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

  Program:   Visualization Toolkit
  Module:    vtkSliceCubes.cxx
  Language:  C++
  Date:      $Date$
  Version:   $Revision$

  Copyright (c) 1993-2002 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.

     THIS CLASS IS PATENTED UNDER UNITED STATES PATENT NUMBER 4,710,876
     "System and Method for the Display of Surface Structures Contained
     Within the Interior Region of a Solid Body".
     Application of this software for commercial purposes requires 
     a license grant from GE. Contact:

         Carl B. Horton
         Sr. Counsel, Intellectual Property
         3000 N. Grandview Blvd., W-710
         Waukesha, WI  53188
         Phone:  (262) 513-4022
         E-Mail: Carl.Horton@med.ge.com

     for more information.

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

#include "vtkByteSwap.h"
#include "vtkCharArray.h"
#include "vtkDoubleArray.h"
#include "vtkFloatArray.h"
#include "vtkImageData.h"
#include "vtkIntArray.h"
#include "vtkLongArray.h"
#include "vtkMarchingCubesCases.h"
#include "vtkMath.h"
#include "vtkObjectFactory.h"
#include "vtkShortArray.h"
#include "vtkUnsignedCharArray.h"
#include "vtkUnsignedIntArray.h"
#include "vtkUnsignedLongArray.h"
#include "vtkUnsignedShortArray.h"
#include "vtkVolumeReader.h"

vtkCxxRevisionMacro(vtkSliceCubes, "1.58");
vtkStandardNewMacro(vtkSliceCubes);

vtkCxxSetObjectMacro(vtkSliceCubes,Reader,vtkVolumeReader);

// Description:
// Construct with NULL reader, output FileName specification, and limits 
// FileName.
vtkSliceCubes::vtkSliceCubes()
{
  this->Reader = NULL;
  this->FileName = NULL;
  this->LimitsFileName = NULL;
  this->Value = 0.0;
}

vtkSliceCubes::~vtkSliceCubes()
{
  if (this->FileName)
    {
    delete [] this->FileName;
    }
  if (this->LimitsFileName)
    {
    delete [] this->LimitsFileName;
    }
  this->SetReader(NULL);
}

// Description:
// Method causes object to read slices and generate isosurface.
void vtkSliceCubes::Update()
{
  this->Execute();
}

// Calculate the gradient using central difference.
// NOTE: We calculate the negative of the gradient for efficiency
template <class T>
void ComputePointGradient(int i, int j, int k, int dims[3], 
                          float Spacing[3], float n[3], T *s0, T *s1, T *s2)
{
  float sp, sm;

  // x-direction
  if ( i == 0 )
    {
    sp = s1[i+1 + j*dims[0]];
    sm = s1[i + j*dims[0]];
    n[0] = (sm - sp) / Spacing[0];
    }
  else if ( i == (dims[0]-1) )
    {
    sp = s1[i + j*dims[0]];
    sm = s1[i-1 + j*dims[0]];
    n[0] = (sm - sp) / Spacing[0];
    }
  else
    {
    sp = s1[i+1 + j*dims[0]];
    sm = s1[i-1 + j*dims[0]];
    n[0] = 0.5 * (sm - sp) / Spacing[0];
    }

  // y-direction
  if ( j == 0 )
    {
    sp = s1[i + (j+1)*dims[0]];
    sm = s1[i + j*dims[0]];
    n[1] = (sm - sp) / Spacing[1];
    }
  else if ( j == (dims[1]-1) )
    {
    sp = s1[i + j*dims[0]];
    sm = s1[i + (j-1)*dims[0]];
    n[1] = (sm - sp) / Spacing[1];
    }
  else

    {
    sp = s1[i + (j+1)*dims[0]];
    sm = s1[i + (j-1)*dims[0]];
    n[1] = 0.5 * (sm - sp) / Spacing[1];
    }

