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

  Program:   Visualization Toolkit
  Module:    vtkImageConnectivityFilter.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.

=========================================================================*/
/*=========================================================================
  Copyright (c) 2014 David Gobbi
  All rights reserved.

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  * Redistributions of source code must retain the above copyright
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  * Redistributions in binary form must reproduce the above copyright
    notice, this list of conditions and the following disclaimer in the
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  * Neither the name of David Gobbi nor the names of any contributors
    may be used to endorse or promote products derived from this software
    without specific prior written permission.

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=========================================================================*/
/**
 * @class   vtkImageConnectivityFilter
 * @brief   Label an image by connectivity
 *
 * vtkImageConnectivityFilter will identify connected regions within an
 * image and label them.  Only points with scalar values within a
 * prescribed range are considered for inclusion, by default this range
 * includes all scalar values with a value greater than zero.  Points
 * within the prescribed scalar range are considered to be connected
 * if a path exists between the points that does not traverse any
 * points that are not within the prescribed scalar range.
 * Adjacency of points is governed by 4-connectivity for 2D images, and
 * 6-connectivity for 3D images.
 *
 * The output of this filter is a label image.  By default, each region
 * is assigned a different label, where the labels are integer values
 * starting at a value of 1.  The SetLabelMode() method can be used to
 * change the way that labels are assigned.  Labels can be assigned
 * by providing input seed points for each region to be labelled, or
 * they can be assigned by ranking the regions by size.
 *
 * If a set of seeds is provided with the SetSeedData() method,
 * then the default behavior is to only output the regions that are
 * connected to the seeds, and if the seeds have scalars, then these
 * scalars will be used to label the regions.  Seeds with a scalar
 * value equal to zero are ignored.  See the documentation for the
 * SetExtractionMode() method for details on how to control which
 * regions will labeled.
 *
 * Regions can be selected by size with the SetSizeRange() method,
 * which can be useful for identifying objects of a certain size,
 * e.g. for rejecting small regions that are likely to be noise.
 * It is also possible to label only the largest region and ignore
 * all others, with SetExtractionModeToLargestRegion().
 *
 * In addition to the labels, the following additional information
 * is provided: the number of regions identified, the size of each
 * region, a list of all label values used, and the seed for each
 * region (if seeds were used).  Optionally, this filter can also
 * compute the extent of each region if GenerateRegionExtentsOn()
 * is called.  These extents can be useful for cropping the output
 * of the filter.
 *
 * @sa
 * vtkConnectivityFilter, vtkPolyDataConnectivityFilter
*/

#ifndef vtkImageConnectivityFilter_h
#define vtkImageConnectivityFilter_h

#include "vtkImagingMorphologicalModule.h" // For export macro
#include "vtkImageAlgorithm.h"

class vtkIdTypeArray;
class vtkIntArray;
class vtkDataSet;
class vtkImageData;
class vtkImageStencilData;

class VTKIMAGINGMORPHOLOGICAL_EXPORT vtkImageConnectivityFilter :
  public vtkImageAlgorithm
{
public:
  static vtkImageConnectivityFilter *New();
  vtkTypeMacro(vtkImageConnectivityFilter, vtkImageAlgorithm);
  void PrintSelf(ostream& os, vtkIndent indent) override;

  /**
   * Enum constants for SetLabelMode().
   */
  enum LabelModeEnum {
    SeedScalar = 0,
    ConstantValue = 1,
    SizeRank = 2
  };

  /**
   * Enum constants for SetExtractionMode().
   */
  enum ExtractionModeEnum {
    SeededRegions = 0,
    AllRegions = 1,
    LargestRegion = 2
  };

  //@{
  /**
   * The input for seed locations (input port 1).
   * Each point in the supplied data set will be used as a seed, unless
   * the data set has scalars, in which case only the points with scalar
   * values that are not equal to zero will be used as seeds.
   */
  void SetSeedConnection(vtkAlgorithmOutput *port);
  vtkAlgorithmOutput *GetSeedConnection();
  void SetSeedData(vtkDataSet *data);
  //@}

  //@{
  /**
   * The input for a stencil (input port 2).
   * The output labels will be restricted to the region inside the stencil,
   * as if no input voxels existed outside the stencil.  This allows you to
   * apply this filter within an arbitrary region of interest.
   */
  void SetStencilConnection(vtkAlgorithmOutput *port);
  vtkAlgorithmOutput *GetStencilConnection();
  void SetStencilData(vtkImageStencilData *data);
  //@}

  //@{
  /**
   * Set the scalar type for the output label image.
   * This should be one of UnsignedChar, Short, UnsignedShort, or Int
   * depending on how many labels are expected.  The default is UnsignedChar,
   * which allows for 255 label values.  If the total number of regions is
   * greater than the maximum label value N, then only the largest N regions
   * will be kept and the rest will be discarded.
   */
  void SetLabelScalarTypeToUnsignedChar() {
    this->SetLabelScalarType(VTK_UNSIGNED_CHAR); }
  void SetLabelScalarTypeToShort() {
    this->SetLabelScalarType(VTK_SHORT); }
  void SetLabelScalarTypeToUnsignedShort() {
    this->SetLabelScalarType(VTK_UNSIGNED_SHORT); }
  void SetLabelScalarTypeToInt() {
    this->SetLabelScalarType(VTK_INT); }
  const char *GetLabelScalarTypeAsString();
  vtkSetMacro(LabelScalarType, int);
  vtkGetMacro(LabelScalarType, int);
  //@}

