Merge branch 'XdmfArraySmartPointer'

Conflicts:
	Xdmf.py
	XdmfPython.cpp

Xdmf.i

@@ -61,24 +61,81 @@ namespace boost {
 %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>;
-
+// Provide accessors from python lists to XdmfArrays
 %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>;
+  void copyValueAsChar(int index, char value) {
+    $self->copyValues(index, &value);
+  }
+
+  void copyValueAsShort(int index, short value) {
+    $self->copyValues(index, &value);
+  }
+
+  void copyValueAsInt(int index, int value) {
+    $self->copyValues(index, &value);
+  }
+
+  void copyValueAsLong(int index, long value) {
+    $self->copyValues(index, &value);
+  }
+
+  void copyValueAsFloat(int index, float value) {
+    $self->copyValues(index, &value);
+  }
+  
+  void copyValueAsDouble(int index, double value) {
+    $self->copyValues(index, &value);
+  }
+
+  void copyValueAsUChar(int index, unsigned char value) {
+    $self->copyValues(index, &value);
+  }
+
+  void copyValueAsUShort(int index, unsigned short value) {
+    $self->copyValues(index, &value);
+  }
+
+  void copyValueAsUInt(int index, unsigned int value) {
+    $self->copyValues(index, &value);
+  }
+};
+
+%extend boost::shared_ptr<XdmfArray> {
+  %pythoncode {
+    def copyValuesAsChar(self, startIndex, values):
+      for i in range(0, len(values)):
+        self.copyValueAsChar(i+startIndex, values[i])
+
+    def copyValuesAsShort(self, startIndex, values):
+      for i in range(0, len(values)):
+        self.copyValueAsShort(i+startIndex, values[i])
+
+    def copyValuesAsInt(self, startIndex, values):
+      for i in range(0, len(values)):
+        self.copyValueAsInt(i+startIndex, values[i])
+
+    def copyValuesAsLong(self, startIndex, values):
+      for i in range(0, len(values)):
+        self.copyValueAsLong(i+startIndex, values[i])
+
+    def copyValuesAsFloat(self, startIndex, values):
+      for i in range(0, len(values)):
+        self.copyValueAsFloat(i+startIndex, values[i])
+
+    def copyValuesAsDouble(self, startIndex, values):
+      for i in range(0, len(values)):
+        self.copyValueAsDouble(i+startIndex, values[i])
+
+    def copyValuesAsUChar(self, startIndex, values):
+      for i in range(0, len(values)):
+        self.copyValueAsUChar(i+startIndex, values[i])
+
+    def copyValuesAsUShort(self, startIndex, values):
+      for i in range(0, len(values)):
+        self.copyValueAsUShort(i+startIndex, values[i])
+
+    def copyValuesAsUInt(self, startIndex, values):
+      for i in range(0, len(values)):
+        self.copyValueAsUInt(i+startIndex, values[i])
+  };
 };

XdmfArray.cpp

@@ -9,159 +9,210 @@
 #include "XdmfVisitor.hpp"
 #include <sstream>
 
-class XdmfArrayGetPrecision : public boost::static_visitor <int> {
+class XdmfArrayClear : public boost::static_visitor <void> {
 public:
-	XdmfArrayGetPrecision()
+
+	XdmfArrayClear()
 	{
 	}
 
-	int operator()(const std::vector<char> & array) const
+	template<typename T> void operator()(const boost::shared_ptr<std::vector<T> > & array) const
 	{
-		return 1;
+		return array->clear();
 	}
+};
+
+class XdmfArrayCopyArrayValues : public boost::static_visitor <void> {
+public:
 
-	int operator()(const std::vector<short> & array) const
+	XdmfArrayCopyArrayValues(int startIndex, int valuesStartIndex, int numValues, int arrayStride, int valuesStride) :
+		mStartIndex(startIndex),
+		mValuesStartIndex(valuesStartIndex),
+		mNumValues(numValues),
+		mArrayStride(arrayStride),
+		mValuesStride(valuesStride)
 	{
-		return 2;
 	}
 
-	int operator()(const std::vector<int> & array) const
+	template<typename T, typename U> void operator()(const boost::shared_ptr<std::vector<T> > & array, const boost::shared_ptr<std::vector<U> > & arrayToCopy) const
 	{
-		return 4;
+		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->operator[](mStartIndex + i*mArrayStride) = (T)arrayToCopy->operator[](mValuesStartIndex + i*mValuesStride);
+		}
 	}
 
-	int operator()(const std::vector<long> & array) const
+private:
+
+	int mStartIndex;
+	int mValuesStartIndex;
+	int mNumValues;
+	int mArrayStride;
+	int mValuesStride;
+};
+
+class XdmfArrayGetHDF5Type : public boost::static_visitor <hid_t> {
+public:
+	XdmfArrayGetHDF5Type()
 	{
-		return 8;
 	}
 
