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

  Program:   Visualization Toolkit
  Module:    $RCSfile: vtkReebGraph.h,v $

  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.

=========================================================================*/
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 Copyright (c) Sandia Corporation
 See Copyright.txt or http://www.paraview.org/HTML/Copyright.html for details.
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// .NAME vtkReebGraph - Reeb graph computation for PL scalar fields.
//
// .SECTION Description
// vtkReebGraph is a class that computes a Reeb graph given a PL scalar
// field (vtkDataArray) defined on a simplicial mesh.
// A Reeb graph is a concise representation of the connectivity evolution of
// the level sets of a scalar function.
//
// It is particularly useful in visualization (optimal seed set computation,
// fast flexible isosurface extraction, automated transfer function design,
// feature-driven visualization, etc.) and computer graphics (shape
// deformation, shape matching, shape compression, etc.).
//
// Reference:
// "Sur les points singuliers d'une forme de Pfaff completement integrable ou
// d'une fonction numerique",
// G. Reeb,
// Comptes-rendus de l'Academie des Sciences, 222:847-849, 1946.
//
// vtkReebGraph implements one of the latest and most robust Reeb graph
// computation algorithms.
//
// Reference:
// "Robust on-line computation of Reeb graphs: simplicity and speed",
// V. Pascucci, G. Scorzelli, P.-T. Bremer, and A. Mascarenhas,
// ACM Transactions on Graphics, Proc. of SIGGRAPH 2007.
//
// vtkReebGraph provides methods for computing multi-resolution topological
// hierarchies through topological simplification.
// Topoligical simplification can be either driven by persistence homology
// concepts (default behavior) or by application specific metrics (see
// vtkReebGraphSimplificationMetric).
// In the latter case, designing customized simplification metric evaluation
// algorithms enables the user to control the definition of what should be
// considered as noise or signal in the topological filtering process.
//
// References:
// "Topological persistence and simplification",
// H. Edelsbrunner, D. Letscher, and A. Zomorodian,
// Discrete Computational Geometry, 28:511-533, 2002.
//
// "Extreme elevation on a 2-manifold",
// P.K. Agarwal, H. Edelsbrunner, J. Harer, and Y. Wang,
// ACM Symposium on Computational Geometry, pp. 357-365, 2004.
//
// "Simplifying flexible isosurfaces using local geometric measures",
// H. Carr, J. Snoeyink, M van de Panne,
// IEEE Visualization, 497-504, 2004
//
// "Loop surgery for volumetric meshes: Reeb graphs reduced to contour trees",
// J. Tierny, A. Gyulassy, E. Simon, V. Pascucci,
// IEEE Trans. on Vis. and Comp. Graph. (Proc of IEEE VIS), 15:1177-1184, 2009.
//
//
//
// Reeb graphs can be computed from 2D data (vtkPolyData, with triangles only)
// or 3D data (vtkUnstructuredGrid, with tetrahedra only), sequentially (see
// the "Build" calls) or in streaming (see the "StreamTriangle" and
// "StreamTetrahedron" calls).
//
// vtkReebGraph inherits from vtkMutableDirectedGraph.
//
// Each vertex of a vtkReebGraph object represents a critical point of the
// scalar field where the connectivity of the related level set changes
// (creation, deletion, split or merge of connected components).
// A vtkIdTypeArray (called "Vertex Ids") is associated with the VertexData of
// a vtkReebGraph object, in order to retrieve if necessary the exact Ids of
// the corresponding vertices in the input mesh.
//
// The edges of a vtkReebGraph object represent the regions of the input mesh
// separated by the critical contours of the field, and where the connectivity
// of the input field does not change.
// A vtkVariantArray is associated with the EdgeDta of a vtkReebGraph object and
// each entry of this array is a vtkAbstractArray containing the Ids of the
// vertices of those regions, sorted by function value (useful for flexible
// isosurface extraction or level set signature computation, for instance).
//
// See Graphics/Testing/Cxx/TestReebGraph.cxx for examples of traversals and
// typical usages (customized simplification, skeletonization, contour spectra,
//  etc.) of a vtkReebGraph object.
//
//
// .SECTION See Also
//      vtkReebGraphSimplificationMetric
//      vtkPolyDataToReebGraphFilter
//      vtkUnstructuredGridToReebGraphFilter
//      vtkReebGraphSimplificationFilter
//      vtkReebGraphSurfaceSkeletonFilter
//      vtkReebGraphVolumeSkeletonFilter
//      vtkAreaContourSpectrumFilter
//      vtkVolumeContourSpectrumFilter
//
// .SECTION Tests
//      Graphics/Testing/Cxx/TestReebGraph.cxx

