ReactionPlot.java

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package cedar.hepdata.webapp.pages;

import cedar.hepdata.model.*;
import cedar.hepdata.xml.*;
import cedar.hepdata.db.*;

import org.apache.tapestry5.annotations.*;
import org.apache.tapestry5.ioc.annotations.*;
import org.apache.tapestry5.services.*;

import org.hibernate.*;
//import org.hibernate.criterion.*;
import java.util.*;

import java.awt.image.BufferedImage;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.util.List;

import java.awt.Graphics2D;
import java.awt.geom.Rectangle2D;
import java.io.File;
import java.io.OutputStream;
import java.io.BufferedOutputStream;
import java.io.FileOutputStream;
 
import com.lowagie.text.Document;
import com.lowagie.text.Rectangle;
import com.lowagie.text.DocumentException;
import com.lowagie.text.pdf.PdfWriter;
import com.lowagie.text.pdf.PdfContentByte;
import com.lowagie.text.pdf.DefaultFontMapper;

import org.apache.tapestry5.ComponentResources;
import org.apache.tapestry5.Link;
import org.apache.tapestry5.MarkupWriter;
import org.apache.tapestry5.StreamResponse;
import org.apache.tapestry5.annotations.*;
import org.apache.tapestry5.ioc.annotations.*;
import org.apache.tapestry5.annotations.*;
import org.apache.tapestry5.ioc.annotations.*;
import org.apache.tapestry5.ioc.services.TypeCoercer;
import org.apache.tapestry5.dom.Element;
import org.apache.tapestry5.services.Response;
import org.apache.tapestry5.annotations.*;
import org.apache.tapestry5.ioc.annotations.*;
import org.apache.tapestry5.annotations.*;
import org.apache.tapestry5.ioc.annotations.*;
import org.jfree.chart.ChartUtilities;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.title.TextTitle;
import org.jfree.data.xy.*;

import com.lowagie.text.Document;

import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.NumberAxis;
import org.jfree.chart.axis.ValueAxis;
import org.jfree.chart.axis.LogarithmicAxis;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.xy.XYErrorRenderer;
import org.jfree.chart.renderer.xy.XYItemRenderer;
import org.jfree.data.xy.XYIntervalSeries;
import org.jfree.data.xy.XYIntervalSeriesCollection;
import org.jfree.data.Range;
import org.jfree.ui.HorizontalAlignment;


public class ReactionPlot{

    @Inject
    private RequestGlobals _reqGlobals;

    @Inject
    private org.hibernate.Session _session;

//    @Persist       
//    List <String> _saved = new ArrayList();
    
    @InjectPage
    private SavePlot saveplot;

//    private YAxis _yaxis;
    
    public String getQueryParam(String param){
       return _reqGlobals.getRequest().getParameter(param);
    }
    
    @Persist
    private String hepid="123";
    public String setHepId(){
        hepid = _reqGlobals.getRequest().getParameter("hepid");
        return "";
    }
    public String getHepId(){
       return _reqGlobals.getRequest().getParameter("hepid");
    }
    public String getDsId(){
       return _reqGlobals.getRequest().getParameter("dsid");
    }
    public String getXId(){
       return _reqGlobals.getRequest().getParameter("xid");
    }
    public String getYId(){
       return _reqGlobals.getRequest().getParameter("yid");
    }
//    static private String _pdfwidth;
//    public int getPdfWidth(){
//       _pdfwidth = _reqGlobals.getRequest().getParameter("pdfwidth");
//       System.out.println("pdfwidth is: " + _pdfwidth);
//       return Integer.parseInt(_pdfwidth);
//    }
//    static private String _pdfheight;
//    public int getPdfHeight(){
//       _pdfheight = _reqGlobals.getRequest().getParameter("pdfheight");
//       System.out.println("pdfheight is: " + _pdfheight);
//       return Integer.parseInt(_pdfheight);
//    }

    public Long getSpiresId(){
       return _paper.getSpiresId();
    }

    public String getQueryString(){
       return _reqGlobals.getRequest().getParameter("string");
    }

