ENH: Add XdmfSet. Remove getName() method from ItemProperties.

CMakeLists.txt

@@ -48,6 +48,8 @@ set(XdmfSources
 	XdmfItemProperty
 	XdmfObject
 	XdmfReader
+	XdmfSet
+	XdmfSetType
 	XdmfTopology
 	XdmfTopologyType
 	XdmfVisitor

Xdmf.i

@@ -20,6 +20,8 @@ swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
 	#include <XdmfItemProperty.hpp>
 	#include <XdmfObject.hpp>
 	#include <XdmfReader.hpp>
+	#include <XdmfSet.hpp>
+	#include <XdmfSetType.hpp>
 	#include <XdmfTopology.hpp>
 	#include <XdmfTopologyType.hpp>
 	#include <XdmfVisitor.hpp>
@@ -60,6 +62,7 @@ namespace boost {
 %template(XdmfItemPtr) boost::shared_ptr<XdmfItem>;
 %template(XdmfObjPtr) boost::shared_ptr<XdmfObject>;
 %template(XdmfReaderPtr) boost::shared_ptr<XdmfReader>;
+%template(XdmfSetPtr) boost::shared_ptr<XdmfSet>;
 %template(XdmfTopologyPtr) boost::shared_ptr<XdmfTopology>;
 %template(XdmfVisitorPtr) boost::shared_ptr<XdmfVisitor>;
 %template(XdmfWriterPtr) boost::shared_ptr<XdmfWriter>;
@@ -94,6 +97,9 @@ SWIG_SHARED_PTR_DERIVED(XdmfHDF5Writer, Loki::BaseVisitor);
 SWIG_SHARED_PTR_DERIVED(XdmfHDF5Writer, XdmfObject);
 SWIG_SHARED_PTR_DERIVED(XdmfItem, XdmfObject);
 SWIG_SHARED_PTR_DERIVED(XdmfReader, XdmfObject);
+SWIG_SHARED_PTR_DERIVED(XdmfSet, XdmfDataItem);
+SWIG_SHARED_PTR_DERIVED(XdmfSet, XdmfItem);
+SWIG_SHARED_PTR_DERIVED(XdmfSet, XdmfObject);
 SWIG_SHARED_PTR_DERIVED(XdmfTopology, XdmfDataItem);
 SWIG_SHARED_PTR_DERIVED(XdmfTopology, XdmfItem);
 SWIG_SHARED_PTR_DERIVED(XdmfTopology, XdmfObject);
@@ -123,6 +129,8 @@ SWIG_SHARED_PTR_DERIVED(XdmfWriter, XdmfObject);
 %include XdmfGeometry.hpp
 %include XdmfGeometryType.hpp
 %include XdmfGrid.hpp
+%include XdmfSet.hpp
+%include XdmfSetType.hpp
 %include XdmfTopology.hpp
 %include XdmfTopologyType.hpp
 

XdmfArray.cpp

@@ -558,6 +558,11 @@ void XdmfArray::initialize(const std::string & type, const unsigned int precisio
 	}
 }
 
+bool XdmfArray::isInitialized()
+{
+	return mHaveArray || mHaveArrayPointer;
+}
+
 void XdmfArray::internalizeArrayPointer()
 {
 	if(mHaveArrayPointer)

XdmfArray.hpp

@@ -179,6 +179,11 @@ public:
 	template <typename T>
 	boost::shared_ptr<std::vector<T> > initialize();
 
+	/**
+	 * Returns whether the array is initialized (contains values in memory).
+	 */
+	bool isInitialized();
+
 	/**
 	 * Copy a value to the back of this array
 	 */

XdmfAttributeCenter.cpp

@@ -77,7 +77,7 @@ XdmfAttributeCenter XdmfAttributeCenter::New(const std::map<std::string, std::st
 	assert(false);
 }
 
-XdmfAttributeCenter& XdmfAttributeCenter::operator=(const XdmfAttributeCenter & attributeCenter)
+XdmfAttributeCenter & XdmfAttributeCenter::operator=(const XdmfAttributeCenter & attributeCenter)
 {
   if(this != &attributeCenter)
   {
@@ -96,11 +96,6 @@ bool XdmfAttributeCenter::operator!=(const XdmfAttributeCenter & attributeCenter
   return !this->operator==(attributeCenter);
 }
 
-std::string XdmfAttributeCenter::getName() const
-{
-	return mName;
-}
-
 void XdmfAttributeCenter::getProperties(std::map<std::string, std::string> & collectedProperties) const
 {
 	collectedProperties["Center"] = mName;

