/*=========================================================================
 *
 *  Program:   Visualization Toolkit
 *  Module:    vtkCDIReader.cxx
 *
 *  Copyright (c) 2018 Niklas Roeber, DKRZ Hamburg
 *  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 "vtkCDIReader.h"

#include "vtkCallbackCommand.h"
#include "vtkCellArray.h"
#include "vtkCellData.h"
#include "vtkCellType.h"
#include "vtkDataObject.h"
#include "vtkDoubleArray.h"
#include "vtkDummyController.h"
#include "vtkFieldData.h"
#include "vtkFileSeriesReader.h"
#include "vtkFloatArray.h"
#include "vtkIdTypeArray.h"
#include "vtkInformation.h"
#include "vtkInformationVector.h"
#include "vtkPointData.h"
#include "vtkStreamingDemandDrivenPipeline.h"
#include "vtkStringArray.h"
#include "vtkUnstructuredGrid.h"

#include "vtksys/FStream.hxx"
#include "vtksys/SystemTools.hxx"

#include "cdi_tools.h"

#include <set>
#include <sstream>

constexpr static int MAX_VARS = 100;

struct Point
{
  double Lon;
  double Lat;
};

struct PointWithIndex
{
  Point Pt;
  int Idx;
};

//----------------------------------------------------------------------------
// Internal class to avoid name pollution
//----------------------------------------------------------------------------
class vtkCDIReader::Internal
{
public:
  Internal()
  {
    for (int i = 0; i < MAX_VARS; i++)
    {
      this->CellVarIDs[i] = -1;
      this->DomainVars[i] = std::string("");
    }
  }
  ~Internal() = default;

  int CellVarIDs[MAX_VARS];
  cdi_tools::CDIVar CellVars[MAX_VARS];
  cdi_tools::CDIVar PointVars[MAX_VARS];
  std::string DomainVars[MAX_VARS];

  // The Point data we expect to receive from each process.
  vtkSmartPointer<vtkIdTypeArray> PointsExpectedFromProcessesLengths;
  vtkSmartPointer<vtkIdTypeArray> PointsExpectedFromProcessesOffsets;

  // The Point data we have to send to each process.  Stored as global ids.
  vtkSmartPointer<vtkIdTypeArray> PointsToSendToProcesses;
  vtkSmartPointer<vtkIdTypeArray> PointsToSendToProcessesLengths;
  vtkSmartPointer<vtkIdTypeArray> PointsToSendToProcessesOffsets;
};

namespace
{
//----------------------------------------------------------------------------
// Macro to check new didn't return an error
//----------------------------------------------------------------------------
#define CHECK_NEW(ptr)                                                                             \
  if ((ptr) == nullptr)                                                                            \
  {                                                                                                \
    vtkErrorMacro("new failed!");                                                                  \
    return 0;                                                                                      \
  }

//----------------------------------------------------------------------------
//  Macros for template calls to load cell/Point variables
//----------------------------------------------------------------------------
#define vtkICONTemplateMacro(call)                                                                 \
  vtkTemplateMacroCase(VTK_DOUBLE, double, call);                                                  \
  vtkTemplateMacroCase(VTK_FLOAT, float, call);

#define vtkICONTemplateDispatch(type, call)                                                        \
  switch (type)                                                                                    \
  {                                                                                                \
    vtkICONTemplateMacro(call);                                                                    \
    default:                                                                                       \
      vtkErrorMacro("Unsupported data type: " << (type));                                          \
      abort();                                                                                     \
  }

//----------------------------------------------------------------------------
// Routines for sorting and efficient removal of duplicates
// (c) and thanks to Moritz Hanke (DKRZ)
//----------------------------------------------------------------------------
int ComparePointWithIndex(const void* a, const void* b)
{
  const struct PointWithIndex* a_ = (struct PointWithIndex*)a;
  const struct PointWithIndex* b_ = (struct PointWithIndex*)b;
  double threshold = 1e-22;

  int lon_diff = fabs(a_->Pt.Lon - b_->Pt.Lon) > threshold;
  if (lon_diff)
  {
    return (a_->Pt.Lon > b_->Pt.Lon) ? -1 : 1;
  }

  int lat_diff = fabs(a_->Pt.Lat - b_->Pt.Lat) > threshold;
  if (lat_diff)
  {
    return (a_->Pt.Lat > b_->Pt.Lat) ? -1 : 1;
  }
  return 0;
}
} // end of anonymous namepace

vtkStandardNewMacro(vtkCDIReader);

vtkCxxSetObjectMacro(vtkCDIReader, Controller, vtkMultiProcessController);

//----------------------------------------------------------------------------
// Constructor for vtkCDIReader
//----------------------------------------------------------------------------
vtkCDIReader::vtkCDIReader()
  : Internals(new Internal())
{
  vtkDebugMacro("Starting to create vtkCDIReader...");
  this->Initialized = false;

  this->SetNumberOfInputPorts(0);
  this->SetNumberOfOutputPorts(1);

  this->StreamID = -1;
  this->VListID = -1;
  this->VariableDimensions = vtkSmartPointer<vtkStringArray>::New();
  this->AllDimensions = vtkSmartPointer<vtkStringArray>::New();
  this->AllVariableArrayNames = vtkSmartPointer<vtkStringArray>::New();
  this->InfoRequested = false;
  this->DataRequested = false;
  this->HaveDomainData = false;

  // Setup selection callback to modify this object when array selection changes
  this->SelectionObserver->SetCallback(&vtkCDIReader::SelectionCallback);
  this->SelectionObserver->SetClientData(this);
  this->CellDataArraySelection->AddObserver(vtkCommand::ModifiedEvent, this->SelectionObserver);
  this->PointDataArraySelection->AddObserver(vtkCommand::ModifiedEvent, this->SelectionObserver);
  this->DomainDataArraySelection->AddObserver(vtkCommand::ModifiedEvent, this->SelectionObserver);

  this->Controller = nullptr;
  this->SetController(vtkMultiProcessController::GetGlobalController());
  if (!this->Controller)
  {
    vtkNew<vtkDummyController> dummyController;
    this->SetController(dummyController);
  }

  this->SetDefaults();

  vtkDebugMacro("MAX_VARS:" << MAX_VARS);
  vtkDebugMacro("Created vtkCDIReader");
}

//----------------------------------------------------------------------------
//  Destroys data stored for variables, points, and cells, but
//  doesn't destroy the list of variables or toplevel cell/pointVarDataArray.
//----------------------------------------------------------------------------
void vtkCDIReader::DestroyData()
{
  vtkDebugMacro("DestroyData...");
  vtkDebugMacro("Destructing double cell var data...");

  this->CellVarDataArray->Initialize();

  vtkDebugMacro("Destructing double Point var array...");
  this->PointVarDataArray->Initialize();

  this->DomainVarDataArray->Initialize();

  vtkDebugMacro("Out DestroyData...");
}

//----------------------------------------------------------------------------
// Destructor for vtkCDIReader
//----------------------------------------------------------------------------
vtkCDIReader::~vtkCDIReader()
{
  vtkDebugMacro("Destructing vtkCDIReader...");
  this->SetFileName(nullptr);

  if (this->StreamID >= 0)
  {
    streamClose(this->StreamID);
    this->StreamID = -1;
  }

  this->DestroyData();

  vtkDebugMacro("Destructing other stuff...");
  this->PointDataArraySelection->RemoveObserver(this->SelectionObserver);
  this->CellDataArraySelection->RemoveObserver(this->SelectionObserver);
  this->DomainDataArraySelection->RemoveObserver(this->SelectionObserver);

  this->SetController(nullptr);

  vtkDebugMacro("Destructed vtkCDIReader");
}

// Grab info from outInfo object (method extracted from RequestInformation)
//----------------------------------------------------------------------------
void vtkCDIReader::GetFileSeriesInformation(vtkInformation* outInfo)
{
  if (outInfo->Has(vtkFileSeriesReader::FILE_SERIES_NUMBER_OF_FILES()))
  {
    this->NumberOfFiles = outInfo->Get(vtkFileSeriesReader::FILE_SERIES_NUMBER_OF_FILES());
  }
  if (outInfo->Has(vtkFileSeriesReader::FILE_SERIES_CURRENT_FILE_NUMBER()))
  {
    this->FileSeriesNumber = outInfo->Get(vtkFileSeriesReader::FILE_SERIES_CURRENT_FILE_NUMBER());
  }
  if (outInfo->Has(vtkFileSeriesReader::FILE_SERIES_FIRST_FILENAME()))
  {
    this->FileSeriesFirstName = outInfo->Get(vtkFileSeriesReader::FILE_SERIES_FIRST_FILENAME());
  }
}

//----------------------------------------------------------------------------
// Verify that the file exists, get dimension sizes and variables
//----------------------------------------------------------------------------
int vtkCDIReader::RequestInformation(
  vtkInformation* reqInfo, vtkInformationVector** inVector, vtkInformationVector* outVector)
{
  vtkDebugMacro("In vtkCDIReader::RequestInformation");
  if (!this->Superclass::RequestInformation(reqInfo, inVector, outVector))
  {
    return 0;
  }

  if (this->FileName.empty())
  {
    vtkErrorMacro("No filename specified");
    return 0;
  }

  if (this->Controller->GetNumberOfProcesses() > 1)
  {
    this->Decomposition = true;
    this->NumberOfProcesses = this->Controller->GetNumberOfProcesses();
  }

  vtkDebugMacro("In vtkCDIReader::RequestInformation read filename ok: " << this->FileName.c_str());
  vtkInformation* outInfo = outVector->GetInformationObject(0);

  vtkDebugMacro("FileName: " << this->FileName.c_str());

  if (!this->GetDims())
  {
    return 0;
  }

  this->InfoRequested = true;

  vtkDebugMacro("In vtkCDIReader::RequestInformation setting VerticalLevelRange");
  this->VerticalLevelRange[0] = 0;
  this->VerticalLevelRange[1] = this->MaximumNVertLevels - 1;

  if (!this->BuildVarArrays())
  {
    return 0;
  }

  this->ResetVarDataArrays();

  this->GetFileSeriesInformation(outInfo);

  vtkSmartPointer<vtkDoubleArray> timeValues = this->ReadTimeAxis();

  this->OutputTimeAxis(outInfo, timeValues);

  outInfo->Set(CAN_HANDLE_PIECE_REQUEST(), 1);
  vtkDebugMacro("Out vtkCDIReader::RequestInformation");

  return 1;
}

//----------------------------------------------------------------------------
vtkSmartPointer<vtkDoubleArray> vtkCDIReader::ReadTimeAxis()
{
  if ((this->FileSeriesNumber == 0) && (!this->TimeSet))
  {

    int taxisID = vlistInqTaxis(this->VListID);
    int calendar = taxisInqCalendar(taxisID);
    streamInqTimestep(this->StreamID, 0);
    int vdate = taxisInqVdate(taxisID);
    int vtime = taxisInqVtime(taxisID);

    this->FirstDay = date_to_julday(calendar, vdate);
    this->TimeUnits = cdi_tools::ParseTimeUnits(vdate, vtime);
    this->Calendar = cdi_tools::ParseCalendar(calendar);
    this->TimeSet = true;
  }

  if (!this->TimeSeriesTimeStepsAllSet)
  {
    if (this->TimeSeriesTimeSteps.size() < this->FileSeriesNumber + 1)
      this->TimeSeriesTimeSteps.resize(this->FileSeriesNumber + 1);
    this->TimeSeriesTimeSteps[this->FileSeriesNumber] = this->NumberOfTimeSteps;
  }

  this->NumberOfAllTimeSteps = 0;
  for (int step = 0; step < this->NumberOfFiles; step++)
  {
    this->NumberOfAllTimeSteps += this->TimeSeriesTimeSteps[step];
  }

  auto timeValues = vtkSmartPointer<vtkDoubleArray>::New();
  timeValues->Allocate(this->NumberOfTimeSteps);
  timeValues->SetNumberOfComponents(1);
  int start = 0;
  int counter = 0;
  for (int step = 0; step < this->FileSeriesNumber; step++)
  {
    start += this->TimeSeriesTimeSteps[step];
  }
  int end = start + this->NumberOfTimeSteps;
  for (int step = start; step < end; step++)
  {
    int taxisID = vlistInqTaxis(this->VListID);
    int calendar = taxisInqCalendar(taxisID);
    streamInqTimestep(this->StreamID, counter);
    int vdate = taxisInqVdate(taxisID);
    int vtime = taxisInqVtime(taxisID);
    double timevalue = date_to_julday(calendar, vdate);
    if (vtime > 0)
    {
      timevalue += (double)((time_to_sec(vtime)) / 86400.0);
    }
    timevalue -= this->FirstDay;
    if (timevalue >= 0.0)
    {
      timeValues->InsertNextTuple1(timevalue);
      if (!this->TimeSeriesTimeStepsAllSet)
      {
        if (TimeSteps.size() < step + 1)
          TimeSteps.resize(step + 1);
        this->TimeSteps[step] = timevalue;
      }
    }
    else
    {
      this->NumberOfTimeSteps -= 1;
    }
    counter++;
  }

  if (this->FileSeriesNumber == (this->NumberOfFiles - 1))
  {
    this->TimeSeriesTimeStepsAllSet = true;
  }

  return timeValues;
}

// Call DestroyData() before calling this!
//----------------------------------------------------------------------------
void vtkCDIReader::ResetVarDataArrays()
{
  this->PointVarDataArray->AllocateArrays(this->NumberOfPointVars);
  this->CellVarDataArray->AllocateArrays(this->NumberOfCellVars);
  this->DomainVarDataArray->AllocateArrays(this->NumberOfDomainVars);
}

// Add the time axis to the out info
//----------------------------------------------------------------------------
void vtkCDIReader::OutputTimeAxis(
  vtkInformation* outInfo, const vtkSmartPointer<vtkDoubleArray>& timeValues)
{
  if (this->NumberOfTimeSteps > 0)
  {
    outInfo->Set(vtkStreamingDemandDrivenPipeline::TIME_STEPS(), timeValues->GetPointer(0),
      timeValues->GetNumberOfTuples());
    double timeRange[2];
    timeRange[0] = timeValues->GetValue(0);
    timeRange[1] = timeValues->GetValue(timeValues->GetNumberOfTuples() - 1);
    outInfo->Set(vtkStreamingDemandDrivenPipeline::TIME_RANGE(), timeRange, 2);
  }
}

//----------------------------------------------------------------------------
int vtkCDIReader::GetTimeIndex(double dataTimeStep)
{
  int start = 0;
  for (int step = 0; step < this->FileSeriesNumber; step++)
    start += this->TimeSeriesTimeSteps[step];
  int end = start + this->TimeSeriesTimeSteps[this->FileSeriesNumber];
  for (int step = start; step < end; step++)
  {
    if (this->TimeSteps[step] == dataTimeStep)
      return (step - start);
  }
  return 0;
}

//----------------------------------------------------------------------------
int vtkCDIReader::RequestUpdateExtent(
  vtkInformation*, vtkInformationVector**, vtkInformationVector* outputVector)
{
  vtkInformation* outInfo = outputVector->GetInformationObject(0);
  int piece = outInfo->Get(vtkStreamingDemandDrivenPipeline::UPDATE_PIECE_NUMBER());
  int numPieces = outInfo->Get(vtkStreamingDemandDrivenPipeline::UPDATE_NUMBER_OF_PIECES());
  // make sure piece is valid
  return (piece < 0 || piece >= numPieces) ? 0 : 1;
}

