PlusFidSegmentation.h

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/*=Plus=header=begin======================================================
  Program: Plus
  Copyright (c) Laboratory for Percutaneous Surgery. All rights reserved.
  See License.txt for details.
=========================================================Plus=header=end*/

#ifndef _FIDUCIAL_SEGMENTATION_H
#define _FIDUCIAL_SEGMENTATION_H

#include "PlusFidPatternRecognitionCommon.h"
#include "PlusConfigure.h"
#include "vtkXMLDataElement.h"
#include <string.h>

//-----------------------------------------------------------------------------

class vtkPlusCalibrationExport PlusCoordinate2D
{
public:
  PlusCoordinate2D() { Y = 0; X = 0; };
  PlusCoordinate2D(int y, int x) { Y = y; X = x; };
  bool operator== (const PlusCoordinate2D& data) const { return (Y == data.Y && X == data.X) ; }

public:
  int Y;
  int X;
};

//-----------------------------------------------------------------------------

class vtkPlusCalibrationExport PlusFidSegmentation
{
public:
  static const double DEFAULT_APPROXIMATE_SPACING_MM_PER_PIXEL;
  static const double DEFAULT_MORPHOLOGICAL_OPENING_CIRCLE_RADIUS_MM;
  static const double DEFAULT_MORPHOLOGICAL_OPENING_BAR_SIZE_MM;
  static const int DEFAULT_CLIP_ORIGIN[2];
  static const int DEFAULT_CLIP_SIZE[2];
  static const double DEFAULT_MAX_LINE_PAIR_DISTANCE_ERROR_PERCENT;
  static const double DEFAULT_ANGLE_TOLERANCE_DEGREES;
  static const double DEFAULT_MAX_ANGLE_DIFFERENCE_DEGREES;
  static const double DEFAULT_MIN_THETA_DEGREES;
  static const double DEFAULT_MAX_THETA_DEGREES;
  static const double DEFAULT_MAX_LINE_SHIFT_MM;
  static const double DEFAULT_THRESHOLD_IMAGE_PERCENT;
  static const double DEFAULT_COLLINEAR_POINTS_MAX_DISTANCE_FROM_LINE_MM;
  static const char* DEFAULT_USE_ORIGINAL_IMAGE_INTENSITY_FOR_DOT_INTENSITY_SCORE;
  static const int DEFAULT_NUMBER_OF_MAXIMUM_FIDUCIAL_POINT_CANDIDATES;

  typedef unsigned char PixelType;

  enum FiducialGeometryType
  {
    CALIBRATION_PHANTOM_MULTI_NWIRE, //PerkLab Multi-Nwire phantom
    CIRS_PHANTOM_13_POINT, //CIRS phantom model 45
    CALIBRATION_PHANTOM_6_POINT //PerkLab Double-N phantom, deprecated (superceded by CALIBRATION_PHANTOM_MULTI_NWIRE)
  };

  PlusFidSegmentation();
  virtual ~PlusFidSegmentation();

  /* Read the configuration file */
  PlusStatus ReadConfiguration(vtkXMLDataElement* rootConfigElement);

  void SetFrameSize(const FrameSizeType& frameSize);
  void SetFiducialGeometry(FiducialGeometryType geometryType);

  void UpdateParameters();

  void Clear();

  void ValidateRegionOfInterest();

  inline PlusFidSegmentation::PixelType ErodePoint0(PlusFidSegmentation::PixelType* image, unsigned int ir, unsigned int ic);
  void Erode0(PlusFidSegmentation::PixelType* dest, PlusFidSegmentation::PixelType* image);
  inline PlusFidSegmentation::PixelType ErodePoint45(PlusFidSegmentation::PixelType* image, unsigned int ir, unsigned int ic);
  void Erode45(PlusFidSegmentation::PixelType* dest, PlusFidSegmentation::PixelType* image);
  inline PlusFidSegmentation::PixelType ErodePoint90(PlusFidSegmentation::PixelType* image, unsigned int ir, unsigned int ic);
  void Erode90(PlusFidSegmentation::PixelType* dest, PlusFidSegmentation::PixelType* image);
  inline PlusFidSegmentation::PixelType ErodePoint135(PlusFidSegmentation::PixelType* image, unsigned int ir, unsigned int ic);
  void Erode135(PlusFidSegmentation::PixelType* dest, PlusFidSegmentation::PixelType* image);
  void ErodeCircle(PlusFidSegmentation::PixelType* dest, PlusFidSegmentation::PixelType* image);
  inline PlusFidSegmentation::PixelType DilatePoint0(PlusFidSegmentation::PixelType* image, unsigned int ir, unsigned int ic);
  void Dilate0(PlusFidSegmentation::PixelType* dest, PlusFidSegmentation::PixelType* image);
  inline PlusFidSegmentation::PixelType DilatePoint45(PlusFidSegmentation::PixelType* image, unsigned int ir, unsigned int ic);
  void Dilate45(PlusFidSegmentation::PixelType* dest, PlusFidSegmentation::PixelType* image);
  inline PlusFidSegmentation::PixelType DilatePoint90(PlusFidSegmentation::PixelType* image, unsigned int ir, unsigned int ic);
  void Dilate90(PlusFidSegmentation::PixelType* dest, PlusFidSegmentation::PixelType* image);
  inline PlusFidSegmentation::PixelType DilatePoint135(PlusFidSegmentation::PixelType* image, unsigned int ir, unsigned int ic);
  void Dilate135(PlusFidSegmentation::PixelType* dest, PlusFidSegmentation::PixelType* image);
  inline PlusFidSegmentation::PixelType DilatePoint(PlusFidSegmentation::PixelType* image, unsigned int ir, unsigned int ic, PlusCoordinate2D* shape, int slen);
  void DilateCircle(PlusFidSegmentation::PixelType* dest, PlusFidSegmentation::PixelType* image);
  void Subtract(PlusFidSegmentation::PixelType* image, PlusFidSegmentation::PixelType* vals);