    public String getXscale(){
       return _reqGlobals.getRequest().getParameter("xscale");
    }
    public String getNotXscale(){
       if(_reqGlobals.getRequest().getParameter("xscale").equals("lin")){ return "log";}
       else { return "lin";}
    }

    public String getYscale(){
       return _reqGlobals.getRequest().getParameter("yscale");
    }
    public String getNotYscale(){
       if(_reqGlobals.getRequest().getParameter("yscale").equals("lin")){ return "log";}
       else { return "lin";}
    }

    public String getSys(){
       return _reqGlobals.getRequest().getParameter("sys");
    }
    public String getNotSys(){
       if(_reqGlobals.getRequest().getParameter("sys").equals("yes")){ return "no";}
       else { return "yes";}
    }

    
    static private String _pdfname;
    public String getPdfName(){
       _pdfname = _reqGlobals.getRequest().getParameter("pdfname");
//       if(_pdfname == null || _pdfname.equals("") ){
//            _pdfname = System.getProperty("user.home") + "/";
//       }
//       else if( !_pdfname.startsWith("/") ) { 
//           _pdfname = System.getProperty("user.home") + "/" + _pdfname;
//       }
       return _pdfname;
    }
    public String setPdfName(){
      _pdfname = getPdfName();
      return ""; 
    }
    static private String _pdfselect;
    public String getPdfSelect(){
       return _reqGlobals.getRequest().getParameter("pdfselect");
    }
    public String setPdfSelect(){
      _pdfselect = getPdfSelect();
      return ""; 
    }

    private String _select;
    public String getSelect() { return _select; }
    public void setSelect(String select) { _select = select; }
    public List <String> getSelects(){
        List <String> _selected= new ArrayList();
        List <String> _names = _reqGlobals.getRequest().getParameterNames();
        int size= _names.size();
        for (int i=0; i<size; i++){
            if(_names.get(i).startsWith("plot")){
                _selected.add(_names.get(i));
            }
        }
        return _selected;
    }

//    private String _save;
//    public String getSave() { return _save; }
//    public void setSave(String save) { _save = save; }
//    public List <String> getSaved(){
//      List <String> _names = _reqGlobals.getRequest().getParameterNames();
//      int size= _names.size();
//      for (int i=0; i<size; i++){
//          if(_names.get(i).startsWith("save")){
//              _saved.add(_names.get(i));
//          }
//      }
//      return _saved;
//   }
    
//    public String writePlots(){
//      List <String> _names = _reqGlobals.getRequest().getParameterNames();
//      int size= _names.size();
//       boolean save = false;
//      for (int i=0; i<size; i++){
//          if(_names.get(i).startsWith("save")){save=true;}
//      }
//      for (int i=0; i<size; i++){
//          if(_names.get(i).startsWith("plot")){
//              int i1 = _names.get(i).indexOf("d");
//              int i2 = _names.get(i).indexOf("y");
//                String ds = _names.get(i).substring(i1+2,i2);
//                String ya = _names.get(i).substring(i2+2);
//              // add to save file /tmp/hepdataplot for the moment
//              System.out.println("attempting to write to a file");
//              System.out.println("saved size is " + _saved.size() );
//              try{
//                 BufferedWriter out = new BufferedWriter(new FileWriter("/tmp/hepdataplot",true));
//                 out.write(_paper.getDataset(Integer.parseInt(ds)).getYAxis(Integer.parseInt(ya)).getAxisId() + "\n");
//                   out.close();
//              } catch(IOException e) {
//              //
//              }
//              //
//          }
//      }
//       return "";
//    }

