cxReconstructPreprocessor.h

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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.
=========================================================================*/

#ifndef CXRECONSTRUCTPREPROCESSOR_H_
#define CXRECONSTRUCTPREPROCESSOR_H_

#include "org_custusx_usreconstruction_Export.h"

#include "cxBoundingBox3D.h"
#include "cxReconstructedOutputVolumeParams.h"
#include "cxReconstructCore.h"
#include "cxUSReconstructInputData.h"

namespace cx
{
typedef boost::shared_ptr<class ReconstructPreprocessor> ReconstructPreprocessorPtr;

class org_custusx_usreconstruction_EXPORT ReconstructPreprocessor
{
public:
        ReconstructPreprocessor(PatientModelServicePtr patientModelService);
    virtual ~ReconstructPreprocessor();

    // used for reconstruction algo
    void initialize(ReconstructCore::InputParams input, USReconstructInputData fileData);
    OutputVolumeParams getOutputVolumeParams() { return mOutputVolumeParams; }
    ReconstructCore::InputParams getInputParams() { return mInput; }

    std::vector<ProcessedUSInputDataPtr> createProcessedInput(std::vector<bool> angio);

private:
    void cropInputData();
                IntBoundingBox3D reduceCropboxToImageSize(IntBoundingBox3D cropbox, QSize size);
    void updateFromOriginalFileData();
    void findExtentAndOutputTransform();
    Transform3D applyOutputOrientation();
        std::vector<Vector3D> generateInputRectangle();
        void interpolatePositions();
        double timeToPosition(unsigned i_frame, unsigned i_pos);
    void filterPositions(); // Noise-supressing position filter, averaging filter, configurable length
    void positionThinning(); // If enabled, try to remove "suspect" data (large jumps etc.)
    void applyTimeCalibration();
    void alignTimeSeries();
        void calibrateTimeStamps(double offset, double scale);

    // input data
    ReconstructCore::InputParams mInput;
    USReconstructInputData mFileData;
    double mMaxTimeDiff;

    // generated data
    OutputVolumeParams mOutputVolumeParams;

        PatientModelServicePtr mPatientModelService;
};

} /* namespace cx */

#endif // CXRECONSTRUCTPREPROCESSOR_H_