star_recognizer.cpp

/**
 * Star recognizer using the CImg library and CCFits.
 *
 * Copyright (C) 2015 Carsten Schmitt
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * 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, see <http://www.gnu.org/licenses/>.
 */
#include <iostream>
#include <filesystem>
//#include <stdexcept> // Standrd runtime_exception...

#include <assert.h>
#include <CImg.h>
#include <CCfits/CCfits>
 
#include <tuple>
#include <functional>
#include <list>
#include <set>
#include <array>
#include <vector>

// See https://en.cppreference.com/w/cpp/ranges
// Not yet part of gcc-9
// See https://stackoverflow.com/questions/56118941/do-we-have-c20-ranges-library-in-gcc-9
//#include <ranges>
// Using boost as long as ranges lib made it into the std.
//#include <boost/range/adaptors.hpp>
//#include <boost/range/algorithm.hpp>

#include <gsl/gsl_multifit_nlin.h>

#include <boost/program_options.hpp>
#include <boost/algorithm/string/case_conv.hpp>

using namespace std;
using namespace cimg_library;
using namespace CCfits;
 
typedef tuple<int /*x*/,int /*y*/> PixelPosT;
typedef set<PixelPosT> PixelPosSetT;
typedef list<PixelPosT> PixelPosListT;
 
typedef tuple<float, float> PixSubPosT;
typedef tuple<float /*x1*/, float /*y1*/, float /*x2*/, float /*y2*/> FrameT;
 
struct StarInfoT {
  FrameT clusterFrame;
  FrameT cogFrame;
  FrameT hfdFrame;
  PixSubPosT cogCentroid;
  PixSubPosT subPixelInterpCentroid;
  float hfd;
  float fwhmHorz;
  float fwhmVert;
  float maxPixValue;
  bool saturated;
};
typedef list<StarInfoT> StarInfoListT;
 
/**
* Get all pixels inside a radius: http://stackoverflow.com/questions/14487322/get-all-pixel-array-inside-circle
* Algorithm: http://en.wikipedia.org/wiki/Midpoint_circle_algorithm
*/
bool
insideCircle(float inX /*pos of x*/, float inY /*pos of y*/, float inCenterX, float inCenterY, float inRadius)
{
  return (pow(inX - inCenterX, 2.0) + pow(inY - inCenterY, 2.0) <= pow(inRadius, 2.0));
}


void
readViaCimg(CImg<float> * inImg, const string & inFilename, long * outBitPix) {
  
  inImg->load(inFilename.c_str());

  *outBitPix = 8; // TODO: Is this correct?
}


void
readFits(CImg<float> * inImg, const string & inFilename, long * outBitPix) {
  std::unique_ptr<FITS> pInfile(new FITS(inFilename, Read, true));
  PHDU & image = pInfile->pHDU(); 
 
  if (outBitPix) {
    *outBitPix = image.bitpix();
  }
 
  inImg->resize(image.axis(0) /*x*/, image.axis(1) /*y*/, 1/*z*/, 1 /*1 color*/);
  
  // NOTE: At this point we assume that there is only 1 layer.
  std::valarray<unsigned long> imgData;
  image.read(imgData);
  cimg_forXY(*inImg, x, y) { (*inImg)(x, inImg->height() - y - 1) = imgData[inImg->offset(x, y)]; }
}


void
readFile(CImg<float> * inImg, const string & inFilename, long * outBitPix = 0)
{
  namespace fs = std::filesystem;
  fs::path filePath = fs::path(inFilename);
  std::string ext = filePath.extension();
  
  boost::algorithm::to_lower(ext);

  static std::vector<std::string> fitsExtensions = { ".fts", ".fits" };

  auto it = std::find(fitsExtensions.begin(), fitsExtensions.end(), ext);
  bool isFitsExt = (it != fitsExtensions.end());

  if (isFitsExt) {
	readFits(inImg, inFilename, outBitPix);
  }
  else {
	// Try to load via CImg directly...
	readViaCimg(inImg, inFilename, outBitPix);
  }
} 
 

void
thresholdOtsu(const CImg<float> & inImg, long inBitPix, CImg<float> * outBinImg)
{
  CImg<> hist = inImg.get_histogram(pow(2.0, inBitPix));
 
  float sum = 0;
  cimg_forX(hist, pos) { sum += pos * hist[pos]; }
 
  float numPixels = inImg.width() * inImg.height();
  float sumB = 0, wB = 0, max = 0.0;
  float threshold1 = 0.0, threshold2 = 0.0;
  
  cimg_forX(hist, i) {
    wB += hist[i];
 
    if (! wB) { continue; }    
 
    float wF = numPixels - wB;
    
    if (! wF) { break; }
    
    sumB += i * hist[i];
 
    float mF = (sum - sumB) / wF;
    float mB = sumB / wB;
    float diff = mB - mF;
    float bw = wB * wF * pow(diff, 2.0);
    
    if (bw >= max) {
      threshold1 = i;
      if (bw > max) {
         threshold2 = i;
      }
      max = bw;            
    }
  } // end loop
  
  float th = (threshold1 + threshold2) / 2.0;
 
