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

  Program:   Visualization Toolkit
  Module:    vtkPolyDataConnectivityFilter.cxx

  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.

=========================================================================*/
#include "vtkPolyDataConnectivityFilter.h"

#include "vtkCellArray.h"
#include "vtkCellData.h"
#include "vtkCell.h"
#include "vtkFloatArray.h"
#include "vtkIdList.h"
#include "vtkIdTypeArray.h"
#include "vtkInformation.h"
#include "vtkInformationVector.h"
#include "vtkMath.h"
#include "vtkObjectFactory.h"
#include "vtkPointData.h"
#include "vtkPolyData.h"

#include <algorithm> // for fill_n

vtkStandardNewMacro(vtkPolyDataConnectivityFilter);

// Construct with default extraction mode to extract largest regions.
vtkPolyDataConnectivityFilter::vtkPolyDataConnectivityFilter()
{
  this->RegionSizes = vtkIdTypeArray::New();
  this->ExtractionMode = VTK_EXTRACT_LARGEST_REGION;
  this->ColorRegions = 0;

  this->ScalarConnectivity = 0;
  this->FullScalarConnectivity = 0;
  this->ScalarRange[0] = 0.0;
  this->ScalarRange[1] = 1.0;

  this->ClosestPoint[0] = this->ClosestPoint[1] = this->ClosestPoint[2] = 0.0;

  this->CellScalars = vtkFloatArray::New();
  this->CellScalars->Allocate(8);

  this->NeighborCellPointIds = vtkIdList::New();
  this->NeighborCellPointIds->Allocate(8);

  this->Seeds = vtkIdList::New();
  this->SpecifiedRegionIds = vtkIdList::New();

  this->MarkVisitedPointIds = 0;
  this->VisitedPointIds = vtkIdList::New();

  this->OutputPointsPrecision = DEFAULT_PRECISION;
}

vtkPolyDataConnectivityFilter::~vtkPolyDataConnectivityFilter()
{
  this->RegionSizes->Delete();
  this->CellScalars->Delete();
  this->NeighborCellPointIds->Delete();
  this->Seeds->Delete();
  this->SpecifiedRegionIds->Delete();
  this->VisitedPointIds->Delete();
}

int vtkPolyDataConnectivityFilter::RequestData(
  vtkInformation *vtkNotUsed(request),
  vtkInformationVector **inputVector,
  vtkInformationVector *outputVector)
{
  // get the info objects
  vtkInformation *inInfo = inputVector[0]->GetInformationObject(0);
  vtkInformation *outInfo = outputVector->GetInformationObject(0);

  // get the input and output
  vtkPolyData *input = vtkPolyData::SafeDownCast(
    inInfo->Get(vtkDataObject::DATA_OBJECT()));
  vtkPolyData *output = vtkPolyData::SafeDownCast(
    outInfo->Get(vtkDataObject::DATA_OBJECT()));

  vtkIdType cellId, newCellId, i, pt;
  vtkPoints *inPts;
  vtkPoints *newPts;
  vtkIdType *cells, *pts, npts, id, n;
  unsigned short ncells;
  vtkIdType maxCellsInRegion;
  vtkIdType largestRegionId = 0;
  vtkPointData *pd=input->GetPointData(), *outputPD=output->GetPointData();
  vtkCellData *cd=input->GetCellData(), *outputCD=output->GetCellData();

  vtkDebugMacro(<<"Executing polygon connectivity filter.");

  //  Check input/allocate storage
  //
  inPts = input->GetPoints();

  if (inPts == NULL)
    {
    vtkErrorMacro("No points!");
    return 1;
    }

  const vtkIdType numPts = inPts->GetNumberOfPoints();
  const vtkIdType numCells = input->GetNumberOfCells();

  if ( numPts < 1 || numCells < 1 )
    {
    vtkDebugMacro(<<"No data to connect!");
    return 1;
    }

  // See whether to consider scalar connectivity
  //
  this->InScalars = input->GetPointData()->GetScalars();
  if ( !this->ScalarConnectivity )
    {
    this->InScalars = NULL;
    }
  else
    {
    if ( this->ScalarRange[1] < this->ScalarRange[0] )
      {
      this->ScalarRange[1] = this->ScalarRange[0];
      }
    }

  // Build cell structure
  //
  this->Mesh = vtkPolyData::New();
  this->Mesh->CopyStructure(input);
  this->Mesh->BuildLinks();
  this->UpdateProgress(0.10);

