source: tags/release-1.1.7/src/Cubes/plotting.cc @ 533

// -----------------------------------------------------------------------
// plotting.cc: Plot the moment map and detection maps, showing the
//              location 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 <math.h>
#include <cpgplot.h>
#include <wcslib/cpgsbox.h>
#include <wcslib/pgwcsl.h>
#include <wcslib/wcs.h>
#include <duchamp/duchamp.hh>
#include <duchamp/param.hh>
#include <duchamp/fitsHeader.hh>
#include <duchamp/PixelMap/Object3D.hh>
#include <duchamp/Cubes/cubes.hh>
#include <duchamp/Cubes/cubeUtils.hh>
#include <duchamp/Cubes/plots.hh>
#include <duchamp/Utils/utils.hh>
#include <duchamp/Utils/mycpgplot.hh>

using namespace mycpgplot;
using namespace PixelInfo;

namespace duchamp
{

void Cube::plotDetectionMap(std::string pgDestination)
{
  ///  @details
  ///  Creates a map of the spatial locations of the detections, which is 
  ///   written to the PGPlot device given by pgDestination.
  ///  The map is done in greyscale, where the scale indicates the number of 
  ///   velocity channels that each spatial pixel is detected in.
  ///  The boundaries of each detection are drawn, and each object is numbered
  ///   (to match the output list and spectra).
  ///  The primary grid scale is pixel coordinate, and if the WCS is valid, 
  ///   the correct WCS gridlines are also drawn.
  /// \param pgDestination The PGPLOT device to be opened, in the typical PGPLOT format.

  // These are the minimum values for the X and Y ranges of the box drawn by 
  //   pgplot (without the half-pixel difference).
  // The -1 is necessary because the arrays we are dealing with start at 0 
  //  index, while the ranges given in the subsection start at 1... 
  float boxXmin = this->par.getXOffset() - 1;
  float boxYmin = this->par.getYOffset() - 1;

  long xdim=this->axisDim[0];
  long ydim=this->axisDim[1];
  Plot::ImagePlot newplot;
  int flag = newplot.setUpPlot(pgDestination.c_str(),float(xdim),float(ydim));

  if(flag<=0){
    duchampError("Plot Detection Map", 
                 "Could not open PGPlot device " + pgDestination + ".\n");
  }
  else{

    newplot.makeTitle(this->pars().getImageFile());

    newplot.drawMapBox(boxXmin+0.5,boxXmin+xdim+0.5,
                       boxYmin+0.5,boxYmin+ydim+0.5,
                       "X pixel","Y pixel");

    //     if(this->objectList.size()>0){ 
    // if there are no detections, there will be nothing to plot here

    float *detectMap = new float[xdim*ydim];
    int maxNum = this->detectMap[0];
    detectMap[0] = float(maxNum);
    for(int pix=1;pix<xdim*ydim;pix++){
      detectMap[pix] = float(this->detectMap[pix]);  
      if(this->detectMap[pix] > maxNum)  maxNum = this->detectMap[pix];
    }

    if(maxNum>0){ // if there are no detections, it will be 0.

      maxNum = 5 * ((maxNum-1)/5 + 1);  // move to next multiple of 5

      float tr[6] = {boxXmin,1.,0.,boxYmin,0.,1.};
      cpggray(detectMap,xdim,ydim,1,xdim,1,ydim,maxNum,0,tr);  
        
      //       delete [] detectMap;
      cpgbox("bcnst",0.,0,"bcnst",0.,0);
      cpgsch(1.5);
      cpgwedg("rg",3.2,2,maxNum,0,"Number of detected channels");
    }
    delete [] detectMap;
      
    drawBlankEdges(this->array,this->axisDim[0],this->axisDim[1],this->par);
      
    if(this->head.isWCS()) this->plotWCSaxes();
  
    if(this->objectList->size()>0){ 
      // now show and label each detection, drawing over the WCS lines.

