public void run(String arg) {
    ImageWindow iw = WindowManager.getCurrentWindow();
    pw = jutils.getPW4SelCopy(iw);
    String title = pw.getTitle();
    float[][] yvals = pw.getYValues();
    float[][] xvals = pw.getXValues();
    int length = yvals[0].length;
    if (pw.getShowErrors()) errs = pw.getErrors(0, false);
    int[] colors = pw.getColors();
    colors[0] = 0;
    ScriptEngineManager manager = new ScriptEngineManager();
    engine = manager.getEngineByName("js");
    ce = (Compilable) engine;
    // hitcounter=0;

    c2 = 0.0f;
    iterations = 0;
    checkc2 = false;

    double[] stats = new double[3];
    tempx = new float[length];
    tempdata = new float[length];
    System.arraycopy(xvals[0], 0, tempx, 0, length);
    System.arraycopy(yvals[0], 0, tempdata, 0, length);
    pw.addPoints(tempx, new float[tempx.length], false);
    series = pw.getNpts().length - 1;
    double[] params = new double[10];
    int[] fixes = {0, 0, 0, 1, 1, 1, 1, 1, 1, 1};
    init_options(params, fixes);
    if (!init_functions()) {
      return;
    }

    while (showoptions(params, fixes)) {
      NLLSfit_v2 fitclass;
      if (checkc2) {
        fitclass = new NLLSfit_v2(this, 0);
      } else {
        fitclass = new NLLSfit_v2(this, 0.0001, 50, 0.1);
      }
      float[] fit = fitclass.fitdata(params, fixes, constraints, yvals[0], weights, stats, true);
      pw.updateSeries(fit, series, false);
      c2 = (float) stats[1];
      iterations = (int) stats[0];
    }

    IJ.log("Chi Squared = " + (float) stats[1]);
    IJ.log("Iterations = " + (int) stats[0]);
    for (int i = 0; i < 10; i++) {
      IJ.log("P" + (i + 1) + " = " + (float) params[i] + " fixed = " + fixes[i]);
    }
    IJ.log("AIC = " + (float) stats[2]);
    // IJ.log("hits = "+hitcounter);
    set_options(params, fixes);
  }
 boolean init_functions() {
   GenericDialog gd = new GenericDialog("Fitting Options");
   gd.addStringField("Extra Definitions", exdef, 50);
   gd.addCheckbox("Weight Using Plot Errors", false);
   gd.addStringField("Weighting Equation (y is for data)", weightfunction, 50);
   gd.addStringField("Fit_Equation", function, 50);
   gd.showDialog();
   if (gd.wasCanceled()) {
     return false;
   }
   exdef = gd.getNextString();
   boolean errweights = gd.getNextBoolean();
   weightfunction = gd.getNextString();
   function = gd.getNextString();
   // first initialize the weights
   weights = new float[tempdata.length];
   if (errweights
       || weightfunction.equals("")
       || weightfunction == null
       || weightfunction == "1.0") {
     if (errweights) {
       for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f / (errs[i] * errs[i]);
     } else {
       for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f;
     }
   } else {
     for (int i = 0; i < tempdata.length; i++) {
       String script =
           "y =" + tempdata[i] + "; " + "x =" + tempx[i] + "; " + "retval=" + weightfunction + ";";
       Double temp = new Double(0.0);
       try {
         temp = (Double) engine.eval(script);
       } catch (Exception e) {
         IJ.log(e.getMessage());
       }
       if (!(temp.isInfinite() || temp.isNaN())) {
         weights[i] = temp.floatValue();
       }
     }
   }
   // now compile the function script
   try {
     String script1 = exdef + "; retval=" + function + ";";
     cs = ce.compile(script1);
   } catch (Exception e) {
     IJ.log(e.toString());
     return false;
   }
   return true;
 }
 public double[] fitfunc(double[] fitparams) {
   Bindings b = engine.createBindings();
   for (int i = 0; i < 10; i++) b.put("P" + (i + 1), fitparams[i]);
