From 71994af79becf05a83a73f4698a94f4586bb3ee7 Mon Sep 17 00:00:00 2001
From: srit <srit>
Date: Thu, 4 Mar 2010 10:08:05 +0000
Subject: [PATCH] Moved signal files to clitk-tests/signal

---
 tools/CMakeLists.txt                          |   9 -
 tools/clitkEllipse.cxx                        | 398 -----------------
 tools/clitkEllipse.h                          |  92 ----
 tools/clitkSignalApparentMotionTracking.cxx   |  51 ---
 tools/clitkSignalApparentMotionTracking.ggo   |  38 --
 ...litkSignalApparentMotionTrackingFilter.cxx | 419 ------------------
 .../clitkSignalApparentMotionTrackingFilter.h |  77 ----
 tools/clitkSignalFilter.cxx                   |  80 ----
 tools/clitkSignalFilter.ggo                   |  27 --
 tools/clitkSignalMeanPositionFilter.cxx       | 362 ---------------
 tools/clitkSignalMeanPositionFilter.h         |  85 ----
 tools/clitkSignalMeanPositionTracking.cxx     |  52 ---
 tools/clitkSignalMeanPositionTracking.ggo     |  27 --
 tools/clitkTrajectory2D.cxx                   | 172 -------
 tools/clitkTrajectory2D.h                     |  80 ----
 15 files changed, 1969 deletions(-)
 delete mode 100644 tools/clitkEllipse.cxx
 delete mode 100644 tools/clitkEllipse.h
 delete mode 100644 tools/clitkSignalApparentMotionTracking.cxx
 delete mode 100644 tools/clitkSignalApparentMotionTracking.ggo
 delete mode 100644 tools/clitkSignalApparentMotionTrackingFilter.cxx
 delete mode 100644 tools/clitkSignalApparentMotionTrackingFilter.h
 delete mode 100644 tools/clitkSignalFilter.cxx
 delete mode 100644 tools/clitkSignalFilter.ggo
 delete mode 100644 tools/clitkSignalMeanPositionFilter.cxx
 delete mode 100644 tools/clitkSignalMeanPositionFilter.h
 delete mode 100644 tools/clitkSignalMeanPositionTracking.cxx
 delete mode 100644 tools/clitkSignalMeanPositionTracking.ggo
 delete mode 100644 tools/clitkTrajectory2D.cxx
 delete mode 100644 tools/clitkTrajectory2D.h

diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index fe4048e..e4f561f 100644
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -67,15 +67,6 @@ TARGET_LINK_LIBRARIES(clitkInvertVF clitkCommon ITKIO clitkFilters)
 ADD_EXECUTABLE(clitkAffineTransform clitkAffineTransform.cxx  clitkAffineTransform_ggo.c)
 TARGET_LINK_LIBRARIES(clitkAffineTransform clitkCommon ITKIO  clitkFilters)
 
-ADD_EXECUTABLE(clitkSignalMeanPositionTracking clitkSignalMeanPositionTracking.cxx clitkSignalMeanPositionFilter.cxx clitkEllipse.cxx clitkSignalMeanPositionTracking_ggo.c)
-TARGET_LINK_LIBRARIES(clitkSignalMeanPositionTracking clitkCommon ITKIO )
-
-ADD_EXECUTABLE(clitkSignalApparentMotionTracking clitkSignalApparentMotionTracking.cxx clitkTrajectory2D.cxx clitkSignalApparentMotionTrackingFilter.cxx clitkEllipse.cxx clitkSignalApparentMotionTracking_ggo.c)
-TARGET_LINK_LIBRARIES(clitkSignalApparentMotionTracking clitkCommon ITKIO)
-
-ADD_EXECUTABLE(clitkSignalFilter clitkSignalFilter.cxx clitkSignalFilter_ggo.c)
-TARGET_LINK_LIBRARIES(clitkSignalFilter clitkCommon ITKIO ) 
-
 ADD_EXECUTABLE(clitkSetBackground clitkSetBackground.cxx
 clitkSetBackgroundGenericFilter.cxx clitkSetBackground_ggo.c)
 TARGET_LINK_LIBRARIES(clitkSetBackground clitkCommon ITKIO )
diff --git a/tools/clitkEllipse.cxx b/tools/clitkEllipse.cxx
deleted file mode 100644
index 4e2bd56..0000000
--- a/tools/clitkEllipse.cxx
+++ /dev/null
@@ -1,398 +0,0 @@
-/*=========================================================================
-                                                                                
-  Program:   clitk
-  Module:    $RCSfile: clitkEllipse.cxx,v $
-  Language:  C++
-  Date:      $Date: 2010/03/03 10:47:48 $
-  Version:   $Revision: 1.3 $
-                                                                                
-  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
-  l'Image). All rights reserved. See Doc/License.txt or
-  http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
-                                                                                
-  This software is distributed WITHOUT ANY WARRANTY; without even
-  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-  PURPOSE.  See the above copyright notices for more information.
-                                                                             
-  =========================================================================*/
-
-#include "clitkEllipse.h"
-
-typedef itk::Vector<double,2> Vector2d;
-typedef itk::Vector<double,6> Vector6d;
-typedef itk::Matrix<double,6,6> Matrix6x6d;
-typedef itk::Matrix<double,3,3> Matrix3x3d;
-
-//---------------------------------------------------------------------
-clitk::Ellipse::Ellipse():a((*this)[0]), b((*this)[1]), 
-                          c((*this)[2]), d((*this)[3]), 
-                          e((*this)[4]), f((*this)[5]) {
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-clitk::Ellipse::Ellipse(const Ellipse & e):a((*this)[0]), b((*this)[1]), 
-                                           c((*this)[2]), d((*this)[3]), 
-                                           e((*this)[4]), f((*this)[5]) {
-  for(int i=0; i<6; i++) (*this)[i] = e[i];
-}
-
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-Vector2d clitk::Ellipse::ComputeCenter() {
-  // See http://mathworld.wolfram.com/Ellipse.html
-  // see Ruan 2008
-  Vector2d center;
-  center[0] = (2*c*d - b*e)/(b*b-4*a*c);
-  center[1] = (2*a*e - b*d)/(b*b-4*a*c);
-  return center;
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-Vector2d clitk::Ellipse::ComputeSemiAxeLengths() {
-  // See http://www.geometrictools.com/Documentation/InformationAboutEllipses.pdf
-  Vector2d axis;
-  Vector2d center = ComputeCenter();
-  double & k1 = center[0];
-  double & k2 = center[1];
-  // DD(f);
-  double mu = 1.0/(a*k1*k1 + b*k1*k2 + c*k2*k2 - f);
-  // DD(a*k1*k1);
-  //   DD(b*k1*k2);
-  //   DD(c*k2*k2);
-  //   DD(a*k1*k1 + b*k1*k2 + c*k2*k2 - f);
-  //   DD(mu);
-  double m11 = mu * a;
-  double m12 = mu * 0.5 * b;
-  double m22 = mu * c;
-  double l1 = ( (m11+m22) + sqrt((m11-m22)*(m11-m22)+4*m12*m12) )/2.0;
-  // DD(k1);
-  //   DD(k2);
-  //   DD(mu);
-  //   DD(m11);
-  //   DD(m12);
-  //   DD(m22);
-  //   DD(l1);
-  assert(l1>=0.0);
-  axis[1] = 1.0/sqrt(l1);
-  double l2 = ((m11+m22)-sqrt((m11-m22)*(m11-m22)+4*m12*m12))/2.0;
-  // DD(l2);
-  assert(l2>0.0);
-  axis[0] = 1.0/sqrt(l2);
-  return axis;
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-double clitk::Ellipse::ComputeAngleInRad() {
-  // See http://www.geometrictools.com/Documentation/InformationAboutEllipses.pdf
-  double theta;
-  if (b==0) {
-    if (a<c) { theta = 0; }
-    else     { theta = 0.5*M_PI; }      
-  }
-  else {
-    if (a<c) {
-      theta = 0.5*atan(-b/(c-a));
-    }
-    else {
-      theta = M_PI/2+0.5*atan(-b/(c-a));
-    }
-  }
-  return theta;
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::Ellipse::InitialiseEllipseFitting(double eta, unsigned int n, clitk::Signal & inputX, clitk::Signal & inputY) {
-  // Store data
-  mEta = eta;
-  mInputX = &inputX;
-  mInputY = &inputY;
-
-  // Initialise ellipse to global fit
-  std::vector<double> extremaX(2);
-  std::vector<double> extremaY(2);
-  double x0 = 0.0;
-  double y0 = 0.0;
-  extremaX[0] = extremaY[0] = numeric_limits<double>::max();
-  extremaX[1] = extremaY[1] = -numeric_limits<double>::max();
-  for(unsigned int i=0; i<n; i++) {
-    if (inputX[i] < extremaX[0]) extremaX[0] = inputX[i];
-    if (inputX[i] > extremaX[1]) extremaX[1] = inputX[i];
-    if (inputY[i] < extremaY[0]) extremaY[0] = inputY[i];
-    if (inputY[i] > extremaY[1]) extremaY[1] = inputY[i];
-    x0 += inputX[i];
-    y0 += inputY[i];
-  }
-  x0 /= n;
-  y0 /= n;
-
-  // initialisation with an ellipse more small than real points extends
-  double ax1 = (extremaX[1]-extremaX[0])/2.0;
-  double ax2 = (extremaY[1]-extremaY[0])/2.0;
-  if (ax2 >= ax1) ax2 = 0.99*ax1;
-  SetCenterAndSemiAxes(x0, y0, ax1, ax2);
-
-  // Initialisation of C
-  C.Fill(0.0);
-  C(0,0) = 0; C(0,1) = 0;  C(0,2) = 2;
-  C(1,0) = 0; C(1,1) = -1; C(1,2) = 0;
-  C(2,0) = 2; C(2,1) = 0;  C(2,2) = 0;
-  Ct = C.GetVnlMatrix().transpose();
-  
-  // Compute initial S
-  UpdateSMatrix(0,n, inputX, inputY);
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::Ellipse::CopyBlock(Matrix6x6d & out, const Matrix6x6d & in, 
-                               int ox, int oy, int l, double factor) {
-  for(int x=ox; x<ox+l; x++)
-    for(int y=oy; y<oy+l; y++) {
-      out(x,y) = factor * in(x,y);
