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

  Program:   Visualization Toolkit
  Module:    vtkStatisticalOutlierRemoval.cxx

  Copyright (c) Kitware, Inc.
  All rights reserved.
  See LICENSE file 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 "vtkStatisticalOutlierRemoval.h"

#include "vtkAbstractPointLocator.h"
#include "vtkIdList.h"
#include "vtkMath.h"
#include "vtkObjectFactory.h"
#include "vtkPointSet.h"
#include "vtkPoints.h"
#include "vtkSMPThreadLocalObject.h"
#include "vtkSMPTools.h"
#include "vtkStaticPointLocator.h"

vtkStandardNewMacro(vtkStatisticalOutlierRemoval);
vtkCxxSetObjectMacro(vtkStatisticalOutlierRemoval, Locator, vtkAbstractPointLocator);

//----------------------------------------------------------------------------
// Helper classes to support efficient computing, and threaded execution.
namespace
{

//----------------------------------------------------------------------------
// The threaded core of the algorithm (first pass)
template <typename T>
struct ComputeMeanDistance
{
  const T* Points;
  vtkAbstractPointLocator* Locator;
  int SampleSize;
  float* Distance;
  double Mean;

  // Don't want to allocate working arrays on every thread invocation. Thread local
  // storage lots of new/delete.
  vtkSMPThreadLocalObject<vtkIdList> PIds;
  vtkSMPThreadLocal<double> ThreadMean;
  vtkSMPThreadLocal<vtkIdType> ThreadCount;

  ComputeMeanDistance(T* points, vtkAbstractPointLocator* loc, int size, float* d)
    : Points(points)
    , Locator(loc)
    , SampleSize(size)
    , Distance(d)
    , Mean(0.0)
  {
  }

  // Just allocate a little bit of memory to get started.
  void Initialize()
  {
    vtkIdList*& pIds = this->PIds.Local();
    pIds->Allocate(128); // allocate some memory

    double& threadMean = this->ThreadMean.Local();
    threadMean = 0.0;

    vtkIdType& threadCount = this->ThreadCount.Local();
    threadCount = 0;
  }

  // Compute average distance for each point, plus accumulate summation of
  // mean distances and count (for averaging in the Reduce() method).
  void operator()(vtkIdType ptId, vtkIdType endPtId)
  {
    const T* px = this->Points + 3 * ptId;
    const T* py;
    double x[3], y[3];
    vtkIdList*& pIds = this->PIds.Local();
    double& threadMean = this->ThreadMean.Local();
    vtkIdType& threadCount = this->ThreadCount.Local();

    for (; ptId < endPtId; ++ptId)
    {
      x[0] = static_cast<double>(*px++);
      x[1] = static_cast<double>(*px++);
      x[2] = static_cast<double>(*px++);

      // The method FindClosestNPoints will include the current point, so
      // we increase the sample size by one.
      this->Locator->FindClosestNPoints(this->SampleSize + 1, x, pIds);
      vtkIdType numPts = pIds->GetNumberOfIds();

      double sum = 0.0;
      vtkIdType nei;
      for (int sample = 0; sample < numPts; ++sample)
      {
        nei = pIds->GetId(sample);
        if (nei != ptId) // exclude ourselves
        {
          py = this->Points + 3 * nei;
          y[0] = static_cast<double>(*py++);
          y[1] = static_cast<double>(*py++);
          y[2] = static_cast<double>(*py);
          sum += sqrt(vtkMath::Distance2BetweenPoints(x, y));
        }
      } // sum the lengths of all samples exclusing current point

      // Average the lengths; again exclude ourselves
      if (numPts > 0)
      {
        this->Distance[ptId] = sum / static_cast<double>(numPts - 1);
        threadMean += this->Distance[ptId];
        threadCount++;
      }
      else // ignore if no points are found, something bad has happened
      {
        this->Distance[ptId] = VTK_FLOAT_MAX; // the effect is to eliminate it
      }
    }
  }

  // Compute the mean by compositing all threads
  void Reduce()
  {
    double mean = 0.0;
    vtkIdType count = 0;

    vtkSMPThreadLocal<double>::iterator mItr;
    vtkSMPThreadLocal<double>::iterator mEnd = this->ThreadMean.end();
    for (mItr = this->ThreadMean.begin(); mItr != mEnd; ++mItr)
    {
      mean += *mItr;
    }

    vtkSMPThreadLocal<vtkIdType>::iterator cItr;
    vtkSMPThreadLocal<vtkIdType>::iterator cEnd = this->ThreadCount.end();
    for (cItr = this->ThreadCount.begin(); cItr != cEnd; ++cItr)
    {
      count += *cItr;
    }

    count = (count < 1 ? 1 : count);
    this->Mean = mean / static_cast<double>(count);
  }

  static void Execute(
    vtkStatisticalOutlierRemoval* self, vtkIdType numPts, T* points, float* distances, double& mean)
  {
    ComputeMeanDistance compute(points, self->GetLocator(), self->GetSampleSize(), distances);
    vtkSMPTools::For(0, numPts, compute);
    mean = compute.Mean;
  }

}; // ComputeMeanDistance

//----------------------------------------------------------------------------
// Now that the mean is known, compute the standard deviation
struct ComputeStdDev
{
  float* Distances;
  double Mean;
  double StdDev;
  vtkSMPThreadLocal<double> ThreadSigma;
  vtkSMPThreadLocal<vtkIdType> ThreadCount;

