/*
*
* Mathematics Subpackage (VrMath)
*
*
* Author: Samuel R. Buss, sbuss@ucsd.edu.
* Web page: http://math.ucsd.edu/~sbuss/MathCG
*
*
This software is provided 'as-is', without any express or implied warranty.
In no event will the authors be held liable for any damages arising from the use of this software.
Permission is granted to anyone to use this software for any purpose,
including commercial applications, and to alter it and redistribute it freely,
subject to the following restrictions:

1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required.
2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software.
3. This notice may not be removed or altered from any source distribution.
*
*
*/


//Alterations:
//Remove register keyword to fix compile errors with some linux compilers (clang)

#include "stdafx_shared.h"
#include "pragma/buss_ik/MathMisc.h"
#include "pragma/buss_ik/LinearR3.h"
#include "pragma/buss_ik/Spherical.h"

// ******************************************************
// * VectorR3 class - math library functions				*
// * * * * * * * * * * * * * * * * * * * * * * * * * * **
const VectorR3 UnitVecIR3(1.0, 0.0, 0.0);
const VectorR3 UnitVecJR3(0.0, 1.0, 0.0);
const VectorR3 UnitVecKR3(0.0, 0.0, 1.0);

const VectorR3 VectorR3::Zero(0.0, 0.0, 0.0);
const VectorR3 VectorR3::UnitX( 1.0, 0.0, 0.0);
const VectorR3 VectorR3::UnitY( 0.0, 1.0, 0.0);
const VectorR3 VectorR3::UnitZ( 0.0, 0.0, 1.0);
const VectorR3 VectorR3::NegUnitX(-1.0, 0.0, 0.0);
const VectorR3 VectorR3::NegUnitY( 0.0,-1.0, 0.0);
const VectorR3 VectorR3::NegUnitZ( 0.0, 0.0,-1.0);

const Matrix3x3 Matrix3x3::Identity(1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0);
const Matrix3x4 Matrix3x4::Identity(1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0);

double VectorR3::MaxAbs() const
{
    double m;
	m = (x>0.0) ? x : -x;
	if ( y>m ) m=y;
	else if ( -y >m ) m = -y;
	if ( z>m ) m=z;
	else if ( -z>m ) m = -z;
	return m;
}

VectorR3& VectorR3::Set( const Quaternion& q )
{
	double sinhalf = sqrt( Square(q.x)+Square(q.y)+Square(q.z) );
	if (sinhalf>0.0) {
		double theta = atan2( sinhalf, q.w );
		theta += theta;
		this->Set( q.x, q.y, q.z );
		(*this) *= (theta/sinhalf);
	}
	else {
		this->SetZero();
	}
	return *this;
}


// *********************************************************************
// Rotation routines												   *
// *********************************************************************

// s.Rotate(theta, u) rotates s and returns s 
//        rotated theta degrees around unit vector w.
VectorR3& VectorR3::Rotate( double theta, const VectorR3& w) 
{
	double c = cos(theta);
	double s = sin(theta);
	double dotw = (x*w.x + y*w.y + z*w.z);
	double v0x = dotw*w.x;
	double v0y = dotw*w.y;		// v0 = provjection onto w
	double v0z = dotw*w.z;
	double v1x = x-v0x;
	double v1y = y-v0y;			// v1 = projection onto plane normal to w
	double v1z = z-v0z;
	double v2x = w.y*v1z - w.z*v1y;
	double v2y = w.z*v1x - w.x*v1z;	// v2 = w * v1 (cross product)
	double v2z = w.x*v1y - w.y*v1x;
	
	x = v0x + c*v1x + s*v2x;
	y = v0y + c*v1y + s*v2y;
	z = v0z	+ c*v1z + s*v2z;

	return ( *this );
}

// Rotate unit vector x in the direction of "dir": length of dir is rotation angle.
//		x must be a unit vector.  dir must be perpindicular to x.
VectorR3& VectorR3::RotateUnitInDirection ( const VectorR3& dir)
{	
	double theta = dir.NormSq();
	if ( theta==0.0 ) {
		return *this;
	}
	else {
		theta = sqrt(theta);
		double costheta = cos(theta);
		double sintheta = sin(theta);
		VectorR3 dirUnit = dir/theta;
		*this = costheta*(*this) + sintheta*dirUnit;
		return ( *this );
	}
}