-    }
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::Ellipse::CopyBlock(Matrix6x6d & out, const Matrix3x3d & in, 
-                               int ox, int oy, double factor) {
-  for(int x=0; x<3; x++)
-    for(int y=0; y<3; y++) {
-      out(ox+x,oy+y) = factor * in(x,y);
-    }
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-Matrix3x3d clitk::Ellipse::GetBlock3x3(const Matrix6x6d & M, int x, int y) {
-  Matrix3x3d B;
-  for(int i=0; i<3; i++) {
-    for(int j=0; j<3; j++) {
-      B(i,j) = M(x+i,y+j);
-    }
-  }
-  return B;
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-double clitk::Ellipse::EllipseFittingNextIteration() {  
-  Vector6d & current = (*this);
-
-  // Normalize current vector. This allow to have a decreasing
-  // residual r (no need to optimize)
-  GetVnlVector().normalize();
-  double r = (St*current)*current;
-  // DD(r);
-
-  // Temporary parameters
-  Vector6d an;
-
-  // Iterative update
-  an = Sinv * C * current;
-  double num = (Wt*current)*current; // anT W an = (WT an) an
-  double denom = (Ct*current)*current;
-  an = (mEta * num/denom) * an;
-  an += (1.0-mEta)*current;
-  SetVnlVector(an.GetVnlVector());
-
-  // return residual
-  return r;
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::Ellipse::SetCenterAndSemiAxes(double x0, double y0, 
-                                          double r1, double r2) {
-  a = 1.0/(r1*r1);
-  b = 0;
-  c = 1.0/(r2*r2);
-  if (a>c) {
-    std::cerr << "Error major axis should be r1, not r2 (r1=" << r1
-              << " r2=" << r2 << ")" << std::endl;
-    exit(0);
-  }
-  d = (-2.0*x0)/(r1*r1);
-  e = (-2.0*y0)/(r2*r2); 
-  f = (x0*x0)/(r1*r1) + (y0*y0)/(r2*r2) - 1.0;
-  GetVnlVector().normalize();
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::Ellipse::UpdateSMatrix(unsigned int begin, unsigned int n, 
-                                   clitk::Signal & inputX, clitk::Signal & inputY) {
-  // Initialisation of z
-  z.resize(n);
-  int j = 0;
-  for(unsigned int i=begin; i<begin+n; i++) {
-    z[j][0] = inputX[i]*inputX[i];
-    z[j][1] = inputX[i]*inputY[i];
-    z[j][2] = inputY[i]*inputY[i];
-    z[j][3] = inputX[i];
-    z[j][4] = inputY[i];
-    z[j][5] = 1;
-    j++;
-  }
-
-  // Initialisation of S
-  S.Fill(0.0);
-  // j = 0;
-  for(unsigned int i=0; i<n; i++) {
-    for(unsigned int x=0; x<6; x++)
-      for(unsigned int y=0; y<6; y++) 
-        S(x,y) += z[i][x]*z[i][y];
-    // j++;
-  }
-  Sinv = S.GetInverse();
-  St = S.GetVnlMatrix().transpose();
-  
-  // Initialisation of W
-  W.Fill(0.0);
-  CopyBlock(W, S, 0, 0, 3);
-  CopyBlock(W, S, 3, 3, 3, -1);
-  Wt = W.GetVnlMatrix().transpose();
-
-  // Automated computation of mEta
-  if (mEta<0) {
-    Matrix3x3d E  = GetBlock3x3(S, 0, 0);
-    Matrix3x3d B  = GetBlock3x3(S, 0, 3);
-    Matrix3x3d Bt = GetBlock3x3(S, 3, 0);
-    Matrix3x3d D  = GetBlock3x3(S, 3, 3);
-    Matrix3x3d Dinv(D.GetInverse());    
-    Matrix3x3d Stilde;
-    Stilde = E - B*Dinv*Bt;
-    
-    Matrix3x3d Ctilde;
-    Ctilde(0,0) = 0; Ctilde(0,1) = 0;  Ctilde(0,2) = 2;
-    Ctilde(1,0) = 0; Ctilde(1,1) = -1; Ctilde(1,2) = 0;
-    Ctilde(2,0) = 2; Ctilde(2,1) = 0;  Ctilde(2,2) = 0;
-    
-    // Ctilde is not inonneg-definite, so vnl print error on std cerr
-    // the following "disableStdCerr" disable it ...
-    disableStdCerr();
-    vnl_generalized_eigensystem solver(Stilde.GetVnlMatrix(), Ctilde.GetVnlMatrix());
-    //vnl_generalized_eigensystem solver(Ctilde.GetVnlMatrix(), Stilde.GetVnlMatrix());
-    enableStdCerr();
-    double dmax=0.0, dmin=9999999.9;
-    dmax = solver.D(2);
-    dmin = solver.D(1);
-    mEta = 2.0/(fabs(dmax/dmin)+1);
-    assert(mEta<1.0);
-  }  
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::ComputeIsoPhaseFromListOfEllipses(std::vector<clitk::Ellipse*> & l, 
-                                              clitk::Signal & sx, 
-                                              clitk::Signal & sy, 
-                                              int nbIsoPhase, 
-                                              int delay, 
-                                              int L, 
-                                              clitk::Signal & phase) {
-  // Init
-  DD(nbIsoPhase);
-  std::vector<double> mIsoPhaseRefAngle(nbIsoPhase);
-  phase.resize(l.size());
-  double refphaseangle=0;
-  double previousangle=0;
-
-  // Loop on ellipses
-  // DD(l.size());
-  for (unsigned int i=0; i<l.size(); i++) {
-    // DD("=================================");
-    //     DD(i);
-    clitk::Ellipse & An = *l[i];
-    // DD(An);
-    //     DD(An.ComputeCenter());
-    //     DD(An.ComputeSemiAxeLengths());
-    //     DD(rad2deg(An.ComputeAngleInRad()));
-
-    // Compute current signed angle
-    Vector2d x1(An.ComputeCenter());
-    double a = l[0]->ComputeSemiAxeLengths()[0]; 
-    double theta = l[0]->ComputeAngleInRad(); 
-    Vector2d x2; x2[0] = x1[0]+a * cos(theta); x2[1] = x1[1]+a * sin(theta);
-    Vector2d x3(x1);
-    Vector2d x4; x4[0] = sx[i+L]; x4[1] = sy[i+L];
-    Vector2d A(x2-x1);
-    Vector2d B(x4-x3);
-    // DD(sx[i+L]);
-    //     DD(sy[i+L]);
-    // http://www.euclideanspace.com/maths/algebra/vectors/angleBetween/index.htm
-    double signed_angle = atan2(B[1], B[0]) - atan2(A[1], A[0]);
-    if (signed_angle<0) signed_angle = 2*M_PI+signed_angle;
-    
-    // First time : set the angle
-    if (i==0) {
-      // DD(signed_angle);
-      refphaseangle = signed_angle;
-      for(int a=0; a<nbIsoPhase; a++) {
-        if (a==0) mIsoPhaseRefAngle[a] = refphaseangle;//signed_angle;
-        else mIsoPhaseRefAngle[a] = (refphaseangle //signed_angle
-                                     + (2*M_PI)*a/nbIsoPhase);
-        if (mIsoPhaseRefAngle[a] > 2*M_PI) mIsoPhaseRefAngle[a] -= 2*M_PI;
-        if (mIsoPhaseRefAngle[a] < 0) mIsoPhaseRefAngle[a] = 2*M_PI-mIsoPhaseRefAngle[a];
-      }
-      int a=0;
-      while ((a<nbIsoPhase) && (signed_angle>=mIsoPhaseRefAngle[a])) { a++; }
-      phase[i] = a-1;
-      if (nbIsoPhase == 1) phase[i] = 1;
-    }
-    else {
-      phase[i] = phase[i-1];
-      
-      // Check if angle cross a ref angle
-      for(int a=0; a<nbIsoPhase; a++) {
-        // std::cout << "a=" << rad2deg(signed_angle) << " prev=" << rad2deg(previousangle)
-        //                   << " ref=" << rad2deg(mIsoPhaseRefAngle[a]) << " " << phase[i] << std::endl;
-        if (signed_angle > previousangle) {
-          // DD("cas1");
-          //             (((signed_angle > mIsoPhaseRefAngle[a]) && (previousangle < mIsoPhaseRefAngle[a]))) ||
-          //             ((mIsoPhaseRefAngle[a]==0) && (signed_angle < previousangle)))
-          if ((previousangle < mIsoPhaseRefAngle[a]) && 
-              (signed_angle >= mIsoPhaseRefAngle[a]))
-            {
-              // DD(a);
-              if (nbIsoPhase == 1) { // single phase, alternate 0 and 1
-                phase[i] = -phase[i-1];
-              }
-              else phase[i] = a;
-            }
-        }
-        else { // previousangle >= signed_angle (we turn around 0)
-          // DD("cas2");
-          if ((mIsoPhaseRefAngle[a] > previousangle) ||
-              (mIsoPhaseRefAngle[a] < signed_angle)) {
-            // DD(a);
-            if (nbIsoPhase == 1) { // single phase, alternate 0 and 1
-              phase[i] = -phase[i-1];
-            }
-            else phase[i] = a;
-          }
-        }
-      }
-    } 
-    previousangle = signed_angle;
-  }
-}
-//---------------------------------------------------------------------
-
diff --git a/tools/clitkEllipse.h b/tools/clitkEllipse.h
deleted file mode 100644
index 5633968..0000000
--- a/tools/clitkEllipse.h
+++ /dev/null
@@ -1,92 +0,0 @@
-/*=========================================================================
-                                                                                
-  Program:   clitk
-  Module:    $RCSfile: clitkEllipse.h,v $
-  Language:  C++
-  Date:      $Date: 2010/03/03 10:47:48 $
-  Version:   $Revision: 1.3 $
-                                                                                
-  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
-  l'Image). All rights reserved. See Doc/License.txt or
-  http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
-                                                                                
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE.  See the above copyright notices for more information.
