cxElastixExecuter.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.

Redistribution and use in source and binary forms, with or without 
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, 
   this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, 
   this list of conditions and the following disclaimer in the documentation 
   and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors 
   may be used to endorse or promote products derived from this software 
   without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
=========================================================================*/


#include "cxElastixExecuter.h"

#include <QProcess>
#include <QFile>
#include <QDir>
#include <QtGlobal>

#include "cxTypeConversions.h"
#include "cxTime.h"
#include "cxData.h"
#include "cxBoundingBox3D.h"
#include "cxTransformFile.h"
#include "cxCustomMetaImage.h"

#include "cxPatientModelService.h"

namespace cx
{

ElastixExecuter::ElastixExecuter(RegServicesPtr services, QObject* parent) :
        TimedBaseAlgorithm("ElastiX", 1000),
        mServices(services)
{
        mProcess = new QProcess(this);
        connect(mProcess, SIGNAL(stateChanged(QProcess::ProcessState)), this, SLOT(processStateChanged(QProcess::ProcessState)));
        connect(mProcess, SIGNAL(error(QProcess::ProcessError)), this, SLOT(processError(QProcess::ProcessError)));
        connect(mProcess, SIGNAL(finished(int, QProcess::ExitStatus)), this, SLOT(processFinished(int, QProcess::ExitStatus)));
}

ElastixExecuter::~ElastixExecuter()
{
        disconnect(mProcess, SIGNAL(error(QProcess::ProcessError)), this, SLOT(processError(QProcess::ProcessError)));
        mProcess->close();
}

void ElastixExecuter::setDisplayProcessMessages(bool on)
{
        disconnect(mProcess, SIGNAL(readyRead()), this, SLOT(processReadyRead()));

        if (on)
        {
                connect(mProcess, SIGNAL(readyRead()), this, SLOT(processReadyRead()));
                //      mProcess->setProcessChannelMode(QProcess::ForwardedChannels);
                mProcess->setProcessChannelMode(QProcess::MergedChannels);
                mProcess->setReadChannel(QProcess::StandardOutput);
        }
}


bool ElastixExecuter::setInput(QString application,
                                DataPtr fixed,
                                DataPtr moving,
                                QString outdir,
                                QStringList parameterfiles)
{
        mFixed = fixed;
        mMoving = moving;

        if (!fixed || !moving)
        {
                reportWarning("Failed to start elastiX registration, fixed or missing image missing.");
                return false;
        }

        if (mProcess->state() != QProcess::NotRunning)
        {
                reportWarning("Failed to start elastiX registration, process already running");
                return false;
        }

        // create output dir (required by ElastiX)
        QDir().mkpath(outdir);

        QString initFilename = this->writeInitTransformToElastixfile(fixed, moving, outdir);
        this->writeInitTransformToCalfile(fixed, moving, outdir);

        mLastOutdir = outdir;

        QStringList cmd;
        cmd << "\"" + application + "\"";
        cmd << "-f" << mServices->patient()->getActivePatientFolder()+"/"+fixed->getFilename();
        cmd << "-m" << mServices->patient()->getActivePatientFolder()+"/"+moving->getFilename();
        cmd << "-out" << outdir;
        cmd << "-t0" << initFilename;
        for (int i=0; i<parameterfiles.size(); ++i)
                cmd << "-p" << parameterfiles[i];

        QString commandLine = cmd.join(" ");
        report(QString("Executing registration with command line: [%1]").arg(commandLine));

#ifdef Q_OS_LINUX
        // hack that inserts . into library path for linux. Solveds issue with elastix lib not being fixed up on linux.
        QString path = QFileInfo(application).absolutePath();
        QProcessEnvironment env = QProcessEnvironment::systemEnvironment();
        env.insert("LD_LIBRARY_PATH", path);
        mProcess->setProcessEnvironment(env);
#endif
    mProcess->start(commandLine);
    return true;
}

void ElastixExecuter::execute()
{
        emit aboutToStart(); // if properly set: triggers the setInput()
}

bool ElastixExecuter::isFinished() const
{
        std::cout << "TODO: check ElastixExecuter::isFinished()" << std::endl;
        return mProcess->atEnd();
}

bool ElastixExecuter::isRunning() const
{
        return mProcess->state()!=QProcess::NotRunning;
}