  // Remove all visited point ids
  this->VisitedPointIds->Reset();

  // Initialize.  Keep track of points and cells visited.
  //
  this->RegionSizes->Reset();
  this->Visited = new vtkIdType[numCells];
  std::fill_n(this->Visited, numCells, -1);
  this->PointMap = new vtkIdType[numPts];
  std::fill_n(this->PointMap, numPts, -1);

  this->NewScalars = vtkIdTypeArray::New();
  this->NewScalars->SetName("RegionId");
  this->NewScalars->SetNumberOfTuples(numPts);
  newPts = vtkPoints::New();

  // Set the desired precision for the points in the output.
  if(this->OutputPointsPrecision == vtkAlgorithm::DEFAULT_PRECISION)
    {
    newPts->SetDataType(inPts->GetDataType());
    }
  else if(this->OutputPointsPrecision == vtkAlgorithm::SINGLE_PRECISION)
    {
    newPts->SetDataType(VTK_FLOAT);
    }
  else if(this->OutputPointsPrecision == vtkAlgorithm::DOUBLE_PRECISION)
    {
    newPts->SetDataType(VTK_DOUBLE);
    }

  newPts->Allocate(numPts);

  // Traverse all cells marking those visited.  Each new search
  // starts a new connected region. Connected region grows
  // using a connected wave propagation.
  //
  this->Wave.reserve(numPts);
  this->Wave2.reserve(numPts);

  this->PointNumber = 0;
  this->RegionNumber = 0;
  maxCellsInRegion = 0;

  this->CellIds = vtkIdList::New();
  this->CellIds->Allocate(8, VTK_CELL_SIZE);
  this->PointIds = vtkIdList::New();
  this->PointIds->Allocate(8, VTK_CELL_SIZE);

  if ( this->ExtractionMode != VTK_EXTRACT_POINT_SEEDED_REGIONS &&
  this->ExtractionMode != VTK_EXTRACT_CELL_SEEDED_REGIONS &&
  this->ExtractionMode != VTK_EXTRACT_CLOSEST_POINT_REGION )
    { //visit all cells marking with region number
    for (cellId=0; cellId < numCells; cellId++)
      {
      if ( cellId && !(cellId % 5000) )
        {
        this->UpdateProgress (0.1 + 0.8*cellId/numCells);
        }

      if ( this->Visited[cellId] < 0 )
        {
        this->NumCellsInRegion = 0;
        this->Wave.push_back(cellId);
        this->TraverseAndMark ();

        if ( this->NumCellsInRegion > maxCellsInRegion )
          {
          maxCellsInRegion = this->NumCellsInRegion;
          largestRegionId = this->RegionNumber;
          }

        this->RegionSizes->InsertValue(this->RegionNumber++,
                                       this->NumCellsInRegion);
        this->Wave.clear();
        this->Wave2.clear();
       }
      }
    }
  else // regions have been seeded, everything considered in same region
    {
    this->NumCellsInRegion = 0;

    if ( this->ExtractionMode == VTK_EXTRACT_POINT_SEEDED_REGIONS )
      {
      for (i=0; i < this->Seeds->GetNumberOfIds(); i++)
        {
        pt = this->Seeds->GetId(i);
        if ( pt >= 0 )
          {
          this->Mesh->GetPointCells(pt,ncells,cells);
          for (unsigned short j = 0; j < ncells; ++j)
            {
            this->Wave.push_back(cells[j]);
            }
          }
        }
      }
    else if ( this->ExtractionMode == VTK_EXTRACT_CELL_SEEDED_REGIONS )
      {
      for (i=0; i < this->Seeds->GetNumberOfIds(); i++)
        {
        cellId = this->Seeds->GetId(i);
        if ( cellId >= 0 )
          {
          this->Wave.push_back(cellId);
          }
        }
      }
    else if ( this->ExtractionMode == VTK_EXTRACT_CLOSEST_POINT_REGION )
      {//loop over points, find closest one
      double minDist2, dist2, x[3];
      int minId = 0;
      for (minDist2=VTK_DOUBLE_MAX, i=0; i<numPts; i++)
        {
        inPts->GetPoint(i,x);
        dist2 = vtkMath::Distance2BetweenPoints(x,this->ClosestPoint);
        if ( dist2 < minDist2 )
          {
          minId = i;
          minDist2 = dist2;
          }
        }
      this->Mesh->GetPointCells(minId,ncells,cells);
      for (unsigned short j=0; j < ncells; ++j)
        {
        this->Wave.push_back(cells[j]);
        }
      }
    this->UpdateProgress (0.5);

