ENH:

	Add XdmfArray to store values --- modify XdmfDataItem to contain an XdmfArray.
	Modify Tests to use new XdmfArray.
	Modify XdmfVisitor to use new XdmfArray.
	Add Python Tests and move Cxx tests to their own directory.

CMake/UsePythonTest.cmake

+# Add a python test from a python file
+# One cannot simply do:
+# SET(ENV{PYTHONPATH} ${LIBRARY_OUTPUT_PATH})
+# SET(my_test "from test_mymodule import *\;test_mymodule()")
+# ADD_TEST(PYTHON-TEST-MYMODULE  python -c ${my_test})
+# Since cmake is only transmitting the ADD_TEST line to ctest thus you are loosing
+# the env var. The only way to store the env var is to physically write in the cmake script
+# whatever PYTHONPATH you want and then add the test as 'cmake -P python_test.cmake'
+# 
+# Usage:
+# SET_SOURCE_FILES_PROPERTIES(test.py PROPERTIES PYTHONPATH
+#   "${LIBRARY_OUTPUT_PATH}:${VTK_DIR}")
+# ADD_PYTHON_TEST(PYTHON-TEST test.py)
+
+# Need python interpreter:
+FIND_PACKAGE(PythonInterp REQUIRED)
+
+MACRO(ADD_PYTHON_TEST TESTNAME FILENAME)
+  GET_SOURCE_FILE_PROPERTY(loc ${FILENAME} LOCATION)
+  GET_SOURCE_FILE_PROPERTY(pyenv ${FILENAME} PYTHONPATH)
+  STRING(REGEX REPLACE ";" " " wo_semicolumn "${ARGN}")
+  FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/${TESTNAME}.cmake
+"
+  SET(ENV{PYTHONPATH} ${pyenv})
+  EXECUTE_PROCESS(
+  	COMMAND ${PYTHON_EXECUTABLE} ${loc} ${wo_semicolumn}
+  	#WORKING_DIRECTORY @LIBRARY_OUTPUT_PATH@
+  	RESULT_VARIABLE import_res
+  	OUTPUT_VARIABLE import_output
+  	ERROR_VARIABLE  import_output
+  )
+  
+  # Pass the output back to ctest
+  MESSAGE("\${import_output}")
+  IF(import_res)
+    MESSAGE(SEND_ERROR "\${import_res}")
+  ENDIF(import_res)
+"
+)
+  ADD_TEST(${TESTNAME} cmake -P ${CMAKE_CURRENT_BINARY_DIR}/${TESTNAME}.cmake)
+ENDMACRO(ADD_PYTHON_TEST)
+
+# Byte compile recursively a directory (DIRNAME)
+MACRO(ADD_PYTHON_COMPILEALL_TEST DIRNAME)
+  # First get the path:
+  GET_FILENAME_COMPONENT(temp_path "${PYTHON_LIBRARIES}" PATH)
+  # Find the python script:
+  GET_FILENAME_COMPONENT(PYTHON_COMPILE_ALL_PY "${temp_path}/../compileall.py" ABSOLUTE)
+  # add test, use DIRNAME to create uniq name for the test:
+  ADD_TEST(COMPILE_ALL-${DIRNAME} ${PYTHON_EXECUTABLE} "${PYTHON_COMPILE_ALL_PY}" -q ${DIRNAME})
+ENDMACRO(ADD_PYTHON_COMPILEALL_TEST)
+

CMakeLists.txt

 project(Xdmf2)
 cmake_minimum_required(VERSION 2.6)
 