    

    public List <YAxis> getSelectedYAxes(){
        List <YAxis> _selected = new ArrayList();
        List <String> _names = _reqGlobals.getRequest().getParameterNames();
        System.out.println(_names);
        int size= _names.size();
        for (int i=0; i<size; i++){
            if(_names.get(i).startsWith("plot")){
                int i1 = _names.get(i).indexOf("d");
                int i2 = _names.get(i).indexOf("y");
                String ds = _names.get(i).substring(i1+2,i2);
                String ya = _names.get(i).substring(i2+2);
                _selected.add(_paper.getDataset(Integer.parseInt(ds)).getYAxis(Integer.parseInt(ya)));
            }
        }
        return _selected;
    }

   public String getFirstAuthorName(){
       int n = 0;
       String _firstauthor = "";
       for (String author : _paper.getAuthors()){
         n += 1;
         if(n == 1) {_firstauthor = author;}
       }
       String _refdate = "xx";
       for (Reference reference : _paper.getReferences()){
          _refdate = reference.getDate();
       }
        int _lref = _refdate.length();
       _firstauthor = _firstauthor + " " + _refdate.substring(_lref-2,_lref);
       return _firstauthor;
   }

   public String getFirstPublished(){
       int n = 0;
       String _firstpublished = "Not Published";
       for (Reference ref : _paper.getReferences()){
           String refdesc = ref.getDescription();
           if(refdesc.startsWith("PL")  ||
              refdesc.startsWith("PR")  ||
              refdesc.startsWith("ZP")  ||
              refdesc.startsWith("EPJ") ||
              refdesc.startsWith("NC")  ||
              refdesc.startsWith("JPG") ||
              refdesc.startsWith("JHEP") ){
                 n += 1;
                 if(n == 1) { _firstpublished = refdesc;}
           }
       }
       return _firstpublished;
   }
   public String getFirstPreprint(){
       int n = 0;
       String _firstpreprint= "Not Known";
       for (Reference reference : _paper.getReferences()){
           String ref = reference.getDescription();
           if(ref.startsWith("PL")  ||
              ref.startsWith("PR")  ||
              ref.startsWith("ZP")  ||
              ref.startsWith("EPJ") ||
              ref.startsWith("NC")  ||
              ref.startsWith("JPG") ||
              ref.startsWith("JHEP") ){
            }
           else{
                 n += 1;
                 if(n == 1) { _firstpreprint = ref;}
             
           }
       }
       return _firstpreprint;
   }
   public String getFirstExperimentName(){
       int n = 0;
       String _firstexperiment = "";
       for (Experiment experiment : _paper.getExperiments()){
           n += 1;
           if(n == 1) { _firstexperiment = experiment.getName();}
       }
       return _firstexperiment;
   }
  public String getFirstInformalName(){
       int n = 0;
       String _firstinformal = "";
       for (Experiment experiment : _paper.getExperiments()){
           n += 1;
           if(n == 1) { _firstinformal = experiment.getInformalName();}
       }
       return _firstinformal;
   }
   public String getTitle(){
       return _paper.getTitle();
    }

   public String getFirstDatasetComment(){
       int n = 0;
       String _firstcomment = "";
       for ( String comment : _paper.getDataset(Integer.parseInt(getDsId())).getComments() ){
          n += 1;
          if(n == 1) { _firstcomment = comment;}
       }
       return _firstcomment;
   }

//YAxis 
    private static YAxis _yaxis;
    public YAxis getYAxis() {  return _yaxis; }
    public void setYAxis(YAxis yaxis) {  _yaxis = yaxis; }

//YAxes 
    
    private Paper _paper=null;
    public List <YAxis> getYAxes(){
       List <YAxis> _ylist = new ArrayList();
       Query q=null;
       StringBuffer b = new StringBuffer();
//       b.append("select distinct p from Paper p where p._hepdataId = ");
       b.append("select distinct p from Paper p where p._id = ");
       b.append(getHepId());
       q = _session.createQuery(b.toString());
       _paper = (Paper) q.uniqueResult();
       String yid=getYId();
       if(yid.equals("0")){yid = "1";} 
       _ylist.add(_paper.getDataset(Integer.parseInt(getDsId())).getYAxis(Integer.parseInt(yid)));
       return _ylist;
    }
// now for the plotting stuff    
    @Inject 
    private ComponentResources _resources;
  
    
    public String setTitleStringBlank(){
       titlestring="";
//       return "zeroed titlrestring";
       return "";
    }  
    
    static private int numberRun = 0;
    static private HashMap seriesMap = new HashMap();
    static private HashMap xLabelMap = new HashMap();
    static private HashMap yLabelMap = new HashMap();
    static private HashMap commentMap = new HashMap();
    static private String titlestring = "";
    static private String caption = "";