    //mark all seeded regions
    this->TraverseAndMark ();
    this->RegionSizes->InsertValue(this->RegionNumber,this->NumCellsInRegion);
    this->UpdateProgress (0.9);
    }//else extracted seeded cells

  vtkDebugMacro (<<"Extracted " << this->RegionNumber << " region(s)");

  // Now that points and cells have been marked, traverse these lists pulling
  // everything that has been visited.
  //
  //Pass through point data that has been visited
  outputPD->CopyAllocate(pd);
  outputCD->CopyAllocate(cd);

  for (i=0; i < numPts; i++)
    {
    if ( this->PointMap[i] > -1 )
      {
      newPts->InsertPoint(this->PointMap[i],inPts->GetPoint(i));
      outputPD->CopyData(pd,i,this->PointMap[i]);
      }
    }

  // if coloring regions; send down new scalar data
  if ( this->ColorRegions )
    {
    int idx = outputPD->AddArray(this->NewScalars);
    outputPD->SetActiveAttribute(idx, vtkDataSetAttributes::SCALARS);
    }
  this->NewScalars->Delete();

  output->SetPoints(newPts);
  newPts->Delete();

  // Create output cells. Have to allocate storage first.
  //
  if ( (n=input->GetVerts()->GetNumberOfCells()) > 0 )
    {
    vtkCellArray *newVerts = vtkCellArray::New();
    newVerts->Allocate(n,n);
    output->SetVerts(newVerts);
    newVerts->Delete();
    }
  if ( (n=input->GetLines()->GetNumberOfCells()) > 0 )
    {
    vtkCellArray *newLines = vtkCellArray::New();
    newLines->Allocate(2*n,n);
    output->SetLines(newLines);
    newLines->Delete();
    }
  if ( (n=input->GetPolys()->GetNumberOfCells()) > 0 )
    {
    vtkCellArray *newPolys = vtkCellArray::New();
    newPolys->Allocate(3*n,n);
    output->SetPolys(newPolys);
    newPolys->Delete();
    }
  if ( (n=input->GetStrips()->GetNumberOfCells()) > 0 )
    {
    vtkCellArray *newStrips = vtkCellArray::New();
    newStrips->Allocate(5*n,n);
    output->SetStrips(newStrips);
    newStrips->Delete();
    }

  if ( this->ExtractionMode == VTK_EXTRACT_POINT_SEEDED_REGIONS ||
  this->ExtractionMode == VTK_EXTRACT_CELL_SEEDED_REGIONS ||
  this->ExtractionMode == VTK_EXTRACT_CLOSEST_POINT_REGION ||
  this->ExtractionMode == VTK_EXTRACT_ALL_REGIONS)
    { // extract any cell that's been visited
    for (cellId=0; cellId < numCells; cellId++)
      {
      if ( this->Visited[cellId] >= 0 )
        {
        this->Mesh->GetCellPoints(cellId, npts, pts);
        this->PointIds->Reset();
        for (i=0; i < npts; i++)
          {
          id = this->PointMap[pts[i]];
          this->PointIds->InsertId(i,id);

          // If we asked to mark the visited point ids, mark them.
          if (this->MarkVisitedPointIds)
            {
            this->VisitedPointIds->InsertUniqueId(id);
            }
          }
        newCellId = output->InsertNextCell(this->Mesh->GetCellType(cellId),
                                           this->PointIds);
        outputCD->CopyData(cd,cellId,newCellId);
        }
      }
    }
  else if ( this->ExtractionMode == VTK_EXTRACT_SPECIFIED_REGIONS )
    {
    for (cellId=0; cellId < numCells; cellId++)
      {
      int inReg, regionId;
      if ( (regionId=this->Visited[cellId]) >= 0 )
        {
        for (inReg=0,i=0; i<this->SpecifiedRegionIds->GetNumberOfIds(); i++)
          {
          if ( regionId == this->SpecifiedRegionIds->GetId(i) )
            {
            inReg = 1;
            break;
            }
          }
        if ( inReg )
          {
          this->Mesh->GetCellPoints(cellId, npts, pts);
          this->PointIds->Reset ();
          for (i=0; i < npts; i++)
            {
            id = this->PointMap[pts[i]];
            this->PointIds->InsertId(i,id);

