/*****************************************************************************
** File IDENTIFICATION
**
**     Name:            procsignal.cpp
**     Purpose:         Routines for processing signals and projections
**     Progammer:           Kevin Rosenberg
**     Date Started:    Aug 1984
**
**  This is part of the CTSim program
**  Copyright (c) 1983-2009 Kevin Rosenberg
**
**  This program is free software; you can redistribute it and/or modify
**  it under the terms of the GNU General Public License (version 2) as
**  published by the Free Software Foundation.
**
**  This program is distributed in the hope that it will be useful,
**  but WITHOUT ANY WARRANTY; without even the implied warranty of
**  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
**  GNU General Public License for more details.
**
**  You should have received a copy of the GNU General Public License
**  along with this program; if not, write to the Free Software
**  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
******************************************************************************/

#include "ct.h"

#ifdef HAVE_WXWINDOWS
#include "nographics.h"
#endif

// FilterMethod ID/Names
const int ProcessSignal::FILTER_METHOD_INVALID = -1;
const int ProcessSignal::FILTER_METHOD_CONVOLUTION = 0;
const int ProcessSignal::FILTER_METHOD_FOURIER = 1;
const int ProcessSignal::FILTER_METHOD_FOURIER_TABLE = 2;
const int ProcessSignal::FILTER_METHOD_FFT = 3;
#if HAVE_FFTW
const int ProcessSignal::FILTER_METHOD_FFTW = 4;
const int ProcessSignal::FILTER_METHOD_RFFTW =5 ;
#endif
const char* const ProcessSignal::s_aszFilterMethodName[] = {
  "convolution",
  "fourier",
  "fouier-table",
  "fft",
#if HAVE_FFTW
  "fftw",
  "rfftw",
#endif
};
const char* const ProcessSignal::s_aszFilterMethodTitle[] = {
  "Convolution",
  "Fourier",
  "Fouier Trigometric Table",
  "FFT",
#if HAVE_FFTW
  "FFTW",
  "Real/Half-Complex FFTW",
#endif
};
const int ProcessSignal::s_iFilterMethodCount = sizeof(s_aszFilterMethodName) / sizeof(const char*);

// FilterGeneration ID/Names
const int ProcessSignal::FILTER_GENERATION_INVALID = -1;
const int ProcessSignal::FILTER_GENERATION_DIRECT = 0;
const int ProcessSignal::FILTER_GENERATION_INVERSE_FOURIER = 1;
const char* const ProcessSignal::s_aszFilterGenerationName[] = {
  "direct",
  "inverse-fourier",
};
const char* const ProcessSignal::s_aszFilterGenerationTitle[] = {
  "Direct",
  "Inverse Fourier",
};
const int ProcessSignal::s_iFilterGenerationCount = sizeof(s_aszFilterGenerationName) / sizeof(const char*);


// CLASS IDENTIFICATION
//   ProcessSignal
//
ProcessSignal::ProcessSignal (const char* szFilterName, const char* szFilterMethodName, double dBandwidth,
                              double dSignalIncrement, int nSignalPoints, double dFilterParam, const char* szDomainName,
                              const char* szFilterGenerationName, int iZeropad, int iPreinterpolationFactor, int iTraceLevel,
                              int iGeometry, double dFocalLength, double dSourceDetectorLength, SGP* pSGP)
                              : m_adFourierCosTable(NULL), m_adFourierSinTable(NULL), m_adFilter(NULL), m_fail(false)
{
  m_idFilterMethod = convertFilterMethodNameToID (szFilterMethodName);
  if (m_idFilterMethod == FILTER_METHOD_INVALID) {
    m_fail = true;
    m_failMessage = "Invalid filter method name ";
    m_failMessage += szFilterMethodName;
    return;
  }
  m_idFilterGeneration = convertFilterGenerationNameToID (szFilterGenerationName);
  if (m_idFilterGeneration == FILTER_GENERATION_INVALID) {
    m_fail = true;
    m_failMessage = "Invalid frequency filter name ";
    m_failMessage += szFilterGenerationName;
    return;
  }
  m_idFilter = SignalFilter::convertFilterNameToID (szFilterName);
  if (m_idFilter == SignalFilter::FILTER_INVALID) {
    m_fail = true;
    m_failMessage = "Invalid Filter name ";
    m_failMessage += szFilterName;
    return;
  }
  m_idDomain = SignalFilter::convertDomainNameToID (szDomainName);
  if (m_idDomain == SignalFilter::DOMAIN_INVALID) {
    m_fail = true;
    m_failMessage = "Invalid domain name ";
    m_failMessage += szDomainName;
    return;
  }

  init (m_idFilter, m_idFilterMethod, dBandwidth, dSignalIncrement, nSignalPoints, dFilterParam, m_idDomain,
    m_idFilterGeneration, iZeropad, iPreinterpolationFactor, iTraceLevel, iGeometry, dFocalLength,
    dSourceDetectorLength, pSGP);
}


