/*=========================================================================

  Program:   Visualization Toolkit
  Module:    vtkVectorFieldTopology.h

  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
  All rights reserved.
  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notice for more information.

=========================================================================*/
/**
 * @class   vtkVectorFieldTopology
 * @brief   Extract the topological skeleton as output datasets
 *
 * vtkVectorFieldTopology is a filter that extracts the critical points and the 1D separatrices
 * (lines) If the data is 3D and the user enables ComputeSurfaces, also the 2D separatrices are
 * computed (surfaces)
 *
 * @par Thanks:
 * Developed by Roxana Bujack and Karen Tsai at Los Alamos National Laboratory under LDRD 20190143ER
 */

#ifndef vtkVectorFieldTopology_h
#define vtkVectorFieldTopology_h

#include "vtkFiltersFlowPathsModule.h" // For export macro
#include "vtkPolyDataAlgorithm.h"
#include "vtkStreamTracer.h" // for vtkStreamSurface::CELL_LENGTH_UNIT

class vtkGradientFilter;
class vtkImageData;
class vtkPolyData;
class vtkStreamSurface;
class vtkUnstructuredGrid;

class VTKFILTERSFLOWPATHS_EXPORT vtkVectorFieldTopology : public vtkPolyDataAlgorithm
{
public:
  static vtkVectorFieldTopology* New();
  vtkTypeMacro(vtkVectorFieldTopology, vtkPolyDataAlgorithm);
  void PrintSelf(ostream& os, vtkIndent indent) override;

  ///@{
  /**
   * Specify a uniform integration step unit for MinimumIntegrationStep,
   * InitialIntegrationStep, and MaximumIntegrationStep.
   * 1 = LENGTH_UNIT, i.e. all sizes are expresed in coordinate scale or cell scale
   * 2 = CELL_LENGTH_UNIT, i.e. all sizes are expresed in cell scale
   */
  vtkSetMacro(IntegrationStepUnit, int);
  vtkGetMacro(IntegrationStepUnit, int);
  ///@}

  ///@{
  /**
   * Specify/see the maximal number of iterations in this class and in vtkStreamTracer
   */
  vtkSetMacro(MaxNumSteps, int);
  vtkGetMacro(MaxNumSteps, int);
  ///@}

  ///@{
  /**
   * Specify the Initial, minimum, and maximum step size used for line integration,
   * expressed in IntegrationStepUnit
   */
  vtkSetMacro(IntegrationStepSize, double);
  vtkGetMacro(IntegrationStepSize, double);
  ///@}

  ///@{
  /**
   * Specify/see the distance by which the seedpoints of the separatrices are placed away from the
   * saddle expressed in IntegrationStepUnit
   */
  vtkSetMacro(SeparatrixDistance, double);
  vtkGetMacro(SeparatrixDistance, double);
  ///@}

  ///@{
  /**
   * Specify/see if the simple (fast) or iterative (correct) version is called
   */
  vtkSetMacro(UseIterativeSeeding, bool);
  vtkGetMacro(UseIterativeSeeding, bool);
  ///@}

  ///@{
  /**
   * Specify/see if the separatring surfaces (separatrices in 3D) are computed or not
   */
  vtkSetMacro(ComputeSurfaces, bool);
  vtkGetMacro(ComputeSurfaces, bool);
  ///@}

  ///@{
  /**
   * Specify/see if the boundary cells are treated or not
   */
  vtkSetMacro(ExcludeBoundary, bool);
  vtkGetMacro(ExcludeBoundary, bool);
  ///@}

  //@{
  /**
   * Specify/see whether to use boundary switch points/lines points as seeds or not
   */
  vtkSetMacro(UseBoundarySwitchPoints, bool);
  vtkGetMacro(UseBoundarySwitchPoints, bool);
  //@}

  //@{
  /**
   * Specify the VectorAngleThreshold to remove noisy boundary switch points/lines
   * When computing boundary switch point, if the vecotrs of the two points within a cell are almost
   * parallel, the boundary switch point computed is considered as a noise point. Let v0 and v1 be
   * the vectors of the two points, and their norm equal to 1. The dot product between them
   * Dot(v0,v1) = cos(theta), where theta is the angle between v0 and v1. When v0 and v1 are almost
   * parallel, abs(Dot(v0,v1)) is close to 1. The range of this threshold is [0,1]. For any
   * abs(Dot(v0,v1)) > VectorAngleThreshold, the boundary switch point computed is a noise point.
   */
  vtkSetMacro(VectorAngleThreshold, double);
  vtkGetMacro(VectorAngleThreshold, double);
  //@}

