source: trunk/src/Cubes/outputSpectra.cc @ 326

// -----------------------------------------------------------------------
// outputSpectra.cc: Print the spectra of the detected objects.
// -----------------------------------------------------------------------
// 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 <iostream>
#include <iomanip>
#include <sstream>
#include <string>
#include <cpgplot.h>
#include <math.h>
#include <wcs.h>
#include <param.hh>
#include <duchamp.hh>
#include <fitsHeader.hh>
#include <PixelMap/Object3D.hh>
#include <Cubes/cubes.hh>
#include <Cubes/plots.hh>
#include <Utils/utils.hh>
#include <Utils/mycpgplot.hh>

using namespace mycpgplot;
using namespace PixelInfo;

void getSmallVelRange(Detection &obj, FitsHeader head, float *minvel, float *maxvel);
void getSmallZRange(Detection &obj, float *minz, float *maxz);

void Cube::outputSpectra()
{
  /** 
   * The way to print out the spectra of the detected objects.
   * Make use of the SpectralPlot class in plots.h, which sizes everything 
   *   correctly.
   * Main choice is whether to use the peak pixel, in which case the 
   *  spectrum is just that of the peak pixel, or the sum, where the 
   *  spectrum is summed over all spatial pixels that are in the object.
   * If a reconstruction has been done, that spectrum is plotted in red.
   * The limits of the detection are marked in blue.
   * A 0th moment map of the detection is also plotted, with a scale bar 
   *  indicating the spatial scale.
   */

  if(this->fullCols.size()==0) this->setupColumns(); 
  // in case cols haven't been set -- need the precisions for printing values.

  std::string spectrafile = this->par.getSpectraFile() + "/vcps";
  Plot::SpectralPlot newplot;
  if(newplot.setUpPlot(spectrafile.c_str())>0) {

    for(int nobj=0;nobj<this->objectList->size();nobj++){
      // for each object in the cube:
      this->plotSpectrum(this->objectList->at(nobj),newplot);
      
    }// end of loop over objects.

    cpgclos();
  }
}

void Cube::plotSpectrum(Detection obj, Plot::SpectralPlot &plot)
{
  /** 
   * The way to print out the spectrum of a Detection.
   * Makes use of the SpectralPlot class in plots.hh, which sizes 
   *  everything correctly.
   *
   * The main choice for the user is whether to use the peak pixel, in
   * which case the spectrum is just that of the peak pixel, or the
   * sum, where the spectrum is summed over all spatial pixels that
   * are in the object.
   *
   * If a reconstruction has been done, that spectrum is plotted in
   * red, and if a baseline has been calculated that is also shown, in
   * yellow.  The spectral limits of the detection are marked in blue.
   * A 0th moment map of the detection is also plotted, with a scale
   * bar indicating the spatial size.
   *
   * \param obj The Detection to be plotted.
   * \param plot The PGPLOT device to plot the spectrum on.
   */

  long xdim = this->axisDim[0];
  long ydim = this->axisDim[1];
  long zdim = this->axisDim[2];
  float beam = this->par.getBeamSize();

  obj.calcFluxes(this->array, this->axisDim);

  double minMWvel,maxMWvel,xval,yval,zval;
  xval = double(obj.getXcentre());
  yval = double(obj.getYcentre());
  if(this->par.getFlagMW()){
    zval = double(this->par.getMinMW());
    minMWvel = this->head.pixToVel(xval,yval,zval);
    zval = double(this->par.getMaxMW());
    maxMWvel = this->head.pixToVel(xval,yval,zval);
  }

  float *specx  = new float[zdim];
  float *specy  = new float[zdim];
  for(int i=0;i<zdim;i++) specy[i] = 0.;
  float *specy2 = new float[zdim];
  for(int i=0;i<zdim;i++) specy2[i] = 0.;
  float *base   = new float[zdim];
  for(int i=0;i<zdim;i++) base[i] = 0.;

  for(int i=0;i<zdim;i++) specy[i] = 0.;
  if(this->par.getFlagATrous())  
    for(int i=0;i<zdim;i++) specy2[i] = 0.;
    
  if(this->head.isWCS())
    for(zval=0;zval<zdim;zval++) 
      specx[int(zval)] = this->head.pixToVel(xval,yval,zval);
  else 
    for(zval=0;zval<zdim;zval++) specx[int(zval)] = zval;

  std::string fluxLabel = "Flux";

