示例#1
0
  public void run(String arg) {
    GenericDialog gd = new GenericDialog("Options");
    double sfreq = 20000.0;
    gd.addNumericField("Sampling Frequency?", sfreq, 1, 10, null);
    String[] psfchoice = {"3D Gaussian", "Gaus-Lorentz^2", "2D Gaussian"};
    gd.addChoice("PSF Type?", psfchoice, psfchoice[0]);
    String[] filetypechoice = {
      "Confocor 3 raw", "Short binary trajectory", "PlotWindow trajectory", "Ascii Text File"
    };
    gd.addChoice("File Type?", filetypechoice, filetypechoice[0]);
    boolean ch2green = true;
    gd.addCheckbox("Ch2 is green?", ch2green);
    gd.showDialog();
    if (gd.wasCanceled()) {
      return;
    }
    sfreq = gd.getNextNumber();
    int psfflag = gd.getNextChoiceIndex();
    int fileflag = gd.getNextChoiceIndex();
    ch2green = gd.getNextBoolean();
    int nfiles = 0;
    Object[] histograms = null;
    int xmax = 0;
    int ymax = 0;
    String[] names = null;
    if (fileflag < 2) {
      jdataio ioclass = new jdataio();
      File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance());
      if (filearray.length == 0) {
        return;
      }
      String dir = filearray[0].getAbsolutePath();
      int sepindex = dir.lastIndexOf(File.separator);
      String newdir = dir.substring(0, sepindex + 1);
      OpenDialog.setDefaultDirectory(newdir);
      nfiles = filearray.length / 2;
      if (nfiles > 25) {
        nfiles = 25;
      }
      histograms = new Object[nfiles];
      names = organize_c3_files(filearray);
      for (int i = 0; i < nfiles; i++) {
        try {
          int length1 = (int) (((double) filearray[2 * i].length() - 128.0) / 4.0);
          int length2 = (int) (((double) filearray[2 * i + 1].length() - 128.0) / 4.0);
          int length3 = (int) (((double) filearray[2 * i].length()) / 2.0);
          int length4 = (int) (((double) filearray[2 * i + 1].length()) / 2.0);
          InputStream instream = new BufferedInputStream(new FileInputStream(filearray[2 * i]));
          InputStream instream2 =
              new BufferedInputStream(new FileInputStream(filearray[2 * i + 1]));
          if (fileflag == 0) {
            int[] pmdata = new int[length1];
            int[] pmdata2 = new int[length2];
            if (!ioclass.skipstreambytes(instream, 128)) {
              showioerror();
              instream.close();
              return;
            }
            if (!ioclass.skipstreambytes(instream2, 128)) {
              showioerror();
              instream2.close();
              return;
            }
            if (!ioclass.readintelintfile(instream, length1, pmdata)) {
              showioerror();
              instream.close();
              return;
            }
            if (!ioclass.readintelintfile(instream2, length2, pmdata2)) {
              showioerror();
              instream2.close();
              return;
            }
            if (ch2green) {
              histograms[i] = (new pmodeconvert()).pm2pch(pmdata2, pmdata, sfreq, 20000000);
            } else {
              histograms[i] = (new pmodeconvert()).pm2pch(pmdata, pmdata2, sfreq, 20000000);
            }
          } else {
            float[] tmdata = new float[length3];
            float[] tmdata2 = new float[length4];
            if (!ioclass.readintelshortfile(instream, length3, tmdata)) {
              showioerror();
              instream.close();
              return;
            }
            if (!ioclass.readintelshortfile(instream2, length4, tmdata2)) {
              showioerror();
              instream2.close();
              return;
            }
            if (ch2green) {
              histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata2, tmdata);
            } else {
              histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata, tmdata2);
            }
          }
          if (((float[][]) histograms[i]).length > xmax) {
            xmax = ((float[][]) histograms[i]).length;
          }
          if (((float[][]) histograms[i])[0].length > ymax) {
            ymax = ((float[][]) histograms[i])[0].length;
          }
