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cxWirePhantomWidget.cpp
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1 /*=========================================================================
2 This file is part of CustusX, an Image Guided Therapy Application.
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32 
33 #include "cxWirePhantomWidget.h"
34 
35 #include <QPushButton>
36 #include <QTextEdit>
37 #include <vtkPolyData.h>
38 #include <vtkPoints.h>
39 #include "cxMesh.h"
40 #include "cxDataLocations.h"
42 #include "cxPointMetric.h"
43 #include "cxDistanceMetric.h"
44 #include "cxTool.h"
45 #include "cxTypeConversions.h"
46 #include "cxPipelineWidget.h"
47 #include "cxDataReaderWriter.h"
48 #include "cxSmoothingImageFilter.h"
51 #include "cxSpaceProvider.h"
52 #include "cxReporter.h"
53 #include "cxRegistrationService.h"
55 #include "cxPatientModelService.h"
56 #include "cxViewGroupData.h"
57 
58 #include "cxProfile.h"
59 #include "cxViewService.h"
62 #include "cxTrackingService.h"
64 
65 namespace cx
66 {
67 
68 WirePhantomWidget::WirePhantomWidget(ctkPluginContext *pluginContext, QWidget* parent) :
69  RegistrationBaseWidget(RegServices::create(pluginContext), parent, "WirePhantomWidget", "Wire Phantom Test"),
70  mUsReconstructionService(new UsReconstructionServiceProxy(pluginContext))
71 {
72  mLastRegistration = Transform3D::Identity();
73 
74  // fill the pipeline with filters:
75  mPipeline.reset(new Pipeline(mServices->patient()));
76  XmlOptionFile options = profile()->getXmlSettings().descend("registration").descend("WirePhantomWidget");
77  FilterGroupPtr filters(new FilterGroup(options));
78  filters->append(FilterPtr(new SmoothingImageFilter(mServices)));
79  filters->append(FilterPtr(new BinaryThresholdImageFilter(mServices)));
81  mPipeline->initialize(filters);
82 
83  mPipeline->getNodes()[0]->setValueName("US Image:");
84  mPipeline->getNodes()[0]->setHelp("Select an US volume acquired from the wire phantom.");
85  mPipeline->setOption("Color", QVariant(QColor("red")));
86 
87  mLayout = new QVBoxLayout(this);
88 
89  mPipelineWidget = new PipelineWidget(mServices->view(), mServices->patient(), NULL, mPipeline);
90 
91  QPushButton* showCrossButton = new QPushButton("Show Cross");
92  showCrossButton->setToolTip("Load the centerline description of the wire cross");
93  connect(showCrossButton, SIGNAL(clicked()), this, SLOT(loadNominalCross()));
94 
95  mMeasureButton = new QPushButton("Execute");
96  mMeasureButton->setToolTip("Measure deviation of input volume from nominal wire cross.");
97  connect(mMeasureButton, SIGNAL(clicked()), this, SLOT(measureSlot()));
98 
99  mCalibrationButton = new QPushButton("Probe calib");
100  mCalibrationButton->setToolTip(""
101  "Estimate probe calibration sMt\n"
102  "based on last accuracy test and\n"
103  "the current probe orientation");
104  connect(mCalibrationButton, SIGNAL(clicked()), this, SLOT(generate_sMt()));
105 
106  QLayout* buttonsLayout = new QHBoxLayout;
107  buttonsLayout->addWidget(mMeasureButton);
108  buttonsLayout->addWidget(mCalibrationButton);
109 
110  mResults = new QTextEdit;
111 
112  mLayout->addWidget(showCrossButton);
113  mLayout->addWidget(mPipelineWidget);
114  mLayout->addLayout(buttonsLayout);
115  mLayout->addWidget(mResults, 1);
116  mLayout->addStretch();
117 }
118 
120 {
121 }
122 
124 {
125  return "<html>"
126  "<h3>Measure US accuracy using the wire phantom.</h3>"
127  "<p>"
128  "Select a US recording of the wire phantom, then press"
129  "the register button to find deviation from the nominal"
130  "data. The output is given as a distance from measured"
131  "to nominal."