QString ElastixExecuter::writeInitTransformToElastixfile(
        DataPtr fixed,
        DataPtr moving,
        QString outdir)
{
        // elastiX uses the transforms present in the mhd files. If the mhd info is up to date
        // with the dataManager info, the T0=I, i.e we dont need to tell elastiX anything.
        // If NOT up to date, then compare file and dataManager, then insert the difference as T0:
        //
        // Let f be fixed, m be moving, mm and ff be the intermediate spaces between the file and r:
        //      rMd is the transform stored in ssc.
        //              ddMd is the transform stored in the mhd file.
        //              T0 is the remainder to be sent to elastiX
        //
        //              mMf = mMr*rMf = mMmm*mmMr*rMff*ffMf = mMmm*T0*ffMf
        //               -->
        //              T0 = mmMm*mMr*rMf*fMff
        //
        Transform3D rMf = fixed->get_rMd();
        Transform3D rMm = moving->get_rMd();
        Transform3D ffMf = this->getFileTransform_ddMd(mFixed);
        Transform3D mmMm = this->getFileTransform_ddMd(mMoving);
//      Transform3D mMf = rMm.inv() * rMf;
        // -->
        // The remainder transform, not stored in mhd files, must be sent to elastiX:
        Transform3D T0 = mmMm*rMm.inv()*rMf*ffMf.inv();

//      Transform3D mMf = moving->get_rMd().inv() * fixed->get_rMd();
        ElastixEulerTransform E = ElastixEulerTransform::create(T0, fixed->boundingBox().center());

        QString elastiXText = QString(""
                "// Input transform file\n"
                "// Auto-generated by CustusX on %1\n"
                "\n"
                "(Transform \"EulerTransform\")\n"
                "(NumberOfParameters 6)\n"
                "(TransformParameters %2 %3)\n"
                "(InitialTransformParametersFileName \"NoInitialTransform\")\n"
                "(HowToCombineTransforms \"Compose\")\n"
                "\n"
                "// EulerTransform specific\n"
                "(CenterOfRotationPoint %4)\n"
                "(ComputeZYX \"false\")\n"
                "").arg(QDateTime::currentDateTime().toString(timestampSecondsFormatNice()),
                        qstring_cast(E.mAngles_xyz),
                        qstring_cast(E.mTranslation),
                        qstring_cast(E.mCenterOfRotation));

        QFile initTransformFile(outdir+"/t0.txt");
        if (!initTransformFile.open(QIODevice::WriteOnly | QIODevice::Text))
        {
                reportWarning(QString("Failed to open file %1 for writing.").arg(initTransformFile.fileName()));
        }
        initTransformFile.write(elastiXText.toLatin1());
        return initTransformFile.fileName();
}

QString ElastixExecuter::writeInitTransformToCalfile(
        DataPtr fixed,
        DataPtr moving,
        QString outdir)
{
        Transform3D mMf = moving->get_rMd().inv() * fixed->get_rMd();

        TransformFile file(outdir+"/moving_M_fixed_initial.cal");
        file.write(mMf);

        return file.fileName();
}

void ElastixExecuter::processReadyRead()
{
        report(QString(mProcess->readAllStandardOutput()));
}

void ElastixExecuter::processError(QProcess::ProcessError error)
{
        QString msg;
        msg += "Registration process reported an error: ";

        switch (error)
        {
        case QProcess::FailedToStart:
                msg += "Failed to start";
                break;
        case QProcess::Crashed:
                msg += "Crashed";
                break;
        case QProcess::Timedout:
                msg += "Timed out";
                break;
        case QProcess::WriteError:
                msg += "Write Error";
                break;
        case QProcess::ReadError:
                msg += "Read Error";
                break;
        case QProcess::UnknownError:
                msg += "Unknown Error";
                break;
        default:
                msg += "Invalid error";
        }

        reportError(msg);
}

void ElastixExecuter::processFinished(int code, QProcess::ExitStatus status)
{
        if (status == QProcess::CrashExit)
                reportError("Registration process crashed");
}


void ElastixExecuter::processStateChanged(QProcess::ProcessState newState)
{
// removed text: to much information

