cxRegistrationImplService.cpp

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/*=========================================================================
This file is part of CustusX, an Image Guided Therapy Application.

Copyright (c) 2008-2014, SINTEF Department of Medical Technology
All rights reserved.

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modification, are permitted provided that the following conditions are met:

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   this list of conditions and the following disclaimer.

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   may be used to endorse or promote products derived from this software 
   without specific prior written permission.

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#include "cxRegistrationImplService.h"

#include <ctkPluginContext.h>
#include <ctkServiceTracker.h>
#include <vtkPoints.h>
#include <vtkLandmarkTransform.h>
#include <vtkMatrix4x4.h>

#include "cxData.h"
#include "cxTypeConversions.h"
#include "cxLogger.h"
#include "cxRegistrationTransform.h"
#include "cxFrameForest.h"
#include "cxPatientModelService.h"
#include "cxRegistrationApplicator.h"
#include "cxLandmark.h"
#include "cxPatientModelServiceProxy.h"
#include "cxLandmarkTranslationRegistration.h"
#include "cxSessionStorageServiceProxy.h"
#include "cxXMLNodeWrapper.h"

namespace cx
{

RegistrationImplService::RegistrationImplService(ctkPluginContext *context) :
        mLastRegistrationTime(QDateTime::currentDateTime()),
        mContext(context),
        mPatientModelService(new PatientModelServiceProxy(context)),
        mSession(SessionStorageServiceProxy::create(context))
{
        connect(mSession.get(), &SessionStorageService::cleared, this, &RegistrationImplService::clearSlot);
    connect(mSession.get(), &SessionStorageService::isLoadingSecond, this, &RegistrationImplService::duringLoadPatientSlot);
        connect(mSession.get(), &SessionStorageService::isSaving, this, &RegistrationImplService::duringSavePatientSlot);
}

RegistrationImplService::~RegistrationImplService()
{
}

void RegistrationImplService::duringSavePatientSlot(QDomElement& node)
{
        XMLNodeAdder root(node);
        QDomElement managerNode = root.descend("managers").node().toElement();
        this->addXml(managerNode);
}

void RegistrationImplService::duringLoadPatientSlot(QDomElement& node)
{
        XMLNodeParser root(node);
        QDomElement registrationManager = root.descend("managers/registrationManager").node().toElement();
        if (!registrationManager.isNull())
                this->parseXml(registrationManager);
}

void RegistrationImplService::addXml(QDomNode& parentNode)
{
        QDomDocument doc = parentNode.ownerDocument();
        QDomElement base = doc.createElement("registrationManager");
        parentNode.appendChild(base);

        QDomElement fixedDataNode = doc.createElement("fixedDataUid");
        DataPtr fixedData = this->getFixedData();
        if(fixedData)
        {
                fixedDataNode.appendChild(doc.createTextNode(fixedData->getUid()));
        }
        base.appendChild(fixedDataNode);

        QDomElement movingDataNode = doc.createElement("movingDataUid");
        DataPtr movingData = this->getMovingData();
        if(movingData)
        {
                movingDataNode.appendChild(doc.createTextNode(movingData->getUid()));
        }
        base.appendChild(movingDataNode);
}

void RegistrationImplService::parseXml(QDomNode& dataNode)
{
        QString fixedData = dataNode.namedItem("fixedDataUid").toElement().text();
        this->setFixedData(fixedData);

        QString movingData = dataNode.namedItem("movingDataUid").toElement().text();
        this->setMovingData(movingData);
}

void RegistrationImplService::clearSlot()
{
        this->setLastRegistrationTime(QDateTime());
        this->setFixedData(DataPtr());
}

void RegistrationImplService::setMovingData(DataPtr data)
{
        this->setMovingData((data) ? data->getUid() : "");
}

void RegistrationImplService::setFixedData(DataPtr data)
{
        this->setFixedData((data) ? data->getUid() : "");
}

void RegistrationImplService::setMovingData(QString uid)
{
        if (uid==mMovingData)
                return;
        mMovingData = uid;
        emit movingDataChanged(mMovingData);
}

void RegistrationImplService::setFixedData(QString uid)
{
        if (uid==mFixedData)
                return;
        mFixedData = uid;
        emit fixedDataChanged(mFixedData);
}

DataPtr RegistrationImplService::getMovingData()
{
        return mPatientModelService->getData(mMovingData);
}

DataPtr RegistrationImplService::getFixedData()
{
        return mPatientModelService->getData(mFixedData);
}

QDateTime RegistrationImplService::getLastRegistrationTime()
{
        return mLastRegistrationTime;
}

void RegistrationImplService::setLastRegistrationTime(QDateTime time)
{
        mLastRegistrationTime = time;
}

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->addPatientRegistration(rMpr, "Patient Landmark");
}

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->addPatientRegistration(rMpr_old*pr_oldMpr_new, "Fast Translation");
}

void RegistrationImplService::doFastRegistration_Orientation(const Transform3D& tMtm, const Transform3D& prMt)
{
        //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();

        Transform3D tmMpr = tMtm * tMpr;

        this->addPatientRegistration(tmMpr, "Fast Orientation");

