cxReconstructCore.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 "cxReconstructCore.h"
#include <vtkImageData.h>
#include "cxTime.h"
#include "cxTypeConversions.h"
#include "cxRegistrationTransform.h"
#include "cxVolumeHelpers.h"
#include "cxTransferFunctions3DPresets.h"
#include "cxTimeKeeper.h"
#include "cxLogger.h"
#include "cxUSFrameData.h"
#include "cxReconstructionMethodService.h"
#include "vtkPointData.h"
#include "vtkDataArray.h"
#include "cxPatientModelService.h"

namespace cx
{


ReconstructCore::ReconstructCore(cx::PatientModelServicePtr patientModelService) :
        mInput(InputParams()),
        mPatientModelService(patientModelService)
{
//      mMaxTimeDiff = 100; // TODO: Change default value for max allowed time difference between tracking and image time tags
        mSuccess = false;
}

ReconstructCore::~ReconstructCore()
{
}

void ReconstructCore::initialize(InputParams input, ReconstructionMethodService* algorithm)
{
        mInput = input;
        mAlgorithm = algorithm;
}

void ReconstructCore::initialize(ProcessedUSInputDataPtr fileData, OutputVolumeParams outputVolumeParams)
{
        mOutputVolumeParams = outputVolumeParams;
        mFileData = fileData;
}

ImagePtr ReconstructCore::reconstruct()
{
        this->threadedPreReconstruct();
//      this->threadablePreReconstruct();
        this->threadedReconstruct();
        this->threadedPostReconstruct();
        return mOutput;
}

void ReconstructCore::threadedPreReconstruct()
{
        if (!this->validInputData())
                return;
        mRawOutput = this->generateRawOutputVolume();
}

void ReconstructCore::threadedReconstruct()
{
        if (!this->validInputData())
                return;
    CX_ASSERT(mRawOutput);

        TimeKeeper timer;

        mSuccess = mAlgorithm->reconstruct(mFileData, mRawOutput, mInput.mAlgoSettings);

        timer.printElapsedSeconds("Reconstruct core time");
}

void ReconstructCore::threadedPostReconstruct()
{
        if (!this->validInputData())
                return;

        if (mSuccess)
        {
                mOutput = this->generateOutputVolume(mRawOutput);

                Eigen::Array3i outputDims(mRawOutput->GetDimensions());
                int total = outputDims[0] * outputDims[1] * outputDims[2];
                report(QString("US Reconstruction complete: %1Mb, output=%2, algo=%3, preset=%4, angio=%5")
                                                                                .arg(total/1024/1024)
                                                                                .arg(mOutput->getName())
                                                                                .arg(mAlgorithm->getName())
                                                                                .arg(mInput.mTransferFunctionPreset)
                                                                                .arg(mInput.mAngio));

                mPatientModelService->insertData(mOutput);
        }
        else
        {
                reportError("Reconstruction failed");
        }
}

ImagePtr ReconstructCore::generateOutputVolume(vtkImageDataPtr rawOutput)
{
        setDeepModified(rawOutput);

//      //If no output path is selecetd, use the same path as the input
//      QString filePath;
//      if (mInput.mOutputBasePath.isEmpty() && mInput.mOutputRelativePath.isEmpty())
//              filePath = qstring_cast(mFileData->getFilePath());
//      else
//              filePath = mInput.mOutputRelativePath;

        QString uid = this->generateOutputUid();
        QString name = this->generateImageName(uid);

        ImagePtr image = mPatientModelService->createSpecificData<Image>(uid + "_%1", name + " %1");
        image->setVtkImageData(rawOutput);

//      ImagePtr image = mPatientModelService->createImage(rawOutput, uid + "_%1", name + " %1", filePath);
        image->get_rMd_History()->setRegistration(mOutputVolumeParams.get_rMd());
        image->setModality("US");
        if (mInput.mAngio)
                image->setImageType("Angio");
        else
                image->setImageType("B-Mode");

        PresetTransferFunctions3DPtr presets = mPatientModelService->getPresetTransferFunctions3D();
        presets->load(mInput.mTransferFunctionPreset, image, true, false);//Only apply to 2D, not 3D
        presets->load("US B-Mode", image, false, true);//Only apply to 3D, not 2D

        return image;
}

vtkImageDataPtr ReconstructCore::generateRawOutputVolume()
{
        Eigen::Array3i dim = mOutputVolumeParams.getDim();
        Vector3D spacing = Vector3D(1, 1, 1) * mOutputVolumeParams.getSpacing();
        vtkImageDataPtr data = generateVtkImageData(dim, spacing, 0);
        return data;
}

QString ReconstructCore::generateOutputUid()
{
        QString base = mFileData->getUid();
        QString name = mFileData->getFilePath().split("/").back();
        name = name.split(".").front();

        QStringList split = name.split("_");
        QStringList prefix = split.front().split("-");
        if (prefix.size() == 2)
        {
                split[0] = prefix[0];
        }
        else
        {
                split[0] += "_rec";
        }

        return split.join("_");
}

QString ReconstructCore::generateImageName(QString uid) const
{
        QString name = uid.split("/").back();
        name = name.split(".").front();
        QString prefix = name.split("_").front(); // retrieve US-Acq part
        prefix = prefix.split("-").front(); // retrieve US part.
        if (prefix.isEmpty())
                prefix = "US";

//      std::cout << "reconstruct input uid " << uid << std::endl;
        if (mInput.mAngio) // tag angio images as such
                prefix += "A";

        // retrieve  index counter from _99_
        QString counter = "";
        QRegExp countReg("_[0-9]{1,2}_");
        if (countReg.indexIn(name) > 0)
        {
                counter = countReg.cap(0).remove("_");
        }

        // retrieve timestamp as HH:MM
        QRegExp tsReg("[0-9]{8}T[0-9]{6}");
        if (tsReg.indexIn(name) > 0)
        {
                QString postfix = name.split("_").back();
                QDateTime datetime = QDateTime::fromString(tsReg.cap(0), timestampSecondsFormat());
                QString timestamp = datetime.toString("hh:mm");
                return prefix + " " + counter + " " + postfix + " " + timestamp;
        }

        return name;
}

ImagePtr ReconstructCore::getOutput()
{
        return mOutput;
}

bool ReconstructCore::validInputData() const
{
        return mAlgorithm!=0;
}

} /* namespace cx */