  // z-direction
  // z-direction
  if ( k == 0 )
    {
    sp = s2[i + j*dims[0]];
    sm = s1[i + j*dims[0]];
    n[2] = (sm - sp) / Spacing[2];
    }
  else if ( k == (dims[2]-1) )
    {
    sp = s1[i + j*dims[0]];
    sm = s0[i + j*dims[0]];
    n[2] = (sm - sp) / Spacing[2];
    }
  else
    {
    sp = s2[i + j*dims[0]];
    sm = s0[i + j*dims[0]];
    n[2] = 0.5 * (sm - sp) / Spacing[2];
    }
}

template <class T, class S>
int vtkSliceCubesContour(T *slice, S *scalars, int imageRange[2], int dims[3], 
                         float origin[3], float Spacing[3], float value, 
                         float xmin[3], float xmax[3], FILE *outFP, 
                         vtkVolumeReader *reader, unsigned char debug)
{
  S *slice0scalars=NULL, *slice1scalars;
  S *slice2scalars, *slice3scalars;
  T *slice0, *slice1, *slice2, *slice3;
  vtkImageData *sp;
  vtkFloatArray *floatScalars=NULL;
  int numTriangles=0, numComp = 0;
  float s[8];
  int i, j, k, idx, jOffset, ii, index, *vert, jj, sliceSize=0;
  static int CASE_MASK[8] = {1,2,4,8,16,32,64,128};
  VTK_TRIANGLE_CASES *triCase, *triCases;
  EDGE_LIST  *edge;
  float pts[8][3], grad[8][3];
  float t, *x1, *x2, *n1, *n2;
  float xp, yp, zp;
  float point[6];
  static int edges[12][2] = { {0,1}, {1,2}, {3,2}, {0,3},
                              {4,5}, {5,6}, {7,6}, {4,7},
                              {0,4}, {1,5}, {3,7}, {2,6}};

  triCases =  VTK_TRIANGLE_CASES::GetCases();

  if ( slice == NULL ) //have to do conversion to float slice-by-slice
    {
    sliceSize = dims[0] * dims[1];
    floatScalars = vtkFloatArray::New();
    floatScalars->Allocate(sliceSize);
    }

  slice1scalars = NULL;
  slice2scalars = scalars;
  slice2scalars->Register(NULL);

  if (debug)  vtkGenericWarningMacro(<< "  Slice# " << imageRange[0]);

  if ( slice2scalars == NULL )
    {
    return 0;
    }
  if ( slice != NULL )
    {
    slice1 = slice2 = slice2scalars->GetPointer(0);
    }
  else
    {//get as float
    numComp = scalars->GetNumberOfComponents();
    slice2scalars->GetData(0,sliceSize-1,0,numComp-1,floatScalars);
    slice1 = slice2 = (T *) floatScalars->GetPointer(0);
    }
    
  sp = reader->GetImage(imageRange[0]+1);
  slice3scalars = (S *) sp->GetPointData()->GetScalars();
  slice3scalars->Register(NULL);
  sp->Delete();

  if (debug)  vtkGenericWarningMacro(<< "  Slice# " << imageRange[0]+1 );

  if ( slice != NULL )
    {
    slice3 = slice3scalars->GetPointer(0);
    }
  else
    {//get as float: cast is ok because this code is only executed for float type
    slice3scalars->GetData(0,sliceSize-1,0,numComp-1,floatScalars);
    slice3 = (T *) floatScalars->GetPointer(0);
    }

  if ( !slice2 || !slice3 )
    {
    vtkGenericWarningMacro(<< "Cannot allocate data!");
    return 0;
    }

  // Generate triangles and normals from slices
  for (k=0; k < (dims[2]-1); k++)
    {

    // swap things around
    if ( slice0scalars != NULL )
      {
      slice0scalars->Delete();
      }
    slice0scalars = slice1scalars;
    slice0 = slice1;
    slice1scalars = slice2scalars;
    slice1 = slice2;
    slice2scalars = slice3scalars;
    slice2 = slice3;
    if ( k < (dims[2]-2) )
      {
      if (debug)  vtkGenericWarningMacro(<< "  Slice# " << imageRange[0]+k+2);
      sp = reader->GetImage(imageRange[0]+k+2);
      slice3scalars = (S *) sp->GetPointData()->GetScalars();
      if ( slice3scalars == NULL )
        {
        vtkGenericWarningMacro(<< "Can't read all the requested slices");
        goto PREMATURE_TERMINATION;
        }
      slice3scalars->Register(NULL);
      sp->Delete();
      if ( slice != NULL )
        {
        slice3 = slice3scalars->GetPointer(0);
        }
      else
        {//get as float
        slice3scalars->GetData(0,sliceSize-1,0,numComp-1,floatScalars);
        slice3 = (T *) floatScalars->GetPointer(0);
        }
      }

