Exemple #1
0
 /**
  * ** Encodes the specified DBRecordKyes into XML and writes it to ** a specified PrintWriter
  * ** @param out The PrintWriter ** @param dbrk The list of DBRecordKeys
  */
 public static void printXML(PrintWriter out, DBRecordKey... dbrk) {
   if (out != null) {
     out.write("<" + DBFactory.TAG_RecordKeys + ">\n");
     for (int i = 0; i < dbrk.length; i++) {
       dbrk[i].printXML(out, 4);
     }
     out.write("</" + DBFactory.TAG_RecordKeys + ">\n");
     out.flush();
   }
 }
  public void handlePageBody(PageContext pc) throws ServletException, IOException {
    ServletContext context = pc.getServletContext();
    Document doc = null;
    try {
      DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
      DocumentBuilder builder = factory.newDocumentBuilder();
      doc = builder.newDocument();
    } catch (Exception e) {
      throw new ServletException(e);
    }

    Element rootElem = doc.createElement("xaf");
    doc.appendChild(rootElem);

    try {
      DatabaseContextFactory.createCatalog(pc, rootElem);
      transform(pc, doc, ACE_CONFIG_ITEM_PROPBROWSERXSL);
    } catch (NamingException e) {
      PrintWriter out = pc.getResponse().getWriter();
      out.write(e.toString());
      e.printStackTrace(out);
    }
  }
  public static void main(String[] args) {
    //////////////////////////
    // The values in following 4 lines should be user input
    int startPos = 200;
    int endPos = 1000;
    int totalNumPixel = 1044;
    double threshhold = 0.0001;
    /////////////////////////
    int numPixel = endPos - startPos;
    double wavelength[] = new double[totalNumPixel];
    double photonCount[] = new double[totalNumPixel];
    double SpecNoBk[] = new double[numPixel];
    double ThisSpectrum[] = new double[numPixel];
    double ThisXaxis[] = new double[numPixel];
    double Po[] = new double[numPixel];
    double Re[] = new double[numPixel];
    double P[] = new double[6];
    double Re2[] = new double[numPixel - 1];
    double mySUM[] = new double[numPixel];
    int ind[];
    double DEV;
    double prevDEV;
    Connection connection = null;
    Statement stmt = null;
    String pattern = "##.##";

    try {
      Scanner in = new Scanner(new FileReader(args[0]));
      int i = 0;
      while (in.hasNextDouble()) {
        wavelength[i] = in.nextDouble();
        photonCount[i] = in.nextDouble();
        ++i;
      }
    } catch (FileNotFoundException e) {
      e.printStackTrace();
    }

    ThisSpectrum = Arrays.copyOfRange(photonCount, startPos, endPos);
    ThisXaxis = Arrays.copyOfRange(wavelength, startPos, endPos);
    final WeightedObservedPoints obs = new WeightedObservedPoints();

    for (int i = 0; i < numPixel; i++) {
      obs.add(ThisXaxis[i], ThisSpectrum[i]);
    }

    final PolynomialCurveFitter fitter = PolynomialCurveFitter.create(5);
    P = fitter.fit(obs.toList());
    Polyval pVal = new Polyval(P, ThisXaxis, numPixel);
    Po = pVal.evl();

    for (int i = 0; i < numPixel; i++) {
      Re[i] = ThisSpectrum[i] - Po[i];
    }

    for (int i = 0; i < numPixel - 1; i++) {
      Re2[i] = Re[i + 1] - Re[i];
    }

    DEV = Math.sqrt(StatUtils.populationVariance(Re2, 0, Re2.length));
    for (int i = 0; i < numPixel; i++) {
      mySUM[i] = Po[i] + DEV;
    }

    int jj = 0; // jj is the length of points to be removed
    for (int i = 0; i < numPixel; i++) {
      if (ThisSpectrum[i] > mySUM[i]) {
        jj++;
        ;
      }
    }
    ind = new int[jj];

    int jjj = 0;
    for (int i = 0; i < numPixel; i++) {
      if (ThisSpectrum[i] > mySUM[i]) {
        ind[jjj] = i;
        jjj++;
      }
    }

