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cxRegistrationImplService.cpp
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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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18  may be used to endorse or promote products derived from this software
19  without specific prior written permission.
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31 =========================================================================*/
32 
34 
35 #include <ctkPluginContext.h>
36 #include <ctkServiceTracker.h>
37 #include <vtkPoints.h>
38 #include <vtkLandmarkTransform.h>
39 #include <vtkMatrix4x4.h>
40 
41 #include "cxData.h"
42 #include "cxTypeConversions.h"
43 #include "cxLogger.h"
45 #include "cxFrameForest.h"
46 #include "cxPatientModelService.h"
48 #include "cxLandmark.h"
52 #include "cxXMLNodeWrapper.h"
53 
54 namespace cx
55 {
56 
58  mLastRegistrationTime(QDateTime::currentDateTime()),
59  mContext(context),
60  mPatientModelService(new PatientModelServiceProxy(context)),
61  mSession(SessionStorageServiceProxy::create(context))
62 {
63  connect(mSession.get(), &SessionStorageService::cleared, this, &RegistrationImplService::clearSlot);
64  connect(mSession.get(), &SessionStorageService::isLoadingSecond, this, &RegistrationImplService::duringLoadPatientSlot);
65  connect(mSession.get(), &SessionStorageService::isSaving, this, &RegistrationImplService::duringSavePatientSlot);
66 }
67 
69 {
70 }
71 
72 void RegistrationImplService::duringSavePatientSlot(QDomElement& node)
73 {
74  XMLNodeAdder root(node);
75  QDomElement managerNode = root.descend("managers").node().toElement();
76  this->addXml(managerNode);
77 }
78 
79 void RegistrationImplService::duringLoadPatientSlot(QDomElement& node)
80 {
81  XMLNodeParser root(node);
82  QDomElement registrationManager = root.descend("managers/registrationManager").node().toElement();
83  if (!registrationManager.isNull())
84  this->parseXml(registrationManager);
85 }
86 
87 void RegistrationImplService::addXml(QDomNode& parentNode)
88 {
89  QDomDocument doc = parentNode.ownerDocument();
90  QDomElement base = doc.createElement("registrationManager");
91  parentNode.appendChild(base);
92 
93  QDomElement fixedDataNode = doc.createElement("fixedDataUid");
94  DataPtr fixedData = this->getFixedData();
95  if(fixedData)
96  {
97  fixedDataNode.appendChild(doc.createTextNode(fixedData->getUid()));
98  }
99  base.appendChild(fixedDataNode);
100 
101  QDomElement movingDataNode = doc.createElement("movingDataUid");
102  DataPtr movingData = this->getMovingData();
103  if(movingData)
104  {
105  movingDataNode.appendChild(doc.createTextNode(movingData->getUid()));
106  }
107  base.appendChild(movingDataNode);
108 }
109 
110 void RegistrationImplService::parseXml(QDomNode& dataNode)
111 {
112  QString fixedData = dataNode.namedItem("fixedDataUid").toElement().text();
113  this->setFixedData(fixedData);
114 
115  QString movingData = dataNode.namedItem("movingDataUid").toElement().text();
116  this->setMovingData(movingData);
117 }
118 
119 void RegistrationImplService::clearSlot()
120 {
121  this->setLastRegistrationTime(QDateTime());
122  this->setFixedData(DataPtr());
123 }
124 
126 {
127  this->setMovingData((data) ? data->getUid() : "");
128 }
129 
131 {
132  this->setFixedData((data) ? data->getUid() : "");
133 }
134 
136 {
137  if (uid==mMovingData)
138  return;
139  mMovingData = uid;
140  emit movingDataChanged(mMovingData);
141 }
142 
144 {
145  if (uid==mFixedData)
146  return;
147  mFixedData = uid;
148  emit fixedDataChanged(mFixedData);
149 }
150 
152 {
153  return mPatientModelService->getData(mMovingData);
154 }
155 
157 {
158  return mPatientModelService->getData(mFixedData);
159 }
160 
162 {
163  return mLastRegistrationTime;
164 }
165 
167 {
168  mLastRegistrationTime = time;
169 }
170 
172 {
173  DataPtr fixedImage = this->getFixedData();
174 
175  if(!fixedImage)
176  {
177  reportError("The fixed data is not set, cannot do patient registration!");
178  return;
179  }
180  LandmarkMap fixedLandmarks = fixedImage->getLandmarks()->getLandmarks();
181  LandmarkMap toolLandmarks = mPatientModelService->getPatientLandmarks()->getLandmarks();
182 
183  this->writePreLandmarkRegistration(fixedImage->getName(), fixedImage->getLandmarks()->getLandmarks());
184  this->writePreLandmarkRegistration("physical", toolLandmarks);
185 
186  std::vector<QString> landmarks = this->getUsableLandmarks(fixedLandmarks, toolLandmarks);
187 
188  vtkPointsPtr p_ref = this->convertTovtkPoints(landmarks, fixedLandmarks, fixedImage->get_rMd());
189  vtkPointsPtr p_pr = this->convertTovtkPoints(landmarks, toolLandmarks, Transform3D::Identity());
190 
191  // ignore if too few data.