  *outBinImg = inImg; // Create a copy
  outBinImg->threshold(th); 
}
 
/**
 * Removes all white neighbours arond pixel from whitePixels
 * if they exist and adds them to pixelsToBeProcessed.
 */
void
getAndRemoveNeighbours(PixelPosT inCurPixelPos, PixelPosSetT * inoutWhitePixels, PixelPosListT * inoutPixelsToBeProcessed)
{
  const size_t _numPixels = 8, _x = 0, _y = 1;
  const int offsets[_numPixels][2] = { { -1, -1 }, { 0, -1 }, { 1, -1 },
                                       { -1, 0 },              { 1, 0 },
                                       { -1, 1 }, { 0, 1 }, { 1, 1 } };
  
  for (size_t p = 0; p < _numPixels; ++p) {
    PixelPosT curPixPos(std::get<0>(inCurPixelPos) + offsets[p][_x], std::get<1>(inCurPixelPos) + offsets[p][_y]);
    PixelPosSetT::iterator itPixPos = inoutWhitePixels->find(curPixPos);
 
    if (itPixPos != inoutWhitePixels->end()) {
      const PixelPosT & curPixPos = *itPixPos;
      inoutPixelsToBeProcessed->push_back(curPixPos);
      inoutWhitePixels->erase(itPixPos); // Remove white pixel from "white set" since it has been now processed
    }
  }
  return;
}
 
template<typename T> void
clusterStars(const CImg<T> & inImg, StarInfoListT * outStarInfos)
{
  PixelPosSetT whitePixels;
 
  cimg_forXY(inImg, x, y) {
    if (inImg(x, y)) {
      whitePixels.insert(whitePixels.end(), PixelPosT(x, y));
    }
  }
 
  // Iterate over white pixels as long as set is not empty
  while (whitePixels.size()) {
    PixelPosListT pixelsToBeProcessed;
 
    PixelPosSetT::iterator itWhitePixPos = whitePixels.begin();
    pixelsToBeProcessed.push_back(*itWhitePixPos);
    whitePixels.erase(itWhitePixPos);
 
    FrameT frame(inImg.width(), inImg.height(), 0, 0);
 
    while(! pixelsToBeProcessed.empty()) {
      PixelPosT curPixelPos = pixelsToBeProcessed.front();
 
      // Determine boundaries (min max in x and y directions)
      if (std::get<0>(curPixelPos) /*x*/ < std::get<0>(frame) /*x1*/) {    std::get<0>(frame) = std::get<0>(curPixelPos); }
      if (std::get<0>(curPixelPos) /*x*/ > std::get<2>(frame) /*x2*/) { std::get<2>(frame) = std::get<0>(curPixelPos); }
      if (std::get<1>(curPixelPos) /*y*/ < std::get<1>(frame) /*y1*/) {    std::get<1>(frame) = std::get<1>(curPixelPos); }
      if (std::get<1>(curPixelPos) /*y*/ > std::get<3>(frame) /*y2*/) { std::get<3>(frame) = std::get<1>(curPixelPos); }
 
      getAndRemoveNeighbours(curPixelPos, & whitePixels, & pixelsToBeProcessed);
      pixelsToBeProcessed.pop_front();
    }
 
    // Create new star-info and set cluster-frame.
    // NOTE: we may use new to avoid copy of StarInfoT...
    StarInfoT starInfo;
    starInfo.clusterFrame = frame;
    outStarInfos->push_back(starInfo);
  }
}
 
float
calcIx2(const CImg<float> & img, int x)
{
  float Ix = 0;
  cimg_forY(img, y) { Ix += pow(img(x, y), 2.0) * (float) x; }
  return Ix;
}
 
float
calcJy2(const CImg<float> & img, int y)
{
  float Iy = 0;
  cimg_forX(img, x) { Iy += pow(img(x, y), 2.0) * (float) y; }
  return Iy;
}
 
// Calculate Intensity Weighted Center (IWC)
void
calcIntensityWeightedCenter(const CImg<float> & inImg, float * outX, float * outY)
{
  assert(outX && outY);
  
  // Determine weighted centroid - See http://cdn.intechopen.com/pdfs-wm/26716.pdf
  float Imean2 = 0, Jmean2 = 0, Ixy2 = 0;
  
  for(size_t i = 0; i < inImg.width(); ++i) {
    Imean2 += calcIx2(inImg, i);
    cimg_forY(inImg, y) { Ixy2 += pow(inImg(i, y), 2.0); }
  }
 
  for(size_t i = 0; i < inImg.height(); ++i) {
    Jmean2 += calcJy2(inImg, i);
  }
  
