ENH: Revert changes to XdmfSet to go back to XdmfArray implementation. Add Attributes to XdmfSet.

Xdmf.i

@@ -92,12 +92,6 @@ swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
 	}
 }
 
-%include std_set.i
-%template(std_set_uint) std::set<unsigned int>;
-
-// Abstract Base Classes
-%template() Loki::Visitor<XdmfSet>;
-
 // Shared Pointer Templates
 %shared_ptr(XdmfAttribute)
 %shared_ptr(XdmfAttributeCenter)

XdmfSet.cpp

@@ -5,7 +5,7 @@
  *      Author: kleiter
  */
 
-#include "XdmfArray.hpp"
+#include "XdmfAttribute.hpp"
 #include "XdmfHDF5Controller.hpp"
 #include "XdmfSet.hpp"
 #include "XdmfSetType.hpp"
@@ -17,7 +17,6 @@ boost::shared_ptr<XdmfSet> XdmfSet::New()
 }
 
 XdmfSet::XdmfSet() :
-	mHDF5Controller(boost::shared_ptr<XdmfHDF5Controller>()),
 	mName(""),
 	mSetType(XdmfSetType::NoSetType())
 {
@@ -29,14 +28,35 @@ XdmfSet::~XdmfSet()
 
 const std::string XdmfSet::ItemTag = "Set";
 
-boost::shared_ptr<XdmfHDF5Controller> XdmfSet::getHDF5Controller()
+boost::shared_ptr<XdmfAttribute> XdmfSet::getAttribute(const unsigned int index)
 {
-	return boost::const_pointer_cast<XdmfHDF5Controller>(static_cast<const XdmfSet &>(*this).getHDF5Controller());
+	return boost::const_pointer_cast<XdmfAttribute>(static_cast<const XdmfSet &>(*this).getAttribute(index));
 }
 
-boost::shared_ptr<const XdmfHDF5Controller> XdmfSet::getHDF5Controller() const
+boost::shared_ptr<const XdmfAttribute> XdmfSet::getAttribute(const unsigned int index) const
 {
-	return mHDF5Controller;
+	if(index < mAttributes.size())
+	{
+		return mAttributes[index];
+	}
+	return boost::shared_ptr<XdmfAttribute>();
+}
+
+boost::shared_ptr<XdmfAttribute> XdmfSet::getAttribute(const std::string & name)
+{
+	return boost::const_pointer_cast<XdmfAttribute>(static_cast<const XdmfSet &>(*this).getAttribute(name));
+}
+
+boost::shared_ptr<const XdmfAttribute> XdmfSet::getAttribute(const std::string & name) const
+{
+	for(std::vector<boost::shared_ptr<XdmfAttribute> >::const_iterator iter = mAttributes.begin(); iter != mAttributes.end(); ++iter)
+	{
+		if((*iter)->getName().compare(name) == 0)
+		{
+			return *iter;
+		}
+	}
+	return boost::shared_ptr<XdmfAttribute>();
 }
 
 std::map<std::string, std::string> XdmfSet::getItemProperties() const
@@ -57,14 +77,19 @@ std::string XdmfSet::getName() const
 	return mName;
 }
 
+unsigned int XdmfSet::getNumberAttributes() const
+{
+	return mAttributes.size();
+}
+
 boost::shared_ptr<const XdmfSetType> XdmfSet::getType() const
 {
 	return mSetType;
 }
 
-bool XdmfSet::isInitialized() const
+void XdmfSet::insert(const boost::shared_ptr<XdmfAttribute> attribute)
 {
-	return std::set<unsigned int>::size() > 0;
+	mAttributes.push_back(attribute);
 }
 