          instream.close();
          instream2.close();
        } catch (IOException e) {
          showioerror();
          return;
        }
      }
    } else {
      if (fileflag == 2) {
        ImageWindow iw = WindowManager.getCurrentWindow();
        float[][] trajectories = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues");
        float[][] tempxvals = (float[][]) jutils.runPW4VoidMethod(iw, "getXValues");
        sfreq = 1.0 / ((double) tempxvals[0][1]);
        nfiles = trajectories.length / 2;
        if (nfiles > 25) {
          nfiles = 25;
        }
        names = new String[nfiles + 1];
        names[nfiles] = "avg";
        histograms = new Object[nfiles];
        for (int i = 0; i < nfiles; i++) {
          names[i] = "trajectory " + (i + 1);
          if (ch2green) {
            histograms[i] =
                (new pmodeconvert())
                    .create_2Dhistogram(trajectories[2 * i + 1], trajectories[2 * i]);
          } else {
            histograms[i] =
                (new pmodeconvert())
                    .create_2Dhistogram(trajectories[2 * i], trajectories[2 * i + 1]);
          }
          if (((float[][]) histograms[i]).length > xmax) {
            xmax = ((float[][]) histograms[i]).length;
          }
          if (((float[][]) histograms[i])[0].length > ymax) {
            ymax = ((float[][]) histograms[i])[0].length;
          }
        }
      } else {
        // here we read tab delimited lines from files
        jdataio ioclass = new jdataio();
        File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance());
        if (filearray.length == 0) {
          return;
        }
        String dir = filearray[0].getAbsolutePath();
        int sepindex = dir.lastIndexOf(File.separator);
        String newdir = dir.substring(0, sepindex + 1);
        OpenDialog.setDefaultDirectory(newdir);
        nfiles = filearray.length;
        if (nfiles > 25) {
          nfiles = 25;
        }
        histograms = new Object[nfiles];
        names = new String[nfiles + 1];
        names[nfiles] = "avg";
        for (int i = 0; i < nfiles; i++) {
          try {
            names[i] = filearray[i].getName();
            BufferedReader d = new BufferedReader(new FileReader(filearray[i]));
            String[] lines = new String[256];
            int counter = 0;
            do {
              lines[counter] = d.readLine();
              counter++;
            } while ((lines[counter - 1] != null && lines[counter - 1] != "") && counter < 256);
            int numcolumns = 0;
            for (int j = 0; j < counter - 1; j++) {
              int temp = getncolumns(lines[j]);
              if (temp > numcolumns) {
                numcolumns = temp;
              }
            }
            float[][] temphist2 = null;
            if (ch2green) {
              temphist2 = new float[numcolumns][counter - 1];
            } else {
              temphist2 = new float[counter - 1][numcolumns];
            }
            for (int k = 0; k < counter - 1; k++) {
              float[] temp = tab_delim2float(lines[k]);
              for (int j = 0; j < numcolumns; j++) {
                if (ch2green) {
                  temphist2[j][k] = temp[j];
                } else {
                  temphist2[k][j] = temp[j];
                }
              }
            }
            histograms[i] = temphist2;
            d.close();
          } catch (IOException e) {
            showioerror();
            return;
          }
        }
        for (int i = 0; i < nfiles; i++) {
          if (((float[][]) histograms[i]).length > xmax) {
            xmax = ((float[][]) histograms[i]).length;
          }
          if (((float[][]) histograms[i])[0].length > ymax) {
            ymax = ((float[][]) histograms[i])[0].length;
          }
        }
      }
    }
    // note that here x is green and y is red
    float[][][] pch = new float[nfiles][xmax][ymax];
    for (int i = 0; i < nfiles; i++) {
      for (int j = 0; j < ((float[][]) histograms[i]).length; j++) {
        for (int k = 0; k < ((float[][]) histograms[i])[j].length; k++) {
