source: trunk/src/ATrous/ReconSearch.cc @ 377

// -----------------------------------------------------------------------
// ReconSearch.cc: Searching a wavelet-reconstructed cube.
// -----------------------------------------------------------------------
// Copyright (C) 2006, Matthew Whiting, ATNF
//
// 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 2 of the License, or (at your
// option) any later version.
//
// Duchamp 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 Duchamp; if not, write to the Free Software Foundation,
// Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA
//
// Correspondence concerning Duchamp may be directed to:
//    Internet email: Matthew.Whiting [at] atnf.csiro.au
//    Postal address: Dr. Matthew Whiting
//                    Australia Telescope National Facility, CSIRO
//                    PO Box 76
//                    Epping NSW 1710
//                    AUSTRALIA
// -----------------------------------------------------------------------
#include <fstream>
#include <iostream>
#include <iomanip>
#include <vector>
#include <duchamp.hh>
#include <PixelMap/Object3D.hh>
#include <Cubes/cubes.hh>
#include <Detection/detection.hh>
#include <ATrous/atrous.hh>
#include <Utils/utils.hh>
#include <Utils/feedback.hh>
#include <Utils/Statistics.hh>

using namespace PixelInfo;
using namespace Statistics;

void Cube::ReconSearch()
{
  /**
   * The Cube is first reconstructed, using Cube::ReconCube().
   * The statistics of the cube are calculated next.
   * It is then searched, using searchReconArray.
   * The resulting object list is stored in the Cube, and outputted
   *  to the log file if the user so requests.
   */

  if(!this->par.getFlagATrous()){
    duchampWarning("ReconSearch",
                   "You've requested a reconSearch, but not allocated space for the reconstructed array.\nDoing the basic CubicSearch.\n");
    this->CubicSearch();
  }
  else {
  
    this->ReconCube();

    if(this->par.isVerbose()) std::cout << "  ";

    this->setCubeStats();
    
    if(this->par.isVerbose()) std::cout << "  Searching... " << std::flush;
  
    *this->objectList = searchReconArraySimple(this->axisDim,this->array,
                                               this->recon,
                                               this->par,this->Stats);
    //   this->objectList = searchReconArray(this->axisDim,this->array,
    //                                this->recon,this->par,this->Stats);

    if(this->par.isVerbose()) std::cout << "  Updating detection map... " 
                                        << std::flush;
    this->updateDetectMap();
    if(this->par.isVerbose()) std::cout << "Done.\n";

    if(this->par.getFlagLog()){
      if(this->par.isVerbose()) 
        std::cout << "  Logging intermediate detections... " << std::flush;
      this->logDetectionList();
      if(this->par.isVerbose()) std::cout << "Done.\n";
    }

  }
}

/////////////////////////////////////////////////////////////////////////////
void Cube::ReconCube()
{
  /**
   * A front-end to the various reconstruction functions, the choice of 
   *  which is determined by the use of the reconDim parameter.
   * Differs from ReconSearch only in that no searching is done.
   */
  int dimRecon = this->par.getReconDim();
  // Test whether we have eg. an image, but have requested a 3-d 
  //  reconstruction.
  // If dimension of data array is less than dimRecon, change dimRecon 
  //  to the dimension of the array.
  int numGoodDim = this->head.getNumAxes();
  if(numGoodDim<dimRecon){
    dimRecon = numGoodDim;
    this->par.setReconDim(dimRecon);
    std::stringstream errmsg;
    errmsg << "You requested a " << dimRecon << "-dimensional reconstruction,"
           << " but the FITS file is only " << numGoodDim << "-dimensional.\n"
           << "Changing reconDim to " << numGoodDim << ".\n";
    duchampWarning("Reconstruction",errmsg.str());
  }

  switch(dimRecon)
    {
    case 1: this->ReconCube1D(); break;
    case 2: this->ReconCube2D(); break;
    case 3: this->ReconCube3D(); break;
    default:
      if(dimRecon<=0){
        std::stringstream errmsg;
        errmsg << "reconDim (" << dimRecon
               << ") is less than 1. Performing 1-D reconstruction.\n";
        duchampWarning("Reconstruction", errmsg.str());
        this->par.setReconDim(1);
        this->ReconCube1D();
      }
      else if(dimRecon>3){ 
        //this probably won't happen with new code above, but just in case...
        std::stringstream errmsg;
        errmsg << "reconDim (" << dimRecon
               << ") is more than 3. Performing 3-D reconstruction.\n";
        duchampWarning("Reconstruction", errmsg.str());
        this->par.setReconDim(3);
        this->ReconCube3D();
      }
      break;
    }
}

/////////////////////////////////////////////////////////////////////////////
void Cube::ReconCube1D()
{
  /**
   * This reconstructs a cube by performing a 1D a trous reconstruction
   *  in the spectrum of each spatial pixel.
   */
  long xySize = this->axisDim[0] * this->axisDim[1];

  long zdim = this->axisDim[2];