  if(this->par.getSpectralMethod()=="sum"){
    fluxLabel = "Integrated " + fluxLabel;
    if(this->head.isWCS()) 
      fluxLabel += " ["+this->head.getIntFluxUnits()+"]";
    bool *done = new bool[xdim*ydim]; 
    for(int i=0;i<xdim*ydim;i++) done[i]=false;
    std::vector<Voxel> voxlist = obj.pixels().getPixelSet();
    for(int pix=0;pix<voxlist.size();pix++){
      int pos = voxlist[pix].getX() + xdim * voxlist[pix].getY();
      if(!done[pos]){
        done[pos] = true;
        for(int z=0;z<zdim;z++){
          if(!(this->isBlank(pos+z*xdim*ydim))){
            specy[z] += this->array[pos + z*xdim*ydim] / beam;
            if(this->reconExists)
              specy2[z] += this->recon[pos + z*xdim*ydim] / beam;
            if(this->par.getFlagBaseline())
              base[z] += this->baseline[pos + z*xdim*ydim] / beam;
          }         
        }
      }
    }
    delete [] done;
  }
  else {// if(par.getSpectralMethod()=="peak"){
    fluxLabel = "Peak " + fluxLabel;
    if(this->head.isWCS()) fluxLabel += " ["+this->head.getFluxUnits()+"]";
    int pos = obj.getXPeak() + xdim*obj.getYPeak();
    for(int z=0;z<zdim;z++){
      specy[z] = this->array[pos + z*xdim*ydim];
      if(this->reconExists) 
        specy2[z] = this->recon[pos + z*xdim*ydim];
      if(this->par.getFlagBaseline()) 
        base[z] = this->baseline[pos + z*xdim*ydim];
    }
  }
    
  float vmax,vmin,width;
  vmax = vmin = specx[0];
  for(int i=1;i<zdim;i++){
    if(specx[i]>vmax) vmax=specx[i];
    if(specx[i]<vmin) vmin=specx[i];
  }
  
  float max,min;
  int loc=0;
  if(this->par.getMinMW()>0) max = min = specy[0];
  else max = min = specx[this->par.getMaxMW()+1];
  for(int i=0;i<zdim;i++){
    if(!this->par.isInMW(i)){
      if(specy[i]>max) max=specy[i];
      if(specy[i]<min){
        min=specy[i];
        loc = i;
      }
    }
  }
  // widen the ranges slightly so that the top & bottom & edges don't 
  // lie on the axes.
  width = max - min;
  max += width * 0.05;
  min -= width * 0.05;
  width = vmax -vmin;
  vmax += width * 0.01;
  vmin -= width * 0.01;

  // now plot the resulting spectrum
  std::string label;
  if(this->head.isWCS()){
    label = this->head.getSpectralDescription() + " [" + 
      this->head.getSpectralUnits() + "]";
    plot.gotoHeader(label);
  }
  else plot.gotoHeader("Spectral pixel value");

  if(this->head.isWCS()){
    label = obj.outputLabelWCS();
    plot.firstHeaderLine(label);
    label = obj.outputLabelFluxes();
    plot.secondHeaderLine(label);
  }
  label = obj.outputLabelWidths();
  plot.thirdHeaderLine(label);
  label = obj.outputLabelPix();
  plot.fourthHeaderLine(label);
    
  plot.gotoMainSpectrum(vmin,vmax,min,max,fluxLabel);
  cpgline(zdim,specx,specy);
  if(this->par.getFlagBaseline()){
    cpgsci(DUCHAMP_BASELINE_SPECTRA_COLOUR);
    cpgline(zdim,specx,base);
    cpgsci(FOREGND);
  }
  if(this->reconExists){
    cpgsci(DUCHAMP_RECON_SPECTRA_COLOUR);
    cpgline(zdim,specx,specy2);    
    cpgsci(FOREGND);
  }
  if(this->par.getFlagMW()) plot.drawMWRange(minMWvel,maxMWvel);
  if(this->head.isWCS()) plot.drawVelRange(obj.getVelMin(),obj.getVelMax());
  else plot.drawVelRange(obj.getZmin(),obj.getZmax());

  /**************************/
  // ZOOM IN SPECTRALLY ON THE DETECTION.

  float minvel,maxvel;
  if(this->head.isWCS()) getSmallVelRange(obj,this->head,&minvel,&maxvel);
  else getSmallZRange(obj,&minvel,&maxvel);