    pts[0][2] = origin[2] + k*Spacing[2];
    zp = origin[2] + (k+1)*Spacing[2];
    for ( j=0; j < (dims[1]-1); j++)
      {
      jOffset = j*dims[0];
      pts[0][1] = origin[1] + j*Spacing[1];
      yp = origin[1] + (j+1)*Spacing[1];
      for ( i=0; i < (dims[0]-1); i++)
        {
        //get scalar values
        idx = i + jOffset;
        s[0] = slice1[idx];
        s[1] = slice1[idx+1];
        s[2] = slice1[idx+1 + dims[0]];
        s[3] = slice1[idx + dims[0]];
        s[4] = slice2[idx];
        s[5] = slice2[idx+1];
        s[6] = slice2[idx+1 + dims[0]];
        s[7] = slice2[idx + dims[0]];

        // Build the case table
        for ( ii=0, index = 0; ii < 8; ii++)
          {
          if ( s[ii] >= value )
            {
            index |= CASE_MASK[ii];
            }
          }

        if ( index == 0 || index == 255 ) // no surface
          {
          continue;
          }
        //create voxel points
        pts[0][0] = origin[0] + i*Spacing[0];
        xp = origin[0] + (i+1)*Spacing[0];

        pts[1][0] = xp;
        pts[1][1] = pts[0][1];
        pts[1][2] = pts[0][2];

        pts[2][0] = xp;
        pts[2][1] = yp;
        pts[2][2] = pts[0][2];

        pts[3][0] = pts[0][0];
        pts[3][1] = yp;
        pts[3][2] = pts[0][2];

        pts[4][0] = pts[0][0];
        pts[4][1] = pts[0][1];
        pts[4][2] = zp;

        pts[5][0] = xp;
        pts[5][1] = pts[0][1];
        pts[5][2] = zp;

        pts[6][0] = xp;
        pts[6][1] = yp;
        pts[6][2] = zp;

        pts[7][0] = pts[0][0];
        pts[7][1] = yp;
        pts[7][2] = zp;

        //create gradients
        ComputePointGradient(i,j, k, dims, Spacing, grad[0],
                             slice0, slice1, slice2);
        ComputePointGradient(i+1,j, k, dims, Spacing, grad[1],
                             slice0, slice1, slice2);
        ComputePointGradient(i+1,j+1, k, dims, Spacing, grad[2],
                             slice0, slice1, slice2);
        ComputePointGradient(i,j+1, k, dims, Spacing, grad[3],
                             slice0, slice1, slice2);
        ComputePointGradient(i,j, k+1, dims, Spacing, grad[4],
                             slice1, slice2, slice3);
        ComputePointGradient(i+1,j, k+1, dims, Spacing, grad[5],
                             slice1, slice2, slice3);
        ComputePointGradient(i+1,j+1, k+1, dims, Spacing, grad[6],
                             slice1, slice2, slice3);
        ComputePointGradient(i,j+1, k+1, dims, Spacing, grad[7],
                             slice1, slice2, slice3);

        triCase = triCases + index;
        edge = triCase->edges;

        for ( ; edge[0] > -1; edge += 3 )
          {
          for (ii=0; ii<3; ii++) //insert triangle
            {
            vert = edges[edge[ii]];
            t = (value - s[vert[0]]) / (s[vert[1]] - s[vert[0]]);
            x1 = pts[vert[0]];
            x2 = pts[vert[1]];
            n1 = grad[vert[0]];
            n2 = grad[vert[1]];
            for (jj=0; jj<3; jj++)
              {
              point[jj] = x1[jj] + t * (x2[jj] - x1[jj]);
              point[jj+3] = n1[jj] + t * (n2[jj] - n1[jj]);
              if (point[jj] < xmin[jj] )
                {
                xmin[jj] = point[jj];
                }
              if (point[jj] > xmax[jj] )
                {
                xmax[jj] = point[jj];
                }
              }
            vtkMath::Normalize(point+3);
            // swap bytes if necessary
            vtkByteSwap::SwapWrite4BERange(point,6,outFP);
            }
          numTriangles++;
          }//for each triangle
        }//for i
      }//for j
    }//for k