-                                                                             
-=========================================================================*/
-
-#ifndef CLITKELLIPSE_H
-#define CLITKELLIPSE_H
-
-#include "clitkCommon.h"
-#include "clitkSignal.h"
-#include "itkVector.h"
-#include <vnl/algo/vnl_generalized_eigensystem.h>
-#include <vnl/algo/vnl_symmetric_eigensystem.h>
-#include <vnl/algo/vnl_real_eigensystem.h>
-
-namespace clitk {
-
-  //---------------------------------------------------------------------
-  class Ellipse : public itk::Vector<double,6> {
-  public:
-    typedef itk::Vector<double,2> Vector2d;
-    typedef itk::Vector<double,6> Vector6d;
-    typedef itk::Matrix<double,6,6> Matrix6x6d;
-    typedef itk::Matrix<double,3,3> Matrix3x3d;
-
-    Ellipse();
-    Ellipse(const Ellipse & e);
-    void InitialiseEllipseFitting(double eta, unsigned int n, clitk::Signal & inputX, clitk::Signal & inputY);
-    double EllipseFittingNextIteration();
-    Vector2d ComputeCenter();
-    Vector2d ComputeSemiAxeLengths();
-    double ComputeAngleInRad();
-    void SetCenterAndSemiAxes(double x0, double y0, double r1, double r2);
-    void Copy(const Vector6d & a);
-    double GetEta() { return mEta; }
-    void UpdateSMatrix(unsigned int begin, unsigned int n, 
-                       clitk::Signal & inputX, clitk::Signal & inputY);
-
-  protected:
-    double mEta;
-    double & a;
-    double & b;
-    double & c;
-    double & d;
-    double & e;
-    double & f;
-    Matrix6x6d C;
-    Matrix6x6d Ct;
-    Matrix6x6d W;
-    Matrix6x6d Wt;
-    Matrix6x6d S;
-    Matrix6x6d Sinv;
-    Matrix6x6d St;
-    std::vector<Vector6d> z;
-    clitk::Signal * mInputX;
-    clitk::Signal * mInputY;
-
-    void CopyBlock(Matrix6x6d & out, const Matrix6x6d & in, 
-                   int ox, int oy, int l, double factor=1.0);
-    void CopyBlock(Matrix6x6d & out, const Matrix3x3d & in, 
-                   int ox, int oy, double factor=1.0);
-    Matrix3x3d GetBlock3x3(const Matrix6x6d & M, int x, int y);
-
-  };
-  //---------------------------------------------------------------------
-
-
-  void ComputeIsoPhaseFromListOfEllipses(std::vector<clitk::Ellipse*> & l, 
-                                         clitk::Signal & sx, 
-                                         clitk::Signal & sy, 
-                                         int nbIsoPhase, 
-                                         int delay, 
-                                         int L,
-                                         clitk::Signal & phase);
-
-    
-} // end namespace
-
-#endif
diff --git a/tools/clitkSignalApparentMotionTracking.cxx b/tools/clitkSignalApparentMotionTracking.cxx
deleted file mode 100644
index 949c647..0000000
--- a/tools/clitkSignalApparentMotionTracking.cxx
+++ /dev/null
@@ -1,51 +0,0 @@
-/*=========================================================================
-                                                                                
-  Program:   clitk
-  Module:    $RCSfile: clitkSignalApparentMotionTracking.cxx,v $
-  Language:  C++
-  Date:      $Date: 2010/03/03 12:47:31 $
-  Version:   $Revision: 1.1 $
-                                                                                
-  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
-  l'Image). All rights reserved. See Doc/License.txt or
-  http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
-                                                                                
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE.  See the above copyright notices for more information.
-                                                                             
-=========================================================================*/
-
-#ifndef CLITKSIGNALAPPARENTMOTIONTRACKING_CXX
-#define CLITKSIGNALAPPARENTMOTIONTRACKING_CXX
-/**
-   =================================================
-   * @file   clitkSignalApparentMotionTracking.cxx
-   * @author David Sarrut <david.sarrut@creatis.insa-lyon.fr>
-   * @date   Sept 2009
-   * 
-   =================================================*/
-
-// clitk include
-#include "clitkSignalApparentMotionTracking_ggo.h"
-#include "clitkSignalApparentMotionTrackingFilter.h"
-#include "clitkCommon.h"
-
-int main(int argc, char * argv[]) {
-
-  // Init command line
-  GGO(clitkSignalApparentMotionTracking,args_info);
-  CLITK_INIT;
-
-  // Init filter
-  clitk::SignalApparentMotionTrackingFilter filter;
-  filter.SetParameters(args_info);
-
-  // Run
-  filter.Update();
-
-  // This is the end my friend
-  return EXIT_SUCCESS;  
-}
-
-#endif
diff --git a/tools/clitkSignalApparentMotionTracking.ggo b/tools/clitkSignalApparentMotionTracking.ggo
deleted file mode 100644
index 8bbb9c7..0000000
--- a/tools/clitkSignalApparentMotionTracking.ggo
+++ /dev/null
@@ -1,38 +0,0 @@
-#File clitkSignalApparentMotionTrackingFilter.ggo
-package "clitkSignalMeanPositionTracking"
-version "1.0"
-purpose "See Ruan 2008, compute mean position from a signal"
-
-option "config"	  	-	"Config file"                            string  	no
-option "input"		i	"Input trajectory filename"		 string  	yes
-option "ref"		r	"Input reference trajectory filename"	 string  	yes
-
-option "refsampling"  	-  	"Sampling between ref samples"	         double         yes
-option "inputsampling"  -  	"Sampling between input samples"         double         yes
-
-option "refphase"    	p  	"Input phase file"	                 string 	yes
-option "delay"    	d  	"Delay for augmented space"	         int            no default="5"
-option "windowLength"   L  	"Sliding window length for ellipse fit"  int            no default="25"
-option "nbiso"    	n       "Number of iso phase"	                  int           no default="4"
-
-option "output"    	o  	"Output phase (debug)"	  string 	no
-
-
-
-
-option "eta"    	e  	"Convergence param (auto if not given)"	          double no
-option "iter"    	-  	"Max # of iterations"	          int no default="100"
-option "t"    	        t  	"DEBUG"	                          int no default="1000"
-
-option "phase"    	-  	"Input phase file for validation"	  string 	no
-option "delta"    	-  	"Input learn delta phase file"	          string 	no
-
-
-section "Output"
-option "residual"    	-  	"Output optimisation residual filemane"	  string 	no
-option "augmented"    	a  	"Output augmented signal filemane"	  string 	no
-
-section "Verbose"
-option "verbose"   	        v   	"Verbose"			  flag		off
-option "verbose_iteration"   	-   	"Verbose each iteration"	  flag		off
-
diff --git a/tools/clitkSignalApparentMotionTrackingFilter.cxx b/tools/clitkSignalApparentMotionTrackingFilter.cxx
deleted file mode 100644
index 24a0b1c..0000000
--- a/tools/clitkSignalApparentMotionTrackingFilter.cxx
+++ /dev/null
@@ -1,419 +0,0 @@
-/*=========================================================================
-                                                                                
-  Program:   clitk
-  Module:    $RCSfile: clitkSignalApparentMotionTrackingFilter.cxx,v $
-  Language:  C++
-  Date:      $Date: 2010/03/03 12:41:27 $
-  Version:   $Revision: 1.1 $
-                                                                                
-  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
-  l'Image). All rights reserved. See Doc/License.txt or
-  http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
-                                                                                
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE.  See the above copyright notices for more information.
-                                                                             
-=========================================================================*/
-
-#include "clitkSignalApparentMotionTrackingFilter.h"
-#include <limits>
-#include <fstream>
-
-//---------------------------------------------------------------------
-void clitk::SignalApparentMotionTrackingFilter::SetParameters(args_info_clitkSignalApparentMotionTracking & a) {
-  args_info = a;
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::SignalApparentMotionTrackingFilter::ComputeMeanAndIsoPhase(clitk::Signal & s, 
-                                                                       int delay, 
-                                                                       int L,
-                                                                       int nbIsoPhase, 
-                                                                       clitk::Signal & mean, 
-                                                                       clitk::Signal & isoPhase) {
-  int mMaxIteration = 1;
-
-  // Compute augmented signal
-  clitk::Signal sx;
-  clitk::Signal sy;
-  s.ComputeAugmentedSpace(sx, sy, delay);
-  
-  // DEBUG augmented space
-  static int tt=0;
-  ofstream os;
-  if (tt==0) os.open("augmentedU.sig");
-  else os.open("augmentedV.sig");
-  tt++;
-  for(uint i=0; i<sx.size(); i++) {
-    os << i << " " << sx[i] << " " << sy[i] << std::endl;
-  }
-  os.close();
-
-  // Compute starting ellipse
-  Ellipse An;
-  An.InitialiseEllipseFitting(-1, L, sx, sy); // -1 is auto eta
-  DD(An.ComputeSemiAxeLengths());
-  
-  // Fit successive ellipses
-  std::vector<clitk::Ellipse*> e;
-  int n = s.size()-L-delay;
-  for(int t=0; t<n; t++) {
-    // An.InitialiseEllipseFitting(-1, L, sx, sy); // -1 is auto eta
-    An.UpdateSMatrix(t, L, sx, sy);
-    // DD(An.GetEta());
-//     DD(An);
-//     DD(An.ComputeSemiAxeLengths());
-    int nn = 0;
-    while (nn<mMaxIteration) {
-      An.EllipseFittingNextIteration();
-      // DD(nn);
-//       DD(An);
-//       DD(An.ComputeSemiAxeLengths());
-      nn++;
-    }
-    clitk::Ellipse * B = new clitk::Ellipse(An);
-    e.push_back(B);
-    DD(t);
-    DD(B->ComputeCenter());
-//      DD(B->ComputeSemiAxeLengths());
-  }
-
-  // Get mean and isoPhase
-  //mean.resize(n);
-  isoPhase.resize(n);
-  ComputeIsoPhaseFromListOfEllipses(e, sx, sy, nbIsoPhase, delay, L, isoPhase);
-  for(unsigned int i=0; i<e.size(); i++) {
-    clitk::Ellipse & An = *e[i];
-    mean[i+delay+L] = An.ComputeCenter()[0];
-    //    DD(An.ComputeCenter());
-  }
-  DD("------------------------");
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::SignalApparentMotionTrackingFilter::ComputeMeanAndIsoPhase(clitk::Trajectory2D & s, 
-                                                                       int delay, 
-                                                                       int L,
-                                                                       int nbIsoPhase, 
-                                                                       clitk::Trajectory2D & mean, 
-                                                                       std::vector<int> & isoPhase) {
-  // Extract signal (slow I know)
-  clitk::Signal U(s.GetU());
-  clitk::Signal V(s.GetV());
-  
-  clitk::Signal & meanU = mean.GetU();
-  clitk::Signal & meanV = mean.GetV();
-
-  meanU.resize(s.size());
-  meanV.resize(s.size());
-
-  clitk::Signal isoPhaseU;
-  clitk::Signal isoPhaseV;
-  
-  DD(U.size());
-  DD(V.size());
-  
-  // Compute mean and iso independently
-  ComputeMeanAndIsoPhase(U, delay, L, nbIsoPhase, meanU, isoPhaseU);
-  ComputeMeanAndIsoPhase(V, delay, L, nbIsoPhase, meanV, isoPhaseV);
-
-  // Check isphase ??? ???