 //-----------------------------------------getChart3()
    public Link getChart3(){          
        if (numberRun > 10000) {
            numberRun=0;
        }
        int numberRunStart  = numberRun;
        XYIntervalSeries series1 = null;
        if(!getSelectedYAxes().isEmpty()){
            System.out.println("there are selected plots");
            for (YAxis ya : getSelectedYAxes()){
                numberRun +=1;
                series1 = getDataSeries(ya,Integer.parseInt(getXId()),getXscale(),getYscale(),true);
                seriesMap.put(numberRun,series1);
                xLabelMap.put(numberRun,ya.getDataset().getXAxis(1).getHeader());
                yLabelMap.put(numberRun,ya.getHeader());
            }
           
        }
        else if(getYId().equals("0")){
            for (YAxis ya : _yaxis.getDataset().getYAxes()){
                numberRun +=1;
                if(getSys().equals("yes")){
                   series1 = getDataSeries(ya,Integer.parseInt(getXId()),getXscale(),getYscale(),true);
                }
                else{
                   series1 = getDataSeries(ya,Integer.parseInt(getXId()),getXscale(),getYscale(),false);
                }     
            seriesMap.put(numberRun,series1);
            xLabelMap.put(numberRun,ya.getDataset().getXAxis(1).getHeader());
            yLabelMap.put(numberRun,ya.getHeader());
            }
        }
        else{
            numberRun +=1;
            if(getSys().equals("yes")){
                 series1 = getDataSeries(_yaxis,Integer.parseInt(getXId()),getXscale(),getYscale(),true);
            }
            else{
                 series1 = getDataSeries(_yaxis,Integer.parseInt(getXId()),getXscale(),getYscale(),false);
            }     
            seriesMap.put(numberRun,series1);
            xLabelMap.put(numberRun,_yaxis.getDataset().getXAxis(1).getHeader());
            yLabelMap.put(numberRun,_yaxis.getHeader());
        }
       int number = numberRun-numberRunStart;
       String xsize = "500";
       String ysize = "500";
//      String ysize = Integer.toString(400+number*100);
       return _resources.createActionLink("chart", false, new Object[]{xsize,ysize,numberRunStart,number,getXscale(),getYscale()});
    }

//-----------------------------------------getDataSeries(YAxis yaxis)
    public XYIntervalSeries getDataSeries(YAxis yaxis,int xid, String xscale,String yscale,Boolean systematics){
        XAxis _xaxis =  yaxis.getDataset().getXAxis(xid);
        titlestring=titlestring.concat("\n" + yaxis.getDataset().getId().toString() + "/" + yaxis.getId().toString());
        for (String comment : yaxis.getDataset().getComments()){
             if(comment.startsWith("Location:")){
                 titlestring=titlestring.concat(" - " + comment);
             }
             else{
                 caption=comment;
             }
        }
        XYIntervalSeries series = new  XYIntervalSeries(" ");
//      if(!systematics){series.setKey(caption);}
//       series.setKey(caption);
       series.setKey(yaxis.getDataset().getId().toString() + "/" + yaxis.getId().toString());
       for (int ip=1; ip<=yaxis.getPoints().size(); ip++){
            try{
            double y = yaxis.getPoint(ip).getValue();
            double eplus = 0.0;
            double eminus = 0.0;
            for (Uncertainty e : yaxis.getPoint(ip).getErrors()){
               Boolean use = true;
               if(e.getSourceType().toString().equals("systematic") && !systematics) { use = false; }
               if(use) {
                   if(e.getNormType() == ErrorNorm.PCT){
                     eplus = eplus + (y*e.getPlus()/100.0)*(y*e.getPlus()/100.0);
                     eminus = eminus + (y*e.getMinus()/100.0)*(y*e.getMinus()/100.0);
                   } 
                   else{
                     eplus = eplus + e.getPlus()*e.getPlus(); 
                     eminus = eminus - e.getMinus()*e.getMinus();
                   }
               }
            }
            eplus = Math.sqrt(eplus);
            eminus = Math.sqrt(eminus);
            double yhigh = y + eplus;
            double ylow = y - eplus;
            double x;
            double xhigh;
            double xlow;
            if(_xaxis.getBin(ip).getLowValue() != null  && _xaxis.getBin(ip).getHighValue() != null){
                x = (_xaxis.getBin(ip).getLowValue()+_xaxis.getBin(ip).getHighValue())/2;
                xlow =  _xaxis.getBin(ip).getLowValue();
                xhigh =  _xaxis.getBin(ip).getHighValue();
            }
            else{
                x = _xaxis.getBin(ip).getFocus();
                xhigh = _xaxis.getBin(ip).getFocus();
                xlow = _xaxis.getBin(ip).getFocus();
            }
            if(xscale.equals("lin") && yscale.equals("lin") )                             {series.add(x,xlow,xhigh,y,ylow,yhigh);}
            if(xscale.equals("log") && yscale.equals("lin") &&  xlow > 0.0 )              {series.add(x,xlow,xhigh,y,ylow,yhigh);}
            if(xscale.equals("lin") && yscale.equals("log") &&  ylow > 0.0 )              {series.add(x,xlow,xhigh,y,ylow,yhigh);}
            if(xscale.equals("log") && yscale.equals("log") &&  ylow > 0.0 && xlow > 0.0) {series.add(x,xlow,xhigh,y,ylow,yhigh);}
           } catch(Exception e){}
        }
        return series;
    }
        