  // Close things down
  PREMATURE_TERMINATION:

  fclose(outFP);
  if ( slice == NULL )
    {
    floatScalars->Delete();
    }
  if (slice0scalars && slice0scalars != slice1scalars)
    {
    slice0scalars->Delete();
    }
  if (slice3scalars && slice3scalars != slice2scalars)
    {
    slice3scalars->Delete();
    }
  slice1scalars->Delete();
  slice2scalars->Delete();

  return numTriangles;
}

void vtkSliceCubes::Execute() 
{
  FILE *outFP;
  vtkImageData *tempStructPts;
  vtkDataArray *inScalars;
  int dims[3], imageRange[2];
  float xmin[3], xmax[3];
  float origin[3], Spacing[3];
  int numTriangles = 0;

  // check input/initalize
  vtkDebugMacro(<< "Executing slice cubes");
  if ( this->Reader == NULL )
   {
   vtkErrorMacro(<<"No reader specified...can't generate isosurface");
   return;
   }

  if ( this->FileName == NULL )
   {
   vtkErrorMacro(<<"No FileName specified...can't output isosurface");
   return;
   }

  if ( (outFP = fopen(this->FileName, "wb")) == NULL )
   {
   vtkErrorMacro(<<"Cannot open specified output file...");
   return;
   }

  // get image dimensions from the readers first slice
  this->Reader->GetImageRange(imageRange);
  tempStructPts = this->Reader->GetImage(imageRange[0]);
  tempStructPts->GetDimensions(dims);
  tempStructPts->GetOrigin(origin);
  tempStructPts->GetSpacing(Spacing);
  
  dims[2] = (imageRange[1] - imageRange[0] + 1);

  if ( (dims[0]*dims[1]*dims[2]) <= 1 || dims[2] < 2 )
    {
    vtkErrorMacro(<<"Bad dimensions...slice must be 3D volume");
    return;
    }

  xmin[0]=xmin[1]=xmin[2] = VTK_LARGE_FLOAT;
  xmax[0]=xmax[1]=xmax[2] = -VTK_LARGE_FLOAT;

  inScalars = tempStructPts->GetPointData()->GetScalars();
  if ( inScalars == NULL )
    {
    vtkErrorMacro(<<"Must have scalars to generate isosurface");
    tempStructPts->Delete();
    return;
    }
  inScalars->Register(this);
  tempStructPts->Delete();