132  "</p>"
133  "</html>";
134 }
135 
136 MeshPtr WirePhantomWidget::loadNominalCross()
137 {
138  QString nominalCrossFilename = DataLocations::getRootConfigPath()+"/models/wire_phantom_cross_pts.vtk";
139  MeshPtr retval;
140 
141  std::map<QString, MeshPtr> meshes = mServices->patient()->getDataOfType<Mesh>();
142  for (std::map<QString, MeshPtr>::iterator iter=meshes.begin(); iter!=meshes.end(); ++iter)
143  if (iter->first.contains("wire_phantom_cross_pts"))
144  retval = iter->second;
145 
146  if (!retval)
147  {
148  QString infoText;
149  retval = boost::dynamic_pointer_cast<Mesh>(mServices->patient()->importData(nominalCrossFilename, infoText));
150  }
151 
152  if (!retval)
153  {
154  reportError(QString("failed to load %s.").arg(nominalCrossFilename));
155  }
156 
157  retval->setColor(QColor("green"));
158  this->showData(retval);
159 
160  return retval;
161 }
162 
163 void WirePhantomWidget::showData(DataPtr data)
164 {
165  mServices->view()->getGroup(0)->addData(data->getUid());
166 }
167 
168 void WirePhantomWidget::measureSlot()
169 {
170  if (mPipeline->getPipelineTimedAlgorithm()->isRunning())
171  return;
172  connect(mPipeline->getPipelineTimedAlgorithm().get(), SIGNAL(finished()), this, SLOT(registration()));
173  mPipeline->execute();
174 }
175 
178 Vector3D WirePhantomWidget::findCentroid(MeshPtr mesh)
179 {
180  vtkPolyDataPtr poly = mesh->getVtkPolyData();
181  vtkPointsPtr points = poly->GetPoints();
182  int N = points->GetNumberOfPoints();
183  if (N==0)
184  return Vector3D(0,0,0);
185 
186  Vector3D acc(0,0,0);
187  for (int i = 0; i < N; ++i)
188  acc += Vector3D(points->GetPoint(i));
189  return acc/N;
190 }
191 
192 void WirePhantomWidget::registration()
193 {
194 // // disconnect the connection that started this registration
195  disconnect(mPipeline->getPipelineTimedAlgorithm().get(), SIGNAL(finished()), this, SLOT(registration()));
196 
197  // Verify that a centerline is available:
198  // - if no centerline, run centerline algo on segmentation,
199  // - if no segmentation, run segmentation
200  //
201  // Set centerline as Registration: moving data.
202  // Load nominal cross
203  // find center in nominal
204  // Execute V2V algo
205  // Find transform matrix fMm
206  // apply fMm to nominal, return diff
207  //
208 
209  DataPtr measuredCross = mPipeline->getNodes().back()->getData();
210  MeshPtr nominalCross = this->loadNominalCross();
211  if (!nominalCross || !measuredCross)
212  {
213  reportError("Missing fixed/moving data. WirePhantom measurement failed.");
214  return;
215  }
216 
217  mServices->registration()->setFixedData(nominalCross);
218  mServices->registration()->setMovingData(measuredCross);
219 
220  this->showData(nominalCross);
221  this->showData(measuredCross);
222 
223  SeansVesselReg vesselReg;
224  vesselReg.mt_auto_lts = true;
225  vesselReg.mt_ltsRatio = 80;
226  vesselReg.mt_doOnlyLinear = true;
227  QString logPath = mServices->patient()->getActivePatientFolder() + "/Logs/";
228 // vesselReg.setDebugOutput(true);
229 
230  bool success = vesselReg.initialize(mServices->registration()->getMovingData(), mServices->registration()->getFixedData(), logPath);
231  success = success && vesselReg.execute();
232  if (!success)
233  {
234  reportWarning("Vessel registration failed.");
235  return;
236  }
237 
238  Transform3D linearTransform = vesselReg.getLinearResult();
239  std::cout << "v2v linear result:\n" << linearTransform << std::endl;
240 
241  vesselReg.checkQuality(linearTransform);
242  mLastRegistration = linearTransform;
243 
244  // The registration is performed in space r. Thus, given an old data position rMd, we find the
245  // new one as rM'd = Q * rMd, where Q is the inverted registration output.