//----------------------------------------------------------------------------
long vtkCDIReader::GetPartitioning(int piece, int numPieces, int numCellsPerLevel,
  int numPointsPerCell, int& beginPoint, int& endPoint, int& beginCell, int& endCell)
{
  if (numPieces == 1)
  {
    beginPoint = 0;
    endPoint = (numCellsPerLevel * numPointsPerCell) - 1;
    beginCell = 0;
    endCell = numCellsPerLevel - 1;

    return numCellsPerLevel;
  }
  else
  {
    long localCells = 0;
    int cells_per_piece = numCellsPerLevel / numPieces;
    if (piece == 0)
    {
      beginCell = 0;
      endCell = (piece + 1) * cells_per_piece - 1;
      beginPoint = 0;
      endPoint = ((endCell + 1) * numPointsPerCell) - 1;
      localCells = 1 + endCell;
    }
    else if (piece < (numPieces - 1))
    {
      beginCell = piece * cells_per_piece;
      endCell = (piece + 1) * cells_per_piece;
      beginPoint = beginCell * numPointsPerCell;
      endPoint = (endCell * numPointsPerCell) - 1;
      localCells = endCell - beginCell;
    }
    else if (piece == (numPieces - 1))
    {
      beginCell = piece * cells_per_piece;
      endCell = numCellsPerLevel - 1;
      beginPoint = beginCell * numPointsPerCell;
      endPoint = ((endCell + 1) * numPointsPerCell) - 1;
      localCells = 1 + endCell - beginCell;
    }
    return localCells;
  }
}

//----------------------------------------------------------------------------
// Default method: Data is read into a vtkUnstructuredGrid
//----------------------------------------------------------------------------
int vtkCDIReader::RequestData(vtkInformation* vtkNotUsed(reqInfo),
  vtkInformationVector** vtkNotUsed(inVector), vtkInformationVector* outVector)
{
  vtkDebugMacro("In vtkCDIReader::RequestData");
  vtkInformation* outInfo = outVector->GetInformationObject(0);

  if (outInfo->Has(vtkFileSeriesReader::FILE_SERIES_CURRENT_FILE_NUMBER()))
  {
    this->FileSeriesNumber = outInfo->Get(vtkFileSeriesReader::FILE_SERIES_CURRENT_FILE_NUMBER());
  }

  this->Piece = outInfo->Get(vtkStreamingDemandDrivenPipeline::UPDATE_PIECE_NUMBER());
  this->NumPieces = outInfo->Get(vtkStreamingDemandDrivenPipeline::UPDATE_NUMBER_OF_PIECES());
  this->NumberLocalCells = this->GetPartitioning(this->Piece, this->NumPieces, this->NumberOfCells,
    this->PointsPerCell, this->BeginPoint, this->EndPoint, this->BeginCell, this->EndCell);

  if (this->DataRequested)
  {
    this->DestroyData();
  }
  if ((!this->Initialized) || (!this->SkipGrid))
  {
    if (!this->ReadAndOutputGrid(true))
    {
      return 0;
    }
  }
  this->Initialized = true;

  double requestedTimeStep = 0.;
#ifndef NDEBUG
  int numRequestedTimeSteps = 0;
#endif

  vtkInformationDoubleKey* timeKey =
    static_cast<vtkInformationDoubleKey*>(vtkStreamingDemandDrivenPipeline::UPDATE_TIME_STEP());
  if (outInfo->Has(timeKey))
  {
#ifndef NDEBUG
    numRequestedTimeSteps = 1;
#endif
    requestedTimeStep = outInfo->Get(timeKey);
  }

  vtkDebugMacro("Num Time steps requested: " << numRequestedTimeSteps);
  this->DTime = requestedTimeStep;
  vtkDebugMacro("this->DTime: " << this->DTime);
  double dTimeTemp = this->DTime;
  this->Output->GetInformation()->Set(vtkDataObject::DATA_TIME_STEP(), dTimeTemp);
  vtkDebugMacro("dTimeTemp: " << dTimeTemp);
  this->DTime = dTimeTemp;

  for (int var = 0; var < this->NumberOfCellVars; var++)
  {
    if (this->GetCellArrayStatus(this->Internals->CellVars[var].Name))
    {
      vtkDebugMacro("Loading Cell Variable: " << this->Internals->CellVars[var].Name);
      this->LoadCellVarData(var, this->DTime);
    }
    else
      vtkDebugMacro(
        "Ignoring Cell Variable: " << this->Internals->CellVars[var].Name << " as requested ");
  }
  this->Output->GetCellData()->ShallowCopy(this->CellVarDataArray);

  for (int var = 0; var < this->NumberOfPointVars; var++)
  {
    if (this->GetPointArrayStatus(this->Internals->PointVars[var].Name))
    {
      vtkDebugMacro("Loading Point Variable: " << var);
      this->LoadPointVarData(var, this->DTime);
    }
  }
  this->Output->GetPointData()->ShallowCopy(this->PointVarDataArray);

  for (int var = 0; var < this->NumberOfDomainVars; var++)
  {
    if (this->GetDomainArrayStatus(this->Internals->DomainVars[var].c_str()))
    {
      vtkDebugMacro("Loading Domain Variable: " << this->Internals->DomainVars[var].c_str());
      this->LoadDomainVarData(var);
    }
  }
  this->Output->GetFieldData()->ShallowCopy(this->DomainVarDataArray);

  if (!this->TimeUnits.empty())
  {
    vtkNew<vtkStringArray> arr;
    arr->SetName("time_units");
    arr->InsertNextValue(this->TimeUnits);
    this->Output->GetFieldData()->AddArray(arr);
  }
  if (!this->Calendar.empty())
  {
    vtkNew<vtkStringArray> arr;
    arr->SetName("time_calendar");
    arr->InsertNextValue(this->Calendar);
    this->Output->GetFieldData()->AddArray(arr);
  }

  if (this->BuildDomainArrays)
  {
    this->BuildDomainArrays = this->BuildDomainCellVars();
  }

  this->DataRequested = true;
  vtkDebugMacro("Returning from RequestData");

  vtkUnstructuredGrid::GetData(outVector)->ShallowCopy(this->Output);

  return 1;
}

//----------------------------------------------------------------------------
// Regenerate and reread the data variables available
//----------------------------------------------------------------------------
int vtkCDIReader::RegenerateVariables()
{
  vtkDebugMacro("In RegenerateVariables");
  this->NumberOfPointVars = 0;
  this->NumberOfCellVars = 0;
  this->NumberOfDomainVars = 0;

  if (!this->GetDims())
  {
    return 0;
  }

  this->VerticalLevelRange[0] = 0;
  this->VerticalLevelRange[1] = this->MaximumNVertLevels - 1;

  if (!this->BuildVarArrays())
  {
    return 0;
  }

  // Allocate the ParaView data arrays which will hold the variables
  this->ResetVarDataArrays();

  vtkDebugMacro("Returning from RegenerateVariables");
  return 1;
}

//----------------------------------------------------------------------------
// If the user changes the projection, or singlelayer to
// multilayer, we need to regenerate the geometry.
//----------------------------------------------------------------------------
int vtkCDIReader::RegenerateGeometry()
{
  vtkDebugMacro("RegenerateGeometry ...");

  if (this->GridReconstructed)
  {
    vtkDebugMacro("GridReconstructed!");
    if (!this->ReadAndOutputGrid(true))
    {
      return 0;
    }
  }
  else
  {
    vtkDebugMacro("GridReconstructed=false");
  }

  double dTimeTemp = this->DTime;
  this->Output->GetInformation()->Set(vtkDataObject::DATA_TIME_STEP(), dTimeTemp);
  this->DTime = dTimeTemp;

  for (int var = 0; var < this->NumberOfCellVars; var++)
  {
    if (this->GetCellArrayStatus(this->Internals->CellVars[var].Name))
    {
      vtkDebugMacro("Loading Cell Variable: " << this->Internals->CellVars[var].Name);
      this->LoadCellVarData(var, this->DTime);
    }
  }
  this->Output->GetCellData()->ShallowCopy(this->CellVarDataArray);
  for (int var = 0; var < this->NumberOfPointVars; var++)
  {
    if (this->GetPointArrayStatus(this->Internals->PointVars[var].Name))
    {
      vtkDebugMacro("Loading Point Variable: " << var);
      this->LoadPointVarData(var, this->DTime);
    }
  }
  this->Output->GetPointData()->ShallowCopy(this->PointVarDataArray);

  for (int var = 0; var < this->NumberOfDomainVars; var++)
  {
    if (this->GetDomainArrayStatus(this->Internals->DomainVars[var].c_str()))
    {
      vtkDebugMacro("Loading Domain Variable: " << this->Internals->DomainVars[var].c_str());
      this->LoadDomainVarData(var);
    }
  }
  this->Output->GetFieldData()->ShallowCopy(this->DomainVarDataArray);

  this->PointDataArraySelection->Modified();
  this->CellDataArraySelection->Modified();
  this->Modified();

  return 1;
}

//----------------------------------------------------------------------------
// Set defaults for various parameters and initialize some variables
//----------------------------------------------------------------------------
void vtkCDIReader::SetDefaults()
{
  this->Grib = false;

  this->VerticalLevelRange[0] = 0;
  this->VerticalLevelRange[1] = 1;
  this->VerticalLevelSelected = 0;
  this->LayerThicknessRange[0] = 0;
  this->LayerThicknessRange[1] = 100;
  this->LayerThickness = 50;
  this->Bloat = 2.0;

  this->Layer0OffsetRange[0] = -50;
  this->Layer0OffsetRange[1] = 51;
  this->Layer0Offset = 1e-30;

  // this is hard coded for now but will change when data generation gets more mature
  this->PerformanceDataFile = "timer.atmo.";
  this->DomainVarName = "cell_owner";
  this->DomainDimension = "domains";
  this->HaveDomainVariable = false;
  this->HaveDomainData = false;

  this->DimensionSelection = 0;
  this->InvertZAxis = false;
  this->DoublePrecision = false;
  this->ShowClonClat = false;
  this->ProjectionMode = projection::SPHERICAL;
  this->ShowMultilayerView = false;
  this->ReconstructNew = false;
  this->CellDataSelected = 0;
  this->PointDataSelected = 0;
  this->MaskingVarname = "";
  this->GotMask = false;
  this->AddCoordinateVars = false;
  this->NumberOfTimeSteps = 0;
  this->NumberOfAllTimeSteps = 0;
  this->TimeSeriesTimeSteps.reserve(5);
  this->TimeSteps.reserve(100 * 250 + 25);
  this->TimeSeriesTimeStepsAllSet = false;
  this->GridReconstructed = false;
  this->CustomMaskValue = 0.0;
  this->InvertMask = false;
  this->UseMask = false;
  this->UseCustomMaskValue = false;
  this->Decomposition = false;

  this->SkipGrid = false;

  this->BeginCell = 0;
  this->FirstDay = -1;
  this->TimeSet = false;

  this->DTime = 0;
  this->FileSeriesNumber = 0;
  this->NumberOfFiles = 1;
  this->NeedHorizontalGridFile = false;
  this->NeedVerticalGridFile = false;

  this->NumberOfProcesses = 1;

  this->BuildDomainArrays = false;
  this->MaximumNVertLevels = 0;
  this->MaximumPoints = 0;
  this->MaximumCells = 0;
  this->DepthVar = nullptr;

  this->NumberOfPoints = 0;
}

//----------------------------------------------------------------------------
// Get dimensions of key NetCDF variables
//----------------------------------------------------------------------------
int vtkCDIReader::OpenFile()
{
  // check if we got either *.Grib or *.nc data
  std::string file = this->FileName;
  std::string check = file.substr((file.size() - 4), file.size());
  if (check == "grib" || check == ".grb")
  {
    this->Grib = true;
  }
  else
  {
    this->Grib = false;
  }

  if (this->StreamID >= 0)
  {
    streamClose(this->StreamID);
    this->StreamID = -1;
    this->VListID = -1;
  }

  this->StreamID = streamOpenRead(this->FileNameGrid.c_str());
  if (this->StreamID < 0)
  {
    return 0;
  }

  vtkDebugMacro("In vtkCDIReader::RequestInformation read file okay");
  this->VListID = streamInqVlist(this->StreamID);

  int nvars = vlistNvars(this->VListID);
  char varname[CDI_MAX_NAME];
  for (int varID = 0; varID < nvars; ++varID)
  {
    vlistInqVarName(this->VListID, varID, varname);
  }

  return 1;
}

//----------------------------------------------------------------------------
void vtkCDIReader::GuessGridFile()
{
  std::string fallback = vtksys::SystemTools::GetParentDirectory(this->FileName) + "/grid.nc";

  std::string guess;
  if (!this->Grib)
    guess = cdi_tools::GuessGridFileFromUri(this->FileName);

  if (!guess.empty())
  {
    if (vtksys::SystemTools::TestFileAccess(guess, vtksys::TEST_FILE_READ))
    {
      this->FileNameGrid = guess;
      return;
    }
    else
      vtkWarningMacro("Could not find grid file "
        << guess << " indicated by grid_file_uri attribute in " << this->FileName
        << " Trying fallback guess " << fallback);
  }
  this->FileNameGrid = fallback;
}