          pch[i][j][k] = ((float[][]) histograms[i])[j][k];
        }
      }
    }

    final PCH2DFitWindow cw = new PCH2DFitWindow();
    cw.init(names, pch, psfflag);

    final Frame f = new Frame("PCH 2D Analysis");
    f.setLocation(10, 10);
    f.addWindowListener(
        new WindowAdapter() {
          public void windowClosing(WindowEvent e) {
            f.dispose();
          }
        });

    f.add(cw);
    f.pack();
    f.setResizable(false);
    Insets ins = f.getInsets();
    cw.totalSize.height = PCH2DFitWindow.H + ins.bottom + ins.top + 65;
    cw.totalSize.width = PCH2DFitWindow.WR + ins.left + ins.right;
    f.setSize(cw.totalSize);
    f.setVisible(true);
    cw.requestFocus();
  }
示例#2
0
  private void geterrors() {
    GenericDialog gd = new GenericDialog("Options");
    float conf = 0.67f;
    gd.addNumericField("Confidence Limit", (int) (conf * 100.0f), 5, 10, null);
    gd.addChoice("Error Parameter", paramsnames, paramsnames[0]);
    double spacing = 0.01;
    gd.addNumericField("Chi^2 plot spacing (% of value)?", spacing * 100.0, 2, 10, null);
    boolean globalerror = false;
    gd.addCheckbox("Global Fit Error?", globalerror);
    int dataset = 0;
    gd.addNumericField("Data Set (for Global Error)", dataset, 0);
    gd.showDialog();
    if (gd.wasCanceled()) {
      return;
    }
    conf = 0.01f * (float) gd.getNextNumber();
    int paramindex = (int) gd.getNextChoiceIndex();
    spacing = 0.01 * gd.getNextNumber();
    globalerror = gd.getNextBoolean();
    dataset = (int) gd.getNextNumber();

    if (globalerror) {
      support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, true, 0.1);
      int[] erindeces = {paramindex, dataset};
      // need to set up all the matrices
      int nsel = 0;
      int nparams = 11;
      for (int i = 0; i < ncurves; i++) {
        if (include[i]) {
          nsel++;
        }
      }
      double[][] params = new double[nsel][nparams];
      String[][] tempformulas = new String[nsel][nparams];
      double[][][] constraints = new double[2][nsel][nparams];
      int[][] vflmatrix = new int[nsel][nparams];

      float[][] tempdata = new float[nsel][xpts * ypts];
      float[][] tempweights = new float[nsel][xpts * ypts];

      int nfit = 0;
      int counter = 0;
      for (int i = 0; i < ncurves; i++) {
        if (include[i]) {
          for (int j = 0; j < nparams; j++) {
            params[counter][j] = globalparams[i][j];
            tempformulas[counter][j] = globalformulas[i][j];
            constraints[0][counter][j] = globalconstraints[0][i][j];
            constraints[1][counter][j] = globalconstraints[1][i][j];
            vflmatrix[counter][j] = globalvflmatrix[i][j];
            if (vflmatrix[counter][j] == 0 || (j == 0 && vflmatrix[counter][j] == 2)) {
              nfit++;
            }
          }
          for (int j = 0; j < xpts; j++) {
            for (int k = 0; k < ypts; k++) {
              tempdata[counter][j + k * xpts] = (float) ((double) pch[i][j][k] / (double) nmeas[i]);
              tempweights[counter][j + k * xpts] = weights[i][j][k];
            }
          }
          counter++;
        }
      }
      int dofnum = xpts * ypts * nsel - (nfit - 1) - 1;
      int dofden = xpts * ypts * nsel - nfit - 1;
      // double flim=FLimit(dofnum,dofden,(double)conf);
      double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf);
      IJ.log("FLimit = " + (float) flim);
      if (flim == Double.NaN && flim < 1.0) {
        IJ.showMessage("Invalid Limiting F Value");
        return;
      }
      double truespacing = Math.abs(params[erindeces[1]][erindeces[0]] * spacing);
      double[][] c2plot =
          erclass.geterrorsglobal(
              params,
              vflmatrix,
              tempformulas,
              paramsnames,
              constraints,
              tempdata,
              tempweights,
              flim,
              truespacing,
              erindeces);
      IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]);
      int templength = c2plot[0].length;