-  isoPhase.resize(s.size());
-  for(unsigned int i=0; i<isoPhaseU.size(); i++) {
-
-    // ********************* U OR V ??????????
-
-    isoPhase[i+delay+L] = isoPhaseV[i]; 
-    //isoPhase[i+delay+L] = isoPhaseU[i]; 
-
-    //    mean[i+delay+L] = mean[i];
-    //DD(isoPhase[i]);
-  }
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::SignalApparentMotionTrackingFilter::ReadDB(std::string filename, 
-                                                       std::vector<Trajectory2D> & bd) {
-  // File format : 2 columns by point (U,V), time by line
-  std::ifstream is(filename.c_str());
-  skipComment(is);
-  std::string line;
-  std::getline(is, line);
-  
-  // Compute nb of column in this first line
-  std::istringstream iss(line);
-  std::string s;
-  int nb = 0;
-  while (iss>>s) {
-    nb++;
-  }
-  DD(nb);
-
-  if (nb%2 == 1) {
-    std::cout << "ERROR in the file '" << filename << "', I read " << nb 
-              << " columns, which is not odd." << std::endl;
-  }
-  nb = nb/2;
-  DD(nb);
-
-  // Read trajectories
-  bd.resize(nb);
-  while (is) {
-    std::istringstream iss(line);
-    std::string s;
-    int i=0;
-    while (iss>>s) {
-      double u = atof(s.c_str());
-      iss >> s;
-      double v = atof(s.c_str());
-      bd[i].push_back(u,v);
-      i++;
-    }
-    std::getline(is, line);
-  }
-  DD(bd[0].size());
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::SignalApparentMotionTrackingFilter::Update() {
-
-  // -----------------------------------------------------
-  // Read and build initial DB
-  ReadDB(args_info.ref_arg, mReferenceTrajectoriesBD);
-  mReferencePhase.Read(args_info.refphase_arg);
-  mReferencePhase.SetSamplingPeriod(args_info.refsampling_arg);
-
-  DD(mReferencePhase.GetSamplingPeriod());
-  DD(mReferencePhase.size());  
-  DD(mReferenceTrajectoriesBD.size());
-
-  mReferenceMean.resize(mReferenceTrajectoriesBD.size());
-  for(unsigned int i=0; i<mReferenceMean.size(); i++) {
-    mReferenceTrajectoriesBD[i].GetMean(mReferenceMean[i]);
-    // DD(mReferenceMean[i]);
-  }
-  
-  for(uint i=0; i<mReferenceTrajectoriesBD.size(); i++)
-    mReferenceTrajectoriesBD[i].SetSamplingPeriod(mReferencePhase.GetSamplingPeriod());
-
-  // Relative reference motion
-  for(uint i=0; i<mReferenceTrajectoriesBD.size(); i++) {
-    // DD(i);
-    // mReferenceTrajectoriesBD[i].Print();
-    mReferenceTrajectoriesBD[i].Substract(mReferenceMean[i]);
-    // mReferenceTrajectoriesBD[i].Print();
-  }
-
-  // -----------------------------------------------------
-  // Read trajectory
-  mInput.Read(args_info.input_arg);
-  DD(mInput.size());
-  mInput.SetSamplingPeriod(args_info.inputsampling_arg);
-  mInputMean.SetSamplingPeriod(args_info.inputsampling_arg);
-  mInputRelative.SetSamplingPeriod(args_info.inputsampling_arg);
-  DD(mInput.GetSamplingPeriod());
-
-  // -----------------------------------------------------
-  // Compute input mean and isophase
-  std::cout << "Compute Mean and IsoPhase" << std::endl;
-  std::vector<int> isophase;
-  double d = args_info.delay_arg;
-  int L = args_info.windowLength_arg;
-  int nbiso = args_info.nbiso_arg;
-  isophase.resize(mInput.size());
-  ComputeMeanAndIsoPhase(mInput, d, L, nbiso, mInputMean, isophase);
-  
-  // -----------------------------------------------------
-  // Substract mean to trajectory
-  std::cout << "Build relative traj" << std::endl;
-  mInputRelative.resize(mInput.size());
-  for(int i=0; i<mInput.size(); i++) {
-     // DD(i);
-//      DD(mInput.GetU(i));
-//      DD(mInput.GetV(i));
-//      DD(mInputMean.GetU(i));
-//      DD(mInputMean.GetV(i));
-     mInputRelative.SetPoint(i, mInput.GetU(i) - mInputMean.GetU(i),
-                            mInput.GetV(i) - mInputMean.GetV(i));
-    // DD(mInputRelative.GetU(i));
-//     DD(mInputRelative.GetV(i));
-  }
-
-  // DEBUG : output mean
-  ofstream osm("mean-phase.sig");
-  for(int i=0; i<mInput.size(); i++) {
-    osm << mInputMean.GetU(i) << " " << mInputMean.GetV(i) << " " << isophase[i] << std::endl;
-  }
-  osm.close();
-
-  // -----------------------------------------------------
-  // Loop on each iso-phase segment
-  std::cout << "Loop on each isophase" << std::endl;
-  clitk::Signal mEstimatedPhase;
-  mEstimatedPhase.resize(mInput.size());
-
-  std::vector<int> isophaseIndex;
-  int previous = isophase[0];
-  for(uint i=0; i<isophase.size(); i++) {
-    if (isophase[i] != previous) {
-      isophaseIndex.push_back(i);
-      previous = isophase[i];
-    }
-  }
-  DDV(isophaseIndex, isophaseIndex.size());
-
-  for(uint ips=0; ips<isophaseIndex.size()-1; ips++) {  
-    DD(ips);
-    int begin = isophaseIndex[ips];
-    int end = isophaseIndex[ips+1];
-    DD(begin);
-    DD(end);
-
-
-    std::cout << "-----------------------------------------------" << std::endl;
-    std::cout << "-----------------------------------------------" << std::endl;
-    std::cout << "Find traj from " << begin << " to " << end << std::endl;
-    mInput.Print("mInput", begin, end);
-    mInputRelative.Print("mInputRelativ", begin, end);
-    
-
-    // Get current mean position
-    Vector2d currentMeanPosition;
-    mInputMean.GetPoint(begin, currentMeanPosition);
-    DD(currentMeanPosition);
-
-    // Find closest ref trajectory
-    int index = FindClosestTrajectory(mReferenceMean, currentMeanPosition);
-    DD(index);
-    clitk::Trajectory2D & currentClosestReferenceTrajectory = mReferenceTrajectoriesBD[index];
-    
-    DD(mReferenceMean[index]);
-    currentClosestReferenceTrajectory.Print("currentClosestReferenceTrajectory");
-
-    // Estimate phase delta
-    clitk::Signal tempPhase;
-    EstimatePhase(mInputRelative, begin, end, 
-                  currentClosestReferenceTrajectory, 
-                  mReferencePhase, tempPhase);
-
-    // Cat current phase
-    int n=0;
-    for(int i=begin; i<end; i++) {
-      mEstimatedPhase[i] = tempPhase[n];
-      n++;
-    }
-  }
-  
-  // -----------------------------------------------------
-  // Output time - phase
-  // DEBUG OUTPUT
-  ofstream os(args_info.output_arg);
-  for(int t=0; t<mInput.size(); t++) {
-    os << t << " " << t*mInput.GetSamplingPeriod() << " " << mEstimatedPhase[t] << std::endl;
-  }
-  os.close();
-
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::SignalApparentMotionTrackingFilter::EstimatePhase(const clitk::Trajectory2D & input, 
-                                                              const int begin, const int end, 
-                                                              const clitk::Trajectory2D & ref, 
-                                                              const clitk::Signal & phaseref, 
-                                                              clitk::Signal & phase) {
-
-  // Create time-warped resampled trajectory
-  clitk::Trajectory2D T;
-  T.SetSamplingPeriod(ref.GetSamplingPeriod());
-  DD(input.size());
-  input.ResampleWithTimeWarpTo(begin, end, T);
-  DD(input.GetSamplingPeriod());
-  DD(ref.GetSamplingPeriod());
-  ref.Print("ref");
-  input.Print("input", begin, end);
-  T.Print("T");
-
-  // Find optimal delta
-  int delta = FindPhaseDelta(T, ref);
-  DD(delta);
-
-  // Shift phase
-  clitk::Signal temp(phaseref);
-  DD(temp.GetSamplingPeriod());
-  DDV(temp, temp.size());
-  temp.Shift(delta, (int)lrint((end-begin)*input.GetSamplingPeriod()/phaseref.GetSamplingPeriod()));
-  DD(temp.GetSamplingPeriod());
-  DDV(temp, temp.size());
-  
-
-  // Output result with time-unwarp
-  phase.resize(end-begin);
-  phase.SetSamplingPeriod(input.GetSamplingPeriod());
-  DD(phase.GetSamplingPeriod());
-  DD(phaseref.GetSamplingPeriod());
-  DD(temp.GetSamplingPeriod());
-  DD(temp.size());
-  DD(phase.size());
-  temp.ResampleWithTimeWarpTo(phase, true); // linear
-  DDV(phase, phase.size());
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-int clitk::SignalApparentMotionTrackingFilter::FindPhaseDelta(const clitk::Trajectory2D & A, 
-                                                                 const clitk::Trajectory2D & B) const {
-  assert(A.GetSamplingPeriod() == B.GetSamplingPeriod());
-  
-  DD("A");
-  A.Print("A");
-  DD("B");
-  B.Print("B");
-
-  // exhaustive search
-  double min=numeric_limits<double>::max();
-  int imin =0;
-  for(int i=0; i<B.size(); i++) {
-    double d = A.DistanceTo(i, B);
-    std::cout.precision(10);
-    std::cout << "i=" << i << " d=" << d << " (min=" << min << " imin=" << imin << ")" << std::endl;
-    if (d < min) {
-      imin = i;
-      min = d;
-    }
-  }
-  DD(imin);
-  return imin;
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-int clitk::SignalApparentMotionTrackingFilter::FindClosestTrajectory(const std::vector<Vector2d> & meanlist, 
-                                                                     const Vector2d & mean) {
-  // Brute force for the moment
-  double dmin = numeric_limits<double>::max();
-  double imin=0;
-  for(uint i=0; i<meanlist.size(); i++) {
-    double d = (meanlist[i]-mean).GetNorm();
-    if (d< dmin) {
-      dmin = d;
-      imin = i;
-    }
-  }
-  DD(dmin);
-  DD(imin);
-  return imin;
-}
-//---------------------------------------------------------------------
diff --git a/tools/clitkSignalApparentMotionTrackingFilter.h b/tools/clitkSignalApparentMotionTrackingFilter.h
deleted file mode 100644
index 0d9cb30..0000000
--- a/tools/clitkSignalApparentMotionTrackingFilter.h
+++ /dev/null
@@ -1,77 +0,0 @@
-/*=========================================================================
-                                                                                
-  Program:   clitk
-  Module:    $RCSfile: clitkSignalApparentMotionTrackingFilter.h,v $
-  Language:  C++
-  Date:      $Date: 2010/03/03 12:41:27 $
-  Version:   $Revision: 1.1 $
-                                                                                
-  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
-  l'Image). All rights reserved. See Doc/License.txt or
-  http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
-                                                                                
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE.  See the above copyright notices for more information.
