void ManualImage2ImageRegistrationWidget::updateAverageAccuracyLabel()
{
QString fixedName;
QString movingName;
DataPtr fixedData = boost::dynamic_pointer_cast<Data>(mServices->registration()->getFixedData());
DataPtr movingData = boost::dynamic_pointer_cast<Data>(mServices->registration()->getMovingData());
if (fixedData)
fixedName = fixedData->getName();
if (movingData)
movingName = movingData->getName();
int numberOfActiveLandmarks = 0;
if(this->isAverageAccuracyValid(numberOfActiveLandmarks))
{
mAvarageAccuracyLabel->setText(tr("Root mean square accuracy (Landmarks) %1 mm, calculated in %2 landmarks").
arg(this->getAverageAccuracy(numberOfActiveLandmarks), 0, 'f', 2).arg(numberOfActiveLandmarks));
mAvarageAccuracyLabel->setToolTip(QString("Root Mean Square landmark accuracy from target [%1] to fixed [%2].").
arg(movingName).arg(fixedName));
}
else
{
mAvarageAccuracyLabel->setText(" ");
mAvarageAccuracyLabel->setToolTip("");
}
}
void RegistrationImplService::doPatientRegistration()
{
DataPtr fixedImage = this->getFixedData();
if(!fixedImage)
{
reportError("The fixed data is not set, cannot do patient registration!");
return;
}
LandmarkMap fixedLandmarks = fixedImage->getLandmarks()->getLandmarks();
LandmarkMap toolLandmarks = mPatientModelService->getPatientLandmarks()->getLandmarks();
this->writePreLandmarkRegistration(fixedImage->getName(), fixedImage->getLandmarks()->getLandmarks());
this->writePreLandmarkRegistration("physical", toolLandmarks);
std::vector<QString> landmarks = this->getUsableLandmarks(fixedLandmarks, toolLandmarks);
vtkPointsPtr p_ref = this->convertTovtkPoints(landmarks, fixedLandmarks, fixedImage->get_rMd());
vtkPointsPtr p_pr = this->convertTovtkPoints(landmarks, toolLandmarks, Transform3D::Identity());
// ignore if too few data.
if (p_ref->GetNumberOfPoints() < 3)
return;
bool ok = false;
Transform3D rMpr = this->performLandmarkRegistration(p_pr, p_ref, &ok);
if (!ok)
{
reportError("P-I Landmark registration: Failed to register: [" + qstring_cast(p_pr->GetNumberOfPoints()) + "p]");
return;
}
this->applyPatientRegistration(rMpr, "Patient Landmark");
}
QString ImageLandmarksWidget::getTargetName() const
{
DataPtr image = this->getCurrentData();
if (!image)
return "None";
return image->getName();
}
void ImageLandmarksWidget::enableButtons()
{
bool selected = !mLandmarkTableWidget->selectedItems().isEmpty();
bool loaded = this->getCurrentData() != 0;
mEditLandmarkButton->setEnabled(selected);
mRemoveLandmarkButton->setEnabled(selected);
mDeleteLandmarksButton->setEnabled(loaded);
mAddLandmarkButton->setEnabled(loaded);
mImportLandmarksFromPointMetricsButton->setEnabled(loaded);
DataPtr image = this->getCurrentData();
if (image)
{
mAddLandmarkButton->setToolTip(QString("Add landmark to image %1").arg(image->getName()));
mEditLandmarkButton->setToolTip(QString("Resample landmark in image %1").arg(image->getName()));
}
}
/** Apply the transform from the parent frame to the imported data.
*
*/
void ImportDataDialog::importParentTransform()
{
if (!mTransformFromParentFrameCheckBox->isChecked())
return;
if(!mData)
return;
DataPtr parent = mPatientModelService->getData(mData->getParentSpace());
if (!parent)
return;
mData->get_rMd_History()->setRegistration(parent->get_rMd());
report("Assigned rMd from data [" + parent->getName() + "] to data [" + mData->getName() + "]");
}
void FrameTreeWidget::fill(QTreeWidgetItem* parent, QDomNode node)
{
for (QDomNode child = node.firstChild(); !child.isNull(); child = child.nextSibling())
{
QString frameName = child.toElement().tagName();
// if frame refers to a data, use its name instead.
