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

  Program:   Visualization Toolkit
  Module:    vtkPOPReader.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.

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

#include "vtkExtentTranslator.h"
#include "vtkFloatArray.h"
#include "vtkImageData.h"
#include "vtkImageReader.h"
#include "vtkImageWrapPad.h"
#include "vtkMath.h"
#include "vtkObjectFactory.h"
#include "vtkPointData.h"
#include "vtkStructuredGrid.h"

#include <ctype.h>
#include <math.h>

vtkCxxRevisionMacro(vtkPOPReader, "1.15");
vtkStandardNewMacro(vtkPOPReader);

//----------------------------------------------------------------------------
vtkPOPReader::vtkPOPReader()
{
  this->Radius = 60000.0;
  
  this->Dimensions[0] = 3600;
  this->Dimensions[1] = 2400;
  
  this->GridFileName = NULL;
  this->FileName = NULL;
  
  this->NumberOfArrays = 0;
  this->MaximumNumberOfArrays = 0;
  this->ArrayNames = NULL;
  this->ArrayFileNames = NULL;
  this->ArrayOffsets = NULL;
  this->ArrayFileDimensionality = 3;

  this->UFlowFileName = NULL;
  this->UFlowFileOffset = 0;
  this->VFlowFileName = NULL;
  this->VFlowFileOffset = 0;

  this->DepthValues = vtkFloatArray::New();

  this->ClipExtent[0] = -VTK_LARGE_INTEGER;
  this->ClipExtent[1] = VTK_LARGE_INTEGER;
  this->ClipExtent[2] = -VTK_LARGE_INTEGER;
  this->ClipExtent[3] = VTK_LARGE_INTEGER;
  this->ClipExtent[4] = -VTK_LARGE_INTEGER;
  this->ClipExtent[5] = VTK_LARGE_INTEGER;

  this->NumberOfGhostLevels = 1;
} 

//----------------------------------------------------------------------------
vtkPOPReader::~vtkPOPReader()
{ 
  this->SetFileName(NULL);
  this->SetGridFileName(NULL);
  this->DeleteArrays();
  
  this->DepthValues->Delete();
  this->DepthValues = NULL;
}


//----------------------------------------------------------------------------
void vtkPOPReader::DeleteArrays()
{
  int i;

  for (i = 0; i < this->NumberOfArrays; ++i)
    {
    if (this->ArrayNames && this->ArrayNames[i])
      {
      delete [] this->ArrayNames[i];
      this->ArrayNames[i] = NULL;
      }
    if (this->ArrayFileNames && this->ArrayFileNames[i])
      {
      delete [] this->ArrayFileNames[i];
      this->ArrayFileNames[i] = NULL;
      }
    }
  if (this->ArrayNames)
    {
    delete [] this->ArrayNames;
    this->ArrayNames = NULL;
    }
  if (this->ArrayFileNames)
    {
    delete [] this->ArrayFileNames;
    this->ArrayFileNames = NULL;
    }
  if (this->ArrayOffsets)
    {
    delete [] this->ArrayOffsets;
    this->ArrayOffsets = NULL;
    }

  this->NumberOfArrays = 0;
  this->MaximumNumberOfArrays = 0;
}

//----------------------------------------------------------------------------
void vtkPOPReader::AddArray(char *arrayName, char *fileName, unsigned long offset)
{
  if (this->NumberOfArrays == this->MaximumNumberOfArrays)
    {
    int idx;
    char **tmp1, **tmp2;
    unsigned long *tmp3;

    this->MaximumNumberOfArrays += 20;
    tmp1 = new char*[this->MaximumNumberOfArrays];
    tmp2 = new char*[this->MaximumNumberOfArrays];
    tmp3 = new unsigned long[this->MaximumNumberOfArrays];
    for (idx = 0; idx < this->NumberOfArrays; ++idx)
      {
      tmp1[idx] = this->ArrayNames[idx];
      tmp2[idx] = this->ArrayFileNames[idx];
      tmp3[idx] = this->ArrayOffsets[idx];
      }
    delete [] this->ArrayNames;
    this->ArrayNames = tmp1;
    delete [] this->ArrayFileNames;
    this->ArrayFileNames = tmp2;
    delete [] this->ArrayOffsets;
    this->ArrayOffsets = tmp3;
    }
  
  this->ArrayNames[this->NumberOfArrays] = new char[strlen(arrayName)+1];
  strcpy(this->ArrayNames[this->NumberOfArrays], arrayName);

  this->ArrayFileNames[this->NumberOfArrays] = new char[strlen(fileName)+1];
  strcpy(this->ArrayFileNames[this->NumberOfArrays], fileName);

  this->ArrayOffsets[this->NumberOfArrays] = offset;