        QString msg;
        msg += "Registration process";

        if (newState == QProcess::Running)
        {
//              report(msg + " running.");
                emit started(0);
        }
        if (newState == QProcess::NotRunning)
        {
                emit finished();
//              report(msg + " not running.");
        }
        if (newState == QProcess::Starting)
        {
//              report(msg + " starting.");
        }
}

QString ElastixExecuter::findMostRecentTransformOutputFile() const
{
        QString retval;
        for (int i=0; ; ++i)
        {
                QString filename = QString(mLastOutdir + "/TransformParameters.%1.txt").arg(i);
                if (!QFileInfo(filename).exists())
                        break;
                retval = filename;
        }
        return retval;
}

Transform3D ElastixExecuter::getFileTransform_ddMd(DataPtr volume)
{
        QString patFolder = mServices->patient()->getActivePatientFolder();
        CustomMetaImagePtr reader = CustomMetaImage::create(patFolder+"/"+volume->getFilename());
        Transform3D ddMd = reader->readTransform();
        return ddMd;
}

Transform3D ElastixExecuter::getAffineResult_mMf(bool* ok)
{
        Transform3D mmMff = this->getAffineResult_mmMff(ok);
        Transform3D ffMf = this->getFileTransform_ddMd(mFixed);
        Transform3D mmMm = this->getFileTransform_ddMd(mMoving);

        return mmMm.inv() * mmMff * ffMf;
}

Transform3D ElastixExecuter::getAffineResult_mmMff(bool* ok)
{
        QString filename = this->findMostRecentTransformOutputFile();
        Transform3D mMf = Transform3D::Identity();

        if (filename.isEmpty())
        {
                if (ok)
                        *ok = false;

                TransformFile file(mLastOutdir+"/moving_M_fixed_registered.cal");
                mMf = file.read(ok);

                if (ok && !*ok)
                {
                        reportWarning("Failed to read registration results.");
                }

                return mMf;
        }

        while (true)
        {
                ElastixParameterFile file(filename);

                bool useDirectionCosines = file.readParameterBool("UseDirectionCosines");
                if (useDirectionCosines)
                {
                        reportWarning("Elastix UseDirectionCosines is not supported. Result is probably wrong.");
                }

                QString transformType = file.readParameterString("Transform");
                if (transformType=="EulerTransform")
                {
                        if (ok)
                                *ok = true;
                        Transform3D mQf = file.readEulerTransform();
                        // concatenate transforms:
                        mMf = mQf * mMf;
                }
                else if (transformType=="AffineTransform")
                {
                        if (ok)
                                *ok = true;
                        Transform3D mQf = file.readAffineTransform();
                        // concatenate transforms:
                        mMf = mQf * mMf;
                }
                else
                {
                        // accept invalid transforms, but emit warning.
//                      if (ok)
//                              *ok = false;
                        reportWarning(QString("TransformType [%1] is not supported by CustusX. Registration result from %2 ignored.").arg(transformType).arg(filename));
                }

                filename = file.readParameterString("InitialTransformParametersFileName");
                if (filename.isEmpty() || filename=="NoInitialTransform")
                        break;
        }

        return mMf;
}


QString ElastixExecuter::getNonlinearResultVolume(bool* ok)
{
        if (ok)
                *ok = false;

        QString retval;
        int i=0;
        for (; ; ++i)
        {
                //TODO only mhd supported
                QString filename = QString(mLastOutdir + "/result.%1.mhd").arg(i);
                if (!QFileInfo(filename).exists())
                        break;
                retval = filename;
        }

        if (retval.isEmpty())
                return retval;

        QString paramFilename = QString(mLastOutdir + "/TransformParameters.%1.txt").arg(i-1);
        ElastixParameterFile file(paramFilename);
        QString transform = file.readParameterString("Transform");

        if ((transform=="BSplineTransform") || (transform=="SplineKernelTransform"))
        {
                report(QString("Reading result file %1 created with transform %2").arg(retval).arg(transform));
                if (ok)
                        *ok = true;
                return retval;
        }
        else
        {
                return "";
        }