//-----------------------------------------onChart(..................)
    public StreamResponse onChart(final int width, final int height, final int numberRunStart, int number,  String _xscale, String _yscale){
 
//        String _yscale=_yscalein;
        final XYIntervalSeriesCollection collection = new XYIntervalSeriesCollection();
        double xlow = 1000000.0;
        double xhigh = -1000000.0;
        double ylow = 1000000.0;
        double yhigh = -1000000.0;
        for (int n=1; n<=number; n++){
            
            XYIntervalSeries series = (XYIntervalSeries) seriesMap.get(numberRunStart+n);
            int nitems = series.getItemCount();
            for (int nn=0; nn<nitems; nn++){
              if(series.getXLowValue(nn) < xlow){ xlow = series.getXLowValue(nn);};     
              if(series.getXHighValue(nn) > xhigh){ xhigh = series.getXHighValue(nn);};     
              if(series.getYLowValue(nn) < ylow){ ylow = series.getYLowValue(nn);};     
              if(series.getYHighValue(nn) > yhigh){ yhigh = series.getYHighValue(nn);};     
            }
//          double ratio=yhigh/ylow;
//          if(_yscalein.equals("auto") && ratio > 100) { _yscale="log";} else {_yscale="lin";}
            seriesMap.remove(numberRunStart+n);
            collection.addSeries(series);
        }
        xlow = xlow - 0.05*(xhigh-xlow);
        xhigh = xhigh + 0.05*(xhigh-xlow);
        ylow = ylow - 0.05*(yhigh-ylow);
        yhigh = yhigh + 0.05*(yhigh-ylow);
        if(xlow == xhigh){
              xlow = 0.90*xlow;
              xhigh= 1.10*xhigh;
        }
        IntervalXYDataset data1 = collection;
 
//        final XYItemRenderer renderer1 = new XYErrorRenderer();
        final XYErrorRenderer renderer1 = new XYErrorRenderer();
        renderer1.setCapLength(3); 
        final Range rangex = new Range(xlow,xhigh);
        final Range rangey = new Range(ylow,yhigh);

        NumberAxis rangeAxisX = null;
        if(_xscale.equals("lin")){
            rangeAxisX = new NumberAxis();
            rangeAxisX.setRange(rangex);
        } else{
            LogarithmicAxis logaxistemp = new LogarithmicAxis("header");
            rangeAxisX = logaxistemp;
        }
        try {
            String xlabel = (String) xLabelMap.get(numberRunStart+1);
            rangeAxisX.setLabel(xlabel);
        } 
        catch(Exception e){          
            rangeAxisX.setLabel("xaxis label ?");
        }
//        rangeAxisX.setAutoRangeIncludesZero(false);