-	int operator()(const std::vector<float> & array) const
+	hid_t operator()(const boost::shared_ptr<std::vector<char> > & array) const
 	{
-		return 4;
+		return H5T_NATIVE_CHAR;
 	}
 
-	int operator()(const std::vector<double> & array) const
+	hid_t operator()(const boost::shared_ptr<std::vector<short> > & array) const
 	{
-		return 8;
+		return H5T_NATIVE_SHORT;
 	}
 
-	int operator()(const std::vector<unsigned char> & array) const
+	hid_t operator()(const boost::shared_ptr<std::vector<int> > & array) const
 	{
-		return 1;
+		return H5T_NATIVE_INT;
 	}
 
-	int operator()(const std::vector<unsigned short> & array) const
+	hid_t operator()(const boost::shared_ptr<std::vector<long> > & array) const
 	{
-		return 2;
+		return H5T_NATIVE_LONG;
 	}
 
-	int operator()(const std::vector<unsigned int> & array) const
+	hid_t operator()(const boost::shared_ptr<std::vector<float> > & array) const
 	{
-		return 4;
+		return H5T_NATIVE_FLOAT;
+	}
+
+	hid_t operator()(const boost::shared_ptr<std::vector<double> > & array) const
+	{
+		return H5T_NATIVE_DOUBLE;
+	}
+
+	hid_t operator()(const boost::shared_ptr<std::vector<unsigned char> > & array) const
+	{
+		return H5T_NATIVE_UCHAR;
+	}
+
+	hid_t operator()(const boost::shared_ptr<std::vector<unsigned short> > & array) const
+	{
+		return H5T_NATIVE_USHORT;
+	}
+
+	hid_t operator()(const boost::shared_ptr<std::vector<unsigned int> > & array) const
+	{
+		return H5T_NATIVE_UINT;
 	}
 };
 
-class XdmfArrayGetType : public boost::static_visitor <std::string> {
+class XdmfArrayGetPrecision : public boost::static_visitor <int> {
 public:
-	XdmfArrayGetType()
+	XdmfArrayGetPrecision()
 	{
 	}
 
-	std::string operator()(const std::vector<char> & array) const
+	int operator()(const boost::shared_ptr<std::vector<char> > & array) const
 	{
-		return "Char";
+		return 1;
 	}
 
-	std::string operator()(const std::vector<short> & array) const
+	int operator()(const boost::shared_ptr<std::vector<short> > & array) const
 	{
-		return "Short";
+		return 2;
 	}
 
-	std::string operator()(const std::vector<int> & array) const
+	int operator()(const boost::shared_ptr<std::vector<int> > & array) const
 	{
-		return "Int";
+		return 4;
 	}
 
-	std::string operator()(const std::vector<long> & array) const
+	int operator()(const boost::shared_ptr<std::vector<long> > & array) const
 	{
-		return "Int";
+		return 8;
 	}
 
-	std::string operator()(const std::vector<float> & array) const
+	int operator()(const boost::shared_ptr<std::vector<float> > & array) const
 	{
-		return "Float";
+		return 4;
 	}
 
-	std::string operator()(const std::vector<double> & array) const
+	int operator()(const boost::shared_ptr<std::vector<double> > & array) const
 	{
-		return "Float";
+		return 8;
 	}
 
-	std::string operator()(const std::vector<unsigned char> & array) const
+	int operator()(const boost::shared_ptr<std::vector<unsigned char> > & array) const
 	{
-		return "UChar";
+		return 1;
 	}
 
-	std::string operator()(const std::vector<unsigned short> & array) const
+	int operator()(const boost::shared_ptr<std::vector<unsigned short> > & array) const
 	{
-		return "UShort";
+		return 2;
 	}
 
-	std::string operator()(const std::vector<unsigned int> & array) const
+	int operator()(const boost::shared_ptr<std::vector<unsigned int> > & array) const
 	{
-		return "UInt";
+		return 4;
 	}
 };
 
-class XdmfArrayGetHDF5Type : public boost::static_visitor <hid_t> {
+class XdmfArrayGetType : public boost::static_visitor <std::string> {
 public:
-	XdmfArrayGetHDF5Type()
+	XdmfArrayGetType()
 	{
 	}
 
-	hid_t operator()(const std::vector<char> & array) const
+	std::string operator()(const boost::shared_ptr<std::vector<char> > & array) const
 	{
-		return H5T_NATIVE_CHAR;
+		return "Char";
 	}
 
-	hid_t operator()(const std::vector<short> & array) const
+	std::string operator()(const boost::shared_ptr<std::vector<short> > & array) const
 	{
-		return H5T_NATIVE_SHORT;
+		return "Short";
 	}
 