  ComputeStdDev(float* d, double mean)
    : Distances(d)
    , Mean(mean)
    , StdDev(0.0)
  {
  }

  void Initialize()
  {
    double& threadSigma = this->ThreadSigma.Local();
    threadSigma = 0.0;

    vtkIdType& threadCount = this->ThreadCount.Local();
    threadCount = 0;
  }

  void operator()(vtkIdType ptId, vtkIdType endPtId)
  {
    double& threadSigma = this->ThreadSigma.Local();
    vtkIdType& threadCount = this->ThreadCount.Local();
    float d;

    for (; ptId < endPtId; ++ptId)
    {
      d = this->Distances[ptId];
      if (d < VTK_FLOAT_MAX)
      {
        threadSigma += (this->Mean - d) * (this->Mean - d);
        threadCount++;
      }
      else
      {
        continue; // skip bad point
      }
    }
  }

  void Reduce()
  {
    double sigma = 0.0;
    vtkIdType count = 0;

    vtkSMPThreadLocal<double>::iterator sItr;
    vtkSMPThreadLocal<double>::iterator sEnd = this->ThreadSigma.end();
    for (sItr = this->ThreadSigma.begin(); sItr != sEnd; ++sItr)
    {
      sigma += *sItr;
    }

    vtkSMPThreadLocal<vtkIdType>::iterator cItr;
    vtkSMPThreadLocal<vtkIdType>::iterator cEnd = this->ThreadCount.end();
    for (cItr = this->ThreadCount.begin(); cItr != cEnd; ++cItr)
    {
      count += *cItr;
    }

    this->StdDev = sqrt(sigma / static_cast<double>(count));
  }

  static void Execute(vtkIdType numPts, float* distances, double mean, double& sigma)
  {
    ComputeStdDev stdDev(distances, mean);
    vtkSMPTools::For(0, numPts, stdDev);
    sigma = stdDev.StdDev;
  }

}; // ComputeStdDev

//----------------------------------------------------------------------------
// Statistics are computed, now filter the points
struct RemoveOutliers
{
  double Mean;
  double Sigma;
  float* Distances;
  vtkIdType* PointMap;

  RemoveOutliers(double mean, double sigma, float* distances, vtkIdType* map)
    : Mean(mean)
    , Sigma(sigma)
    , Distances(distances)
    , PointMap(map)
  {
  }

  void operator()(vtkIdType ptId, vtkIdType endPtId)
  {
    vtkIdType* map = this->PointMap + ptId;
    float* d = this->Distances + ptId;
    double mean = this->Mean, sigma = this->Sigma;

    for (; ptId < endPtId; ++ptId)
    {
      *map++ = (fabs(*d++ - mean) <= sigma ? 1 : -1);
    }
  }

  static void Execute(vtkIdType numPts, float* distances, double mean, double sigma, vtkIdType* map)
  {
    RemoveOutliers remove(mean, sigma, distances, map);
    vtkSMPTools::For(0, numPts, remove);
  }

}; // RemoveOutliers

} // anonymous namespace

//================= Begin class proper =======================================
//----------------------------------------------------------------------------
vtkStatisticalOutlierRemoval::vtkStatisticalOutlierRemoval()
{
  this->SampleSize = 25;
  this->StandardDeviationFactor = 1.0;
  this->Locator = vtkStaticPointLocator::New();

  this->ComputedMean = 0.0;
  this->ComputedStandardDeviation = 0.0;
}

//----------------------------------------------------------------------------
vtkStatisticalOutlierRemoval::~vtkStatisticalOutlierRemoval()
{
  this->SetLocator(nullptr);
}

//----------------------------------------------------------------------------
// Traverse all the input points and gather statistics about average distance
// between them, and the standard deviation of variation. Then filter points
// within a specified deviation from the mean.
int vtkStatisticalOutlierRemoval::FilterPoints(vtkPointSet* input)
{
  // Perform the point removal
  // Start by building the locator
  if (!this->Locator)
  {
    vtkErrorMacro(<< "Point locator required\n");
    return 0;
  }
  this->Locator->SetDataSet(input);
  this->Locator->BuildLocator();

  // Compute statistics across the point cloud. Start my computing
  // mean distance to N closest neighbors.
  vtkIdType numPts = input->GetNumberOfPoints();
  float* dist = new float[numPts];
  void* inPtr = input->GetPoints()->GetVoidPointer(0);
  double mean = 0.0, sigma = 0.0;
  switch (input->GetPoints()->GetDataType())
  {
    vtkTemplateMacro(
      ComputeMeanDistance<VTK_TT>::Execute(this, numPts, (VTK_TT*)inPtr, dist, mean));
  }

  // At this point the mean distance for each point, and across the point
  // cloud is known. Now compute global standard deviation.
  ComputeStdDev::Execute(numPts, dist, mean, sigma);

  // Finally filter the points based on specified deviation range.
  RemoveOutliers::Execute(
    numPts, dist, mean, this->StandardDeviationFactor * sigma, this->PointMap);

  // Assign derived variable
  this->ComputedMean = mean;
  this->ComputedStandardDeviation = sigma;

  // Clean up
  delete[] dist;

  return 1;
}

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

  os << indent << "Sample Size: " << this->SampleSize << "\n";
  os << indent << "Standard Deviation Factor: " << this->StandardDeviationFactor << "\n";
  os << indent << "Locator: " << this->Locator << "\n";

  os << indent << "Computed Mean: " << this->ComputedMean << "\n";
  os << indent << "Computed Standard Deviation: " << this->ComputedStandardDeviation << "\n";
}