  ++this->NumberOfArrays;
}


//----------------------------------------------------------------------------
void vtkPOPReader::ExecuteInformation()
{
  int xDim, yDim, zDim;
  
  this->ReadInformationFile();  
  
  xDim = this->Dimensions[0]+1;
  yDim = this->Dimensions[1];
  zDim = this->DepthValues->GetNumberOfTuples();  

  // Clip should be no larger than the whole extent.
  if (this->ClipExtent[0] < 0 ||
      this->ClipExtent[0] - this->NumberOfGhostLevels < 0)
    {
    this->ClipExtent[0] = 0;
    }
  else
    {
    this->ClipExtent[0] -= this->NumberOfGhostLevels;
    }
  if (this->ClipExtent[2] < this->NumberOfGhostLevels)
    {
    this->ClipExtent[2] = 0;
    }
  else
    {
    this->ClipExtent[2] -= this->NumberOfGhostLevels;
    }
  if (this->ClipExtent[4] < this->NumberOfGhostLevels)
    {
    this->ClipExtent[4] = 0;
    }
  else
    {
    this->ClipExtent[4] -= this->NumberOfGhostLevels;
    }
  if (this->ClipExtent[1] > xDim-1 - this->NumberOfGhostLevels)
    {
    this->ClipExtent[1] = xDim-1;
    }
  else
    {
    this->ClipExtent[1] += this->NumberOfGhostLevels;
    }
  if (this->ClipExtent[3] > yDim-1 - this->NumberOfGhostLevels)
    {
    this->ClipExtent[3] = yDim-1;
    }
  else
    {
    this->ClipExtent[3] += this->NumberOfGhostLevels;
    }
  if (this->ClipExtent[5] > zDim-1 - this->NumberOfGhostLevels)
    {
    this->ClipExtent[5] = zDim-1;
    }
  else
    {
    this->ClipExtent[5] += this->NumberOfGhostLevels;
    }

  this->GetOutput()->SetWholeExtent(this->ClipExtent);
}

//----------------------------------------------------------------------------
void vtkPOPReader::Execute()
{
  vtkStructuredGrid *output;
  vtkPoints *points;
  vtkImageData *image;
  vtkDataArray *array;
  int ext[6];
  int i;

  output = this->GetOutput();
  
  cout << "Reading POP file\n";
  cout.flush();

  // Set up the extent of the grid image.
  ext[0] = ext[2] = ext[4] = 0;
  ext[1] = this->Dimensions[0]-1;
  ext[3] = this->Dimensions[1]-1;
  ext[5] = 1;
  
  vtkImageReader *reader = vtkImageReader::New();
  reader->SetFileDimensionality(3);
  reader->SetDataExtent(ext);
  reader->SetFileName(this->GridFileName);
  reader->SetDataByteOrderToBigEndian();
  reader->SetNumberOfScalarComponents(1);
  reader->SetDataScalarTypeToDouble();
  reader->SetHeaderSize(0);
  vtkImageWrapPad *wrap = vtkImageWrapPad::New();
  wrap->SetInput(reader->GetOutput());
  ++ext[1];
  wrap->SetOutputWholeExtent(ext);

  image = wrap->GetOutput();
  output->GetUpdateExtent(ext);
  output->SetExtent(ext);
  ext[4] = 0;
  ext[5] = 1;
  image->SetUpdateExtent(ext);
  image->Update();
  
  // Create the grid points from the grid image.
  points = this->ReadPoints(image);
  output->SetPoints(points);
  points->Delete();
  points = NULL;
  