DataPtr data = mPatientService->getData(frameName);
if (data)
frameName = data->getName();
QTreeWidgetItem* item = new QTreeWidgetItem(parent, QStringList() << frameName);
this->fill(item, child);
}
}
/**\brief Identical to doFastRegistration_Orientation(), except data does not move.
*
* When applying a new transform to the patient orientation, all data is moved
* the the inverse of that value, thus giving a net zero change along the path
* pr...d_i.
*
*/
void RegistrationImplService::applyPatientOrientation(const Transform3D& tMtm, const Transform3D& prMt)
{
Transform3D rMpr = mPatientModelService->get_rMpr();
//create a marked(m) space tm, which is related to tool space (t) as follows:
//the tool is defined in DICOM space such that
//the tool points toward the patients feet and the spheres faces the same
//direction as the nose
Transform3D tMpr = prMt.inv();
// this is the new patient registration:
Transform3D tmMpr = tMtm * tMpr;
// the change in pat reg becomes:
Transform3D F = tmMpr * rMpr.inv();
QString description("Patient Orientation");
QDateTime oldTime = this->getLastRegistrationTime(); // time of previous reg
this->applyPatientRegistration(tmMpr, description);
// now apply the inverse of F to all data,
// thus ensuring the total path from pr to d_i is unchanged:
Transform3D delta_pre_rMd = F;
// use the same registration time as generated in the applyPatientRegistration() above:
RegistrationTransform regTrans(delta_pre_rMd, this->getLastRegistrationTime(), description);
std::map<QString,DataPtr> data = mPatientModelService->getData();
// update the transform on all target data:
for (std::map<QString,DataPtr>::iterator iter = data.begin(); iter!=data.end(); ++iter)
{
DataPtr current = iter->second;
RegistrationTransform newTransform = regTrans;
newTransform.mValue = regTrans.mValue * current->get_rMd();
current->get_rMd_History()->updateRegistration(oldTime, newTransform);
report("Updated registration of data " + current->getName());
std::cout << "rMd_new\n" << newTransform.mValue << std::endl;
}
this->setLastRegistrationTime(regTrans.mTimestamp);
reportSuccess("Patient Orientation has been performed");
}
void LandmarkRegistrationWidget::updateAverageAccuracyLabel()
{
QString fixedName;
DataPtr fixedData = boost::dynamic_pointer_cast<Data>(mServices->registration()->getFixedData());
if (fixedData)
fixedName = fixedData->getName();
if(this->isAverageAccuracyValid())
{
mAvarageAccuracyLabel->setText(tr("Mean accuracy %1 mm").arg(this->getAverageAccuracy(), 0, 'f', 2));
mAvarageAccuracyLabel->setToolTip(QString("Average landmark accuracy from target [%1] to fixed [%2].").arg(this->getTargetName()).arg(fixedName));
}
else
{
mAvarageAccuracyLabel->setText(" ");
mAvarageAccuracyLabel->setToolTip("");
}
}
void DataManagerImpl::loadData(DataPtr data)
{
if (data->getUid().contains('%'))
{
QString uid = data->getUid();
QString name = data->getName();
this->generateUidAndName(&uid, &name);
data->setName(name);
data->setUid(uid);
}
if (data)
{
if (mData.count(data->getUid()) && mData[data->getUid()]!=data)
reportError(QString("Overwriting Data with uid=%1 with new object into PasM").arg(data->getUid()));
// this->verifyParentFrame(data);
mData[data->getUid()] = data;
emit dataAddedOrRemoved();
}
}
void ClipperWidget::createNewCheckboxesBasedOnData()
{
std::map<QString, DataPtr> datas = this->getDatas();
std::map<QString, DataPtr>::iterator iter = datas.begin();
int row = 0;
for(; iter != datas.end(); ++iter)
{
