  
  #endif /*  __ICM_H__ */
  
-diff -rupNb MRF2.1/LinkedBlockList.cpp MRF_new/LinkedBlockList.cpp
+diff -rupN MRF2.1/LinkedBlockList.cpp MRF-v2.1.src-patched/LinkedBlockList.cpp
 --- MRF2.1/LinkedBlockList.cpp	2006-11-15 04:27:04.000000000 +0100
-+++ MRF_new/LinkedBlockList.cpp	2012-05-24 13:56:07.000000000 +0200
++++ MRF-v2.1.src-patched/LinkedBlockList.cpp	2012-08-13 12:25:46.000000000 +0200
 @@ -1,5 +1,7 @@
  #include "LinkedBlockList.h"
  

 
     if (!m_grid_graph)
     {
diff -rupNb MRF2.1/ICM.h MRF_new/ICM.h
--- MRF2.1/ICM.h	2006-11-15 04:27:04.000000000 +0100
+++ MRF_new/ICM.h	2012-05-24 13:56:07.000000000 +0200
@@ -1,5 +1,5 @@
-#ifndef __ICM_H__
-#define __ICM_H__

+	}
+}
+
+#endif
diff -rupN MRF2.1/typeTruncatedQuadratic2D_old.h MRF-v2.1.src-patched/typeTruncatedQuadratic2D_old.h
--- MRF2.1/typeTruncatedQuadratic2D_old.h	1970-01-01 01:00:00.000000000 +0100
+++ MRF-v2.1.src-patched/typeTruncatedQuadratic2D_old.h	2012-08-13 12:25:46.000000000 +0200
@@ -0,0 +1,574 @@
+/******************************************************************
+typeTruncatedQuadratic2D.h
+
+Energy function with 2-dimensional truncated quadratic interactions:
+   E(x)   =   \sum_i D_i(x_i)   +   \sum_ij V_ij(x_i,x_j)
+   where x_i \in {0, 1, ..., KX-1} x {0, 1, ..., KY-1}
+   (i.e. x_i = (x_i(1), x_i(2))).
+   V_ij(ki, kj) = min { alpha1_ij*(ki(1)-kj(2))^2 + alpha2_ij*(ki(2)-kj(2))^2, lambda_ij }.
+   alpha1_ij, alpha2_ij and lambda_ij must be non-negative.
+
+Example usage:
+
+Minimize function E(x,y) = Dx(x) + Dy(y) + min { alpha1*(x(1) - y(1))^2 + alpha2*(x(2) - y(2))^2, lambda } 
+where 
+  x,y \in {0,1} x {0,1,2}
+  Dx(0,0) = 0, Dx(0,1) = 1, Dx(0,2) = 2,
+  Dx(1,0) = 3, Dx(1,1) = 4, Dx(1,2) = 5,
+  Dy(y) = 0 for all y,
+  alpha1 = 6,
+  alpha2 = 7,
+  lambda = 8
+
+
+
+
+#include <stdio.h>
+#include "MRFEnergy.h"
+
+void testTruncatedQuadratic2D()
+{
+	MRFEnergy<TypeTruncatedQuadratic2D>* mrf;
+	MRFEnergy<TypeTruncatedQuadratic2D>::NodeId* nodes;
+	MRFEnergy<TypeTruncatedQuadratic2D>::Options options;
+	TypeTruncatedQuadratic2D::REAL energy, lowerBound;
+
+	const int nodeNum = 2; // number of nodes
+	const int KX = 2; //   label
+	const int KY = 3; // dimensions
+	const int K = KX*KY; // number of labels
+	TypeTruncatedQuadratic2D::REAL D[K];
+	TypeTruncatedQuadratic2D::Label x, y;
+
+	mrf = new MRFEnergy<TypeTruncatedQuadratic2D>(TypeTruncatedQuadratic2D::GlobalSize(KX, KY));
+	nodes = new MRFEnergy<TypeTruncatedQuadratic2D>::NodeId[nodeNum];
+
+	// construct energy
+	D[0] = 0; D[1] = 1; D[2] = 2;
+	D[3] = 3; D[4] = 4; D[5] = 5;
+	nodes[0] = mrf->AddNode(TypeTruncatedQuadratic2D::LocalSize(), TypeTruncatedQuadratic2D::NodeData(D));
+	D[0] = 0; D[1] = 0; D[2] = 0;
+	D[3] = 0; D[4] = 0; D[5] = 0;
+	nodes[1] = mrf->AddNode(TypeTruncatedQuadratic2D::LocalSize(), TypeTruncatedQuadratic2D::NodeData(D));
+	mrf->AddEdge(nodes[0], nodes[1], TypeTruncatedQuadratic2D::EdgeData(6, 7, 8));
+
+	// Function below is optional - it may help if, for example, nodes are added in a random order
+	// mrf->SetAutomaticOrdering();
+
+	/////////////////////// TRW-S algorithm //////////////////////
+	options.m_iterMax = 30; // maximum number of iterations
+	mrf->Minimize_TRW_S(options, lowerBound, energy);
+
+	// read solution
+	x = mrf->GetSolution(nodes[0]);
+	y = mrf->GetSolution(nodes[1]);
+
+	printf("Solution: %d %d\n", x, y);
+
+	//////////////////////// BP algorithm ////////////////////////
