cxBronchoscopyRegistrationWidget.cpp

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

Copyright (c) SINTEF Department of Medical Technology.
All rights reserved.

CustusX is released under a BSD 3-Clause license.

See Lisence.txt (https://github.com/SINTEFMedtek/CustusX/blob/master/License.txt) for details.
=========================================================================*/

#include "cxBronchoscopyRegistrationWidget.h"
#include <vtkPolyData.h>
#include "cxTransform3D.h"
#include "cxDataSelectWidget.h"
#include "cxTrackingService.h"
#include "cxMesh.h"
#include "cxSelectDataStringProperty.h"
#include "cxRecordSessionWidget.h"
#include "cxRecordSession.h"
#include "cxView.h"
#include "cxToolRep3D.h"
#include "cxToolTracer.h"
#include "cxBronchoscopyRegistration.h"
#include "cxLogger.h"
#include "cxTypeConversions.h"
#include "cxPatientModelService.h"
#include "cxRegistrationService.h"
#include "cxViewService.h"
#include "cxStringProperty.h"
#include "cxLabeledComboBoxWidget.h"
#include "cxTrackingService.h"
#include "cxDoubleProperty.h"
#include "cxProfile.h"
#include "cxHelperWidgets.h"
#include "cxBoolProperty.h"
#include "cxCheckBoxWidget.h"
#include "cxRepContainer.h"
#include "cxWidgetObscuredListener.h"
#include "cxViewGroupData.h"
#include "cxStringPropertySelectTool.h"
#include "cxHelperWidgets.h"
#include "cxAcquisitionService.h"
#include "cxRegServices.h"
#include "cxRecordTrackingWidget.h"


namespace cx
{
BronchoscopyRegistrationWidget::BronchoscopyRegistrationWidget(RegServicesPtr services, QWidget* parent) :
        RegistrationBaseWidget(services, parent, "org_custusx_registration_method_bronchoscopy_widget",
                                                                                                 "Bronchoscopy Registration"),
        mBronchoscopyRegistration(new BronchoscopyRegistration()),
        mServices(services),
        mRecordTrackingWidget(NULL)
{
        mVerticalLayout = new QVBoxLayout(this);
}

void BronchoscopyRegistrationWidget::prePaintEvent()
{
        if (!mRecordTrackingWidget)
        {
                this->setup();
        }
}

void BronchoscopyRegistrationWidget::setup()
{
        mOptions = profile()->getXmlSettings().descend("bronchoscopyregistrationwidget");

        mSelectMeshWidget = StringPropertySelectMesh::New(mServices->patient());
        mSelectMeshWidget->setValueName("Centerline: ");

        //this->initializeTrackingService();

        connect(mServices->patient().get(),&PatientModelService::patientChanged,this,&BronchoscopyRegistrationWidget::clearDataOnNewPatient);

        mProcessCenterlineButton = new QPushButton("Process centerline");
        connect(mProcessCenterlineButton, SIGNAL(clicked()), this, SLOT(processCenterlineSlot()));
        mProcessCenterlineButton->setToolTip(this->defaultWhatsThis());

        //      mBronchoscopeRegistrationPtr = BronchoscopeRegistrationPtr(new BronchoscopePositionProjection());
        //      mProjectionCenterlinePtr->createMaxDistanceToCenterlineOption(mOptions.getElement());

        mRegisterButton = new QPushButton("Register");
        connect(mRegisterButton, SIGNAL(clicked()), this, SLOT(registerSlot()));
        mRegisterButton->setToolTip(this->defaultWhatsThis());

        mRecordTrackingWidget = new RecordTrackingWidget(mOptions.descend("recordTracker"),
                                                                                                                                                                                                         mServices->acquisition(), mServices,
                                                                                                                                                                                                         "bronc_path",
                                                                                                                                                                                                         this);
        mRecordTrackingWidget->getSessionSelector()->setHelp("Select bronchoscope path for registration");
        mRecordTrackingWidget->getSessionSelector()->setDisplayName("Bronchoscope path");

        mVerticalLayout->setMargin(0);
        mVerticalLayout->addWidget(new DataSelectWidget(mServices->view(), mServices->patient(), this, mSelectMeshWidget));

        this->selectSubsetOfBranches(mOptions.getElement());
        this->createMaxNumberOfGenerations(mOptions.getElement());
        this->useEBUSprobe(mOptions.getElement());
        this->useLocalRegistration(mOptions.getElement());
        this->createMaxLocalRegistrationDistance(mOptions.getElement());

        //      PropertyPtr maxLocalRegistrationDistance = mProjectionCenterlinePtr->getMaxLocalRegistrationDistanceOption();

        mVerticalLayout->addWidget(new CheckBoxWidget(this, mUseSubsetOfGenerations));
        mVerticalLayout->addWidget(createDataWidget(mServices->view(), mServices->patient(), this, mMaxNumberOfGenerations));
        mVerticalLayout->addWidget(mProcessCenterlineButton);
        mVerticalLayout->addWidget(new CheckBoxWidget(this, mUseEBUSProbe));
        mVerticalLayout->addWidget(mRecordTrackingWidget);
        mVerticalLayout->addWidget(new CheckBoxWidget(this, mUseLocalRegistration));
        mVerticalLayout->addWidget(createDataWidget(mServices->view(), mServices->patient(), this, mMaxLocalRegistrationDistance));
        mVerticalLayout->addWidget(mRegisterButton);

        mVerticalLayout->addStretch();
}

QString BronchoscopyRegistrationWidget::defaultWhatsThis() const
{
        return QString();
}