            // If we asked to mark the visited point ids, mark them.
            if (this->MarkVisitedPointIds)
              {
              this->VisitedPointIds->InsertUniqueId(id);
              }

            }
          newCellId = output->InsertNextCell(this->Mesh->GetCellType(cellId),
                                             this->PointIds);
          outputCD->CopyData(cd,cellId,newCellId);
          }
        }
      }
    }
  else //extract largest region
    {
    for (cellId=0; cellId < numCells; cellId++)
      {
      if ( this->Visited[cellId] == largestRegionId )
        {
        this->Mesh->GetCellPoints(cellId, npts, pts);
        this->PointIds->Reset ();
        for (i=0; i < npts; i++)
          {
          id = this->PointMap[pts[i]];
          this->PointIds->InsertId(i,id);

          // If we asked to mark the visited point ids, mark them.
          if (this->MarkVisitedPointIds)
            {
            this->VisitedPointIds->InsertUniqueId(id);
            }
          }
        newCellId = output->InsertNextCell(this->Mesh->GetCellType(cellId),
                                           this->PointIds);
        outputCD->CopyData(cd,cellId,newCellId);
        }
      }
   }

  delete [] this->Visited;
  delete [] this->PointMap;
  this->Mesh->Delete();
  output->Squeeze();
  this->CellIds->Delete();
  this->PointIds->Delete();

  int num = this->GetNumberOfExtractedRegions();
  vtkIdType count = 0;

  for (int ii = 0; ii < num; ii++)
    {
    count += this->RegionSizes->GetValue (ii);
    }
  vtkDebugMacro (<< "Total # of cells accounted for: " << count);
  vtkDebugMacro (<<"Extracted " << output->GetNumberOfCells() << " cells");

  return 1;
}

// Mark current cell as visited and assign region number.  Note:
// traversal occurs across shared vertices.
//
void vtkPolyDataConnectivityFilter::TraverseAndMark ()
{
  vtkIdType cellId, ptId, numIds, i;
  int j, k;
  vtkIdType *pts, *cells, npts;
  unsigned short ncells;
  const vtkIdType numCells = this->Mesh->GetNumberOfCells();

  while ( (numIds=static_cast<vtkIdType>(this->Wave.size())) > 0 )
    {
    for ( i=0; i < numIds; i++ )
      {
      cellId = this->Wave[i];
      if ( this->Visited[cellId] < 0 )
        {
        this->Visited[cellId] = this->RegionNumber;
        this->NumCellsInRegion++;
        this->Mesh->GetCellPoints(cellId, npts, pts);

        for (j=0; j < npts; j++)
          {
          if ( this->PointMap[ptId=pts[j]] < 0 )
            {
            this->PointMap[ptId] = this->PointNumber++;
            vtkArrayDownCast<vtkIdTypeArray>(this->NewScalars)->SetValue(
              this->PointMap[ptId], this->RegionNumber);

            this->Mesh->GetPointCells(ptId,ncells,cells);

            // check connectivity criterion (geometric + scalar)
            if ( this->InScalars )
              {
              for (k = 0; k < ncells; ++k)
                {
                if (this->IsScalarConnected(cells[k]))
                  {
                  this->Wave2.push_back(cells[k]);
                  }
                }
              }
            else
              {
              for (k = 0; k < ncells; ++k)
                {
                this->Wave2.push_back(cells[k]);
                }
              }
            }
          }//for all points of this cell
        }//if cell not yet visited
      }//for all cells in this wave

    this->Wave = this->Wave2;
    this->Wave2.clear();
    this->Wave2.reserve(numCells);
    } //while wave is not empty

  return;
}

// --------------------------------------------------------------------------
int vtkPolyDataConnectivityFilter::IsScalarConnected( vtkIdType cellId )
{
  double s;

  this->Mesh->GetCellPoints(cellId, this->NeighborCellPointIds);
  const int numScalars = this->NeighborCellPointIds->GetNumberOfIds();

  this->CellScalars->SetNumberOfTuples(numScalars);
  this->InScalars->GetTuples(this->NeighborCellPointIds,
                             this->CellScalars);

  double range[2] = {VTK_DOUBLE_MAX, VTK_DOUBLE_MIN};