// ******************************************************
// * Matrix3x3 class - math library functions			*
// * * * * * * * * * * * * * * * * * * * * * * * * * * **

Matrix3x3& Matrix3x3::ReNormalize()	// Re-normalizes nearly orthonormal matrix
{
     double alpha = m11*m11+m21*m21+m31*m31;	// First column's norm squared
     double beta  = m12*m12+m22*m22+m32*m32;	// Second column's norm squared
     double gamma = m13*m13+m23*m23+m33*m33;	// Third column's norm squared
	alpha = 1.0 - 0.5*(alpha-1.0);				// Get mult. factor
	beta  = 1.0 - 0.5*(beta-1.0);
	gamma = 1.0 - 0.5*(gamma-1.0);
	m11 *= alpha;								// Renormalize first column
	m21 *= alpha;
	m31 *= alpha;
	m12 *= beta;								// Renormalize second column
	m22 *= beta;
	m32 *= beta;
	m13 *= gamma;
	m23 *= gamma;
	m33 *= gamma;
	alpha = m11*m12+m21*m22+m31*m32;		// First and second column dot product
	beta  = m11*m13+m21*m23+m31*m33;		// First and third column dot product
	gamma = m12*m13+m22*m23+m32*m33;		// Second and third column dot product
	alpha *= 0.5;
	beta *= 0.5;
	gamma *= 0.5;
    double temp1, temp2;
	temp1 = m11-alpha*m12-beta*m13;			// Update row1
	temp2 = m12-alpha*m11-gamma*m13;
	m13 -= beta*m11+gamma*m12;
	m11 = temp1;
	m12 = temp2;
	temp1 = m21-alpha*m22-beta*m23;			// Update row2
	temp2 = m22-alpha*m21-gamma*m23;
	m23 -= beta*m21+gamma*m22;
	m21 = temp1;
	m22 = temp2;
	temp1 = m31-alpha*m32-beta*m33;			// Update row3
	temp2 = m32-alpha*m31-gamma*m33;
	m33 -= beta*m31+gamma*m32;
	m31 = temp1;
	m32 = temp2;
	return *this;
}

void Matrix3x3::OperatorTimesEquals(const Matrix3x3& B)	 // Matrix product
{
	double t1, t2;		// temporary values
	t1 =  m11*B.m11 + m12*B.m21 + m13*B.m31;
	t2 =  m11*B.m12 + m12*B.m22 + m13*B.m32;
	m13 = m11*B.m13 + m12*B.m23 + m13*B.m33;
	m11 = t1;
	m12 = t2;

	t1 =  m21*B.m11 + m22*B.m21 + m23*B.m31;
	t2 =  m21*B.m12 + m22*B.m22 + m23*B.m32;
	m23 = m21*B.m13 + m22*B.m23 + m23*B.m33;
	m21 = t1;
	m22 = t2;

	t1 =  m31*B.m11 + m32*B.m21 + m33*B.m31;
	t2 =  m31*B.m12 + m32*B.m22 + m33*B.m32;
	m33 = m31*B.m13 + m32*B.m23 + m33*B.m33;
	m31 = t1;
	m32 = t2;
	return;
}

VectorR3 Matrix3x3::Solve(const VectorR3& u) const	// Returns solution
{												// based on Cramer's rule
	double sd11 = m22*m33-m23*m32;
	double sd21 = m32*m13-m12*m33;
	double sd31 = m12*m23-m22*m13;
	double sd12 = m31*m23-m21*m33;
	double sd22 = m11*m33-m31*m13;
	double sd32 = m21*m13-m11*m23;
	double sd13 = m21*m32-m31*m22;
	double sd23 = m31*m12-m11*m32;
	double sd33 = m11*m22-m21*m12;

    double detInv = 1.0/(m11*sd11 + m12*sd12 + m13*sd13);

	double rx = (u.x*sd11 + u.y*sd21 + u.z*sd31)*detInv;
	double ry = (u.x*sd12 + u.y*sd22 + u.z*sd32)*detInv;
	double rz = (u.x*sd13 + u.y*sd23 + u.z*sd33)*detInv;

	return ( VectorR3( rx, ry, rz ) );
}


// ******************************************************
// * Matrix3x4 class - math library functions			*
// * * * * * * * * * * * * * * * * * * * * * * * * * * **