  // Find new max & min flux values
  std::swap(max,min);
  int ct = 0;
  for(int i=0;i<zdim;i++){
    if((!this->par.isInMW(i))&&(specx[i]>=minvel)&&(specx[i]<=maxvel)){
      ct++;
      if(specy[i]>max) max=specy[i];
      if(specy[i]<min) min=specy[i];
    }
  }
  // widen the flux range slightly so that the top & bottom don't lie
  // on the axes.
  width = max - min;
  max += width * 0.05;
  min -= width * 0.05;

  plot.gotoZoomSpectrum(minvel,maxvel,min,max);
  cpgline(zdim,specx,specy);
  if(this->par.getFlagBaseline()){
    cpgsci(DUCHAMP_BASELINE_SPECTRA_COLOUR);
    cpgline(zdim,specx,base);
    cpgsci(FOREGND);
  }
  if(this->reconExists){
    cpgsci(DUCHAMP_RECON_SPECTRA_COLOUR);
    cpgline(zdim,specx,specy2);    
    cpgsci(FOREGND);
  }
  if(this->par.getFlagMW()) plot.drawMWRange(minMWvel,maxMWvel);
  if(this->head.isWCS()) plot.drawVelRange(obj.getVelMin(),obj.getVelMax());
  else plot.drawVelRange(obj.getZmin(),obj.getZmax());
    
  /**************************/

  // DRAW THE MOMENT MAP OF THE DETECTION -- SUMMED OVER ALL CHANNELS
  plot.gotoMap();
  this->drawMomentCutout(obj);

  delete [] specx;
  delete [] specy;
  delete [] specy2;
  delete [] base;
  
}


void getSmallVelRange(Detection &obj, FitsHeader head, 
                      float *minvel, float *maxvel)
{
  /** 
   *  Routine to calculate the velocity range for the zoomed-in region.
   *  This range should be the maximum of 20 pixels, or 3x the wdith of 
   *   the detection.
   *  Need to :
   *      Calculate pixel width of a 3x-detection-width region.
   *      If smaller than 20, calculate velocities of central vel +- 10 pixels
   *      If not, use the 3x-detection-width
   *  Range returned via "minvel" and "maxvel" parameters.
   *  \param obj Detection under examination.
   *  \param head FitsHeader, containing the WCS information.
   *  \param minvel Returned value of minimum velocity
   *  \param maxvel Returned value of maximum velocity
   */

  double *pixcrd = new double[3];
  double *world  = new double[3];
  float minpix,maxpix;
  // define new velocity extrema 
  //    -- make it 3x wider than the width of the detection.
  *minvel = 0.5*(obj.getVelMin()+obj.getVelMax()) - 1.5*obj.getVelWidth();
  *maxvel = 0.5*(obj.getVelMin()+obj.getVelMax()) + 1.5*obj.getVelWidth();
  // Find velocity range in number of pixels:
  world[0] = obj.getRA();
  world[1] = obj.getDec();
  world[2] = head.velToSpec(*minvel);
  head.wcsToPix(world,pixcrd);
  minpix = pixcrd[2];
  world[2] = head.velToSpec(*maxvel);
  head.wcsToPix(world,pixcrd);
  maxpix = pixcrd[2];
  if(maxpix<minpix) std::swap(maxpix,minpix);
    
  if((maxpix - minpix + 1) < 20){
    pixcrd[0] = double(obj.getXcentre());
    pixcrd[1] = double(obj.getYcentre());
    pixcrd[2] = obj.getZcentre() - 10.;
    head.pixToWCS(pixcrd,world);
    //    *minvel = setVel_kms(wcs,world[2]);
    *minvel = head.specToVel(world[2]);
    pixcrd[2] = obj.getZcentre() + 10.;
    head.pixToWCS(pixcrd,world);
    //     *maxvel = setVel_kms(wcs,world[2]);
    *maxvel = head.specToVel(world[2]);
    if(*maxvel<*minvel) std::swap(*maxvel,*minvel);
  }
  delete [] pixcrd;
  delete [] world;

}

void getSmallZRange(Detection &obj, float *minz, float *maxz)
{
  /** 
   *  Routine to calculate the pixel range for the zoomed-in spectrum.
   *  This range should be the maximum of 20 pixels, or 3x the width 
   *   of the detection.
   *  Need to :
   *      Calculate pixel width of a 3x-detection-width region.
   *       If smaller than 20, use central pixel +- 10 pixels
   *  Range returned via "minz" and "maxz" parameters.
   *  \param obj Detection under examination.
   *  \param minz Returned value of minimum z-pixel coordinate
   *  \param maxz Returned value of maximum z-pixel coordinate
   */

  *minz = 2.*obj.getZmin() - obj.getZmax();
  *maxz = 2.*obj.getZmax() - obj.getZmin();
    
  if((*maxz - *minz + 1) < 20){
    *minz = obj.getZcentre() - 10.;
    *maxz = obj.getZcentre() + 10.;
  }

}