  //@{
  /**
   * Specify the OffsetAwayFromBoundary to shift seeds for computing separating lines/surfaces
   */
  vtkSetMacro(OffsetAwayFromBoundary, double);
  vtkGetMacro(OffsetAwayFromBoundary, double);
  //@}

  //@{
  /**
   * Specify EpsilonCriticalPoint for classifying critical points. The default is 1e-10.
   */
  vtkSetMacro(EpsilonCriticalPoint, double);
  vtkGetMacro(EpsilonCriticalPoint, double);
  //@}

  /**
   * Set the type of the velocity field interpolator to determine whether
   * INTERPOLATOR_WITH_DATASET_POINT_LOCATOR or INTERPOLATOR_WITH_CELL_LOCATOR is employed for
   * locating cells during streamline integration.
   */
  void SetInterpolatorType(int interpType);

  /**
   * Set the velocity field interpolator type to the one involving a cell locator.
   */
  void SetInterpolatorTypeToCellLocator();

  /**
   * Set the velocity field interpolator type to the one involving a dataset point locator.
   */
  void SetInterpolatorTypeToDataSetPointLocator();

protected:
  vtkVectorFieldTopology();
  ~vtkVectorFieldTopology() override;

  int FillInputPortInformation(int port, vtkInformation* info) override;
  int FillOutputPortInformation(int port, vtkInformation* info) override;
  int RequestData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) override;

private:
  vtkVectorFieldTopology(const vtkVectorFieldTopology&) = delete;
  void operator=(const vtkVectorFieldTopology&) = delete;

  /**
   * This function checks the values of flags, such as UseBoundarySwitchPoints and ExcludeBoundary
   */
  int Validate();

  /**
   * main function if input is vtkImageData
   * triangulate, compute critical points, separatrices, and surfaces
   * @param dataset: the input dataset
   * @param tridataset: the triangulated version of the input dataset
   * @return 1 if successfully terminated
   */
  int ImageDataPrepare(vtkDataSet* dataSetInput, vtkUnstructuredGrid* tridataset);

  /**
   * main function if input is vtkUnstructuredGrid
   * triangulate if necessary, compute critical points, separatrices, and surfaces
   * @param dataset: the input dataset
   * @param tridataset: the triangulated version of the input dataset
   * @return 1 if successfully terminated
   */
  int UnstructuredGridPrepare(vtkDataSet* dataSetInput, vtkUnstructuredGrid* tridataset);

  /**
   * delete the cells that touch the boundary
   * @param tridataset: input vector field after triangulation
   * @return 1 if successful, 0 if not
   */
  int RemoveBoundary(vtkSmartPointer<vtkUnstructuredGrid> tridataset);

  /**
   * for each triangle, we solve the linear vector field analytically for its zeros
   *  if this location is inside the triangle, we have found a critical point
   * @param criticalPoints: list of the locations where the vf is zero
   * @param tridataset: input vector field after triangulation
   * @return 1 if successful, 0 if not
   */
  int ComputeCriticalPoints2D(
    vtkSmartPointer<vtkPolyData> criticalPoints, vtkSmartPointer<vtkUnstructuredGrid> tridataset);

  /**
   * for each tetrahedron, we solve the linear vector field analytically for its zeros
   *  if this location is inside the tetrahedron, we have found a critical point
   * @param criticalPoints: list of the locations where the vf is zero
   * @param tridataset: input vector field after tetrahedrization
   * @return 1 if successfully terminated
   */
  int ComputeCriticalPoints3D(
    vtkSmartPointer<vtkPolyData> criticalPoints, vtkSmartPointer<vtkUnstructuredGrid> tridataset);