+	mrf->ZeroMessages(); // in general not necessary - it may be faster to start 
+	                     // with messages computed in previous iterations
+
+	options.m_iterMax = 30; // maximum number of iterations
+	mrf->Minimize_BP(options, energy);
+
+	// read solution
+	x = mrf->GetSolution(nodes[0]);
+	y = mrf->GetSolution(nodes[1]);
+
+	printf("Solution: (%d, %d) (%d, %d)\n", x.m_kx, x.m_ky, y.m_kx, y.m_ky);
+
+	// done
+	delete nodes;
+	delete mrf;
+}
+
+*******************************************************************/
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+#ifndef __TYPETRUNCATEDQUADRATIC2D_H__
+#define __TYPETRUNCATEDQUADRATIC2D_H__
+
+#include <string.h>
+#include <assert.h>
+
+
+template <class T> class MRFEnergy;
+
+
+class TypeTruncatedQuadratic2D
+{
+private:
+	struct Vector; // node parameters and messages
+	struct Edge; // stores edge information and either forward or backward message
+
+public:
+	// types declarations
+	struct Label
+	{
+		int		m_kx, m_ky;
+	};
+	typedef double REAL;
+	struct GlobalSize; // global information about number of labels
+	struct LocalSize; // local information about number of labels (stored at each node)
+	struct NodeData; // argument to MRFEnergy::AddNode()
+	struct EdgeData; // argument to MRFEnergy::AddEdge()
+
+
+	struct GlobalSize
+	{
+		GlobalSize(int KX, int KY);
+
+	private:
+	friend struct Vector;
+	friend struct Edge;
+		int		m_KX, m_KY; // label dimensions
+		int		m_K; // number of labels
+	};
+
+	struct LocalSize // number of labels is stored at MRFEnergy::m_Kglobal
+	{
+	};
+
+	struct NodeData
+	{
+		NodeData(REAL* data); // data = pointer to array of size MRFEnergy::m_Kglobal
+
+	private:
+	friend struct Vector;
+	friend struct Edge;
+		REAL*		m_data;
+	};
+
+	struct EdgeData
+	{
+		EdgeData(REAL alphaX, REAL alphaY, REAL lambda);
+
+	private:
+	friend struct Vector;
+	friend struct Edge;
+		REAL		m_alphaX, m_alphaY;
+		REAL		m_lambda;
+	};
+
+
+
+
+
+
+
+	//////////////////////////////////////////////////////////////////////////////////
+	////////////////////////// Visible only to MRFEnergy /////////////////////////////
+	//////////////////////////////////////////////////////////////////////////////////
+
+private:
+friend class MRFEnergy<TypeTruncatedQuadratic2D>;
+
+	struct Vector
+	{
+		static int GetSizeInBytes(GlobalSize Kglobal, LocalSize K); // returns -1 if invalid K's
+		void Initialize(GlobalSize Kglobal, LocalSize K, NodeData data);  // called once when user adds a node
+		void Add(GlobalSize Kglobal, LocalSize K, NodeData data); // called once when user calls MRFEnergy::AddNodeData()
+
+		void SetZero(GlobalSize Kglobal, LocalSize K);                            // set this[k] = 0
+		void Copy(GlobalSize Kglobal, LocalSize K, Vector* V);                    // set this[k] = V[k]
+		void Add(GlobalSize Kglobal, LocalSize K, Vector* V);                     // set this[k] = this[k] + V[k]
+		REAL GetValue(GlobalSize Kglobal, LocalSize K, Label k);                  // return this[k]
+		REAL ComputeMin(GlobalSize Kglobal, LocalSize K, Label& kMin);            // return vMin = min_k { this[k] }, set kMin
+		REAL ComputeAndSubtractMin(GlobalSize Kglobal, LocalSize K);              // same as previous, but additionally set this[k] -= vMin (and kMin is not returned)
+
+		static int GetArraySize(GlobalSize Kglobal, LocalSize K);
+		REAL GetArrayValue(GlobalSize Kglobal, LocalSize K, int k); // note: k is an integer in [0..GetArraySize()-1].