 void XdmfSet::populateItem(const std::map<std::string, std::string> & itemProperties, std::vector<boost::shared_ptr<XdmfItem> > & childItems, const XdmfCoreReader * const reader)
@@ -78,47 +103,40 @@ void XdmfSet::populateItem(const std::map<std::string, std::string> & itemProper
 	{
 		assert(false);
 	}
+	mSetType = XdmfSetType::New(itemProperties);
 	for(std::vector<boost::shared_ptr<XdmfItem> >::const_iterator iter = childItems.begin(); iter != childItems.end(); ++iter)
 	{
 		if(boost::shared_ptr<XdmfArray> array = boost::shared_dynamic_cast<XdmfArray>(*iter))
 		{
-			if(array->isInitialized())
-			{
-				for(unsigned int i=0; i<array->size(); ++i)
-				{
-					this->insert(array->getValueCopy<unsigned int>(i));
-				}
-			}
-			else
-			{
-				mHDF5Controller = array->getHDF5Controller();
-			}
+			this->swap(array);
+			// TODO: If multiple dataitems.
 		}
-	}
-	mSetType = XdmfSetType::New(itemProperties);
-}
-
-void XdmfSet::read()
-{
-	if(mHDF5Controller)
-	{
-		boost::shared_ptr<XdmfArray> setValues = XdmfArray::New();
-		mHDF5Controller->read(setValues.get());
-		for(unsigned int i=0; i<setValues->size(); ++i)
+		else if(boost::shared_ptr<XdmfAttribute> attribute = boost::shared_dynamic_cast<XdmfAttribute>(*iter))
 		{
-			this->insert(setValues->getValueCopy<unsigned int>(i));
+			this->insert(attribute);
 		}
 	}
 }
 
-void XdmfSet::release()
+void XdmfSet::removeAttribute(const unsigned int index)
 {
-	std::set<unsigned int>::clear();
+	if(index < mAttributes.size())
+	{
+		mAttributes.erase(mAttributes.begin() + index);
+	}
 }
 
-void XdmfSet::setHDF5Controller(const boost::shared_ptr<XdmfHDF5Controller> hdf5Controller)
+void XdmfSet::removeAttribute(const std::string & name)
 {
-	mHDF5Controller = hdf5Controller;
+	for(std::vector<boost::shared_ptr<XdmfAttribute> >::iterator iter = mAttributes.begin(); iter != mAttributes.end(); ++iter)
+	{
+		if((*iter)->getName().compare(name) == 0)
+		{
+			mAttributes.erase(iter);
+			return;
+		}
+	}
+	return;
 }
 
 void XdmfSet::setName(const std::string & name)
@@ -131,28 +149,11 @@ void XdmfSet::setType(const boost::shared_ptr<const XdmfSetType> setType)
 	mSetType = setType;
 }
 
-std::size_t XdmfSet::size() const
-{
-	if(std::set<unsigned int>::size() != 0)
-	{
-		return std::set<unsigned int>::size();
-	}
-	else if(mHDF5Controller)
-	{
-		return mHDF5Controller->size();
-	}
-	return 0;
-}
-
 void XdmfSet::traverse(const boost::shared_ptr<XdmfBaseVisitor> visitor)
 {
-	boost::shared_ptr<XdmfArray> setValues = XdmfArray::New();
-	setValues->reserve(std::set<unsigned int>::size());
-	for(XdmfSet::const_iterator iter = this->begin(); iter != this->end(); ++iter)
+	XdmfArray::traverse(visitor);
+	for(std::vector<boost::shared_ptr<XdmfAttribute> >::const_iterator iter = mAttributes.begin(); iter != mAttributes.end(); ++iter)
 	{
-		setValues->pushBack(*iter);
+		(*iter)->accept(visitor);
 	}
-	setValues->setHDF5Controller(mHDF5Controller);
-	setValues->accept(visitor);
-	mHDF5Controller = setValues->getHDF5Controller();
 }

XdmfSet.hpp

@@ -2,12 +2,12 @@
 #define XDMFSET_HPP_
 
 // Forward Declarations
+class XdmfAttribute;
 class XdmfHDF5Controller;
 class XdmfSetType;
 
 // Includes
-#include <set>
-#include "XdmfItem.hpp"
+#include "XdmfArray.hpp"
 
 /**
  * @brief Holds a collection of individual nodes, cells, faces, or edges that are part of an XdmfGrid.
@@ -17,8 +17,7 @@ class XdmfSetType;
  * set are determined by their id.  An XdmfSet can have XdmfAttributes attached that contain extra values
  * attached to the elements in the set.
  */
-class XdmfSet : public XdmfItem,
-	public std::set<unsigned int> {
+class XdmfSet : public XdmfArray {
 
 public:
 