//----------------------------------------------------------------------------
// Get dimensions of key NetCDF variables
//----------------------------------------------------------------------------
int vtkCDIReader::GetDims()
{
  if (!this->FileName.empty())
  {
    this->FileNameGrid = this->FileName;
    if (this->VListID < 0 || this->StreamID < 0)
    {
      if (!this->OpenFile())
      {
        return 0;
      }
    }

    this->ReadHorizontalGridData();
    if (this->NeedHorizontalGridFile)
    {
      // if there is no grid information in the data file, try opening
      // an additional grid file named grid.nc in the same directory to
      // read in the grid information
      if (this->StreamID >= 0)
      {
        streamClose(this->StreamID);
        this->StreamID = -1;
        this->VListID = -1;
      }

      char* directory = new char[strlen(this->FileName.c_str()) + 1];
      strcpy(directory, this->FileName.c_str());

      this->GuessGridFile();
      if (!this->OpenFile())
      {
        return 0;
      }
      if (!this->ReadHorizontalGridData())
      {
        vtkErrorMacro("Couldn't open grid information in data nor in the grid file.");
        return 0;
      }

      this->FileNameGrid = this->FileName;
      if (!this->OpenFile())
      {
        return 0;
      }
    }

    this->ReadVerticalGridData();
    if (this->NeedVerticalGridFile)
    {
      // if there is no grid information in the data file, try opening
      // an additional grid file named grid.nc in the same directory to
      // read in the grid information
      if (this->StreamID >= 0)
      {
        streamClose(this->StreamID);
        this->StreamID = -1;
        this->VListID = -1;
      }

      char* directory = new char[strlen(this->FileName.c_str()) + 1];
      strcpy(directory, this->FileName.c_str());
      if (!this->OpenFile())
      {
        return 0;
      }

      if (!this->ReadVerticalGridData())
      {
        vtkDebugMacro("Couldn't neither open grid information within the data netCDF file, nor "
                      "in the grid.nc file.");
        vtkErrorMacro("Couldn't neither open grid information within the data netCDF file, nor "
                      "in the grid.nc file.");
        return 0;
      }

      this->FileNameGrid = this->FileName;
      if (!this->OpenFile())
      {
        return 0;
      }
    }

    if (this->DimensionSelection > 0)
    {
      vlistNgrids(this->VListID);
      int nzaxis = vlistNzaxis(this->VListID);

      this->GridID = vlistGrid(this->VListID, this->DimensionSelection / nzaxis);
      this->ZAxisID = vlistZaxis(
        this->VListID, this->DimensionSelection - (nzaxis * this->DimensionSelection / nzaxis));
    }

    if (this->GridID != -1)
    {
      this->NumberOfCells = static_cast<int>(gridInqSize(this->GridID));

      if (this->NumberOfPoints and
        this->NumberOfPoints != static_cast<int>(gridInqSize(this->GridID)))
        vtkDebugMacro("GetDims: Changing number of points from  "
          << this->NumberOfPoints << " to " << static_cast<int>(gridInqSize(this->GridID)));
      this->NumberOfPoints = static_cast<int>(gridInqSize(this->GridID));
      this->PointsPerCell = gridInqNvertex(this->GridID);
    }

    int ntsteps = 0;
    if (this->Grib)
    {
      while (streamInqTimestep(this->StreamID, ntsteps))
        ntsteps++;
    }
    else
    {
      ntsteps = vlistNtsteps(this->VListID);
    }
    this->NumberOfTimeSteps = ntsteps;

    this->MaximumNVertLevels = 1;
    if (this->ZAxisID != -1)
    {
      this->MaximumNVertLevels = zaxisInqSize(this->ZAxisID);
    }

    this->FillGridDimensions();
  }
  else
  {
    vtkDebugMacro("No Filename yet set!");
  }

  return 1;
}

//----------------------------------------------------------------------------
// Read Horizontal Grid Data
//----------------------------------------------------------------------------
int vtkCDIReader::ReadHorizontalGridData()
{
  int vlistID_l = this->VListID;
  this->GridID = -1;
  this->ZAxisID = -1;
  this->SurfID = -1;

  int ngrids = vlistNgrids(vlistID_l);
  for (int i = 0; i < ngrids; ++i)
  {
    int gridID_l = vlistGrid(vlistID_l, i);
    int nv = gridInqNvertex(gridID_l);

    if (nv >= 3) //  ((nv == 3 || nv == 4)) // && gridInqType(gridID_l) == GRID_UNSTRUCTURED)
    {
      this->GridID = gridID_l;
      break;
    }
  }

  if (this->GridID == -1)
  {
    this->NeedHorizontalGridFile = true;
    return 0;
  }

  return 1;
}

//----------------------------------------------------------------------------
// Read Vertical Grid Data
//----------------------------------------------------------------------------
int vtkCDIReader::ReadVerticalGridData()
{
  this->ZAxisID = -1;
  this->SurfID = -1;
  int nzaxis = vlistNzaxis(this->VListID);

  for (int i = 0; i < nzaxis; ++i)
  {
    int zaxisID_l = vlistZaxis(this->VListID, i);
    if (zaxisInqSize(zaxisID_l) == 1 || zaxisInqType(zaxisID_l) == ZAXIS_SURFACE)
    {
      this->SurfID = zaxisID_l;
      this->ZAxisID = zaxisID_l;
      break;
    }
  }

  for (int i = 0; i < nzaxis; ++i)
  {
    int zaxisID_l = vlistZaxis(this->VListID, i);
    if (zaxisInqSize(zaxisID_l) > 1)
    {
      this->ZAxisID = zaxisID_l;
      break;
    }
  }

  if (this->ZAxisID == -1)
  {
    this->NeedVerticalGridFile = true;
    return 0;
  }

  return 1;
}

//----------------------------------------------------------------------------
// Get the NetCDF variables on cell and vertex and check for domain data
//----------------------------------------------------------------------------
int vtkCDIReader::GetVars()
{
  int cellVarIndex = -1;
  int pointVarIndex = -1;
  int domainVarIndex = -1;

  int numVars = vlistNvars(this->VListID);
  for (int i = 0; i < numVars; i++)
  {
    int varID = i;
    cdi_tools::CDIVar aVar;

    aVar.StreamID = this->StreamID;
    aVar.VarID = varID;
    aVar.GridID = vlistInqVarGrid(this->VListID, varID);
    aVar.ZAxisID = vlistInqVarZaxis(this->VListID, varID);
    aVar.GridSize = static_cast<int>(gridInqSize(aVar.GridID));
    aVar.NLevel = zaxisInqSize(aVar.ZAxisID);
    aVar.Type = 0;
    aVar.ConstTime = 0;

    // to do multiple grids:
    // - Check how many grids are available
    // - Check if all grids can be reconstructed, or if bnds are all zero
    // - Reform gui to load either Cell, Point or Edge data

    if (vlistInqVarTsteptype(this->VListID, varID) == TIME_CONSTANT)
    {
      aVar.ConstTime = 1;
    }
    if (aVar.ZAxisID != this->ZAxisID && aVar.ZAxisID != this->SurfID)
    {
      continue;
    }

    vlistInqVarName(this->VListID, varID, aVar.Name);
    aVar.Type = 2;
    if (aVar.NLevel > 1)
    {
      aVar.Type = 3;
    }
    int varType = aVar.Type;

    // check for dim 2 being cell or Point
    bool isCellData = false;
    bool isPointData = false;
    if (aVar.GridSize == this->NumberOfCells)
    {
      isCellData = true;
    }
    else if ((aVar.GridSize < this->NumberOfCells) && (this->PointsPerCell == 3))
    {
      if (this->NumberOfPoints and this->NumberOfPoints != aVar.GridSize)
      {
        vtkWarningMacro("Not adding "
          << aVar.Name << " as point var, as it's size " << aVar.GridSize
          << " does not correspond to our understanding of the correct size for 'the' point grid: "
          << this->NumberOfPoints);
        break;
      }
      isPointData = true;
      this->NumberOfPoints = aVar.GridSize;
    }
    else
    {
      continue;
    }

    // 3D variables ...
    if (varType == 3)
    {
      if (isCellData)
      {
        cellVarIndex++;
        if (cellVarIndex > MAX_VARS - 1)
        {
          vtkErrorMacro("Exceeded number of cell vars.");
          return 0;
        }
        this->Internals->CellVars[cellVarIndex] = aVar;
        vtkDebugMacro("Adding var " << aVar.Name << " to CellVars");
      }
      else if (isPointData)
      {
        pointVarIndex++;
        if (pointVarIndex > MAX_VARS - 1)
        {
          vtkErrorMacro("Exceeded number of Point vars.");
          return 0;
        }
        this->Internals->PointVars[pointVarIndex] = aVar;
        vtkDebugMacro("Adding var " << aVar.Name << " to PointVars");
      }
    }
    // 2D variables
    else if (varType == 2)
    {
      vtkDebugMacro("check for " << aVar.Name << ".");
      if (isCellData)
      {
        cellVarIndex++;
        if (cellVarIndex > MAX_VARS - 1)
        {
          vtkDebugMacro("Exceeded number of cell vars.");
          return 0;
        }
        this->Internals->CellVars[cellVarIndex] = aVar;
        vtkDebugMacro("Adding var " << aVar.Name << " to CellVars");
      }
      else if (isPointData)
      {
        pointVarIndex++;
        if (pointVarIndex > MAX_VARS - 1)
        {
          vtkErrorMacro("Exceeded number of Point vars.");
          return 0;
        }
        this->Internals->PointVars[pointVarIndex] = aVar;
        vtkDebugMacro("Adding var " << aVar.Name << " to PointVars");
      }
    }
  }

  // check if domain var is defined and how many domains are available
  for (int var = 0; var < pointVarIndex + 1; var++)
  {
    if (!strcmp(this->Internals->PointVars[var].Name, this->DomainVarName.c_str()))
    {
      this->HaveDomainVariable = true;
    }
  }
  for (int var = 0; var < cellVarIndex + 1; var++)
  {
    if (!strcmp(this->Internals->CellVars[var].Name, this->DomainVarName.c_str()))
    {
      this->HaveDomainVariable = true;
    }
  }

  // prepare data structure and read in names
  std::string filename = this->PerformanceDataFile + "0000";
  vtksys::ifstream file(filename.c_str());
  if (file.good())
  {
    this->HaveDomainData = true;
  }

  if (this->SupportDomainData())
  {
    vtkDebugMacro("Found Domain Data and loading it.");
    this->BuildDomainArrays = true;
  }

  this->NumberOfPointVars = pointVarIndex + 1;
  this->NumberOfCellVars = cellVarIndex + 1;
  this->NumberOfDomainVars = domainVarIndex + 1;
  this->NumberAllCells = this->NumberOfCells;
  this->NumberAllPoints = this->NumberOfPoints;

  return 1;
}

//----------------------------------------------------------------------------
// Build the selection Arrays for points and cells in the GUI.
//----------------------------------------------------------------------------
int vtkCDIReader::BuildVarArrays()
{
  vtkDebugMacro("In vtkCDIReader::BuildVarArrays");

  if (!this->FileName.empty())
  {
    if (!GetVars())
    {
      return 0;
    }

    vtkDebugMacro("NumberOfCellVars: " << this->NumberOfCellVars
                                       << " NumberOfPointVars: " << this->NumberOfPointVars);
    if (this->NumberOfCellVars == 0)
    {
      vtkErrorMacro("No cell variables found!");
    }

    for (int var = 0; var < this->NumberOfPointVars; var++)
    {
      this->PointDataArraySelection->EnableArray(this->Internals->PointVars[var].Name);
      vtkDebugMacro("Adding Point var: " << this->Internals->PointVars[var].Name);
    }

    for (int var = 0; var < this->NumberOfCellVars; var++)
    {
      vtkDebugMacro("Adding cell var: " << this->Internals->CellVars[var].Name);
      this->CellDataArraySelection->EnableArray(this->Internals->CellVars[var].Name);
    }

    for (int var = 0; var < this->NumberOfDomainVars; var++)
    {
      vtkDebugMacro("Adding domain var: " << this->Internals->DomainVars[var].c_str());
      this->DomainDataArraySelection->EnableArray(this->Internals->DomainVars[var].c_str());
    }
  }
  else
  {
    vtkDebugMacro("No Filename yet set.");
  }

  vtkDebugMacro("Leaving vtkCDIReader::BuildVarArrays");
  return 1;
}

//----------------------------------------------------------------------------
//  Read the data from the ncfile, allocate the geometry and create the
//  vtk data structures for points and cells.
//----------------------------------------------------------------------------
int vtkCDIReader::ReadAndOutputGrid(bool init)
{
  vtkDebugMacro("In vtkCDIReader::ReadAndOutputGrid");

  if (this->ProjectionMode == projection::SPHERICAL)
  {
    if (!this->AllocSphereGeometry())
    {
      return 0;
    }
  }
  else
  {
    if (!this->AllocLatLonGeometry())
    {
      return 0;
    }

    if (this->ProjectionMode == projection::CASSINI)
    {
      if (!this->Wrap(2))
      {
        return 0;
      }
    }
    else
    {
      if (!this->Wrap(1))
      {
        return 0;
      }
    }
  }

  if ((this->ProjectionMode == projection::CYLINDRICAL_EQUIDISTANT) ||
    (this->ProjectionMode == projection::CASSINI))
  {
    this->AddMaskHalo();
    this->AddClonClatHalo();
  }
  this->OutputPoints(init);
  this->OutputCells(init);

  vtkDebugMacro("Leaving vtkCDIReader::ReadAndOutputGrid");

  return 1;
}

//----------------------------------------------------------------------------
// Mirrors the triangle mesh in z direction
//----------------------------------------------------------------------------
int vtkCDIReader::MirrorMesh()
{
  for (int i = 0; i < this->NumberLocalPoints; i++)
  {
    this->PointZ[i] = (this->PointZ[i] * (-1.0));
  }

  return 1;
}

//----------------------------------------------------------------------------
void vtkCDIReader::RemoveDuplicates(
  double* pointLon, double* pointLat, int temp_nbr_vertices, int* triangle_list, int* nbr_cells)
{
  struct PointWithIndex* sort_array = new PointWithIndex[temp_nbr_vertices];

  for (int i = 0; i < temp_nbr_vertices; ++i)
  {
    double curr_lon, curr_lat;
    double threshold = (vtkMath::Pi() / 2.0) - 1e-4;
    curr_lon = ((double*)pointLon)[i];
    curr_lat = ((double*)pointLat)[i];

    while (curr_lon < 0.0)
    {
      curr_lon += 2 * vtkMath::Pi();
    }
    while (curr_lon >= vtkMath::Pi())
    {
      curr_lon -= 2 * vtkMath::Pi();
    }

    if (curr_lat > threshold)
    {
      curr_lon = 0.0;
    }
    else if (curr_lat < (-1.0 * threshold))
    {
      curr_lon = 0.0;
    }

    sort_array[i].Pt.Lon = curr_lon;
    sort_array[i].Pt.Lat = curr_lat;
    sort_array[i].Idx = i;
  }

  qsort(sort_array, temp_nbr_vertices, sizeof(*sort_array), ::ComparePointWithIndex);
  triangle_list[sort_array[0].Idx] = 1;

  int last_unique_idx = sort_array[0].Idx;
  for (int i = 1; i < temp_nbr_vertices; ++i)
  {
    if (::ComparePointWithIndex(sort_array + i - 1, sort_array + i))
    {
      triangle_list[sort_array[i].Idx] = 1;
      last_unique_idx = sort_array[i].Idx;
    }
    else
    {
      triangle_list[sort_array[i].Idx] = -last_unique_idx;
    }
  }

  int new_nbr_vertices = 0;
  for (int i = 0; i < temp_nbr_vertices; ++i)
  {
    if (triangle_list[i] == 1)
    {
      pointLon[new_nbr_vertices] = pointLon[i];
      pointLat[new_nbr_vertices] = pointLat[i];
      triangle_list[i] = new_nbr_vertices;
      new_nbr_vertices++;
    }
  }

  for (int i = 0; i < temp_nbr_vertices; ++i)
  {
    if (triangle_list[i] <= 0)
    {
      triangle_list[i] = triangle_list[-triangle_list[i]];
    }
  }

  nbr_cells[0] = temp_nbr_vertices;
  nbr_cells[1] = new_nbr_vertices;
  delete[] sort_array;
}