void
ProcessSignal::init (const int idFilter, const int idFilterMethod, double dBandwidth, double dSignalIncrement,
                     int nSignalPoints, double dFilterParam, const int idDomain, const int idFilterGeneration,
                     const int iZeropad, const int iPreinterpolationFactor, int iTraceLevel, int iGeometry,
                     double dFocalLength, double dSourceDetectorLength, SGP* pSGP)
{
  int i;
  m_idFilter = idFilter;
  m_idDomain = idDomain;
  m_idFilterMethod = idFilterMethod;
  m_idFilterGeneration = idFilterGeneration;
  m_idGeometry = iGeometry;
  m_dFocalLength = dFocalLength;
  m_dSourceDetectorLength = dSourceDetectorLength;

  if (m_idFilter == SignalFilter::FILTER_INVALID || m_idDomain == SignalFilter::DOMAIN_INVALID || m_idFilterMethod == FILTER_METHOD_INVALID || m_idFilterGeneration == FILTER_GENERATION_INVALID) {
    m_fail = true;
    return;
  }
  m_traceLevel = iTraceLevel;
  m_nameFilterMethod = convertFilterMethodIDToName (m_idFilterMethod);
  m_nameFilterGeneration = convertFilterGenerationIDToName (m_idFilterGeneration);
  m_dBandwidth = dBandwidth;
  m_nSignalPoints = nSignalPoints;
  m_dSignalInc = dSignalIncrement;
  m_dFilterParam = dFilterParam;
  m_iZeropad = iZeropad;
  m_iPreinterpolationFactor = iPreinterpolationFactor;

  // scale signalInc/BW to adjust for imaginary detector through origin of phantom
  // see Kak-Slaney Fig 3.22, for Collinear diagram
  if (m_idGeometry == Scanner::GEOMETRY_EQUILINEAR) {
    double dEquilinearScale = m_dSourceDetectorLength / m_dFocalLength;
    m_dSignalInc /= dEquilinearScale;
    m_dBandwidth *= dEquilinearScale;
  }

  if (m_idFilterMethod == FILTER_METHOD_FFT) {
#if HAVE_FFTW
    m_idFilterMethod = FILTER_METHOD_RFFTW;
#else
    m_fail = true;
    m_failMessage = "FFT not yet implemented";
    return;
#endif
  }

  bool m_bFrequencyFiltering = true;
  if (m_idFilterMethod == FILTER_METHOD_CONVOLUTION)
    m_bFrequencyFiltering = false;

  // Spatial-based filtering
  if (! m_bFrequencyFiltering) {

    if (m_idFilterGeneration == FILTER_GENERATION_DIRECT) {
      m_nFilterPoints = 2 * (m_nSignalPoints - 1) + 1;
      m_dFilterMin = -m_dSignalInc * (m_nSignalPoints - 1);
      m_dFilterMax = m_dSignalInc * (m_nSignalPoints - 1);
      m_dFilterInc = (m_dFilterMax - m_dFilterMin) / (m_nFilterPoints - 1);
      SignalFilter filter (m_idFilter, m_dFilterMin, m_dFilterMax, m_nFilterPoints, m_dBandwidth, m_dFilterParam, SignalFilter::DOMAIN_SPATIAL);
      m_adFilter = new double[ m_nFilterPoints ];
      filter.copyFilterData (m_adFilter, 0, m_nFilterPoints);
    } else if (m_idFilterGeneration == FILTER_GENERATION_INVERSE_FOURIER) {
      m_nFilterPoints = 2 * (m_nSignalPoints - 1) + 1;
      m_dFilterMin = -1. / (2 * m_dSignalInc);
      m_dFilterMax = 1. / (2 * m_dSignalInc);
      m_dFilterInc = (m_dFilterMax - m_dFilterMin) / (m_nFilterPoints - 1);
      SignalFilter filter (m_idFilter, m_dFilterMin, m_dFilterMax, m_nFilterPoints, m_dBandwidth, m_dFilterParam, SignalFilter::DOMAIN_FREQUENCY);
      m_adFilter = new double[ m_nFilterPoints ];
      double* adFrequencyFilter = new double [m_nFilterPoints];
      filter.copyFilterData (adFrequencyFilter, 0, m_nFilterPoints);
#if defined(HAVE_WXWINDOWS) && (defined(DEBUG) || defined(_DEBUG))
      if (g_bRunningWXWindows && m_traceLevel > 0) {
        EZPlotDialog dlgEZPlot;
        dlgEZPlot.getEZPlot()->ezset ("title Filter Response: Natural Order");
        dlgEZPlot.getEZPlot()->addCurve (adFrequencyFilter, m_nFilterPoints);
        dlgEZPlot.ShowModal();
      }
#endif
      Fourier::shuffleNaturalToFourierOrder (adFrequencyFilter, m_nFilterPoints);
#ifdef HAVE_SGP
      if (g_bRunningWXWindows && m_traceLevel > 0) {
        EZPlotDialog dlgEZPlot;
        dlgEZPlot.getEZPlot()->ezset ("title Filter Response: Fourier Order");
        dlgEZPlot.getEZPlot()->addCurve (adFrequencyFilter, m_nFilterPoints);
        dlgEZPlot.ShowModal();
      }
#endif
      ProcessSignal::finiteFourierTransform (adFrequencyFilter, m_adFilter, m_nFilterPoints, FORWARD);
      delete adFrequencyFilter;
#if defined(HAVE_WXWINDOWS) && (defined(DEBUG) || defined(_DEBUG))
      if (g_bRunningWXWindows && m_traceLevel > 0) {
        EZPlotDialog dlgEZPlot;
        dlgEZPlot.getEZPlot()->ezset ("title Inverse Fourier Frequency: Fourier Order");
        dlgEZPlot.getEZPlot()->addCurve (m_adFilter, m_nFilterPoints);
        dlgEZPlot.ShowModal();
      }
#endif
      Fourier::shuffleFourierToNaturalOrder (m_adFilter, m_nFilterPoints);
#if defined(HAVE_WXWINDOWS) && (defined(DEBUG) || defined(_DEBUG))
      if (g_bRunningWXWindows && m_traceLevel > 0) {
        EZPlotDialog dlgEZPlot;
        dlgEZPlot.getEZPlot()->ezset ("title Inverse Fourier Frequency: Natural Order");
        dlgEZPlot.getEZPlot()->addCurve (m_adFilter, m_nFilterPoints);
        dlgEZPlot.ShowModal();
      }
#endif
      for (i = 0; i < m_nFilterPoints; i++) {
        m_adFilter[i] /= m_dSignalInc;
      }
    }
    if (m_idGeometry == Scanner::GEOMETRY_EQUILINEAR) {
      for (i = 0; i < m_nFilterPoints; i++)
        m_adFilter[i] *= 0.5;
    } else if (m_idGeometry == Scanner::GEOMETRY_EQUIANGULAR) {
      for (i = 0; i < m_nFilterPoints; i++) {
        int iDetFromZero = i - ((m_nFilterPoints - 1) / 2);
        double sinScale = 1 / SignalFilter::sinc (iDetFromZero * m_dSignalInc);
        double dScale = 0.5 * sinScale * sinScale;
        m_adFilter[i] *= dScale;
      }
#if defined(HAVE_WXWINDOWS) && (defined(DEBUG) || defined(_DEBUG))
      if (g_bRunningWXWindows && m_traceLevel > 0) {
        EZPlotDialog dlgEZPlot;
        dlgEZPlot.getEZPlot()->ezset ("title Scaled Inverse Fourier Frequency: Natural Order");
        dlgEZPlot.getEZPlot()->addCurve (m_adFilter, m_nFilterPoints);
        dlgEZPlot.ShowModal();
      }
#endif
    } // if (geometry)
  } // if (spatial filtering)