}


// --------------------------------------------------------
// --------------------------------------------------------
// --------------------------------------------------------




Transform3D ElastixParameterFile::readEulerTransform()
{
        QString transformType = this->readParameterString("Transform");
        if (transformType!="EulerTransform")
                reportError("Assert failure: attempting to read EulerTransform");

        int numberOfParameters = this->readParameterInt("NumberOfParameters");
        if (numberOfParameters!=6)
        {
                reportWarning(QString("Expected 6 Euler parameters, got %1").arg(numberOfParameters));
                return Transform3D::Identity();
        }
        std::vector<double> tp = this->readParameterDoubleVector("TransformParameters");
        std::vector<double> cor = this->readParameterDoubleVector("CenterOfRotationPoint");

        ElastixEulerTransform E = ElastixEulerTransform::create(
                Vector3D(tp[0], tp[1], tp[2]),
                Vector3D(tp[3], tp[4], tp[5]),
                Vector3D(cor[0], cor[1], cor[2]));

        return E.toMatrix();
}

Transform3D ElastixParameterFile::readAffineTransform()
{
        QString transformType = this->readParameterString("Transform");
        if (transformType!="AffineTransform")
                reportError("Assert failure: attempting to read AffineTransform");

        int numberOfParameters = this->readParameterInt("NumberOfParameters");
        if (numberOfParameters!=12)
        {
                reportWarning(QString("Expected 12 Euler parameters, got %1").arg(numberOfParameters));
                return Transform3D::Identity();
        }
        std::vector<double> tp = this->readParameterDoubleVector("TransformParameters");
//      std::vector<double> cor = this->readParameterDoubleVector("CenterOfRotationPoint");

        Transform3D M = Transform3D::Identity();

        for (int r=0; r<3; ++r)
                for (int c=0; c<3; ++c)
                        M(r,c) = tp[3*r+c];
        for (int r=0; r<3; ++r)
                M(r,3) = tp[9+r];

        return M;
}

ElastixParameterFile::ElastixParameterFile(QString filename) : mFile(filename)
{
        if (!mFile.open(QIODevice::ReadOnly | QIODevice::Text))
        {
                reportWarning(QString("Can't open ElastiX result file %1").arg(filename));
        }
        mText = QString(mFile.readAll());
//      std::cout << "Loaded text from " << filename << ":\n" << mText << std::endl;
}

QString ElastixParameterFile::readParameterRawValue(QString key)
{
        QStringList lines = mText.split('\n');

        QString regexpStr = QString(""
                "\\s*" // match zero or more whitespace
                "\\("  // match beginning (
                "\\s*" // match zero or more whitespace
                "%1"   // key
                "\\s+" // match one or more whitespace
                "("    // start grab value
                "[^\\)]*" // value - anything up to the closing )
                ")"    // end grab value
                "\\)"  // match ending )
                "[^\\n]*" // rest of line - ignore
                ).arg(key);
        QRegExp rx(regexpStr);
//      std::cout << regexpStr << std::endl;

        lines.indexOf(rx);

//      if (lines.indexOf(rx)>=0)
//      {
//              std::cout << "FOUND0 " << rx.cap(0) << std::endl;
//              std::cout << "FOUND1 " << rx.cap(1) << std::endl;
//      }

        return rx.cap(1);
}

QString ElastixParameterFile::readParameterString(QString key)
{
        QString retval =  this->readParameterRawValue(key);
        if (retval.startsWith("\"") && retval.endsWith("\""))
        {
                retval = retval.replace(0, 1, "");
                retval = retval.replace(retval.size()-1, 1, "");
        }

        return retval;
}

bool ElastixParameterFile::readParameterBool(QString key)
{
        QString text = this->readParameterString(key);
        return (text=="true") ? true : false;
}

int ElastixParameterFile::readParameterInt(QString key)
{
        QString retval =  this->readParameterRawValue(key);
        return retval.toInt();
}

std::vector<double> ElastixParameterFile::readParameterDoubleVector(QString key)
{
        QString retval =  this->readParameterRawValue(key);
        return convertQString2DoubleVector(retval);
}

} /* namespace cx */