   /*String script1="P1="+fitparams[0]+"; "+
   "P2="+fitparams[1]+"; "+
   "P3="+fitparams[2]+"; "+
   "P4="+fitparams[3]+"; "+
   "P5="+fitparams[4]+"; "+
   "P6="+fitparams[5]+"; "+
   "P7="+fitparams[6]+"; "+
   "P8="+fitparams[7]+"; "+
   "P9="+fitparams[8]+"; "+
   "P10="+fitparams[9]+"; "+
   exdef+"; x=";
   String script2="; retval="+function+";";*/
   try {
     double[] temp = new double[tempx.length];
     for (int i = 0; i < tempx.length; i++) {
       // temp[i]=((Double)engine.eval(script1+(double)tempx[i]+script2)).doubleValue();
       b.put("x", tempx[i]);
       b.put("y", tempdata[i]);
       temp[i] = (Double) cs.eval(b);
     }
     return temp;
   } catch (Exception e) {
     IJ.log(e.getMessage());
     return null;
   }
 }
 public void run(String arg) {
   ImagePlus[] imps = jutils.selectImages(false, 2, new String[] {"Histogram", "Image"});
   if (imps == null) return;
   ImageWindow iw = imps[0].getWindow();
   int[] indices = (int[]) jutils.runReflectionMethod(iw, "getroiindices", null);
   if (indices == null) {
     IJ.error("Select Roi First");
     return;
   }
   int width = imps[1].getWidth();
   int height = imps[1].getHeight();
   int[] mask = new int[width * height];
   // for(int i=0;i<mask.length;i++) mask[i]=0xff000000;
   for (int i = 0; i < indices.length; i++) mask[indices[i]] = 0xffff0000;
   ColorProcessor cp = new ColorProcessor(width, height, mask);
   ImageRoi roi = new ImageRoi(0, 0, cp);
   roi.setZeroTransparent(true);
   imps[1].setOverlay(new Overlay(roi));
 }
  private void fitglobal() {
    int nparams = 11;
    int nsel = 0;
    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];

    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];
        }
        counter++;
      }
      for (int j = 0; j < nparams; j++) {
        undoparams[i][j] = globalparams[i][j];
        undoformulas[i][j] = globalformulas[i][j];
        undovflmatrix[i][j] = globalvflmatrix[i][j];
      }
      for (int j = 0; j < xpts; j++) {
        for (int k = 0; k < ypts; k++) {
          undofit[i][j][k] = fit[i][j][k];
        }
      }
      undoc2[i] = c2[i];
    }
    undoglobalc2 = globalc2;
    if (showglobalfitdialog(params, tempformulas, vflmatrix)) {
      counter = 0;
      for (int i = 0; i < ncurves; i++) {
        if (include[i]) {
          for (int j = 0; j < nparams; j++) {
            globalparams[i][j] = params[counter][j];
            globalformulas[i][j] = tempformulas[counter][j];
            globalvflmatrix[i][j] = vflmatrix[counter][j];
          }
          counter++;
        }
      }
      double[] stats = new double[2];
      float[][] tempdata = new float[nsel][xpts * ypts];
      float[][] tempweights = new float[nsel][xpts * ypts];
      counter = 0;
      for (int i = 0; i < ncurves; i++) {
        if (include[i]) {
          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 tempmaxiter = globalfitclass.maxiter;
      if (checkc2) {
        globalfitclass.changemaxiter(0);
      }
      double[] tempc2vals = new double[nsel];
      IJ.showStatus("Fitting Globally");
      float[][] tempfit =
          globalfitclass.fitdata(
              params,
              vflmatrix,
              tempformulas,
              paramsnames,
              constraints,
              tempdata,
              tempweights,
              stats,
              tempc2vals,
              false);
      IJ.showStatus("Fit Complete");
      globalfitclass.changemaxiter(tempmaxiter);
      globalc2 = stats[1];
      globalc2label.setText("Global chi^2 = " + (float) globalc2);
      counter = 0;
      for (int i = 0; i < ncurves; i++) {
        if (include[i]) {