//----------------------------------------------------------------------------
// Construct grid geometry
//----------------------------------------------------------------------------
int vtkCDIReader::ConstructGridGeometry()
{
  vtkDebugMacro("Starting grid reconstruction ...");
  if (this->NumberOfCellVars == 0 && this->NumberOfPointVars == 0)
  {
    vtkErrorMacro("No cell variables - can't construct grid");
    return 0;
  }

  this->NumberLocalCells = this->GetPartitioning(this->Piece, this->NumPieces, this->NumberOfCells,
    this->PointsPerCell, this->BeginPoint, this->EndPoint, this->BeginCell, this->EndCell);

  int size = this->NumberLocalCells * this->PointsPerCell;
  int size2 = this->NumberAllCells * this->PointsPerCell;
  std::vector<double> cLonVertices;
  std::vector<double> cLatVertices;
  if (size > cLonVertices.max_size())
  {
    vtkErrorMacro("Too many points to construct geometry.");
    return 0;
  }
  cLonVertices.resize(size);
  cLatVertices.resize(size);
  this->DepthVar = new double[this->MaximumNVertLevels];
  CHECK_NEW(this->DepthVar);

  vtkDebugMacro("Start reading Vertices");
  gridInqXboundsPart(
    this->GridID, (this->BeginCell * this->PointsPerCell), size, cLonVertices.data());
  gridInqYboundsPart(
    this->GridID, (this->BeginCell * this->PointsPerCell), size, cLatVertices.data());
  vtkDebugMacro("Done reading Vertices");
  zaxisInqLevels(this->ZAxisID, this->DepthVar);
  char units[CDI_MAX_NAME];
  this->OrigConnections.resize(size);
  int new_cells[2];

  if (this->ProjectionMode != projection::CATALYST)
  {
    gridInqXunits(this->GridID, units);
    if (strncmp(units, "degree", 6) == 0)
    {
      for (int i = 0; i < size; i++)
      {
        cLonVertices[i] = vtkMath::RadiansFromDegrees(cLonVertices[i]);
      }
    }
    gridInqYunits(this->GridID, units);
    if (strncmp(units, "degree", 6) == 0)
    {
      for (int i = 0; i < size; i++)
      {
        cLatVertices[i] = vtkMath::RadiansFromDegrees(cLatVertices[i]);
      }
    }
  }

  // check for duplicates in the Point list and update the triangle list
  this->RemoveDuplicates(
    cLonVertices.data(), cLatVertices.data(), size, &this->OrigConnections[0], new_cells);
  this->NumberLocalCells = new_cells[0] / this->PointsPerCell;
  this->NumberLocalPoints = new_cells[1];
  if (this->NumberOfPoints and this->NumberOfPoints != new_cells[1])
    vtkDebugMacro("ConstructGridGeometry: Changing number of points from  "
      << this->NumberOfPoints << " to " << new_cells[1]);

  this->NumberOfPoints = new_cells[1];

  this->ModNumPoints = (int)floor(this->NumberLocalPoints * (this->Bloat * this->Bloat));
  this->ModNumCells = (int)floor(this->NumberLocalCells * (this->Bloat));

  this->PointMap.resize((size_t)floor(this->NumberOfPoints * (this->Bloat * this->Bloat)));
  this->CellMap.resize((size_t)floor(this->NumberOfCells * this->Bloat));

  this->PointX.resize(this->ModNumPoints);
  this->PointY.resize(this->ModNumPoints);
  this->PointZ.resize(this->ModNumPoints);

  // now get the individual coordinates out of the clon/clat vertices
  for (int i = 0; i < this->NumberLocalPoints; i++)
  {
    projection::longLatToCartesian(
      cLonVertices[i], cLatVertices[i], &PointX[i], &PointY[i], &PointZ[i], this->ProjectionMode);
  }

  // mirror the mesh if needed
  if (this->ProjectionMode == projection::SPHERICAL)
  {
    this->MirrorMesh();
  }
  this->GridReconstructed = true;
  this->ReconstructNew = false;

  // if we run with data decomposition, we need to know the mapping of points
  this->VertexIds.resize(size);
  std::vector<int> vertex_ids2;
  if (size2 > vertex_ids2.max_size())
  {
    vtkErrorMacro("Too many points to construct geometry.");
    return 0;
  }
  vertex_ids2.resize(size2);
#if VTK_MODULE_ENABLE_VTK_ParallelMPI
  if (this->Decomposition)
  {
    if (this->Piece == 0)
    {
      int new_cells2[2];
      double clon_vert2[size2];
      double clat_vert2[size2];

      gridInqXboundsPart(this->GridID, 0, size2, clon_vert2);
      gridInqYboundsPart(this->GridID, 0, size2, clat_vert2);

      gridInqXunits(this->GridID, units);
      if (strncmp(units, "degree", 6) == 0)
      {
        for (int i = 0; i < size2; i++)
        {
          clon_vert2[i] = vtkMath::RadiansFromDegrees(clon_vert2[i]);
        }
      }

      gridInqYunits(this->GridID, units);
      if (strncmp(units, "degree", 6) == 0)
      {
        for (int i = 0; i < size2; i++)
        {
          clat_vert2[i] = vtkMath::RadiansFromDegrees(clat_vert2[i]);
        }
      }

      this->RemoveDuplicates(clon_vert2, clat_vert2, size2, vertex_ids2.data(), new_cells2);
      for (int i = 1; i < this->NumPieces; i++)
      {
        this->Controller->Send(vertex_ids2.data(), size2, i, 101);
      }
    }
    else
    {
      this->Controller->Receive(vertex_ids2.data(), size2, 0, 101);

      for (int i = this->BeginPoint; i < (this->EndPoint + 1); i++)
      {
        this->VertexIds[i - this->BeginPoint] = vertex_ids2[i];
      }
    }

    this->SetupPointConnectivity();
  }
#endif

  this->CurrentExtraPoint = this->NumberLocalPoints;
  this->CurrentExtraCell = this->NumberLocalCells;

  cLonVertices.clear();
  cLatVertices.clear();
  vtkDebugMacro("Grid Reconstruction complete...");
  return 1;
}

//----------------------------------------------------------------------------
// Allocate into sphere view of geometry
// This is work in progress, but as almost all variables are cell based, it
// is not that urgent.
//----------------------------------------------------------------------------
void vtkCDIReader::SetupPointConnectivity()
{
  this->Internals->PointsExpectedFromProcessesLengths = vtkSmartPointer<vtkIdTypeArray>::New();
  this->Internals->PointsExpectedFromProcessesLengths->SetNumberOfTuples(this->NumPieces);
  this->Internals->PointsExpectedFromProcessesOffsets = vtkSmartPointer<vtkIdTypeArray>::New();
  this->Internals->PointsExpectedFromProcessesOffsets->SetNumberOfTuples(this->NumPieces);
  this->Internals->PointsToSendToProcesses = vtkSmartPointer<vtkIdTypeArray>::New();
  this->Internals->PointsToSendToProcessesLengths = vtkSmartPointer<vtkIdTypeArray>::New();
  this->Internals->PointsToSendToProcessesLengths->SetNumberOfTuples(this->NumPieces);
  this->Internals->PointsToSendToProcessesOffsets = vtkSmartPointer<vtkIdTypeArray>::New();
  this->Internals->PointsToSendToProcessesOffsets->SetNumberOfTuples(this->NumPieces);
}

//----------------------------------------------------------------------------
// Allocate into sphere view of geometry
//----------------------------------------------------------------------------
int vtkCDIReader::AllocSphereGeometry()
{
  vtkDebugMacro("In AllocSphereGeometry...");

  if (!GridReconstructed || this->ReconstructNew)
  {
    this->ConstructGridGeometry();
  }

  if (this->ShowMultilayerView)
  {
    this->MaximumCells = this->NumberLocalCells * this->MaximumNVertLevels;
    this->MaximumPoints = this->NumberLocalPoints * (this->MaximumNVertLevels + 1);
  }
  else
  {
    this->MaximumCells = this->NumberLocalCells;
    this->MaximumPoints = this->NumberLocalPoints;
  }

  if (this->ShowClonClat)
  {
    this->LoadClonClatVars();
  }
  this->CheckForMaskData();
  vtkDebugMacro("Leaving AllocSphereGeometry...");
  return 1;
}

//----------------------------------------------------------------------------
// Allocate the lat/lon or Cassini projection of geometry.
//----------------------------------------------------------------------------
int vtkCDIReader::AllocLatLonGeometry()
{
  vtkDebugMacro("In AllocLatLonGeometry...");
  if (this->NumberOfCellVars == 0 && this->NumberOfPointVars == 0)
  {
    vtkErrorMacro("No cell or point variables - can't construct grid");
    return 0;
  }

  if (!GridReconstructed || this->ReconstructNew)
  {
    this->ConstructGridGeometry();
  }

  this->ModConnections.resize(this->ModNumCells * this->PointsPerCell);

  if (this->ShowMultilayerView)
  {
    this->MaximumCells = this->CurrentExtraCell * this->MaximumNVertLevels;
    this->MaximumPoints = this->CurrentExtraPoint * (this->MaximumNVertLevels + 1);
  }
  else
  {
    this->MaximumPoints = this->CurrentExtraPoint;
    this->MaximumCells = this->CurrentExtraCell;
  }

  if (this->ShowClonClat)
  {
    this->LoadClonClatVars();
  }
  this->CheckForMaskData();
  vtkDebugMacro("Leaving AllocLatLonGeometry...");
  return 1;
}

//----------------------------------------------------------------------------
// Construct grid geometry
//----------------------------------------------------------------------------
int vtkCDIReader::LoadClonClatVars()
{
  vtkDebugMacro("In LoadClonClatVars...");

  std::vector<double> cLon_l(this->NumberLocalCells);
  std::vector<double> cLat_l(this->NumberLocalCells);

  gridInqXvalsPart(this->GridID, this->BeginCell, this->NumberLocalCells, cLon_l.data());
  gridInqYvalsPart(this->GridID, this->BeginCell, this->NumberLocalCells, cLat_l.data());

  char units[CDI_MAX_NAME];
  gridInqXunits(this->GridID, units);
  if (strncmp(units, "degree", 6) == 0)
  {
    for (int i = 0; i < this->NumberLocalCells; i++)
    {
      cLon_l[i] = vtkMath::RadiansFromDegrees(cLon_l[i]);
    }
  }
  gridInqYunits(this->GridID, units);
  if (strncmp(units, "degree", 6) == 0)
  {
    for (int i = 0; i < this->NumberLocalCells; i++)
    {
      cLat_l[i] = vtkMath::RadiansFromDegrees(cLat_l[i]);
    }
  }

  if (this->ShowMultilayerView)
  {
    int tmp = this->MaximumCells * this->Bloat;
    this->CLon.resize(tmp);
    this->CLat.resize(tmp);

    for (int j = 0; j < this->NumberLocalCells; j++)
    {
      for (int levelNum = 0; levelNum < this->MaximumNVertLevels; levelNum++)
      {
        int i = j * this->MaximumNVertLevels;
        this->CLon[i + levelNum] = static_cast<double>(cLon_l[j]);
        this->CLat[i + levelNum] = static_cast<double>(cLat_l[j]);
      }
    }
  }
  else
  {
    int tmp = this->NumberLocalCells * this->Bloat;
    this->CLon.resize(tmp);
    this->CLat.resize(tmp);

    for (int j = 0; j < this->NumberLocalCells; j++)
    {
      this->CLon[j] = static_cast<double>(cLon_l[j]);
      this->CLat[j] = static_cast<double>(cLat_l[j]);
    }
  }

  this->AddCoordinateVars = true;
  vtkDebugMacro("Out LoadClonClatVars...");
  return 1;
}

//----------------------------------------------------------------------------
int vtkCDIReader::AddClonClatHalo()
{
  if ((this->AddCoordinateVars) && (this->NumberLocalCells < this->CurrentExtraCell))
  {
    if (this->ShowMultilayerView)
    {
      // put out data for extra cells
      for (int j = this->NumberLocalCells; j < this->CurrentExtraCell; j++)
      {
        for (int levelNum = 0; levelNum < this->MaximumNVertLevels; levelNum++)
        {
          int l = j * this->MaximumNVertLevels;
          int k = this->MaximumNVertLevels * this->CellMap[j - this->NumberLocalCells];
          this->CLon[l + levelNum] = static_cast<int>(CLon[k + levelNum]);
          this->CLat[l + levelNum] = static_cast<int>(CLat[k + levelNum]);
        }
      }
    }
    else
    {
      // put out data for extra cells
      for (int j = this->NumberLocalCells; j < this->CurrentExtraCell; j++)
      {
        int k = this->CellMap[j - this->NumberLocalCells];
        this->CLon[j] = static_cast<int>(CLon[k]);
        this->CLat[j] = static_cast<int>(CLat[k]);
      }
    }

    return 1;
  }

  return 0;
}

//----------------------------------------------------------------------------
//  Read in Missing value mask. We probably should not read this, but just fetch it, but hell,
//  whatever.
//----------------------------------------------------------------------------
int vtkCDIReader::CheckForMaskData()
{
  int numVars = this->NumberOfCellVars;
  this->GotMask = false;
  int mask_pos = 0;

  std::string mask_name;
  if (this->PointsPerCell == 3)
    mask_name = "wet_c";
  if (this->PointsPerCell == 4)
    mask_name = "wet_e";
  if (this->PointsPerCell == 6)
    mask_name = "wet_v";

  for (int i = 0; i < numVars; i++)
  {
    if (!strcmp(this->Internals->CellVars[i].Name, this->MaskingVarname.c_str()))
    {
      if (this->MaskingVarname.empty())
      {
        vtkWarningMacro(<< "Found empty var at position " << i << " of Internals->CellVars ");
        break;
      }

      this->GotMask = true;
      mask_pos = i;
      break;
    }
  }
  if (this->GotMask == false)
  {
    this->MaskingVarname = mask_name;
    for (int i = 0; i < numVars; i++)
    {
      if (!strcmp(this->Internals->CellVars[i].Name, this->MaskingVarname.c_str()))
      {
        if (this->MaskingVarname.empty())
        {
          vtkWarningMacro(<< "Found empty var at position " << i << " of Internals->CellVars ");
          break;
        }
        this->GotMask = true;
        mask_pos = i;
        break;
      }
    }
  }

  if (this->GotMask)
  {
    const double maskVal = this->UseCustomMaskValue
      ? this->CustomMaskValue
      : vlistInqVarMissval(this->VListID, this->Internals->CellVars[mask_pos].VarID);

    cdi_tools::CDIVar* cdiVar = &(this->Internals->CellVars[mask_pos]);
    if (this->ShowMultilayerView)
    {
      this->CellMask.resize(this->MaximumCells * this->Bloat);
      float* dataTmpMask = new float[this->MaximumCells * sizeof(float)];
      CHECK_NEW(dataTmpMask);

      cdi_set_cur(cdiVar, 0, 0);
      cdi_tools::cdi_get_part<float>(cdiVar, this->BeginCell, this->NumberLocalCells, dataTmpMask,
        this->MaximumNVertLevels, this->Grib);
      vtkDebugMacro("Done with read of 3d Mask data");

      // readjust the data
      for (int j = 0; j < this->NumberLocalCells; j++)
      {
        for (int levelNum = 0; levelNum < this->MaximumNVertLevels; levelNum++)
        {
          int i = j * this->MaximumNVertLevels;
          this->CellMask[i + levelNum] =
            (dataTmpMask[j + (levelNum * this->NumberLocalCells)] == maskVal);
        }
      }

      delete[] dataTmpMask;
      vtkDebugMacro("Got data for missing value mask (3D)");
    }
    else
    {
      this->CellMask.resize(this->NumberLocalCells * this->Bloat);
      float* dataTmpMask = new float[this->NumberLocalCells];

      cdi_set_cur(cdiVar, 0, this->VerticalLevelSelected);
      cdi_tools::cdi_get_part<float>(
        cdiVar, this->BeginCell, this->NumberLocalCells, dataTmpMask, 1, this->Grib);