  else if (m_bFrequencyFiltering) {  // Frequency-based filtering

    if (m_idFilterGeneration == FILTER_GENERATION_DIRECT) {
      // calculate number of filter points with zeropadding
      m_nFilterPoints = addZeropadFactor (m_nSignalPoints, m_iZeropad);
      m_nOutputPoints = m_nFilterPoints * m_iPreinterpolationFactor;

      if (isOdd (m_nFilterPoints)) { // Odd
        m_dFilterMin = -1. / (2 * m_dSignalInc);
        m_dFilterMax = 1. / (2 * m_dSignalInc);
        m_dFilterInc = (m_dFilterMax - m_dFilterMin) / (m_nFilterPoints - 1);
      } else { // Even
        m_dFilterMin = -1. / (2 * m_dSignalInc);
        m_dFilterMax = 1. / (2 * m_dSignalInc);
        m_dFilterInc = (m_dFilterMax - m_dFilterMin) / m_nFilterPoints;
        m_dFilterMax -= m_dFilterInc;
      }

      SignalFilter filter (m_idFilter, m_dFilterMin, m_dFilterMax, m_nFilterPoints, m_dBandwidth,
        m_dFilterParam, SignalFilter::DOMAIN_FREQUENCY);
      m_adFilter = new double [m_nFilterPoints];
      filter.copyFilterData (m_adFilter, 0, m_nFilterPoints);

#if defined(HAVE_WXWINDOWS) && (defined(DEBUG) || defined(_DEBUG))
      if (g_bRunningWXWindows && m_traceLevel > 0) {
        EZPlotDialog dlgEZPlot;
        dlgEZPlot.getEZPlot()->ezset ("title Frequency Filter: Natural Order");
        dlgEZPlot.getEZPlot()->addCurve (m_adFilter, m_nFilterPoints);
        dlgEZPlot.ShowModal();
      }
#endif

