cxtestSyntheticReconstructInput.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 "cxtestSyntheticReconstructInput.h"
#include "cxDummyTool.h"
#include "cxSimpleSyntheticVolume.h"
#include "cxtestSphereSyntheticVolume.h"
#include "cxTypeConversions.h"
#include "cxMathUtils.h"


namespace cxtest
{

SyntheticReconstructInput::SyntheticReconstructInput()
{
        mBounds = cx::Vector3D(99,99,99);

        mProbeMovementDefinition.mRangeNormalizedTranslation = cx::Vector3D::UnitX();
//      mProbeMovementDefinition.mRangeAngle = M_PI/8;
//      mProbeMovementDefinition.mSteps = 100;
        mProbeMovementDefinition.mRangeAngle = 0;
        mProbeMovementDefinition.mSteps = 200;

        mProbe = cx::DummyToolTestUtilities::createProbeDefinitionLinear(100, 100, Eigen::Array2i(200,200));
}

void SyntheticReconstructInput::defineProbeMovementNormalizedTranslationRange(double range)
{
        mProbeMovementDefinition.mRangeNormalizedTranslation = cx::Vector3D::UnitX() * range;
}
void SyntheticReconstructInput::defineProbeMovementAngleRange(double range)
{
        mProbeMovementDefinition.mRangeAngle = range;
}
void SyntheticReconstructInput::defineProbeMovementSteps(int steps)
{
        mProbeMovementDefinition.mSteps = steps;
}
void SyntheticReconstructInput::defineProbe(cx::ProbeDefinition probe)
{
        mProbe = probe;
}

void SyntheticReconstructInput::setOverallBoundsAndSpacing(double size, double spacing)
{
        // factors controlling sample rate:
        //  - output volume spacing
        //  - probe plane in-plane spacing
        //  - probe planes spacing (between the planes)
        //
        // set all these rates to the input spacing:

        mBounds = cx::Vector3D::Ones() * size;
        mProbe = cx::DummyToolTestUtilities::createProbeDefinitionLinear(size, size, Eigen::Array2i(1,1)*(int(cx::roundAwayFromZero(size/spacing))+1));
        mProbeMovementDefinition.mRangeNormalizedTranslation = cx::Vector3D::UnitX();
        mProbeMovementDefinition.mRangeAngle = 0;
        mProbeMovementDefinition.mSteps = size/spacing+1;
}

void SyntheticReconstructInput::printConfiguration()
{
        QString indent("");
        mPhantom->printInfo();
        std::cout << indent << "Probe:\n" << streamXml2String(mProbe) << std::endl;
        std::cout << indent << "ProbeMovement RangeNormalizedTranslation: " << mProbeMovementDefinition.mRangeNormalizedTranslation << std::endl;
        std::cout << indent << "ProbeMovement RangeAngle: " << mProbeMovementDefinition.mRangeAngle << std::endl;
        std::cout << indent << "ProbeMovement Steps: " << mProbeMovementDefinition.mSteps<< std::endl;
}

void SyntheticReconstructInput::setBoxAndLinesPhantom()
{
        mPhantom.reset(new cx::cxSimpleSyntheticVolume(mBounds));
}

void SyntheticReconstructInput::setSpherePhantom()
{
        mPhantom.reset(new cxtest::SphereSyntheticVolume(mBounds));
}

void SyntheticReconstructInput::setWireCrossPhantom()
{

}

std::vector<cx::Transform3D> SyntheticReconstructInput::generateFrames_rMt_tilted()
{
        cx::Vector3D p0(mBounds[0]/2, mBounds[1]/2, 0); //probe starting point. pointing along z
        cx::Vector3D range_translation = mBounds[0] * mProbeMovementDefinition.mRangeNormalizedTranslation;
        double range_angle = mProbeMovementDefinition.mRangeAngle;
        int steps = mProbeMovementDefinition.mSteps;

        // generate transforms from tool to reference.
        return this->generateFrames(p0,
                                                                range_translation,
                                                                range_angle,
                                                                Eigen::Vector3d::UnitY(),
                                                                steps);
}

std::vector<cx::Transform3D> SyntheticReconstructInput::generateFrames(cx::Vector3D p0,
                                                                                                                                                 cx::Vector3D range_translation,
                                                                                                                                                 double range_angle,
                                                                                                                                                 cx::Vector3D rotation_axis,
                                                                                                                                                 int steps)
{
        // generate transforms from tool to reference.
        std::vector<cx::Transform3D> planes;
        for(int i = 0; i < steps; ++i)
        {
                double R = steps-1;
                double t = (i-R/2)/R; // range [-0.5 .. 0.5]
                cx::Transform3D transform = cx::Transform3D::Identity();
                transform.translation() = p0 + range_translation*t;
                transform.rotate(Eigen::AngleAxisd(t*range_angle, rotation_axis));
                planes.push_back(transform);
        }
        return planes;
}

cx::USReconstructInputData SyntheticReconstructInput::generateSynthetic_USReconstructInputData()
{
        cx::Vector3D p0(mBounds[0]/2, mBounds[1]/2, 0); //probe starting point. pointing along z
        cx::Vector3D range_translation = mBounds[0] * mProbeMovementDefinition.mRangeNormalizedTranslation;
        double range_angle = mProbeMovementDefinition.mRangeAngle;
        int steps_full = 3*mProbeMovementDefinition.mSteps;

        // generate oversampled list of positions, for use both in tracking and imaging.
        std::vector<cx::Transform3D> rMt_full;
        rMt_full = this->generateFrames(p0,
                                                                        range_translation,
                                                                        range_angle,
                                                                        Eigen::Vector3d::UnitY(),
                                                                        steps_full);

        cx::USReconstructInputData result;

        // sample out tracking positions from the full list
        for (unsigned i=0; i<steps_full; i+=2)
        {
                cx::TimedPosition pos;
                pos.mTime = i;
                pos.mPos = rMt_full[i]; // TODO: skrell av rMpr
                result.mPositions.push_back(pos);
        }

        // sample out image frames from the full list
        std::vector<vtkImageDataPtr> frames;
        for (unsigned i=0; i<steps_full; i+=3)
        {
                cx::TimedPosition pos;
                pos.mTime = i;
                result.mFrames.push_back(pos);

                frames.push_back(mPhantom->sampleUsData(rMt_full[i], mProbe));
        }
        result.mUsRaw = cx::USFrameData::create("virtual", frames);

        // fill rest of info
        result.rMpr = cx::Transform3D::Identity(); // if <>Identity, remember to also change mPositions
        result.mProbeUid = "testProbe";
        result.mProbeDefinition.setData(mProbe);

        return result;
}

cx::ProcessedUSInputDataPtr SyntheticReconstructInput::generateSynthetic_ProcessedUSInputData(cx::Transform3D dMr)
{
        std::vector<cx::Transform3D> planes = this->generateFrames_rMt_tilted();
//      std::cout << "Starting sampling\n";
        cx::ProcessedUSInputDataPtr retval;
        retval = mPhantom->sampleUsData(planes, mProbe, dMr);
//      std::cout << "Done sampling\n";
        return retval;
}


} // namespace cxtest