XdmfAttributeCenter.hpp

@@ -32,13 +32,6 @@ public:
 	static XdmfAttributeCenter Edge();
 	static XdmfAttributeCenter Node();
 
-	/**
-	 * Get the name of this attribute center.
-	 *
-	 * @return a string containing the name.
-	 */
-	std::string getName() const;
-
 	void getProperties(std::map<std::string, std::string> & collectedProperties) const;
 
 	/**
@@ -58,7 +51,7 @@ public:
 	bool operator!=(const XdmfAttributeCenter & attributeCenter) const;
 
 	XdmfAttributeCenter(const XdmfAttributeCenter & attributeCenter);
-	XdmfAttributeCenter& operator=(const XdmfAttributeCenter & attributeCenter);
+	XdmfAttributeCenter & operator=(const XdmfAttributeCenter & attributeCenter);
 
 protected:
 

XdmfAttributeType.cpp

@@ -95,7 +95,7 @@ XdmfAttributeType XdmfAttributeType::New(const std::map<std::string, std::string
 	assert(false);
 }
 
-XdmfAttributeType& XdmfAttributeType::operator=(const XdmfAttributeType & attributeType)
+XdmfAttributeType & XdmfAttributeType::operator=(const XdmfAttributeType & attributeType)
 {
 	if(this != &attributeType)
 	{
@@ -114,11 +114,6 @@ bool XdmfAttributeType::operator!=(const XdmfAttributeType & attributeType) cons
 	return !this->operator==(attributeType);
 }
 
-std::string XdmfAttributeType::getName() const
-{
-	return mName;
-}
-
 void XdmfAttributeType::getProperties(std::map<std::string, std::string> & collectedProperties) const
 {
 	collectedProperties["AttributeType"] = mName;

XdmfAttributeType.hpp

@@ -36,13 +36,6 @@ public:
 	static XdmfAttributeType Tensor6();
 	static XdmfAttributeType GlobalId();
 
-	/**
-	 * Get the name of this attribute type
-	 *
-	 * @return a string containing the name.
-	 */
-	std::string getName() const;
-
 	void getProperties(std::map<std::string, std::string> & collectedProperties) const;
 
 	/*
@@ -62,7 +55,7 @@ public:
 	bool operator!=(const XdmfAttributeType & attributeType) const;
 
 	XdmfAttributeType(const XdmfAttributeType & attributeType);
-	XdmfAttributeType& operator=(const XdmfAttributeType & attributeType);
+	XdmfAttributeType & operator=(const XdmfAttributeType & attributeType);
 
 protected:
 

XdmfGeometryType.cpp

@@ -116,7 +116,7 @@ XdmfGeometryType XdmfGeometryType::New(const std::map<std::string, std::string>
 	assert(false);
 }
 
-XdmfGeometryType& XdmfGeometryType::operator=(const XdmfGeometryType& geometryType)
+XdmfGeometryType & XdmfGeometryType::operator=(const XdmfGeometryType& geometryType)
 {
 	if(this != &geometryType)
 	{
@@ -141,11 +141,6 @@ int XdmfGeometryType::getDimensions() const
 	return mDimensions;
 }
 
-std::string XdmfGeometryType::getName() const
-{
-	return mName;
-}
-
 void XdmfGeometryType::getProperties(std::map<std::string, std::string> & collectedProperties) const
 {
 	collectedProperties["GeometryType"] = this->mName;

XdmfGeometryType.hpp

@@ -47,17 +47,10 @@ public:
 	 */
 	int getDimensions() const;
 
-	/**
-	 * Get the name of this geometry type
-	 *
-	 * @return a string containing the name.
-	 */
-	std::string getName() const;
-
 	void getProperties(std::map<std::string, std::string> & collectedProperties) const;
 
 	/*
-	 * Compare two XdmfGeometry types for equality.
+	 * Compare two XdmfGeometryTypes for equality.
 	 *
 	 * @param geometryType a XdmfGeometryType to compare equality to.
 	 * @return true if the XdmfGeometryTypes are equal.
@@ -65,7 +58,7 @@ public:
 	bool operator==(const XdmfGeometryType & geometryType) const;
 
 	/**
-	 * Compare two XdmfGeometry types for inequality.
+	 * Compare two XdmfGeometryTypes for inequality.
 	 *
 	 * @param geometryType a XdmfGeometryType to compare inequality to.
 	 * @return true if the XdmfGeometryTypes are not equal.
@@ -73,7 +66,7 @@ public:
 	bool operator!=(const XdmfGeometryType & geometryType) const;
 