    int indKeepLength = numPixel - ind.length;
    int indKeep[] = new int[indKeepLength];
    int k = 0;
    for (int i = 0; i < numPixel; i++) {
      if (!ArrayUtils.contains(ind, i)) {
        indKeep[k] = i;
        k++;
      }
    }
    double ThisSpectrumKeep[] = new double[indKeepLength];
    double ThisXaxisKeep[] = new double[indKeepLength];
    double PoKeep[] = new double[indKeepLength];
    double ReKeep[] = new double[indKeepLength];
    double Re2Keep[] = new double[indKeepLength - 1];
    double mySUMKeep[] = new double[indKeepLength];

    for (int i = 0; i < indKeepLength; i++) {
      ThisSpectrumKeep[i] = ThisSpectrum[indKeep[i]];
      ThisXaxisKeep[i] = ThisXaxis[indKeep[i]];
    }

    prevDEV = DEV;

    // at the point, ThisSpectrum and ThisXaxis should have reduced size
    final WeightedObservedPoints obs1 = new WeightedObservedPoints();

    for (int i = 0; i < indKeepLength; i++) {
      obs1.add(ThisXaxisKeep[i], ThisSpectrumKeep[i]);
    }

    while (true) {
      final PolynomialCurveFitter fitter1 = PolynomialCurveFitter.create(5);
      P = fitter1.fit(obs1.toList());
      Polyval pVal1 = new Polyval(P, ThisXaxisKeep, indKeepLength);
      PoKeep = pVal1.evl();

      for (int i = 0; i < indKeepLength; i++) {
        ReKeep[i] = ThisSpectrumKeep[i] - PoKeep[i];
      }

      for (int i = 0; i < indKeepLength - 1; i++) {
        Re2Keep[i] = ReKeep[i + 1] - ReKeep[i];
      }

      DEV = Math.sqrt(StatUtils.populationVariance(Re2Keep, 0, Re2Keep.length));

      for (int i = 0; i < indKeepLength; i++) {
        mySUMKeep[i] = PoKeep[i] + DEV;
      }

      for (int i = 0; i < indKeepLength; i++) {
        if (ThisSpectrumKeep[i] > mySUMKeep[i]) ThisSpectrumKeep[i] = mySUMKeep[i];
      }
      if ((Math.abs(DEV - prevDEV) / DEV) < threshhold) break;
      prevDEV = DEV;

      obs1.clear();
      for (int i = 0; i < indKeepLength; i++) {
        obs1.add(ThisXaxisKeep[i], ThisSpectrumKeep[i]);
      }
    }
    Polyval pVal2 = new Polyval(P, ThisXaxis, numPixel);
    double FLbk[] = pVal2.evl();
    for (int i = 0; i < ThisXaxis.length; i++) {
      SpecNoBk[i] = ThisSpectrum[i] - FLbk[i];
    }

    // the write-to-file part is only for testing purpose, ThisXaxis and SpecNoBk are two outputs
    try {
      FileWriter fr = new FileWriter(args[1]);
      BufferedWriter br = new BufferedWriter(fr);
      PrintWriter out = new PrintWriter(br);
      DecimalFormat df = new DecimalFormat(pattern);
      for (int j = 0; j < ThisXaxis.length; j++) {
        if (Double.toString(wavelength[j]) != null) out.write(ThisXaxis[j] + "\t" + SpecNoBk[j]);
        out.write("\r\n");
      }
      out.close();
    } catch (IOException e) {
      System.out.println(e);
    }
  }
Exemple #4
0
 /**
  * ** Encodes this DBRecordKey into XML and writes it to a specified PrintWriter ** @param out The
  * PrintWriter ** @param indent The number of spaces to indent ** @param sequence Optional
  * sequence value ** @param soapXML True for SOAP XML
  */
 public void printXML(PrintWriter out, int indent, int sequence, boolean soapXML) {
   if (out != null) {
     out.write(this.toXML(null, indent, sequence, soapXML).toString());
     out.flush();
   }
 }