      float[][] c2plotf = new float[2][templength - 1];
      for (int i = 0; i < (templength - 1); i++) {
        c2plotf[0][i] = (float) c2plot[0][i + 1];
        c2plotf[1][i] = (float) c2plot[1][i + 1];
      }
      new PlotWindow4(
              "c2 plot",
              paramsnames[paramindex] + "[" + dataset + "]",
              "Chi^2",
              c2plotf[0],
              c2plotf[1])
          .draw();
    } else {
      support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, false, 0.1);
      int errindex = paramindex;

      float[] tempdata = new float[xpts * ypts];
      float[] tempweights = new float[xpts * ypts];
      for (int i = 0; i < xpts; i++) {
        for (int j = 0; j < ypts; j++) {
          tempdata[i + j * xpts] = (float) ((double) avg[i][j] / (double) nmeas[ncurves]);
          tempweights[i + j * xpts] = avgweights[i][j];
        }
      }

      int nfit = 0;
      for (int i = 0; i < 7; i++) {
        if (avgfixes[i] == 0) {
          nfit++;
        }
      }
      int dofnum = xpts * ypts - (nfit - 1) - 1;
      int dofden = xpts * ypts - nfit - 1;
      double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf);
      IJ.log("FLimit = " + (float) flim);
      if (flim == Double.NaN && flim < 1.0) {
        IJ.showMessage("Invalid Limiting F Value");
        return;
      }
      double truespacing = Math.abs(avgparams[errindex] * spacing);
      double[][] c2plot =
          erclass.geterrors(
              avgparams,
              avgfixes,
              avgconstraints,
              tempdata,
              tempweights,
              flim,
              truespacing,
              errindex);
      IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]);
      int templength = c2plot[0].length;
      float[][] c2plotf = new float[2][templength - 1];
      for (int i = 0; i < (templength - 1); i++) {
        c2plotf[0][i] = (float) c2plot[0][i + 1];
        c2plotf[1][i] = (float) c2plot[1][i + 1];
      }
      new PlotWindow4("c2 plot", paramsnames[errindex], "Chi^2", c2plotf[0], c2plotf[1]).draw();
    }
  }
示例#3
0
 public void run(String arg) {
   Frame[] niframes = WindowManager.getNonImageWindows();
   String[] titles = new String[niframes.length + 1];
   for (int i = 0; i < niframes.length; i++) {
     titles[i] = niframes[i].getTitle();
   }
   titles[niframes.length] = "Clipboard";
   GenericDialog gd = new GenericDialog("Windows");
   boolean importfile = false;
   gd.addCheckbox("Import from file?", importfile);
   gd.addChoice("Windows", titles, titles[0]);
   boolean hasxvals = false;
   gd.addCheckbox("X Vals Column?", hasxvals);
   boolean multix = false;
   gd.addCheckbox("Multi_X_Columns?", multix);
   boolean skipendzeros = false;
   gd.addCheckbox("Skip_end_zeros?", skipendzeros);
   String[] delimiters = {"Tab", "Comma", "Space"};
   gd.addChoice("Delimiter", delimiters, delimiters[0]);
   gd.showDialog();
   if (gd.wasCanceled()) {
     return;
   }
   importfile = gd.getNextBoolean();
   int index = gd.getNextChoiceIndex();
   hasxvals = gd.getNextBoolean();
   multix = gd.getNextBoolean();
   skipendzeros = gd.getNextBoolean();
   int delimindex = gd.getNextChoiceIndex();
   if (multix) hasxvals = true;
   String textdata = "";
   if (importfile) {
     OpenDialog od = new OpenDialog("Open File", "", ".txt");
     String directory = od.getDirectory();
     String name = od.getFileName();
     if (name == null) {
       return;
     }
     try {
       File infile = new File(directory + name);
       BufferedReader b = new BufferedReader(new FileReader(infile));
       textdata = (new jdataio()).readstringfile(b);
       b.close();
     } catch (IOException e) {
       return;
     }
   } else {
     if (index == niframes.length) {
       // here we get the data from the clipboard
       Transferable t = Toolkit.getDefaultToolkit().getSystemClipboard().getContents(null);
       try {
         if (t != null && t.isDataFlavorSupported(DataFlavor.stringFlavor)) {
           textdata = (String) t.getTransferData(DataFlavor.stringFlavor);
         }
       } catch (UnsupportedFlavorException e) {