@@ -31,22 +30,40 @@ public:
 
 	virtual ~XdmfSet();
 
-	LOKI_DEFINE_VISITABLE(XdmfSet, XdmfItem)
+	LOKI_DEFINE_VISITABLE(XdmfSet, XdmfArray)
 	static const std::string ItemTag;
 
 	/**
-	 * Get the hdf5 controller attached to this set.
+	 * Get an attribute attached to this set by index.
 	 *
-	 * @return the hdf5 controller attached to this set.
+	 * @param index of the attribute to retrieve.
+	 * @return requested attribute.  If not found a NULL pointer is returned.
 	 */
-	boost::shared_ptr<XdmfHDF5Controller> getHDF5Controller();
+	boost::shared_ptr<XdmfAttribute> getAttribute(const unsigned int index);
 
 	/**
-	 * Get the hdf5 controller attached to this set (const version).
+	 * Get an attribute attached to this set by index (const version).
 	 *
-	 * @return the hdf5 controller attached to this set.
+	 * @param index of the attribute to retrieve.
+	 * @return requested attribute.  If not found a NULL pointer is returned.
 	 */
-	boost::shared_ptr<const XdmfHDF5Controller> getHDF5Controller() const;
+	boost::shared_ptr<const XdmfAttribute> getAttribute(const unsigned int index) const;
+
+	/**
+	 * Get an attribute attached to this set by name.
+	 *
+	 * @param name of the attribute to retrieve.
+	 * @return requested attribute.  If not found a NULL pointer is returned.
+	 */
+	boost::shared_ptr<XdmfAttribute> getAttribute(const std::string & name);
+
+	/**
+	 * Get an attribute attached to this set by name (const version).
+	 *
+	 * @param name the name of the attribute to retrieve.
+	 * @return requested attribute.  If not found a NULL pointer is returned.
+	 */
+	boost::shared_ptr<const XdmfAttribute> getAttribute(const std::string & name) const;
 
 	std::map<std::string, std::string> getItemProperties() const;
 
@@ -60,33 +77,39 @@ public:
 	std::string getName() const;
 
 	/**
-	 * Get the XdmfSetType associated with this set.
+	 * Get the number of attributes attached to this grid.
 	 *
-	 * @return XdmfSetType of this set.
+	 * @return the number of attributes attached to this grid.
 	 */
-	boost::shared_ptr<const XdmfSetType> getType() const;
+	unsigned int getNumberAttributes() const;
 
 	/**
-	 * Returns whether the set is initialized (contains values in memory).
+	 * Get the XdmfSetType associated with this set.
+	 *
+	 * @return XdmfSetType of this set.
 	 */
-	bool isInitialized() const;
+	boost::shared_ptr<const XdmfSetType> getType() const;
 
 	/**
-	 * Read data from disk into memory.
+	 * Insert an attribute into the set.
+	 *
+	 * @param attribute an XdmfAttribute to attach to this set.
 	 */
-	void read();
+	void insert(const boost::shared_ptr<XdmfAttribute> attribute);
 
 	/**
-	 * Release all data held in memory.  The HDF5Controller remains attached.
+	 * Remove an attribute from the set by index.  If no attribute is at that index, no attributes are removed.
+	 *
+	 * @param index of the attribute to remove.
 	 */
-	void release();
+	void removeAttribute(const unsigned int index);
 
 	/**
-	 * Attach an hdf5 controller to this set.
+	 * Remove an attribute from the set by name.  If no attribute having the name is found, no attributes are removed.
 	 *
-	 * @param hdf5Controller to attach to this set.
+	 * @param name of the attribute to remove.
 	 */
-	void setHDF5Controller(const boost::shared_ptr<XdmfHDF5Controller> hdf5Controller);
+	void removeAttribute(const std::string & name);
 
 	/**
 	 * Set the name of the set.
@@ -102,8 +125,6 @@ public:
 	 */
 	void setType(const boost::shared_ptr<const XdmfSetType> setType);
 
-	std::size_t size() const;
-
 	void traverse(const boost::shared_ptr<XdmfBaseVisitor> visitor);
 
 protected:
@@ -116,8 +137,8 @@ private:
 	XdmfSet(const XdmfSet & set);  // Not implemented.
 	void operator=(const XdmfSet & set);  // Not implemented.
 