  // Now read in the arrays.
  // Set up the extent of the grid image.
  ext[0] = ext[2] = ext[4] = 0;
  ext[1] = this->Dimensions[0]-1;
  ext[3] = this->Dimensions[1]-1;
  ext[5] = this->DepthValues->GetNumberOfTuples()-1;
  reader->SetDataExtent(ext);
  reader->SetDataScalarTypeToFloat();
  reader->SetFileDimensionality(this->ArrayFileDimensionality);
  ++ext[1];
  wrap->SetOutputWholeExtent(ext);
  for (i = 0; i < this->NumberOfArrays; ++i)
    {
    if (this->ArrayFileNames[i] && this->ArrayNames[i])
      {
      if (this->ArrayFileDimensionality == 3)
        {
        reader->SetFileName(this->ArrayFileNames[i]);
        }
      else if (this->ArrayFileDimensionality == 2)
        {
        reader->SetFilePattern("%s.%02d");
        reader->SetFilePrefix(this->ArrayFileNames[i]);
        }
      else
        {
        vtkErrorMacro("FileDimensionality can only be 2 or 3.");
        reader->Delete();
        wrap->Delete();
        return;
        }
      reader->SetHeaderSize(this->ArrayOffsets[i] * 4 
                            * this->Dimensions[0] * this->Dimensions[1]);
      // Just in case.
      //reader->SetHeaderSize(0);
      output->GetUpdateExtent(ext);
      image = wrap->GetOutput();
      image->SetUpdateExtent(ext);
      image->Update();
      array = image->GetPointData()->GetScalars();
      array->SetName(this->ArrayNames[i]);
      
      output->GetPointData()->AddArray(array);
      image->ReleaseData();
      }
    }
  reader->Delete();
  reader = NULL;
  wrap->Delete();
  wrap = NULL;

  // If there is flow defined.
  this->ReadFlow();
}


//----------------------------------------------------------------------------
vtkPoints *vtkPOPReader::GeneratePoints()
{
  /*
  vtkPoints *points;
  vtkImageData *temp;
  double x, y, z, radius;
  double theta, phi;
  int i, j;
  int *wholeExt;
  int xDim, yDim;
  int *ext;  
  int id;
  
  //temp = this->GetInput();
  wholeExt = temp->GetWholeExtent();
  if (wholeExt[0] != 0 || wholeExt[2] != 0 || wholeExt[4] != 0)
    {
    vtkErrorMacro("Expecting whole extent to start at 0.");
    return NULL;
    }
  xDim = wholeExt[1]+1;
  yDim = wholeExt[3]+1;  
  ext = temp->GetExtent();
  
  points = vtkPoints::New();
  points->Allocate(xDim*yDim);
  id = 0;
  radius = 20000.0;
  for (j = ext[2]; j <= ext[3]; ++j)
    {
    phi = (double)j * vtkMath::Pi() / (double)(yDim);
    for (i = ext[0]; i <= ext[1]; ++i)
      {
      theta = (double)i * 2.0 * vtkMath::Pi() / (double)(xDim);
      y = cos(phi)*radius;
      x = sin(theta)*sin(phi)*radius;
      z = cos(theta)*sin(phi)*radius;
      points->SetPoint(id, x, y, z);
      ++id;
      }
    }
  
  return points;
  */
  return NULL;
}




//----------------------------------------------------------------------------
vtkPoints *vtkPOPReader::ReadPoints(vtkImageData *image)
{
  vtkPoints *points;
  double x, y, z, depth, radius;
  double theta, phi;
  int i, j, k;
  int id, num;
  // The only different between these two is the z extent.
  // We should probably ditch ext and user update extent to make things simpler.
  int *updateExt = this->GetOutput()->GetUpdateExtent();
  int *ext = image->GetExtent();
  
  points = vtkPoints::New();
  num = (ext[1]-ext[0]+1)*(ext[3]-ext[2]+1)*(updateExt[5]-updateExt[4]+1);
  points->Allocate(num);
  points->SetNumberOfPoints(num);
  