  /**
   * Given 1D position x0 <= x <= x1, and two 3-vectors v0 and v1, this functions interpolates a
   * 3-vector at x.
   * @param x0: minimum 1D position
   * @param x1: maximum 1D position
   * @param x: target 1D position
   * @param v0: 3-vector at x0
   * @param v1: 3-vector at x1
   * @param v: output 3-vector at x
   */
  static void InterpolateVector(
    double x0, double x1, double x, const double v0[3], const double v1[3], double v[3]);

  /**
   * This functions compute boundary switch points from boundaries that are lines.
   * @param boundarySwitchPoints: list of the locations of the boundary switch points
   * @param tridataset: input vector field after triangulation
   * @return 1 if successful, 0 if not
   */
  int ComputeBoundarySwitchPoints(
    vtkPolyData* boundarySwitchPoints, vtkUnstructuredGrid* tridataset);

  /**
   * This function computes separatrix lines using boundary switch points, by using the
   * vtkStreamTracer filter
   * @param boundarySwitchPoints: list of the locations of boundaries where the directions of the
   * flow change
   * @param separatrices: inegration lines
   * @param dataset: input vector field
   * @param interestPoints: a set of points that includes both critical points and boundary switch
   * points
   * @param integrationStepUnit: whether the sizes are expresed in coordinate scale or cell scale
   * @param dist: size of the offset of the seeding
   * @param stepSize: stepsize of the integrator
   * @param maxNumSteps: maximal number of integration steps
   * @return 1 if successfully terminated
   */
  int ComputeSeparatricesBoundarySwitchPoints(vtkPolyData* boundarySwitchPoints,
    vtkPolyData* separatrices, vtkDataSet* dataset, vtkPoints* interestPoints,
    int integrationStepUnit, double dist, int maxNumSteps);

  /**
   * This function computes boundary switch lines from boundaries that surfaces.
   * It then computes separatrix surfaces using boundary switch lines, by using the
   * vtkStreamSurfaces filter.
   * @param boundarySwitchLines: list of the locations of boundaries where the directions of the
   * flow change
   * @param separatrices: inegration surfaces
   * @param dataset: input vector field
   * @param integrationStepUnit: whether the sizes are expresed in coordinate scale or cell scale
   * @param dist: size of the offset of the seeding
   * @param stepSize: stepsize of the integrator
   * @param maxNumSteps: maximal number of integration steps
   * @param computeSurfaces: depending on this boolen the separatring surfaces are computed or not
   * @param useIterativeSeeding: depending on this boolen the separatring surfaces  are computed
   * either good or fast
   * @return 1 if successfully terminated
   */
  int ComputeSeparatricesBoundarySwitchLines(vtkPolyData* boundarySwitchLines,
    vtkPolyData* separatrices, vtkDataSet* dataset, int integrationStepUnit, double dist,
    int maxNumSteps, bool computeSurfaces, bool useIterativeSeeding);

  /**
   * we classify the critical points based on the eigenvalues of the jacobian
   * for the saddles, we seed in an offset of dist and integrate
   * @param criticalPoints: list of the locations where the vf is zero
   * @param separatrices: inegration lines starting at saddles
   * @param surfaces: inegration surfaces starting at saddles
   * @param dataset: input vector field
   * @param interestPoints: a set of points that includes both critical points and boundary switch
   * points
   * @param integrationStepUnit: whether the sizes are expresed in coordinate scale or cell scale
   * @param dist: size of the offset of the seeding
   * @param stepSize: stepsize of the integrator
   * @param maxNumSteps: maximal number of integration steps
   * @param computeSurfaces: depending on this boolen the separatring surfaces are computed or not
   * @param useIterativeSeeding: depending on this boolen the separatring surfaces  are computed
   * either good or fast
   * @return 1 if successfully terminated
   */
  int ComputeSeparatrices(vtkPolyData* criticalPoints, vtkPolyData* separatrices,
    vtkPolyData* surfaces, vtkDataSet* dataset, vtkPoints* interestPoints, int integrationStepUnit,
    double dist, double stepSize, int maxNumSteps, bool computeSurfaces, bool useIterativeSeeding);

