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cxElastixExecuter.h
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1 /*=========================================================================
2 This file is part of CustusX, an Image Guided Therapy Application.
3 
4 Copyright (c) 2008-2014, SINTEF Department of Medical Technology
5 All rights reserved.
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7 Redistribution and use in source and binary forms, with or without
8 modification, are permitted provided that the following conditions are met:
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10 1. Redistributions of source code must retain the above copyright notice,
11  this list of conditions and the following disclaimer.
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13 2. Redistributions in binary form must reproduce the above copyright notice,
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21 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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31 =========================================================================*/
32 
33 
34 #ifndef CXELASTIXEXECUTER_H_
35 #define CXELASTIXEXECUTER_H_
36 
37 #include <QString>
38 #include "cxForwardDeclarations.h"
39 #include "cxTransform3D.h"
40 #include <QObject>
41 #include <QProcess>
42 #include <QFile>
43 #include "cxTimedAlgorithm.h"
44 #include "cxLogger.h"
45 #include "cxRegServices.h"
46 #include "org_custusx_registration_method_commandline_Export.h"
47 
48 namespace cx
49 {
70 class org_custusx_registration_method_commandline_EXPORT ElastixExecuter : public TimedBaseAlgorithm
71 {
72  Q_OBJECT
73 public:
74  ElastixExecuter(RegServicesPtr services, QObject* parent=NULL);
75  virtual ~ElastixExecuter();
76 
77  void setDisplayProcessMessages(bool on);
78 
79  bool setInput(QString application,
80  DataPtr fixed,
81  DataPtr moving,
82  QString outdir,
83  QStringList parameterfiles);
84  virtual void execute();
85  virtual bool isFinished() const;
86  virtual bool isRunning() const;
87 
93  Transform3D getAffineResult_mMf(bool* ok = 0) ;
94  QString getNonlinearResultVolume(bool* ok = 0);
95 
96 private slots:
97  void processStateChanged(QProcess::ProcessState newState);
98  void processError(QProcess::ProcessError error);
99  void processFinished(int, QProcess::ExitStatus);
100  void processReadyRead();
101 
102 private:
106  QString writeInitTransformToElastixfile(DataPtr fixed, DataPtr moving, QString outdir);
110  QString writeInitTransformToCalfile(DataPtr fixed, DataPtr moving, QString outdir);
115  QString findMostRecentTransformOutputFile() const;
134  Transform3D getAffineResult_mmMff(bool* ok = 0) ;
141  Transform3D getFileTransform_ddMd(DataPtr volume);
142 
143  QString mLastOutdir;
144  QProcess* mProcess;
145  DataPtr mFixed;
146  DataPtr mMoving;
147  RegServicesPtr mServices;
148 };
149 
154 {
155 public:
156  ElastixParameterFile(QString filename);
157 
158  bool isValid() const;
159  QString readParameterString(QString key) ;
160  bool readParameterBool(QString key) ;
161  int readParameterInt(QString key) ;
162  std::vector<double> readParameterDoubleVector(QString key) ;
163 // void writeParameter(QString key, QStringList value);
166 
167 private:
168  QString readParameterRawValue(QString key);
169  QFile mFile;
170  QString mText;
171 };
172 
178 {
179 public:
183 
184  static ElastixEulerTransform create(Vector3D angles_xyz, Vector3D translation, Vector3D centerOfRotation)
185  {
186  ElastixEulerTransform retval;
187  retval.mAngles_xyz = angles_xyz;
188  retval.mTranslation = translation;
189  retval.mCenterOfRotation = centerOfRotation;
190  return retval;
191  }
192  static ElastixEulerTransform create(Transform3D M, Vector3D centerOfRotation)
193  {
194  ElastixEulerTransform retval;
195  retval.mAngles_xyz = M.matrix().block<3, 3> (0, 0).eulerAngles(0, 1, 2);
196  retval.mCenterOfRotation = centerOfRotation;
197 
198  Transform3D R = retval.getRotationMatrix();
200  // solve M = T*Tc*R*Tc.inv() with respect to T:
201  Transform3D T = M*C*R.inv()*C.inv();
202 
203  retval.mTranslation = T.matrix().block<3, 1> (0, 3);
204 // retval.mCenterOfRotation = Vector3D(0,0,0);
205  return retval;
206  }
208  {
211  Transform3D R = this->getRotationMatrix();
212  Transform3D Q = T*C*R*C.inv();
213  return Q;
214  }
215  static void test()
216  {
217  std::cout << "==========TEST==============" << std::endl;
219 
220  ElastixEulerTransform E = create(M, Vector3D(30,40,50));
221  Transform3D Q = E.toMatrix();
222 
223  std::cout << "M\n" << M << std::endl;
224  std::cout << "Q\n" << Q << std::endl;
225  Transform3D diff = Q*M.inv();
226  std::cout << "Q*M.inv\n" << diff << std::endl;
227  if (!similar(Transform3D::Identity(), diff))
228  reportError("assertion failure in ElastixEulerTransform");
229  }
230 private:
232 
233  Transform3D getRotationMatrix() const
234  {
235  Eigen::Matrix3d m;
236  m = Eigen::AngleAxisd(mAngles_xyz[0], Eigen::Vector3d::UnitX())
237  * Eigen::AngleAxisd(mAngles_xyz[1], Eigen::Vector3d::UnitY())
238  * Eigen::AngleAxisd(mAngles_xyz[2], Eigen::Vector3d::UnitZ());
239 
240  Transform3D R = Transform3D::Identity();
241  R.matrix().block<3, 3> (0, 0) = m;
242  return R;
243  }
244 };
245 
246 
250 } /* namespace cx */
251 #endif /* CXELASTIXEXECUTER_H_ */
ElastixParameterFile(QString filename)
Transform3D createTransformRotateY(const double angle)
QString readParameterString(QString key)
void reportError(QString msg)
Definition: cxLogger.cpp:92
Base class for algorithms that wants to time their execution.
boost::shared_ptr< class RegServices > RegServicesPtr
Definition: cxRegServices.h:41
static ElastixEulerTransform create(Vector3D angles_xyz, Vector3D translation, Vector3D centerOfRotation)
int readParameterInt(QString key)
Transform3D Transform3D
Transform3D is a representation of an affine 3D transform.
Transform3D toMatrix() const
static ElastixEulerTransform create(Transform3D M, Vector3D centerOfRotation)
bool similar(const DoubleBoundingBox3D &a, const DoubleBoundingBox3D &b, double tol)
boost::shared_ptr< class Data > DataPtr
ElastiX command-line wrapper.
Transform3D createTransformTranslate(const Vector3D &translation)
bool readParameterBool(QString key)
Eigen::Vector3d Vector3D
Vector3D is a representation of a point or vector in 3D.
Definition: cxVector3D.h:63
std::vector< double > readParameterDoubleVector(QString key)
Transform3D createTransformRotateX(const double angle)
#define M_PI