cxtestSyntheticVolumeComparer.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 "cxtestSyntheticVolumeComparer.h"
#include "cxVolumeHelpers.h"
#include "catch.hpp"
#include "cxImage.h"
#include "cxtestUtilities.h"
#include <vtkImageData.h>
#include "cxRegistrationTransform.h"
#include <QDir>
#include <QString>
#include "cxTypeConversions.h"
#include "cxFileManagerService.h"

namespace cxtest
{

SyntheticVolumeComparer::SyntheticVolumeComparer() : mVerbose(false)
{
}

void SyntheticVolumeComparer::setPhantom(cx::cxSyntheticVolumePtr phantom)
{
        mPhantom = phantom;
        mNominalImage.reset();
}

void SyntheticVolumeComparer::setTestImage(cx::ImagePtr image)
{
        mTestImage = image;
        mNominalImage.reset();
}

//vtkImageDataPtr Utilities::create3DVtkImageData(Eigen::Array3i dim, const unsigned int voxelValue)
//{
//      return cx::generateVtkImageData(dim, cx::Vector3D(1,1,1), voxelValue);
//}

//cx::ImagePtr Utilities::create3DImage(Eigen::Array3i dim, const unsigned int voxelValue)
//{
//      vtkImageDataPtr vtkImageData = create3DVtkImageData(dim, voxelValue);
//      QString unique_string = qstring_cast(reinterpret_cast<long>(vtkImageData.GetPointer()));
//      QString imagesUid = QString("TESTUID_%2_%1").arg(unique_string);
//      cx::ImagePtr image(new cx::Image(imagesUid, vtkImageData));

//      return image;
//}


cx::ImagePtr SyntheticVolumeComparer::getNominalOutputImage() const
{
        REQUIRE(mTestImage);

        if (!mNominalImage)
        {
                Eigen::Array3i dim(mTestImage->getBaseVtkImageData()->GetDimensions());
                cx::Vector3D spacing(mTestImage->getBaseVtkImageData()->GetSpacing());
                mNominalImage = cxtest::Utilities::create3DImage(dim, spacing, 0);
                mNominalImage->get_rMd_History()->setRegistration(mTestImage->get_rMd());

                mPhantom->fillVolume(mNominalImage);
        }

        return mNominalImage;
}

void SyntheticVolumeComparer::checkRMSBelow(double threshold)
{
        float sse = this->getRMS();
        if (this->getVerbose())
                std::cout << "RMS value: " << sse << std::endl;
        CHECK(sse < threshold);
}

double SyntheticVolumeComparer::getRMS() const
{
        double sse = cx::calculateRMSError(mTestImage->getBaseVtkImageData(), this->getNominalOutputImage()->getBaseVtkImageData());
//      float sse = mPhantom->computeRMSError(mOutputData);
//      std::cout << "RMS value: " << sse << std::endl;
        return sse;
}

void SyntheticVolumeComparer::checkCentroidDifferenceBelow(double val)
{
        cx::Vector3D c_n = calculateCentroid(this->getNominalOutputImage());
        cx::Vector3D c_r = calculateCentroid(mTestImage);

        double difference = (c_n-c_r).norm();

        if (this->getVerbose())
                std::cout << "c_n=[" << c_n << "] c_r=[" << c_r << "] diff=[" << difference << "]" << std::endl;

        CHECK(difference < val);
}

void SyntheticVolumeComparer::checkMassDifferenceBelow(double val)
{
        double v_n = calculateMass(this->getNominalOutputImage());
        double v_r = calculateMass(mTestImage);
        double normalized_difference = fabs(v_n-v_r)/(v_n+v_r);

        if (this->getVerbose())
                std::cout << "v_n=[" << v_n << "] v_r=[" << v_r << "] diff=[" << normalized_difference << "]" << std::endl;

        CHECK(normalized_difference<val);
}

void SyntheticVolumeComparer::checkValueWithin(cx::Vector3D p_r, int lowerLimit, int upperLimit)
{
        int val = this->getValue(mTestImage, p_r);
        if (this->getVerbose())
                std::cout << QString("p_r[%1]=%2, limit=[%3, %4]").arg(qstring_cast(p_r)).arg(val).arg(lowerLimit).arg(upperLimit) << std::endl;
        CHECK(val>=lowerLimit);
        CHECK(val<=upperLimit);
}

double SyntheticVolumeComparer::getValue(cx::ImagePtr image, cx::Vector3D p_r)
{
        vtkImageDataPtr raw = image->getBaseVtkImageData();
        cx::Vector3D p_d = image->get_rMd().inv().coord(p_r);
        Eigen::Array3d spacing(raw->GetSpacing());
        Eigen::Array3i voxel = cx::round(p_r.array() / spacing).cast<int>();
        double val = raw->GetScalarComponentAsDouble(voxel.data()[0],voxel.data()[1],voxel.data()[2], 0);
        return val;
}

void SyntheticVolumeComparer::saveNominalOutputToFile(QString filename, cx::FileManagerServicePtr port)
{
        port->save(this->getNominalOutputImage(), this->addFullPath(filename));
}

void SyntheticVolumeComparer::saveOutputToFile(QString filename, cx::FileManagerServicePtr port)
{
        port->save(mTestImage, this->addFullPath(filename));
}

QString SyntheticVolumeComparer::addFullPath(QString filename)
{
        QDir dir(QDir::homePath() + "/test/");
        dir.mkdir(".");
        QString fullFilename = dir.absoluteFilePath(filename);
        return fullFilename;
}

} // namespace cxtest