  *outX = Imean2 / Ixy2;
  *outY = Jmean2 / Ixy2;
}
 
void
calcSubPixelCenter(const CImg<float> & inImg, float * outX, float * outY, size_t inNumIter = 10 /*num iterations*/)
{
  // Sub pixel interpolation
  float c, a1, a2, a3, a4, b1, b2, b3, b4;
  float a1n, a2n, a3n, a4n, b1n, b2n, b3n, b4n;
 
  assert(inImg.width() == 3 && inImg.height() == 3);
 
  b1 = inImg(0, 0); a2 = inImg(1, 0); b2 = inImg(2, 0);
  a1 = inImg(0, 1);  c = inImg(1, 1); a3 = inImg(2, 1);
  b4 = inImg(0, 2); a4 = inImg(1, 2); b3 = inImg(2, 2);
 
  for (size_t i = 0; i < inNumIter; ++i) {
    float c2 = 2 * c;
    float sp1 = (a1 + a2 + c2) / 4;
    float sp2 = (a2 + a3 + c2) / 4;
    float sp3 = (a3 + a4 + c2) / 4;
    float sp4 = (a4 + a1 + c2) / 4;
    
    // New maximum is center
    float newC = std::max({ sp1, sp2, sp3, sp4 });
    
    // Calc position of new center
    float ad = pow(2.0, -((float) i + 1));
 
    if (newC == sp1) {
      *outX = *outX - ad; // to the left
      *outY = *outY - ad; // to the top
 
      // Calculate new sub pixel values
      b1n = (a1 + a2 + 2 * b1) / 4;
      b2n = (c + b2 + 2 * a2) / 4;
      b3n = sp3;
      b4n = (b4 + c + 2 * a1) / 4;
      a1n = (b1n + c + 2 * a1) / 4;
      a2n = (b1n + c + 2 * a2) / 4;
      a3n = sp2;
      a4n = sp4;
 
    } else if (newC == sp2) {
      *outX = *outX + ad; // to the right
      *outY = *outY - ad; // to the top
 
      // Calculate new sub pixel values
      b1n = (2 * a2 + b1 + c) / 4;
      b2n = (2 * b2 + a3 + a2) / 4;
      b3n = (2 * a3 + b3 + c) / 4;
      b4n = sp4;
      a1n = sp1;
      a2n = (b2n + c + 2 * a2) / 4;
      a3n = (b2n + c + 2 * a3) / 4;
      a4n = sp3;
    } else if (newC == sp3) {
      *outX = *outX + ad; // to the right
      *outY = *outY + ad; // to the bottom
 
      // Calculate new sub pixel values
      b1n = sp1;
      b2n = (b2 + 2 * a3 + c) / 4;
      b3n = (2 * b3 + a3 + a4) / 4;
      b4n = (2 * a4 + b4 + c) / 4;
      a1n = sp4;
      a2n = sp2;
      a3n = (b3n + 2 * a3 + c) / 4;
      a4n = (b3n + 2 * a4 + c) / 4;
    } else {
      *outX = *outX - ad; // to the left
      *outY = *outY + ad; // to the bottom  
 
      // Calculate new sub pixel values
      b1n = (2 * a1 + b1 + c) / 4;
      b2n = sp2;
      b3n = (c + b3 + 2 * a4) / 4;
      b4n = (2 * b4 + a1 + a4) / 4;
      a1n = (b4n + 2 * a1 + c) / 4;
      a2n = sp1;
      a3n = sp3;
      a4n = (b4n + 2 * a4 + c) / 4;
    }
 
    c = newC; // Oi = Oi+1
 
    a1 = a1n;
    a2 = a2n;
    a3 = a3n;
    a4 = a4n;
 
    b1 = b1n;
    b2 = b2n;
    b3 = b3n;
    b4 = b4n;
  }
}
 
void
calcCentroid(const CImg<float> & inImg, const FrameT & inFrame, PixSubPosT * outPixelPos, PixSubPosT * outSubPixelPos = 0, size_t inNumIterations = 10)
{
  // Get frame sub img
  CImg<float> subImg = inImg.get_crop(std::get<0>(inFrame), std::get<1>(inFrame), std::get<2>(inFrame), std::get<3>(inFrame));
 
  float & xc = std::get<0>(*outPixelPos);
  float & yc = std::get<1>(*outPixelPos);
  
  // 1. Calculate the IWC
  calcIntensityWeightedCenter(subImg, & xc, & yc);
 
  if (outSubPixelPos) {
    // 2. Round to nearest integer and then iteratively improve.
    int xi = floor(xc + 0.5);
    int yi = floor(yc + 0.5);
  
    CImg<float> img3x3 = inImg.get_crop(xi - 1 /*x0*/, yi - 1 /*y0*/, xi + 1 /*x1*/, yi + 1 /*y1*/);
    
    // 3. Interpolate using sub-pixel algorithm
    float xsc = xi, ysc = yi;
    calcSubPixelCenter(img3x3, & xsc, & ysc, inNumIterations);
    
    std::get<0>(*outSubPixelPos) = xsc;
    std::get<1>(*outSubPixelPos) = ysc;
  }
}
 