      // readjust the data
      for (int j = 0; j < this->NumberLocalCells; j++)
      {
        this->CellMask[j] = (dataTmpMask[j] == maskVal);
      }

      delete[] dataTmpMask;
      vtkDebugMacro("Got data for missing value mask (2D)");
    }
    this->GotMask = true;
  }

  return 1;
}

//----------------------------------------------------------------------------
//  Add halo to the land sea mask (for points on 180 deg line / ... )
//----------------------------------------------------------------------------
int vtkCDIReader::AddMaskHalo()
{
  if ((this->GotMask) && (this->NumberLocalCells < this->CurrentExtraCell))
  {
    if (this->ShowMultilayerView)
    {
      // put out data for extra cells
      for (int j = this->NumberLocalCells; j < this->CurrentExtraCell; j++)
      {
        for (int levelNum = 0; levelNum < this->MaximumNVertLevels; levelNum++)
        {
          int l = j * this->MaximumNVertLevels;
          int k = this->MaximumNVertLevels * this->CellMap[j - this->NumberLocalCells];
          this->CellMask[l + levelNum] = (CellMask[k + levelNum]);
        }
      }
    }
    else
    {
      // put out data for extra cells
      for (int j = this->NumberLocalCells; j < this->CurrentExtraCell; j++)
      {
        int k = this->CellMap[j - this->NumberLocalCells];
        this->CellMask[j] = this->CellMask[k];
      }
    }

    return 1;
  }

  return 0;
}

//----------------------------------------------------------------------------
//  Load domain (performance data) variables and integrate them as
//  cell vars. //  Check http://www.kitware.com/blog/home/post/817 if it
//  is possible to adapt to this technique.
//----------------------------------------------------------------------------
bool vtkCDIReader::BuildDomainCellVars()
{
  this->DomainCellVar = new double[this->NumberOfCells * this->NumberOfDomainVars];
  std::vector<double> domainTMP(this->NumberOfCells);
  CHECK_NEW(this->DomainCellVar);
  double val = 0;
  int mask_pos = 0;
  int numVars = vlistNvars(this->VListID);

  for (int i = 0; i < numVars; i++)
  {
    if (!strcmp(this->Internals->CellVars[i].Name, this->DomainVarName.c_str()))
    {
      mask_pos = i;
    }
  }

  cdi_tools::CDIVar* cdiVar = &(this->Internals->CellVars[mask_pos]);
  cdi_set_cur(cdiVar, 0, 0);
  cdi_tools::cdi_get_part<double>(
    cdiVar, this->BeginCell, this->NumberLocalCells, domainTMP.data(), 1, this->Grib);

  for (int j = 0; j < this->NumberOfDomainVars; j++)
  {
    vtkNew<vtkDoubleArray> domainVar;
    for (int k = 0; k < this->NumberOfCells; k++)
    {
      val = this->DomainVarDataArray->GetArray(j)->GetComponent(domainTMP[k], 0l);
      this->DomainCellVar[k + (j * this->NumberOfCells)] = val;
    }
    domainVar->SetArray(this->DomainCellVar + (j * this->NumberOfCells), this->NumberLocalCells, 0,
      vtkDoubleArray::VTK_DATA_ARRAY_FREE);
    domainVar->SetName(this->Internals->DomainVars[j].c_str());
    this->Output->GetCellData()->AddArray(domainVar);
  }

  vtkDebugMacro("Built cell vars from domain data");
  return 1;
}

//------------------------------------------------------------------------------
//  Add a "mirror point" X -- a point on the opposite side of the lat/lon projection.
//------------------------------------------------------------------------------
int vtkCDIReader::AddMirrorPointX(int index, double dividerX, double offset)
{
  vtkDebugMacro("In AddMirrorPoint X...");
  double x = this->PointX[index];
  double y = this->PointY[index];

  // add on east
  if (x < dividerX)
  {
    x += offset;
  }
  else
  {
    // add on west
    x -= offset;
  }

  this->PointX[this->CurrentExtraPoint] = x;
  this->PointY[this->CurrentExtraPoint] = y;

  size_t mirrorPoint = this->CurrentExtraPoint;

  // record mapping
  this->PointMap[this->CurrentExtraPoint - this->NumberLocalPoints] = index;
  this->CurrentExtraPoint++;

  vtkDebugMacro("Out AddMirrorPoint X...");
  return static_cast<int>(mirrorPoint);
}

//------------------------------------------------------------------------------
//  Add a "mirror point" Y -- a point on the opposite side of the Cassini projection.
//------------------------------------------------------------------------------
int vtkCDIReader::AddMirrorPointY(int index, double dividerY, double offset)
{
  vtkDebugMacro("In AddMirrorPoint Y...");
  double x = this->PointX[index];
  double y = this->PointY[index];

  // add on south
  if (y < dividerY)
  {
    y += offset;
  }
  else
  {
    // add on north
    y -= offset;
  }

  this->PointX[this->CurrentExtraPoint] = x;
  this->PointY[this->CurrentExtraPoint] = y;

  size_t mirrorPoint = this->CurrentExtraPoint;

  // record mapping
  this->PointMap[this->CurrentExtraPoint - this->NumberLocalPoints] = index;
  this->CurrentExtraPoint++;

  vtkDebugMacro("Out AddMirrorPoint Y...");
  return static_cast<int>(mirrorPoint);
}

//----------------------------------------------------------------------------
// Elimate Wrap for lon/lat Projection   1 = x-Axis, 2 = Y-Axis
//----------------------------------------------------------------------------
int vtkCDIReader::Wrap(int axis)
{
  vtkDebugMacro("In Wrapping...");

  if ((this->WrapOn) &&
    ((this->ProjectionMode == projection::CYLINDRICAL_EQUIDISTANT) ||
      (this->ProjectionMode == projection::CASSINI)))
  {
    double xyLength = 2 * vtkMath::Pi();
    double xyCenter = 0.0;
    const double toleranceXY = 1.0;

    // For each cell, examine vertices
    // Add new points and cells where needed to account for wraparound.
    for (size_t j = 0; j < this->NumberLocalCells; j++)
    {
      int* conns = &this->OrigConnections[j * this->PointsPerCell];
      int* modConns = &this->ModConnections[j * this->PointsPerCell];

      // Determine if we are wrapping in X direction
      size_t lastk = this->PointsPerCell - 1;
      bool xyWrap = false;
      for (size_t k = 0; k < this->PointsPerCell; k++)
      {
        if ((std::abs(this->PointX[conns[k]] - this->PointX[conns[lastk]]) > toleranceXY) &&
          (axis == 1))
        {
          xyWrap = true;
        }
        if ((std::abs(this->PointY[conns[k]] - this->PointY[conns[lastk]]) > toleranceXY) &&
          (axis == 2))
        {
          xyWrap = true;
        }
        lastk = k;
      }

      // If we wrapped in X direction, modify cell and add mirror cell
      if (xyWrap)
      {
        // first point is anchor it doesn't move
        double anchorX = this->PointX[conns[0]];
        double anchorY = this->PointY[conns[0]];

        modConns[0] = conns[0];
        int numExtraPoints = 0;

        // modify existing cell, so it doesn't wrap
        // move points to one side
        for (size_t k = 1; k < this->PointsPerCell; k++)
        {
          int neigh = conns[k];

          // add a new point, figure out east or west
          if ((axis == 1) && (std::abs(this->PointX[neigh] - anchorX) > toleranceXY))
          {
            modConns[k] = this->AddMirrorPointX(neigh, anchorX, xyLength);
            numExtraPoints++;
          }
          else if ((axis == 2) && (std::abs(this->PointY[neigh] - anchorY) > toleranceXY))
          {
            modConns[k] = this->AddMirrorPointY(neigh, anchorY, xyLength);
            numExtraPoints++;
          }
          else
          {
            // use existing kth point
            modConns[k] = neigh;
          }
        }

        // move addedConns to this->ModConnections extra cells area
        int* addedConns = &this->ModConnections[this->CurrentExtraCell * this->PointsPerCell];

        // add a mirroring cell to other side
        // add mirrored anchor first
        if (axis == 1)
        {
          addedConns[0] = this->AddMirrorPointX(conns[0], xyCenter, xyLength);
          anchorX = this->PointX[addedConns[0]];
        }
        else if (axis == 2)
        {
          addedConns[0] = this->AddMirrorPointY(conns[0], xyCenter, xyLength);
          anchorY = this->PointY[addedConns[0]];
        }
        numExtraPoints++;

        // add mirror cell points if needed
        for (size_t k = 1; k < this->PointsPerCell; k++)
        {
          int neigh = conns[k];

          // add a new point for neighbor, figure out east or west
          if ((axis == 1) && (std::abs(this->PointX[neigh] - anchorX) > toleranceXY))
          {
            addedConns[k] = this->AddMirrorPointX(neigh, anchorX, xyLength);
            numExtraPoints++;
          }
          else if ((axis == 2) && (std::abs(this->PointY[neigh] - anchorY) > toleranceXY))
          {
            addedConns[k] = this->AddMirrorPointY(neigh, anchorY, xyLength);
            numExtraPoints++;
          }
          else
          {
            // use existing kth point
            addedConns[k] = neigh;
          }
        }
        this->CellMap[this->CurrentExtraCell - this->NumberLocalCells] = j;
        this->CurrentExtraCell++;
      }
      else
      {
        // just add cell "as is" to this->ModConnections
        for (size_t k = 0; k < this->PointsPerCell; k++)
        {
          modConns[k] = conns[k];
        }
      }
      if (this->CurrentExtraCell > this->ModNumCells)
      {
        vtkErrorMacro(<< "Exceeded storage for extra cells!");
        return (0);
      }
      if (this->CurrentExtraPoint > this->ModNumPoints)
      {
        vtkErrorMacro(<< "Exceeded storage for extra points!");
        return (0);
      }
    }

    if (!ShowMultilayerView)
    {
      this->MaximumCells = static_cast<int>(this->CurrentExtraCell);
      this->MaximumPoints = static_cast<int>(this->CurrentExtraPoint);
      vtkDebugMacro(<< "elim xwrap: singlelayer: setting this->MaximumPoints to "
                    << this->MaximumPoints);
    }
    else
    {
      this->MaximumCells = static_cast<int>(this->CurrentExtraCell * this->MaximumNVertLevels);
      this->MaximumPoints =
        static_cast<int>(this->CurrentExtraPoint * (this->MaximumNVertLevels + 1));
      vtkDebugMacro(<< "elim xwrap: multilayer: setting this->MaximumPoints to "
                    << this->MaximumPoints);
    }

    vtkDebugMacro("Out Wrapping...");
    return 1;
  }
  else
  {
    for (int j = 0; j < this->NumberLocalCells; j++)
    {
      int* conns = &this->OrigConnections[j * this->PointsPerCell];
      int* modConns = &this->ModConnections[j * this->PointsPerCell];
      int lastk = this->PointsPerCell - 1;
      bool xyWrap = false;

      for (int k = 0; k < this->PointsPerCell; k++)
      {
        if ((abs(this->PointX[conns[k]] - this->PointX[conns[lastk]]) > 1.0) && (axis == 1))
        {
          xyWrap = true;
        }
        if ((abs(this->PointY[conns[k]] - this->PointY[conns[lastk]]) > 1.0) && (axis == 2))
        {
          xyWrap = true;
        }

        lastk = k;
      }

      if (xyWrap)
      {
        for (int k = 0; k < this->PointsPerCell; k++)
        {
          modConns[k] = 0;
        }
      }
      else
      {
        for (int k = 0; k < this->PointsPerCell; k++)
        {
          modConns[k] = conns[k];
        }
      }
    }
    vtkDebugMacro("Out Wrapping...");
    return 1;
  }
}

//----------------------------------------------------------------------------
//  Add points to vtk data structures
//----------------------------------------------------------------------------
void vtkCDIReader::OutputPoints(bool init)
{
  vtkDebugMacro("In OutputPoints...");
  float layerThicknessScaleFactor = 5000.0;
  vtkSmartPointer<vtkPoints> points;
  float adjustedLayerThickness = (this->LayerThickness / layerThicknessScaleFactor);

  if (this->InvertZAxis)
  {
    adjustedLayerThickness = -1.0 * (this->LayerThickness / layerThicknessScaleFactor);
  }

  vtkDebugMacro("OutputPoints: this->MaximumPoints: "
    << this->MaximumPoints << " this->MaximumNVertLevels: " << this->MaximumNVertLevels
    << " LayerThickness: " << this->LayerThickness
    << " ShowMultilayerView: " << this->ShowMultilayerView);
  if (init)
  {
    points = vtkSmartPointer<vtkPoints>::New();
    points->Allocate(this->MaximumPoints, this->MaximumPoints);
    this->Output->SetPoints(points);
  }
  else
  {
    points = this->Output->GetPoints();
    points->Initialize();
    points->Allocate(this->MaximumPoints, this->MaximumPoints);
  }

  if (this->DepthVar == nullptr)
  {
    vtkDebugMacro("OutputPoints: this->MaximumPoints: "
      << this->MaximumPoints << " this->MaximumNVertLevels: " << this->MaximumNVertLevels
      << " LayerThickness: " << this->LayerThickness
      << " ShowMultilayerView: " << this->ShowMultilayerView);
    return; // We don't have any data anyways.
  }

  double sx, sy, sz;
  get_scaling(this->ProjectionMode, this->ShowMultilayerView,
    this->DepthVar[this->VerticalLevelSelected], adjustedLayerThickness, sx, sy, sz);

  for (int j = 0; j < this->CurrentExtraPoint; j++)
  {
    double x = this->PointX[j] * sx;
    double y = this->PointY[j] * sy;
    double z = this->PointZ[j] * sz;

    if (!this->ShowMultilayerView)
    {
      points->InsertNextPoint(x, y, z);
    }
    else
    {
      double rho = 0.0, rholevel = 0.0, theta = 0.0, phi = 0.0;
      int retval = -1;

      if (this->ProjectionMode == projection::SPHERICAL)
      {
        if ((x != 0.0) || (y != 0.0) || (z != 0.0))
        {
          retval = projection::cartesianToSpherical(x, y, z, &rho, &phi, &theta);
          if (!retval)
            retval = projection::sphericalToCartesian(
              rho + this->Layer0Offset * adjustedLayerThickness, phi, theta, &x, &y, &z);
        }
      }

      if (this->ProjectionMode != projection::SPHERICAL)
      {
        z = this->Layer0Offset * adjustedLayerThickness; // to avoid 0 layer thickness / ...
      }

      points->InsertNextPoint(x, y, z);

      for (int levelNum = 0; levelNum < this->MaximumNVertLevels; levelNum++)
      {
        if ((this->ProjectionMode != projection::SPHERICAL) &&
          (this->ProjectionMode != projection::CATALYST))
        {
          z = -(this->DepthVar[levelNum] * adjustedLayerThickness);
        }
        else if (this->ProjectionMode == projection::SPHERICAL)
        {
          if (!retval && ((x != 0.0) || (y != 0.0) || (z != 0.0)))
          {
            rholevel = rho - (adjustedLayerThickness * this->DepthVar[levelNum]);
            retval = projection::sphericalToCartesian(rholevel, phi, theta, &x, &y, &z);
          }
        }
        else if (this->ProjectionMode == projection::CATALYST)
        {
          z = -(this->DepthVar[levelNum] * (adjustedLayerThickness * 0.04));
        }
        points->InsertNextPoint(x, y, z);
      }
    }
  }
  if (abs(this->DepthVar[0] - this->Layer0Offset) < 1 && this->ShowMultilayerView)
  {
    vtkWarningMacro(<< this->FileName << ": First vertical level thickness is close to 0 ("
                    << abs(this->DepthVar[0] - this->Layer0Offset)
                    << " to be precise). It will be rendered as basically flat. Use \"3D Surface Z "
                       "offset for first Layer\" to adjust. Current value is "
                    << this->Layer0Offset << ".");
  }
  vtkDebugMacro("Leaving OutputPoints...");
}