-	hid_t operator()(const std::vector<int> & array) const
+	std::string operator()(const boost::shared_ptr<std::vector<int> > & array) const
 	{
-		return H5T_NATIVE_INT;
+		return "Int";
 	}
 
-	hid_t operator()(const std::vector<long> & array) const
+	std::string operator()(const boost::shared_ptr<std::vector<long> > & array) const
 	{
-		return H5T_NATIVE_LONG;
+		return "Int";
 	}
 
-	hid_t operator()(const std::vector<float> & array) const
+	std::string operator()(const boost::shared_ptr<std::vector<float> > & array) const
 	{
-		return H5T_NATIVE_FLOAT;
+		return "Float";
 	}
 
-	hid_t operator()(const std::vector<double> & array) const
+	std::string operator()(const boost::shared_ptr<std::vector<double> > & array) const
 	{
-		return H5T_NATIVE_DOUBLE;
+		return "Float";
 	}
 
-	hid_t operator()(const std::vector<unsigned char> & array) const
+	std::string operator()(const boost::shared_ptr<std::vector<unsigned char> > & array) const
 	{
-		return H5T_NATIVE_UCHAR;
+		return "UChar";
 	}
 
-	hid_t operator()(const std::vector<unsigned short> & array) const
+	std::string operator()(const boost::shared_ptr<std::vector<unsigned short> > & array) const
 	{
-		return H5T_NATIVE_USHORT;
+		return "UShort";
 	}
 
-	hid_t operator()(const std::vector<unsigned int> & array) const
+	std::string operator()(const boost::shared_ptr<std::vector<unsigned int> > & array) const
 	{
-		return H5T_NATIVE_UINT;
+		return "UInt";
 	}
 };
 
@@ -172,62 +223,64 @@ public:
 	{
 	}
 
-	template<typename T> int operator()(const std::vector<T> & array) const
+	template<typename T> int operator()(const boost::shared_ptr<std::vector<T> > & array) const
+	{
+		return array->size();
+	}
+};
+
+class XdmfArrayGetValuesPointer : public boost::static_visitor <const void* const> {
+public:
+
+	XdmfArrayGetValuesPointer()
+	{
+	}
+
+	template<typename T> const void* const operator()(const boost::shared_ptr<std::vector<T> > & array) const
 	{
-		return array.size();
+		return &array->operator[](0);
 	}
 };
 
-class XdmfArrayGetValues : public boost::static_visitor <std::string> {
+class XdmfArrayGetValuesString : public boost::static_visitor <std::string> {
 public:
 
-	XdmfArrayGetValues()
+	XdmfArrayGetValuesString()
 	{
 	}
 
-	std::string operator()(const std::vector<char> & array) const
+	std::string operator()(const boost::shared_ptr<std::vector<char> > & array) const
 	{
 		std::stringstream toReturn;
-		for(int i=0; i<array.size(); ++i)
+		for(int i=0; i<array->size(); ++i)
 		{
-			toReturn << (int)(array[i]) << " ";
+			toReturn << (int)(array->operator[](i)) << " ";
 		}
 		return toReturn.str();
 	}
 
-	template<typename T> std::string operator()(const std::vector<T> & array) const
+	template<typename T> std::string operator()(const boost::shared_ptr<std::vector<T> > & array) const
 	{
 		std::stringstream toReturn;
-		for(int i=0; i<array.size(); ++i)
+		for(int i=0; i<array->size(); ++i)
 		{
-			toReturn << array[i] << " ";
+			toReturn << array->operator[](i) << " ";
 		}
 		return toReturn.str();
 	}
 };
 
-class XdmfArrayGetValuesPointer : public boost::static_visitor <void*> {
+class XdmfArrayNewArray : public boost::static_visitor <void> {
 public:
-	XdmfArrayGetValuesPointer()
-	{
-	}
 
-	template<typename T> void* operator()(std::vector<T> & array) const
+	XdmfArrayNewArray()
 	{
-		return &array[0];
 	}
-};
 
-class XdmfArrayGetValuesPointerConst : public boost::static_visitor <const void* const> {
-public:
-
-	XdmfArrayGetValuesPointerConst()
+	template<typename T> void operator()(boost::shared_ptr<std::vector<T> > & array) const
 	{
-	}
-
-	template<typename T> const void* const operator()(const std::vector<T> & array) const
-	{
-		return &array[0];
+		boost::shared_ptr<std::vector<T> > newArray(new std::vector<T>());
+		array = newArray;
 	}
 };
 
@@ -242,6 +295,28 @@ XdmfArray::~XdmfArray()
 	std::cout << "Deleted Array " << this << std::endl;
 }
 