      cpgsch(1.0);
      cpgslw(2);    
      float xoff=0.;
      float yoff=newplot.cmToCoord(0.5);
      if(this->par.drawBorders()){
        cpgsci(DUCHAMP_OBJECT_OUTLINE_COLOUR);
        for(int i=0;i<this->objectList->size();i++) 
          this->objectList->at(i).drawBorders(0,0);
      }
      cpgsci(DUCHAMP_ID_TEXT_COLOUR);
      std::stringstream label;
      cpgslw(1);
      for(int i=0;i<this->objectList->size();i++){
        cpgpt1(this->par.getXOffset()+this->objectList->at(i).getXPeak(), 
               this->par.getYOffset()+this->objectList->at(i).getYPeak(), 
               CROSS);
        label.str("");
        label << this->objectList->at(i).getID();
        cpgptxt(this->par.getXOffset()+this->objectList->at(i).getXPeak()-xoff, 
                this->par.getYOffset()+this->objectList->at(i).getYPeak()-yoff, 
                0, 0.5, label.str().c_str());
      }

    }

    cpgclos();
  }
}

/*********************************************************/

void Cube::plotMomentMap(std::string pgDestination)
{
  ///  @details
  ///  Uses the other function
  ///  Cube::plotMomentMap(std::vector<std::string>) to plot the moment
  ///  map.
  /// \param pgDestination The PGPLOT device that the map is to be written to.

  std::vector<std::string> devicelist;
  devicelist.push_back(pgDestination);
  this->plotMomentMap(devicelist);
}

/*********************************************************/

void Cube::plotMomentMap(std::vector<std::string> pgDestination)
{
  ///  @details
  ///  Creates a 0th moment map of the detections, which is written to each
  ///   of the PGPlot devices mentioned in pgDestination.
  ///  The advantage of this function is that the map is only calculated once,
  ///   even if multiple maps are required.
  ///  The map is done in greyscale, where the scale indicates the integrated 
  ///   flux at each spatial pixel.
  ///  The boundaries of each detection are drawn, and each object is numbered
  ///   (to match the output list and spectra).
  ///  The primary grid scale is pixel coordinate, and if the WCS is valid, 
  ///   the correct WCS gridlines are also drawn.
  /// \param pgDestination A set of PGPLOT devices that are to be
  /// opened, each in the typical PGPLOT format.

  float boxXmin = this->par.getXOffset() - 1;
  float boxYmin = this->par.getYOffset() - 1;

  long xdim=this->axisDim[0];
  long ydim=this->axisDim[1];
  long zdim=this->axisDim[2];

  int numPlots = pgDestination.size();
  std::vector<Plot::ImagePlot> plotList(numPlots);
  std::vector<int> plotFlag(numPlots,0);
  std::vector<bool> doPlot(numPlots,false);
  bool plotNeeded = false;

  for(int i=0;i<numPlots;i++){
    
    plotFlag[i] = plotList[i].setUpPlot(pgDestination[i],
                                        float(xdim),float(ydim));
       
    if(plotFlag[i]<=0) duchampError("Plot Moment Map", 
                                    "Could not open PGPlot device " 
                                    + pgDestination[i] + ".\n");
    else{
      doPlot[i] = true;
      plotNeeded = true;
    }

  }

  if(plotNeeded){

    if(this->objectList->size()==0){ 
      // if there are no detections, we plot an empty field.

      for(int iplot=0; iplot<numPlots; iplot++){
        plotList[iplot].goToPlot();
        plotList[iplot].makeTitle(this->pars().getImageFile());
        
        plotList[iplot].drawMapBox(boxXmin+0.5,boxXmin+xdim+0.5,
                                   boxYmin+0.5,boxYmin+ydim+0.5,
                                   "X pixel","Y pixel");
        
        drawBlankEdges(this->array,this->axisDim[0],this->axisDim[1],this->par);
        
        if(this->head.isWCS()) this->plotWCSaxes();
      }

    }
    else {  
      // if there are some detections, do the calculations first before
      //  plotting anything.
  
      for(int iplot=0; iplot<numPlots; iplot++){
        // Although plot the axes so that the user knows something is 
        //  being done (at least, they will if there is an /xs plot)
        plotList[iplot].goToPlot();
        plotList[iplot].makeTitle(this->pars().getImageFile());
    
        plotList[iplot].drawMapBox(boxXmin+0.5,boxXmin+xdim+0.5,
                                   boxYmin+0.5,boxYmin+ydim+0.5,
                                   "X pixel","Y pixel");
        
        if(pgDestination[iplot]=="/xs") 
          cpgptxt(boxXmin+0.5+xdim/2., boxYmin+0.5+ydim/2., 0, 0.5,
                  "Calculating map...");
      }

      bool *isObj = new bool[xdim*ydim*zdim];
      for(int i=0;i<xdim*ydim*zdim;i++) isObj[i] = false;
      for(int i=0;i<this->objectList->size();i++){
        std::vector<Voxel> voxlist = 
          this->objectList->at(i).pixels().getPixelSet();
        for(int p=0;p<voxlist.size();p++){
          int pixelpos = voxlist[p].getX() + xdim*voxlist[p].getY() + 
            xdim*ydim*voxlist[p].getZ();
          isObj[pixelpos] = true;
        }
      }

      float *momentMap = new float[xdim*ydim];
      // Initialise to zero
      for(int i=0;i<xdim*ydim;i++) momentMap[i] = 0.;