 
/**
* Expects star centered in the middle of the image (in x and y) and mean background subtracted from image.
*
* HDF calculation: http://www005.upp.so-net.ne.jp/k_miyash/occ02/halffluxdiameter/halffluxdiameter_en.html
*                  http://www.cyanogen.com/help/maximdl/Half-Flux.htm
*
* NOTE: Currently the accuracy is limited by the insideCircle function (-> sub-pixel accuracy).
* NOTE: The HFD is estimated in case there is no flux (HFD ~ sqrt(2) * inOuterDiameter / 2).
* NOTE: The outer diameter is usually a value which depends on the properties of the optical
*       system and also on the seeing conditions. The HFD value calculated depends on this
*       outer diameter value.
*/
float
calcHfd(const CImg<float> & inImage, unsigned int inOuterDiameter)
{
  // Sum up all pixel values in whole circle
  float outerRadius = inOuterDiameter / 2;
  float sum = 0, sumDist = 0;
  int centerX = ceil(inImage.width() / 2.0);
  int centerY = ceil(inImage.height() / 2.0);
 
  cimg_forXY(inImage, x, y) {
    if (insideCircle(x, y, centerX, centerY, outerRadius)) {
      sum += inImage(x, y);
      sumDist += inImage(x, y) * sqrt(pow((float) x - (float) centerX, 2.0f) + pow((float) y - (float) centerY, 2.0f));
    }
  }
  // NOTE: Multiplying with 2 is required since actually just the HFR is calculated above
  return (sum ? 2.0 * sumDist / sum : sqrt(2.0) * outerRadius);
}
 
/**********************************************************************
* Helper classes
**********************************************************************/
struct DataPointT {
  float x;
  float y;
  DataPointT(float inX = 0, float inY = 0) : x(inX), y(inY) {}
};
  
typedef vector<DataPointT> DataPointsT;
  
struct GslMultiFitDataT {
  float y;
  float sigma;
  DataPointT pt;
};
  
typedef vector<GslMultiFitDataT> GslMultiFitParmsT;
 
 
/**********************************************************************
* Curve to fit to is supplied by traits.
**********************************************************************/
template <class FitTraitsT>
class CurveFitTmplT {
public:
  typedef typename FitTraitsT::CurveParamsT CurveParamsT;
 
  /**
   * DataAccessor allows specifying how x,y data is accessed.
   * See http://en.wikipedia.org/wiki/Approximation_error for expl. of rel and abs errors.
   */
  template<typename DataAccessorT> static int  
  fitGslLevenbergMarquart(const typename DataAccessorT::TypeT & inData, typename CurveParamsT::TypeT * outResults,
          double inEpsAbs, double inEpsRel, size_t inNumMaxIter = 500) {
    GslMultiFitParmsT gslMultiFitParms(inData.size());
      
    // Fill in the parameters
    for (typename DataAccessorT::TypeT::const_iterator it = inData.begin(); it != inData.end(); ++it) {
      size_t idx = std::distance(inData.begin(), it);
      const DataPointT & dataPoint = DataAccessorT::getDataPoint(idx, it);
      gslMultiFitParms[idx].y     = dataPoint.y;
      gslMultiFitParms[idx].sigma = 0.1f;
      gslMultiFitParms[idx].pt    = dataPoint;
    }
 
    // Fill in function info
    gsl_multifit_function_fdf f;
    f.f      = FitTraitsT::gslFx;
    f.df     = FitTraitsT::gslDfx;
    f.fdf    = FitTraitsT::gslFdfx;
    f.n      = inData.size();
    f.p      = FitTraitsT::CurveParamsT::_Count;
    f.params = & gslMultiFitParms;
    
 
    gsl_vector * guess = gsl_vector_alloc(FitTraitsT::CurveParamsT::_Count);  // Allocate the guess vector
    
    FitTraitsT::makeGuess(gslMultiFitParms, guess);  // Make initial guesses based on the data
    
    // Create a Levenberg-Marquardt solver with n data points and m parameters
    gsl_multifit_fdfsolver * solver = gsl_multifit_fdfsolver_alloc(gsl_multifit_fdfsolver_lmsder,
                                                                  inData.size(), FitTraitsT::CurveParamsT::_Count);
    gsl_multifit_fdfsolver_set(solver, & f, guess);  // Initialize the solver
    
    int status, i = 0;
    
    // Iterate to to find a result
    do {
      i++;
      status = gsl_multifit_fdfsolver_iterate(solver); // returns 0 in case of success
      if (status) {  break; }
      status = gsl_multifit_test_delta(solver->dx, solver->x, inEpsAbs, inEpsRel);
    } while (status == GSL_CONTINUE && i < inNumMaxIter);
    
    // Store the results to be returned to the user (copy from gsl_vector to result structure)
    for (size_t i = 0; i < FitTraitsT::CurveParamsT::_Count; ++i) {
      typename FitTraitsT::CurveParamsT::TypeE idx = static_cast<typename FitTraitsT::CurveParamsT::TypeE>(i);
      (*outResults)[idx] = gsl_vector_get(solver->x, idx);
    }
 
    // Free GSL memory
    gsl_multifit_fdfsolver_free(solver);
    gsl_vector_free(guess);
 
    return status;
  }
};
 