Matrix3x4& Matrix3x4::ReNormalize()	// Re-normalizes nearly orthonormal matrix
{
    double alpha = m11*m11+m21*m21+m31*m31;	// First column's norm squared
    double beta  = m12*m12+m22*m22+m32*m32;	// Second column's norm squared
    double gamma = m13*m13+m23*m23+m33*m33;	// Third column's norm squared
	alpha = 1.0 - 0.5*(alpha-1.0);				// Get mult. factor
	beta  = 1.0 - 0.5*(beta-1.0);
	gamma = 1.0 - 0.5*(gamma-1.0);
	m11 *= alpha;								// Renormalize first column
	m21 *= alpha;
	m31 *= alpha;
	m12 *= beta;								// Renormalize second column
	m22 *= beta;
	m32 *= beta;
	m13 *= gamma;
	m23 *= gamma;
	m33 *= gamma;
	alpha = m11*m12+m21*m22+m31*m32;		// First and second column dot product
	beta  = m11*m13+m21*m23+m31*m33;		// First and third column dot product
	gamma = m12*m13+m22*m23+m32*m33;		// Second and third column dot product
	alpha *= 0.5;
	beta *= 0.5;
	gamma *= 0.5;
    double temp1, temp2;
	temp1 = m11-alpha*m12-beta*m13;			// Update row1
	temp2 = m12-alpha*m11-gamma*m13;
	m13 -= beta*m11+gamma*m12;
	m11 = temp1;
	m12 = temp2;
	temp1 = m21-alpha*m22-beta*m23;			// Update row2
	temp2 = m22-alpha*m21-gamma*m23;
	m23 -= beta*m21+gamma*m22;
	m21 = temp1;
	m22 = temp2;
	temp1 = m31-alpha*m32-beta*m33;			// Update row3
	temp2 = m32-alpha*m31-gamma*m33;
	m33 -= beta*m31+gamma*m32;
	m31 = temp1;
	m32 = temp2;
	return *this;
}

void Matrix3x4::OperatorTimesEquals (const Matrix3x4& B)	// Composition
{
	m14 += m11*B.m14 + m12*B.m24 + m13*B.m34;
	m24 += m21*B.m14 + m22*B.m24 + m23*B.m34;
	m34 += m31*B.m14 + m32*B.m24 + m33*B.m34;

	double t1, t2;		// temporary values
	t1 =  m11*B.m11 + m12*B.m21 + m13*B.m31;
	t2 =  m11*B.m12 + m12*B.m22 + m13*B.m32;
	m13 = m11*B.m13 + m12*B.m23 + m13*B.m33;
	m11 = t1;
	m12 = t2;

	t1 =  m21*B.m11 + m22*B.m21 + m23*B.m31;
	t2 =  m21*B.m12 + m22*B.m22 + m23*B.m32;
	m23 = m21*B.m13 + m22*B.m23 + m23*B.m33;
	m21 = t1;
	m22 = t2;

	t1 =  m31*B.m11 + m32*B.m21 + m33*B.m31;
	t2 =  m31*B.m12 + m32*B.m22 + m33*B.m32;
	m33 = m31*B.m13 + m32*B.m23 + m33*B.m33;
	m31 = t1;
	m32 = t2;
}

void Matrix3x4::OperatorTimesEquals (const Matrix3x3& B)	// Composition
{
	double t1, t2;		// temporary values
	t1 =  m11*B.m11 + m12*B.m21 + m13*B.m31;
	t2 =  m11*B.m12 + m12*B.m22 + m13*B.m32;
	m13 = m11*B.m13 + m12*B.m23 + m13*B.m33;
	m11 = t1;
	m12 = t2;

	t1 =  m21*B.m11 + m22*B.m21 + m23*B.m31;
	t2 =  m21*B.m12 + m22*B.m22 + m23*B.m32;
	m23 = m21*B.m13 + m22*B.m23 + m23*B.m33;
	m21 = t1;
	m22 = t2;

	t1 =  m31*B.m11 + m32*B.m21 + m33*B.m31;
	t2 =  m31*B.m12 + m32*B.m22 + m33*B.m32;
	m33 = m31*B.m13 + m32*B.m23 + m33*B.m33;
	m31 = t1;
	m32 = t2;
}

// ******************************************************
// * LinearMapR3 class - math library functions			*
// * * * * * * * * * * * * * * * * * * * * * * * * * * **