  ProgressBar bar;
  if(!this->reconExists){
    std::cout<<"  Reconstructing... ";
    if(par.isVerbose()) bar.init(xySize);
    for(int npix=0; npix<xySize; npix++){

      if( par.isVerbose() ) bar.update(npix+1);

      float *spec = new float[zdim];
      float *newSpec = new float[zdim];
      for(int z=0;z<zdim;z++) spec[z] = this->array[z*xySize + npix];
      bool verboseFlag = this->par.isVerbose();
      this->par.setVerbosity(false);
      atrous1DReconstruct(this->axisDim[2],spec,newSpec,this->par);
      this->par.setVerbosity(verboseFlag);
      for(int z=0;z<zdim;z++) this->recon[z*xySize+npix] = newSpec[z];
      delete [] spec;
      delete [] newSpec;
    }
    this->reconExists = true;
    bar.fillSpace(" All Done.");
    printSpace(22);
    std::cout << "\n";
  }

}

/////////////////////////////////////////////////////////////////////////////
void Cube::ReconCube2D()
{
  /**
   * This reconstructs a cube by performing a 2D a trous reconstruction
   *  in each spatial image (ie. each channel map) of the cube.
   */
  long xySize = this->axisDim[0] * this->axisDim[1];
  ProgressBar bar;
  bool useBar = (this->axisDim[2]>1);

  if(!this->reconExists){
    std::cout<<"  Reconstructing... ";
    if(useBar&&par.isVerbose()) bar.init(this->axisDim[2]);
    for(int z=0;z<this->axisDim[2];z++){

      if( par.isVerbose() && useBar ) bar.update((z+1));

      if(!this->par.isInMW(z)){
        float *im = new float[xySize];
        float *newIm = new float[xySize];
        for(int npix=0; npix<xySize; npix++) 
          im[npix] = this->array[z*xySize+npix];
        bool verboseFlag = this->par.isVerbose();
        this->par.setVerbosity(false);
        atrous2DReconstruct(this->axisDim[0],this->axisDim[1],
                            im,newIm,this->par);
        this->par.setVerbosity(verboseFlag);
        for(int npix=0; npix<xySize; npix++) 
          this->recon[z*xySize+npix] = newIm[npix];
        delete [] im;
        delete [] newIm;
      }
      else {
        for(int i=z*xySize; i<(z+1)*xySize; i++) 
          this->recon[i] = this->array[i];
      }
    }
    this->reconExists = true;
    if(useBar) bar.fillSpace(" All Done.");
    printSpace(22);
    std::cout << "\n";
  }
}

/////////////////////////////////////////////////////////////////////////////
void Cube::ReconCube3D()
{
  /**
   * This performs a full 3D a trous reconstruction of the cube
   */
  if(this->axisDim[2]==1) this->ReconCube2D();
  else {

    if(!this->reconExists){
      std::cout<<"  Reconstructing... "<<std::flush;
      atrous3DReconstruct(this->axisDim[0],this->axisDim[1],this->axisDim[2],
                          this->array,this->recon,this->par);
      this->reconExists = true;
      std::cout << "  All Done.";
      printSpace(22);
      std::cout << "\n";
    }

  }
}

/////////////////////////////////////////////////////////////////////////////
std::vector <Detection> searchReconArray(long *dim, float *originalArray, 
                                         float *reconArray, Param &par,
                                         StatsContainer<float> &stats)
{
  /**
   *  This searches for objects in a cube that has been reconstructed.
   *
   *  The search is conducted first in each spatial pixel (xdim*ydim 1D 
   *   searches), then in each channel image (zdim 2D searches).
   *  The searches are done on the reconstructed array, although the detected
   *   objects have fluxes drawn from the corresponding pixels of the original
   *   array.
   *
   *  \param dim Array of dimension sizes
   *  \param originalArray Original, un-reconstructed image array.
   *  \param reconArray Reconstructed image array
   *  \param par The Param set.
   *  \param stats The StatsContainer that defines what a detection is.
   *
   *  \return A vector of Detections resulting from the search.
   */
  std::vector <Detection> outputList;
  long zdim = dim[2];
  long xySize = dim[0] * dim[1];
  int num=0;
  ProgressBar bar;