  void WritePossibleFiducialOverlayImage(const std::vector< std::vector<double> >& fiducials, PlusFidSegmentation::PixelType* unalteredImage, const char* namePrefix, int frameIndex);

  void WritePossibleFiducialOverlayImage(const std::vector<PlusFidDot>& fiducials, PlusFidSegmentation::PixelType* unalteredImage, const char* namePrefix, int frameIndex);

  void MorphologicalOperations();

  void Suppress(PlusFidSegmentation::PixelType* image, double percent_thresh);

  inline bool AcceptDot(PlusFidDot& dot);

  bool Cluster(bool& tooManyCandidates);

  static void WritePng(PlusFidSegmentation::PixelType* modifiedImage, std::string outImageName, int cols, int rows);

  static void SetDefaultSegmentationParameters(vtkXMLDataElement* segmentationElement);

  bool ShapeContains(std::vector<PlusCoordinate2D>& shape, PlusCoordinate2D point);

  inline void ClusteringAddNeighbors(PlusFidSegmentation::PixelType* image, int r, int c, std::vector<PlusFidDot>& m_Test, std::vector<PlusFidDot>& m_Set, std::vector<PlusFidSegmentation::PixelType>& m_Vals);

  // Accessors and mutators

  void SetPossibleFiducialsImageFilename(std::string value) { m_PossibleFiducialsImageFilename = value; };

  double GetThresholdImagePercent() { return m_ThresholdImagePercent; };

  bool GetDebugOutput() { return m_DebugOutput; };

  void SetDebugOutput(bool value) { m_DebugOutput = value; };

  unsigned int GetMorphologicalOpeningBarSizePx();

  FrameSizeType GetFrameSize() { return m_FrameSize; };

  std::vector<PlusFidDot>& GetDotsVector() {return m_DotsVector; };

  void SetCandidateFidValues(const std::vector<PlusFidDot>& value) { m_CandidateFidValues = value; };

  std::vector<PlusFidDot>& GetCandidateFidValues() { return m_CandidateFidValues; };

  void SetNumberOfMaximumFiducialPointCandidates(int aValue);

  FiducialGeometryType  GetFiducialGeometry() { return m_FiducialGeometry; };

  PlusFidSegmentation::PixelType* GetWorking() {return m_Working; };

  PlusFidSegmentation::PixelType* GetUnalteredImage() {return m_UnalteredImage; };

  void  SetApproximateSpacingMmPerPixel(double value) { m_ApproximateSpacingMmPerPixel = value; };

  void  SetMorphologicalOpeningCircleRadiusMm(double value) { m_MorphologicalOpeningCircleRadiusMm = value; };

  void  SetMorphologicalOpeningBarSizeMm(double value) { m_MorphologicalOpeningBarSizeMm = value; };

  void  SetRegionOfInterest(unsigned int xMin, unsigned int yMin, unsigned int xMax, unsigned int yMax);

  void  GetRegionOfInterest(unsigned int& xMin, unsigned int& yMin, unsigned int& xMax, unsigned int& yMax);

  void  SetThresholdImagePercent(double value) { m_ThresholdImagePercent = value; };

  void  SetUseOriginalImageIntensityForDotIntensityScore(bool value) { m_UseOriginalImageIntensityForDotIntensityScore = value; };

protected:
  FrameSizeType m_FrameSize;
  std::array<unsigned int, 4> m_RegionOfInterest; // xmin, ymin; xmax, ymax
  bool m_UseOriginalImageIntensityForDotIntensityScore;

  unsigned int m_NumberOfMaximumFiducialPointCandidates;

  double m_ThresholdImagePercent;

  double m_MorphologicalOpeningBarSizeMm;
  double m_MorphologicalOpeningCircleRadiusMm;

  std::string m_PossibleFiducialsImageFilename;

  FiducialGeometryType m_FiducialGeometry;

  std::vector<PlusCoordinate2D> m_MorphologicalCircle;

  double m_ApproximateSpacingMmPerPixel;
  double m_ImageScalingTolerancePercent[4];
  double m_ImageNormalVectorInPhantomFrameEstimation[3];
  double m_ImageNormalVectorInPhantomFrameMaximumRotationAngleDeg[6];
  double m_ImageToPhantomTransform[16];

  bool m_DotsFound;

  std::vector<std::vector<double>> m_FoundDotsCoordinateValue;

  double m_NumDots;

  std::vector<PlusFidDot> m_CandidateFidValues;

  PlusFidSegmentation::PixelType* m_Working;
  PlusFidSegmentation::PixelType* m_Dilated;
  PlusFidSegmentation::PixelType* m_Eroded;
  PlusFidSegmentation::PixelType* m_UnalteredImage;

  std::vector<PlusFidDot> m_DotsVector;

  bool m_DebugOutput;
};

#endif // _FIDUCIAL_SEGMENTATION_H