-                                                                             
-=========================================================================*/
-
-#ifndef SIGNALAPPARENTMOTIONTRACKINGFILTER_H
-#define SIGNALAPPARENTMOTIONTRACKINGFILTER_H
-
-#include "clitkSignalApparentMotionTracking_ggo.h"
-#include "clitkSignal.h"
-#include "clitkEllipse.h"
-#include "clitkTrajectory2D.h"
-#include "itkVector.h"
-#include <math.h>
-
-namespace clitk {
-
-  //---------------------------------------------------------------------
-  class SignalApparentMotionTrackingFilter {
-  public:
-    typedef itk::Vector<double,2> Vector2d;
-
-    void SetParameters(args_info_clitkSignalApparentMotionTracking & args_info);
-    void Update();
-    
-  protected:    
-    args_info_clitkSignalApparentMotionTracking args_info;
-    clitk::Signal mRefU;
-    clitk::Signal mRefV;
-    clitk::Signal mRefPhase;
-    clitk::Signal mInputU;
-    clitk::Signal mInputV;
-    clitk::Signal mMeanU;
-    clitk::Signal mMeanV;
-    clitk::Signal mIsoPhaseU;
-    clitk::Signal mIsoPhaseV;
-    double mRefSampling;
-
-    std::vector<Trajectory2D> mReferenceTrajectoriesBD;
-    clitk::Signal mReferencePhase;
-    clitk::Trajectory2D mInput;
-    clitk::Trajectory2D mInputRelative;
-    clitk::Trajectory2D mInputMean;
-    std::vector<Vector2d> mReferenceMean;
-
-    void ComputeMeanAndIsoPhase(clitk::Signal & s, int delay, int L, int nbIso,
-                                clitk::Signal & mean, clitk::Signal & isoPhase);
-    void ComputeMeanAndIsoPhase(clitk::Trajectory2D & s, int delay, int L,
-                                int nbIsoPhase, clitk::Trajectory2D & mean, 
-                                std::vector<int> & isoPhase);
-    void EstimatePhase(const clitk::Trajectory2D & input, 
-                       const int begin, const int end, 
-                       const clitk::Trajectory2D & ref, 
-                       const clitk::Signal & phaseref, 
-                       clitk::Signal & phase);
-    int FindPhaseDelta(const clitk::Trajectory2D & A, const clitk::Trajectory2D & B) const;
-    int FindClosestTrajectory(const std::vector<Vector2d> & meanlist, const Vector2d & mean);
-    void ReadDB(std::string filename, std::vector<Trajectory2D> & bd);
-  };
-  //---------------------------------------------------------------------
-  
-} // end namespace
-
-#endif
diff --git a/tools/clitkSignalFilter.cxx b/tools/clitkSignalFilter.cxx
deleted file mode 100644
index 04a6f10..0000000
--- a/tools/clitkSignalFilter.cxx
+++ /dev/null
@@ -1,80 +0,0 @@
-/*=========================================================================
-                                                                                
-  Program:   clitk
-  Language:  C++
-                                                                                
-  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
-  l'Image). All rights reserved. See Doc/License.txt or
-  http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
-                                                                                
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE.  See the above copyright notices for more information.
-                                                                             
-=========================================================================*/
-
-#ifndef CLITKSIGNALFILTER_CXX
-#define CLITKSIGNALFILTER_CXX
-/**
-   =================================================
-   * @file   clitkSignalFilter.cxx
-   * @author Jef Vandemeulebroucke <jefvdmb@gmail.com>
-   * @date   23 April 2008
-   * 
-   * @brief  "Apply a filter to the signal"                  
-   =================================================*/
-
-// clitk include
-#include "clitkSignalFilter_ggo.h"
-#include "clitkSignal.h"
-#include "clitkIO.h"
-#include "clitkImageCommon.h"
-
-int main(int argc, char * argv[]) {
-
-  // Init command line
-  GGO(clitkSignalFilter, args_info);
-  CLITK_INIT;
-
-  //input
-  clitk::Signal input;
-  input.Read (args_info.input_arg);
-  clitk::Signal input2;
-  if (args_info.input2_given) input2.Read(args_info.input2_arg);
-
-  double p1 = args_info.p1_arg;
-  double p2 = args_info.p2_arg;
-
-  //process
-
-  if( args_info.multiply_flag) input*=input2;
-  if( args_info.divide_flag) input/=input2;
-  if( args_info.norm_flag) input=input.Normalize (p1, p2);
-  //if( args_info.highPass_flag) input=input.HighPassFilter(p1,p2);
-  //if( args_info.lowPass_flag) input=input.LowPassFilter(p1,p2);
-  if( args_info.detect_flag) input=input.DetectLocalExtrema(static_cast<unsigned int >(p1));
-  if( args_info.limPhase_flag) input=input.LimPhase();
-  if( args_info.monPhase_flag) input=input.MonPhase();
-  if( args_info.monPhaseDE_flag) input=input.MonPhaseDE(p1,p2);
-  if( args_info.average_flag) input=input.MovingAverageFilter(static_cast<unsigned int> (p1));
-  if( args_info.ssd_flag) std::cout<<"The sqrt of the mean SSD is "<< input.SSD(input2)<<std::endl;
-  if (args_info.gauss_flag)input=input.GaussLikeFilter();
-  if (args_info.rescale_flag)input=input.NormalizeMeanStdDev(p1, p2);
-  if (args_info.interp_flag)input=input.LinearlyInterpolateScatteredValues();
-  // if( args_info.approx_flag) input=input.ApproximateScatteredValuesWithBSplines(static_cast<unsigned int>(p1),static_cast<unsigned int>(p2));
-  if( args_info.limit_flag) input=input.LimitSignalRange();
-//   if( args_info._flag) input=input;
-//   if( args_info._flag) input=input;
-//   if( args_info._flag) input=input;
-//   if( args_info._flag) input=input;
-  // if( args_info._flag) input=input;
-  // if( args_info._flag) input=input;
-  // if( args_info._flag) input=input;
-
-  if (args_info.output_given) input.Write(args_info.output_arg);
-
-  return EXIT_SUCCESS;
-  
-}
-
-#endif
diff --git a/tools/clitkSignalFilter.ggo b/tools/clitkSignalFilter.ggo
deleted file mode 100644
index 0ae384a..0000000
--- a/tools/clitkSignalFilter.ggo
+++ /dev/null
@@ -1,27 +0,0 @@
-#File clitkSignalFilter.ggo
-package "clitk"
-version "Pass an filter on an signal"
-
-option "config"	  	-	"Config file"			  string  	no
-option "verbose"   	v   	"Verbose"			  flag		off
-option "input"		i	"Input grid filename"		  string  	yes
-option "input2"		j	"Second Input grid filename"	  string  	no
-option "p1"		-	"p1"				  double  	no
-option "p2"		-	"p2"				  double  	no
-option "output"    	o  	"Output grid filename"		  string 	no
-option "multiply"	-	"Mulitply values of input 1 with input 2 (same size)"      flag		off    
-option "divide"		-	"Divide values of input 1 with input 2 (same size, zeros are skipped)"   flag		off     
-option "norm"    	n  	"Normalize signal between p1=min and p2=max"		  flag 		off
-option "rescale"    	-  	"Rescale signal to p1=mean and p2=StdDev"	  	  flag 		off
-#option "highPass"   	-  	"High Pass Filter: p1=sampPeriod, p2= cutOffFrequecy"	  flag 		off
-#option "lowPass"   	-  	"Low Pass Filter: p1=sampPeriod, p2= cutOffFrequecy"	  flag 		off
-option "detect"   	-  	"Detect Local extrema: local window= 2*p1+1, p1>=1"	  	  flag 		off
-option "limPhase"   	-  	"Convert extrema signal into limited phase [0, 1["	  	  flag 		off
-option "monPhase"   	-  	"Convert extrema signal into monotone phase [0, inf["	  	  flag 		off
-option "monPhaseDE"   	-  	"Convert extrema signal into scattered monotone phase, taking into account both extrema (p1=eEPhaseValue,p2=eIPhaseValue)"	  	  flag 		off
-option "average"   	-  	"Moving Average filter: window= 2*p1+1 [0, inf["	  	  flag 		off
-option "ssd"	   	-  	"Calculate the sqrt of the mean SSD between i and j"	  	  flag 		off
-option "gauss"	   	-  	"Pass a small gauss-like kernel (121-mask)"		  	  flag 		off
-option "interp"	   	-  	"Linearly interpolate scattered values (unknow values=-1)"		  	  flag 		off
-option "approx"	   	-  	"Bspline approximate scattered values(unknow values=-1, p1=Order, p2=number of control points"	 flag 		off
-option "limit"	   	-  	"Limit the range to [0, 1[ (signal-floor (signal))"	 flag 		off
diff --git a/tools/clitkSignalMeanPositionFilter.cxx b/tools/clitkSignalMeanPositionFilter.cxx
deleted file mode 100644
index f0c6ac1..0000000
--- a/tools/clitkSignalMeanPositionFilter.cxx
+++ /dev/null
@@ -1,362 +0,0 @@
-/*=========================================================================
-                                                                                
-  Program:   clitk
-  Module:    $RCSfile: clitkSignalMeanPositionFilter.cxx,v $
-  Language:  C++
-  Date:      $Date: 2010/03/03 12:51:06 $
-  Version:   $Revision: 1.7 $
-                                                                                
-  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
-  l'Image). All rights reserved. See Doc/License.txt or
-  http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
-                                                                                
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE.  See the above copyright notices for more information.