LinearMapR3 operator* ( const LinearMapR3& A, const LinearMapR3& B)
{
	return( LinearMapR3( A.m11*B.m11 + A.m12*B.m21 + A.m13*B.m31,
							A.m21*B.m11 + A.m22*B.m21 + A.m23*B.m31,
							A.m31*B.m11 + A.m32*B.m21 + A.m33*B.m31,
						 A.m11*B.m12 + A.m12*B.m22 + A.m13*B.m32,
							A.m21*B.m12 + A.m22*B.m22 + A.m23*B.m32,
							A.m31*B.m12 + A.m32*B.m22 + A.m33*B.m32,
						 A.m11*B.m13 + A.m12*B.m23 + A.m13*B.m33,
							A.m21*B.m13 + A.m22*B.m23 + A.m23*B.m33,
							A.m31*B.m13 + A.m32*B.m23 + A.m33*B.m33 ) );
}

double LinearMapR3::Determinant () const		// Returns the determinant
{
	return ( m11*(m22*m33-m23*m32) 
				- m12*(m21*m33-m31*m23)
				+ m13*(m21*m23-m31*m22) );
}

LinearMapR3 LinearMapR3::Inverse() const			// Returns inverse
{
	double sd11 = m22*m33-m23*m32;
	double sd21 = m32*m13-m12*m33;
	double sd31 = m12*m23-m22*m13;
	double sd12 = m31*m23-m21*m33;
	double sd22 = m11*m33-m31*m13;
	double sd32 = m21*m13-m11*m23;
	double sd13 = m21*m32-m31*m22;
	double sd23 = m31*m12-m11*m32;
	double sd33 = m11*m22-m21*m12;

    double detInv = 1.0/(m11*sd11 + m12*sd12 + m13*sd13);

	return( LinearMapR3( sd11*detInv, sd12*detInv, sd13*detInv,
						 sd21*detInv, sd22*detInv, sd23*detInv,
						 sd31*detInv, sd32*detInv, sd33*detInv ) );
}

LinearMapR3& LinearMapR3::Invert() 			// Converts into inverse.
{
	double sd11 = m22*m33-m23*m32;
	double sd21 = m32*m13-m12*m33;
	double sd31 = m12*m23-m22*m13;
	double sd12 = m31*m23-m21*m33;
	double sd22 = m11*m33-m31*m13;
	double sd32 = m21*m13-m11*m23;
	double sd13 = m21*m32-m31*m22;
	double sd23 = m31*m12-m11*m32;
	double sd33 = m11*m22-m21*m12;

    double detInv = 1.0/(m11*sd11 + m12*sd12 + m13*sd13);

	m11 = sd11*detInv;
	m12 = sd21*detInv;
	m13 = sd31*detInv;
	m21 = sd12*detInv;
	m22 = sd22*detInv;
	m23 = sd32*detInv;
	m31 = sd13*detInv;
	m32 = sd23*detInv;
	m33 = sd33*detInv;

	return ( *this );
}


// ******************************************************
// * AffineMapR3 class - math library functions			*
// * * * * * * * * * * * * * * * * * * * * * * * * * * **

AffineMapR3 operator* ( const AffineMapR3& A, const AffineMapR3& B )
{
	return( AffineMapR3( A.m11*B.m11 + A.m12*B.m21 + A.m13*B.m31,
							A.m21*B.m11 + A.m22*B.m21 + A.m23*B.m31,
							A.m31*B.m11 + A.m32*B.m21 + A.m33*B.m31,
						 A.m11*B.m12 + A.m12*B.m22 + A.m13*B.m32,
							A.m21*B.m12 + A.m22*B.m22 + A.m23*B.m32,
							A.m31*B.m12 + A.m32*B.m22 + A.m33*B.m32,
						 A.m11*B.m13 + A.m12*B.m23 + A.m13*B.m33,
							A.m21*B.m13 + A.m22*B.m23 + A.m23*B.m33,
							A.m31*B.m13 + A.m32*B.m23 + A.m33*B.m33,
						 A.m11*B.m14 + A.m12*B.m24 + A.m13*B.m34 + A.m14,
						    A.m21*B.m14 + A.m22*B.m24 + A.m23*B.m34 + A.m24,
							A.m31*B.m14 + A.m32*B.m24 + A.m33*B.m34 + A.m34));
}