        NumberAxis rangeAxisY = null;        
        if(_yscale.equals("lin")) {
           rangeAxisY = new NumberAxis();
           rangeAxisY.setRange(rangey);
        } else{
           LogarithmicAxis logaxistemp = new LogarithmicAxis(_yaxis.getHeader());
//           LogarithmicAxis logaxistemp = new LogarithmicAxis("abc");
//           logaxistemp.setAllowNegativesFlag(true);
//           logaxistemp.setStrictValuesFlag(false);
//           logaxistemp.setAutoRangeNextLogFlag(true);
           rangeAxisY = logaxistemp;
        }       
        try{
            String ylabel = (String) yLabelMap.get(numberRunStart+1);
            rangeAxisY.setLabel(ylabel);
        }
        catch (Exception e){
             rangeAxisY.setLabel("yaxis label ?");
        }
        final XYPlot subplot1 = new XYPlot(data1, rangeAxisX, rangeAxisY, renderer1);
        final TextTitle title = new TextTitle(titlestring);
        title.setTextAlignment(HorizontalAlignment.LEFT);
        final JFreeChart chart = new JFreeChart(subplot1);
        chart.addSubtitle(title);
        System.out.println("pdfselect: " + _pdfselect + " pdfname: " + _pdfname);
        if(_pdfselect != null && _pdfselect.equals("yes")){
            if(_pdfname != null && !_pdfname.equals("")){
                File filename = new File(_pdfname);
                try {
                   saveChartAsPDF(filename, chart, 500, 500);
//                   saveChartAsPDF( filename, chart, Integer.parseInt(_pdfwidth), Integer.parseInt(_pdfheight) );
                } catch (IOException ie) { 
                  //
                }
            }
        }
        return new StreamResponse(){
            public String getContentType(){
                return "image/png";
            }
            public InputStream getStream() throws IOException {
                BufferedImage image  = chart.createBufferedImage(width, height);
                ByteArrayOutputStream byteArray = new ByteArrayOutputStream() ;
                ChartUtilities.writeBufferedImageAsJPEG(byteArray, image) ;
                return new ByteArrayInputStream(byteArray.toByteArray());
            }
            public void prepareResponse(Response response){}
        };
    }
    public static void saveChartAsPDF(File file,
                                      JFreeChart chart,
                                      int width,
                                      int height) throws IOException{
       OutputStream out = new BufferedOutputStream(new FileOutputStream(file));
       writeChartAsPDF(out, chart, width, height);
       out.close();
    }
    public static void writeChartAsPDF(OutputStream out,
                                       JFreeChart chart,
                                       int width, int height) throws IOException{
       Rectangle pagesize = new Rectangle(width,height);
       Document document = new Document(pagesize, 50, 50, 50, 50);
       try {
           PdfWriter writer = PdfWriter.getInstance(document, out);
           document.addAuthor("JFreeChart");
           document.open();
           PdfContentByte cb = writer.getDirectContent();
           Graphics2D g2 = cb.createGraphics(width, height);
           Rectangle2D r2D = new Rectangle2D.Double(0, 0, width, height);
           chart.draw(g2, r2D, null);
           g2.dispose();
       }
       catch(DocumentException de){
          System.err.println(de.getMessage());
       }
       document.close();
    }
   
//---------------------------------------end of onChart(..................)

    private Class nextPage;
    Object onSubmitFromSavePlot()
    {
        return nextPage;
    }
    @OnEvent(component="submit2Button")
    void onsubmitFromSavePage()
    {
        this.setHepId(); 
        saveplot.setHepId(getHepId());
        saveplot.setDsId(getDsId());
        saveplot.setYId(getYId());
        saveplot.setXId(getXId());
        saveplot.setYscale(getYscale());
        saveplot.setXscale(getXscale());
        saveplot.setSys(getSys());
        saveplot.setQueryString(getQueryString());
        nextPage=SavePlot.class;
    }
        
      
}

---