-                                                                             
-=========================================================================*/
-
-#include "clitkSignalMeanPositionFilter.h"
-#include <fstream>
-
-//---------------------------------------------------------------------
-void clitk::SignalMeanPositionFilter::SetParameters(args_info_clitkSignalMeanPositionTracking & args) {
-  args_info = args;
-  mEtaIsSet = false;
-  mOutputFilenameIsSet = false;
-  mOutputResidualFilenameIsSet = false;
-  mInput.Read(args_info.input_arg);
-  mAugmentationDelay = args_info.delay_arg;
-  mIsAdaptiveMethod = false;
-  mWindowLength = -1;
-  mValidationWithRealPhase = false;
-  mUseLearnedDeltaPhase = false;
-  if (args_info.eta_given) {
-    mEta = args_info.eta_arg;
-    mEtaIsSet = true;
-  }
-  mMaxIteration = args_info.iter_arg;
-  if (args_info.output_given) {
-    mOutputFilenameIsSet = true;
-    mOutputFilename = args_info.output_arg;
-  }
-  if (args_info.residual_given) {
-    mOutputResidualFilenameIsSet = true;
-    mOutputResidualFilename = args_info.residual_arg;
-  }
-  if (args_info.augmented_given) {
-    mOutputAugmentedFilenameIsSet = true;
-    mOutputAugmentedFilename = args_info.augmented_arg;
-  }
-  mVerbose = args_info.verbose_flag;
-  mVerboseIteration = args_info.verbose_iteration_flag;
-  if (args_info.L_given) {
-    mIsAdaptiveMethod = true;
-    mWindowLength = args_info.L_arg;
-  }
-  if (args_info.phase_given) {
-    mValidationWithRealPhase = true;
-    mInputPhaseFilename = args_info.phase_arg;
-    mInputPhase.Read(mInputPhaseFilename);
-  }
-  mNumberOfIsoPhase = args_info.nbiso_arg;
-  if (args_info.delta_given) {
-    mUseLearnedDeltaPhase = true;
-    mLearnIsoPhaseDelta.Read(args_info.delta_arg);
-    mNumberOfIsoPhase = mLearnIsoPhaseDelta.size();
-  }
-
-  // DEBUG
-  if (args_info.phase_given) {
-    std::cout << "PLEASE DO NO USE THIS OPTION --phase YET ..." << std::endl;
-    exit(0);
-  }
-  if (args_info.delta_given) {
-    std::cout << "PLEASE DO NO USE THIS OPTION --delta YET ..." << std::endl;
-    exit(0);
-  }
-
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::SignalMeanPositionFilter::Update() {
-
-  // Compute augmented space
-  if (mVerbose) {
-    std::cout << "Computing augmented space with delay = " << mAugmentationDelay
-              << ", number of samples is " << mInput.size()-mAugmentationDelay 
-              << std::endl;
-  }
-  mInput.ComputeAugmentedSpace(mAugmentedInputX, mAugmentedInputY, mAugmentationDelay);
-
-  // Output augmented state
-  if (mOutputAugmentedFilenameIsSet) {
-    std::ofstream os;
-    openFileForWriting(os, mOutputAugmentedFilename);
-    for(unsigned int i=0; i<(unsigned int)mAugmentedInputX.size(); i++) {
-      os << mAugmentedInputX[i] << " " << mAugmentedInputY[i] << std::endl;
-    }
-    os.close();
-  }
-
-  // Initial starting ellipse
-  Ellipse An; // starting point
-  if (!mEtaIsSet) mEta = -1;
-  DD(mWindowLength);
-  if (mWindowLength == -1) {
-    mWindowLength = mAugmentedInputY.size();
-  }
-  An.InitialiseEllipseFitting(mEta, mWindowLength, mAugmentedInputX, mAugmentedInputY);
-  mEta = An.GetEta();
-  if (mVerbose) {
-    std::cout << "Eta is " << mEta << std::endl;
-  }
-  Ellipse AnInitial(An);
-  if (mVerbose) {
-    std::cout << "Set initial ellipse to c=" << An.ComputeCenter() 
-              << " and axes=" << An.ComputeSemiAxeLengths() << std::endl;
-  }
-
-  // Fitting method
-  if (mIsAdaptiveMethod) {
-    AdaptiveFitEllipse(An);
-  }
-  else FitEllipse(An);
-
-  // Output
-  if (mVerbose) {
-    std::cout << "Result    is "  << An << std::endl;
-    std::cout << "Center    is "  << An.ComputeCenter() << std::endl;
-    std::cout << "SemiAxis are " << An.ComputeSemiAxeLengths() << std::endl;
-    std::cout << "Angle     is " << rad2deg(An.ComputeAngleInRad()) << " deg" << std::endl;
-  }
-  if (mOutputFilenameIsSet) {
-    std::ofstream os;
-    openFileForWriting(os, mOutputFilename);
-    
-    std::vector<double> phase;
-    ComputeIsoPhase(mListOfEllipses, phase, mCycles);
-    
-    //int currentCycle = 0;
-    for (unsigned int i=0; i<mListOfEllipses.size(); i++) {
-      clitk::Ellipse & An = *mListOfEllipses[i];
-      int time = i+mAugmentationDelay+mWindowLength;
-      os << time << " " // current 'time' in input
-         << mInput[time] << " " // current value in input
-         << An.ComputeCenter()[0] << " " << An.ComputeCenter()[1] << " " 
-         << An.ComputeSemiAxeLengths()[0] << " " << An.ComputeSemiAxeLengths()[1] << " " 
-         << An.ComputeAngleInRad() << " "
-         << rad2deg(An.ComputeAngleInRad()) << " _Phase_ "
-         << mIsoPhaseIndex[i] << " " ;
-
-      /*
-        if (mUseLearnedDeltaPhase) { 
-        os << mIsoPhaseDelta[mIsoPhaseIndex[i]] << " " << phase[i] << " ";
-        }
-      */
-
-      os << " _Ellipse_ ";
-      for(int j=0; j<6; j++) os << An[j] << " ";
-      os << std::endl;
-    }
-    os.close();
-  }
-  
-  if (mOutputResidualFilenameIsSet) {
-    std::ofstream os;
-    openFileForWriting(os, mOutputResidualFilename);
-    for(unsigned int i=0; i<mCurrentResidual.size(); i++) {
-      os.precision(10);
-      os << mCurrentResidual[i] << std::endl;
-    }
-  os.close();
-  }
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::SignalMeanPositionFilter::FitEllipse(clitk::Ellipse & An) {
-  int n = 0;
-  mCurrentResidual.clear();
-  while (n<mMaxIteration) {
-    double r = An.EllipseFittingNextIteration();
-    mCurrentResidual.push_back(r);
-    n++;
-    if (mVerboseIteration) {
-      std::cout.precision(3);
-      std::cout << "A(" << n << ")=" << An
-                << " c="  << An.ComputeCenter() 
-                << " ax=" << An.ComputeSemiAxeLengths()
-                << " theta=" << rad2deg(An.ComputeAngleInRad());
-      std::cout.precision(10);
-      std::cout << " R=" << r << std::endl;
-    }
-  }
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::SignalMeanPositionFilter::AdaptiveFitEllipse(clitk::Ellipse & An) {  
-  // Compute the total number of iteration : 
-  //     = nb of inputs minus the delay, minus the windowL, minus the first one
-  int maxN = std::min((unsigned int)args_info.t_arg, 
-                      mInput.size()-mWindowLength-mAugmentationDelay);
-  for(int t=0; t<maxN; t++) {
-    An.UpdateSMatrix(t, mWindowLength, mAugmentedInputX, mAugmentedInputY);
-    FitEllipse(An);
-    clitk::Ellipse * B = new clitk::Ellipse(An);
-    mListOfEllipses.push_back(B);
-  }
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::SignalMeanPositionFilter::ComputeIsoPhase(std::vector<clitk::Ellipse*> & l, 
-                                                      std::vector<double> & phase, 
-                                                      std::vector<int> & cycles) {
-  double refphaseangle=0;
-  double previousangle=0;
-  phase.resize(mListOfEllipses.size());
-
-  // DD(mListOfEllipses.size());
-  mIsoPhaseIndex.resize(mListOfEllipses.size());
-  // mIsoPhaseDelta.resize(mNumberOfIsoPhase);
-  //   mIsoPhaseDeltaNb.resize(mNumberOfIsoPhase);
-  mIsoPhaseRefAngle.resize(mNumberOfIsoPhase); 
-
-  for (unsigned int i=0; i<mListOfEllipses.size(); i++) {
-    clitk::Ellipse & An = *mListOfEllipses[i];
-    
-    // Current time accordint to initial input signal
-    // int time = i+mAugmentationDelay+mWindowLength;   // not use yet
-    
-    // Compute current signed angle
-    Vector2d x1(An.ComputeCenter());
-    double a = mListOfEllipses[0]->ComputeSemiAxeLengths()[0]; 
-    double theta = mListOfEllipses[0]->ComputeAngleInRad(); 
-    Vector2d x2; x2[0] = x1[0]+a * cos(theta); x2[1] = x1[1]+a * sin(theta);
-    Vector2d x3(x1);
-    Vector2d x4; x4[0] = mAugmentedInputX[i+mWindowLength]; x4[1] = mAugmentedInputY[i+mWindowLength];
-    Vector2d A(x2-x1);
-    Vector2d B(x4-x3);
-    double signed_angle = atan2(B[1], B[0]) - atan2(A[1], A[0]);