+set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/CMake ${CMAKE_MODULE_PATH})
 include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 
 set(BUILD_SHARED_LIBS true)
@@ -29,12 +30,12 @@ if(XDMF_WRAP_PYTHON)
 endif(XDMF_WRAP_PYTHON)
 
 set(XdmfSources
+	XdmfArray
 	XdmfAttribute
 	XdmfAttributeCenter
 	XdmfAttributeType
 	XdmfDataItem
-	XdmfDataItemType
-	XdmfDomain
+  XdmfDomain
 	XdmfGeometry
 	XdmfGeometryType
 	XdmfGrid
@@ -63,6 +64,4 @@ option(BUILD_TESTING OFF)
 if(BUILD_TESTING)
 	enable_testing()
 	add_subdirectory(tests)
-	add_executable(XdmfTest test.cpp)
-	target_link_libraries(XdmfTest Xdmf)
 endif(BUILD_TESTING)

Xdmf.i

@@ -15,6 +15,7 @@ namespace boost {
 }
 
 %template(XdmfAttributePtr) boost::shared_ptr<XdmfAttribute>;
+%template(XdmfArrayPtr) boost::shared_ptr<XdmfArray>;
 %template(XdmfDataItemPtr) boost::shared_ptr<XdmfDataItem>;
 %template(XdmfDomainPtr) boost::shared_ptr<XdmfDomain>;
 %template(XdmfGeometryPtr) boost::shared_ptr<XdmfGeometry>;
@@ -26,11 +27,11 @@ namespace boost {
 
 %module Xdmf
 %{
+  #include <XdmfArray.hpp>
   #include <XdmfAttribute.hpp>
   #include <XdmfAttributeCenter.hpp>
   #include <XdmfAttributeType.hpp>
   #include <XdmfDataItem.hpp>
-  #include <XdmfDataItemType.hpp>
   #include <XdmfDomain.hpp>
   #include <XdmfGeometry.hpp>
   #include <XdmfGeometryType.hpp>
@@ -48,14 +49,36 @@ namespace boost {
 %include XdmfVisitor.hpp
 
 %include XdmfDataItem.hpp
-%include XdmfDataItemType.hpp
 
 %include XdmfAttribute.hpp
 %include XdmfAttributeCenter.hpp
 %include XdmfAttributeType.hpp
+%include XdmfArray.hpp
 %include XdmfDomain.hpp
 %include XdmfGeometry.hpp
 %include XdmfGeometryType.hpp
 %include XdmfGrid.hpp
 %include XdmfTopology.hpp
 %include XdmfTopologyType.hpp
+
+%template(CharVector) std::vector<char>;
+%template(ShortVector) std::vector<short>;
+%template(IntVector) std::vector<int>;
+%template(LongVector) std::vector<long>;
+%template(FloatVector) std::vector<float>;
+%template(DoubleVector) std::vector<double>;
+%template(UCharVector) std::vector<unsigned char>;
+%template(UShortVector) std::vector<unsigned short>;
+%template(UIntVector) std::vector<unsigned int>;
+
+%extend XdmfArray {
+  %template(setValues) setValues<char>;
+  %template(setValues) setValues<short>;
+  %template(setValues) setValues<int>;
+  %template(setValues) setValues<long>;
+  %template(setValues) setValues<float>;
+  %template(setValues) setValues<double>;
+  %template(setValues) setValues<unsigned char>;
+  %template(setValues) setValues<unsigned short>;
+  %template(setValues) setValues<unsigned int>;
+};