AffineMapR3 operator* ( const LinearMapR3& A, const AffineMapR3& B )
{
	return( AffineMapR3( A.m11*B.m11 + A.m12*B.m21 + A.m13*B.m31,
							A.m21*B.m11 + A.m22*B.m21 + A.m23*B.m31,
							A.m31*B.m11 + A.m32*B.m21 + A.m33*B.m31,
						 A.m11*B.m12 + A.m12*B.m22 + A.m13*B.m32,
							A.m21*B.m12 + A.m22*B.m22 + A.m23*B.m32,
							A.m31*B.m12 + A.m32*B.m22 + A.m33*B.m32,
						 A.m11*B.m13 + A.m12*B.m23 + A.m13*B.m33,
							A.m21*B.m13 + A.m22*B.m23 + A.m23*B.m33,
							A.m31*B.m13 + A.m32*B.m23 + A.m33*B.m33,
						 A.m11*B.m14 + A.m12*B.m24 + A.m13*B.m34,
						    A.m21*B.m14 + A.m22*B.m24 + A.m23*B.m34,
							A.m31*B.m14 + A.m32*B.m24 + A.m33*B.m34  ));

}
 
AffineMapR3 operator* ( const AffineMapR3& A, const LinearMapR3& B )
{
	return( AffineMapR3( A.m11*B.m11 + A.m12*B.m21 + A.m13*B.m31,
							A.m21*B.m11 + A.m22*B.m21 + A.m23*B.m31,
							A.m31*B.m11 + A.m32*B.m21 + A.m33*B.m31,
						 A.m11*B.m12 + A.m12*B.m22 + A.m13*B.m32,
							A.m21*B.m12 + A.m22*B.m22 + A.m23*B.m32,
							A.m31*B.m12 + A.m32*B.m22 + A.m33*B.m32,
						 A.m11*B.m13 + A.m12*B.m23 + A.m13*B.m33,
							A.m21*B.m13 + A.m22*B.m23 + A.m23*B.m33,
							A.m31*B.m13 + A.m32*B.m23 + A.m33*B.m33,
						 A.m14,
							A.m24,
							A.m34   ) );
}
 

AffineMapR3 AffineMapR3::Inverse() const				// Returns inverse
{
	double sd11 = m22*m33-m23*m32;
	double sd21 = m32*m13-m12*m33;
	double sd31 = m12*m23-m22*m13;
	double sd12 = m31*m23-m21*m33;
	double sd22 = m11*m33-m31*m13;
	double sd32 = m21*m13-m11*m23;
	double sd13 = m21*m32-m31*m22;
	double sd23 = m31*m12-m11*m32;
	double sd33 = m11*m22-m21*m12;

    double detInv = 1.0/(m11*sd11 + m12*sd12 + m13*sd13);

	// Make sd's hold the (transpose of) the inverse of the 3x3 part
	sd11 *= detInv;
	sd12 *= detInv;
	sd13 *= detInv;
	sd21 *= detInv;
	sd22 *= detInv;
	sd23 *= detInv;
	sd31 *= detInv;
	sd32 *= detInv;
	sd33 *= detInv;
	double sd41 = -(m14*sd11 + m24*sd21 + m34*sd31);
	double sd42 = -(m14*sd12 + m24*sd22 + m34*sd32);
	double sd43 = -(m14*sd12 + m24*sd23 + m34*sd33);

	return( AffineMapR3( sd11, sd12, sd13,
						 sd21, sd22, sd23,
						 sd31, sd32, sd33,
						 sd41, sd42, sd43 ) );
}

AffineMapR3& AffineMapR3::Invert()					// Converts into inverse.
{
	double sd11 = m22*m33-m23*m32;
	double sd21 = m32*m13-m12*m33;
	double sd31 = m12*m23-m22*m13;
	double sd12 = m31*m23-m21*m33;
	double sd22 = m11*m33-m31*m13;
	double sd32 = m21*m13-m11*m23;
	double sd13 = m21*m32-m31*m22;
	double sd23 = m31*m12-m11*m32;
	double sd33 = m11*m22-m21*m12;

    double detInv = 1.0/(m11*sd11 + m12*sd12 + m13*sd13);

	m11 = sd11*detInv;
	m12 = sd21*detInv;
	m13 = sd31*detInv;
	m21 = sd12*detInv;
	m22 = sd22*detInv;
	m23 = sd32*detInv;
	m31 = sd13*detInv;
	m32 = sd23*detInv;
	m33 = sd33*detInv;
	double sd41 = -(m14*m11 + m24*m12 + m34*m13);  // Compare to ::Inverse.
	double sd42 = -(m14*m21 + m24*m22 + m34*m23);
	double sd43 = -(m14*m31 + m24*m32 + m34*m33);
	m14 = sd41;
	m24 = sd42;
	m34 = sd43;

	return ( *this );
}

// **************************************************************
// * RotationMapR3 class - math library functions				*
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * **

RotationMapR3 operator*(const RotationMapR3& A, const RotationMapR3& B) 
										// Matrix product (composition)
{
	return(RotationMapR3(A.m11*B.m11 + A.m12*B.m21 + A.m13*B.m31,
							A.m21*B.m11 + A.m22*B.m21 + A.m23*B.m31,
							A.m31*B.m11 + A.m32*B.m21 + A.m33*B.m31,
						 A.m11*B.m12 + A.m12*B.m22 + A.m13*B.m32,
							A.m21*B.m12 + A.m22*B.m22 + A.m23*B.m32,
							A.m31*B.m12 + A.m32*B.m22 + A.m33*B.m32,
						 A.m11*B.m13 + A.m12*B.m23 + A.m13*B.m33,
							A.m21*B.m13 + A.m22*B.m23 + A.m23*B.m33,
							A.m31*B.m13 + A.m32*B.m23 + A.m33*B.m33 ) );
}

RotationMapR3& RotationMapR3::Set( const Quaternion& quat )
{
	double wSq = quat.w*quat.w;
	double xSq = quat.x*quat.x;
	double ySq = quat.y*quat.y;
	double zSq = quat.z*quat.z;
	double Dqwx = 2.0*quat.w*quat.x;
	double Dqwy = 2.0*quat.w*quat.y;
	double Dqwz = 2.0*quat.w*quat.z;
	double Dqxy = 2.0*quat.x*quat.y;
	double Dqyz = 2.0*quat.y*quat.z;
	double Dqxz = 2.0*quat.x*quat.z;
	m11 = wSq+xSq-ySq-zSq;
	m22 = wSq-xSq+ySq-zSq;
	m33 = wSq-xSq-ySq+zSq;
	m12 = Dqxy-Dqwz;
	m21 = Dqxy+Dqwz;
	m13 = Dqxz+Dqwy;
	m31 = Dqxz-Dqwy;
	m23 = Dqyz-Dqwx;
	m32 = Dqyz+Dqwx;
	return *this;
}

RotationMapR3& RotationMapR3::Set( const VectorR3& u, double theta )
{
	assert ( fabs(u.NormSq()-1.0)<2.0e-6 );
    double c = cos(theta);
    double s = sin(theta);
    double mc = 1.0-c;
	double xmc = u.x*mc;
	double xymc = xmc*u.y;
	double xzmc = xmc*u.z;
	double yzmc = u.y*u.z*mc;
	double xs = u.x*s;
	double ys = u.y*s;
	double zs = u.z*s;
	Matrix3x3::Set( u.x*u.x*mc+c, xymc+zs,      xzmc-ys,
					xymc-zs,	  u.y*u.y*mc+c, yzmc+xs,
					xzmc+ys,	  yzmc-xs,	    u.z*u.z*mc+c );
	return *this;
}

// The rotation axis vector u MUST be a UNIT vector!!! 
RotationMapR3& RotationMapR3::Set( const VectorR3& u, double s, double c )
{
	assert ( fabs(u.NormSq()-1.0)<2.0e-6 );
	double mc = 1.0-c;
	double xmc = u.x*mc;
	double xymc = xmc*u.y;
	double xzmc = xmc*u.z;
	double yzmc = u.y*u.z*mc;
	double xs = u.x*s;
	double ys = u.y*s;
	double zs = u.z*s;
	Matrix3x3::Set( u.x*u.x*mc+c, xymc+zs,      xzmc-ys,
					xymc-zs,	  u.y*u.y*mc+c, yzmc+xs,
					xzmc+ys,	  yzmc-xs,	    u.z*u.z*mc+c );
	return *this;
}


// ToAxisAndAngle - find a unit vector in the direction of the rotation axis,
//	and the angle theta of rotation.  Returns true if the rotation angle is non-zero,
//  and false if it is zero.
bool RotationMapR3::ToAxisAndAngle( VectorR3* u, double *theta ) const
{
	double alpha = m11+m22+m33-1.0;
	double beta = sqrt(Square(m32-m23)+Square(m13-m31)+Square(m21-m12));
	if ( beta==0.0 ) {
		*u = VectorR3::UnitY;
		*theta = 0.0;
		return false;
	}
	else {
		u->Set(m32-m23, m13-m31, m21-m12);
		*u /= beta;
		*theta = atan2( beta, alpha );
		return true;
	}
}