+		                                                            // For Potts functions GetArrayValue() and GetValue() are the same,
+		                                                            // but they are different for, say, 2-dimensional labels.
+		void SetArrayValue(GlobalSize Kglobal, LocalSize K, int k, REAL x);
+
+	private:
+	friend struct Edge;
+		REAL		m_data[1]; // actual size is MRFEnergy::m_Kglobal
+	};
+
+	struct Edge
+	{
+		static int GetSizeInBytes(GlobalSize Kglobal, LocalSize Ki, LocalSize Kj, EdgeData data); // returns -1 if invalid data
+		static int GetBufSizeInBytes(int vectorMaxSizeInBytes); // returns size of buffer need for UpdateMessage()
+		void Initialize(GlobalSize Kglobal, LocalSize Ki, LocalSize Kj, EdgeData data, Vector* Di, Vector* Dj); // called once when user adds an edge
+		Vector* GetMessagePtr();
+		void Swap(GlobalSize Kglobal, LocalSize Ki, LocalSize Kj); // if the client calls this function, then the meaning of 'dir'
+								                                               // in distance transform functions is swapped
+
+		// When UpdateMessage() is called, edge contains message from dest to source.
+		// The function must replace it with the message from source to dest.
+		// The update rule is given below assuming that source corresponds to tail (i) and dest corresponds
+		// to head (j) (which is the case if dir==0).
+		//
+		// 1. Compute Di[ki] = gamma*source[ki] - message[ki].  (Note: message = message from j to i).
+		// 2. Compute distance transform: set
+		//       message[kj] = min_{ki} (Di[ki] + V(ki,kj)). (Note: message = message from i to j).
+		// 3. Compute vMin = min_{kj} m_message[kj].
+		// 4. Set m_message[kj] -= vMin.
+		// 5. Return vMin.
+		//
+		// If dir==1 then source corresponds to j, sink corresponds to i. Then the update rule is
+		//
+		// 1. Compute Dj[kj] = gamma*source[kj] - message[kj].  (Note: message = message from i to j).
+		// 2. Compute distance transform: set
+		//       message[ki] = min_{kj} (Dj[kj] + V(ki,kj)). (Note: message = message from j to i).
+		// 3. Compute vMin = min_{ki} m_message[ki].
+		// 4. Set m_message[ki] -= vMin.
+		// 5. Return vMin.
+		//
+		// If Edge::Swap has been called odd number of times, then the meaning of dir is swapped.
+		//
+		// Vector 'source' must not be modified. Function may use 'buf' as a temporary storage.
+		REAL UpdateMessage(GlobalSize Kglobal, LocalSize Ksource, LocalSize Kdest, Vector* source, REAL gamma, int dir, void* buf);
+
+		// If dir==0, then sets dest[kj] += V(ksource,kj).
+		// If dir==1, then sets dest[ki] += V(ki,ksource).
+		// If Swap() has been called odd number of times, then the meaning of dir is swapped.