      // This works fairly well. I'm not sure why since scaling for geometries is done on
      // frequency filter rather than spatial filter as it should be.
      // It gives values slightly off than freq/inverse filtering
      if (m_idGeometry == Scanner::GEOMETRY_EQUILINEAR) {
        for (i = 0; i < m_nFilterPoints; i++)
          m_adFilter[i] *= 0.5;
      } else if (m_idGeometry == Scanner::GEOMETRY_EQUIANGULAR) {
        for (i = 0; i < m_nFilterPoints; i++) {
          int iDetFromZero = i - ((m_nFilterPoints - 1) / 2);
          double sinScale = 1 / SignalFilter::sinc (iDetFromZero * m_dSignalInc);
          double dScale = 0.5 * sinScale * sinScale;
          m_adFilter[i] *= dScale;
        }
      }
#if defined(HAVE_WXWINDOWS) && (defined(DEBUG) || defined(_DEBUG))
      if (g_bRunningWXWindows && m_traceLevel > 0) {
        EZPlotDialog dlgEZPlot;
        dlgEZPlot.getEZPlot()->ezset ("title Filter Geometry Scaled: Natural Order");
        dlgEZPlot.getEZPlot()->addCurve (m_adFilter, m_nFilterPoints);
        dlgEZPlot.ShowModal();
      }
#endif
      Fourier::shuffleNaturalToFourierOrder (m_adFilter, m_nFilterPoints);
#if defined(HAVE_WXWINDOWS) && (defined(DEBUG) || defined(_DEBUG))
      if (g_bRunningWXWindows && m_traceLevel > 0) {
        EZPlotDialog dlgEZPlot;
        dlgEZPlot.getEZPlot()->ezset ("title Filter Geometry Scaled: Fourier Order");
        dlgEZPlot.getEZPlot()->addCurve (m_adFilter, m_nFilterPoints);
        dlgEZPlot.ShowModal();
      }
#endif

      // FILTERING:  FREQUENCY - INVERSE FOURIER

    } else if (m_idFilterGeneration == FILTER_GENERATION_INVERSE_FOURIER) {
      // calculate number of filter points with zeropadding
      int nSpatialPoints = 2 * (m_nSignalPoints - 1) + 1;
      m_dFilterMin = -m_dSignalInc * (m_nSignalPoints - 1);
      m_dFilterMax = m_dSignalInc * (m_nSignalPoints - 1);
      m_dFilterInc = (m_dFilterMax - m_dFilterMin) / (nSpatialPoints - 1);
      m_nFilterPoints = nSpatialPoints;
      if (m_iZeropad > 0) {
        double logBase2 = log(nSpatialPoints) / log(2);
        int nextPowerOf2 = static_cast<int>(floor(logBase2));
        if (logBase2 != floor(logBase2))
          nextPowerOf2++;
        nextPowerOf2 += (m_iZeropad - 1);
        m_nFilterPoints = 1 << nextPowerOf2;
      }
      m_nOutputPoints = m_nFilterPoints * m_iPreinterpolationFactor;
#if defined(DEBUG) || defined(_DEBUG)
      if (m_traceLevel >= Trace::TRACE_CONSOLE)
        sys_error (ERR_TRACE, "nFilterPoints = %d", m_nFilterPoints);
#endif
      double* adSpatialFilter = new double [m_nFilterPoints];
      SignalFilter filter (m_idFilter, m_dFilterMin, m_dFilterMax, nSpatialPoints, m_dBandwidth,
        m_dFilterParam, SignalFilter::DOMAIN_SPATIAL);
      filter.copyFilterData (adSpatialFilter, 0, nSpatialPoints);
#if defined(HAVE_WXWINDOWS) && (defined(DEBUG) || defined(_DEBUG))
      if (g_bRunningWXWindows && m_traceLevel > 0) {
        EZPlotDialog dlgEZPlot;;
        dlgEZPlot.getEZPlot()->ezset ("title Spatial Filter: Natural Order");
        dlgEZPlot.getEZPlot()->addCurve (adSpatialFilter, nSpatialPoints);
        dlgEZPlot.ShowModal();
      }
#endif

      if (m_idGeometry == Scanner::GEOMETRY_EQUILINEAR) {
        for (i = 0; i < nSpatialPoints; i++)
          adSpatialFilter[i] *= 0.5;
      } else if (m_idGeometry == Scanner::GEOMETRY_EQUIANGULAR) {
        for (i = 0; i < nSpatialPoints; i++) {
          int iDetFromZero = i - ((nSpatialPoints - 1) / 2);
          double sinScale = sin (iDetFromZero * m_dSignalInc);
          if (fabs(sinScale) < 1E-7)
            sinScale = 1;
          else
            sinScale = (iDetFromZero * m_dSignalInc) / sinScale;
          double dScale = 0.5 * sinScale * sinScale;
          adSpatialFilter[i] *= dScale;
        }
      }
#if defined(HAVE_WXWINDOWS) && (defined(DEBUG) || defined(_DEBUG))
      if (g_bRunningWXWindows && m_traceLevel > 0) {
        EZPlotDialog dlgEZPlot;;
        dlgEZPlot.getEZPlot()->ezset ("title Scaled Spatial Filter: Natural Order");
        dlgEZPlot.getEZPlot()->addCurve (adSpatialFilter, nSpatialPoints);
        dlgEZPlot.ShowModal();
      }
#endif
      for (i = nSpatialPoints; i < m_nFilterPoints; i++)
        adSpatialFilter[i] = 0;

      m_adFilter = new double [m_nFilterPoints];
      std::complex<double>* acInverseFilter = new std::complex<double> [m_nFilterPoints];
      finiteFourierTransform (adSpatialFilter, acInverseFilter, m_nFilterPoints, BACKWARD);
      delete adSpatialFilter;
      for (i = 0; i < m_nFilterPoints; i++)
        m_adFilter[i] = std::abs (acInverseFilter[i]) * m_dSignalInc;
      delete acInverseFilter;
#if defined(HAVE_WXWINDOWS) && (defined(DEBUG) || defined(_DEBUG))
      if (g_bRunningWXWindows && m_traceLevel > 0) {
        EZPlotDialog dlgEZPlot;
        dlgEZPlot.getEZPlot()->ezset ("title Fourier Scaled Spatial Filter: Fourier Order");
        dlgEZPlot.getEZPlot()->addCurve (m_adFilter, m_nFilterPoints);
        dlgEZPlot.ShowModal();
      }
#endif
    }
  }