      // if we are looking for negative features, we need to invert the 
      //  detected pixels for the moment map
      float sign = 1.;
      if(this->pars().getFlagNegative()) sign = -1.;

      float deltaVel;
      double x,y;

      double *zArray  = new double[zdim];
      for(int z=0; z<zdim; z++) zArray[z] = double(z);
    
      double *world  = new double[zdim];

      for(int pix=0; pix<xdim*ydim; pix++){ 

        x = double(pix%xdim);
        y = double(pix/xdim);

        delete [] world;
        world = this->head.pixToVel(x,y,zArray,zdim);
      
        for(int z=0; z<zdim; z++){      
          int pos =  z*xdim*ydim + pix;  // the voxel in the cube
          if(isObj[pos]){ // if it's an object pixel...
            // delta-vel is half the distance between adjacent channels.
            // if at end, then just use 0-1 or (zdim-1)-(zdim-2) distance
            if(z==0){
              if(zdim==1) deltaVel=1.; // pathological case -- if 2D image.
              else deltaVel = world[z+1] - world[z];
            }
            else if(z==(zdim-1)) deltaVel = world[z-1] - world[z];
            else deltaVel = (world[z+1] - world[z-1]) / 2.;

            momentMap[pix] += sign * this->array[pos] * fabs(deltaVel);

          }
        }

      }
    
      delete [] world;
      delete [] zArray;

      float *temp = new float[xdim*ydim];
      int count=0;
      for(int i=0;i<xdim*ydim;i++) {
        if(momentMap[i]>0.){
          bool addPixel = false;
          for(int z=0;z<zdim;z++) addPixel = addPixel || isObj[z*xdim*ydim+i];
          if(addPixel) temp[count++] = log10(momentMap[i]);
        }
      }
      float z1,z2;
      z1 = z2 = temp[0];
      for(int i=1;i<count;i++){
        if(temp[i]<z1) z1 = temp[i];
        if(temp[i]>z2) z2 = temp[i];
      }
      delete [] temp;

      for(int i=0;i<xdim*ydim;i++) {
        bool addPixel = false;
        for(int z=0;z<zdim;z++) addPixel = addPixel || isObj[z*xdim*ydim+i];
        addPixel = addPixel && (momentMap[i]>0.);
        if(!addPixel) momentMap[i] = z1-1.;
        else momentMap[i] = log10(momentMap[i]);
      }

      delete [] isObj;

      // Have now done all necessary calculations for moment map.
      // Now produce the plot

      for(int iplot=0; iplot<numPlots; iplot++){
        plotList[iplot].goToPlot();
      
        float tr[6] = {boxXmin,1.,0.,boxYmin,0.,1.};
        cpggray(momentMap,xdim,ydim,1,xdim,1,ydim,z2,z1,tr);
        cpgbox("bcnst",0.,0,"bcnst",0.,0);
        cpgsch(1.5);
        std::string wedgeLabel = "Integrated Flux ";
        if(this->par.getFlagNegative()) 
          wedgeLabel = "-1. " + times + " " + wedgeLabel;
        if(this->head.isWCS())
          wedgeLabel += "[" + this->head.getIntFluxUnits() + "]";
        else wedgeLabel += "[" + this->head.getFluxUnits() + "]";
        cpgwedglog("rg",3.2,2,z2,z1,wedgeLabel.c_str());


        drawBlankEdges(this->array,this->axisDim[0],this->axisDim[1],this->par);

        if(this->head.isWCS()) this->plotWCSaxes();
  
