TubeSegmentationAndCenterlineExtraction.hpp

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#ifndef TUBE_SEGMENTATION_AND_CENTERLINE_EXTRACTION_HPP
#define TUBE_SEGMENTATION_AND_CENTERLINE_EXTRACTION_HPP
 
#include "FAST/ProcessObject.hpp"
#include "FAST/Data/Image.hpp"
#include "FAST/Data/Mesh.hpp"
#include "FAST/Data/Segmentation.hpp"
 
namespace fast {
 
class FAST_EXPORT  TubeSegmentationAndCenterlineExtraction : public ProcessObject {
    FAST_OBJECT(TubeSegmentationAndCenterlineExtraction)
    public:
        void setKeepLargestTree(bool keep);
        void setMinimumTreeSize(int nrOfVoxels);
        void setMinimumRadius(float radius);
        void setMaximumRadius(float radius);
        void setRadiusStep(float step);
        void setSensitivity(float sensitivity);
        // The voxel intensities are capped to these values
        void setMinimumIntensity(float intensity);
        // The voxel intensities are capped to these values
        void setMaximumIntensity(float intensity);
        void extractDarkTubes();
        void extractBrightTubes();
        void disableSegmentation();
        void enableSegmentation();
        // TODO move cropping out of this algorithm
        void disableAutomaticCropping();
        void enableAutomaticCropping(bool lungCropping = false);
        DataChannel::pointer getSegmentationOutputPort();
        DataChannel::pointer getCenterlineOutputPort();
        DataChannel::pointer getTDFOutputPort();
    private:
        TubeSegmentationAndCenterlineExtraction();
        void execute();
 
        Image::pointer createGradients(Image::pointer image);
        void runTubeDetectionFilter(Image::pointer gradients, float minimumRadius, float maximumRadius, Image::pointer& TDF, Image::pointer& radius);
        void runNonCircularTubeDetectionFilter(Image::pointer gradients, float minimumRadius, float maximumRadius, Image::pointer& TDF, Image::pointer& radius);
        Image::pointer runGradientVectorFlow(Image::pointer vectorField);
        void keepLargestObjects(Segmentation::pointer segmentation, Mesh::pointer& centerlines);
 
        // Parameters
 
        // General
        bool mSegmentation, mThresholdCropping, mLungCropping;
        float mStDevBlurSmall, mStDevBlurLarge; // This should be tuned to the amount of noise in the image.
        float mMinimumIntensity, mMaximumIntensity; // The voxel intensities are capped to these values
        bool mExtractDarkStructures; // true and this extract dark structures, false and it extract bright structures
 
        // Radius
        float mMinimumRadius, mMaximumRadius, mRadiusStep;
 
        // Centerline extraction
        float mSensitivity; // A number between 0 and 1 influencing how much is extracted (including noise).
 
        bool mOnlyKeepLargestTree;
        int mMinimumTreeSize;
};
 
} // end namespace fast
 
#endif