-    // double signed_angle = atan2(B[1], B[0]) - atan2(0, 1);
-    if (signed_angle<0) signed_angle = 2*M_PI+signed_angle;
-    // http://www.euclideanspace.com/maths/algebra/vectors/angleBetween/index.htm
-    
-    // First time : set the angle
-    if (i==0) {
-      refphaseangle = signed_angle;
-      for(int a=0; a<mNumberOfIsoPhase; a++) {
-        if (a==0) mIsoPhaseRefAngle[a] = signed_angle;
-        else mIsoPhaseRefAngle[a] = (signed_angle
-                                     + (2*M_PI)*a/mNumberOfIsoPhase);
-        if (mIsoPhaseRefAngle[a] > 2*M_PI) mIsoPhaseRefAngle[a] -= 2*M_PI;
-        if (mIsoPhaseRefAngle[a] < 0) mIsoPhaseRefAngle[a] = 2*M_PI-mIsoPhaseRefAngle[a];
-        // DD(rad2deg(mIsoPhaseRefAngle[a]));
-        // mIsoPhaseDelta[a] = 0.0;
-        // mIsoPhaseDeltaNb[a] = 0;
-      }
-      int a=0;
-      // DD(rad2deg(signed_angle));
-      while ((a<mNumberOfIsoPhase) && (signed_angle>=mIsoPhaseRefAngle[a])) { a++; }
-      // DD(a);
-      mIsoPhaseIndex[i] = a-1;
-      // DD(mIsoPhaseIndex[0]);
-      cycles.push_back(0);
-    }
-    else {
-      mIsoPhaseIndex[i] = mIsoPhaseIndex[i-1];
-      
-      // Check if angle cross a ref angle
-      for(int a=0; a<mNumberOfIsoPhase; a++) {
-        std::cout << "a=" << rad2deg(signed_angle) << " p=" << rad2deg(previousangle)
-                  << " ref=" << rad2deg(mIsoPhaseRefAngle[a]) << std::endl;
-        if (
-            (((signed_angle > mIsoPhaseRefAngle[a]) && (previousangle < mIsoPhaseRefAngle[a]))) ||
-            ((mIsoPhaseRefAngle[a]==0) && (signed_angle < previousangle)))
-          {
-            // if (mValidationWithRealPhase) {
-            //             mIsoPhaseDelta[a] += mInputPhase[time];
-            //             mIsoPhaseDeltaNb[a]++;
-            //           }
-            mIsoPhaseIndex[i] = a;
-            // DD(a);
-            cycles.push_back(i);
-          }
-      }
-      // DD(mIsoPhaseIndex[i]);      
-    }
-    
-    previousangle = signed_angle;
-  }
-  
-  /*
-  if (mValidationWithRealPhase) {
-    // Mean of all deltas
-    for(unsigned int a=0; a<mIsoPhaseDelta.size(); a++) {
-      if (mIsoPhaseDelta[a] == 0) {
-        std::cerr << "Error : less than one cyle ?" << std::endl;
-        exit(0);
-      }
-      mIsoPhaseDelta[a] /= mIsoPhaseDeltaNb[a];
-      DD(mIsoPhaseDelta[a]);
-    }
-    std::ofstream os;
-    openFileForWriting(os, "delta.sig");
-    for(unsigned int a=0; a<mIsoPhaseDelta.size(); a++) {
-      os << mIsoPhaseDelta[a] << std::endl;
-    }
-    os.close();    
-  }
-  */
-
-  /*
-  if (mUseLearnedDeltaPhase) {
-    for(unsigned int a=0; a<mIsoPhaseDelta.size(); a++) {
-      mIsoPhaseDelta[a] = mLearnIsoPhaseDelta[a];
-      DD(mIsoPhaseDelta[a]);
-    }
-  }
-  */
-  
-  // DEBUG UNUSED
-  /*
-  int j=0;
-  for (unsigned int i=0; i<cycles.size(); i++) {
-    DD(cycles[i]);
-    int n;
-    if (i!=0) {
-      n=cycles[i]-cycles[i-1];
-      for(int index=0; index<n; index++) {
-        
-        int indexOfPhase1 = mIsoPhaseIndex[cycles[i-1]];
-        int indexOfPhase2 = mIsoPhaseIndex[cycles[i]];
-        DD(indexOfPhase1);
-        DD(indexOfPhase2);
-        double ph1 = mIsoPhaseDelta[indexOfPhase1];
-        double ph2 = mIsoPhaseDelta[indexOfPhase2];
-        DD(ph1);
-        DD(ph2);
-        
-        phase[j] = (ph1+(double)index*(ph2-ph1)/(double)n);
-        if (phase[j]>1.0) phase[j] = 1.0-phase[j];
-        DD(phase[j]);
-        j++;
-      }
-    }
-    else j+=cycles[0];
-  }  
-  */
-  for (unsigned int i=0; i<cycles.size(); i++) {
-    DD(cycles[i]);
-  }
-
-}
-//---------------------------------------------------------------------
-
diff --git a/tools/clitkSignalMeanPositionFilter.h b/tools/clitkSignalMeanPositionFilter.h
deleted file mode 100644
index fbe214e..0000000
--- a/tools/clitkSignalMeanPositionFilter.h
+++ /dev/null
@@ -1,85 +0,0 @@
-/*=========================================================================
-                                                                                
-  Program:   clitk
-  Module:    $RCSfile: clitkSignalMeanPositionFilter.h,v $
-  Language:  C++
-  Date:      $Date: 2010/03/03 10:47:48 $
-  Version:   $Revision: 1.6 $
-                                                                                
-  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
-  l'Image). All rights reserved. See Doc/License.txt or
-  http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
-                                                                                
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE.  See the above copyright notices for more information.
-                                                                             
-=========================================================================*/
-
-#ifndef CLITKSIGNALMEANPOSITIONFILTER_H
-#define CLITKSIGNALMEANPOSITIONFILTER_H
-
-#include "clitkSignalMeanPositionTracking_ggo.h"
-#include "clitkSignal.h"
-#include "clitkEllipse.h"
-#include "itkVector.h"
-#include <math.h>
-
-namespace clitk {
-
-  //---------------------------------------------------------------------
-  class SignalMeanPositionFilter {
-  public:
-    typedef itk::Vector<double,2> Vector2d;
-
-    void SetParameters(args_info_clitkSignalMeanPositionTracking & args_info);
-    void Update();
-    
-  protected:    
-    args_info_clitkSignalMeanPositionTracking args_info;
-    clitk::Signal mInput;
-    clitk::Signal mAugmentedInputX;
-    clitk::Signal mAugmentedInputY;
-    int mAugmentationDelay;
-    int mMaxIteration;
-    double mEta;
-    bool mEtaIsSet;
-    bool mOutputFilenameIsSet;
-    bool mOutputResidualFilenameIsSet;
-    bool mOutputAugmentedFilenameIsSet;
-    std::string mOutputFilename;
-    std::string mOutputResidualFilename;
-    std::string mOutputAugmentedFilename;
-    bool mVerbose;
-    bool mVerboseIteration;
-    bool mIsAdaptiveMethod;
-    std::vector<double> mCurrentResidual;
-    int mWindowLength;
-    std::vector<clitk::Ellipse*> mListOfEllipses;
-    
-    bool mValidationWithRealPhase;
-    std::string mInputPhaseFilename;
-    clitk::Signal mInputPhase;
-    std::vector<int> mCycles;
-
-    std::vector<int> mIsoPhaseIndex;
-    std::vector<double> mIsoPhaseDelta;
-    std::vector<int> mIsoPhaseDeltaNb;
-    std::vector<double> mIsoPhaseRefAngle;
-
-    bool mUseLearnedDeltaPhase;
-    clitk::Signal mLearnIsoPhaseDelta;
-    int mNumberOfIsoPhase;
-
-    void FitEllipse(clitk::Ellipse & An);
-    void AdaptiveFitEllipse(clitk::Ellipse & An);
-
-    void ComputeIsoPhase(std::vector<clitk::Ellipse*> & l, 
-                         std::vector<double> & phase,
-                         std::vector<int> & cycles);
-  };
-  //---------------------------------------------------------------------
-  
-} // end namespace
-
-#endif
diff --git a/tools/clitkSignalMeanPositionTracking.cxx b/tools/clitkSignalMeanPositionTracking.cxx
deleted file mode 100644
index b2f4591..0000000
--- a/tools/clitkSignalMeanPositionTracking.cxx
+++ /dev/null
@@ -1,52 +0,0 @@
-/*=========================================================================
-                                                                                
-  Program:   clitk
-  Module:    $RCSfile: clitkSignalMeanPositionTracking.cxx,v $
-  Language:  C++
-  Date:      $Date: 2010/03/03 10:47:48 $
-  Version:   $Revision: 1.6 $
-                                                                                
-  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
-  l'Image). All rights reserved. See Doc/License.txt or
-  http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
-                                                                                
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE.  See the above copyright notices for more information.