//----------------------------------------------------------------------------
// Determine if cell is one of VTK_TRIANGLE, VTK_WEDGE, VTK_QUAD or
// VTK_HEXAHEDRON
//----------------------------------------------------------------------------
unsigned char vtkCDIReader::GetCellType()
{
  // write cell types
  switch (this->PointsPerCell)
  {
    case 3:
      return (!this->ShowMultilayerView) ? VTK_TRIANGLE : VTK_WEDGE;
    case 4:
      return (!this->ShowMultilayerView) ? VTK_QUAD : VTK_HEXAHEDRON;
    case 5:
      return (!this->ShowMultilayerView) ? VTK_POLYGON : VTK_PENTAGONAL_PRISM;
    case 6:
      return (!this->ShowMultilayerView) ? VTK_POLYGON : VTK_HEXAGONAL_PRISM;
    default:
      return (!this->ShowMultilayerView) ? VTK_POLYGON : VTK_POLYHEDRON;
  }
  return VTK_TRIANGLE;
}

//----------------------------------------------------------------------------
//  Add cells to vtk data structures
//----------------------------------------------------------------------------
void vtkCDIReader::OutputCells(bool init)
{
  vtkDebugMacro("In OutputCells...");
  vtkUnstructuredGrid* output = this->Output;

  output->GetCellData()->Initialize();
  output->GetCellData()->SetNumberOfTuples(this->MaximumCells);
  output->Allocate(this->MaximumCells, this->MaximumCells);

  vtkSmartPointer<vtkCellArray> cells;
  int pointsPerPolygon = this->PointsPerCell * (this->ShowMultilayerView ? 2 : 1);
  int cellType = this->GetCellType();

  if (init)
  {
    cells = vtkSmartPointer<vtkCellArray>::New();
    cells->Allocate(this->MaximumCells, this->MaximumCells);
    output->SetCells(cellType, cells);
    cells->SetNumberOfCells(this->MaximumCells);
  }
  else
  {
    cells = output->GetCells();
    cells->Initialize();
    cells->Allocate(this->MaximumCells, this->MaximumCells);
    cells->SetNumberOfCells(this->MaximumCells);
  }

  vtkDebugMacro("OutputCells: init: " << init << " this->MaximumCells: " << this->MaximumCells
                                      << " cellType: " << cellType
                                      << " this->MaximumNVertLevels: " << this->MaximumNVertLevels
                                      << " LayerThickness: " << this->LayerThickness
                                      << " ShowMultilayerView: " << this->ShowMultilayerView
                                      << " CurrentExtraCell: " << this->CurrentExtraCell);

  if (this->DepthVar == nullptr)
  {
    vtkErrorMacro(
      "File " << this->FileName << " OutputCells: this->MaximumCells: " << this->MaximumCells
              << " this->MaximumNVertLevels: " << this->MaximumNVertLevels << " LayerThickness: "
              << this->LayerThickness << " ShowMultilayerView: " << this->ShowMultilayerView);
    return; // We don't have any data anyways.
  }

  std::vector<vtkIdType> polygon(pointsPerPolygon);
  for (int j = 0; j < this->CurrentExtraCell; j++)
  {
    int* conns;
    if (this->ProjectionMode != projection::SPHERICAL)
    {
      conns = &this->ModConnections[j * this->PointsPerCell];
    }
    else
    {
      conns = &this->OrigConnections[j * this->PointsPerCell];
    }

    // check for outer boundary cell
    bool boundary = false;
    if (this->ProjectionMode == projection::CYLINDRICAL_EQUIDISTANT ||
      this->ProjectionMode == projection::CASSINI)
    {

      double borderX, borderY;
      if (this->ProjectionMode == projection::CYLINDRICAL_EQUIDISTANT)
      {
        borderX = vtkMath::Pi() + 0.5;
        borderY = (vtkMath::Pi() / 2.0) + 0.5;
      }
      else
      {
        borderX = (vtkMath::Pi() / 2.0) + 0.5;
        borderY = vtkMath::Pi() + 0.5;
      }
      for (size_t k = 0; k < this->PointsPerCell; k++)
      {
        double x = this->PointX[conns[k]];
        double y = this->PointY[conns[k]];
        if (((x > borderX) || (x < (0.0 - borderX)) || (y > borderY) || (y < (0.0 - borderY))))
        {
          boundary = true;
        }
      }
    }

    if (!this->ShowMultilayerView)
    { // singlelayer
      if (((this->GotMask) && (this->UseMask) && (this->CellMask[j] ^ this->InvertMask)) ||
        boundary)
      {
        output->InsertNextCell(VTK_EMPTY_CELL, 0, polygon.data());
      }
      else
      {
        for (int k = 0; k < this->PointsPerCell; k++)
        {
          polygon[k] = conns[k];
        }

        output->InsertNextCell(cellType, pointsPerPolygon, polygon.data());
      }
    }
    else
    { // multilayer
      for (int levelNum = 0; levelNum < this->MaximumNVertLevels; levelNum++)
      {
        int i = j * this->MaximumNVertLevels;
        if (((this->GotMask) && (this->UseMask) && (this->CellMask[i + levelNum])) || boundary)
        {
          output->InsertNextCell(VTK_EMPTY_CELL, 0, polygon.data());
        }
        else
        {
          for (int k = 0; k < this->PointsPerCell; k++)
          {
            int val = (conns[k] * (this->MaximumNVertLevels + 1)) + levelNum;
            polygon[k] = val;
          }
          for (int k = 0; k < this->PointsPerCell; k++)
          {
            int val = (conns[k] * (this->MaximumNVertLevels + 1)) + levelNum + 1;
            polygon[k + this->PointsPerCell] = val;
          }
          if (cellType == VTK_POLYHEDRON)
            this->InsertPolyhedron(polygon);
          else
            output->InsertNextCell(cellType, pointsPerPolygon, polygon.data());
        }
      }
    }
  }

  if (this->AddCoordinateVars && this->ShowClonClat)
  {
    this->ClonArray = vtkSmartPointer<vtkDoubleArray>::New();
    this->ClonArray->SetName("Center Longitude (CLON)");
    this->ClonArray->SetNumberOfTuples(this->NumberLocalCells * this->MaximumNVertLevels);
    this->ClatArray = vtkSmartPointer<vtkDoubleArray>::New();
    this->ClatArray->SetName("Center Latitude (CLAT)");
    this->ClatArray->SetNumberOfTuples(this->NumberLocalCells * this->MaximumNVertLevels);
    if (this->ShowMultilayerView)
    {
      this->ClonArray->SetArray(
        &this->CLon[0], this->CurrentExtraCell * this->MaximumNVertLevels, 1);
      this->ClatArray->SetArray(
        &this->CLat[0], this->CurrentExtraCell * this->MaximumNVertLevels, 1);
    }
    else
    {
      this->ClonArray->SetArray(&this->CLon[0], this->CurrentExtraCell,
        1); // 1 at the end = No freeing these. They are our vectors.
      this->ClatArray->SetArray(&this->CLat[0], this->CurrentExtraCell,
        1); // 1 at the end = No freeing these. They are our vectors.
    }
    output->GetCellData()->AddArray(this->ClonArray);
    output->GetCellData()->AddArray(this->ClatArray);
  }

  vtkDebugMacro("Leaving OutputCells...");
}

//------------------------------------------------------------------------------
void vtkCDIReader::InsertPolyhedron(std::vector<vtkIdType> polygon)
{

  std::vector<vtkIdType>::iterator it;
  it = std::unique(polygon.begin(), polygon.end());
  polygon.resize(std::distance(polygon.begin(), it));
  const int pointsPerPolygon = polygon.size();

  const int pointsPerCell = pointsPerPolygon / 2;
  const int numFaces = pointsPerCell + 2;
  std::vector<vtkIdType> facestream(7 * pointsPerCell + 2);
  // number of points of the face, then the points of the face
  // 1 + pointsPerCell values for lid / bottom
  // 1 + 4 values for each of the pointsPerCell side faces
  // bottom
  size_t next = 0;
  facestream[next++] = pointsPerCell;
  for (int k = 0; k < pointsPerCell; k++)
  {
    facestream[next++] = polygon[pointsPerCell - 1 - k];
  }
  // lid
  facestream[next++] = pointsPerCell;
  for (int k = pointsPerCell; k < pointsPerCell * 2; k++)
  {
    facestream[next++] = polygon[k];
  }
  for (int k = 0; k < pointsPerCell - 1; k++)
  {
    facestream[next++] = 4;
    facestream[next++] = polygon[k];
    facestream[next++] = polygon[k + 1];
    facestream[next++] = polygon[k + 1 + pointsPerCell];
    facestream[next++] = polygon[k + pointsPerCell];
  }
  facestream[next++] = 4;
  facestream[next++] = polygon[pointsPerCell - 1];
  facestream[next++] = polygon[0];
  facestream[next++] = polygon[pointsPerCell];
  facestream[next++] = polygon[pointsPerCell * 2 - 1];
  this->Output->InsertNextCell(
    VTK_POLYHEDRON, pointsPerPolygon, polygon.data(), numFaces, facestream.data());
};

//----------------------------------------------------------------------------
//  Load the data for a Point variable specified.
//----------------------------------------------------------------------------
int vtkCDIReader::LoadPointVarData(int variableIndex, double dTimeStep)
{
  if (!(this->PointsPerCell == 3))
    return 0;

  this->PointDataSelected = variableIndex;

  vtkSmartPointer<vtkDataArray> dataArray =
    this->PointVarDataArray->GetArray(this->Internals->PointVars[variableIndex].Name);

  // Allocate data array for this variable
  if (dataArray == nullptr)
  {
    if (this->DoublePrecision)
    {
      dataArray = vtkSmartPointer<vtkDoubleArray>::New();
    }
    else
    {
      dataArray = vtkSmartPointer<vtkFloatArray>::New();
    }

    vtkDebugMacro("Allocated Point var index: " << this->Internals->PointVars[variableIndex].Name);
    dataArray->SetName(this->Internals->PointVars[variableIndex].Name);
    dataArray->SetNumberOfTuples(this->MaximumPoints);
    dataArray->SetNumberOfComponents(1);

    this->PointVarDataArray->AddArray(dataArray);
  }

  int success = false;
  if (this->DoublePrecision)
  {
    vtkICONTemplateDispatch(
      VTK_DOUBLE,
      success = this->LoadPointVarDataTemplate<VTK_TT>(variableIndex, dTimeStep, dataArray););
  }
  else
  {
    vtkICONTemplateDispatch(
      VTK_FLOAT,
      success = this->LoadPointVarDataTemplate<VTK_TT>(variableIndex, dTimeStep, dataArray););
  }

  return success;
}

//----------------------------------------------------------------------------
//  Load the data for a cell variable specified.
//----------------------------------------------------------------------------
int vtkCDIReader::LoadCellVarData(int variableIndex, double dTimeStep)
{
  this->CellDataSelected = variableIndex;

  vtkSmartPointer<vtkDataArray> dataArray =
    this->CellVarDataArray->GetArray(this->Internals->CellVars[variableIndex].Name);
  // Allocate data array for this variable
  if (dataArray == nullptr)
  {
    if (this->DoublePrecision)
    {
      dataArray = vtkSmartPointer<vtkDoubleArray>::New();
    }
    else
    {
      dataArray = vtkSmartPointer<vtkFloatArray>::New();
    }

    vtkDebugMacro("Allocated cell var index: " << this->Internals->CellVars[variableIndex].Name);
    dataArray->SetName(this->Internals->CellVars[variableIndex].Name);
    dataArray->SetNumberOfTuples(this->MaximumCells);
    dataArray->SetNumberOfComponents(1);

    this->CellVarDataArray->AddArray(dataArray);
  }

  int success = false;
  if (this->DoublePrecision)
  {
    vtkICONTemplateDispatch(
      VTK_DOUBLE,
      success = this->LoadCellVarDataTemplate<VTK_TT>(variableIndex, dTimeStep, dataArray););
  }
  else
  {
    vtkICONTemplateDispatch(
      VTK_FLOAT,
      success = this->LoadCellVarDataTemplate<VTK_TT>(variableIndex, dTimeStep, dataArray););
  }

  return success;
}

//----------------------------------------------------------------------------
//  Load the data for a cell variable specified.
//----------------------------------------------------------------------------
template <typename ValueType>
int vtkCDIReader::LoadCellVarDataTemplate(
  int variableIndex, double dTimeStep, vtkDataArray* dataArray)
{
  vtkDebugMacro("In vtkCDIReader::LoadCellVarData");
  ValueType* dataBlock = static_cast<ValueType*>(dataArray->GetVoidPointer(0));
  cdi_tools::CDIVar* cdiVar = &(this->Internals->CellVars[variableIndex]);
  int varType = cdiVar->Type;

  int timestep = this->GetTimeIndex(dTimeStep);
  vtkDebugMacro("Time: " << timestep);
  vtkDebugMacro("Dimensions: " << varType);

  if (varType == 3) // 3D arrays
  {
    if (!this->ShowMultilayerView)
    {
      cdi_set_cur(cdiVar, timestep, this->VerticalLevelSelected);
      cdi_tools::cdi_get_part<ValueType>(
        cdiVar, this->BeginCell, this->NumberLocalCells, dataBlock, 1, this->Grib);

      // put out data for extra cells
      for (int j = this->NumberLocalCells; j < this->CurrentExtraCell; j++)
      {
        int k = this->CellMap[j - this->NumberLocalCells];
        dataBlock[j] = dataBlock[k];
      }
    }
    else
    {
      ValueType* dataTmp = new ValueType[this->MaximumCells];
      cdi_set_cur(cdiVar, timestep, 0);
      cdi_tools::cdi_get_part<ValueType>(cdiVar, this->BeginCell, this->NumberLocalCells, dataTmp,
        this->MaximumNVertLevels, this->Grib);

      // readjust the data
      for (int j = 0; j < this->NumberLocalCells; j++)
      {
        for (int levelNum = 0; levelNum < this->MaximumNVertLevels; levelNum++)
        {
          int i = j * this->MaximumNVertLevels;
          dataBlock[i + levelNum] = dataTmp[j + (levelNum * this->NumberLocalCells)];
        }
      }