        // now show and label each detection, drawing over the WCS lines.
        cpgsch(1.0);
        cpgslw(2);
        float xoff=0.;
        float yoff=plotList[iplot].cmToCoord(0.5);
        if(this->par.drawBorders()){
          cpgsci(DUCHAMP_OBJECT_OUTLINE_COLOUR);
          for(int i=0;i<this->objectList->size();i++) 
            this->objectList->at(i).drawBorders(0,0);
        }
        cpgsci(DUCHAMP_ID_TEXT_COLOUR);
        std::stringstream label;
        cpgslw(1);
        for(int i=0;i<this->objectList->size();i++){
          cpgpt1(this->par.getXOffset()+this->objectList->at(i).getXPeak(), 
                 this->par.getYOffset()+this->objectList->at(i).getYPeak(),
                 CROSS);
          label.str("");
          label << this->objectList->at(i).getID();
          cpgptxt(this->par.getXOffset()+this->objectList->at(i).getXPeak()-xoff,
                  this->par.getYOffset()+this->objectList->at(i).getYPeak()-yoff,
                  0, 0.5, label.str().c_str());
        }

      } // end of iplot loop over number of devices

      delete [] momentMap;

    } // end of else (from if(numdetections==0) )

  
    for(int iplot=0; iplot<numPlots; iplot++){
      plotList[iplot].goToPlot();
      cpgclos();
    }

  }
  
}

/*********************************************************/


void Cube::plotWCSaxes(int textColour, int axisColour)
{
  /// @details
  ///  A front-end to the cpgsbox command, to draw the gridlines for the WCS 
  ///    over the current plot.
  ///  Lines are drawn in dark green over the full plot area, and the axis 
  ///    labels are written on the top and on the right hand sides, so as not 
  ///    to conflict with other labels.
  ///  \param textColour The colour index to use for the text labels --
  ///  defaults to duchamp::DUCHAMP_ID_TEXT_COLOUR 
  ///  \param axisColour The colour index to use for the axes --
  ///  defaults to duchamp::DUCHAMP_WCS_AXIS_COLOUR

  float boxXmin=0,boxYmin=0;

  char idents[3][80], opt[2], nlcprm[1];

  struct wcsprm *tempwcs;
  tempwcs = this->head.getWCS();

  strcpy(idents[0], tempwcs->lngtyp);
  strcpy(idents[1], tempwcs->lattyp);
  strcpy(idents[2], "");
  if(strcmp(tempwcs->lngtyp,"RA")==0) opt[0] = 'G';
  else opt[0] = 'D';
  opt[1] = 'E';

  float  blc[2], trc[2];
  //   float  scl; // --> unused here.
  blc[0] = boxXmin + 0.5;
  blc[1] = boxYmin + 0.5;
  trc[0] = boxXmin + this->axisDim[0]+0.5;
  trc[1] = boxYmin + this->axisDim[1]+0.5;
  
  int existingLineWidth;
  cpgqlw(&existingLineWidth);
  int existingColour;
  cpgqci(&existingColour);
  float existingSize;
  cpgqch(&existingSize);
  //  cpgsci(DUCHAMP_ID_TEXT_COLOUR);
  cpgsci(textColour);
  cpgsch(0.8);
  int    c0[7], ci[7], gcode[2], ic, ierr;
  for(int i=0;i<7;i++) c0[i] = -1;
  /* define the WCS axes colour */
  setWCSGreen();

  gcode[0] = 2;  // type of grid to draw: 0=none, 1=ticks only, 2=full grid
  gcode[1] = 2;

  double cache[257][4], grid1[9], grid2[9], nldprm[8];
  grid1[0] = 0.0;  
  grid2[0] = 0.0;

  // Draw the celestial grid with no intermediate tick marks.
  // Set LABCTL=2100 to write 1st coord on top, and 2nd on right

  //Colour indices used by cpgsbox: make it all the same colour for thin 
  // line case.
  ci[0] = axisColour; // grid lines, coord 1
  ci[1] = axisColour; // grid lines, coord 2
  ci[2] = axisColour; // numeric labels, coord 1
  ci[3] = axisColour; // numeric labels, coord 2
  ci[4] = axisColour; // axis annotation, coord 1
  ci[5] = axisColour; // axis annotation, coord 2
  ci[6] = axisColour; // title

  cpgsbox(blc, trc, idents, opt, 2100, 0, ci, gcode, 0.0, 0, grid1, 0, grid2,
          0, pgwcsl_, 1, WCSLEN, 1, nlcprm, (int *)tempwcs, 
          nldprm, 256, &ic, cache, &ierr);

  wcsfree(tempwcs);
  free(tempwcs);

  cpgsci(existingColour);
  cpgsch(existingSize);
  cpgslw(existingLineWidth);
}

}