192  if (p_ref->GetNumberOfPoints() < 3)
193  return;
194 
195  bool ok = false;
196  Transform3D rMpr = this->performLandmarkRegistration(p_pr, p_ref, &ok);
197  if (!ok)
198  {
199  reportError("P-I Landmark registration: Failed to register: [" + qstring_cast(p_pr->GetNumberOfPoints()) + "p]");
200  return;
201  }
202 
203  this->applyPatientRegistration(rMpr, "Patient Landmark");
204 }
205 
207 {
208  DataPtr fixedImage = this->getFixedData();
209  if(!fixedImage)
210  {
211  reportError("The fixed data is not set, cannot do image registration!");
212  return;
213  }
214 
215  LandmarkMap fixedLandmarks = fixedImage->getLandmarks()->getLandmarks();
216  LandmarkMap toolLandmarks = mPatientModelService->getPatientLandmarks()->getLandmarks();
217 
218  this->writePreLandmarkRegistration(fixedImage->getName(), fixedImage->getLandmarks()->getLandmarks());
219  this->writePreLandmarkRegistration("physical", toolLandmarks);
220 
221  std::vector<QString> landmarks = this->getUsableLandmarks(fixedLandmarks, toolLandmarks);
222 
223  Transform3D rMd = fixedImage->get_rMd();
224  Transform3D rMpr_old = mPatientModelService->get_rMpr();
225  std::vector<Vector3D> p_pr_old = this->convertAndTransformToPoints(landmarks, fixedLandmarks, rMpr_old.inv()*rMd);
226  std::vector<Vector3D> p_pr_new = this->convertAndTransformToPoints(landmarks, toolLandmarks, Transform3D::Identity());
227 
228  // ignore if too few data.
229  if (p_pr_old.size() < 1)
230  return;
231 
232  LandmarkTranslationRegistration landmarkTransReg;
233  bool ok = false;
234  Transform3D pr_oldMpr_new = landmarkTransReg.registerPoints(p_pr_old, p_pr_new, &ok);
235  if (!ok)
236  {
237  reportError("Fast translation registration: Failed to register: [" + qstring_cast(p_pr_old.size()) + "points]");
238  return;
239  }
240 
241  this->applyPatientRegistration(rMpr_old*pr_oldMpr_new, "Fast Translation");
242 }
243 
251 {
252  //create a marked(m) space tm, which is related to tool space (t) as follows:
253  //the tool is defined in DICOM space such that
254  //the tool points toward the patients feet and the spheres faces the same
255  //direction as the nose
256  Transform3D tMpr = prMt.inv();
257 
258  Transform3D tmMpr = tMtm * tMpr;
259 
260  this->applyPatientRegistration(tmMpr, "Fast Orientation");
261 
262  // also apply the fast translation registration if any (this frees us form doing stuff in a well-defined order.)