DataPtr data = iter->second;
QCheckBox *checkbox = new QCheckBox();
checkbox->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Fixed);
mDataTableWidget->setCellWidget(row, 0, checkbox);
QTableWidgetItem *descriptionItem = new QTableWidgetItem(data->getName());
mDataTableWidget->setItem(row++, 1, descriptionItem);
boost::function<void()> func = boost::bind(&ClipperWidget::dataSelectorClicked, this, checkbox, data);
connect(checkbox, &QCheckBox::clicked, this, func);
this->updateCheckBoxFromClipper(checkbox, data);
}
}
void RegistrationImplService::doFastRegistration_Translation()
{
DataPtr fixedImage = this->getFixedData();
if(!fixedImage)
{
reportError("The fixed data is not set, cannot do image registration!");
return;
}
LandmarkMap fixedLandmarks = fixedImage->getLandmarks()->getLandmarks();
LandmarkMap toolLandmarks = mPatientModelService->getPatientLandmarks()->getLandmarks();
this->writePreLandmarkRegistration(fixedImage->getName(), fixedImage->getLandmarks()->getLandmarks());
this->writePreLandmarkRegistration("physical", toolLandmarks);
std::vector<QString> landmarks = this->getUsableLandmarks(fixedLandmarks, toolLandmarks);
Transform3D rMd = fixedImage->get_rMd();
Transform3D rMpr_old = mPatientModelService->get_rMpr();
std::vector<Vector3D> p_pr_old = this->convertAndTransformToPoints(landmarks, fixedLandmarks, rMpr_old.inv()*rMd);
std::vector<Vector3D> p_pr_new = this->convertAndTransformToPoints(landmarks, toolLandmarks, Transform3D::Identity());
// ignore if too few data.
if (p_pr_old.size() < 1)
return;
LandmarkTranslationRegistration landmarkTransReg;
bool ok = false;
Transform3D pr_oldMpr_new = landmarkTransReg.registerPoints(p_pr_old, p_pr_new, &ok);
if (!ok)
{
reportError("Fast translation registration: Failed to register: [" + qstring_cast(p_pr_old.size()) + "points]");
return;
}
this->applyPatientRegistration(rMpr_old*pr_oldMpr_new, "Fast Translation");
}
void RegistrationImplService::doImageRegistration(bool translationOnly)
{
//check that the fixed data is set
DataPtr fixedImage = this->getFixedData();
if(!fixedImage)
{
reportError("The fixed data is not set, cannot do landmark image registration!");
return;
}
//check that the moving data is set
DataPtr movingImage = this->getMovingData();
if(!movingImage)
{
reportError("The moving data is not set, cannot do landmark image registration!");
return;
}
// ignore self-registration, this gives no effect bestcase, buggy behaviour worstcase (has been observed)
if(movingImage==fixedImage)
{
reportError("The moving and fixed are equal, ignoring landmark image registration!");
return;
}
LandmarkMap fixedLandmarks = fixedImage->getLandmarks()->getLandmarks();
LandmarkMap imageLandmarks = movingImage->getLandmarks()->getLandmarks();
this->writePreLandmarkRegistration(fixedImage->getName(), fixedImage->getLandmarks()->getLandmarks());
this->writePreLandmarkRegistration(movingImage->getName(), movingImage->getLandmarks()->getLandmarks());
std::vector<QString> landmarks = getUsableLandmarks(fixedLandmarks, imageLandmarks);
vtkPointsPtr p_fixed_r = convertTovtkPoints(landmarks, fixedLandmarks, fixedImage->get_rMd());
vtkPointsPtr p_moving_r = convertTovtkPoints(landmarks, imageLandmarks, movingImage->get_rMd());
int minNumberOfPoints = 3;
if (translationOnly)
minNumberOfPoints = 1;
// ignore if too few data.
if (p_fixed_r->GetNumberOfPoints() < minNumberOfPoints)
{
reportError(
QString("Found %1 corresponding landmarks, need %2, cannot do landmark image registration!")