 	XdmfGeometryType(const XdmfGeometryType & geometryType);
-	XdmfGeometryType& operator=(const XdmfGeometryType & geometryType);
+	XdmfGeometryType & operator=(const XdmfGeometryType & geometryType);
 
 protected:
 

XdmfGrid.cpp

@@ -8,6 +8,7 @@
 #include "XdmfAttribute.hpp"
 #include "XdmfGrid.hpp"
 #include "XdmfGeometry.hpp"
+#include "XdmfSet.hpp"
 #include "XdmfTopology.hpp"
 
 XdmfGrid::XdmfGrid() :
@@ -30,7 +31,6 @@ boost::shared_ptr<XdmfAttribute> XdmfGrid::getAttribute(unsigned int index)
 	if(index >= mAttributes.size())
 	{
 		assert(false);
-		// Out of range --- should we throw exceptions?
 	}
 	return mAttributes[index];
 }
@@ -40,7 +40,6 @@ boost::shared_ptr<const XdmfAttribute> XdmfGrid::getAttribute(unsigned int index
 	if(index >= mAttributes.size())
 	{
 		assert(false);
-		// Out of range --- should we throw exceptions?
 	}
 	return mAttributes[index];
 }
@@ -77,6 +76,29 @@ unsigned int XdmfGrid::getNumberOfAttributes() const
 	return mAttributes.size();
 }
 
+unsigned int XdmfGrid::getNumberOfSets() const
+{
+	return mSets.size();
+}
+
+boost::shared_ptr<XdmfSet> XdmfGrid::getSet(unsigned int index)
+{
+	if(index >= mSets.size())
+	{
+		assert(false);
+	}
+	return mSets[index];
+}
+
+boost::shared_ptr<const XdmfSet> XdmfGrid::getSet(unsigned int index) const
+{
+	if(index >= mSets.size())
+	{
+		assert(false);
+	}
+	return mSets[index];
+}
+
 boost::shared_ptr<XdmfTopology> XdmfGrid::getTopology()
 {
 	return mTopology;
@@ -92,6 +114,11 @@ void XdmfGrid::insert(boost::shared_ptr<XdmfAttribute> attribute)
 	mAttributes.push_back(attribute);
 }
 
+void XdmfGrid::insert(boost::shared_ptr<XdmfSet> set)
+{
+	mSets.push_back(set);
+}
+
 void XdmfGrid::populateItem(const std::map<std::string, std::string> & itemProperties, std::vector<boost::shared_ptr<XdmfItem> > & childItems)
 {
 	std::map<std::string, std::string>::const_iterator name = itemProperties.find("Name");
@@ -113,6 +140,10 @@ void XdmfGrid::populateItem(const std::map<std::string, std::string> & itemPrope
 		{
 			mGeometry = geometry;
 		}
+		if(boost::shared_ptr<XdmfSet> set = boost::shared_dynamic_cast<XdmfSet>(*iter))
+		{
+			this->insert(set);
+		}
 		else if(boost::shared_ptr<XdmfTopology> topology = boost::shared_dynamic_cast<XdmfTopology>(*iter))
 		{
 			mTopology = topology;
@@ -143,4 +174,8 @@ void XdmfGrid::traverse(boost::shared_ptr<Loki::BaseVisitor> visitor)
 	{
 		(*iter)->accept(visitor);
 	}
+	for(std::vector<boost::shared_ptr<XdmfSet> >::const_iterator iter = mSets.begin(); iter != mSets.end(); ++iter)
+	{
+		(*iter)->accept(visitor);
+	}
 }

XdmfGrid.hpp

@@ -4,6 +4,7 @@
 // Forward Declarations
 class XdmfAttribute;
 class XdmfGeometry;
+class XdmfSet;
 class XdmfTopology;
 
 // Includes
@@ -15,7 +16,8 @@ class XdmfTopology;
  *
  * XdmfGrid represents a mesh.  It is required to contain two other Xdmf data structures, an XdmfGeometry
  * that stores point locations and an XdmfTopology that store connectivity information.  XdmfAttributes can be inserted
- * into the XdmfGrid to specify values attached at various parts of the mesh.
+ * into the XdmfGrid to specify values attached at various parts of the mesh.  XdmfSets can be inserted in the XdmfGrid
+ * to specify collections of mesh elements.
  */
 class XdmfGrid : public XdmfItem {
 
@@ -73,6 +75,29 @@ public:
 	 */
 	unsigned int getNumberOfAttributes() const;
 