          for (int j = 0; j < xpts; j++) {
            for (int k = 0; k < ypts; k++) {
              fit[i][j][k] = tempfit[counter][j + xpts * k] * (float) nmeas[i];
            }
          }
          if (i == dispcurve) {
            pwfit.updateSeries(fit[dispcurve], 1, true);
          }
          for (int j = 0; j < nparams; j++) {
            globalparams[i][j] = params[counter][j];
          }
          c2[i] = tempc2vals[counter];
          c2array[i].setText("" + (float) c2[i]);
          counter++;
        }
      }
      float[] temp = pwfit.getLimits();
      temp[4] = 1.0f;
      pwfit.setLimits(temp);
    }
  }
 private void showioerror() {
   IJ.showMessage("Error in file io");
 }
  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();
  }
 public void showresults(String results) {
   IJ.showStatus(results);
   IJ.log(results);
 }
  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();
    }
  }
 public void showresults(String results) {
   if (redirect) tw.append(results);
   else IJ.log(results);
 }
 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) {
    GenericDialog gd = new GenericDialog("Options");
    gd.addCheckbox("Acceptor_First", true);
    gd.showDialog();
    if (gd.wasCanceled()) return;
    boolean a1 = gd.getNextBoolean();
    int asp = 0;
    int dsp = 1;
    int aop = 2;
    int dop = 3;
    int atp = 4;
    int dtp = 5;
    if (!a1) {
      asp = 1;
      dsp = 0;
      aop = 3;
      dop = 2;
      atp = 5;
      dtp = 4;
    }
    ImageWindow iw = WindowManager.getCurrentWindow();
    float[][] xvals = (float[][]) jutils.runPW4VoidMethod(iw, "getXValues");
    float[][] yvals = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues");
    int[] npts = (int[]) jutils.runPW4VoidMethod(iw, "getNpts");
    int maxpts = (int) jstatistics.getstatistic("Max", npts, null);
    int nsets = npts.length / 6;
    float[][] rtxvals = new float[nsets][maxpts];
    float[][] rtavals = new float[nsets][maxpts];
    float[][] rtdvals = new float[nsets][maxpts];
    int[] rtnpts = new int[nsets];
    int fretlength = 10;
    float[][] stfretvals = new float[nsets][fretlength];
    float[][] offfretvals = new float[nsets][fretlength];
    TextWindow tw = jutils.selectTable("DNA Damage FRET");
    if (tw == null)
      tw =
          new TextWindow(
              "DNA Damage FRET",
              "title\tacceptor\tdonor\testripe\teoff\tmaxart\tmaxdrt",
              "",
              400,
              200);
    // note that st stands for stripe and off is for areas off the damage stripe
    for (int i = 0; i < npts.length / 6; i++) {
      int len = npts[i * 6];
      int damageindex = findbleach(yvals[i * 6 + dsp], len);
      int fretindex = findbleach(yvals[i * 6 + atp], len);
      IJ.log("set " + i + " damage pos = " + damageindex + " , fret pos = " + fretindex);
      int predamagestart = damageindex - 4;
      int prefretstart = fretindex - 5;
      float staccpredam = getavg(yvals[i * 6 + asp], len, predamagestart, damageindex - 1);
      float stdonpredam = getavg(yvals[i * 6 + dsp], len, predamagestart, damageindex - 1);
      float nucaccpredam = getavg(yvals[i * 6 + atp], len, predamagestart, damageindex - 1);
      float nucdonpredam = getavg(yvals[i * 6 + dtp], len, predamagestart, damageindex - 1);
      float stdonprefret = getavg(yvals[i * 6 + dsp], len, prefretstart, fretindex - 2);
      float stdonafret = getavg(yvals[i * 6 + dsp], len, fretindex, fretindex + 3);
      float offdonprefret = getavg(yvals[i * 6 + dop], len, prefretstart, fretindex - 2);
      float offdonafret = getavg(yvals[i * 6 + dop], len, fretindex, fretindex + 3);