246  // Delta is thus equal to Q:
247  Transform3D delta = linearTransform.inv();
248 // mRegistrationService->restart();
249  mServices->registration()->setLastRegistrationTime(QDateTime::currentDateTime());//Instead of restart
250  mServices->registration()->applyImage2ImageRegistration(delta, "Wire Phantom Measurement");
251 
252 
253  Vector3D t_delta = linearTransform.matrix().block<3, 1>(0, 3);
254  Eigen::AngleAxisd angleAxis = Eigen::AngleAxisd(linearTransform.matrix().block<3, 3>(0, 0));
255  double angle = angleAxis.angle();
256 
257  // Compute the centroid of the wire phantom.
258  // This should be the wire centre, given that the
259  // model is symmetrical.
260  Vector3D cross_r = this->findCentroid(nominalCross);
261  // Vector3D cross(134.25, 134.25, 99.50); // old hardcoded value: obsole after new measurements
262  // should be (CA20121022): <134.212 134.338 100.14>
263 // std::cout << "cross2 " << cross2 << std::endl;
264 
265 
266  // find transform to probe space t_us, i.e. the middle position from the us acquisition
267  std::pair<QString, Transform3D> probePos = this->getLastProbePosition();
268  Transform3D rMt_us = probePos.second;
269 
270  Vector3D cross_moving_r = linearTransform.coord(cross_r);
271  Vector3D diff_r = (cross_r - cross_moving_r);
272  Vector3D diff_tus = rMt_us.inv().vector(diff_r);
273 
274  struct Fmt
275  {
276  QString operator()(double val)
277  {
278  return QString("%1").arg(val, 2, 'f', 2);
279  }
280  };
281  Fmt fmt;
282 
283  QString result;
284  result += QString("Results for: %1\n").arg(mServices->registration()->getMovingData()->getName());
285  result += QString("Shift vector (r): \t%1\t%2\t%3\n").arg(fmt(diff_r[0])).arg(fmt(diff_r[1])).arg(fmt(diff_r[2]));
286  if (!probePos.first.isEmpty())
287  result += QString("Shift vector (probe): \t%1\t%2\t%3\t(used tracking data from %4)\n").arg(fmt(diff_tus[0])).arg(fmt(diff_tus[1])).arg(fmt(diff_tus[2])).arg(probePos.first);
288  result += QString("Accuracy |v|: \t%1\tmm\n").arg(fmt(diff_r.length()));
289  result += QString("Angle: \t%1\t*\n").arg(fmt(angle / M_PI * 180.0));
290 
291  mResults->append(result);
292  report("Wire Phantom Test Results:\n"+result);
293 
294  this->showDataMetrics(cross_r);
295 }
296 
302 void WirePhantomWidget::showDataMetrics(Vector3D cross_r)
303 {
304  // add metrics displaying the distance from cross in the nominal and us spaces:
305  Transform3D usMnom = mServices->spaceProvider()->get_toMfrom(
306  mServices->spaceProvider()->getD(mServices->registration()->getFixedData()),
307  mServices->spaceProvider()->getD(mServices->registration()->getMovingData()));
308  Vector3D cross_us = usMnom.coord(cross_r);
309 
310  PointMetricPtr p1 = boost::dynamic_pointer_cast<PointMetric>(mServices->patient()->getData("cross_nominal"));
311  if (!p1)
312  p1 = mServices->patient()->createSpecificData<PointMetric>("cross_nominal");
313 // p1 = PointMetric::create("cross_nominal", "cross_nominal");
314  p1->get_rMd_History()->setParentSpace(mServices->registration()->getFixedData()->getUid());
315  p1->setSpace(mServices->spaceProvider()->getD(mServices->registration()->getFixedData()));
316  p1->setCoordinate(cross_r);
317 // dataManager()->loadData(p1);
318  mServices->patient()->insertData(p1);