  // Loop through the cell points.
  for (int ii=0; ii < numScalars;  ii++)
    {
    s = this->CellScalars->GetComponent(ii, 0);
    if ( s < range[0] )
      {
      range[0] = s;
      }
    if ( s > range[1] )
      {
      range[1] = s;
      }
    }

  // Check if the scalars lie within the user supplied scalar range.

  if ( this->FullScalarConnectivity )
    {
    // All points in this cell must lie in the user supplied scalar range
    // for this cell to qualify as being connected.
    if (range[0] >= this->ScalarRange[0] &&
        range[1] <= this->ScalarRange[1])
      {
      return 1;
      }
    }
  else
    {
    // Any point from this cell must lie is the user supplied scalar range
    // for this cell to qualify as being connected
    if ( range[1] >= this->ScalarRange[0] &&
         range[0] <= this->ScalarRange[1] )
      {
      return 1;
      }
    }

  return 0;
}

// --------------------------------------------------------------------------
// Obtain the number of connected regions.
int vtkPolyDataConnectivityFilter::GetNumberOfExtractedRegions()
{
  return this->RegionSizes->GetMaxId() + 1;
}

// Initialize list of point ids/cell ids used to seed regions.
void vtkPolyDataConnectivityFilter::InitializeSeedList()
{
  this->Modified();
  this->Seeds->Reset();
}

// Add a seed id (point or cell id). Note: ids are 0-offset.
void vtkPolyDataConnectivityFilter::AddSeed(int id)
{
  this->Modified();
  this->Seeds->InsertNextId(id);
}

// Delete a seed id (point or cell id). Note: ids are 0-offset.
void vtkPolyDataConnectivityFilter::DeleteSeed(int id)
{
  this->Modified();
  this->Seeds->DeleteId(id);
}

// Initialize list of region ids to extract.
void vtkPolyDataConnectivityFilter::InitializeSpecifiedRegionList()
{
  this->Modified();
  this->SpecifiedRegionIds->Reset();
}

// Add a region id to extract. Note: ids are 0-offset.
void vtkPolyDataConnectivityFilter::AddSpecifiedRegion(int id)
{
  this->Modified();
  this->SpecifiedRegionIds->InsertNextId(id);
}

// Delete a region id to extract. Note: ids are 0-offset.
void vtkPolyDataConnectivityFilter::DeleteSpecifiedRegion(int id)
{
  this->Modified();
  this->SpecifiedRegionIds->DeleteId(id);
}

void vtkPolyDataConnectivityFilter::PrintSelf(ostream& os, vtkIndent indent)
{
  this->Superclass::PrintSelf(os,indent);

  os << indent << "Extraction Mode: ";
  os << this->GetExtractionModeAsString() << "\n";

  os << indent << "Closest Point: (" << this->ClosestPoint[0] << ", "
     << this->ClosestPoint[1] << ", " << this->ClosestPoint[2] << ")\n";

  os << indent << "Color Regions: " << (this->ColorRegions ? "On\n" : "Off\n");

  os << indent << "Scalar Connectivity: "
     << (this->ScalarConnectivity ? "On\n" : "Off\n");

  if (this->ScalarConnectivity)
    {
    os << indent << "Full Connectivity: "
       << (this->FullScalarConnectivity ? "On\n" : "Off\n");
    }

  os << indent << "Mark visited point ids: "
     << (this->MarkVisitedPointIds ? "On\n" : "Off\n");
  if (this->MarkVisitedPointIds)
    {
    this->VisitedPointIds->PrintSelf(os, indent.GetNextIndent());
    }

  double *range = this->GetScalarRange();
  os << indent << "Scalar Range: (" << range[0] << ", " << range[1] << ")\n";

  os << indent << "RegionSizes: ";
  if (this->GetNumberOfExtractedRegions() > 10)
    {
    os << "Only first ten of "
       << this->GetNumberOfExtractedRegions() << " listed";
    }
  os << std::endl;

  for (vtkIdType id = 0;
       id < (this->GetNumberOfExtractedRegions() > 10
             ? 10 : this->GetNumberOfExtractedRegions());
       id++)
    {
    os << indent << indent
       << id << ": " << this->RegionSizes->GetValue(id) << std::endl;
    }

  os << indent << "Output Points Precision: " << this->OutputPointsPrecision << "\n";
}