      // put out data for extra cells
      for (int j = this->NumberLocalCells; j < this->CurrentExtraCell; j++)
      {
        for (int levelNum = 0; levelNum < this->MaximumNVertLevels; levelNum++)
        {
          int l = j * this->MaximumNVertLevels;
          int k = this->CellMap[j - this->NumberLocalCells];
          dataBlock[l + levelNum] = dataTmp[k + (levelNum * this->NumberLocalCells)];
        }
      }

      delete[] dataTmp;
    }
    vtkDebugMacro("Got data for cell var: " << this->Internals->CellVars[variableIndex].Name);
  }
  else // 2D arrays
  {
    if (!this->ShowMultilayerView)
    {
      cdi_set_cur(cdiVar, timestep, 0);
      cdi_tools::cdi_get_part<ValueType>(
        cdiVar, this->BeginCell, this->NumberLocalCells, dataBlock, 1, this->Grib);

      // put out data for extra cells
      for (int j = this->NumberLocalCells; j < this->CurrentExtraCell; j++)
      {
        int k = this->CellMap[j - this->NumberLocalCells];
        dataBlock[j] = dataBlock[k];
      }
    }
    else
    {
      ValueType* dataTmp = new ValueType[this->NumberLocalCells];
      cdi_set_cur(cdiVar, timestep, 0);
      cdi_tools::cdi_get_part<ValueType>(
        cdiVar, this->BeginCell, this->NumberLocalCells, dataTmp, 1, this->Grib);

      for (int j = 0; j < +this->NumberLocalCells; j++)
      {
        for (int levelNum = 0; levelNum < this->MaximumNVertLevels; levelNum++)
        {
          int i = j * this->MaximumNVertLevels;
          dataBlock[i + levelNum] = dataTmp[j];
        }
      }

      // put out data for extra cells
      for (int j = this->NumberLocalCells; j < this->CurrentExtraCell; j++)
      {
        for (int levelNum = 0; levelNum < this->MaximumNVertLevels; levelNum++)
        {
          int l = j * this->MaximumNVertLevels;
          int k = this->CellMap[j - this->NumberLocalCells];
          dataBlock[l + levelNum] = dataTmp[k];
        }
      }

      delete[] dataTmp;
    }

    vtkDebugMacro("Got data for cell var: " << this->Internals->CellVars[variableIndex].Name);
  }

  vtkDebugMacro("Stored data for cell var: " << this->Internals->CellVars[variableIndex].Name);

  this->ReplaceFillWithNan(cdiVar->VarID, dataArray);
  return 1;
}

//------------------------------------------------------------------------------
int vtkCDIReader::ReplaceFillWithNan(const int varID, vtkDataArray* dataArray)
{
  double miss = vlistInqVarMissval(this->VListID, varID);

  // NaN only available with float and double.
  if (dataArray->GetDataType() == VTK_FLOAT)
  {

    float fillValue = miss;
    std::replace(reinterpret_cast<float*>(dataArray->GetVoidPointer(0)),
      reinterpret_cast<float*>(dataArray->GetVoidPointer(dataArray->GetNumberOfTuples())),
      fillValue, static_cast<float>(vtkMath::Nan()));
  }
  else if (dataArray->GetDataType() == VTK_DOUBLE)
  {
    double fillValue = miss;
    std::replace(reinterpret_cast<double*>(dataArray->GetVoidPointer(0)),
      reinterpret_cast<double*>(dataArray->GetVoidPointer(dataArray->GetNumberOfTuples())),
      fillValue, vtkMath::Nan());
  }
  else
  {
    vtkWarningMacro(<< "No NaN available for data of type " << dataArray->GetDataType());
  }

  return 1;
}

//----------------------------------------------------------------------------
//  Load the data for a Point variable specified.
//----------------------------------------------------------------------------
template <typename ValueType>
int vtkCDIReader::LoadPointVarDataTemplate(
  int variableIndex, double dTimeStep, vtkDataArray* dataArray)
{
  vtkDebugMacro("In vtkICONReader::LoadPointVarData");
  cdi_tools::CDIVar* cdiVar = &this->Internals->PointVars[variableIndex];
  int varType = cdiVar->Type;

  vtkDebugMacro("getting pointer in vtkICONReader::LoadPointVarData");
  ValueType* dataBlock = static_cast<ValueType*>(dataArray->GetVoidPointer(0));
  ValueType* dataTmp;
  if (this->ShowMultilayerView)
  {
    dataTmp = new ValueType[this->MaximumPoints];
  }
  else
  {
    dataTmp = new ValueType[this->NumberLocalPoints];
  }

  int timestep = this->GetTimeIndex(dTimeStep);
  vtkDebugMacro("Time: " << timestep);
  vtkDebugMacro("dTimeStep requested: " << dTimeStep);

  if (this->Piece < 1)
  {
    // 3D arrays ...
    vtkDebugMacro("Dimensions: " << varType);
    if (varType == 3)
    {
      if (!this->ShowMultilayerView)
      {
        cdi_set_cur(cdiVar, timestep, this->VerticalLevelSelected);
        cdi_tools::cdi_get_part<ValueType>(
          cdiVar, this->BeginPoint, this->NumberLocalPoints, dataBlock, 1, this->Grib);
        dataBlock[0] = dataBlock[1];

        // put out data for extra points
        for (int j = this->NumberLocalPoints; j < this->CurrentExtraPoint; j++)
        {
          int k = this->PointMap[j - this->NumberLocalPoints];
          dataBlock[j] = dataBlock[k];
        }
      }
      else
      {
        cdi_set_cur(cdiVar, timestep, 0);
        cdi_tools::cdi_get_part<ValueType>(cdiVar, this->BeginPoint, this->NumberLocalPoints,
          dataTmp, this->MaximumNVertLevels, this->Grib);
        dataTmp[0] = dataTmp[1];

        // put out data for extra points
        for (int j = this->NumberLocalPoints; j < this->CurrentExtraPoint; j++)
        {
          for (int levelNum = 0; levelNum < this->MaximumNVertLevels; levelNum++)
          {
            int l = j * this->MaximumNVertLevels;
            int k = this->PointMap[j - this->NumberLocalPoints];
            dataBlock[l + levelNum] = dataTmp[k + (levelNum * this->NumberLocalPoints)];
          }
        }
      }
    }
    // 2D arrays ...
    else if (varType == 2)
    {
      if (!this->ShowMultilayerView)
      {
        cdi_set_cur(cdiVar, timestep, 0);
        cdi_tools::cdi_get_part<ValueType>(
          cdiVar, this->BeginPoint, this->NumberLocalPoints, dataBlock, 1, this->Grib);
        dataBlock[0] = dataBlock[1];
      }
      else
      {
        cdi_set_cur(cdiVar, timestep, 0);
        cdi_tools::cdi_get_part<ValueType>(
          cdiVar, this->BeginPoint, this->NumberLocalPoints, dataTmp, 1, this->Grib);
        dataTmp[0] = dataTmp[1];
      }
    }
    vtkDebugMacro("got Point data in vtkICONReader::LoadPointVarDataSP");

    if (this->ShowMultilayerView)
    {
      // put in some dummy points
      for (int levelNum = 0; levelNum < this->MaximumNVertLevels; levelNum++)
      {
        dataBlock[levelNum] = dataTmp[this->MaximumNVertLevels + levelNum];
      }

      // write highest level dummy Point (duplicate of last level)
      dataBlock[this->MaximumNVertLevels] =
        dataTmp[this->MaximumNVertLevels + this->MaximumNVertLevels - 1];
      vtkDebugMacro("Wrote dummy vtkICONReader::LoadPointVarDataSP");

      // readjust the data
      for (int j = 0; j < this->NumberLocalPoints; j++)
      {
        int i = j * (this->MaximumNVertLevels + 1);
        // write data for one Point -- lowest level to highest
        for (int levelNum = 0; levelNum < this->MaximumNVertLevels; levelNum++)
        {
          dataBlock[i++] = dataTmp[j + (levelNum * this->NumberLocalPoints)];
        }

        // layer below, which is repeated ...
        dataBlock[i++] = dataTmp[j + ((MaximumNVertLevels - 1) * this->NumberLocalPoints)];
      }
    }
  }
  else
  {
    int length = (this->NumberAllPoints / this->NumPieces);
    int start = (length * this->Piece);
    ValueType* dataTmp2 = new ValueType[length];

    // 3D arrays ...
    vtkDebugMacro("Dimensions: " << varType);
    if (varType == 3)
    {
      if (!this->ShowMultilayerView)
      {
        cdi_set_cur(cdiVar, timestep, this->VerticalLevelSelected);
        cdi_tools::cdi_get_part<ValueType>(cdiVar, start, length, dataTmp2, 1, this->Grib);
        dataTmp2[0] = dataTmp2[1];

        // readjust the data
        size_t size = this->NumberLocalCells * this->PointsPerCell;
        for (size_t j = 0; j < size; j++)
        {
          int pos = this->VertexIds[j];
          int pos_conn = this->OrigConnections[j];
          if ((pos > start) && (pos < (start + length + 1)))
          {
            dataBlock[pos_conn] = dataTmp2[pos - start];
          }
          else
          {
            dataBlock[pos_conn] = 0.0;
          }
        }
      }
      else
      {
        cdi_set_cur(cdiVar, timestep, 0);
        cdi_tools::cdi_get_part<ValueType>(
          cdiVar, start, length, dataTmp, this->MaximumNVertLevels, this->Grib);
        dataTmp[0] = dataTmp[1];
      }
    }
    // 2D arrays ...
    else if (varType == 2)
    {
      if (!this->ShowMultilayerView)
      {
        cdi_set_cur(cdiVar, timestep, 0);
        cdi_tools::cdi_get_part<ValueType>(cdiVar, start, length, dataTmp2, 1, this->Grib);
        dataTmp2[0] = dataTmp2[1];

        // readjust the data
        size_t size = this->NumberLocalCells * this->PointsPerCell;
        for (size_t j = 0; j < size; j++)
        {
          int pos = this->VertexIds[j];
          int pos_conn = this->OrigConnections[j];
          if ((pos > start) && (pos < (start + length + 1)))
          {
            dataBlock[pos_conn] = dataTmp2[pos - start];
          }
          else
          {
            dataBlock[pos_conn] = 0.0;
          }
        }
      }
      else
      {
        cdi_set_cur(cdiVar, timestep, 0);
        cdi_tools::cdi_get_part<ValueType>(cdiVar, start, length, dataTmp, 1, this->Grib);
        dataTmp[0] = dataTmp[1];
      }
    }
    delete[] dataTmp2;
    vtkDebugMacro("got Point data in vtkICONReader::LoadPointVarDataSP");
  }

  vtkDebugMacro("this->NumberOfPoints: " << this->NumberOfPoints << " this->NumberLocalPoints: "
                                         << this->NumberLocalPoints);
  delete[] dataTmp;

  return 1;
}

//----------------------------------------------------------------------------
//  Load the data for a domain variable specified
//----------------------------------------------------------------------------
int vtkCDIReader::LoadDomainVarData(int variableIndex)
{
  // This is not very well implemented, also due to the organization of
  // the data available. Needs to be improved together with the modellers.
  vtkDebugMacro("In vtkCDIReader::LoadDomainVarData");
  std::string variable = this->Internals->DomainVars[variableIndex];
  this->DomainDataSelected = variableIndex;

  // Allocate data array for this variable
  if (!this->DomainVarDataArray->HasArray(variable.c_str()))
  {
    vtkNew<vtkDoubleArray> dataArray;
    vtkDebugMacro("Allocated domain var index: " << variable.c_str());
    dataArray->SetName(variable.c_str());
    dataArray->SetNumberOfTuples(this->NumberOfDomains);
    // 6 components
    dataArray->SetNumberOfComponents(1);
    this->DomainVarDataArray->AddArray(dataArray);
  }

  for (int i = 0; i < this->NumberOfDomains; i++)
  {
    std::string filename;
    if (i < 10)
    {
      filename = this->PerformanceDataFile + "000" + std::to_string(i);
    }
    else if (i < 100)
    {
      filename = this->PerformanceDataFile + "00" + std::to_string(i);
    }
    else if (i < 1000)
    {
      filename = this->PerformanceDataFile + "0" + std::to_string(i);
    }
    else
    {
      filename = this->PerformanceDataFile + std::to_string(i);
    }

    std::vector<std::string> wordVec;
    vtksys::ifstream file(filename.c_str());
    std::string str, word;
    double temp[1];

    getline(file, str);
    std::stringstream ss(str);
    while (ss.good())
    {
      ss >> word;

      word.erase(word.begin(),
        std::find_if(word.begin(), word.end(), [](int c) { return !std::ispunct(c); }));
      word.erase(
        std::find_if(word.rbegin(), word.rend(), [](int c) { return !std::ispunct(c); }).base(),
        word.end());

      wordVec.push_back(word);
    }
    //  0    1      	2     		3      	4       	5      	6 7		  8
    //  th  L 	name   	#calls 	t_min 	t_ave	t_max 	t_total	   t_total2
    // 00   L		physics   251    	0.4222s  0.9178s  10.52s    03m50s     230.21174
    // for (int l=0; l<6 ; l++)
    //  temp[l] = atof(wordVec.at(2+l).c_str());

    if (wordVec.at(1) != "L")
    {
      temp[0] = atof(wordVec.at(7).c_str());
    }
    else
    {
      temp[0] = atof(wordVec.at(8).c_str());
    }

    // for now, we just use t_average
    this->DomainVarDataArray->GetArray(variableIndex)->InsertTuple(i, temp);
  }

  vtkDebugMacro("Out vtkCDIReader::LoadDomainVarData");
  return 1;
}

//----------------------------------------------------------------------------
//  Specify the netCDF dimension names
//-----------------------------------------------------------------------------
int vtkCDIReader::FillGridDimensions()
{
  int ngrids = vlistNgrids(this->VListID);
  int nzaxis = vlistNzaxis(this->VListID);
  int nvars = vlistNvars(this->VListID);
  this->AllDimensions->SetNumberOfValues(0);
  this->VariableDimensions->SetNumberOfValues(ngrids * nzaxis);
  char nameGridX[CDI_MAX_NAME];
  char nameGridY[CDI_MAX_NAME];
  char nameLev[CDI_MAX_NAME];

  std::set<std::string> hits;

  for (int k = 0; k < nvars; k++)
  {
    int i = vlistInqVarGrid(this->VListID, k);
    int j = vlistInqVarZaxis(this->VListID, k);
    hits.insert(std::to_string(i) + "x" + std::to_string(j));
    // IDs are not 0 to n-1 but can be 30-ish for a file with 3 grids.
    // they map to the gridID_l and zaxisID_l values below.
    // Thus we need to a map to catch rather unpredictable values.
  }

  for (int i = 0; i < ngrids; ++i)
  {
    for (int j = 0; j < nzaxis; ++j)
    {
      std::string dimEncoding("(");
      int gridID_l = vlistGrid(this->VListID, i);
      gridInqXname(gridID_l, nameGridX);
      gridInqYname(gridID_l, nameGridY);
      dimEncoding += nameGridX;
      dimEncoding += ", ";
      dimEncoding += nameGridY;
      dimEncoding += ", ";
      int zaxisID_l = vlistZaxis(this->VListID, j);
      zaxisInqName(zaxisID_l, nameLev);
      dimEncoding += nameLev;
      dimEncoding += ")";

      if (hits.count(std::to_string(gridID_l) + "x" + std::to_string(zaxisID_l)) == 0)
      {
        continue; // skip empty grid combinations
      }

      this->AllDimensions->InsertNextValue(dimEncoding);
      this->VariableDimensions->SetValue(i * nzaxis + j, dimEncoding.c_str());
    }
  }

  return 1;
}

//----------------------------------------------------------------------------
//  Set dimensions and rebuild geometry
//-----------------------------------------------------------------------------
void vtkCDIReader::SetDimensions(const char* dimensions)
{
  for (vtkIdType i = 0; i < this->VariableDimensions->GetNumberOfValues(); i++)
  {
    if (this->VariableDimensions->GetValue(i) == dimensions)
    {
      this->DimensionSelection = i;
    }
  }

  this->PointDataArraySelection->RemoveAllArrays();
  this->CellDataArraySelection->RemoveAllArrays();
  this->PointDataArraySelection->Modified();
  this->CellDataArraySelection->Modified();

  if (this->DomainDataArraySelection)
  {
    this->DomainDataArraySelection->RemoveAllArrays();
    this->DomainDataArraySelection->Modified();
  }

  this->ReconstructNew = true;
  this->DestroyData();
  this->RegenerateVariables();
  if (this->GridReconstructed)
    this->RegenerateGeometry();
}