  id = 0;
  for (k = updateExt[4]; k <= updateExt[5]; ++k)
    {
    depth = this->DepthValues->GetValue(k);
    radius = this->Radius - depth;
    for (j = ext[2]; j <= ext[3]; ++j)
      {
      for (i = ext[0]; i <= ext[1]; ++i)
        {      
        phi = (double)(image->GetScalarComponentAsFloat(i, j, 0, 0));
        theta = (double)(image->GetScalarComponentAsFloat(i, j, 1, 0));
        phi += vtkMath::Pi()/2.0;
        y = -cos(phi)*radius;
        x = sin(theta)*sin(phi)*radius;
        z = cos(theta)*sin(phi)*radius;
        points->SetPoint(id, x, y, z);
        ++id;
        }
      }
    }
  
  return points;
}


//==================== Stuff for reading the pop file ========================



//----------------------------------------------------------------------------
void vtkPOPReader::ReadInformationFile()
{
  ifstream *file;
  int i=0, num;
  float tempf;
  char str[256];

  this->DeleteArrays();
  this->DepthValues->Reset();
  this->SetUFlowFileName(NULL);
  this->SetVFlowFileName(NULL);
  this->UFlowFileOffset = this->VFlowFileOffset = 0;
  if(!this->FileName)
    {
    return;
    }
  file = new ifstream(this->FileName, ios::in);
  
  while (1)
    {
    // Read Key
    *file >> str;
    if (file->fail())
      {
      file->close();
      delete file;
      return;
      }
    
    if (strcmp(str, "Dimensions") == 0)
      {
      *file >> num;
      this->Dimensions[0] = num;
      *file >> num;
      this->Dimensions[1] = num;
      }

    else if (strcmp(str, "GridFileName") == 0)
      {
      *file >> str;
      this->SetGridName(str);
      }

    else if (strcmp(str, "NumberOfArrays") == 0)
      {
      char str2[256];
      unsigned long offset;
      *file >> num;
      for (i = 0; i < num; ++i)
        {
        *file >> str;
        *file >> str2;
        *file >> offset;
        if (file->fail())
          {
          vtkErrorMacro("Error reading array name " << i);    
          delete file;
          return;
          }
        this->AddArrayName(str, str2, offset);
        }
      }

    else if (strcmp(str, "ArrayFileDimensionality") == 0)
      {
      *file >> num;
      if (file->fail())
        {
        vtkErrorMacro("Error reading array name " << i);    
        delete file;
        return;
        }
      this->ArrayFileDimensionality = num;
      }

    else if (strcmp(str, "Flow") == 0)
      {
      char *tmp = NULL;
      char str2[256];
      unsigned long offset;
      *file >> num;
      for (i = 0; i < num; ++i)
        {
        *file >> str;
        *file >> str2;
        *file >> offset;

        if (file->fail())
          {
          vtkErrorMacro("Error reading flow component " << i);    
          delete file;
          return;
          }
  
        if (strcmp(str,"u") == 0)
          {
          if (str2[0] != '/' && str2[1] != ':')
            {
            tmp = this->MakeFileName(str2);
            this->SetUFlowFileName(tmp);
            delete [] tmp;
            }
          else
            {
            this->SetUFlowFileName(str2);
            }
          this->UFlowFileOffset = offset;
          }
        else if (strcmp(str,"v") == 0)
          {
          if (str2[0] != '/' && str2[1] != ':')
            {
            tmp = this->MakeFileName(str2);
            this->SetVFlowFileName(tmp);
            delete [] tmp;
            }
          else
            {
            this->SetVFlowFileName(str2);
            }
          this->VFlowFileOffset = offset;
          }
        }
      }

    else if (strcmp(str, "NumberOfDepthValues") == 0)
      {
      *file >> num;
      for (i = 0; i < num; ++i)
        {
        *file >> str;
        if (file->fail())
          {
          vtkErrorMacro("Error reading depth value " << i);    
          delete file;
          return;
          }
        tempf = atof(str);
        this->DepthValues->InsertNextValue(tempf);
        }
      }
    }
}