/**********************************************************************
* Gaussian fit traits
**********************************************************************/
class GaussianFitTraitsT {
private:
  
public:
  struct CurveParamsT {
    // b = base, p = peak, c = center in x, w = mean width (FWHM)
    enum TypeE { B_IDX = 0, P_IDX, C_IDX, W_IDX, _Count };
    struct TypeT : public std::array<float, TypeE::_Count> {
      TypeT(const gsl_vector * inVec = 0) {
        for (size_t i = 0; i < TypeE::_Count; ++i) {
          TypeE idx = static_cast<TypeE>(i);
          (*this)[i] = (inVec ? gsl_vector_get(inVec, idx) : 0);
        }
      }
    };
  };
 
  /* Makes a guess for b, p, c and w based on the supplied data */
  static void makeGuess(const GslMultiFitParmsT & inData, gsl_vector * guess) {
    size_t numDataPoints = inData.size();
    float y_mean = 0;
    float y_max = inData.at(0).pt.y;
    float c = inData.at(0).pt.x;
    
    for(size_t i = 0; i < numDataPoints; ++i) {
      const DataPointT & dataPoint = inData.at(i).pt;
 
      y_mean += dataPoint.y;
      
      if(y_max < dataPoint.y) {
        y_max = dataPoint.y;
        c = dataPoint.x;
      }
    }
 
    y_mean /= (float) numDataPoints;
    float w = (inData.at(numDataPoints - 1).pt.x - inData.at(0).pt.x) / 10.0;
    
    gsl_vector_set(guess, CurveParamsT::B_IDX, y_mean);
    gsl_vector_set(guess, CurveParamsT::P_IDX, y_max);
    gsl_vector_set(guess, CurveParamsT::C_IDX, c);
    gsl_vector_set(guess, CurveParamsT::W_IDX, w);
  }
 
  /* y = b + p * exp(-0.5f * ((t - c) / w) * ((t - c) / w)) */
  static float fx(float x, const CurveParamsT::TypeT & inParms) {
    float b = inParms[CurveParamsT::B_IDX];
    float p = inParms[CurveParamsT::P_IDX];
    float c = inParms[CurveParamsT::C_IDX];
    float w = inParms[CurveParamsT::W_IDX];
    float t = ((x - c) / w);
    t *= t;
    return (b + p * exp(-0.5f * t));
  }
 
  /* Calculates f(x) = b + p * e^[0.5*((x-c)/w)] for each data point. */
  static int gslFx(const gsl_vector * x, void * inGslParams, gsl_vector * outResultVec) {    
    CurveParamsT::TypeT curveParams(x);     // Store the current coefficient values
    const GslMultiFitParmsT * gslParams = ((GslMultiFitParmsT*) inGslParams); // Store parameter values
 
    //Execute Levenberg-Marquart on f(x)
    for(size_t i = 0; i < gslParams->size(); ++i) {
      const GslMultiFitDataT & gslData = gslParams->at(i);
      float yi = GaussianFitTraitsT::fx((float) gslData.pt.x, curveParams);
      gsl_vector_set(outResultVec, i, (yi - gslData.y) / gslData.sigma);
    }
    return GSL_SUCCESS;
  }
 
  /* Calculates the Jacobian (derivative) matrix of f(x) = b + p * e^[0.5*((x-c)/w)^2] for each data point */
  static int gslDfx(const gsl_vector * x, void * params, gsl_matrix * J) {
    
    // Store parameter values
    const GslMultiFitParmsT * gslParams = ((GslMultiFitParmsT*) params);
    
    // Store current coefficients
    float p = gsl_vector_get(x, CurveParamsT::P_IDX);
    float c = gsl_vector_get(x, CurveParamsT::C_IDX);
    float w = gsl_vector_get(x, CurveParamsT::W_IDX);
    
    // Store non-changing calculations
    float w2 = w * w;
    float w3 = w2 * w;
    
    for(size_t i = 0; i < gslParams->size(); ++i) {
      const GslMultiFitDataT & gslData = gslParams->at(i);
      float x_minus_c = (gslData.pt.x - c);
      float e = exp(-0.5f * (x_minus_c / w) * (x_minus_c / w));
      
      gsl_matrix_set(J, i, CurveParamsT::B_IDX, 1 / gslData.sigma);
      gsl_matrix_set(J, i, CurveParamsT::P_IDX, e / gslData.sigma);
      gsl_matrix_set(J, i, CurveParamsT::C_IDX, (p * e * x_minus_c) / (gslData.sigma * w2));
      gsl_matrix_set(J, i, CurveParamsT::W_IDX, (p * e * x_minus_c * x_minus_c) / (gslData.sigma * w3));
    }    
    return GSL_SUCCESS;
  }
  
  /* Invokes f(x) and f'(x) */
  static int gslFdfx(const gsl_vector * x, void * params, gsl_vector * f, gsl_matrix * J) {
    gslFx(x, params, f);
    gslDfx(x, params, J);
    
    return GSL_SUCCESS;
  }
};
 
typedef list<PixSubPosT> MyDataContainerT;
 
class MyDataAccessorT {
public:
  typedef MyDataContainerT TypeT;
  static DataPointT getDataPoint(size_t inIdx, TypeT::const_iterator inIt) {
    const PixSubPosT & pos = *inIt;
    DataPointT dp(get<0>(pos) /*inIdx*/, get<1>(pos) /*y*/);
    return dp;
  }
};
 