+		void AddColumn(GlobalSize Kglobal, LocalSize Ksource, LocalSize Kdest, Label ksource, Vector* dest, int dir);
+
+	private:
+		// parabolas must be array of size K
+		// intersections must be array of size K+1
+		void DistanceTransformL2(int K, int stride, REAL alpha, REAL* source, REAL* dest, int* parabolas, int* intersections);
+
+		// edge information
+		REAL		m_alphaX, m_alphaY;
+		REAL		m_lambda;
+
+		// message
+		Vector		m_message;
+	};
+};
+
+
+
+
+//////////////////////////////////////////////////////////////////////////////////
+/////////////////////////////// Implementation ///////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////////
+
+
+inline TypeTruncatedQuadratic2D::GlobalSize::GlobalSize(int KX, int KY)
+{
+	m_KX = KX;
+	m_KY = KY;
+	m_K = KX*KY;
+}
+
+///////////////////// NodeData and EdgeData ///////////////////////
+
+inline TypeTruncatedQuadratic2D::NodeData::NodeData(REAL* data)
+{
+	m_data = data;
+}
+
+inline TypeTruncatedQuadratic2D::EdgeData::EdgeData(REAL alphaX, REAL alphaY, REAL lambda)
+{
+	m_alphaX = alphaX;
+	m_alphaY = alphaY;
+	m_lambda = lambda;
+}
+
+///////////////////// Vector ///////////////////////
+
+inline int TypeTruncatedQuadratic2D::Vector::GetSizeInBytes(GlobalSize Kglobal, LocalSize K)
+{
+	if (Kglobal.m_KX < 1 || Kglobal.m_KY < 1)
+	{
+		return -1;
+	}
+	return Kglobal.m_K*sizeof(REAL);
+}
+inline void TypeTruncatedQuadratic2D::Vector::Initialize(GlobalSize Kglobal, LocalSize K, NodeData data)
+{
+	memcpy(m_data, data.m_data, Kglobal.m_K*sizeof(REAL));
+}
+
+inline void TypeTruncatedQuadratic2D::Vector::Add(GlobalSize Kglobal, LocalSize K, NodeData data)
+{
+	for (int k=0; k<Kglobal.m_K; k++)
+	{
+		m_data[k] += data.m_data[k];
+	}
+}
+
+inline void TypeTruncatedQuadratic2D::Vector::SetZero(GlobalSize Kglobal, LocalSize K)
+{
+	memset(m_data, 0, Kglobal.m_K*sizeof(REAL));
+}
+
+inline void TypeTruncatedQuadratic2D::Vector::Copy(GlobalSize Kglobal, LocalSize K, Vector* V)
+{
+	memcpy(m_data, V->m_data, Kglobal.m_K*sizeof(REAL));
+}
+
+inline void TypeTruncatedQuadratic2D::Vector::Add(GlobalSize Kglobal, LocalSize K, Vector* V)
+{
+	for (int k=0; k<Kglobal.m_K; k++)
+	{
+		m_data[k] += V->m_data[k];
+	}
+}
+
+inline TypeTruncatedQuadratic2D::REAL TypeTruncatedQuadratic2D::Vector::GetValue(GlobalSize Kglobal, LocalSize K, Label k)
+{
+	assert(k.m_kx>=0 && k.m_kx<Kglobal.m_KX && k.m_ky>=0 && k.m_ky<Kglobal.m_KY);
+	return m_data[k.m_kx + k.m_ky*Kglobal.m_KX];
+}
+
+inline TypeTruncatedQuadratic2D::REAL TypeTruncatedQuadratic2D::Vector::ComputeMin(GlobalSize Kglobal, LocalSize K, Label& _kMin)
+{
+	REAL vMin = m_data[0];
+	int kMin = 0;
+	for (int k=1; k<Kglobal.m_K; k++)
+	{
+		if (vMin > m_data[k])
+		{
+			vMin = m_data[k];
+			kMin = k;
+		}
+	}
+
+	_kMin.m_ky = kMin / Kglobal.m_KX;
+	_kMin.m_kx = kMin - _kMin.m_ky * Kglobal.m_KX;
+
+	return vMin;
+}
+