void BronchoscopyRegistrationWidget::initializeTrackingService()
{
        if(mServices->tracking()->getState() < Tool::tsCONFIGURED)
                mServices->tracking()->setState(Tool::tsCONFIGURED);
}

void BronchoscopyRegistrationWidget::processCenterlineSlot()
{
        this->initializeTrackingService();

        if(!mSelectMeshWidget->getMesh())
        {
                reportError("No centerline");
                return;
        }
        vtkPolyDataPtr centerline = mSelectMeshWidget->getMesh()->getVtkPolyData();//input
        Transform3D rMd = mSelectMeshWidget->getMesh()->get_rMd();
        vtkPolyDataPtr processedCenterline;
        if (mUseSubsetOfGenerations->getValue())
                processedCenterline = mBronchoscopyRegistration->processCenterline(centerline, rMd, mMaxNumberOfGenerations->getValue());
        else
                processedCenterline = mBronchoscopyRegistration->processCenterline(centerline, rMd);

        if (!mMesh)
        {
                QString uid = mSelectMeshWidget->getMesh()->getUid() + "_cl%1";
                QString name = mSelectMeshWidget->getMesh()->getName()+" cl_processed%1";
                std::cout << "name: " << name << std::endl;
                std::cout << "uid: " << uid << std::endl;
                mMesh = mServices->patient()->createSpecificData<Mesh>(uid, name);
        }
        mMesh->setVtkPolyData(processedCenterline);
        mMesh->setColor(QColor(0, 0, 255, 255));
        mServices->patient()->insertData(mMesh);
        mServices->view()->autoShowData(mMesh);
}

void BronchoscopyRegistrationWidget::registerSlot()
{
        if(!mBronchoscopyRegistration->isCenterlineProcessed())
        {
                reportError("Centerline not processed");
                return;
        }

        Transform3D old_rMpr = mServices->patient()->get_rMpr();//input to registrationAlgorithm
        //std::cout << "rMpr: " << std::endl;
        //std::cout << old_rMpr << std::endl;

        TimedTransformMap trackerRecordedData;
        if(mUseEBUSProbe->getValue())
                trackerRecordedData = mRecordTrackingWidget->getRecordedTrackerData_prMs();
        else
                trackerRecordedData = mRecordTrackingWidget->getRecordedTrackerData_prMt();

        if(trackerRecordedData.empty())
        {
                reportError("No positions");
                return;
        }

        Transform3D new_rMpr;

        if(mUseLocalRegistration->getValue()){
                std::cout << "Running local registration with max distance " << mMaxLocalRegistrationDistance->getValue() << " mm." << std::endl;
                new_rMpr = Transform3D(mBronchoscopyRegistration->runBronchoscopyRegistration(trackerRecordedData,old_rMpr,mMaxLocalRegistrationDistance->getValue()));
        }
        else{
                std::cout << "Running global registration." << std::endl;
                new_rMpr = Transform3D(mBronchoscopyRegistration->runBronchoscopyRegistration(trackerRecordedData,old_rMpr,0));
        }

        new_rMpr = new_rMpr*old_rMpr;//output
        mServices->registration()->addPatientRegistration(new_rMpr, "Bronchoscopy centerline to tracking data");

        Eigen::Matrix4d display_rMpr = Eigen::Matrix4d::Identity();
        display_rMpr = new_rMpr*display_rMpr;
        std::cout << "New prMt: " << std::endl;
        for (int i = 0; i < 4; i++)
                std::cout << display_rMpr.row(i) << std::endl;

        //      mRecordTrackingWidget->showSelectedRecordingInView();

}

void BronchoscopyRegistrationWidget::createMaxNumberOfGenerations(QDomElement root)
{
        mMaxNumberOfGenerations = DoubleProperty::initialize("Max number of generations in centerline", "",
                                                                                                                                                                                                                         "Set max number of generations centerline", 4, DoubleRange(0, 10, 1), 0,
                                                                                                                                                                                                                         root);
        mMaxNumberOfGenerations->setGuiRepresentation(DoublePropertyBase::grSLIDER);
}

void BronchoscopyRegistrationWidget::selectSubsetOfBranches(QDomElement root)
{
        mUseSubsetOfGenerations = BoolProperty::initialize("Select branch generations to be used in registration", "",
                                                                                                                                                                                                                 "Select branch generations to be used in registration", false,
                                                                                                                                                                                                                 root);
}

void BronchoscopyRegistrationWidget::useEBUSprobe(QDomElement root)
{
        mUseEBUSProbe = BoolProperty::initialize("EBUS probe", "",
                                                                                                                                                                                                                 "Select if EBUS probe is used registration (using prMs to exclude probe calibration)", false,
                                                                                                                                                                                                                 root);
}

void BronchoscopyRegistrationWidget::useLocalRegistration(QDomElement root)
{
        mUseLocalRegistration = BoolProperty::initialize("Use local registration", "",
                                                                                                                                                                                                         "Use local registration", false,
                                                                                                                                                                                                         root);
}

void BronchoscopyRegistrationWidget::createMaxLocalRegistrationDistance(QDomElement root)
{
        mMaxLocalRegistrationDistance = DoubleProperty::initialize("Max local registration distance (mm)", "",
                                                                                                                                                                                                                                                 "Set max distance for local registration in mm", 30, DoubleRange(1, 200, 1), 0,
                                                                                                                                                                                                                                                 root);
        mMaxLocalRegistrationDistance->setGuiRepresentation(DoubleProperty::grSLIDER);
}

void BronchoscopyRegistrationWidget::clearDataOnNewPatient()
{
        mMesh.reset();
}
} //namespace cx