 
FrameT
rectify(const FrameT & inFrame)
{
  float border = 3;
  float border2 = 2.0 * border;
  float width = fabs(std::get<0>(inFrame) - std::get<2>(inFrame)) + border2;
  float height = fabs(std::get<1>(inFrame) - std::get<3>(inFrame)) + border2;
  float L = max(width, height);
  float x0 = std::get<0>(inFrame) - (fabs(width - L) / 2.0) - border;
  float y0 = std::get<1>(inFrame) - (fabs(height - L) / 2.0) - border;
  return FrameT(x0, y0, x0 + L, y0 + L);
}
 
int
main(int argc, char *argv[])
{  
  /* outerHfdDiameter depends on pixel size and focal length (and seeing...).
     Later we may calculate it automatically wihth goven focal length and pixel
     size of the camera. For now it is a "best guess" value.
  */
  const unsigned int outerHfdDiameter = 21;
  StarInfoListT starInfos;
  vector < list<StarInfoT *> > starBuckets;
  CImg<float> img;
  long bitPix = 0;
  std::string filename;

  
  // Commandline options
  namespace po = boost::program_options;
  po::options_description desc("StarRecognizer options");
  
  desc.add_options()
    ("help,h", "Produce this help message.")
    ("input-file,i", po::value<std::string>(), "Path to image file.")
	;

  
  po::positional_options_description p;
  p.add("input-file", -1);

  po::variables_map vm;
  po::store(po::command_line_parser(argc, argv).
			options(desc).positional(p).run(), vm);
  po::notify(vm);


  
  if (vm.count("help")) {
	std::cout << desc << std::endl;
    return 1;
  }

  // So far only one filename at a time is supported
  if (vm.count("input-file")) {
	filename = vm["input-file"].as<std::string>();

	std::cout << "Filename specified: " 
			  << filename
			  << std::endl;
  } else {
	std::cout << "Please specify an image filename." << std::endl;
	std::cout << desc << std::endl;
	return 1;
  }




  
  // Read file to CImg
  try {
	std::cout << "Opening file " << filename << endl;
    readFile(& img, filename, & bitPix);
  } catch (FitsException &) {
	std::cout << "Read FITS failed." << endl;
    return 1;
  }
 
  // Create RGB image from fits file to paint boundaries and centroids (just for visualization)
  CImg<unsigned char> rgbImg(img.width(), img.height(), 1 /*depth*/, 3 /*3 channels - RGB*/);
  float min = img.min(), mm = img.max() - min;
  
  cimg_forXY(img, x, y) {
    int value = 255.0 * (img(x,y) - min) / mm;
    rgbImg(x, y, 0 /*red*/) = value;
    rgbImg(x, y, 1 /*green*/) = value;
    rgbImg(x, y, 2 /*blue*/) = value;
  }
  
  // AD noise reduction --> In: Loaded image, Out: Noise reduced image
  // NOTE: This step takes a while for big images... too long for usage in a loop ->
  //       Should only be used on image segments, later...
  //
  // http://cimg.sourceforge.net/reference/structcimg__library_1_1CImg.html
  std::cout << "Applying anisotropic diffusion..." << std::endl;

  CImg<float> & aiImg = img.blur_anisotropic(30.0f, /*amplitude*/
                         0.7f, /*sharpness*/
                         0.3f, /*anisotropy*/
                         0.6f, /*alpha*/
                         1.1f, /*sigma*/
                         0.8f, /*dl*/
                         30,   /*da*/
                         2,    /*gauss_prec*/
                         0,    /*interpolation_type*/
                         false /*fast_approx*/
                          );
 
  // Thresholding (Otsu) --> In: Noise reduced image, Out: binary image
  std::cout << "Applying OTSU thresholding..." << std::endl;

  CImg<float> binImg;
  thresholdOtsu(aiImg, bitPix, & binImg);
 
  // Clustering --> In: binary image from thresholding, Out: List of detected stars, subimg-boundaries (x1,y1,x2,y2) for each star
  std::cout << "Applying star clustering..." << std::endl;
  clusterStars(binImg, & starInfos);

  
  std::cout << "Recognized " << starInfos.size() << " stars..." << std::endl;
 
  // Calc brightness boundaries for possible focusing stars
  float maxPossiblePixValue = pow(2.0, bitPix) - 1;
 
  // For each star
  std::cout << "Calculating measures for all stars..." << std::endl;
  
  for (StarInfoListT::iterator it = starInfos.begin(); it != starInfos.end(); ++it) {
    const FrameT & frame = it->clusterFrame;
    FrameT & cogFrame = it->cogFrame;
    FrameT & hfdFrame = it->hfdFrame;
    PixSubPosT & cogCentroid = it->cogCentroid;
    PixSubPosT & subPixelInterpCentroid = it->subPixelInterpCentroid;
    float & hfd = it->hfd;
    float & fwhmHorz = it->fwhmHorz;
    float & fwhmVert = it->fwhmVert;
    float & maxPixValue = it->maxPixValue;
    bool & saturated = it->saturated;
    
    FrameT squareFrame = rectify(frame);
    