  /**
   * this method computes streamsurfaces
   * in the plane of the two eigenvectors of the same sign around saddles
   * @param isBackward: is 1 if the integration direction is backward and 0 for forward
   * @param normal: direction along the one eigenvector with opposite sign
   * @param zeroPos: location of the saddle
   * @param streamSurfaces: surfaces that have so far been computed
   * @param dataset: the vector field in which we advect
   * @param integrationStepUnit: whether the sizes are expresed in coordinate scale or cell scale
   * @param dist: size of the offset of the seeding
   * @param stepSize: stepsize of the integrator
   * @param maxNumSteps: maximal number of integration steps
   * @param useIterativeSeeding: depending on this boolen the separatring surfaces  are computed
   * either good or fast
   * @return 1 if successful, 0 if empty
   */
  int ComputeSurface(int numberOfSeparatingSurfaces, bool isBackward, double normal[3],
    double zeroPos[3], vtkPolyData* streamSurfaces, vtkDataSet* dataset, int integrationStepUnit,
    double dist, double stepSize, int maxNumSteps, bool useIterativeSeeding);

  /**
   * simple type that corresponds to the number of positive eigenvalues
   * in analogy to ttk, where the type corresponds to the down directions
   */
  enum CriticalType2D
  {
    DEGENERATE_2D = -1,
    SINK_2D = 0,
    SADDLE_2D = 1,
    SOURCE_2D = 2,
    CENTER_2D = 3
  };

  /**
   * detailed type that additionally distinguishes nodes from foci
   * nomenclature as in James Helman, Hesselink: "Visualizing Vector Field Topology in Fluid Flows"
   */
  enum CriticalTypeDetailed2D
  {
    //    DEGENERATE2D = -1,
    ATTRACTING_NODE_2D = 0,
    ATTRACTING_FOCUS_2D = 1,
    NODE_SADDLE_2D = 2,
    REPELLING_NODE_2D = 3,
    REPELLING_FOCUS_2D = 4,
    CENTER_DETAILED_2D = 5
  };

  /**
   * simple type that corresponds to the number of positive eigenvalues
   * in analogy to ttk, where the type corresponds to the down directions
   */
  enum CriticalType3D
  {
    DEGENERATE_3D = -1,
    SINK_3D = 0,
    SADDLE_1_3D = 1,
    SADDLE_2_3D = 2,
    SOURCE_3D = 3,
    CENTER_3D = 4
  };

  /**
   * detailed type that additionally distinguishes nodes from foci
   * nomenclature as in James Helman, Hesselink: "Visualizing Vector Field Topology in Fluid Flows"
   */
  enum CriticalTypeDetailed3D
  {
    ATTRACTING_NODE_3D = 0,
    ATTRACTING_FOCUS_3D = 1,
    NODE_SADDLE_1_3D = 2,
    FOCUS_SADDLE_1_3D = 3,
    NODE_SADDLE_2_3D = 4,
    FOCUS_SADDLE_2_3D = 5,
    REPELLING_NODE_3D = 6,
    REPELLING_FOCUS_3D = 7,
    CENTER_DETAILED_3D = 8
  };

  /**
   * determine which type of critical point we have based on the eigenvalues of the Jacobian in 2D
   * @param countReal: number of complex valued eigenvalues
   * @param countPos: number of positive eigenvalues
   * @param countNeg: number of negative eigenvalues
   * @return type of critical point: SOURCE_2D 2, SADDLE_2D 1, SINK_2D 0, (CENTER_2D 3)
   */
  static int Classify2D(int countComplex, int countPos, int countNeg);

  /**
   * determine which type of critical point we have including distinction between node and spiral
   * @param countReal: number of complex valued eigenvalues
   * @param countPos: number of positive eigenvalues
   * @param countNeg: number of negative eigenvalues
   * @return type of critical point: ATTRACTING_NODE_2D 0, ATTRACTING_FOCUS_2D 1, NODE_SADDLE_2D 2,
   * REPELLING_NODE_2D 3, REPELLING_FOCUS_2D 4, CENTER_DETAILED_2D 5,
   */
  static int ClassifyDetailed2D(int countComplex, int countPos, int countNeg);

  /**
   * determine which type of critical point we have based on the eigenvalues of the Jacobian in 3D
   * @param countReal: number of complex valued eigenvalues
   * @param countPos: number of positive eigenvalues
   * @param countNeg: number of negative eigenvalues
   * @return type of critical point: SOURCE_3D 3, SADDLE_2_3D 2, SADDLE_1_3D 1, SINK_3D 0,
   * (CENTER_3D 4)
   */
  static int Classify3D(int countComplex, int countPos, int countNeg);