264 }
265 
266 std::vector<Vector3D> RegistrationImplService::convertAndTransformToPoints(const std::vector<QString>& uids, const LandmarkMap& data, Transform3D M)
267 {
268  std::vector<Vector3D> retval;
269 
270  for (unsigned i=0; i<uids.size(); ++i)
271  {
272  QString uid = uids[i];
273  Vector3D p = M.coord(data.find(uid)->second.getCoord());
274  retval.push_back(p);
275  }
276  return retval;
277 }
278 
283 std::vector<QString> RegistrationImplService::getUsableLandmarks(const LandmarkMap& data_a, const LandmarkMap& data_b)
284 {
285  std::vector<QString> retval;
286  std::map<QString, LandmarkProperty> props = mPatientModelService->getLandmarkProperties();
287  std::map<QString, LandmarkProperty>::iterator iter;
288 
289  for (iter=props.begin(); iter!=props.end(); ++iter)
290  {
291  QString uid = iter->first;
292  if (data_a.count(uid) && data_b.count(uid) && iter->second.getActive())
293  retval.push_back(uid);
294  }
295  return retval;
296 }
297 
299 {
300  //check that the fixed data is set
301  DataPtr fixedImage = this->getFixedData();
302  if(!fixedImage)
303  {
304  reportError("The fixed data is not set, cannot do landmark image registration!");
305  return;
306  }
307 
308  //check that the moving data is set
309  DataPtr movingImage = this->getMovingData();
310  if(!movingImage)
311  {
312  reportError("The moving data is not set, cannot do landmark image registration!");
313  return;
314  }
315 
316  // ignore self-registration, this gives no effect bestcase, buggy behaviour worstcase (has been observed)
317  if(movingImage==fixedImage)
318  {
319  reportError("The moving and fixed are equal, ignoring landmark image registration!");
320  return;
321  }
322 
323  LandmarkMap fixedLandmarks = fixedImage->getLandmarks()->getLandmarks();
324  LandmarkMap imageLandmarks = movingImage->getLandmarks()->getLandmarks();
325 
326  this->writePreLandmarkRegistration(fixedImage->getName(), fixedImage->getLandmarks()->getLandmarks());
327  this->writePreLandmarkRegistration(movingImage->getName(), movingImage->getLandmarks()->getLandmarks());
328 
329  std::vector<QString> landmarks = getUsableLandmarks(fixedLandmarks, imageLandmarks);
330  vtkPointsPtr p_fixed_r = convertTovtkPoints(landmarks, fixedLandmarks, fixedImage->get_rMd());
331  vtkPointsPtr p_moving_r = convertTovtkPoints(landmarks, imageLandmarks, movingImage->get_rMd());
332 
333  int minNumberOfPoints = 3;
334  if (translationOnly)
335  minNumberOfPoints = 1;
336 
337  // ignore if too few data.
338  if (p_fixed_r->GetNumberOfPoints() < minNumberOfPoints)
339  {
340  reportError(
341  QString("Found %1 corresponding landmarks, need %2, cannot do landmark image registration!")
342  .arg(p_fixed_r->GetNumberOfPoints())
343  .arg(minNumberOfPoints)
344  );
345  return;
346  }
347 
348  bool ok = false;
349  QString idString;
350  Transform3D delta;
351 
352  if (translationOnly)
353  {
354  LandmarkTranslationRegistration landmarkTransReg;
355  delta = landmarkTransReg.registerPoints(convertVtkPointsToPoints(p_fixed_r), convertVtkPointsToPoints(p_moving_r), &ok);
356  idString = QString("Image to Image Landmark Translation");
357  }
358  else
359  {
360  Transform3D rMd;
361  delta = this->performLandmarkRegistration(p_moving_r, p_fixed_r, &ok);
362  idString = QString("Image to Image Landmark");
363  }
364 
365  if (!ok)
366  {
367  reportError("I-I Landmark registration: Failed to register: [" + qstring_cast(p_moving_r->GetNumberOfPoints()) + "p], "+ movingImage->getName());
368  return;
369  }
370 
371  this->applyImage2ImageRegistration(delta, idString);
372 }
373 
374 std::vector<Vector3D> RegistrationImplService::convertVtkPointsToPoints(vtkPointsPtr base)
375 {
376  std::vector<Vector3D> retval;
377 
378  for (int i=0; i<base->GetNumberOfPoints(); ++i)
379  {
380  Vector3D p(base->GetPoint(i));
381  retval.push_back(p);
382  }
383  return retval;
384 }
385 
389 Transform3D RegistrationImplService::performLandmarkRegistration(vtkPointsPtr source, vtkPointsPtr target, bool* ok) const
390 {
391  *ok = false;
392 
393  // too few data samples: ignore
394  if (source->GetNumberOfPoints() < 3)
395  {
396  return Transform3D::Identity();
397  }
398 
399  vtkLandmarkTransformPtr landmarktransform = vtkLandmarkTransformPtr::New();
400  landmarktransform->SetSourceLandmarks(source);
401  landmarktransform->SetTargetLandmarks(target);
402  landmarktransform->SetModeToRigidBody();
403  source->Modified();
404  target->Modified();
405  landmarktransform->Update();
406 
407  Transform3D tar_M_src(landmarktransform->GetMatrix());
408 
409  if (QString::number(tar_M_src(0,0))=="nan") // harry but quick way to check badness of transform...