  // precalculate sin and cosine tables for fourier transform
  if (m_idFilterMethod == FILTER_METHOD_FOURIER_TABLE) {
    int nFourier = imax (m_nFilterPoints,m_nOutputPoints) * imax (m_nFilterPoints, m_nOutputPoints) + 1;
    double angleIncrement = (2. * PI) / m_nFilterPoints;
    m_adFourierCosTable = new double[ nFourier ];
    m_adFourierSinTable = new double[ nFourier ];
    double angle = 0;
    for (i = 0; i < nFourier; i++) {
      m_adFourierCosTable[i] = cos (angle);
      m_adFourierSinTable[i] = sin (angle);
      angle += angleIncrement;
    }
  }

#if HAVE_FFTW
  if (m_idFilterMethod == FILTER_METHOD_FFTW || m_idFilterMethod == FILTER_METHOD_RFFTW) {
    for (i = 0; i < m_nFilterPoints; i++)  //fftw uses unnormalized fft
      m_adFilter[i] /= m_nFilterPoints;
  }

  if (m_idFilterMethod == FILTER_METHOD_RFFTW) {
    m_adRealFftInput = static_cast<double*>(fftw_malloc (sizeof(double) * m_nFilterPoints));
    m_adRealFftOutput = static_cast<double*>(fftw_malloc (sizeof(double) * m_nFilterPoints));
    m_realPlanForward = fftw_plan_r2r_1d (m_nFilterPoints, m_adRealFftInput, m_adRealFftOutput, FFTW_R2HC, FFTW_ESTIMATE);
    m_adRealFftSignal = static_cast<double*>(fftw_malloc (sizeof(double) *  m_nOutputPoints));
    m_adRealFftBackwardOutput = static_cast<double*>(fftw_malloc (sizeof(double) * m_nOutputPoints));
    m_realPlanBackward = fftw_plan_r2r_1d (m_nOutputPoints, m_adRealFftSignal, m_adRealFftBackwardOutput, FFTW_HC2R, FFTW_ESTIMATE);
    for (i = 0; i < m_nFilterPoints; i++)
      m_adRealFftInput[i] = 0;
  } else if (m_idFilterMethod == FILTER_METHOD_FFTW) {
    m_adComplexFftInput = static_cast<fftw_complex*>(fftw_malloc (sizeof(fftw_complex) * m_nFilterPoints));
    m_adComplexFftOutput = static_cast<fftw_complex*>(fftw_malloc (sizeof(fftw_complex) * m_nFilterPoints));
    m_complexPlanForward = fftw_plan_dft_1d (m_nFilterPoints, m_adComplexFftInput, m_adComplexFftOutput, FFTW_FORWARD,  FFTW_ESTIMATE);
    m_adComplexFftSignal = static_cast<fftw_complex*>(fftw_malloc (sizeof(fftw_complex) * m_nOutputPoints));
    m_adComplexFftBackwardOutput = static_cast<fftw_complex*>(fftw_malloc (sizeof(fftw_complex) * m_nOutputPoints));
    m_complexPlanBackward = fftw_plan_dft_1d (m_nOutputPoints, m_adComplexFftSignal, m_adComplexFftBackwardOutput, FFTW_BACKWARD,  FFTW_ESTIMATE);

    for (i = 0; i < m_nFilterPoints; i++)
      m_adComplexFftInput[i][0] = m_adComplexFftInput[i][1] = 0;
    for (i = 0; i < m_nOutputPoints; i++)
      m_adComplexFftSignal[i][0] = m_adComplexFftSignal[i][1] = 0;
  }
#endif

}

ProcessSignal::~ProcessSignal (void)
{
  delete [] m_adFourierSinTable;
  delete [] m_adFourierCosTable;
  delete [] m_adFilter;

