cxElastixManager.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 "cxElastixManager.h"
 
#include <QDir>
 
#include "cxTime.h"
#include "cxProfile.h"
#include "cxElastixExecuter.h"
#include "cxSettings.h"
#include "cxRegistrationService.h"
#include "cxRegistrationTransform.h"
#include "cxPatientModelService.h"
#include "cxViewService.h"
#include "cxVolumeHelpers.h"
#include "cxLogger.h"
#include "cxFilePathProperty.h"
#include "cxImage.h"
#include "cxFileManagerService.h"
 
namespace cx
{
 
ElastixManager::ElastixManager(RegServicesPtr services) :
        mServices(services)
{
        mOptions = profile()->getXmlSettings().descend(ElastixParameters::getConfigUid());
 
        mParameters.reset(new ElastixParameters(mOptions));
        connect(mParameters.get(), SIGNAL(elastixParametersChanged()), this, SIGNAL(elastixChanged()));
 
        mDisplayProcessMessages = BoolProperty::initialize("displayProcessMessages",
                "Show Messages",
                "Display messages from the running registration process in CustusX",
                false,
                mOptions.getElement());
 
        mDisableRendering = BoolProperty::initialize("disableRendering",
                "Disable Rendering",
                "Disable rendering while running process.\n"
                "Can be used to avoid clash in GPU usage.",
                false,
                mOptions.getElement());
 
        mExecuter.reset(new ElastixExecuter(services));
        connect(mExecuter.get(), SIGNAL(finished()), this, SLOT(executionFinishedSlot()));
        connect(mExecuter.get(), SIGNAL(aboutToStart()), this, SLOT(preprocessExecuter()));
}
 
ElastixManager::~ElastixManager()
{
}
 
void ElastixManager::execute()
{
        mExecuter->execute();
}
 
void ElastixManager::preprocessExecuter()
{
        QStringList parameterFiles = mParameters->getActiveParameterFiles();
        QString timestamp = QDateTime::currentDateTime().toString(timestampSecondsFormat());
        QDir outDir(mServices->patient()->getActivePatientFolder()+"/"+mParameters->getConfigUid()+"/"+timestamp);
 
        mExecuter->setDisplayProcessMessages(mDisplayProcessMessages->getValue());
        mExecuter->setInput(mParameters->getActiveExecutable()->getEmbeddedPath().getAbsoluteFilepath(),
                                         mServices->registration()->getFixedData(),
                                         mServices->registration()->getMovingData(),
                 outDir.absolutePath(),
                 parameterFiles);
 
        if (mDisableRendering->getValue())
        {
                mServices->view()->enableRender(false);
        }
}
 
void ElastixManager::executionFinishedSlot()
{
        if (mDisableRendering->getValue())
                mServices->view()->enableRender(true);
 
        bool ok = false;
        Transform3D mMf = mExecuter->getAffineResult_mMf(&ok);
 
        if (!ok)
                return;
 
//      std::cout << "ElastixManager::executionFinishedSlot(), Linear Result mMf: \n" << mMf << std::endl;
 
        QStringList parameterFiles = mParameters->getActiveParameterFiles();
        QString desc = QString("Image2Image [exe=%1]").arg(QFileInfo(mParameters->getActiveExecutable()->getValue()).fileName());
        for (unsigned i=0; i<parameterFiles.size(); ++i)
                desc += QString("[par=%1]").arg(QFileInfo(parameterFiles[i]).fileName());
 
        // Start with fMr * D * rMm = fMm'
        // where the lhs is the existing data and the delta that is input to regmanager,
        // and the rhs is the (inverse of the) output from ElastiX.
        // This gives
        // D = rMf * fMm' * mMr
        // as the input to regmanager applyImage2ImageRegistration()
 
        Transform3D delta_pre_rMd =
                mServices->registration()->getFixedData()->get_rMd()
                * mMf.inv()
                * mServices->registration()->getMovingData()->get_rMd().inv();
 
//      std::cout << "ElastixManager::executionFinishedSlot(), delta_pre_rMd: \n" << delta_pre_rMd << std::endl;
//      std::cout << "ElastixManager::executionFinishedSlot(), expected new rMdm: \n" << mServices->registration()->getFixedData()->get_rMd() * mMf.inv() << std::endl;
 
//      mServices->registration()->addImage2ImageRegistration(mMf.inv(), desc);
        mServices->registration()->addImage2ImageRegistration(delta_pre_rMd, desc);
 
        // add nonlinear data AFTER registering - we dont want these data to be double-registered!
        this->addNonlinearData();
}
 
void ElastixManager::addNonlinearData()
{
        bool ok = true;
        QString nonlinearVolumeFilename = mExecuter->getNonlinearResultVolume(&ok);
 
        if (!ok)
                return;
 
        ImagePtr movingImage = boost::dynamic_pointer_cast<Image>(mServices->registration()->getMovingData());
        ImagePtr raw = boost::dynamic_pointer_cast<Image>(mServices->file()->load(nonlinearVolumeFilename, nonlinearVolumeFilename));
 
        if (!raw)
        {
                report(QString("Failed to import nonlinear volume %1").arg(nonlinearVolumeFilename));
                return;
        }
 
        QString uid = movingImage->getUid() + "_nl%1";
        QString name = movingImage->getName()+" nl%1";
 
        ImagePtr nlVolume = createDerivedImage(mServices->patient(),
                                                                                 uid, name,
                                                                                 raw->getBaseVtkImageData(), movingImage);
 
        // volume is resampled into the space of the fixed data:
        nlVolume->get_rMd_History()->setRegistration(mServices->registration()->getFixedData()->get_rMd());
 
        mServices->patient()->insertData(nlVolume);
 
        report(QString("Added volume %1, created by a nonlinear transform").arg(nlVolume->getName()));
}
 
} /* namespace cx */