//----------------------------------------------------------------------------
void vtkPOPReader::SetGridName(char *name)
{
  if (name[0] == '/' || name[1] == ':')
    {
    this->SetGridFileName(name);
    return;
    }
  
  char *tmp;
  
  tmp = this->MakeFileName(name);
  this->SetGridFileName(tmp);
  delete [] tmp;
}

//----------------------------------------------------------------------------
// This will append the full path onto the file name. (using the grid path/
void vtkPOPReader::AddArrayName(char *name, char *fileName, unsigned long offset)
{
  char *tmp;

  if (fileName[0] == '/' || fileName[1] == ':')
    {
    this->AddArray(name, fileName, offset);
    return;
    }
  
  tmp = this->MakeFileName(fileName);
  this->AddArray(name, tmp, offset);
  delete [] tmp;
}

//----------------------------------------------------------------------------
int vtkPOPReader::IsFileName(char *name)
{
  while (name && *name)
    {
    if (*name == '/')
      {
      return 1;
      }
    ++name;
    }
  
  return 0;  
}

//----------------------------------------------------------------------------
char *vtkPOPReader::MakeFileName(char *name)
{
  char *fileName;
  char *tmp1;
  char *tmp2;
  char *start;
  
  if (name == NULL)
    {
    vtkErrorMacro("No name.");
    return NULL;
    }
  
  if (this->FileName == NULL)
    {
    fileName = new char[strlen(name) + 1];
    strcpy(fileName, name);
    return fileName;
    }
  
  fileName = new char[strlen(this->FileName) + strlen(name) + 1];
  tmp1 = this->FileName;
  tmp2 = fileName;
  start = fileName;
  while (tmp1 && *tmp1)
    {
    *tmp2 = *tmp1;
    if (*tmp1 == '/')
      {
      start = tmp2+1;
      }
    ++tmp1;
    ++tmp2;
    }
  
  strcpy(start, name);
  
  return fileName;
}

  

//----------------------------------------------------------------------------
void vtkPOPReader::ReadFlow()
{
  vtkStructuredGrid *output;
  vtkDataArray *array;
  vtkImageData *uImage, *vImage, *fImage;
  int updateExt[6], wholeExt[6], ext[6];
  int idx, u, v, w;
  float *pf, *pu, *pv;
  float v0, v2, w0, u0, u2;
  float du, dv, dw;
  int uvInc0, uvInc1, uvInc2;
  int vMin, vMax;
  vtkPoints *pts;
  float *pp;
  int pfInc1, pfInc2;
  float nv[3], axisW[3], axisV[3], axisU[3];
  float tmp;

  if (this->UFlowFileName == NULL || this->VFlowFileName == NULL)
    {
    return;
    }

  output = this->GetOutput();
  pts = output->GetPoints();

  ext[0] = ext[2] = ext[4] = 0;
  ext[1] = this->Dimensions[0]-1;
  ext[3] = this->Dimensions[1]-1;
  ext[5] = this->DepthValues->GetNumberOfTuples()-1;

  vtkImageReader *reader = vtkImageReader::New();
  reader->SetFileDimensionality(this->ArrayFileDimensionality);
  reader->SetDataExtent(ext);
  reader->SetDataByteOrderToBigEndian();
  reader->SetNumberOfScalarComponents(1);
  reader->SetDataScalarTypeToFloat();
  reader->SetHeaderSize(0);
  vtkImageWrapPad *wrap = vtkImageWrapPad::New();
  wrap->SetInput(reader->GetOutput());
  // To complete the last row (shared with the first row).
  ++ext[1];
  // We will need ghost cells. Poles are discontinuities.
  // U is cyclical
  --ext[0];
  ++ext[1];
  wrap->SetOutputWholeExtent(ext);
  