       } catch (IOException e) {
       }
       if (textdata.equals("")) {
         IJ.error("Error copying from clipboard.");
         return;
       }
     } else {
       if (niframes[index] instanceof Editor) {
         Editor tw = (Editor) niframes[index];
         textdata = tw.getText();
       } else {
         if (niframes[index] instanceof TextWindow) {
           TextWindow tw = (TextWindow) niframes[index];
           textdata = tw.getTextPanel().getText();
         } else {
           IJ.showMessage("Not a valid text window");
           return;
         }
       }
     }
   }
   if (textdata == null) {
     IJ.showMessage("Error in Obtaining String");
     return;
   }
   if (textdata.indexOf("\r") >= 0) {
     textdata = textdata.replace('\r', '\n');
   }
   char[] delims = {'\t', ',', ' '};
   delimit_string ds = new delimit_string(delims[delimindex]);
   String[] rows = ds.getrows(textdata);
   int lines = rows.length;
   int columns = ds.getnumcolumns(rows[0]);
   int ycolumns = columns;
   if (hasxvals) {
     if (multix) {
       ycolumns /= 2;
     } else {
       ycolumns--;
     }
   }
   if (multix) {
     float[][] ydata = new float[ycolumns][lines];
     float[][] xdata = new float[ycolumns][lines];
     for (int i = 0; i < lines; i++) {
       float[] temp = ds.delim2float(rows[i], columns);
       for (int j = 0; j < ycolumns; j++) {
         ydata[j][i] = temp[2 * j + 1];
         xdata[j][i] = temp[2 * j];
       }
     }
     int[] npts = new int[ycolumns];
     for (int i = 0; i < ycolumns; i++) {
       npts[i] = lines;
     }
     if (skipendzeros) {
       for (int i = 0; i < ycolumns; i++) {
         int counter = lines - 1;
         while ((xdata[i][counter] == 0.0f || Float.isNaN(xdata[i][counter])) && counter > 0) {
           xdata[i][counter] = 0.0f;
           ydata[i][counter] = 0.0f;
           npts[i]--;
           counter--;
         }
       }
     }
     (new PlotWindow4("Text Plot", "x", "y", xdata, ydata, npts)).draw();
   } else {
     float[][] tempydata = new float[ycolumns][lines];
     float[] tempxdata = new float[lines];
     float[][] xdata = null;
     float[][] ydata = null;
     int startcolumn = 0;
     if (hasxvals) startcolumn = 1;
     for (int i = 0; i < lines; i++) {
       float[] temp = ds.delim2float(rows[i], columns);
       if (hasxvals) {
         tempxdata[i] = temp[0];
       } else {
         tempxdata[i] = (float) (i + 1);
       }
       for (int j = 0; j < ycolumns; j++) {
         tempydata[j][i] = temp[j + startcolumn];
       }
     }
     int[] npts = new int[ycolumns];
     npts[0] = lines;
     if (skipendzeros) {
       int maxpts = 0;
       for (int i = 0; i < ycolumns; i++) {
         int counter = lines - 1;
         npts[i] = lines;
         while ((tempydata[i][counter] == 0.0f || Float.isNaN(tempydata[i][counter]))
             && counter > 0) {
           npts[i]--;
           counter--;
         }
         if (npts[i] > maxpts) maxpts = npts[i];
         IJ.log("" + npts[i]);
       }
       ydata = new float[ycolumns][maxpts];
       xdata = new float[ycolumns][maxpts];
       for (int i = 0; i < ycolumns; i++) {
         // npts[i]=npts[0];
         System.arraycopy(tempxdata, 0, xdata[i], 0, npts[i]);
         System.arraycopy(tempydata[i], 0, ydata[i], 0, npts[i]);
       }
     } else {
       ydata = tempydata;
       xdata = new float[ycolumns][];
       for (int i = 0; i < ycolumns; i++) {
         npts[i] = npts[0];
         xdata[i] = tempxdata.clone();
       }
     }
     (new PlotWindow4("Text Plot", "x", "y", xdata, ydata, npts)).draw();
   }
 }
 public boolean get_errors(double[] params, int[] fixes) {
   GenericDialog gd = new GenericDialog("Error Options");
   String[] methods = {"Support Plane", "Monte Carlo"};
   gd.addChoice("Method", methods, methods[0]);
   float conf = 0.67f;
   gd.addNumericField("SP_Confidence Limit (%)", (int) (conf * 100.0f), 5, 10, null);
   String[] labels = {"P1", "P2", "P3", "P4", "P5", "P6", "P7", "P8", "P9", "P10"};
   gd.addChoice("SP_Parameter", labels, labels[0]);