410  {
411  return Transform3D::Identity();
412  }
413 
414  *ok = true;
415  return tar_M_src;
416 }
417 
419 {
420  this->performImage2ImageRegistration(delta_pre_rMd, description);
421 }
422 
424 {
425  this->performImage2ImageRegistration(delta_pre_rMd, description, true);
426 }
427 
428 void RegistrationImplService::performImage2ImageRegistration(Transform3D delta_pre_rMd, QString description, bool continuous)
429 {
430  RegistrationTransform regTrans(delta_pre_rMd, QDateTime::currentDateTime(), description);
431  regTrans.mFixed = mFixedData;
432  regTrans.mMoving = mMovingData;
433 
434  this->updateRegistration(mLastRegistrationTime, regTrans, this->getMovingData(), continuous);
435 
436  mLastRegistrationTime = regTrans.mTimestamp;
437  if(!continuous)
438  reportSuccess(QString("Image registration [%1] has been performed on %2").arg(description).arg(regTrans.mMoving) );
439 }
440 
442 {
443  this->performPatientRegistration(rMpr_new, description);
444 }
445 
447 {
448  this->performPatientRegistration(rMpr_new, description, true);
449 }
450 
451 void RegistrationImplService::performPatientRegistration(Transform3D rMpr_new, QString description, bool continuous)
452 {
453  RegistrationTransform regTrans(rMpr_new, QDateTime::currentDateTime(), description);
454  regTrans.mFixed = mFixedData;
455 
456  mPatientModelService->updateRegistration_rMpr(mLastRegistrationTime, regTrans, continuous);
457 
458  mLastRegistrationTime = regTrans.mTimestamp;
459  if(!continuous)
460  reportSuccess(QString("Patient registration [%1] has been performed.").arg(description));
461 }
462 
468 void RegistrationImplService::updateRegistration(QDateTime oldTime, RegistrationTransform deltaTransform, DataPtr data, bool continuous)
469 {
470  RegistrationApplicator applicator(mPatientModelService->getData());
471  applicator.updateRegistration(oldTime, deltaTransform, data, continuous);
472  if(!continuous)
473  mPatientModelService->autoSave();
474 }
475 
484 {
485  Transform3D rMpr = mPatientModelService->get_rMpr();
486 
487  //create a marked(m) space tm, which is related to tool space (t) as follows:
488  //the tool is defined in DICOM space such that
489  //the tool points toward the patients feet and the spheres faces the same
490  //direction as the nose
491  Transform3D tMpr = prMt.inv();
492 
493  // this is the new patient registration:
494  Transform3D tmMpr = tMtm * tMpr;
495  // the change in pat reg becomes:
496  Transform3D F = tmMpr * rMpr.inv();
497 
498  QString description("Patient Orientation");
499 
500  QDateTime oldTime = this->getLastRegistrationTime(); // time of previous reg
501  this->applyPatientRegistration(tmMpr, description);
502 
503  // now apply the inverse of F to all data,
504  // thus ensuring the total path from pr to d_i is unchanged:
505  Transform3D delta_pre_rMd = F;
506 
507 
508  // use the same registration time as generated in the applyPatientRegistration() above:
509  RegistrationTransform regTrans(delta_pre_rMd, this->getLastRegistrationTime(), description);
510 
511  std::map<QString,DataPtr> data = mPatientModelService->getData();
512  // update the transform on all target data:
513  for (std::map<QString,DataPtr>::iterator iter = data.begin(); iter!=data.end(); ++iter)
514  {
515  DataPtr current = iter->second;
516  RegistrationTransform newTransform = regTrans;
517  newTransform.mValue = regTrans.mValue * current->get_rMd();
518  current->get_rMd_History()->updateRegistration(oldTime, newTransform);
519 