#if HAVE_FFTW
  if (m_idFilterMethod == FILTER_METHOD_FFTW) {
    fftw_destroy_plan(m_complexPlanForward);
    fftw_destroy_plan(m_complexPlanBackward);
    fftw_free (m_adComplexFftInput);
    fftw_free (m_adComplexFftOutput);
    fftw_free (m_adComplexFftSignal);
    fftw_free (m_adComplexFftBackwardOutput);
  }
  if (m_idFilterMethod == FILTER_METHOD_RFFTW) {
    fftw_destroy_plan(m_realPlanForward);
    fftw_destroy_plan(m_realPlanBackward);
    fftw_free (m_adRealFftInput);
    fftw_free (m_adRealFftOutput);
    fftw_free (m_adRealFftSignal);
    fftw_free (m_adRealFftBackwardOutput);
  }
#endif
}

int
ProcessSignal::convertFilterMethodNameToID (const char* const filterMethodName)
{
  int fmID = FILTER_METHOD_INVALID;

  for (int i = 0; i < s_iFilterMethodCount; i++) {
    if (strcasecmp (filterMethodName, s_aszFilterMethodName[i]) == 0) {
      fmID = i;
      break;
    }
  }
  return (fmID);
}

const char *
ProcessSignal::convertFilterMethodIDToName (const int fmID)
{
  static const char *name = "";

  if (fmID >= 0 && fmID < s_iFilterMethodCount)
    return (s_aszFilterMethodName [fmID]);

  return (name);
}

const char *
ProcessSignal::convertFilterMethodIDToTitle (const int fmID)
{
  static const char *title = "";

  if (fmID >= 0 && fmID < s_iFilterMethodCount)
    return (s_aszFilterMethodTitle [fmID]);

  return (title);
}


int
ProcessSignal::convertFilterGenerationNameToID (const char* const fgName)
{
  int fgID = FILTER_GENERATION_INVALID;

  for (int i = 0; i < s_iFilterGenerationCount; i++) {
    if (strcasecmp (fgName, s_aszFilterGenerationName[i]) == 0) {
      fgID = i;
      break;
    }
  }
  return (fgID);
}

const char *
ProcessSignal::convertFilterGenerationIDToName (const int fgID)
{
  static const char *name = "";

  if (fgID >= 0 && fgID < s_iFilterGenerationCount)
    return (s_aszFilterGenerationName [fgID]);

  return (name);
}

const char *
ProcessSignal::convertFilterGenerationIDToTitle (const int fgID)
{
  static const char *name = "";

  if (fgID >= 0 && fgID < s_iFilterGenerationCount)
    return (s_aszFilterGenerationTitle [fgID]);

  return (name);
}

void
ProcessSignal::filterSignal (const float constInput[], double output[]) const
{
  double* input = new double [m_nSignalPoints];
  int i;

#if HAVE_OPENMP
  #pragma omp parallel for
#endif
  for (i = 0; i < m_nSignalPoints; i++)
    input[i] = constInput[i];

  if (m_idGeometry == Scanner::GEOMETRY_EQUILINEAR) {
#if HAVE_OPENMP
    #pragma omp parallel for
#endif
    for (int i = 0; i < m_nSignalPoints; i++) {
      int iDetFromCenter = i - (m_nSignalPoints / 2);
      input[i] *= m_dFocalLength / sqrt (m_dFocalLength * m_dFocalLength + iDetFromCenter * iDetFromCenter * m_dSignalInc * m_dSignalInc);
    }
  } else if (m_idGeometry == Scanner::GEOMETRY_EQUIANGULAR) {
#if HAVE_OPENMP
    #pragma omp parallel for
#endif
    for (int i = 0; i < m_nSignalPoints; i++) {
      int iDetFromCenter = i - (m_nSignalPoints / 2);
      input[i] *= m_dFocalLength * cos (iDetFromCenter * m_dSignalInc);
    }
  }
  if (m_idFilterMethod == FILTER_METHOD_CONVOLUTION) {
#if HAVE_OPENMP
    #pragma omp parallel for
#endif
    for (i = 0; i < m_nSignalPoints; i++)
      output[i] = convolve (input, m_dSignalInc, i, m_nSignalPoints);
  } else if (m_idFilterMethod == FILTER_METHOD_FOURIER) {
    double* inputSignal = new double [m_nFilterPoints];
    for (i = 0; i < m_nSignalPoints; i++)
      inputSignal[i] = input[i];
    for (i = m_nSignalPoints; i < m_nFilterPoints; i++)
      inputSignal[i] = 0;  // zeropad
    std::complex<double>* fftSignal = new std::complex<double> [m_nFilterPoints];
    finiteFourierTransform (inputSignal, fftSignal, m_nFilterPoints, FORWARD);
    delete inputSignal;
#if HAVE_OPENMP
    #pragma omp parallel for
#endif
    for (i = 0; i < m_nFilterPoints; i++)
      fftSignal[i] *= m_adFilter[i];
    double* inverseFourier = new double [m_nFilterPoints];
    finiteFourierTransform (fftSignal, inverseFourier, m_nFilterPoints, BACKWARD);
    delete fftSignal;
    for (i = 0; i < m_nSignalPoints; i++)
      output[i] = inverseFourier[i];
    delete inverseFourier;
  } else if (m_idFilterMethod == FILTER_METHOD_FOURIER_TABLE) {
    double* inputSignal = new double [m_nFilterPoints];
    for (i = 0; i < m_nSignalPoints; i++)
      inputSignal[i] = input[i];
    for (i = m_nSignalPoints; i < m_nFilterPoints; i++)
      inputSignal[i] = 0;  // zeropad
    std::complex<double>* fftSignal = new std::complex<double> [m_nFilterPoints];
    finiteFourierTransform (inputSignal, fftSignal, FORWARD);
    delete inputSignal;
#if HAVE_OPENMP
    #pragma omp parallel for
#endif
    for (i = 0; i < m_nFilterPoints; i++)
      fftSignal[i] *= m_adFilter[i];
    double* inverseFourier = new double [m_nFilterPoints];
    finiteFourierTransform (fftSignal, inverseFourier, BACKWARD);
    delete fftSignal;
    for (i = 0; i < m_nSignalPoints; i++)
      output[i] = inverseFourier[i];
    delete inverseFourier;
  }
#if HAVE_FFTW
  else if (m_idFilterMethod == FILTER_METHOD_RFFTW) {
    for (i = 0; i < m_nSignalPoints; i++)
      m_adRealFftInput[i] = input[i];