// VrRotate is similar to glRotate.  Returns a matrix (LinearMapR3)
//		that will perform the rotation when multiplied on the left.
// u is supposed to be a *unit* vector.  Otherwise, the LinearMapR3
//		returned will be garbage!
RotationMapR3 VrRotate( double theta, const VectorR3& u )
{
	RotationMapR3 ret;
	ret.Set( u, theta );
	return ret;
}

// This version of rotate takes the cosine and sine of theta
//    instead of theta.  u must still be a unit vector.

RotationMapR3 VrRotate( double c, double s, const VectorR3& u )
{
	RotationMapR3 ret;
	ret.Set( u, s, c );
	return ret;
}

// Returns a RotationMapR3 which rotates the fromVec to be colinear
//		with toVec.

RotationMapR3 VrRotateAlign( const VectorR3& fromVec, const VectorR3& toVec)
{
	VectorR3 crossVec = fromVec;
	crossVec *= toVec;
	double sinetheta = crossVec.Norm();	// Not yet normalized!
	if ( sinetheta < 1.0e-40 ) {
		return ( RotationMapR3( 
					1.0, 0.0, 0.0, 
					0.0, 1.0, 0.0, 
					0.0, 0.0, 1.0) );
	}
	crossVec /= sinetheta;				// Normalize the vector
	double scale = 1.0/sqrt(fromVec.NormSq()*toVec.NormSq());
	sinetheta *= scale;
	double cosinetheta = (fromVec^toVec)*scale;
	return ( VrRotate( cosinetheta, sinetheta, crossVec) );
}

// RotateToMap returns a rotation map which rotates fromVec to have the
//		same direction as toVec.
// fromVec and toVec should be unit vectors
RotationMapR3 RotateToMap( const VectorR3& fromVec, const VectorR3& toVec)
{
	VectorR3 crossVec = fromVec;
	crossVec *= toVec;
	double sintheta = crossVec.Norm();
	double costheta = fromVec^toVec;
	if ( sintheta <= 1.0e-40 ) {
		if ( costheta>0.0 ) {
			return ( RotationMapR3( 
						1.0, 0.0, 0.0, 
						0.0, 1.0, 0.0, 
						0.0, 0.0, 1.0) );
		}
		else {
			GetOrtho ( toVec, crossVec );		// Get arbitrary orthonormal vector
			return( VrRotate(costheta, sintheta, crossVec ) );
		}
	}	
	else {
		crossVec /= sintheta;				// Normalize the vector
		return ( VrRotate( costheta, sintheta, crossVec) );
	}
}

// **************************************************************
// * RigidMapR3 class - math library functions					*
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * **

// The rotation axis vector u MUST be a UNIT vector!!! 
RigidMapR3& RigidMapR3::SetRotationPart( const VectorR3& u, double theta )
{
	assert ( fabs(u.NormSq()-1.0)<2.0e-6 );
    double c = cos(theta);
    double s = sin(theta);
    double mc = 1.0-c;
	double xmc = u.x*mc;
	double xymc = xmc*u.y;
	double xzmc = xmc*u.z;
	double yzmc = u.y*u.z*mc;
	double xs = u.x*s;
	double ys = u.y*s;
	double zs = u.z*s;
	Matrix3x4::Set3x3( u.x*u.x*mc+c, xymc+zs,      xzmc-ys,
					xymc-zs,	  u.y*u.y*mc+c, yzmc+xs,
					xzmc+ys,	  yzmc-xs,	    u.z*u.z*mc+c );
	return *this;
}

// The rotation axis vector u MUST be a UNIT vector!!! 
RigidMapR3& RigidMapR3::SetRotationPart( const VectorR3& u, double s, double c )
{
	assert ( fabs(u.NormSq()-1.0)<2.0e-6 );
	double mc = 1.0-c;
	double xmc = u.x*mc;
	double xymc = xmc*u.y;
	double xzmc = xmc*u.z;
	double yzmc = u.y*u.z*mc;
	double xs = u.x*s;
	double ys = u.y*s;
	double zs = u.z*s;
	Matrix3x4::Set3x3( u.x*u.x*mc+c, xymc+zs,      xzmc-ys,
					xymc-zs,	  u.y*u.y*mc+c, yzmc+xs,
					xzmc+ys,	  yzmc-xs,	    u.z*u.z*mc+c );
	return *this;
}