  /**
   * determine which type of critical point we have including distinction between node and spiral
   * @param countReal: number of complex valued eigenvalues
   * @param countPos: number of positive eigenvalues
   * @param countNeg: number of negative eigenvalues
   * @return type of critical point: ATTRACTING_NODE_3D 0, ATTRACTING_FOCUS_3D 1, NODE_SADDLE_1_3D
   * 2, FOCUS_SADDLE_1_3D 3, NODE_SADDLE_2_3D 4, FOCUS_SADDLE_2_3D 5, REPELLING_NODE_3D 6,
   * REPELLING_FOCUS_3D 7, CENTER_DETAILED_3D 8
   */
  static int ClassifyDetailed3D(int countComplex, int countPos, int countNeg);

  /**
   * number of iterations in this class and in vtkStreamTracer
   */
  int MaxNumSteps = 100;

  /**
   * this value is used as stepsize for the integration
   */
  double IntegrationStepSize = 1;

  /**
   * the separatrices are seeded with this offset from the critical points
   */
  double SeparatrixDistance = 1;

  /**
   * depending on this boolen the simple (fast) or iterative (correct) version is called
   */
  bool UseIterativeSeeding = false;

  /**
   * depending on this boolen the separatring surfaces (separatrices in 3D) are computed or not
   */
  bool ComputeSurfaces = false;

  /**
   * the name of the array in pointdata that is being processed
   */
  const char* NameOfVectorArray;

  /**
   * depending on this boolen the cells touching the boundary of the input dataset are treated or
   * not this prevents detection of the whole boundary in no slip boundary settings
   */
  bool ExcludeBoundary = false;

  /**
   * dimension of the input data: 2 or 3
   */
  int Dimension = 2;

  /**
   * Analogous to integration step unit in vtkStreamTracer
   * Specify a uniform integration step unit for MinimumIntegrationStep,
   * InitialIntegrationStep, and MaximumIntegrationStep. NOTE: The valid
   * unit is now limited to only LENGTH_UNIT (1) and CELL_LENGTH_UNIT (2),
   * EXCLUDING the previously-supported TIME_UNIT.
   */
  int IntegrationStepUnit = vtkStreamTracer::CELL_LENGTH_UNIT;

  /**
   * Use boundary switch points/lines as seeds to compute seperatrix.
   * For 2D data, seeds are boundary switch points
   * For 3D data, seeds are boundary switch lines instead of points.
   * The default is to use critical points only.
   */
  bool UseBoundarySwitchPoints = false;

  /**
   *  It is either vtkStreamTracer::INTERPOLATOR_WITH_DATASET_POINT_LOCATOR or
   * vtkStreamTracer::INTERPOLATOR_WITH_CELL_LOCATOR
   */
  int InterpolatorType = vtkStreamTracer::INTERPOLATOR_WITH_DATASET_POINT_LOCATOR;

  /**
   * When computing boundary switch point, if the vecotrs of the two points within a cell are almost
   * parallel, the boundary switch point computed is considered as a noise point. Let v0 and v1 be
   * the vectors of the two points, and their norm equal to 1. The dot product between them
   * Dot(v0,v1) = cos(theta), where theta is the angle between v0 and v1. When v0 and v1 are almost
   * parallel, abs(Dot(v0,v1)) is close to 1. The range of this threshold is [0,1]. For any
   * abs(Dot(v0,v1)) > VectorAngleThreshold, the boundary switch point computed is a noise point.
   */
  double VectorAngleThreshold = 1;

  /**
   * When computing the separatrix, seeds are used. Seeds need to be inside the boundary.
   * This ratio is used to computed the amount of shift that shifts seeds a little bit inward.
   * It is multiplied with the variable SeparatrixDistance.
   * If users choose integrationStepUnit == vtkStreamTracer::CELL_LENGTH_UNIT, which is default, it
   * is equivalent to OffsetAwayFromBoundary * cell length
   */
  double OffsetAwayFromBoundary = 1e-3;

  /**
   * It is used to classify the type of critical points.
   */
  double EpsilonCriticalPoint = 1e-10;

  vtkNew<vtkStreamSurface> StreamSurface;
};
#endif