+inline TypeTruncatedQuadratic2D::REAL TypeTruncatedQuadratic2D::Vector::ComputeAndSubtractMin(GlobalSize Kglobal, LocalSize K)
+{
+	REAL vMin = m_data[0];
+	for (int k=1; k<Kglobal.m_K; k++)
+	{
+		if (vMin > m_data[k])
+		{
+			vMin = m_data[k];
+		}
+	}
+	for (int k=0; k<Kglobal.m_K; k++)
+	{
+		m_data[k] -= vMin;
+	}
+
+	return vMin;
+}
+
+inline int TypeTruncatedQuadratic2D::Vector::GetArraySize(GlobalSize Kglobal, LocalSize K)
+{
+	return Kglobal.m_K;
+}
+
+inline TypeTruncatedQuadratic2D::REAL TypeTruncatedQuadratic2D::Vector::GetArrayValue(GlobalSize Kglobal, LocalSize K, int k)
+{
+	assert(k>=0 && k<Kglobal.m_K);
+	return m_data[k];
+}
+
+inline void TypeTruncatedQuadratic2D::Vector::SetArrayValue(GlobalSize Kglobal, LocalSize K, int k, REAL x)
+{
+	assert(k>=0 && k<Kglobal.m_K);
+	m_data[k] = x;
+}
+
+///////////////////// EdgeDataAndMessage implementation /////////////////////////
+
+inline int TypeTruncatedQuadratic2D::Edge::GetSizeInBytes(GlobalSize Kglobal, LocalSize Ki, LocalSize Kj, EdgeData data)
+{
+	if (data.m_alphaX < 0 || data.m_alphaY < 0 || data.m_lambda < 0)
+	{
+		return -1;
+	}
+	return sizeof(Edge) - sizeof(Vector) + Kglobal.m_K*sizeof(REAL);
+}
+
+inline int TypeTruncatedQuadratic2D::Edge::GetBufSizeInBytes(int vectorMaxSizeInBytes)
+{
+	int K = vectorMaxSizeInBytes / sizeof(REAL);
+	return K*sizeof(REAL) + (2*K+1)*sizeof(int);
+}
+
+inline void TypeTruncatedQuadratic2D::Edge::Initialize(GlobalSize Kglobal, LocalSize Ki, LocalSize Kj, EdgeData data, Vector* Di, Vector* Dj)
+{
+	m_alphaX = data.m_alphaX;
+	m_alphaY = data.m_alphaY;
+	m_lambda = data.m_lambda;
+	memset(m_message.m_data, 0, Kglobal.m_K*sizeof(REAL));
+}
+
+inline TypeTruncatedQuadratic2D::Vector* TypeTruncatedQuadratic2D::Edge::GetMessagePtr()
+{
+	return &m_message;
+}
+
+inline void TypeTruncatedQuadratic2D::Edge::Swap(GlobalSize Kglobal, LocalSize Ki, LocalSize Kj)
+{
+}
+
+inline TypeTruncatedQuadratic2D::REAL TypeTruncatedQuadratic2D::Edge::UpdateMessage(GlobalSize Kglobal, LocalSize Ksource, LocalSize Kdest, Vector* source, REAL gamma, int dir, void* _buf)
+{
+	REAL* buf = (REAL*) _buf;
+	int* parabolas = (int*) ((char*)_buf + Kglobal.m_K*sizeof(REAL));
+	int* intersections = (int*) ((char*)_buf + Kglobal.m_K*(sizeof(REAL) + sizeof(int)));
+	Label k;
+	REAL vMin;
+	REAL* sourcePtr;
+	REAL* destPtr;
+
+	m_message.m_data[0] = gamma*source->m_data[0] - m_message.m_data[0];
+	vMin = m_message.m_data[0];
+
+	sourcePtr = source->m_data;
+	destPtr = m_message.m_data;
+	for (sourcePtr++, destPtr++ ; sourcePtr<&source->m_data[Kglobal.m_K]; sourcePtr++, destPtr++)
+	{
+		destPtr[0] = gamma*sourcePtr[0] - destPtr[0];
+		if (vMin > destPtr[0])
+		{
+			vMin = destPtr[0];
+		}
+	}
+
+	// distance transform in 'X' direction
+	for (k.m_ky=0; k.m_ky<Kglobal.m_KY; k.m_ky++)
+	{
+		DistanceTransformL2(Kglobal.m_KX, 1, m_alphaX, &m_message.m_data[k.m_ky*Kglobal.m_KX], buf+k.m_ky*Kglobal.m_KX, parabolas, intersections);
