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;
        void convertToQuaternions(Eigen::ArrayXXd qPosArray, int nQuaternions, int nPositions, int filterStrength);
        Eigen::ArrayXXd filterQuaternionArray(Eigen::ArrayXXd qPosArray, int nPositions, int filterLength);
        void convertFromQuaternion(Eigen::ArrayXXd qPosFiltered);
};
 
} /* namespace cx */
 
#endif // CXRECONSTRUCTPREPROCESSOR_H_