    // Centroid calculation --> In: Handle to full noise reduced image, subimg-boundaries (x1,y1,x2,y2), Out: (x,y) - abs. centroid coordinates
    calcCentroid(aiImg, squareFrame, & cogCentroid, & subPixelInterpCentroid, 10 /* num iterations */);
    std::get<0>(cogCentroid) += std::get<0>(squareFrame);
    std::get<1>(cogCentroid) += std::get<1>(squareFrame);
    std::get<0>(subPixelInterpCentroid) += std::get<0>(squareFrame);
    std::get<1>(subPixelInterpCentroid) += std::get<1>(squareFrame);
    
    
    // Calculate cog boundaries
    float maxClusterEdge = std::max(fabs(std::get<0>(frame) - std::get<2>(frame)), fabs(std::get<1>(frame) - std::get<3>(frame)));
    float cogHalfEdge = ceil(maxClusterEdge / 2.0);
    float cogX = std::get<0>(cogCentroid);
    float cogY = std::get<1>(cogCentroid);
    std::get<0>(cogFrame) = cogX - cogHalfEdge - 1;
    std::get<1>(cogFrame) = cogY - cogHalfEdge - 1;
    std::get<2>(cogFrame) = cogX + cogHalfEdge + 1;
    std::get<3>(cogFrame) = cogY + cogHalfEdge + 1;
 
    
    // HFD calculation --> In: image, Out: HFD value
    // Subtract mean value from image which is required for HFD calculation
    size_t hfdRectDist = floor(outerHfdDiameter / 2.0);
    std::get<0>(hfdFrame) = cogX - hfdRectDist;
    std::get<1>(hfdFrame) = cogY - hfdRectDist;
    std::get<2>(hfdFrame) = cogX + hfdRectDist;
    std::get<3>(hfdFrame) = cogY + hfdRectDist;
 
    CImg<float> hfdSubImg = aiImg.get_crop(std::get<0>(hfdFrame), std::get<1>(hfdFrame), std::get<2>(hfdFrame), std::get<3>(hfdFrame));
    maxPixValue = hfdSubImg.max();
    //saturated = (maxPixValue > lowerBound && maxPixValue < upperBound);
    saturated = (maxPixValue == maxPossiblePixValue);
    
    CImg<float> imgHfdSubMean(hfdSubImg);
    double mean = hfdSubImg.mean();
 
    cimg_forXY(hfdSubImg, x, y) {
      imgHfdSubMean(x, y) = (hfdSubImg(x, y) < mean ? 0 : hfdSubImg(x, y) - mean);
    }
 
    // Calc the HFD
    hfd = calcHfd(imgHfdSubMean, outerHfdDiameter /*outer diameter in px*/);
    
    // FWHM calculation --> In: Handle to full noise reduced image, abs. centroid coordinates, Out: FWHM value
    MyDataContainerT vertDataPoints, horzDataPoints;
 
    cimg_forX(imgHfdSubMean, x) {
      horzDataPoints.push_back(make_pair(x, imgHfdSubMean(x, floor(imgHfdSubMean.height() / 2.0 + 0.5))));
    }
    cimg_forY(imgHfdSubMean, y) {
      vertDataPoints.push_back(make_pair(y, imgHfdSubMean(floor(imgHfdSubMean.width() / 2.0 + 0.5), y)));
    }    
    
    // Do the LM fit
    typedef CurveFitTmplT<GaussianFitTraitsT> GaussMatcherT;
    typedef GaussMatcherT::CurveParamsT CurveParamsT;
    CurveParamsT::TypeT gaussCurveParmsHorz, gaussCurveParmsVert;
    
    GaussMatcherT::fitGslLevenbergMarquart<MyDataAccessorT>(horzDataPoints, & gaussCurveParmsHorz, 0.1f /*EpsAbs*/, 0.1f /*EpsRel*/);
    fwhmHorz = gaussCurveParmsHorz[CurveParamsT::W_IDX];
    
    GaussMatcherT::fitGslLevenbergMarquart<MyDataAccessorT>(vertDataPoints, & gaussCurveParmsVert, 0.1f /*EpsAbs*/, 0.1f /*EpsRel*/);
    fwhmVert = gaussCurveParmsVert[CurveParamsT::W_IDX];
  }
  
  // Create result image
  const int factor = 4;
  CImg<unsigned char> & rgbResized = rgbImg.resize(factor * rgbImg.width(), factor * rgbImg.height(),
                           -100 /*size_z*/, -100 /*size_c*/, 1 /*interpolation_type*/);  
 
  // Draw cluster boundaries and square cluster boundaries
  const unsigned char red[3] = { 255, 0, 0 }, green[3] = { 0, 255, 0 }, yellow[3] = { 255, 255, 0 };
  const unsigned char  black[3] = { 0, 0, 0 }, blue[3] = { 0, 0, 255 }, white[3] = { 255, 255, 255 };
  const size_t cCrossSize = 3;
  