+	}
+
+	// distance transform in 'Y' direction
+	for (k.m_kx=0; k.m_kx<Kglobal.m_KX; k.m_kx++)
+	{
+		DistanceTransformL2(Kglobal.m_KY, Kglobal.m_KX, m_alphaY, buf+k.m_kx, &m_message.m_data[k.m_kx], parabolas, intersections);
+	}
+
+	for (destPtr=m_message.m_data; destPtr<&m_message.m_data[Kglobal.m_K]; destPtr++)
+	{
+		destPtr[0] -= vMin;
+		if (destPtr[0] > m_lambda)
+		{
+			destPtr[0] = m_lambda;
+		}
+	}
+
+	return vMin;
+}
+
+inline void TypeTruncatedQuadratic2D::Edge::AddColumn(GlobalSize Kglobal, LocalSize Ksource, LocalSize Kdest, Label ksource, Vector* dest, int dir)
+{
+	assert(ksource.m_kx>=0 && ksource.m_kx<Kglobal.m_KX && ksource.m_ky>=0 && ksource.m_ky<Kglobal.m_KY);
+
+	REAL* destPtr;
+	Label k;
+
+	destPtr = dest->m_data;
+	for (k.m_ky=0; k.m_ky<Kglobal.m_KY; k.m_ky++)
+	for (k.m_kx=0; k.m_kx<Kglobal.m_KX; k.m_kx++, destPtr++)
+	{
+		REAL cost = m_alphaX*(k.m_kx - ksource.m_kx)*(k.m_kx - ksource.m_kx)
+		          + m_alphaY*(k.m_ky - ksource.m_ky)*(k.m_ky - ksource.m_ky);
+		destPtr[0] += (cost < m_lambda) ? cost : m_lambda;
+	}
+}
+
+//////////////////////////////////////////////////////////////////////////////////
+
+
+
+inline void TypeTruncatedQuadratic2D::Edge::DistanceTransformL2(int K, int stride, REAL alpha, REAL* source, REAL* dest, int* parabolas, int* intersections)
+{
+	assert(alpha >= 0);
+
+	if (alpha == 0)
+	{
+		REAL* ptr;
+		REAL vMin = source[0];
+
+		for (ptr=source+stride; ptr<source+K*stride; ptr+=stride)
+		{
+			if (vMin > ptr[0])
+			{
+				vMin = ptr[0];
+			}
+		}
+		for (ptr=dest; ptr<dest+K*stride; ptr+=stride)
+		{
+			ptr[0] = vMin;
+		}
+		return;
+	}
+
+	int i, j, k, p;
+	int r = 0; // = number of parabolas minus 1
+	// parabolas[p] will be base of parabola p (0<=p<=r)
+	// intersections[p] will be intersection between parabolas p-1 and p (1<=p<=r)
+	// intersections[0] will be always 0
+	parabolas[0] = 0;
+	intersections[0] = 0;
+
+	for (i=1; i<K; i++)
+	{
+		while ( 1 )
+		{
+			j = parabolas[r]; // base of previous rightmost visible parabola
+			// k is intersection of parabolas i and j
+			k = (int) ( 1 + ( (i + j)  +  (source[stride*j] - source[stride*i]) / (alpha * (j - i)) ) / 2);
+			if (k >= K)
+			{
+				// i is not visible
+				break;
+			}
+			if (k < 0)
+			{
+				k = 0;
+			}
+
+			if (k > intersections[r])
+			{
+				// intersection is rightmost, add it to end
+				r ++;
+				parabolas[r] = i;
+				intersections[r] = k;
+				break;
+			}
+			// j is not visible
+			if (r == 0)
+			{
+				parabolas[0] = i;
+				break;
+			}
+			r --;
+		}
+	}
+
+	intersections[r + 1] = K;
+
+	i = 0;
+	for (p=0; p<=r; p++)
+	{
+		j = parabolas[p];
+		// i values in [intersections[p], intersections[p+1]) are assigned to j
+		for ( ; i<intersections[p+1]; i++)
+		{
+			dest[stride*i] = source[stride*j] + alpha*(i-j)*(i-j);
+		}
+	}
+}
+
+#endif
