode;
-	xmlCurrentNode = xmlNewChild(xmlCurrentNode, NULL, (xmlChar*)"Geometry", NULL);
-	xmlNewProp(xmlCurrentNode, (xmlChar*)"GeometryType", (xmlChar*)geometry.getGeometryType().getName().c_str());
-
-	dataHierarchy.push_back("XYZ");
-	geometry.traverse(visitor);
-	dataHierarchy.pop_back();
-
-	xmlCurrentNode = parentNode;
+	xmlAddChild(mXMLCurrentNode, xmlNewText((xmlChar*)xmlTextValues.str().c_str()));
+	mXMLCurrentNode = parentNode;
 }
 
-void XdmfWriter::visit(XdmfGrid & grid, boost::shared_ptr<Loki::BaseVisitor> visitor)
+void XdmfWriter::visit(XdmfItem & item, boost::shared_ptr<Loki::BaseVisitor> visitor)
 {
-	std::cout << "Writing Grid" << std::endl;
-	xmlNodePtr parentNode = xmlCurrentNode;
-    xmlCurrentNode = xmlNewChild(xmlCurrentNode, NULL, (xmlChar*)"Grid", NULL);
-	xmlNewProp(xmlCurrentNode, (xmlChar*)"Name", (xmlChar*)grid.getName().c_str());
-
-	dataHierarchy.push_back(grid.getName());
-	grid.traverse(visitor);
-	dataHierarchy.pop_back();
-
-	xmlCurrentNode = parentNode;
-}
-
-void XdmfWriter::visit(XdmfTopology & topology, boost::shared_ptr<Loki::BaseVisitor> visitor)
-{
-	std::cout << "Writing Topology" << std::endl;
-	xmlNodePtr parentNode = xmlCurrentNode;
-	xmlCurrentNode = xmlNewChild(xmlCurrentNode, NULL, (xmlChar*)"Topology", NULL);
-	xmlNewProp(xmlCurrentNode, (xmlChar*)"TopologyType", (xmlChar*)topology.getTopologyType().getName().c_str());
-	std::stringstream numberElementsString;
-	numberElementsString << topology.getNumberElements();
-	xmlNewProp(xmlCurrentNode, (xmlChar*)"NumberOfElements", (xmlChar*)numberElementsString.str().c_str());
-
-	dataHierarchy.push_back("Connectivity");
-	topology.traverse(visitor);
-	dataHierarchy.pop_back();
-
-	xmlCurrentNode = parentNode;
-}
-
-unsigned int XdmfWriter::getLightDataLimit() const
-{
-	return mLightDataLimit;
-}
-
-void XdmfWriter::setLightDataLimit(unsigned int numValues)
-{
-	mLightDataLimit = numValues;
-}
-
-std::string XdmfWriter::getHDF5GroupName()
-{
-	std::stringstream datasetName;
-	for(unsigned int i=0; i<dataHierarchy.size() - 1; ++i)
+	xmlNodePtr parentNode = mXMLCurrentNode;
+	mXMLCurrentNode = xmlNewChild(mXMLCurrentNode, NULL, (xmlChar*)item.getItemTag().c_str(), NULL);
+	const std::map<std::string, std::string> itemProperties = item.getItemProperties();
+	bool pushedHDF5Name = false;
+	for(std::map<std::string, std::string>::const_iterator iter = itemProperties.begin(); iter != itemProperties.end(); ++iter)
 	{
-		datasetName << "/" << dataHierarchy[i];
+		if(iter->first.compare("Name") == 0)
+		{
+			mDataHierarchy.push_back(iter->second);
+			pushedHDF5Name = true;
+		}
+		xmlNewProp(mXMLCurrentNode, (xmlChar*)iter->first.c_str(), (xmlChar*)iter->second.c_str());
 	}
-	return datasetName.str();
+	if(!pushedHDF5Name)
+	{
+		mDataHierarchy.push_back(item.getItemTag());
+	}
+
+	item.traverse(visitor);
+	mXMLCurrentNode = parentNode;
+	mDataHierarchy.pop_back();
 }

XdmfWriter.hpp

@@ -3,16 +3,10 @@
 
 // Forward Declarations
 class XdmfArray;
-class XdmfAttribute;
-class XdmfDomain;
-class XdmfGeometry;
-class XdmfGrid;
-class XdmfTopology;
 
 // Includes
 #include <hdf5.h>
 #include <libxml/tree.h>
-#include <sstream>
 #include <vector>
 #include "XdmfVisitor.hpp"
 