+void XdmfArray::copyValues(int startIndex, boost::shared_ptr<XdmfArray> values, int valuesStartIndex, int numValues, int arrayStride, int valuesStride)
+{
+	if(!mInitialized)
+	{
+		// Copy the values variant in order to get the type (only taking smart pointer so no worries about large copies)
+		mArray = values->getVariant();
+		// Reinitialize variant array to contain new array with same type.
+		boost::apply_visitor( XdmfArrayNewArray(), mArray);
+		//boost::shared_ptr<std::vector<double> > newArray(new std::vector<double>());
+		//mArray = newArray;
+
+		//std::cout << boost::get<boost::shared_ptr<std::vector<double> > >(mArray)->operator[](0) << std::endl;
+		//std::cout << this->getValuesString() << std::endl;
+	}
+	boost::apply_visitor( XdmfArrayCopyArrayValues(startIndex, valuesStartIndex, numValues, arrayStride, valuesStride), mArray, values->getVariant());
+}
+
+void XdmfArray::clear()
+{
+	return boost::apply_visitor( XdmfArrayClear(), mArray);
+}
+
 hid_t XdmfArray::getHDF5Type() const
 {
 	return boost::apply_visitor( XdmfArrayGetHDF5Type(), mArray);
@@ -262,19 +337,14 @@ 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()
+const void* const XdmfArray::getValuesPointer() const
 {
 	return boost::apply_visitor( XdmfArrayGetValuesPointer(), mArray);
 }
 
-const void* const XdmfArray::getValuesPointer() const
+std::string XdmfArray::getValuesString() const
 {
-	return boost::apply_visitor( XdmfArrayGetValuesPointerConst(), mArray);
+	return boost::apply_visitor( XdmfArrayGetValuesString(), mArray);
 }
 
 std::string XdmfArray::printSelf() const

XdmfArray.hpp

@@ -15,10 +15,10 @@
 #include <vector>
 
 template<typename T>
-class XdmfArraySetValues : public boost::static_visitor <void> {
+class XdmfArrayCopyValues : public boost::static_visitor <void> {
 public:
 
-	XdmfArraySetValues(int startIndex, T* valuesPointer, int numValues, int arrayStride = 1, int valuesStride = 1) :
+	XdmfArrayCopyValues(int startIndex, T* valuesPointer, int numValues = 1, int arrayStride = 1, int valuesStride = 1) :
 		mStartIndex(startIndex),
 		mValuesPointer(valuesPointer),
 		mNumValues(numValues),
@@ -27,20 +27,20 @@ public:
 	{
 	}
 
-	template<typename U> void operator()(std::vector<U> & array) const
+	template<typename U> void operator()(boost::shared_ptr<std::vector<U> > array) const
 	{
 		int size = mStartIndex + mNumValues;
 		if(mArrayStride > 1)
 		{
 			size = mStartIndex + mNumValues * mArrayStride - 1;
 		}
-		if(array.size() < size)
+		if(array->size() < size)
 		{
-			array.resize(size);
+			array->resize(size);
 		}
 		for(int i=0; i<mNumValues; ++i)
 		{
-			array[mStartIndex + i*mArrayStride] = (U)mValuesPointer[i*mValuesStride];
+			array->operator[](mStartIndex + i*mArrayStride) = (U)mValuesPointer[i*mValuesStride];
 		}
 	}
 
@@ -53,11 +53,88 @@ private:
 	int mValuesStride;
 };
 
+template <typename T>
+class XdmfArrayGetValues : public boost::static_visitor <boost::shared_ptr<std::vector<T> > > {
+public:
+
+    XdmfArrayGetValues()
+    {
+    }
+
+    boost::shared_ptr<std::vector<T> > operator()(const boost::shared_ptr<std::vector<T> > array) const
+    {
+        return array;
+    }
+
+    template <typename U>
+    boost::shared_ptr<std::vector<T> > operator()(const boost::shared_ptr<std::vector<U> > array) const
+    {
+        return boost::shared_ptr<std::vector<T> >();
+    }
+};
+
+template <typename T>
+class XdmfArrayGetValuesConst : public boost::static_visitor <const boost::shared_ptr<const std::vector<T> > > {
+public:
+
+    XdmfArrayGetValuesConst()
+    {
+    }
+
+    const boost::shared_ptr<const std::vector<T> > operator()(const boost::shared_ptr<const std::vector<T> > array) const
+    {
+        return array;
+    }
+
+    template <typename U>
+    const boost::shared_ptr<const std::vector<T> > operator()(const boost::shared_ptr<const std::vector<U> > array) const
+    {
+        return boost::shared_ptr<std::vector<T> >();
+    }
+};
+
 class XdmfArray : public XdmfItem {
 public:
 
 	XdmfNewMacro(XdmfArray);
 
+	/**
+	 * Copy values from an XdmfArray into this array.
+	 *
+	 * @param startIndex the index in this array to begin insertion.
+	 * @param values a shared pointer to an XdmfArray to copy into this array.
+	 * @param numValues the number of values to copy into this array.