  // First search --  in each spectrum.
  if(zdim > 1){
    if(par.isVerbose()){
      std::cout << "1D: ";
      bar.init(xySize);
    }

    bool *doPixel = new bool[xySize];
    // doPixel is a bool array to say whether to look in a given spectrum
    for(int npix=0; npix<xySize; npix++){
      doPixel[npix] = false;
      for(int z=0;z<zdim;z++) {
        doPixel[npix] = doPixel[npix] || 
          (!par.isBlank(originalArray[npix]) && !par.isInMW(z));
      }
      // doPixel[i] is false only when there are no good pixels in spectrum
      //  of pixel #i.
    }

    long *specdim = new long[2];
    specdim[0] = zdim; specdim[1]=1;
    Image *spectrum = new Image(specdim);
    delete [] specdim;
    spectrum->saveParam(par);
    spectrum->saveStats(stats);
    spectrum->setMinSize(par.getMinChannels());
    spectrum->pars().setBeamSize(2.); 
    // beam size: for spectrum, only neighbouring channels correlated

    for(int y=0; y<dim[1]; y++){
      for(int x=0; x<dim[0]; x++){

        int npix = y*dim[0] + x;
        if( par.isVerbose() ) bar.update(npix+1);

        if(doPixel[npix]){

          spectrum->extractSpectrum(reconArray,dim,npix);
          spectrum->removeMW(); // only works if flagMW is true
          std::vector<Scan> objlist = spectrum->spectrumDetect();
          num += objlist.size();
          for(int obj=0;obj<objlist.size();obj++){
            Detection newObject;
            // Fix up coordinates of each pixel to match original array
            for(int z=objlist[obj].getX();z<=objlist[obj].getXmax();z++) {
              newObject.pixels().addPixel(x,y,z);
            }
            newObject.setOffsets(par);
            mergeIntoList(newObject,outputList,par);
          }
        }

      }
    }

    delete spectrum;
    delete [] doPixel;

    if(par.isVerbose()) {
      bar.fillSpace("Found ");
      std::cout << num <<";" << std::flush;
    }
  }

  // Second search --  in each channel
  if(par.isVerbose()){
    std::cout << "  2D: ";
    bar.init(zdim);
  }

  num = 0;

  long *imdim = new long[2];
  imdim[0] = dim[0]; imdim[1] = dim[1];
  Image *channelImage = new Image(imdim);
  delete [] imdim;
  channelImage->saveParam(par);
  channelImage->saveStats(stats);
  channelImage->setMinSize(par.getMinPix());

  for(int z=0; z<zdim; z++){  // loop over all channels

    if( par.isVerbose() ) bar.update(z+1);

    if(!par.isInMW(z)){ 
      // purpose of this is to ignore the Milky Way channels 
      //  if we are flagging them

      channelImage->extractImage(reconArray,dim,z);
      std::vector<Object2D> objlist = channelImage->lutz_detect();
      num += objlist.size();
      for(int obj=0;obj<objlist.size();obj++){
        Detection newObject;
        newObject.pixels().addChannel(z,objlist[obj]);
        newObject.setOffsets(par);
        mergeIntoList(newObject,outputList,par);
      }
    }
    
  }

  delete channelImage;

  if(par.isVerbose()){
    bar.fillSpace("Found ");
    std::cout << num << ".\n";
  }


  return outputList;
}

/////////////////////////////////////////////////////////////////////////////
std::vector <Detection> 
searchReconArraySimple(long *dim, float *originalArray,
                       float *reconArray, Param &par,
                       StatsContainer<float> &stats)
{
  /**
   *  This searches for objects in a cube that has been reconstructed.
   *
   *  The search is conducted only in each channel image (zdim 2D
   *  searches) -- no searches in 1D are done.
   *
   *  The searches are done on the reconstructed array, although the detected
   *   objects have fluxes drawn from the corresponding pixels of the original
   *   array.
   *
   *  \param dim Array of dimension sizes
   *  \param originalArray Original, un-reconstructed image array.
   *  \param reconArray Reconstructed image array
   *  \param par The Param set.
   *  \param stats The StatsContainer that defines what a detection is.
   *
   *  \return A vector of Detections resulting from the search.
   */
  std::vector <Detection> outputList;
  long zdim = dim[2];
  int num=0;
  ProgressBar bar;
  bool useBar = (zdim>1);
  if(useBar&&par.isVerbose()) bar.init(zdim);
  
  long *imdim = new long[2];
  imdim[0] = dim[0]; imdim[1] = dim[1];
  Image *channelImage = new Image(imdim);
  delete [] imdim;
  channelImage->saveParam(par);
  channelImage->saveStats(stats);
  channelImage->setMinSize(1);

  for(int z=0; z<zdim; z++){  // loop over all channels

    if( par.isVerbose() && useBar ) bar.update(z+1);

    if(!par.isInMW(z)){ 
      // purpose of this is to ignore the Milky Way channels 
      //  if we are flagging them

      channelImage->extractImage(reconArray,dim,z);
      std::vector<Object2D> objlist = channelImage->lutz_detect();
      num += objlist.size();
      for(int obj=0;obj<objlist.size();obj++){
        Detection newObject;
        newObject.pixels().addChannel(z,objlist[obj]);
        newObject.setOffsets(par);
        mergeIntoList(newObject,outputList,par);
      }
    }
    
  }

  delete channelImage;

  if(par.isVerbose()){
    if(useBar) bar.remove();
    std::cout << "Found " << num << ".\n";
  }


  return outputList;
}