   double spacing = 0.01;
   gd.addNumericField("SP_Chi^2_plot_spacing (% of value)?", spacing * 100.0, 2, 10, null);
   int ntrials = 100;
   gd.addNumericField("MC_#_Trials", ntrials, 0);
   gd.showDialog();
   if (gd.wasCanceled()) {
     return false;
   }
   int methodindex = gd.getNextChoiceIndex();
   conf = 0.01f * (float) gd.getNextNumber();
   int paramindex = gd.getNextChoiceIndex();
   spacing = 0.01 * gd.getNextNumber();
   ntrials = (int) gd.getNextNumber();
   if (methodindex == 0) {
     support_plane_errors_v2 erclass = new support_plane_errors_v2(this, 0.0001, 50, false, 0.1);
     int errindex = paramindex;
     int nfit = 0;
     for (int i = 0; i < labels.length; i++) {
       if (fixes[i] == 0) {
         nfit++;
       }
     }
     int npts = tempdata.length;
     int dofnum = npts - (nfit - 1) - 1;
     int dofden = npts - nfit - 1;
     double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf);
     IJ.log("FLimit = " + (float) flim);
     if (flim == Double.NaN && flim < 1.0) {
       IJ.showMessage("Invalid Limiting F Value");
       return false;
     }
     double truespacing = Math.abs(params[errindex] * spacing);
     double[][] c2plot =
         erclass.geterrors(
             params, fixes, constraints, tempdata, weights, flim, truespacing, errindex);
     IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]);
     IJ.log(
         "upper error = "
             + (c2plot[1][0] - params[errindex])
             + " lower error = "
             + (params[errindex] - c2plot[0][0]));
     int templength = c2plot[0].length;
     float[][] c2plotf = new float[2][templength - 1];
     for (int i = 0; i < (templength - 1); i++) {
       c2plotf[0][i] = (float) c2plot[0][i + 1];
       c2plotf[1][i] = (float) c2plot[1][i + 1];
     }
     new PlotWindow4("c2 plot", labels[errindex], "Chi^2", c2plotf[0], c2plotf[1]).draw();
   } else {
     StringBuffer sb = new StringBuffer();
     sb.append("Trial\t");
     for (int i = 0; i < labels.length; i++) {
       if (fixes[i] == 0) sb.append(labels[i] + "\t");
     }
     sb.append("chi^2");
     tw = new TextWindow("Monte Carlo Results", sb.toString(), "", 400, 400);
     redirect = true;
     monte_carlo_errors_v2 erclass = new monte_carlo_errors_v2(this, 0.0001, 50, false, 0.1);
     double[][] errors = erclass.geterrors(params, fixes, constraints, tempdata, weights, ntrials);
     sb = new StringBuffer();
     sb.append("StDev\t");
     for (int i = 0; i < errors.length; i++) {
       float[] ferr = new float[errors[0].length];
       for (int j = 0; j < ferr.length; j++) ferr[j] = (float) errors[i][j];
       float stdev = jstatistics.getstatistic("StDev", ferr, null);
       sb.append("" + stdev);
       if (i < (errors.length - 1)) sb.append("\t");
     }
     tw.append(sb.toString());
     redirect = false;
   }
   return true;
 }
 public void run(String arg) {
   String[] labels = {
     "Masked_Chromosomes", "Unmixed_Image", "Spectral_Image(optional)", "Spectra(optional)"
   };
   ImagePlus[] imps = jutils.selectImages(true, 4, labels);
   if (imps == null) {
     return;
   }
   if (imps[0] == null) {
     return;
   }
   float[] mask = (float[]) imps[0].getStack().getPixels(2);
   findblobs3 fb = new findblobs3(imps[0].getWidth(), imps[0].getHeight());
   float[] objects = fb.dofindblobs(mask, 0.5f);
   WaitForUserDialog dg =
       new WaitForUserDialog(
           "Optional Input", "Place RoiManager Points on Chromosome Segments (if desired)");
   dg.show();
   if (!dg.escPressed()) {
     RoiManager rman = RoiManager.getInstance();
     while (rman != null && rman.getCount() > 1) {
       Roi[] rois = rman.getRoisAsArray();
       int[] ids = new int[rois.length];
       for (int i = 0; i < rois.length; i++) {
         Rectangle r = rois[i].getBounds();
         ids[i] = (int) objects[r.x + fb.width * r.y];
       }
       objects = fb.link_objects(objects, ids);
       rman.reset();
       dg =
           new WaitForUserDialog(
               "Optional Input",
               "Place More RoiManager Points on Chromosome Segments (if desired)");