    fftw_execute (m_realPlanForward);
    for (i = 0; i < m_nFilterPoints; i++)
      m_adRealFftSignal[i] = m_adFilter[i] * m_adRealFftOutput[i];
    for (i = m_nFilterPoints; i < m_nOutputPoints; i++)
             m_adRealFftSignal[i] = 0;

    fftw_execute (m_realPlanBackward);
    for (i = 0; i < m_nSignalPoints * m_iPreinterpolationFactor; i++)
      output[i] = m_adRealFftBackwardOutput[i];
  } else if (m_idFilterMethod == FILTER_METHOD_FFTW) {
    for (i = 0; i < m_nSignalPoints; i++)
      m_adComplexFftInput[i][0] = input[i];

    fftw_execute (m_complexPlanForward);
#if HAVE_OPENMP
    #pragma omp parallel for
#endif
    for (i = 0; i < m_nFilterPoints; i++) {
      m_adComplexFftSignal[i][0] = m_adFilter[i] * m_adComplexFftOutput[i][0];
      m_adComplexFftSignal[i][1] = m_adFilter[i] * m_adComplexFftOutput[i][1];
    }
    fftw_execute (m_complexPlanBackward);
    for (i = 0; i < m_nSignalPoints * m_iPreinterpolationFactor; i++)
      output[i] = m_adComplexFftBackwardOutput[i][0];
  }
#endif
  delete input;
}


/* NAME
*    convolve                   Discrete convolution of two functions
*
* SYNOPSIS
*    r = convolve (f1, f2, dx, n, np, func_type)
*    double r                   Convolved result
*    double f1[], f2[]          Functions to be convolved
*    double dx                  Difference between successive x values
*    int n                      Array index to center convolution about
*    int np                     Number of points in f1 array
*    int func_type              EVEN or ODD or EVEN_AND_ODD function f2
*
* NOTES
*    f1 is the projection data, its indices range from 0 to np - 1.
*    The index for f2, the filter, ranges from -(np-1) to (np-1).
*    There are 3 ways to handle the negative vertices of f2:
*       1. If we know f2 is an EVEN function, then f2[-n] = f2[n].
*          All filters used in reconstruction are even.
*      2. If we know f2 is an ODD function, then f2[-n] = -f2[n]
*      3. If f2 is both ODD AND EVEN, then we must store the value of f2
*          for negative indices.  Since f2 must range from -(np-1) to (np-1),
*          if we add (np - 1) to f2's array index, then f2's index will
*          range from 0 to 2 * (np - 1), and the origin, x = 0, will be
*          stored at f2[np-1].
*/

double
ProcessSignal::convolve (const double func[], const double dx, const int n, const int np) const
{
  double sum = 0.0;

#if UNOPTIMIZED_CONVOLUTION
  for (int i = 0; i < np; i++)
    sum += func[i] * m_adFilter[n - i + (np - 1)];
#else
  double* f2 = m_adFilter + n + (np - 1);
  for (int i = 0; i < np; i++)
    sum += *func++ * *f2--;
#endif

  return (sum * dx);
}


double
ProcessSignal::convolve (const float func[], const double dx, const int n, const int np) const
{
  double sum = 0.0;

#if UNOPTIMIZED_CONVOLUTION
  for (int i = 0; i < np; i++)
    sum += func[i] * m_adFilter[n - i + (np - 1)];
#else
  double* f2 = m_adFilter + n + (np - 1);
  for (int i = 0; i < np; i++)
    sum += *func++ * *f2--;
#endif

  return (sum * dx);
}


void
ProcessSignal::finiteFourierTransform (const double input[], double output[], const int n, int direction)
{
  std::complex<double>* complexOutput = new std::complex<double> [n];

  finiteFourierTransform (input, complexOutput, n, direction);
  for (int i = 0; i < n; i++)
    output[i] = complexOutput[i].real();
  delete [] complexOutput;
}

void
ProcessSignal::finiteFourierTransform (const double input[], std::complex<double> output[], const int n, int direction)
{
  if (direction < 0)
    direction = -1;
  else
    direction = 1;

  double angleIncrement = direction * 2 * PI / n;
  for (int i = 0; i < n; i++) {
    double sumReal = 0;
    double sumImag = 0;
    for (int j = 0; j < n; j++) {
      double angle = i * j * angleIncrement;
      sumReal += input[j] * cos(angle);
      sumImag += input[j] * sin(angle);
    }
    if (direction < 0) {
      sumReal /= n;
      sumImag /= n;
    }
    output[i] = std::complex<double> (sumReal, sumImag);
  }
}