#ifndef __vtkReebGraph_h
#define __vtkReebGraph_h

#include "vtkCommonDataModelModule.h" // For export macro
#include  "vtkMutableDirectedGraph.h"

class vtkDataArray;
class vtkDataSet;
class vtkIdList;
class vtkPolyData;
class vtkReebGraphSimplificationMetric;
class vtkUnstructuredGrid;

class VTKCOMMONDATAMODEL_EXPORT vtkReebGraph : public vtkMutableDirectedGraph
{

public:

  static vtkReebGraph *New();

  vtkTypeMacro(vtkReebGraph, vtkMutableDirectedGraph);
  void PrintSelf(ostream& os, vtkIndent indent);
  void PrintNodeData(ostream& os, vtkIndent indent);

  // Description:
  // Return class name of data type. This is one of VTK_STRUCTURED_GRID, 
  // VTK_STRUCTURED_POINTS, VTK_UNSTRUCTURED_GRID, VTK_POLY_DATA, or
  // VTK_RECTILINEAR_GRID (see vtkSetGet.h for definitions).
  // THIS METHOD IS THREAD SAFE
  virtual int GetDataObjectType() {return VTK_REEB_GRAPH;}


  enum
  {
    ERR_INCORRECT_FIELD = -1,
    ERR_NO_SUCH_FIELD = -2,
    ERR_NOT_A_SIMPLICIAL_MESH = -3
  };

  // Description:
  // Build the Reeb graph of the field 'scalarField' defined on the surface
  // mesh 'mesh'.
  //
  // Returned values:
  //
  // vtkReebGraph::ERR_INCORRECT_FIELD: 'scalarField' does not have as many
  // tuples as 'mesh' has vertices.
  //
  // vtkReebGraph::ERR_NOT_A_SIMPLICIAL_MESH: the input mesh 'mesh' is not a
  // simplicial mesh (for example, the surface mesh contains quads instead of
  // triangles).
  //
  int Build(vtkPolyData *mesh, vtkDataArray *scalarField);

  // Description:
  // Build the Reeb graph of the field 'scalarField' defined on the volume
  // mesh 'mesh'.
  //
  // Returned values:
  //
  // vtkReebGraph::ERR_INCORRECT_FIELD: 'scalarField' does not have as many
  // tuples as 'mesh' has vertices.
  //
  // vtkReebGraph::ERR_NOT_A_SIMPLICIAL_MESH: the input mesh 'mesh' is not a
  // simplicial mesh.
  //
  int Build(vtkUnstructuredGrid *mesh, vtkDataArray *scalarField);


  // Description:
  // Build the Reeb graph of the field given by the Id 'scalarFieldId',
  // defined on the surface mesh 'mesh'.
  //
  // Returned values:
  //
  // vtkReebGraph::ERR_INCORRECT_FIELD: 'scalarField' does not have as many
  // tuples as 'mesh' as vertices.
  //
  // vtkReebGraph::ERR_NOT_A_SIMPLICIAL_MESH: the input mesh 'mesh' is not a
  // simplicial mesh (for example, the surface mesh contains quads instead of
  // triangles).
  //
  // vtkReebGraph::ERR_NO_SUCH_FIELD: the scalar field given by the Id
  // 'scalarFieldId' does not exist.
  //
  int Build(vtkPolyData *mesh, vtkIdType scalarFieldId);

  // Description:
  // Build the Reeb graph of the field given by the Id 'scalarFieldId',
  // defined on the volume mesh 'mesh'.
  //
  // Returned values:
  //
  // vtkReebGraph::ERR_INCORRECT_FIELD: 'scalarField' does not have as many
  // tuples as 'mesh' as vertices.
  //
  // vtkReebGraph::ERR_NOT_A_SIMPLICIAL_MESH: the input mesh 'mesh' is not a
  // simplicial mesh.
  //
  // vtkReebGraph::ERR_NO_SUCH_FIELD: the scalar field given by the Id
  // 'scalarFieldId' does not exist.
  //
  int Build(vtkUnstructuredGrid *mesh, vtkIdType scalarFieldId);


  // Description:
  // Build the Reeb graph of the field given by the name 'scalarFieldName',
  // defined on the surface mesh 'mesh'.
  //
  // Returned values:
  //
  // vtkReebGraph::ERR_INCORRECT_FIELD: 'scalarField' does not have as many
  // tuples as 'mesh' as vertices.
  //
  // vtkReebGraph::ERR_NOT_A_SIMPLICIAL_MESH: the input mesh 'mesh' is not a
  // simplicial mesh (for example, the surface mesh contains quads instead of
  // triangles).
  //
  // vtkReebGraph::ERR_NO_SUCH_FIELD: the scalar field given by the name
  // 'scalarFieldName' does not exist.
  //
  int Build(vtkPolyData *mesh, const char* scalarFieldName);