  //@{
  /**
   * Set the mode for applying labels to the output.
   * Labeling by SeedScalar uses the scalars from the seeds as labels, if
   * present, or the regions will be labeled consecutively starting at 1,
   * if the seeds have no scalars. Labeling by SizeRank means that the
   * largest region is labeled 1 and other regions are labeled consecutively
   * in order of decreasing size (if there is a tie, then the seed point ID
   * is used as a tiebreaker).  Finally, Constant means that all regions
   * will have the value of SetLabelConstantValue().  The default is to
   * label using the seed scalars, if present, or to label consecutively,
   * if no seed scalars are present.
   */
  void SetLabelModeToSeedScalar() { this->SetLabelMode(SeedScalar); }
  void SetLabelModeToConstantValue() { this->SetLabelMode(ConstantValue); }
  void SetLabelModeToSizeRank() { this->SetLabelMode(SizeRank); }
  const char *GetLabelModeAsString();
  vtkSetMacro(LabelMode, int);
  vtkGetMacro(LabelMode, int);
  //@}

  //@{
  /**
   * Set which regions to output from this filter.
   * This can be all the regions, just the seeded regions, or the largest
   * region (which will the the largest seeded region, if there are seeds).
   * The default is to output all the seeded regions, if there are seeds,
   * or to output all the regions, if there are no seeds.
   */
  void SetExtractionModeToSeededRegions(){
    this->SetExtractionMode(SeededRegions); }
  void SetExtractionModeToAllRegions() {
    this->SetExtractionMode(AllRegions); }
  void SetExtractionModeToLargestRegion() {
    this->SetExtractionMode(LargestRegion); }
  const char *GetExtractionModeAsString();
  vtkSetMacro(ExtractionMode, int);
  vtkGetMacro(ExtractionMode, int);
  //@}

  //@{
  /**
   * The label used when LabelMode is ConstantValue.
   * The default value is 255.
   */
  vtkSetMacro(LabelConstantValue, int);
  vtkGetMacro(LabelConstantValue, int);
  //@}

  /**
   * Get the number of extracted regions.
   */
  vtkIdType GetNumberOfExtractedRegions();

  /**
   * Get the label used for each extracted region.
   */
  vtkIdTypeArray *GetExtractedRegionLabels() {
    return this->ExtractedRegionLabels; }

  // Description:
  // Get the size of each extracted region, as a voxel count.
  vtkIdTypeArray *GetExtractedRegionSizes() {
    return this->ExtractedRegionSizes; }

  /**
   * Get the PointId of the seed for each region.
   * If no seed was used, the PointId will be -1.
   */
  vtkIdTypeArray *GetExtractedRegionSeedIds() {
    return this->ExtractedRegionSeedIds; }

  /**
   * Get the extent (a 6-tuples) for each output region.
   * This is only valid if GenerateRegionExtentsOn() was called before
   * the filter was executed.
   */
  vtkIntArray *GetExtractedRegionExtents() {
    return this->ExtractedRegionExtents; }

  //@{
  /**
   * Turn this on to request creation of the ExtractedRegionExtents array.
   */
  vtkSetMacro(GenerateRegionExtents, int);
  vtkBooleanMacro(GenerateRegionExtents, int);
  vtkGetMacro(GenerateRegionExtents, int);
  //@}

  //@{
  /**
   * Set the size range for the extracted regions.
   * Only regions that have sizes within the specified range will be present
   * in the output.  The default range is (1, VTK_ID_MAX).
   */
  vtkSetVector2Macro(SizeRange, vtkIdType);
  vtkGetVector2Macro(SizeRange, vtkIdType);
  //@}

  //@{
  /**
   * Set the scalar range used to define potential regions.
   * Only voxels with values that are within this range will be considered
   * for region membership.  This is an inclusive range, meaning that the
   * upper and lower limits are considered to be within the range.  The
   * default range goes from 0.5 to VTK_DOUBLE_MAX.
   */
  vtkSetVector2Macro(ScalarRange, double);
  vtkGetVector2Macro(ScalarRange, double);
  //@}

  //@{
  /**
   * For multi-component input images, select which component to use.
   */
  vtkSetMacro(ActiveComponent, int);
  vtkGetMacro(ActiveComponent, int);
  //@}

protected:
  vtkImageConnectivityFilter();
  ~vtkImageConnectivityFilter() override;

  int LabelMode;
  int ExtractionMode;

  double ScalarRange[2];
  vtkIdType SizeRange[2];
  int LabelConstantValue;
  int ActiveComponent;
  int LabelScalarType;
  int GenerateRegionExtents;

  vtkIdTypeArray *ExtractedRegionLabels;
  vtkIdTypeArray *ExtractedRegionSizes;
  vtkIdTypeArray *ExtractedRegionSeedIds;
  vtkIntArray *ExtractedRegionExtents;

  void ComputeInputUpdateExtent(int inExt[6], int outExt[6]);

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

private:
  vtkImageConnectivityFilter(const vtkImageConnectivityFilter&) = delete;
  void operator=(const vtkImageConnectivityFilter&) = delete;
};

#endif