+	std::vector<boost::shared_ptr<XdmfAttribute> > mAttributes;
 	std::string mName;
-	boost::shared_ptr<XdmfHDF5Controller> mHDF5Controller;
 	boost::shared_ptr<const XdmfSetType> mSetType;
 };
 

tests/Cxx/TestXdmfSet.cpp

+#include "XdmfAttribute.hpp"
 #include "XdmfSet.hpp"
 #include "XdmfSetType.hpp"
 
@@ -16,11 +17,21 @@ int main(int argc, char* argv[])
 	set->setName("TEST");
 	assert(set->getName().compare("TEST") == 0);
 
-	assert(set->isInitialized() == false);
-	assert(set->find(0) == set->end());
-	set->insert(0);
-	assert(set->isInitialized() == true);
-	assert(set->find(0) != set->end());
-
+	assert(set->getNumberAttributes() == 0);
+	assert(set->getAttribute("") == NULL);
+	assert(set->getAttribute(0) == NULL);
+	boost::shared_ptr<XdmfAttribute> attribute = XdmfAttribute::New();
+	attribute->setName("foo");
+	set->insert(attribute);
+	assert(set->getNumberAttributes() == 1);
+	assert(set->getAttribute(0) == attribute);
+	assert(set->getAttribute("foo") == attribute);
+	set->removeAttribute(0);
+	assert(set->getNumberAttributes() == 0);
+	set->insert(attribute);
+	set->removeAttribute("no");
+	assert(set->getNumberAttributes() == 1);
+	set->removeAttribute("foo");
+	assert(set->getNumberAttributes() == 0);
 	return 0;
 }

tests/Cxx/TestXdmfVisitorValueCounter.cpp

@@ -4,8 +4,7 @@
 
 // Make a new XdmfVisitor that simply counts number of values
 class XdmfVisitorValueCounter : public XdmfVisitor,
-	public Loki::Visitor<XdmfArray>,
-	public Loki::Visitor<XdmfSet> {
+	public Loki::Visitor<XdmfArray> {
 
 public:
 
@@ -34,11 +33,6 @@ public:
 		mCount += array.size();
 	}
 
-	void visit(XdmfSet & set, boost::shared_ptr<Loki::BaseVisitor> visitor)
-	{
-		mCount += set.size();
-	}
-
 protected:
 
 	XdmfVisitorValueCounter() :

tests/Cxx/XdmfTestDataGenerator.hpp

@@ -63,7 +63,7 @@ public:
 		int nodeIds[] = {0, 1, 2};
 		nodeSet->setName("Node Set");
 		nodeSet->setType(XdmfSetType::Node());
-		nodeSet->insert(nodeIds, nodeIds + 3);
+		nodeSet->copyValues(0, &nodeIds[0], 3);
 
 		// Add Time
 		boost::shared_ptr<XdmfTime> time = XdmfTime::New(100);

tests/Python/TestXdmfSet.py

@@ -10,7 +10,6 @@ if __name__ == "__main__":
 	set.setType(XdmfSetType.Node())
 	assert(set.getType() == XdmfSetType.Node())
 	assert(set.size() == 0)
-	set.insert(1)
-	#assert(set.size() == 1)
-	#print set.find("1")
+	set.copyValueAsInt32(0, 1)
+	assert(set.size() == 1)
 

utils/XdmfExodusReader.cpp

@@ -288,16 +288,17 @@ boost::shared_ptr<XdmfGrid> XdmfExodusReader::read(const std::string & fileName,
 
 		if (num_nodes_in_set > 0)
 		{
-			int * node_set_node_list = new int[num_nodes_in_set];
-			ex_get_node_set(exodusHandle, nodeSetIds[i], node_set_node_list);
-
 			boost::shared_ptr<XdmfSet> set = XdmfSet::New();
 			set->setName(node_set_names[i]);
 			set->setType(XdmfSetType::Node());
+			set->initialize(XdmfArrayType::Int32(), num_nodes_in_set);
+			int * setPointer = (int*)set->getValuesPointer();
+			ex_get_node_set(exodusHandle, nodeSetIds[i], setPointer);
 