void
ProcessSignal::finiteFourierTransform (const std::complex<double> input[], std::complex<double> output[], const int n, int direction)
{
  if (direction < 0)
    direction = -1;
  else
    direction = 1;

  double angleIncrement = direction * 2 * PI / n;
  for (int i = 0; i < n; i++) {
    std::complex<double> sum (0,0);
    for (int j = 0; j < n; j++) {
      double angle = i * j * angleIncrement;
      std::complex<double> exponentTerm (cos(angle), sin(angle));
      sum += input[j] * exponentTerm;
    }
    if (direction < 0) {
      sum /= n;
    }
    output[i] = sum;
  }
}

void
ProcessSignal::finiteFourierTransform (const std::complex<double> input[], double output[], const int n, int direction)
{
  if (direction < 0)
    direction = -1;
  else
    direction = 1;

  double angleIncrement = direction * 2 * PI / n;
  for (int i = 0; i < n; i++) {
    double sumReal = 0;
    for (int j = 0; j < n; j++) {
      double angle = i * j * angleIncrement;
      sumReal += input[j].real() * cos(angle) - input[j].imag() * sin(angle);
    }
    if (direction < 0) {
      sumReal /= n;
    }
    output[i] = sumReal;
  }
}

// Table-based routines

void
ProcessSignal::finiteFourierTransform (const double input[], std::complex<double> output[], int direction) const
{
  if (direction < 0)
    direction = -1;
  else
    direction = 1;

  for (int i = 0; i < m_nFilterPoints; i++) {
    double sumReal = 0, sumImag = 0;
    for (int j = 0; j < m_nFilterPoints; j++) {
      int tableIndex = i * j;
      if (direction > 0) {
        sumReal += input[j] * m_adFourierCosTable[tableIndex];
        sumImag += input[j] * m_adFourierSinTable[tableIndex];
      } else {
        sumReal += input[j] * m_adFourierCosTable[tableIndex];
        sumImag -= input[j] * m_adFourierSinTable[tableIndex];
      }
    }
    if (direction < 0) {
      sumReal /= m_nFilterPoints;
      sumImag /= m_nFilterPoints;
    }
    output[i] = std::complex<double> (sumReal, sumImag);
  }
}

// (a+bi) * (c + di) = (ac - bd) + (ad + bc)i
void
ProcessSignal::finiteFourierTransform (const std::complex<double> input[], std::complex<double> output[], int direction) const
{
  if (direction < 0)
    direction = -1;
  else
    direction = 1;

  for (int i = 0; i < m_nFilterPoints; i++) {
    double sumReal = 0, sumImag = 0;
    for (int j = 0; j < m_nFilterPoints; j++) {
      int tableIndex = i * j;
      if (direction > 0) {
        sumReal += input[j].real() * m_adFourierCosTable[tableIndex]
          - input[j].imag() * m_adFourierSinTable[tableIndex];
        sumImag += input[j].real() * m_adFourierSinTable[tableIndex]
          + input[j].imag() * m_adFourierCosTable[tableIndex];
      } else {
        sumReal += input[j].real() * m_adFourierCosTable[tableIndex]
          - input[j].imag() * -m_adFourierSinTable[tableIndex];
        sumImag += input[j].real() * -m_adFourierSinTable[tableIndex]
          + input[j].imag() * m_adFourierCosTable[tableIndex];
      }
    }
    if (direction < 0) {
      sumReal /= m_nFilterPoints;
      sumImag /= m_nFilterPoints;
    }
    output[i] = std::complex<double> (sumReal, sumImag);
  }
}

void
ProcessSignal::finiteFourierTransform (const std::complex<double> input[], double output[], int direction) const
{
  if (direction < 0)
    direction = -1;
  else
    direction = 1;

  for (int i = 0; i < m_nFilterPoints; i++) {
    double sumReal = 0;
    for (int j = 0; j < m_nFilterPoints; j++) {
      int tableIndex = i * j;
      if (direction > 0) {
        sumReal += input[j].real() * m_adFourierCosTable[tableIndex]
          - input[j].imag() * m_adFourierSinTable[tableIndex];
      } else {
        sumReal += input[j].real() * m_adFourierCosTable[tableIndex]
          - input[j].imag() * -m_adFourierSinTable[tableIndex];
      }
    }
    if (direction < 0) {
      sumReal /= m_nFilterPoints;
    }
    output[i] = sumReal;
  }
}


int
ProcessSignal::addZeropadFactor (int n, int iZeropad)
{
  if (iZeropad > 0) {
    double dLogBase2 = log(n) / log(2);
    int iLogBase2 = static_cast<int>(floor (dLogBase2));
    int iPaddedN = 1 << (iLogBase2 + iZeropad);
#ifdef DEBUG
    sys_error (ERR_TRACE, "Zeropadding %d to %d", n, iPaddedN);
#endif
    return iPaddedN;
  }

  return n;
}