XdmfArray.cpp

+/*
+ * XdmfArray.cpp
+ *
+ *  Created on: Jan 29, 2010
+ *      Author: kleiter
+ */
+
+#include "XdmfArray.hpp"
+#include "XdmfVisitor.hpp"
+#include <sstream>
+
+class XdmfArrayGetPrecision : public boost::static_visitor <int> {
+public:
+	XdmfArrayGetPrecision()
+	{
+	}
+
+	int operator()(const std::vector<char> & array) const
+	{
+		return 1;
+	}
+
+	int operator()(const std::vector<short> & array) const
+	{
+		return 2;
+	}
+
+	int operator()(const std::vector<int> & array) const
+	{
+		return 4;
+	}
+
+	int operator()(const std::vector<long> & array) const
+	{
+		return 8;
+	}
+
+	int operator()(const std::vector<float> & array) const
+	{
+		return 4;
+	}
+
+	int operator()(const std::vector<double> & array) const
+	{
+		return 8;
+	}
+
+	int operator()(const std::vector<unsigned char> & array) const
+	{
+		return 1;
+	}
+
+	int operator()(const std::vector<unsigned short> & array) const
+	{
+		return 2;
+	}
+
+	int operator()(const std::vector<unsigned int> & array) const
+	{
+		return 4;
+	}
+};
+
+class XdmfArrayGetType : public boost::static_visitor <std::string> {
+public:
+	XdmfArrayGetType()
+	{
+	}
+
+	std::string operator()(const std::vector<char> & array) const
+	{
+		return "Char";
+	}
+
+	std::string operator()(const std::vector<short> & array) const
+	{
+		return "Short";
+	}
+
+	std::string operator()(const std::vector<int> & array) const
+	{
+		return "Int";
+	}
+
+	std::string operator()(const std::vector<long> & array) const
+	{
+		return "Int";
+	}
+
+	std::string operator()(const std::vector<float> & array) const
+	{
+		return "Float";
+	}
+
+	std::string operator()(const std::vector<double> & array) const
+	{
+		return "Float";
+	}
+
+	std::string operator()(const std::vector<unsigned char> & array) const
+	{
+		return "UChar";
+	}
+
+	std::string operator()(const std::vector<unsigned short> & array) const
+	{
+		return "UShort";
+	}
+
+	std::string operator()(const std::vector<unsigned int> & array) const
+	{
+		return "UInt";
+	}
+};
+
+class XdmfArrayGetHDF5Type : public boost::static_visitor <hid_t> {
+public:
+	XdmfArrayGetHDF5Type()
+	{
+	}
+
+	hid_t operator()(const std::vector<char> & array) const
+	{
+		return H5T_NATIVE_CHAR;
+	}
+
+	hid_t operator()(const std::vector<short> & array) const
+	{
+		return H5T_NATIVE_SHORT;
+	}
+
+	hid_t operator()(const std::vector<int> & array) const
+	{
+		return H5T_NATIVE_INT;
+	}
+
+	hid_t operator()(const std::vector<long> & array) const
+	{
+		return H5T_NATIVE_LONG;
+	}
+
+	hid_t operator()(const std::vector<float> & array) const
+	{
+		return H5T_NATIVE_FLOAT;
+	}
+
+	hid_t operator()(const std::vector<double> & array) const
+	{
+		return H5T_NATIVE_DOUBLE;
+	}
+