// CalcGlideRotation - converts a rigid map into an equivalent
//	glide rotation (screw motion).  It returns the rotation axis
//  as base point u, and a rotation axis v.  The vectors u and v are
//  always orthonormal.  v will be a unit vector.  
//  It also returns the glide distance, which is the translation parallel
//  to v.  Further, it returns the signed rotation angle theta (right hand rule 
//  specifies the direction.
// The glide rotation means a rotation around the point u with axis direction v.
// Return code "true" if the rotation amount is non-zero.  "false" if pure translation.
bool RigidMapR3::CalcGlideRotation( VectorR3* u, VectorR3* v, 
								    double *glideDist, double *rotation ) const
{
	// Compare to the code for ToAxisAndAngle.
	double alpha = m11+m22+m33-1.0;
	double beta = sqrt(Square(m32-m23)+Square(m13-m31)+Square(m21-m12));
	if ( beta==0.0 ) {
		double vN = m14*m14 + m24*m24 + m34*m34;
		if ( vN>0.0 ) {
			vN = sqrt(vN);
			v->Set( m14, m24, m34 );
			*v /= vN;
			*glideDist = vN;
		}
		else {
			*v = VectorR3::UnitX;
			*glideDist = 0.0;
		}
		u->SetZero();
		*rotation = 0;
		return false;
	}
	else {
		v->Set(m32-m23, m13-m31, m21-m12);
		*v /= beta;				// v - unit vector, rotation axis
		*rotation = atan2( beta, alpha );
		u->Set( m14, m24, m34 );
		*glideDist = ((*u)^(*v));
		VectorR3 temp = *v;
		temp *= *glideDist;
		*u -= temp;					// Subtract component in direction of rot. axis v
		temp = *v;
		temp *= *u;
		temp /= tan((*rotation)/2);	// temp = (v \times u) / tan(rotation/2)
		*u += temp;
		*u *= 0.5;
		return true;
	}

}

// ***************************************************************
//  Linear Algebra Utilities									 *
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

// Returns a righthanded orthonormal basis to complement vector u
void GetOrtho( const VectorR3& u,  VectorR3& v, VectorR3& w)
{
	if ( u.x > 0.5 || u.x<-0.5 || u.y > 0.5 || u.y<-0.5 ) {
		v.Set ( u.y, -u.x, 0.0 );
	}
	else {
		v.Set ( 0.0, u.z, -u.y);
	}
	v.Normalize();
	w = u;
	w *= v;
	w.Normalize();
	// w.NormalizeFast();
	return;
}

// Returns a vector v orthonormal to unit vector u
void GetOrtho( const VectorR3& u,  VectorR3& v )
{
	if ( u.x > 0.5 || u.x<-0.5 || u.y > 0.5 || u.y<-0.5 ) {
		v.Set ( u.y, -u.x, 0.0 );
	}
	else {
		v.Set ( 0.0, u.z, -u.y);
	}
	v.Normalize();
	return;
}

// ***************************************************************
//  Stream Output Routines										 *
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

ostream& operator<< ( ostream& os, const VectorR3& u )
{
	return (os << "<" << u.x << "," << u.y << "," << u.z << ">");
}

ostream& operator<< ( ostream& os, const Matrix3x3& A )
{
	os << " <" << A.m11 << ", " << A.m12 << ", " << A.m13  << ">\n"
	   << " <" << A.m21 << ", " << A.m22 << ", " << A.m23  << ">\n"
	   << " <" << A.m31 << ", " << A.m32 << ", " << A.m33  << ">\n" ;
	return (os);
}

ostream& operator<< ( ostream& os, const Matrix3x4& A )
{
	os << " <" << A.m11 << ", " << A.m12 << ", " << A.m13 
			<< "; " << A.m14 << ">\n"
	   << " <" << A.m21 << ", " << A.m22 << ", " << A.m23 
			<< "; " << A.m24 << ">\n"
	   << " <" << A.m31 << ", " << A.m32 << ", " << A.m33 
			<< "; " << A.m34 << ">\n" ;
	return (os);
}