.arg(p_fixed_r->GetNumberOfPoints())
.arg(minNumberOfPoints)
);
return;
}
bool ok = false;
QString idString;
Transform3D delta;
if (translationOnly)
{
LandmarkTranslationRegistration landmarkTransReg;
delta = landmarkTransReg.registerPoints(convertVtkPointsToPoints(p_fixed_r), convertVtkPointsToPoints(p_moving_r), &ok);
idString = QString("Image to Image Landmark Translation");
}
else
{
Transform3D rMd;
delta = this->performLandmarkRegistration(p_moving_r, p_fixed_r, &ok);
idString = QString("Image to Image Landmark");
}
if (!ok)
{
reportError("I-I Landmark registration: Failed to register: [" + qstring_cast(p_moving_r->GetNumberOfPoints()) + "p], "+ movingImage->getName());
return;
}
this->applyImage2ImageRegistration(delta, idString);
}
void LandmarkRegistrationWidget::prePaintEvent()
{
mLandmarkTableWidget->blockSignals(true);
mLandmarkTableWidget->clear();
QString fixedName;
DataPtr fixedData = boost::dynamic_pointer_cast<Data>(mServices->registration()->getFixedData());
if (fixedData)
fixedName = fixedData->getName();
std::vector<Landmark> landmarks = this->getAllLandmarks();
LandmarkMap targetData = this->getTargetLandmarks();
Transform3D rMtarget = this->getTargetTransform();
//ready the table widget
mLandmarkTableWidget->setRowCount((int)landmarks.size());
mLandmarkTableWidget->setColumnCount(4);
QStringList headerItems(QStringList() << "Name" << "Status" << "Coordinates" << "Accuracy (mm)");
mLandmarkTableWidget->setHorizontalHeaderLabels(headerItems);
mLandmarkTableWidget->horizontalHeader()->setSectionResizeMode(QHeaderView::ResizeToContents);
mLandmarkTableWidget->setSelectionBehavior(QAbstractItemView::SelectRows);
for (unsigned i = 0; i < landmarks.size(); ++i)
{
std::vector<QTableWidgetItem*> items(4); // name, status, coordinates, accuracy
LandmarkProperty prop = mServices->patient()->getLandmarkProperties()[landmarks[i].getUid()];
Vector3D coord = landmarks[i].getCoord();
coord = rMtarget.coord(coord); // display coordinates in space r (in principle, this means all coords should be equal)
items[0] = new QTableWidgetItem(qstring_cast(prop.getName()));
items[0]->setToolTip(QString("Landmark name. Double-click to rename."));
items[1] = new QTableWidgetItem;
if (prop.getActive())
items[1]->setCheckState(Qt::Checked);
else
items[1]->setCheckState(Qt::Unchecked);
items[1]->setToolTip(QString("Check to use landmark in current registration."));
QString coordText = "Not sampled";
if (targetData.count(prop.getUid()))
{
int width = 5;
int prec = 1;
coordText = tr("(%1, %2, %3)").arg(coord[0], width, 'f', prec).arg(coord[1], width, 'f', prec).arg(
coord[2], width, 'f', prec);
}
items[2] = new QTableWidgetItem(coordText);
items[2]->setToolTip(QString("Landmark coordinates of target [%1] in reference space.").arg(this->getTargetName()));
items[3] = new QTableWidgetItem(tr("%1").arg(this->getAccuracy(landmarks[i].getUid())));
items[3]->setToolTip(QString("Distance from target [%1] to fixed [%2].").arg(this->getTargetName()).arg(fixedName));
for (unsigned j = 0; j < items.size(); ++j)
{
items[j]->setData(Qt::UserRole, qstring_cast(prop.getUid()));
mLandmarkTableWidget->setItem(i, j, items[j]);
}
//highlight selected row
if (prop.getUid() == mActiveLandmark)
{
mLandmarkTableWidget->setCurrentItem(items[2]);
}
}
this->updateAverageAccuracyLabel();
mLandmarkTableWidget->blockSignals(false);
}