+	hid_t operator()(const std::vector<unsigned char> & array) const
+	{
+		return H5T_NATIVE_UCHAR;
+	}
+
+	hid_t operator()(const std::vector<unsigned short> & array) const
+	{
+		return H5T_NATIVE_USHORT;
+	}
+
+	hid_t operator()(const std::vector<unsigned int> & array) const
+	{
+		return H5T_NATIVE_UINT;
+	}
+};
+
+class XdmfArrayGetSize : public boost::static_visitor <int> {
+public:
+
+	XdmfArrayGetSize()
+	{
+	}
+
+	template<typename T> int operator()(const std::vector<T> & array) const
+	{
+		return array.size();
+	}
+};
+
+class XdmfArrayGetValues : public boost::static_visitor <std::string> {
+public:
+
+	XdmfArrayGetValues()
+	{
+	}
+
+	std::string operator()(const std::vector<char> & array) const
+	{
+		std::stringstream toReturn;
+		for(int i=0; i<array.size(); ++i)
+		{
+			toReturn << (int)(array[i]) << " ";
+		}
+		return toReturn.str();
+	}
+
+	template<typename T> std::string operator()(const std::vector<T> & array) const
+	{
+		std::stringstream toReturn;
+		for(int i=0; i<array.size(); ++i)
+		{
+			toReturn << array[i] << " ";
+		}
+		return toReturn.str();
+	}
+};
+
+class XdmfArrayGetValuesPointer : public boost::static_visitor <void*> {
+public:
+	XdmfArrayGetValuesPointer()
+	{
+	}
+
+	template<typename T> void* operator()(std::vector<T> & array) const
+	{
+		return &array[0];
+	}
+};
+
+class XdmfArrayGetValuesPointerConst : public boost::static_visitor <const void* const> {
+public:
+
+	XdmfArrayGetValuesPointerConst()
+	{
+	}
+
+	template<typename T> const void* const operator()(const std::vector<T> & array) const
+	{
+		return &array[0];
+	}
+};
+
+XdmfArray::XdmfArray() :
+	mInitialized(false)
+{
+	std::cout << "Created Array " << this << std::endl;
+}
+
+XdmfArray::~XdmfArray()
+{
+	std::cout << "Deleted Array " << this << std::endl;
+}
+
+hid_t XdmfArray::getHDF5Type() const
+{
+	return boost::apply_visitor( XdmfArrayGetHDF5Type(), mArray);
+}
+
+int XdmfArray::getPrecision() const
+{
+	return boost::apply_visitor( XdmfArrayGetPrecision(), mArray);
+}
+
+int XdmfArray::getSize() const
+{
+	return boost::apply_visitor( XdmfArrayGetSize(), mArray);
+}
+
+std::string XdmfArray::getType() const
+{
+	return boost::apply_visitor( XdmfArrayGetType(), mArray);
+}
+
+std::string XdmfArray::getValues() const
+{
+	return boost::apply_visitor( XdmfArrayGetValues(), mArray);
+}
+
+void* XdmfArray::getValuesPointer()
+{
+	return boost::apply_visitor( XdmfArrayGetValuesPointer(), mArray);
+}
+
+const void* const XdmfArray::getValuesPointer() const
+{
+	return boost::apply_visitor( XdmfArrayGetValuesPointerConst(), mArray);
+}
+
+std::string XdmfArray::printSelf() const
+{
+	return "";
+}
+
+void XdmfArray::write(boost::shared_ptr<XdmfVisitor> visitor) const
+{
+	visitor->visit(this);
+}