//----------------------------------------------------------------------------
//  Return all variable names
//-----------------------------------------------------------------------------
vtkStringArray* vtkCDIReader::GetAllVariableArrayNames()
{
  int numArrays = this->GetNumberOfVariableArrays();
  this->AllVariableArrayNames->SetNumberOfValues(numArrays);
  for (int arrayIdx = 0; arrayIdx < numArrays; arrayIdx++)
  {
    const char* arrayName = this->GetVariableArrayName(arrayIdx);
    this->AllVariableArrayNames->SetValue(arrayIdx, arrayName);
  }
  return this->AllVariableArrayNames;
}

//----------------------------------------------------------------------------
// Set status of named Point variable selection.
//----------------------------------------------------------------------------
void vtkCDIReader::SetPointArrayStatus(const char* name, int status)
{
  if (status)
  {
    this->PointDataArraySelection->EnableArray(name);
  }
  else
  {
    this->PointDataArraySelection->DisableArray(name);
  }
}

//----------------------------------------------------------------------------
// Set status of named cell variable selection.
//----------------------------------------------------------------------------
void vtkCDIReader::SetCellArrayStatus(const char* name, int status)
{
  if (status)
  {
    this->CellDataArraySelection->EnableArray(name);
  }
  else
  {
    this->CellDataArraySelection->DisableArray(name);
  }
}

//----------------------------------------------------------------------------
// Set status of named domain variable selection.
//----------------------------------------------------------------------------
void vtkCDIReader::SetDomainArrayStatus(const char* name, int status)
{
  if (status)
  {
    this->DomainDataArraySelection->EnableArray(name);
  }
  else
  {
    this->DomainDataArraySelection->DisableArray(name);
  }
}

//----------------------------------------------------------------------------
// Set status of named domain variable selection.
//----------------------------------------------------------------------------
void vtkCDIReader::SetMaskingVariable(const char* name)
{
  vtkDebugMacro("Setting MaskingVariable to " << name);

  this->MaskingVarname = name;

  this->Modified();

  if (!this->InfoRequested || !this->DataRequested)
  {
    return;
  }
  this->DestroyData();
  this->RegenerateGeometry();
}

//----------------------------------------------------------------------------
// Toggle the Use of the custom mask value.
//----------------------------------------------------------------------------
void vtkCDIReader::SetUseCustomMaskValue(bool val)
{
  if (val == this->UseCustomMaskValue)
    return;

  this->UseCustomMaskValue = val;

  this->Modified();

  if (!this->InfoRequested || !this->DataRequested || !this->UseCustomMaskValue)
  {
    return;
  }
  this->DestroyData();
  this->RegenerateGeometry();
}

//----------------------------------------------------------------------------
// Set custom mask value.
//----------------------------------------------------------------------------
void vtkCDIReader::SetCustomMaskValue(double val)
{
  if (val == this->CustomMaskValue)
    return;

  this->CustomMaskValue = val;

  this->Modified();

  if (!this->InfoRequested || !this->DataRequested || !this->UseCustomMaskValue)
  {
    return;
  }
  this->DestroyData();
  this->RegenerateGeometry();
}

//----------------------------------------------------------------------------
// Get name of indexed Point variable
//----------------------------------------------------------------------------
const char* vtkCDIReader::GetPointArrayName(int index)
{
  return this->Internals->PointVars[index].Name;
}

//----------------------------------------------------------------------------
// Get name of indexed cell variable
//----------------------------------------------------------------------------
const char* vtkCDIReader::GetCellArrayName(int index)
{
  return this->Internals->CellVars[index].Name;
}

//----------------------------------------------------------------------------
// Get name of indexed domain variable
//----------------------------------------------------------------------------
const char* vtkCDIReader::GetDomainArrayName(int index)
{
  return this->Internals->DomainVars[index].c_str();
}

//----------------------------------------------------------------------------
// Set to lat/lon (equidistant cylindrical) projection.
//----------------------------------------------------------------------------
void vtkCDIReader::SetFileName(const char* val)
{
  if (this->FileName.empty() || val == nullptr || strcmp(this->FileName.c_str(), val) != 0)
  {
    if (this->StreamID >= 0)
    {
      streamClose(this->StreamID);
      this->StreamID = -1;
      this->VListID = -1;
    }
    this->Modified();
    if (val == nullptr)
    {
      return;
    }
    this->FileName = val;
    vtkDebugMacro("SetFileName to " << this->FileName);

    this->DestroyData();
    this->RegenerateVariables();
  }
}

//----------------------------------------------------------------------------
//  Set vertical level to be viewed.
//----------------------------------------------------------------------------
void vtkCDIReader::SetVerticalLevel(int level)
{
  if (this->VerticalLevelSelected != level)
  {
    if (level < 0 || level > this->MaximumNVertLevels - 1)
    {
      vtkErrorMacro("Requested inexistent vertical level: "
        << level << ".\nThe level must be the in range [ 0 ; " << this->MaximumNVertLevels - 1
        << " ].");
      return;
    }
    this->VerticalLevelSelected = level;
    this->Modified();
    vtkDebugMacro("Set VerticalLevelSelected to: " << level);
  }
  vtkDebugMacro("InfoRequested?: " << this->InfoRequested);

  if (!this->InfoRequested || !this->DataRequested)
  {
    return;
  }

  for (int var = 0; var < this->NumberOfPointVars; var++)
  {
    if (this->PointDataArraySelection->GetArraySetting(var))
    {
      vtkDebugMacro("Loading Point Variable: " << this->Internals->PointVars[var].Name);
      this->LoadPointVarData(var, this->DTime);
    }
  }

  for (int var = 0; var < this->NumberOfCellVars; var++)
  {
    if (this->CellDataArraySelection->GetArraySetting(var))
    {
      vtkDebugMacro("Loading Cell Variable: " << this->Internals->CellVars[var].Name);
      this->LoadCellVarData(var, this->DTime);
    }
  }

  this->PointDataArraySelection->Modified();
  this->CellDataArraySelection->Modified();
}

//----------------------------------------------------------------------------
//  Set layer thickness for multilayer view.
//----------------------------------------------------------------------------
void vtkCDIReader::SetLayerThickness(int val)
{
  if (this->LayerThickness != val)
  {
    this->LayerThickness = val;
    this->Modified();
    vtkDebugMacro("SetLayerThickness: LayerThickness set to " << this->LayerThickness);

    if (this->ShowMultilayerView)
    {
      if (!this->InfoRequested || !this->DataRequested)
      {
        return;
      }
      this->DestroyData();
      this->RegenerateGeometry();
    }
  }
}

//----------------------------------------------------------------------------
//  Set layer 0 offset for multilayer view.
//----------------------------------------------------------------------------
void vtkCDIReader::SetLayer0Offset(double val)
{
  if (this->Layer0Offset != val)
  {
    this->Layer0Offset = val;
    this->Modified();
    vtkDebugMacro("SetLayer0Offset: Layer0Offset set to " << this->Layer0Offset);

    if (this->ShowMultilayerView)
    {
      if (!this->InfoRequested || !this->DataRequested)
      {
        return;
      }
      this->DestroyData();
      this->RegenerateGeometry();
    }
  }
}

//----------------------------------------------------------------------------
// Set the projection mode.
//----------------------------------------------------------------------------
void vtkCDIReader::SetProjection(int val)
{
  if (this->ProjectionMode != val)
  {
    if (!projection::isproj(val))
    {
      vtkErrorMacro(
        "SetProjection: Can't set ProjectionMode to '" << val << "'. Not a valid projection.");
      return;
    }
    this->ProjectionMode = projection::Projection(val);
    this->Modified();
    vtkDebugMacro("SetProjection: ProjectionMode to " << this->ProjectionMode);
    this->ReconstructNew = true;

    if (!this->InfoRequested || !this->DataRequested)
    {
      return;
    }

    this->DestroyData();
    this->RegenerateGeometry();
  }
}

//----------------------------------------------------------------------------
// Set double/float projection.
//----------------------------------------------------------------------------
void vtkCDIReader::SetDoublePrecision(bool val)
{
  if (this->DoublePrecision != val)
  {
    this->DoublePrecision = val;
    this->Modified();
    vtkDebugMacro("DoublePrecision to " << this->DoublePrecision);
    this->ReconstructNew = true;

    if (!this->InfoRequested || !this->DataRequested)
    {
      return;
    }

    this->DestroyData();
    this->RegenerateGeometry();
  }
}

//----------------------------------------------------------------------------
// Set wrapping.
//----------------------------------------------------------------------------
void vtkCDIReader::SetWrapping(bool val)
{
  if (this->WrapOn != val)
  {
    this->WrapOn = val;
    this->Modified();
    vtkDebugMacro("Wrapping set to " << this->WrapOn);
    this->ReconstructNew = true;

    if (!this->InfoRequested || !this->DataRequested)
    {
      return;
    }

    this->DestroyData();
    this->RegenerateGeometry();
  }
}

//----------------------------------------------------------------------------
// Invert the z-axis of the visualization.
//----------------------------------------------------------------------------
void vtkCDIReader::SetInvertZAxis(bool val)
{
  if (this->InvertZAxis != val)
  {
    this->InvertZAxis = val;
    this->Modified();
    vtkDebugMacro("InvertZAxis to " << this->InvertZAxis);

    if (!this->InfoRequested || !this->DataRequested)
    {
      return;
    }

    this->DestroyData();
    this->RegenerateGeometry();
  }
}

//----------------------------------------------------------------------------
// Set visualization with topography/bathymetrie.
//----------------------------------------------------------------------------
void vtkCDIReader::SetUseMask(bool val)
{
  if (this->UseMask != val)
  {
    this->UseMask = val;
    this->Modified();
    vtkDebugMacro("Set UseMask to " << this->UseMask);

    if (!this->InfoRequested || !this->DataRequested)
    {
      return;
    }

    this->DestroyData();
    this->RegenerateGeometry();
  }
}

//----------------------------------------------------------------------------
// Add Clon and Clat to output
//----------------------------------------------------------------------------
void vtkCDIReader::SetShowClonClat(bool val)
{
  if (this->ShowClonClat != val)
  {
    this->ShowClonClat = val;
    this->Modified();
    vtkDebugMacro("Set ShowClonClat to " << this->ShowClonClat);

    if (!this->InfoRequested || !this->DataRequested)
    {
      return;
    }

    this->DestroyData();
    this->RegenerateGeometry();
  }
}

//----------------------------------------------------------------------------
// Set visualization with inverted topography/bathymetrie.
//----------------------------------------------------------------------------
void vtkCDIReader::SetInvertMask(bool val)
{
  if (val == this->InvertMask)
  {
    return;
  }
  this->InvertMask = val;
  this->Modified();

  vtkDebugMacro("Set InvertMask to " << this->InvertMask);

  if (!this->InfoRequested || !this->DataRequested)
  {
    return;
  }

  this->DestroyData();
  this->RegenerateGeometry();
}

//------------------------------------------------------------------------------
void vtkCDIReader::SetSkipGrid(bool val)
{
  this->SkipGrid = val;
}

//----------------------------------------------------------------------------
//  Set view to be multilayered view.
//----------------------------------------------------------------------------
void vtkCDIReader::SetShowMultilayerView(bool val)
{
  if (this->ShowMultilayerView != val)
  {
    this->ShowMultilayerView = val;
    this->Modified();
    vtkDebugMacro("ShowMultilayerView to " << this->ShowMultilayerView);

    if (!this->InfoRequested || !this->DataRequested)
    {
      return;
    }

    this->DestroyData();
    this->RegenerateGeometry();
  }
}

//----------------------------------------------------------------------------
//  Print self.
//----------------------------------------------------------------------------
void vtkCDIReader::PrintSelf(ostream& os, vtkIndent indent)
{
  this->Superclass::PrintSelf(os, indent);
  os << indent << "FileName: " << (this->FileName.c_str() ? this->FileName.c_str() : "nullptr")
     << "\n";
  os << indent << "VariableDimensions: ";
  if (this->VariableDimensions)
  {
    this->VariableDimensions->PrintSelf(os, indent.GetNextIndent());
  }
  else
  {
    os << "(nullptr)"
       << "\n";
  }
  os << indent << "AllDimensions: ";
  if (this->AllDimensions)
  {
    this->AllDimensions->PrintSelf(os, indent.GetNextIndent());
  }
  else
  {
    os << "(nullptr)"
       << "\n";
  }
  os << indent << "NumberOfPointVars: " << this->NumberOfPointVars << "\n";
  os << indent << "NumberOfCellVars: " << this->NumberOfCellVars << "\n";
  os << indent << "NumberOfDomainVars: " << this->NumberOfDomainVars << "\n";
  os << indent << "MaximumPoints: " << this->MaximumPoints << "\n";
  os << indent << "MaximumCells: " << this->MaximumCells << "\n";
  os << indent << "Projection: " << this->ProjectionMode << endl;
  os << indent << "DoublePrecision: " << (this->DoublePrecision ? "ON" : "OFF") << endl;
  os << indent << "Wrapping: " << (this->WrapOn ? "ON" : "OFF") << endl;
  os << indent << "ShowClonClat: " << (this->ShowClonClat ? "ON" : "OFF") << endl;
  os << indent << "ShowMultilayerView: " << (this->ShowMultilayerView ? "ON" : "OFF") << endl;
  os << indent << "InvertZ: " << (this->InvertZAxis ? "ON" : "OFF") << endl;
  os << indent << "UseMask: " << (this->UseMask ? "ON" : "OFF") << endl;
  os << indent << "CustomMaskValue: " << this->CustomMaskValue << endl;
  os << indent << "SkipGrid: " << (this->SkipGrid ? "ON" : "OFF") << endl;
  os << indent << "InvertMask: " << (this->InvertMask ? "ON" : "OFF") << endl;
  os << indent << "VerticalLevel: " << this->VerticalLevelSelected << "\n";
  os << indent << "VerticalLevelRange: " << this->VerticalLevelRange[0] << ","
     << this->VerticalLevelRange[1] << endl;
  os << indent << "LayerThicknessRange: " << this->LayerThicknessRange[0] << ","
     << this->LayerThicknessRange[1] << endl;
  os << indent << "Layer0OffsetRange: " << this->Layer0OffsetRange[0] << ","
     << this->Layer0OffsetRange[1] << endl;
}