  // Figure out what extent we need for the request.
  wrap->GetOutputWholeExtent(wholeExt);
  output->GetUpdateExtent(updateExt);
  if (wholeExt[5] != updateExt[5])
    {
    vtkErrorMacro("Requested extent does not have bottom slice required for correct completion of the flow vectors.");
    }

  output->GetUpdateExtent(ext);
  for (idx = 0; idx < 3; ++idx)
    {
    --ext[idx*2];
    ++ext[idx*2+1];
    if (ext[idx*2] < wholeExt[idx*2])
      {
      ext[idx*2] = wholeExt[idx*2];
      }
    if (ext[idx*2+1] > wholeExt[idx*2+1])
      {
      ext[idx*2+1] = wholeExt[idx*2+1];
      }
    }

  uImage = vtkImageData::New();
  // Set up the reader with the appropriate filename.
      if (this->ArrayFileDimensionality == 3)
        {
        reader->SetFileName(this->UFlowFileName);
        }
      else if (this->ArrayFileDimensionality == 2)
        {
        reader->SetFilePattern("%s.%02d");
        reader->SetFilePrefix(this->UFlowFileName);
        }
      else
        {
        vtkErrorMacro("FileDimensionality can only be 2 or 3.");
        reader->Delete();
        wrap->Delete();
        return;
        }
  reader->SetHeaderSize(this->UFlowFileOffset * 4 
                  * this->Dimensions[0] * this->Dimensions[1]);
  wrap->SetOutput(uImage);
  uImage->SetUpdateExtent(ext);
  uImage->Update();

  vImage = vtkImageData::New();
  // Set up the reader with the appropriate filename.
      if (this->ArrayFileDimensionality == 3)
        {
        reader->SetFileName(this->VFlowFileName);
        }
      else if (this->ArrayFileDimensionality == 2)
        {
        reader->SetFilePattern("%s.%02d");
        reader->SetFilePrefix(this->VFlowFileName);
        }
      else
        {
        vtkErrorMacro("FileDimensionality can only be 2 or 3.");
        reader->Delete();
        wrap->Delete();
        return;
        }
  reader->SetHeaderSize(this->VFlowFileOffset * 4 
                  * this->Dimensions[0] * this->Dimensions[1]);
  wrap->SetOutput(vImage);
  vImage->SetUpdateExtent(ext);
  vImage->Update();

  uvInc0 = 1;
  uvInc1 = ext[1]-ext[0]+1;
  uvInc2 = uvInc1 * (ext[3]-ext[2]+1);
  vMin = ext[2];
  vMax = ext[3];

  reader->Delete();
  reader = NULL;
  wrap->Delete();
  wrap = NULL;

  fImage = vtkImageData::New();
  fImage->SetExtent(updateExt);
  fImage->SetNumberOfScalarComponents(3);
  fImage->SetScalarType(VTK_FLOAT);
  fImage->AllocateScalars();

  pfInc1 = 3*(updateExt[1]-updateExt[0]+1);
  pfInc2 = (updateExt[1]-updateExt[0]+1)*(updateExt[3]-updateExt[2]+1)*3;

  // Central differences is good, but I do not like it for the
  // z/propagation direction (alternation).  Normal difference
  // produces a shift.  As a start, I will use it any way.
  // I could always average the top and bottom versions...

  // Now do the computation from bottom to top.
  // Since dw is uniform across a level, forget about traversing the points
  // back to front.  Just do the first slice always.
  pp = pts->GetPoint(0);  
  for (v = updateExt[2]; v <= updateExt[3]; ++v)
    {
    for (u = updateExt[0]; u <= updateExt[1]; ++u)
      {
      // Loose a little efficiency here, but ...
      pf = (float*)fImage->GetScalarPointer(u, v, updateExt[5]);
      pu = (float*)uImage->GetScalarPointer(u, v, updateExt[5]);
      pv = (float*)vImage->GetScalarPointer(u, v, updateExt[5]);
      // Find the coordinate transform (and deltas as a side effect).
      // Except for dw, these are constant up a column.
      // W is just the noramlize vector 0->p.
      axisW[0] = pp[0];
      axisW[1] = pp[1];
      axisW[2] = pp[2];
      vtkMath::Normalize(axisW);
      // Ignore curvature of earth surface. Handle boundaries.
      if (v == updateExt[2])
        {
        axisV[0] = pp[0] - pp[pfInc1];
        axisV[1] = pp[1] - pp[1+pfInc1];
        axisV[2] = pp[2] - pp[2+pfInc1];
        }
      else
        {
        axisV[0] = pp[-pfInc1] - pp[0];
        axisV[1] = pp[1-pfInc1] - pp[1];
        axisV[2] = pp[2-pfInc1] - pp[2];
        }
      dv = vtkMath::Normalize(axisV);
      // Last U axis.
      if (u == updateExt[0])
        {
        axisU[0] =  pp[3] - pp[0];
        axisU[1] =  pp[4] - pp[1];
        axisU[2] =  pp[5] - pp[2];
        }
      else
        {
        axisU[0] =  pp[0] - pp[-3];
        axisU[1] =  pp[1] - pp[-2];
        axisU[2] =  pp[2] - pp[-1];
        }
      du = vtkMath::Normalize(axisU);