+	/**
+	 * Get the number of XdmfSets attached to this grid.
+	 *
+	 * @return an unsigned int containing the number of XdmfSets attached to this grid.
+	 */
+	unsigned int getNumberOfSets() const;
+
+	/**
+	 * Get an XdmfSet attached to this grid.
+	 *
+	 * @param index of the XdmfSet to retrieve.
+	 * @return pointer to the XdmfSet attached to this grid.
+	 */
+	boost::shared_ptr<XdmfSet> getSet(unsigned int index);
+
+	/**
+	 * Get an XdmfSet attached to this grid (const version).
+	 *
+	 * @param index of the XdmfSet to retrieve.
+	 * @return pointer to the XdmfSet attached to this grid.
+	 */
+	boost::shared_ptr<const XdmfSet> getSet(unsigned int index) const;
+
 	/**
 	 * Get the XdmfTopology associated with this grid.
 	 *
@@ -90,21 +115,28 @@ public:
 	/**
 	 * Insert an XdmfAttribute into the grid.
 	 *
-	 * @param attribute a smart pointer to the XdmfAttribute to attach to this grid.
+	 * @param attribute an XdmfAttribute to attach to this grid.
 	 */
 	void insert(boost::shared_ptr<XdmfAttribute> attribute);
 
+	/**
+	 * Insert an XdmfSet into the grid.
+	 *
+	 * @param set an XdmfSet to attach to this grid.
+	 */
+	void insert(boost::shared_ptr<XdmfSet> set);
+
 	/**
 	 * Set the XdmfGeometry associated with this grid.
 	 *
-	 * @param geometry a smart pointer to the XdmfGeometry to attach to this grid.
+	 * @param geometry an XdmfGeometry to attach to this grid.
 	 */
 	void setGeometry(boost::shared_ptr<XdmfGeometry> geometry);
 
 	/**
 	 * Set the XdmfTopology associated with this grid.
 	 *
-	 * @param topology a smart pointer to the XdmfTopology to attach to this grid.
+	 * @param topology an XdmfTopology to attach to this grid.
 	 */
 	void setTopology(boost::shared_ptr<XdmfTopology> topology);
 
@@ -130,6 +162,7 @@ private:
 
 	std::vector<boost::shared_ptr<XdmfAttribute> > mAttributes;
 	boost::shared_ptr<XdmfGeometry> mGeometry;
+	std::vector<boost::shared_ptr<XdmfSet> > mSets;
 	boost::shared_ptr<XdmfTopology> mTopology;
 	std::string mName;
 };

XdmfReader.cpp

@@ -6,6 +6,7 @@
 #include "XdmfDomain.hpp"
 #include "XdmfGeometry.hpp"
 #include "XdmfGrid.hpp"
+#include "XdmfSet.hpp"
 #include "XdmfTopology.hpp"
 
 
@@ -51,6 +52,10 @@ public:
 		{
 			newItem = XdmfGrid::New();
 		}
+		else if(itemTag.compare(XdmfSet::ItemTag) == 0)
+		{
+			newItem = XdmfSet::New();
+		}
 		else if(itemTag.compare(XdmfTopology::ItemTag) == 0)
 		{
 			newItem = XdmfTopology::New();

XdmfSet.cpp

+/*
+ * XdmfSet.cpp
+ *
+ *  Created on: Jan 29, 2010
+ *      Author: kleiter
+ */
+
+#include "XdmfSet.hpp"
+
+XdmfSet::XdmfSet() :
+	mSetType(XdmfSetType::NoSetType()),
+	mName("")
+{
+	std::cout << "Created Set " << this << std::endl;
+}
+
+XdmfSet::~XdmfSet()
+{
+	std::cout << "Deleted Set " << this << std::endl;
+}
+
+std::string XdmfSet::ItemTag = "Set";
+
+std::string XdmfSet::getName() const
+{
+	return mName;
+}
+
+XdmfSetType XdmfSet::getSetType() const
+{
+	return mSetType;
+}
+
+std::map<std::string, std::string> XdmfSet::getItemProperties() const
+{
+	std::map<std::string, std::string> setProperties;
+	setProperties["Name"] = mName;
+	mSetType.getProperties(setProperties);
+	return setProperties;
+}
+
+std::string XdmfSet::getItemTag() const
+{
+	return ItemTag;
+}
+
+void XdmfSet::populateItem(const std::map<std::string, std::string> & itemProperties, std::vector<boost::shared_ptr<XdmfItem> > & childItems)
+{
+	std::map<std::string, std::string>::const_iterator name = itemProperties.find("Name");
+	if(name != itemProperties.end())
+	{
+		mName = name->second;
+	}
+	else
+	{
+		assert(false);
+	}
+	mSetType = XdmfSetType::New(itemProperties);
+	XdmfDataItem::populateItem(itemProperties, childItems);
+}
+
+void XdmfSet::setName(const std::string & name)
+{
+	mName= name;
+}
+
+void XdmfSet::setSetType(const XdmfSetType & setType)
+{
+	mSetType = setType;
+}