XdmfArray.hpp

+/*
+ * XdmfArray.hpp
+ *
+ *  Created on: Jan 25, 2010
+ *      Author: kleiter
+ */
+
+#ifndef XDMFARRAY_HPP_
+#define XDMFARRAY_HPP_
+
+// Includes
+#include "XdmfItem.hpp"
+#include <boost/variant.hpp>
+#include <hdf5.h>
+#include <vector>
+
+template<typename T>
+class XdmfArraySetValues : public boost::static_visitor <void> {
+public:
+
+	XdmfArraySetValues(int startIndex, T* valuesPointer, int numValues, int arrayStride = 1, int valuesStride = 1) :
+		mStartIndex(startIndex),
+		mValuesPointer(valuesPointer),
+		mNumValues(numValues),
+		mArrayStride(arrayStride),
+		mValuesStride(valuesStride)
+	{
+	}
+
+	template<typename U> void operator()(std::vector<U> & array) const
+	{
+		int size = mStartIndex + mNumValues;
+		if(mArrayStride > 1)
+		{
+			size = mStartIndex + mNumValues * mArrayStride - 1;
+		}
+		if(array.size() < size)
+		{
+			array.resize(size);
+		}
+		for(int i=0; i<mNumValues; ++i)
+		{
+			array[mStartIndex + i*mArrayStride] = (U)mValuesPointer[i*mValuesStride];
+		}
+	}
+
+private:
+
+	int mStartIndex;
+	T* mValuesPointer;
+	int mNumValues;
+	int mArrayStride;
+	int mValuesStride;
+};
+
+class XdmfArray : public XdmfItem {
+public:
+
+	XdmfNewMacro(XdmfArray);
+
+	/**
+     * Get the data type of this array.
+     *
+     * @return a string containing the Xdmf data type for the array, this is one of
+     *      Char, Short, Int, Float, UChar, UShort, UInt.
+     */
+	virtual std::string getType() const;
+
+	/**
+	 * Get the hdf5 data type of this array.
+	 *
+	 * @return a hid_t value containing the hdf5 data type for the array.
+	 */
+	virtual hid_t getHDF5Type() const;
+
+	/**
+	 * Get the precision, in bytes, of the data type of this array.
+	 *
+	 * @return a int containing the precision, in bytes, of the data type of this array.
+	 */
+	virtual int getPrecision() const;
+
+	/**
+	 * Get the number of values stored in this array.
+	 *
+	 * @return a int containing the number of values stored in this array.
+	 */
+	virtual int getSize() const;
+
+	/**
+	 * Get the values stored in this array as a string.
+	 *
+	 * @return a string containing the contents of the array.
+	 */
+	virtual std::string getValues() const;
+
+	/**
+	 * Get a pointer to the values stored in this array.
+	 *
+	 * @return a void pointer to the first value stored in this array.
+	 */
+	virtual void* getValuesPointer();
+
+	/**
+	 * Get a pointer to the values stored in this array (const version).
+	 *
+	 * @return a void pointer to the first value stored in this array.
+	 */
+	virtual const void* const getValuesPointer() const;
+
+	virtual std::string printSelf() const;
+
+	/**
+	 * Copy the values from a pointer into this array.
+	 *
+	 * @param startIndex the index in this array to begin insertion.
+	 * @param valuesPointer a pointer to the values to copy into this array.
+	 * @param numValues the number of values to copy into this array.
+	 * @param arrayStride number of values to stride in this array between each copy.
+	 * @param valuesStride number of values to stride in the pointer between each copy.
+	 */
+	template<typename T> void setValues(int startIndex, T* valuesPointer, int numValues = 1, int arrayStride = 1, int valuesStride = 1)
+	{
+		if(!mInitialized)
+		{
+			// Set type of variant to type of pointer
+			mArray = std::vector<T>();
+			mInitialized = true;
+	    }
+	    boost::apply_visitor( XdmfArraySetValues<T>(startIndex, valuesPointer, numValues, arrayStride, valuesStride), mArray);
+	}
+
+	/**
+	 * Copy the values from a vector into this array
+	 *
+	 * @param array the vector to copy into this array.
+	 */
+	template<typename T> void setValues(std::vector<T> & array)
+	{
+		mArray = array;
+	}
+
+	virtual void write(boost::shared_ptr<XdmfVisitor>) const;
+
+protected:
+
+	XdmfArray();
+	virtual ~XdmfArray();
+
+private:
+
+	bool mInitialized;
+
+	boost::variant<std::vector<char>,
+				   std::vector<short>,
+				   std::vector<int>,
+				   std::vector<long>,
+				   std::vector<float>,
+				   std::vector<double>,
+				   std::vector<unsigned char>,
+				   std::vector<unsigned short>,
+				   std::vector<unsigned int> > mArray;
+};
+
+#endif /* XDMFARRAY_HPP_ */

XdmfAttribute.cpp

@@ -61,11 +61,6 @@ void XdmfAttribute::setName(const std::string& name)
 	mName= name;
 }
 
-void XdmfAttribute::setNumberValues(int numValues)
-{
-	mNumberValues = numValues;
-}
-
 void XdmfAttribute::write(boost::shared_ptr<XdmfVisitor> visitor) const
 {
 	visitor->visit(this);

XdmfAttribute.hpp

@@ -8,6 +8,7 @@
 #ifndef XDMFATTRIBUTE_HPP_
 #define XDMFATTRIBUTE_HPP_
 
+// Includes
 #include "XdmfAttributeCenter.hpp"
 #include "XdmfAttributeType.hpp"
 #include "XdmfDataItem.hpp"
@@ -74,13 +75,6 @@ public:
 	 */
 	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;

XdmfDataItem.cpp

@@ -5,12 +5,11 @@
  *      Author: kleiter
  */