520  report("Updated registration of data " + current->getName());
521  std::cout << "rMd_new\n" << newTransform.mValue << std::endl;
522  }
523 
524  this->setLastRegistrationTime(regTrans.mTimestamp);
525 
526  reportSuccess("Patient Orientation has been performed");
527 }
528 
529 void RegistrationImplService::writePreLandmarkRegistration(QString name, LandmarkMap landmarks)
530 {
531  QStringList lm;
532  for (LandmarkMap::iterator iter=landmarks.begin(); iter!=landmarks.end(); ++iter)
533  {
534  lm << mPatientModelService->getLandmarkProperties()[iter->second.getUid()].getName();
535  }
536 
537  QString msg = QString("Preparing to register [%1] containing the landmarks: [%2]").arg(name).arg(lm.join(","));
538  report(msg);
539 }
540 
547 vtkPointsPtr RegistrationImplService::convertTovtkPoints(const std::vector<QString>& uids, const LandmarkMap& data, Transform3D M)
548 {
549  vtkPointsPtr retval = vtkPointsPtr::New();
550 
551  for (unsigned i=0; i<uids.size(); ++i)
552  {
553  QString uid = uids[i];
554  Vector3D p = M.coord(data.find(uid)->second.getCoord());
555  retval->InsertNextPoint(p.begin());
556  }
557  return retval;
558 }
559 
561 {
562  return false;
563 }
564 
565 } /* namespace cx */
QString qstring_cast(const T &val)
void reportError(QString msg)
Definition: cxLogger.cpp:92
RegistrationImplService(ctkPluginContext *context)
virtual void doFastRegistration_Orientation(const Transform3D &tMtm, const Transform3D &prMt)
vtkSmartPointer< class vtkLandmarkTransform > vtkLandmarkTransformPtr
Transform3D Transform3D
Transform3D is a representation of an affine 3D transform.
void isLoadingSecond(QDomElement &root)
Emitted after the isLoading signal, to allow for structures that must be loaded after core structures...
virtual void doImageRegistration(bool translationOnly)
virtual void setFixedData(DataPtr data)
virtual void doFastRegistration_Translation()
use the landmarks in master image and patient to perform a translation-only landmark registration ...
void fixedDataChanged(QString uid)
boost::shared_ptr< class Data > DataPtr
QDateTime mTimestamp
time the transform was registrated.
Transform3D registerPoints(std::vector< Vector3D > ref, std::vector< Vector3D > target, bool *ok)
Transform3D mValue
value of transform
virtual void setMovingData(DataPtr data)
virtual void doPatientRegistration()
registrates the fixed image to the patient
void reportSuccess(QString msg)
Definition: cxLogger.cpp:93
void cleared()
emitted when session is cleared, before isLoading is called
virtual void setLastRegistrationTime(QDateTime time)
Eigen::Vector3d Vector3D
Vector3D is a representation of a point or vector in 3D.
Definition: cxVector3D.h:63
A registration event and its transform.
void movingDataChanged(QString uid)
virtual void applyPatientOrientation(const Transform3D &tMtm, const Transform3D &prMt)
Identical to doFastRegistration_Orientation(), except data does not move.
void report(QString msg)
Definition: cxLogger.cpp:90
std::map< QString, class Landmark > LandmarkMap
Always provides a PatientModelService.
virtual void applyContinuousPatientRegistration(Transform3D rMpr_new, QString description)
virtual void applyPatientRegistration(Transform3D rMpr_new, QString description)
virtual void applyContinuousImage2ImageRegistration(Transform3D delta_pre_rMd, QString description)
virtual void applyImage2ImageRegistration(Transform3D delta_pre_rMd, QString description)
void isSaving(QDomElement &root)
xml storage is available
vtkSmartPointer< class vtkPoints > vtkPointsPtr