       dg.show();
       if (dg.escPressed()) break;
     }
   }
   int[] areas = fb.get_areas(objects);
   int[] temprank = jsort.get_javasort_order(areas);
   int[] arearank = jsort.get_javasort_order(temprank);
   for (int i = 0; i < fb.nobjects; i++) {
     arearank[i] = fb.nobjects - arearank[i] - 1;
   }
   // if the spectra are available, get them
   float[][][] spectra = null;
   Object[] data = null;
   if (imps[1] != null && imps[2] != null && imps[3] != null) {
     ImageWindow iw = imps[3].getWindow();
     if (iw.getClass().getName().equals("jguis.PlotWindow4")) {
       float[][] yvals = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues");
       data = jutils.stack2array(imps[2].getStack());
       Object[] coef = jutils.stack2array(imps[1].getStack());
       spectra = new float[fb.nobjects][2][];
       for (int i = 0; i < fb.nobjects; i++) {
         spectra[i][0] = fb.get_object_spectrum(objects, (i + 1), data, "Sum");
         spectra[i][1] = new float[yvals[0].length];
         float[] tempcoef = fb.get_object_spectrum(objects, (i + 1), coef, "Sum");
         for (int j = 0; j < yvals[0].length; j++) {
           for (int k = 0; k < 5; k++) {
             spectra[i][1][j] += tempcoef[k] * yvals[k][j];
           }
         }
       }
     }
   }
   CompositeImage imp = (CompositeImage) imps[0];
   imp.setPosition(1, 1, 1);
   LUT graylut = jutils.get_lut_for_color(Color.white);
   imp.setChannelColorModel(graylut);
   imp.setPosition(2, 1, 1);
   LUT redlut = jutils.get_lut_for_color(Color.red);
   imp.setChannelColorModel(redlut);
   imp.setPosition(1, 1, 1);
   imp.updateAndRepaintWindow();
   SkyPanel_v3 sp = new SkyPanel_v3();
   int skychan = 6;
   if (imps[1] != null) skychan = imps[1].getNChannels();
   // assume that the sky image has 6 channels and that the second is the unknown green
   // shift the unknown green to the end
   ImagePlus skyimp = null;
   if (imps[1] != null) {
     Object[] skystack = jutils.stack2array(imps[1].getStack());
     // Object[]
     // skystack2={skystack[0],skystack[2],skystack[3],skystack[4],skystack[5],skystack[1]};
     Object[] skystack2 = null;
     if (skychan == 6)
       skystack2 = new Object[] {skystack[0], skystack[2], skystack[3], skystack[4], skystack[5]};
     else
       skystack2 = new Object[] {skystack[0], skystack[1], skystack[2], skystack[3], skystack[4]};
     skyimp =
         new ImagePlus(
             "rearranged", jutils.array2stack(skystack2, imps[1].getWidth(), imps[1].getHeight()));
   }
   int nch = 5;
   if (skyimp != null) nch = skyimp.getStack().getSize();
   GenericDialog gd2 = new GenericDialog("Options");
   gd2.addNumericField("Area Accuracy (percent)", 30, 0);
   for (int i = 0; i < nch; i++) {
     gd2.addNumericField("Ch_" + (i + 1) + "_Contr_Thresh", 0.35, 5, 15, null);
   }
   // gd2.addNumericField("Contribution Threshold",0.35,5,15,null);
   gd2.addCheckbox("Mouse?", false);
   gd2.addNumericField("Box_Width", 150, 0);
   gd2.addNumericField("Box_Height", 100, 0);
   gd2.showDialog();
   if (gd2.wasCanceled()) {
     return;
   }
   sp.areathresh = (float) gd2.getNextNumber();
   sp.objthresh2 = new float[nch];
   for (int i = 0; i < nch; i++) sp.objthresh2[i] = (float) gd2.getNextNumber();
   // sp.objthresh=(float)gd2.getNextNumber();
   boolean mouse = gd2.getNextBoolean();
   int bwidth = (int) gd2.getNextNumber();
   int bheight = (int) gd2.getNextNumber();
   int[] colorindices = {4, 1, 2, 6, 3};
   GenericDialog gd3 = new GenericDialog("Color Options");
   for (int i = 0; i < 5; i++)
     gd3.addChoice(
         "Ch" + (i + 1) + " Color",
         SkyPanel_v3.colornames,
         SkyPanel_v3.colornames[colorindices[i]]);
   gd3.showDialog();
   if (gd3.wasCanceled()) return;
   for (int i = 0; i < 5; i++) colorindices[i] = gd3.getNextChoiceIndex();
   sp.colorindices = colorindices;
   sp.nch = 5;
   sp.dapilast = false;
   sp.cellwidth = bwidth;
   sp.cellheight = bheight;
   sp.init(imps[0], skyimp, objects, areas, arearank, fb, true, spectra, data, mouse);
   SkyPanel_v3.launch_frame(sp);
 }