319  //this->showData(p1);
320 
321  PointMetricPtr p2 = mServices->patient()->getData<PointMetric>("cross_us");
322  if (!p2)
323  p2 = mServices->patient()->createSpecificData<PointMetric>("cross_us");
324 // p2 = PointMetric::create("cross_us", "cross_us");
325  p2->get_rMd_History()->setParentSpace(mServices->registration()->getMovingData()->getUid());
326  p2->setSpace(mServices->spaceProvider()->getD(mServices->registration()->getMovingData()));
327  p2->setCoordinate(cross_us);
328 // dataManager()->loadData(p2);
329  mServices->patient()->insertData(p2);
330  //this->showData(p2);
331 
332  DistanceMetricPtr d0 = mServices->patient()->getData<DistanceMetric>("accuracy");
333  if (!d0)
334  d0 = mServices->patient()->createSpecificData<DistanceMetric>("accuracy");
335 // d0.reset(new DistanceMetric("accuracy", "accuracy"));
336  d0->get_rMd_History()->setParentSpace("reference");
337  d0->getArguments()->set(0, p1);
338  d0->getArguments()->set(1, p2);
339 // dataManager()->loadData(d0);
340  mServices->patient()->insertData(d0);
341  this->showData(d0);
342 }
343 
350 std::pair<QString, Transform3D> WirePhantomWidget::getLastProbePosition()
351 {
352  // find transform to probe space t_us, i.e. the middle position from the us acquisition
353  USReconstructInputData usData = mUsReconstructionService->getSelectedFileData();
354  Transform3D prMt_us = Transform3D::Identity();
355  if (usData.mPositions.empty())
356  return std::make_pair("", Transform3D::Identity());
357  prMt_us = usData.mPositions[usData.mPositions.size()/2].mPos;
358  return std::make_pair(usData.mFilename, prMt_us);
359 }
360 
361 void WirePhantomWidget::generate_sMt()
362 {
363  bool translateOnly = true;
364 
365 
366  std::pair<QString, Transform3D> probePos = this->getLastProbePosition();
367  Transform3D rMt_us = probePos.second;
368  if (probePos.first.isEmpty())
369  {
370  reportWarning("Cannot find probe position from last recording, aborting calibration test.");
371  return;
372  }
373 
374  USReconstructInputData usData = mUsReconstructionService->getSelectedFileData();
375  ToolPtr probe = mServices->tracking()->getTool(usData.mProbeUid);
376  if (!probe || !probe->hasType(Tool::TOOL_US_PROBE))
377  {
378  reportWarning("Cannot find probe, aborting calibration test.");
379  return;
380  }
381 
382 // ToolPtr probe = toolManager()->getDominantTool();
383 // if (!probe || !probe->getVisible() || !probe->hasType(Tool::TOOL_US_PROBE))
384 // {
385 // reportWarning("Cannot find visible probe, aborting calibration test.");
386 // return;
387 // }
388  if (!mServices->registration()->getMovingData())
389  {
390  reportWarning("Cannot find moving data, aborting calibration test.");
391  return;
392  }
393 
394 
395  if (translateOnly)
396  {
397  Vector3D cross_r = this->findCentroid(this->loadNominalCross());
398  // Vector3D cross(134.25, 134.25, 99.50); // old hardcoded value: obsole after new measurements
399  // should be (CA20121022): <134.212 134.338 100.14>
400  // std::cout << "cross2 " << cross2 << std::endl;
401 
402 
403  // find transform to probe space t_us, i.e. the middle position from the us acquisition
404 // std::pair<QString, Transform3D> probePos = this->getLastProbePosition();
405 // Transform3D rMt_us = probePos.second;
