source: trunk/src/Cubes/plotting.cc @ 621

// -----------------------------------------------------------------------
// 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{

      // get the list of objects that should be plotted. Only applies to outlines and labels.
      std::vector<bool> objectChoice = this->par.getObjectChoices(this->objectList->size());

      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(unsigned int i=0;i<this->objectList->size();i++) 
            if(objectChoice[i]) this->objectList->at(i).drawBorders(0,0);
        }
        cpgsci(DUCHAMP_ID_TEXT_COLOUR);
        std::stringstream label;
        cpgslw(1);
        for(unsigned int i=0;i<this->objectList->size();i++){
          if(objectChoice[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.
  
        // get the list of objects that should be plotted. Only applies to outlines and labels.
        std::vector<bool> objectChoice = this->par.getObjectChoices(this->objectList->size());

        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(unsigned int i=0;i<this->objectList->size();i++){
          if(objectChoice[i]){
            std::vector<Voxel> this->objectList->at(i).pixels().getPixelSet();
            for(unsigned 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);

          if(!this->isBlank(pix)){ // only do this for non-blank pixels. Judge this by the first pixel of the channel.

            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(unsigned int i=0;i<this->objectList->size();i++) 
              if(objectChoice[i]) this->objectList->at(i).drawBorders(0,0);
          }
          cpgsci(DUCHAMP_ID_TEXT_COLOUR);
          std::stringstream label;
          cpgslw(1);
          for(unsigned int i=0;i<this->objectList->size();i++){
            if(objectChoice[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)
//   {
//     duchamp::plotWCSaxes(this->head.getWCS(), this->axisDim, textColour, axisColour);
//   }
  
  
  void plotWCSaxes(struct wcsprm *wcs, long *axes, 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];

    strcpy(idents[0], wcs->lngtyp);
    strcpy(idents[1], wcs->lattyp);
    strcpy(idents[2], "");
    if(strcmp(wcs->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 + axes[0]+0.5;
    trc[1] = boxYmin + axes[1]+0.5;
  
    int existingLineWidth;
    cpgqlw(&existingLineWidth);
    int existingColour;
    cpgqci(&existingColour);
    float existingSize;
    cpgqch(&existingSize);
    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 *)wcs, 
            nldprm, 256, &ic, cache, &ierr);

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



}