XdmfSet.hpp

+#ifndef XDMFSET_HPP_
+#define XDMFSET_HPP_
+
+// Includes
+#include "XdmfDataItem.hpp"
+#include "XdmfSetType.hpp"
+
+/**
+ * @brief Holds a collection of individual nodes, cells, faces, or edges that are part of an XdmfGrid.
+ *
+ * An XdmfSet holds a collection of nodes, cells, faces, or edges that are part of an XdmfGrid.  For instance,
+ * a simulation may want to record a set of nodes along a boundary.  The individual elements making up the
+ * set are determined by their id.  An XdmfSet can have XdmfAttributes attached that give extra values
+ * attached to the components of the set.
+ */
+class XdmfSet : public XdmfDataItem {
+
+public:
+
+	XdmfNewMacro(XdmfSet);
+	LOKI_DEFINE_VISITABLE(XdmfSet, XdmfDataItem)
+	static std::string ItemTag;
+
+	/**
+	 * Get the XdmfSetType associated with this set.
+	 *
+	 * @return XdmfSetType of this set.
+	 */
+	XdmfSetType getSetType() const;
+
+	std::map<std::string, std::string> getItemProperties() const;
+
+	std::string getItemTag() const;
+
+	/**
+	 * Get the name of the set.
+	 *
+	 * @return a string containing the name of the set.
+	 */
+	std::string getName() const;
+
+	/**
+	 * Set the name of the set.
+	 *
+	 * @param name a string containing the name to set.
+	 */
+	void setName(const std::string & name);
+
+	/**
+	 * Set the XdmfSetType associated with this set.
+	 *
+	 * @param setType the XdmfSetType to set.
+	 */
+	void setSetType(const XdmfSetType & setType);
+
+protected:
+
+	XdmfSet();
+	virtual ~XdmfSet();
+	virtual void populateItem(const std::map<std::string, std::string> & itemProperties, std::vector<boost::shared_ptr<XdmfItem> > & childItems);
+
+private:
+
+	XdmfSet(const XdmfSet & set);  // Not implemented.
+	void operator=(const XdmfSet & set);  // Not implemented.
+
+	std::string mName;
+	XdmfSetType mSetType;
+};
+
+#endif /* XDMFSET_HPP_ */

XdmfSetType.cpp

+/*
+ * XdmfSetType.cpp
+ *
+ *  Created on: Jan 29, 2010
+ *      Author: kleiter
+ */
+
+#include "XdmfSetType.hpp"
+
+// Supported XdmfSetTypes
+XdmfSetType XdmfSetType::NoSetType()
+{
+	return XdmfSetType("None");
+}
+
+XdmfSetType XdmfSetType::Node()
+{
+	return XdmfSetType("Node");
+}
+
+XdmfSetType XdmfSetType::Cell()
+{
+	return XdmfSetType("Cell");
+}
+
+XdmfSetType XdmfSetType::Face()
+{
+	return XdmfSetType("Face");
+}
+
+XdmfSetType XdmfSetType::Edge()
+{
+	return XdmfSetType("Edge");
+}
+
+XdmfSetType::XdmfSetType(const XdmfSetType & setType):
+	mName(setType.mName)
+{
+}
+
+XdmfSetType::XdmfSetType(const std::string & name) :
+	mName(name)
+{
+}
+
+XdmfSetType XdmfSetType::New(const std::map<std::string, std::string> & itemProperties)
+{
+	std::map<std::string, std::string>::const_iterator type = itemProperties.find("SetType");
+	if(type != itemProperties.end())
+	{
+		const std::string typeVal = type->second;
+		if(typeVal.compare("None") == 0)
+		{
+			return NoSetType();
+		}
+		else if(typeVal.compare("Node") == 0)
+		{
+			return Node();
+		}
+		else if(typeVal.compare("Cell") == 0)
+		{
+			return Cell();
+		}
+		else if(typeVal.compare("Face") == 0)
+		{
+			return Face();
+		}
+		else if(typeVal.compare("Edge") == 0)
+		{
+			return Edge();
+		}
+		else
+		{
+			assert(false);
+		}
+	}
+	assert(false);
+}
+
+XdmfSetType & XdmfSetType::operator=(const XdmfSetType & setType)
+{
+	if(this != &setType)
+	{
+		mName = setType.mName;