406 
407  Vector3D cross_moving_r = mLastRegistration.coord(cross_r);
408  Vector3D diff_r = (cross_r - cross_moving_r);
409  Vector3D diff_tus = rMt_us.inv().vector(diff_r);
410 
411  Transform3D sMt = probe->getCalibration_sMt();
412  Transform3D sQt; // Q is the new calibration matrix.
413 
414  sQt = sMt * createTransformTranslate(diff_tus);
415 
416  report(QString(""
417  "Calculated new calibration matrix\n"
418  "adding only translation "
419  "from last accuracy test\n"
420  "and raw data %1:\n"
421  "%2").arg(probePos.first).arg(qstring_cast(sQt)));
422  }
423  else
424  {
425  Transform3D prMt = rMt_us;
426  Transform3D sMt = probe->getCalibration_sMt();
427  Transform3D prMs = prMt * sMt.inv();
428  Transform3D usMpr = mServices->registration()->getMovingData()->get_rMd().inv() * mServices->patient()->get_rMpr();
429  Transform3D nomMus = mLastRegistration.inv();
430 
431  Transform3D sQt; // Q is the new calibration matrix.
432  Transform3D usMs = usMpr*prMs;
433 
434  // start with: nomMus * usMpr * prMs * sMt
435  // move usMpr*prMs to the left and collect a new sMt from the remains:
436  // start with: usMpr * prMs * (usMpr * prMs).inv() * nomMus * usMpr * prMs * sMt
437 
438  sQt = usMs.inv() * nomMus * usMs * sMt;
439 
440  report(QString(""
441  "Calculated new calibration matrix\n"
442  "from last accuracy test\n"
443  "and raw data %1.\n"
444  "Old calibration matrix sMt:\n"
445  "%2\n"
446  "New calibration matrix sQt:\n"
447  "%3\n").arg(probePos.first).arg(qstring_cast(sMt)).arg(qstring_cast(sQt)));
448  }
449 
450 }
451 
452 
453 //------------------------------------------------------------------------------
454 }//namespace cx
QString qstring_cast(const T &val)
cxResource_EXPORT ProfilePtr profile()
Definition: cxProfile.cpp:176
void reportError(QString msg)
Definition: cxLogger.cpp:92
A mesh data set.
Definition: cxMesh.h:61
Transform3D Transform3D
Transform3D is a representation of an affine 3D transform.
boost::shared_ptr< class Data > DataPtr
vtkSmartPointer< class vtkPolyData > vtkPolyDataPtr
boost::shared_ptr< class Filter > FilterPtr
void reportWarning(QString msg)
Definition: cxLogger.cpp:91
boost::shared_ptr< FilterGroup > FilterGroupPtr
Definition: cxFilterGroup.h:86
WirePhantomWidget(ctkPluginContext *pluginContext, QWidget *parent=0)
Transform3D createTransformTranslate(const Vector3D &translation)
boost::shared_ptr< class DistanceMetric > DistanceMetricPtr
Eigen::Vector3d Vector3D
Vector3D is a representation of a point or vector in 3D.
Definition: cxVector3D.h:63
static QString getRootConfigPath()
return path to root config folder. May be replaced with getExistingConfigPath()
void report(QString msg)
Definition: cxLogger.cpp:90
boost::shared_ptr< class Mesh > MeshPtr
Ultrasond probe. The tool has a Probe subinterface with a sector and a video stream.
Definition: cxTool.h:108
virtual QString defaultWhatsThis() const
Helper class for xml files used to store ssc/cx data.
#define M_PI
vtkSmartPointer< class vtkPoints > vtkPointsPtr
boost::shared_ptr< class Tool > ToolPtr
boost::shared_ptr< class PointMetric > PointMetricPtr