@@ -24,12 +18,7 @@ class XdmfTopology;
  * The XdmfItem as well as all children attached to the XdmfItem are written to disk.
  */
 class XdmfWriter : public XdmfVisitor,
-	public Loki::Visitor<XdmfArray>,
-	public Loki::Visitor<XdmfAttribute>,
-	public Loki::Visitor<XdmfDomain>,
-	public Loki::Visitor<XdmfGeometry>,
-	public Loki::Visitor<XdmfGrid>,
-	public Loki::Visitor<XdmfTopology> {
+	public Loki::Visitor<XdmfArray> {
 
 public:
 
@@ -58,44 +47,12 @@ public:
 	void visit(XdmfArray & array, boost::shared_ptr<Loki::BaseVisitor> visitor);
 
 	/**
-	 * Write an XdmfAttribute to disk
+	 * Write an XdmfItem to disk
 	 *
-	 * @param attribute a pointer to an XdmfAttribute to write to disk.
+	 * @param item a pointer to an XdmfItem to write to disk.
 	 * @param visitor a smart pointer to this XdmfVisitor --- aids in grid traversal.
 	 */
-	void visit(XdmfAttribute & attribute, boost::shared_ptr<Loki::BaseVisitor> visitor);
-
-	/**
-	 * Write an XdmfDomain to disk
-	 *
-	 * @param domain a pointer to an XdmfDomain to write to disk.
-	 * @param visitor a smart pointer to this XdmfVisitor --- aids in grid traversal.
-	 */
-	void visit(XdmfDomain & domain, boost::shared_ptr<Loki::BaseVisitor> visitor);
-
-	/**
-	 * Write an XdmfGeometry to disk
-	 *
-	 * @param geometry a pointer to an XdmfGeometry to write to disk.
-	 * @param visitor a smart pointer to this XdmfVisitor --- aids in grid traversal.
-	 */
-	void visit(XdmfGeometry & geometry, boost::shared_ptr<Loki::BaseVisitor> visitor);
-
-	/**
-	 * Write an XdmfGrid to disk
-	 *
-	 * @param grid a pointer to an XdmfGrid to write to disk.
-	 * @param visitor a smart pointer to this XdmfVisitor --- aids in grid traversal.
-	 */
-	void visit(XdmfGrid & grid, boost::shared_ptr<Loki::BaseVisitor> visitor);
-
-	/**
-	 * Write an XdmfTopology to disk
-	 *
-	 * @param topology a pointer to an XdmfTopology to write to disk.
-	 * @param visitor a smart pointer to this XdmfVisitor --- aids in grid traversal.
-	 */
-	void visit(XdmfTopology & topology, boost::shared_ptr<Loki::BaseVisitor> visitor);
+	void visit(XdmfItem & item, boost::shared_ptr<Loki::BaseVisitor> visitor);
 
 protected:
 
@@ -108,18 +65,30 @@ private:
 	void operator=(const XdmfWriter & writer);  // Not implemented.
 
 	/**
-	 * Uses the dataHierarchy to construct an appropriate hdf5 group name at the current point in writing.
+	 * Create a new HDF5 group if needed based on the dataHierarchy.  This is a recursive function used by getHDF5GroupHandle to construct
+	 * new hdf5 groups.
+	 *
+	 * @param groupPath the current place in the dataHierarchy being processed.
+	 * @param index the index in the dataHierarchy being processed.
+	 *
+	 * @return a string containing the path to the created group.
+	 */
+	std::string createHDF5Group(std::stringstream & groupPath, int index = 0);
+
+	/**
+	 * Get a handle to a hdf5 group to write into.  Uses the dataHierarchy to construct an appropriate hdf5 group name
+	 * at the current point in writing.
 	 *
-	 * @return a string containing the hdf5 group name.
+	 * @return a string containing the path to the created group.
 	 */
-	std::string getHDF5GroupName();
+	std::string getHDF5GroupHandle();
 
-	std::vector<std::string> dataHierarchy;
-	hid_t hdf5Handle;
+	std::vector<std::string> mDataHierarchy;
+	hid_t mHDF5Handle;
 	std::string mHeavyFileName;
 	unsigned int mLightDataLimit;
-	xmlDocPtr xmlDocument;
-	xmlNodePtr xmlCurrentNode;
+	xmlDocPtr mXMLDocument;
+	xmlNodePtr mXMLCurrentNode;
 };
 
 #endif /* XDMFWRITER_HPP_ */