  if (inScalars->GetNumberOfComponents() == 1 )
    {
    switch (inScalars->GetDataType())
      {
      case VTK_CHAR:
        {
        vtkCharArray *scalars = (vtkCharArray *)inScalars;
        char *s = scalars->GetPointer(0);
        numTriangles = vtkSliceCubesContour(s,scalars,imageRange,dims,origin,
                               Spacing,this->Value,
                               xmin,xmax,outFP,this->Reader,this->Debug);
        }
      break;
      case VTK_UNSIGNED_CHAR:
        {
        vtkUnsignedCharArray *scalars = (vtkUnsignedCharArray *)inScalars;
        unsigned char *s = scalars->GetPointer(0);
        numTriangles = vtkSliceCubesContour(s,scalars,imageRange,dims,origin,
                               Spacing,this->Value,
                               xmin,xmax,outFP,this->Reader,this->Debug);
        }
      break;
      case VTK_SHORT:
        {
        vtkShortArray *scalars = (vtkShortArray *)inScalars;
        short *s = scalars->GetPointer(0);
        numTriangles = vtkSliceCubesContour(s,scalars,imageRange,dims,origin,
                               Spacing,this->Value,
                               xmin,xmax,outFP,this->Reader,this->Debug);
        }
      break;
      case VTK_UNSIGNED_SHORT:
        {
        vtkUnsignedShortArray *scalars = (vtkUnsignedShortArray *)inScalars;
        unsigned short *s = scalars->GetPointer(0);
        numTriangles = vtkSliceCubesContour(s,scalars,imageRange,dims,origin,
                               Spacing,this->Value,
                               xmin,xmax,outFP,this->Reader,this->Debug);
        }
      break;
      case VTK_INT:
        {
        vtkIntArray *scalars = (vtkIntArray *)inScalars;
        int *s = scalars->GetPointer(0);
        numTriangles = vtkSliceCubesContour(s,scalars,imageRange,dims,origin,
                               Spacing,this->Value,
                               xmin,xmax,outFP,this->Reader,this->Debug);
        }
      break;
      case VTK_UNSIGNED_INT:
        {
        vtkUnsignedIntArray *scalars = (vtkUnsignedIntArray *)inScalars;
        unsigned int *s = scalars->GetPointer(0);
        numTriangles = vtkSliceCubesContour(s,scalars,imageRange,dims,origin,
                               Spacing,this->Value,
                               xmin,xmax,outFP,this->Reader,this->Debug);
        }
      break;
      case VTK_LONG:
        {
        vtkLongArray *scalars = (vtkLongArray *)inScalars;
        long *s = scalars->GetPointer(0);
        numTriangles = vtkSliceCubesContour(s,scalars,imageRange,dims,origin,
                               Spacing,this->Value,
                               xmin,xmax,outFP,this->Reader,this->Debug);
        }
      break;
      case VTK_UNSIGNED_LONG:
        {
        vtkUnsignedLongArray *scalars = (vtkUnsignedLongArray *)inScalars;
        unsigned long *s = scalars->GetPointer(0);
        numTriangles = vtkSliceCubesContour(s,scalars,imageRange,dims,origin,
                               Spacing,this->Value,
                               xmin,xmax,outFP,this->Reader,this->Debug);
        }
      break;
      case VTK_FLOAT:
        {
        vtkFloatArray *scalars = (vtkFloatArray *)inScalars;
        float *s = scalars->GetPointer(0);
        numTriangles = vtkSliceCubesContour(s,scalars,imageRange,dims,origin,
                               Spacing,this->Value,
                               xmin,xmax,outFP,this->Reader,this->Debug);
        }
      break;
      case VTK_DOUBLE:
        {
        vtkDoubleArray *scalars = (vtkDoubleArray *)inScalars;
        double *s = scalars->GetPointer(0);
        numTriangles = vtkSliceCubesContour(s,scalars,imageRange,dims,origin,
                               Spacing,this->Value,
                               xmin,xmax,outFP,this->Reader,this->Debug);
        }
      break;
      }//switch
    }

  else //multiple components have to convert
    {
    vtkFloatArray *scalars = (vtkFloatArray *)inScalars;
    float *s = NULL; //clue to convert data to float
    numTriangles = vtkSliceCubesContour(s,scalars,imageRange,dims,origin,
                           Spacing,this->Value,
                           xmin,xmax,outFP,this->Reader,this->Debug);
    }

  inScalars->UnRegister(this);
  vtkDebugMacro(<<"Created: " << 3*numTriangles << " points, " 
                << numTriangles << " triangles");

  if ( this->LimitsFileName )
    {
    int i;
    float t;

    if ( (outFP = fopen(this->LimitsFileName, "wb")) == NULL )
      {
      vtkWarningMacro(<<"Sorry, couldn't write limits file...");
      }
    else
      {
      for (i=0; i<3; i++)
        {
        t = origin[i] + (dims[i] - 1)*Spacing[i];
        vtkByteSwap::SwapWrite4BERange(origin+i,1,outFP);
        // swap if neccessary
        vtkByteSwap::SwapWrite4BERange(&t,1,outFP);
        }
      for (i=0; i<3; i++)
        {
        vtkByteSwap::SwapWrite4BERange(xmin+i,1,outFP);
        vtkByteSwap::SwapWrite4BERange(xmax+i,1,outFP);
        }
      }
     fclose(outFP);
    }
}

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

  os << indent << "Iso Value: " << this->Value << "\n";

  if ( this->Reader )
    {
    os << indent << "Reader:\n";
    this->Reader->PrintSelf(os,indent.GetNextIndent());
    }
  else
    {
    os << indent << "Reader: (none)\n";
    }

  os << indent << "File Name: " 
     << (this->FileName ? this->FileName : "(none)") << "\n";
  os << indent << "Limits File Name: " 
     << (this->LimitsFileName ? this->LimitsFileName : "(none)") << "\n";
}