      // Since the points are not used in the inner most loop,
      // move to the next point here.      
      pp += 3;     

      // Now sum the w flow up the column.
      w0 = 0.0;
      for (w = updateExt[5]; w >= updateExt[4]; --w)
        {
        // Find dw (easy because we have the depth values in an array).
        if (w == 0)
          {
          if (this->DepthValues->GetNumberOfTuples() <= 1)
            {
            dw = 0.0;
            }
          else
            {
            dw = this->DepthValues->GetValue(1) - this->DepthValues->GetValue(0);
            }
          }
        else
          {
          dw = this->DepthValues->GetValue(w) - this->DepthValues->GetValue(w-1);
          }

        // Compute w componenet of flow ...
        // Find the five important values for this point (have w0 already).
        // U is circular so does not have boundary checks.
        v0 = v2 = 0.0;
        u0 = pu[-uvInc0];
        u2 = pu[uvInc0];
        if (v < vMax)
          {
          v0 = pv[uvInc1];
          }
        if (v > vMin)
          {
          v2 = pv[-uvInc1];
          }

        // Now fill the vector for this point (uvw coords).
        pf[0] =  *pu;  // i.e. u1
        pf[1] =  *pv;  // i.e. v1
        tmp = 0.5 * (((u0-u2)*dv*dw + (v0-v2)*du*dw)/(du*dv));
        pf[2] = w0 + tmp;
        //pf[2] = 0.0;

        // Before we transform and loose w1, 
        // save it for summing in the next iteration.
        w0 = pf[2];

        // Now compute the vector in the new coordinate system.
        nv[0] = axisU[0]*pf[0] + axisV[0]*pf[1] + axisW[0]*pf[2];
        nv[1] = axisU[1]*pf[0] + axisV[1]*pf[1] + axisW[1]*pf[2];
        nv[2] = axisU[2]*pf[0] + axisV[2]*pf[1] + axisW[2]*pf[2];
        pf[0] = nv[0];
        pf[1] = nv[1];
        pf[2] = nv[2];

        // Move up the column to the next point.
        pf -= pfInc2;
        pu -= uvInc2;
        pv -= uvInc2;
        }
      }
    }
    
  // Delete 
  uImage->Delete();
  vImage->Delete();

  array = fImage->GetPointData()->GetScalars();
  array->SetName("Flow");
      
  output->GetPointData()->AddArray(array);
  fImage->ReleaseData();
  fImage->Delete();
}






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

  if (this->FileName)
    {
    os << indent << "FileName: " << this->FileName << endl;
    }
  if (this->GridFileName)
    {
    os << indent << "GridFileName: " << this->GridFileName << endl;
    }

  if (this->UFlowFileName)
    {
    os << indent << "UFlowFileName: " << this->UFlowFileName << endl;
    }
  if (this->VFlowFileName)
    {
    os << indent << "VFlowFileName: " << this->VFlowFileName << endl;
    }

  os << indent << "Dimensions: " << this->Dimensions[0] << ", "
     << this->Dimensions[1] << endl;

  os << indent << "Radius: " << this->Radius << endl;

  os << indent << "ClipExtent: " << this->ClipExtent[0] << ", "
     << this->ClipExtent[1] << ", " << this->ClipExtent[2] << ", "
     << this->ClipExtent[3] << ", " << this->ClipExtent[4] << ", "
     << this->ClipExtent[5] << endl;

  os << indent << "NumberOfGhostLevels = " << this->NumberOfGhostLevels << endl;

}