  // Description:
  // Build the Reeb graph of the field given by the name 'scalarFieldName',
  // defined on the volume mesh 'mesh'.
  //
  // Returned values:
  //
  // vtkReebGraph::ERR_INCORRECT_FIELD: 'scalarField' does not have as many
  // tuples as 'mesh' as vertices.
  //
  // vtkReebGraph::ERR_NOT_A_SIMPLICIAL_MESH: the input mesh 'mesh' is not a
  // simplicial mesh.
  //
  // vtkReebGraph::ERR_NO_SUCH_FIELD: the scalar field given by the name
  // 'scalarFieldName' does not exist.
  //
  int Build(vtkUnstructuredGrid *mesh, const char* scalarFieldName);

  // Description:
  // Streaming Reeb graph computation.
  // Add to the streaming computation the triangle of the vtkPolyData surface
  // mesh described by
  // 	vertex0Id, scalar0
  // 	vertex1Id, scalar1
  // 	vertex2Id, scalar2
  //
  // 	where vertex<i>Id is the Id of the vertex in the vtkPolyData structure
  // 	and scalar<i> is the corresponding scalar field value.
  //
  // IMPORTANT: The stream _must_ be finalized with the "CloseStream" call.
  int StreamTriangle(	vtkIdType vertex0Id, double scalar0,
                      vtkIdType vertex1Id, double scalar1,
                      vtkIdType vertex2Id, double scalar2);

  // Description:
  // Streaming Reeb graph computation.
  // Add to the streaming computation the tetrahedra of the vtkUnstructuredGrid
  // volume mesh described by
  // 	vertex0Id, scalar0
  // 	vertex1Id, scalar1
  // 	vertex2Id, scalar2
  // 	vertex3Id, scalar3
  //
  // 	where vertex<i>Id is the Id of the vertex in the vtkUnstructuredGrid
  // 	structure and scalar<i> is the corresponding scalar field value.
  //
  // IMPORTANT: The stream _must_ be finalized with the "CloseStream" call.
  int StreamTetrahedron( vtkIdType vertex0Id, double scalar0,
                         vtkIdType vertex1Id, double scalar1,
                         vtkIdType vertex2Id, double scalar2,
                         vtkIdType vertex3Id, double scalar3);

  // Description:
  // Finalize internal data structures, in the case of streaming computations
  // (with StreamTriangle or StreamTetrahedron).
  // After this call, no more triangle or tetrahedron can be inserted via
  // StreamTriangle or StreamTetrahedron.
  // IMPORTANT: This method _must_ be called when the input stream is finished.
  // If you need to get a snapshot of the Reeb graph during the streaming
  // process (to parse or simplify it), do a DeepCopy followed by a
  // CloseStream on the copy.
  void CloseStream();

  // Descrition:
  // Implements deep copy
  void DeepCopy(vtkDataObject *src);

  // Description:
  // Simplify the Reeb graph given a threshold 'simplificationThreshold'
  // (between 0 and 1).
  //
  // This method is the core feature for Reeb graph multi-resolution hierarchy
  // construction.
  //
  // Return the number of arcs that have been removed through the simplification
  // process.
  //
  // 'simplificationThreshold' represents a "scale", under which each Reeb graph
  // feature is considered as noise. 'simplificationThreshold' is expressed as a
  // fraction of the scalar field overall span. It can vary from 0
  // (no simplification) to 1 (maximal simplification).
  //
  // 'simplificationMetric' is an object in charge of evaluating the importance
  // of a Reeb graph arc at each step of the simplification process.
  // if 'simplificationMetric' is NULL, the default strategy (persitence of the
  // scalar field) is used.
  // Customized simplification metric evaluation algorithm can be designed (see
  // vtkReebGraphSimplificationMetric), enabling the user to control the
  // definition of what should be considered as noise or signal.
  //
  // References:
  //
  // "Topological persistence and simplification",
  // H. Edelsbrunner, D. Letscher, and A. Zomorodian,
  // Discrete Computational Geometry, 28:511-533, 2002.
  //
  // "Extreme elevation on a 2-manifold",
  // P.K. Agarwal, H. Edelsbrunner, J. Harer, and Y. Wang,
  // ACM Symposium on Computational Geometry, pp. 357-365, 2004.
  //
  // "Simplifying flexible isosurfaces using local geometric measures",
  // H. Carr, J. Snoeyink, M van de Panne,
  // IEEE Visualization, 497-504, 2004
  //
  // "Loop surgery for volumetric meshes: Reeb graphs reduced to contour trees",
  // J. Tierny, A. Gyulassy, E. Simon, V. Pascucci,
  // IEEE Trans. on Vis. and Comp. Graph. (Proc of IEEE VIS), 15:1177-1184,2009.
  int Simplify(double simplificationThreshold,
    vtkReebGraphSimplificationMetric *simplificationMetric);

  // Description:
  // Use a pre-defined Reeb graph (post-processing).
  // Use with caution!
  void Set(vtkMutableDirectedGraph *g);

protected:

  vtkReebGraph();
  ~vtkReebGraph();

  class Implementation;
  Implementation* Storage;

private:
  vtkReebGraph(const vtkReebGraph&); // Not implemented.
  void operator=(const vtkReebGraph&); // Not implemented.

};

#endif