  // Mark all stars in RGB image
  for (StarInfoListT::iterator it = starInfos.begin(); it != starInfos.end(); ++it) {
    StarInfoT * curStarInfo = & (*it);
    PixSubPosT & cogCentroid = curStarInfo->cogCentroid;
    float & hfd = curStarInfo->hfd;
    float & fwhmHorz = curStarInfo->fwhmHorz;
    float & fwhmVert = curStarInfo->fwhmVert;
    float & maxPixValue = curStarInfo->maxPixValue;
    
	std::cout << "cogCentroid=(" << setw(9) << std::get<0>(curStarInfo->cogCentroid)
			  << ", " << setw(9) << std::get<1>(curStarInfo->cogCentroid)
			  <<  "), " << setw(8) << ", maxPixValue: " << setw(8) << maxPixValue
			  << ", sat: " << curStarInfo->saturated << ", hfd: " << setw(10) << hfd
			  << ", fwhmHorz: " << setw(10) << fwhmHorz << ", fwhmVert: " << setw(10) << fwhmVert << std::endl;
    
    const FrameT & frame = curStarInfo->clusterFrame;
    FrameT squareFrame(rectify(frame));
    rgbResized.draw_rectangle(floor(factor * (std::get<0>(frame) - 1) + 0.5), floor(factor * (std::get<1>(frame) - 1) + 0.5),
                  floor(factor * (std::get<2>(frame) + 1) + 0.5), floor(factor * (std::get<3>(frame) + 1) + 0.5),
                  red, 1 /*opacity*/, ~0 /*pattern*/);
    
    rgbResized.draw_rectangle(floor(factor * (std::get<0>(squareFrame) - 1) + 0.5), floor(factor * (std::get<1>(squareFrame) - 1) + 0.5),
                  floor(factor * (std::get<2>(squareFrame) + 1) + 0.5), floor(factor * (std::get<3>(squareFrame) + 1) + 0.5),
                  blue, 1 /*opacity*/, ~0 /*pattern*/);
    
    
    // Draw centroid crosses and centroid boundaries
    const PixSubPosT & subPos = curStarInfo->cogCentroid;
    const FrameT & cogFrame = curStarInfo->cogFrame;
    const FrameT & hfdFrame = curStarInfo->hfdFrame;
    
    rgbResized.draw_line(floor(factor * (std::get<0>(subPos) - cCrossSize) + 0.5), floor(factor * std::get<1>(subPos) + 0.5),
             floor(factor * (std::get<0>(subPos) + cCrossSize) + 0.5), floor(factor * std::get<1>(subPos) + 0.5), green, 1 /*opacity*/);
    
    rgbResized.draw_line(floor(factor * std::get<0>(subPos) + 0.5), floor(factor * (std::get<1>(subPos) - cCrossSize) + 0.5),
             floor(factor * std::get<0>(subPos) + 0.5), floor(factor * (std::get<1>(subPos) + cCrossSize) + 0.5), green, 1 /*opacity*/);
    
    rgbResized.draw_rectangle(floor(factor * std::get<0>(cogFrame) + 0.5), floor(factor * std::get<1>(cogFrame) + 0.5),
                  floor(factor * std::get<2>(cogFrame) + 0.5), floor(factor * std::get<3>(cogFrame) + 0.5),
                  green, 1 /*opacity*/, ~0 /*pattern*/);
    
    // Draw HFD
    rgbResized.draw_rectangle(floor(factor * std::get<0>(hfdFrame) + 0.5), floor(factor * std::get<1>(hfdFrame) + 0.5),
                  floor(factor * std::get<2>(hfdFrame) + 0.5), floor(factor * std::get<3>(hfdFrame) + 0.5),
                  yellow, 1 /*opacity*/, ~0 /*pattern*/);
    
    rgbImg.draw_circle(floor(factor * std::get<0>(subPos) + 0.5), floor(factor * std::get<1>(subPos) + 0.5), factor * outerHfdDiameter / 2, yellow, 1 /*pattern*/, 1 /*opacity*/);
    rgbImg.draw_circle(floor(factor * std::get<0>(subPos) + 0.5), floor(factor * std::get<1>(subPos) + 0.5), factor * hfd / 2, yellow, 1 /*pattern*/, 1 /*opacity*/);
    
    // Draw text
    const bool & saturated = curStarInfo->saturated;
    
    ostringstream oss;
    oss.precision(4);
    oss    << "HFD=" << hfd << endl
    << "FWHM H=" << fwhmHorz << endl
    << "FWHM V=" << fwhmVert << endl
    << "MAX=" << (int)maxPixValue << endl
    << "SAT=" << (saturated ? "Y" : "N");
    
    rgbImg.draw_text(floor(factor * std::get<0>(subPos) + 0.5), floor(factor * std::get<1>(subPos) + 0.5), oss.str().c_str(), white /*fg color*/, black /*bg color*/, 0.7 /*opacity*/, 9 /*font-size*/);
  }


  // Saving visualization
  static const char* VISUALIZATION_FILENAME = "star_recognizer_out.jpeg";
  
  std::cout << "Illustration written to '" << VISUALIZATION_FILENAME << "'. Done." << std::endl; 
  rgbResized.save(VISUALIZATION_FILENAME);
  
  return 0;
}