+			// Subtract all node ids by 1 since exodus indices start at 1
 			for(unsigned int j=0; j<num_nodes_in_set; ++j)
 			{
-				set->insert(node_set_node_list[j] - 1);
+				setPointer[i]--;
 			}
 
 			toReturn->insert(set);
@@ -307,8 +308,6 @@ boost::shared_ptr<XdmfGrid> XdmfExodusReader::read(const std::string & fileName,
 				set->accept(heavyDataWriter);
 				set->release();
 			}
-
-			delete [] node_set_node_list;
 		}
 		delete [] node_set_names[i];
 	}

utils/XdmfExodusWriter.cpp

@@ -409,11 +409,11 @@ void XdmfExodusWriter::write(const std::string & filePath, const boost::shared_p
 			{
 				ex_put_side_set_param(exodusHandle, setId + i, numValues, 0);
 				int * values = new int[numValues];
-				unsigned int k=0;
-				for(XdmfSet::const_iterator iter = currSet->begin(); iter != currSet->end(); ++iter, ++k)
+				currSet->getValuesCopy(0, values, numValues);
+				for(unsigned int k=0; k<numValues; ++k)
 				{
 					// Add 1 to xdmf ids because exodus ids begin at 1
-					values[k] = *iter + 1;
+					values[k]++;
 				}
 				ex_put_side_set(exodusHandle, setId + i, values, NULL);
 				ex_put_name(exodusHandle, EX_SIDE_SET, setId + i, name.c_str());
@@ -423,11 +423,11 @@ void XdmfExodusWriter::write(const std::string & filePath, const boost::shared_p
 			{
 				ex_put_node_set_param(exodusHandle, setId + i, numValues, 0);
 				int * values = new int[numValues];
-				unsigned int k=0;
-				for(XdmfSet::const_iterator iter = currSet->begin(); iter != currSet->end(); ++iter, ++k)
+				currSet->getValuesCopy(0, values, numValues);
+				for(unsigned int k=0; k<numValues; ++k)
 				{
 					// Add 1 to xdmf ids because exodus ids begin at 1
-					values[k] = *iter + 1;
+					values[k]++;
 				}
 				ex_put_node_set(exodusHandle, setId + i, values);
 				ex_put_name(exodusHandle, EX_NODE_SET, setId + i, name.c_str());

utils/XdmfPartitioner.cpp

@@ -355,24 +355,24 @@ boost::shared_ptr<XdmfGridCollection> XdmfPartitioner::partition(const boost::sh
 
 				if(currSet->getType() == XdmfSetType::Cell() || currSet->getType() == XdmfSetType::Face() || currSet->getType() == XdmfSetType::Edge())
 				{
-					for(XdmfSet::const_iterator iter = currSet->begin(); iter != currSet->end(); ++iter)
+					for(unsigned int k=0; k<currSet->size(); ++k)
 					{
-						std::vector<unsigned int>::const_iterator val = std::find(currElemIds.begin(), currElemIds.end(), *iter);
+						std::vector<unsigned int>::const_iterator val = std::find(currElemIds.begin(), currElemIds.end(), currSet->getValueCopy<unsigned int>(k));
 						if(val != currElemIds.end())
 						{
 							unsigned int valToPush = val - currElemIds.begin();
-							partitionedSet->insert(valToPush);
+							partitionedSet->pushBack(valToPush);
 						}
 					}
 				}
 				else if(currSet->getType() == XdmfSetType::Node())
 				{
-					for(XdmfSet::const_iterator iter = currSet->begin(); iter != currSet->end(); ++iter)
+					for(unsigned int k=0; k<currSet->size(); ++k)
 					{
-						std::map<unsigned int, unsigned int>::const_iterator val = currNodeMap.find(*iter);
+						std::map<unsigned int, unsigned int>::const_iterator val = currNodeMap.find(currSet->getValueCopy<unsigned int>(k));
 						if(val != currNodeMap.end())
 						{
-							partitionedSet->insert(val->second);
+							partitionedSet->pushBack(val->second);
 						}
 					}
 				}