-                                                                             
-=========================================================================*/
-
-#ifndef CLITKSIGNALMEANPOSITIONTRACKING_CXX
-#define CLITKSIGNALMEANPOSITIONTRACKING_CXX
-/**
-   =================================================
-   * @file   clitkSignalMeanPositionTracking.cxx
-   * @author David Sarrut <david.sarrut@creatis.insa-lyon.fr>
-   * @date   Sept 2009
-   * 
-   * @brief  "See Ruan 2007, compute mean position from a signal"                  
-   =================================================*/
-
-// clitk include
-#include "clitkSignalMeanPositionTracking_ggo.h"
-#include "clitkCommon.h"
-#include "clitkSignalMeanPositionFilter.h"
-
-int main(int argc, char * argv[]) {
-
-  // Init command line
-  GGO(clitkSignalMeanPositionTracking,args_info);
-  CLITK_INIT;
-
-  // Init filter
-  clitk::SignalMeanPositionFilter filter;
-  filter.SetParameters(args_info);
-
-  // Run
-  filter.Update();
-
-  // This is the end my friend
-  return EXIT_SUCCESS;  
-}
-
-#endif
diff --git a/tools/clitkSignalMeanPositionTracking.ggo b/tools/clitkSignalMeanPositionTracking.ggo
deleted file mode 100644
index b3cb8e3..0000000
--- a/tools/clitkSignalMeanPositionTracking.ggo
+++ /dev/null
@@ -1,27 +0,0 @@
-#File clitkSignalMeanPositionTracking.ggo
-package "clitkSignalMeanPositionTracking"
-version "1.0"
-purpose "See Ruan 2008, compute mean position from a signal"
-
-option "config"	  	-	"Config file"			  string  	no
-option "input"		i	"Input signal filename"		  string  	yes
-option "delay"    	d  	"Delay for augmented space"	  int no default="10"
-option "eta"    	e  	"Convergence param (auto if not given)"	          double no
-option "iter"    	-  	"Max # of iterations"	          int no default="100"
-option "L"    	        L  	"Sliding window length"	          int no
-option "t"    	        t  	"DEBUG"	                          int no default="1000"
-
-option "phase"    	p  	"Input phase file for validation"	  string 	no
-option "delta"    	-  	"Input learn delta phase file"	          string 	no
-option "nbiso"    	n       "Number of iso phase"	                  int no default="1"
-
-
-section "Output"
-option "output"    	o  	"Output ellipse param filename (2 lines=initial/final ; 6 quadratic param + 5 parametric param=center/axis/theta)"	  string 	no
-option "residual"    	r  	"Output optimisation residual filemane"	  string 	no
-option "augmented"    	a  	"Output augmented signal filemane"	  string 	no
-
-section "Verbose"
-option "verbose"   	        v   	"Verbose"			  flag		off
-option "verbose_iteration"   	-   	"Verbose each iteration"	  flag		off
-
diff --git a/tools/clitkTrajectory2D.cxx b/tools/clitkTrajectory2D.cxx
deleted file mode 100644
index 8ee6a71..0000000
--- a/tools/clitkTrajectory2D.cxx
+++ /dev/null
@@ -1,172 +0,0 @@
-/*=========================================================================
-                                                                                
-  Program:   clitk
-  Module:    $RCSfile: clitkTrajectory2D.cxx,v $
-  Language:  C++
-  Date:      $Date: 2010/03/03 12:41:27 $
-  Version:   $Revision: 1.1 $
-                                                                                
-  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
-  l'Image). All rights reserved. See Doc/License.txt or
-  http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
-                                                                                
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE.  See the above copyright notices for more information.
-                                                                             
-=========================================================================*/
-
-#include "clitkTrajectory2D.h"
-
-//---------------------------------------------------------------------
-void clitk::Trajectory2D::ResampleWithTimeWarpTo(int begin, int end, Trajectory2D & output) const {
-  DD(begin);
-  DD(end);
-  int n = (int)lrint((end-begin)*GetSamplingPeriod()/output.GetSamplingPeriod());
-  output.resize(n);
-  DD(n);
-  double duration = (end-begin)*GetSamplingPeriod();
-  DD(duration);
-  double sp = output.GetSamplingPeriod();
-  DD(output.GetTotalTimeDuration());
-  //   DD(sp);
-  for(int i=0; i<n; i++) {
-    Vector2d p;
-    // DD(i);
-    GetValueAtLin((i*sp)+(begin*GetSamplingPeriod()), p);
-    // DD(p);
-    output.SetPoint(i, p);
-  }
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-bool clitk::Trajectory2D::Read(std::string filename) {
-  bool b = mU.Read(filename, 0);
-  if (!b) return false;
-  b = mV.Read(filename, 1);
-  return b;
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::Trajectory2D::GetValueAtLin(double t, Vector2d & p) const {
-  // Can be faster, I know ...
-  p[0] = mU.GetValueAtLin(t);
-  p[1] = mV.GetValueAtLin(t);
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------
-void clitk::Trajectory2D::ResampleWithTimeWarpTo(Trajectory2D & output) const {
-  ResampleWithTimeWarpTo(0, size(), output);
-}
-//---------------------------------------------------------------------
-
-
-//---------------------------------------------------------------------        
-void clitk::Trajectory2D::Shift(double s) {
-  std::cout << "Shift s=" << s << std::endl;
-  int d = (int)lrint(s/GetSamplingPeriod()); // closest integer delta
-  DD(d);
-  clitk::Signal tempU((uint)size());
-  clitk::Signal tempV((uint)size());
-  for(int i=0; i<size(); i++) {
-    tempU[0] = mU[(i+d)%size()];
-    tempV[0] = mV[(i+d)%size()];
-  }
-  for(int i=0; i<size(); i++) {
-    mU[i] = tempU[i];
-    mV[i] = tempV[i];
-  }
-}
-//---------------------------------------------------------------------        
-
-
-//---------------------------------------------------------------------        
-void clitk::Trajectory2D::GetPoint(const int index, Vector2d & p) {
-  p[0] = mU[index];
-  p[1] = mV[index];
-}
-//---------------------------------------------------------------------        
-
-
-//---------------------------------------------------------------------        
-clitk::Trajectory2D & clitk::Trajectory2D::operator+(Trajectory2D & d) {
-  for(int i=0; i<size(); i++) {
-    mU[i] += d.GetU(i);
-    mV[i] += d.GetV(i);
-  }
-  return  *this;
-}
-//---------------------------------------------------------------------        
-
-
-//---------------------------------------------------------------------        
-clitk::Trajectory2D & clitk::Trajectory2D::operator-(Trajectory2D & d) {
-  for(int i=0; i<size(); i++) {
-    mU[i] -= d.GetU(i);
-    mV[i] -= d.GetV(i);
-  }
-  return  *this;
-}
-//---------------------------------------------------------------------        
-
-
-//---------------------------------------------------------------------        
-void clitk::Trajectory2D::GetMean(Vector2d & m) {
-  m[0] = 0.0;
-  m[1] = 0.0;
-  for(int i=0; i<size(); i++) {
-    m[0] += mU[i];
-    m[1] += mV[i];
-  }
-  m[0] /= size();
-  m[1] /= size();
-}
-//---------------------------------------------------------------------        
-
-
-//---------------------------------------------------------------------        
-double clitk::Trajectory2D::DistanceTo(int delta, const clitk::Trajectory2D & B) const {
-  double d = 0.0;
-  for(int n=0; n<size(); n++) {
-    int i = n;//(n)%size();
-    int j = (n+delta)%B.size();
-    // DD(j);
-//     DD(i);
-//     DD(n);
-    d += pow(mU[i] - B.GetU(j), 2) + pow(mV[i] - B.GetV(j), 2);
-  }
-  return d;
-}
-//---------------------------------------------------------------------        
-
-
-//---------------------------------------------------------------------        
-void clitk::Trajectory2D::Print(const std::string & name) const {
-  Print(name, 0, size());
-}
-//---------------------------------------------------------------------        
-
-
-//---------------------------------------------------------------------        
-void clitk::Trajectory2D::Print(const std::string & name, int begin, int end) const {
-  std::cout << "Traj " << name << " size = " << size() 
-            << " from " << begin << " to " << end << std ::endl;
-  for(int i=begin; i<end; i++) {
-    std::cout << mU[i] << " " << mV[i] << std::endl;
-  }
-}
-//---------------------------------------------------------------------        
-
-
-//---------------------------------------------------------------------        
-void clitk::Trajectory2D::Substract(const Vector2d & m) {
-  mU.AddValue(-m[0]);
-  mV.AddValue(-m[1]);
-}
-//---------------------------------------------------------------------        
diff --git a/tools/clitkTrajectory2D.h b/tools/clitkTrajectory2D.h
deleted file mode 100644
index f5fdef9..0000000
--- a/tools/clitkTrajectory2D.h
+++ /dev/null
@@ -1,80 +0,0 @@
-/*=========================================================================
-                                                                                
-  Program:   clitk
-  Module:    $RCSfile: clitkTrajectory2D.h,v $
-  Language:  C++
-  Date:      $Date: 2010/03/03 12:41:27 $
-  Version:   $Revision: 1.1 $
-                                                                                
-  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
-  l'Image). All rights reserved. See Doc/License.txt or
-  http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
-                                                                                
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE.  See the above copyright notices for more information.
-                                                                             
-=========================================================================*/
-
-#ifndef CLITKTRAJECTORY2D_H
-#define CLITKTRAJECTORY2D_H
-
-#include "clitkCommon.h"
-#include "clitkSignal.h"
-#include "itkVector.h"
-#include <vnl/algo/vnl_generalized_eigensystem.h>
-#include <vnl/algo/vnl_symmetric_eigensystem.h>
-#include <vnl/algo/vnl_real_eigensystem.h>
-
-namespace clitk {
-
-  //---------------------------------------------------------------------
-  class Trajectory2D {
-  public:
-    typedef itk::Vector<double,2> Vector2d;
-
-    void ResampleWithTimeWarpTo(int begin, int end, Trajectory2D & output) const;
-    void ResampleWithTimeWarpTo(Trajectory2D & output) const; 
-    void Shift(double s);
-    
-    bool Read(std::string filename);
-
-    void GetPoint(const int index, Vector2d & p);
-    void GetMean(Vector2d & m);
-    double GetU(const int index) const { return mU[index]; }
-    double GetV(const int index) const { return mV[index]; }
-    clitk::Signal & GetU() { return mU; }
-    clitk::Signal & GetV() { return mV; }
-    
-    int size() const { return mU.size(); }
-    void resize(int n) { mU.resize(n); mV.resize(n); }
-
-    void SetPoint(const int i, Vector2d & p) { mU[i] = p[0]; mV[i] = p[1]; }
-    void SetPoint(const int i, double u, double v) { mU[i] = u; mV[i] = v; }
-    void GetValueAtLin(double t, Vector2d & p) const;
-
-    double GetSamplingPeriod() const { return mU.GetSamplingPeriod(); }
-    void SetSamplingPeriod(double sp){ mU.SetSamplingPeriod(sp); mV.SetSamplingPeriod(sp); }
-    double DistanceTo(int delta, const clitk::Trajectory2D & B) const;
-
-    Trajectory2D & operator+(Trajectory2D & d);
-    Trajectory2D & operator-(Trajectory2D & d);
-    
-    void Print(const std::string & name) const;
-    void Print(const std::string & name, int begin, int end) const;
-
-    void push_back(double u, double v) { mU.push_back(u); mV.push_back(v); }
-    void Substract(const Vector2d & m);
-    double GetTotalTimeDuration() const { return mU.GetTotalTimeDuration(); }
-
-  protected:
-    clitk::Signal mU;
-    clitk::Signal mV;
-    
-  };
-  //---------------------------------------------------------------------
-
-
-} // end namespace
-
-#endif
-- 
2.47.1