        // also apply the fast translation registration if any (this frees us form doing stuff in a well-defined order.)
        this->doFastRegistration_Translation();
}

std::vector<Vector3D> RegistrationImplService::convertAndTransformToPoints(const std::vector<QString>& uids, const LandmarkMap& data, Transform3D M)
{
        std::vector<Vector3D> retval;

        for (unsigned i=0; i<uids.size(); ++i)
        {
                QString uid = uids[i];
                Vector3D p = M.coord(data.find(uid)->second.getCoord());
                retval.push_back(p);
        }
        return retval;
}

std::vector<QString> RegistrationImplService::getUsableLandmarks(const LandmarkMap& data_a, const LandmarkMap& data_b)
{
        std::vector<QString> retval;
        std::map<QString, LandmarkProperty> props = mPatientModelService->getLandmarkProperties();
        std::map<QString, LandmarkProperty>::iterator iter;

        for (iter=props.begin(); iter!=props.end(); ++iter)
        {
                QString uid = iter->first;
                if (data_a.count(uid) && data_b.count(uid) && iter->second.getActive())
                        retval.push_back(uid);
        }
        return retval;
}

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
        {
                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->addImage2ImageRegistration(delta, idString);
}

std::vector<Vector3D> RegistrationImplService::convertVtkPointsToPoints(vtkPointsPtr base)
{
        std::vector<Vector3D> retval;

        for (int i=0; i<base->GetNumberOfPoints(); ++i)
        {
                Vector3D p(base->GetPoint(i));
                retval.push_back(p);
        }
        return retval;
}

Transform3D RegistrationImplService::performLandmarkRegistration(vtkPointsPtr source, vtkPointsPtr target, bool* ok) const
{
        *ok = false;

        // too few data samples: ignore
        if (source->GetNumberOfPoints() < 3)
        {
                return Transform3D::Identity();
        }

        vtkLandmarkTransformPtr landmarktransform = vtkLandmarkTransformPtr::New();
        landmarktransform->SetSourceLandmarks(source);
        landmarktransform->SetTargetLandmarks(target);
        landmarktransform->SetModeToRigidBody();
        source->Modified();
        target->Modified();
        landmarktransform->Update();

        Transform3D tar_M_src(landmarktransform->GetMatrix());

        if (QString::number(tar_M_src(0,0))=="nan") // harry but quick way to check badness of transform...
        {
                return Transform3D::Identity();
        }

        *ok = true;
        return tar_M_src;
}

void RegistrationImplService::addImage2ImageRegistration(Transform3D dMd, QString description)
{
        this->performImage2ImageRegistration(dMd, description);
}

void RegistrationImplService::updateImage2ImageRegistration(Transform3D dMd, QString description)
{
        this->performImage2ImageRegistration(dMd, description, true);
}

void RegistrationImplService::performImage2ImageRegistration(Transform3D dMd, QString description, bool temporaryRegistration)
{
        RegistrationTransform regTrans(dMd, QDateTime::currentDateTime(), description, temporaryRegistration);
        regTrans.mFixed = mFixedData;
        regTrans.mMoving = mMovingData;

        this->updateRegistration_rMd(mLastRegistrationTime, regTrans, this->getMovingData());

        mLastRegistrationTime = regTrans.mTimestamp;
        if(!temporaryRegistration)
                reportSuccess(QString("Image registration [%1] has been performed on %2").arg(description).arg(regTrans.mMoving) );
}

void RegistrationImplService::addPatientRegistration(Transform3D rMpr_new, QString description)
{
        this->performPatientRegistration(rMpr_new, description);
}

void RegistrationImplService::updatePatientRegistration(Transform3D rMpr_new, QString description)
{
        this->performPatientRegistration(rMpr_new, description, true);
}

void RegistrationImplService::performPatientRegistration(Transform3D rMpr_new, QString description, bool temporaryRegistration)
{
        RegistrationTransform regTrans(rMpr_new, QDateTime::currentDateTime(), description, temporaryRegistration);
        regTrans.mFixed = mFixedData;

        mPatientModelService->updateRegistration_rMpr(mLastRegistrationTime, regTrans);

        mLastRegistrationTime = regTrans.mTimestamp;
        if(!temporaryRegistration)
                reportSuccess(QString("Patient registration [%1] has been performed.").arg(description));
}

void RegistrationImplService::updateRegistration_rMd(QDateTime oldTime, RegistrationTransform dMd, DataPtr data)
{
        RegistrationApplicator applicator(mPatientModelService->getDatas());
        dMd.mMoving = data->getUid();
        applicator.updateRegistration(oldTime, dMd);

        bool silent = dMd.mTemp;
        if(!silent)
                mPatientModelService->autoSave();
}

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->addPatientRegistration(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->getDatas();
        // 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()->addOrUpdateRegistration(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 RegistrationImplService::writePreLandmarkRegistration(QString name, LandmarkMap landmarks)
{
        QStringList lm;
        for (LandmarkMap::iterator iter=landmarks.begin(); iter!=landmarks.end(); ++iter)
        {
                lm << mPatientModelService->getLandmarkProperties()[iter->second.getUid()].getName();
        }

        QString msg = QString("Preparing to register [%1] containing the landmarks: [%2]").arg(name).arg(lm.join(","));
        report(msg);
}

vtkPointsPtr RegistrationImplService::convertTovtkPoints(const std::vector<QString>& uids, const LandmarkMap& data, Transform3D M)
{
        vtkPointsPtr retval = vtkPointsPtr::New();

        for (unsigned i=0; i<uids.size(); ++i)
        {
                QString uid = uids[i];
                Vector3D p = M.coord(data.find(uid)->second.getCoord());
                retval->InsertNextPoint(p.begin());
        }
        return retval;
}

bool RegistrationImplService::isNull()
{
        return false;
}

} /* namespace cx */