      float estripe = 1.0f - stdonprefret / stdonafret;
      float eoff = 1.0f - offdonprefret / offdonafret;
      rtnpts[i] = len;
      for (int j = 0; j < len; j++) {
        rtxvals[i][j] = j - damageindex - 1;
        rtavals[i][j] =
            (yvals[i * 6 + asp][j] / staccpredam) / (yvals[i * 6 + atp][j] / nucaccpredam);
        rtdvals[i][j] =
            (yvals[i * 6 + dsp][j] / stdonpredam) / (yvals[i * 6 + dtp][j] / nucdonpredam);
      }
      float[] smart = (float[]) algutils.get_subarray(rtavals[i], 0, fretindex);
      float[] smdrt = (float[]) algutils.get_subarray(rtdvals[i], 0, fretindex);
      jsmooth.blur1D(smart, 2.0f);
      jsmooth.blur1D(smdrt, 2.0f);
      float maxart = 0.0f;
      float maxdrt = 0.0f;
      for (int j = 0; j < fretindex - 2; j++) {
        if (smart[j] > maxart) maxart = smart[j];
        if (smdrt[j] > maxdrt) maxdrt = smdrt[j];
      }

      stfretvals[i] = getregion(yvals[i * 6 + dsp], len, prefretstart, fretlength);
      offfretvals[i] = getregion(yvals[i * 6 + dop], len, prefretstart, fretlength);
      tw.append(
          iw.getTitle()
              + "-"
              + (i + 1)
              + "\t"
              + staccpredam
              + "\t"
              + stdonpredam
              + "\t"
              + estripe
              + "\t"
              + eoff
              + "\t"
              + maxart
              + "\t"
              + maxdrt);
    }
    new PlotWindow4("Stripe_FRET_profiles", "time", "intensity", stfretvals, null).draw();
    new PlotWindow4("OffStripe_FRET_profiles", "time", "intensity", offfretvals, null).draw();
    new PlotWindow4("Acc_Rt_profiles", "time", "intensity", rtxvals, rtavals, rtnpts).draw();
    new PlotWindow4("Don_Rt_profiles", "time", "intensity", rtxvals, rtdvals, rtnpts).draw();
  }
 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 void run(String arg) {
    ImagePlus imp = WindowManager.getCurrentImage();
    Calibration cal = imp.getCalibration();
    GenericDialog gd = new GenericDialog("Options");
    int subsize = 32;
    gd.addNumericField("Subregion Size (pixels)?", subsize, 0);
    int stepsize = 16;
    gd.addNumericField("Step Size?", stepsize, 0);
    int shift = 3;
    gd.addNumericField("STICS temporal Shift?", shift, 0);
    float xoffset = 0.0f;
    gd.addNumericField("X_Offset", xoffset, 5, 15, null);
    float yoffset = 0.0f;
    gd.addNumericField("Y_Offset", yoffset, 5, 15, null);
    float multiplier = 8.0f;
    gd.addNumericField("Velocity Multiplier", multiplier, 5, 15, null);
    float ftime = 1.0f;
    gd.addNumericField("Frame_Time(min)", ftime, 5, 15, null);
    float scaling = (float) cal.pixelWidth;
    gd.addNumericField("Pixel_Size(um)", scaling, 5, 15, null);
    boolean norm = true;
    gd.addCheckbox("Normalize_Vector_lengths?", norm);
    boolean centered = true;
    gd.addCheckbox("Center_Vectors?", centered);
    float magthresh = 0.0f;
    gd.addNumericField("Magnitude_Threshhold?", magthresh, 5, 15, null);
    int rlength = 10;
    gd.addNumericField("Running_avg_length", rlength, 0);
    int inc = 5;
    gd.addNumericField("Start_frame_increment", inc, 0);
    gd.showDialog();
    if (gd.wasCanceled()) {
      return;
    }
    subsize = (int) gd.getNextNumber();
    stepsize = (int) gd.getNextNumber();
    shift = (int) gd.getNextNumber();
    xoffset = (float) gd.getNextNumber();
    yoffset = (float) gd.getNextNumber();
    multiplier = (float) gd.getNextNumber();
    ftime = (float) gd.getNextNumber();
    scaling = (float) gd.getNextNumber();
    norm = gd.getNextBoolean();
    centered = gd.getNextBoolean();
    magthresh = (float) gd.getNextNumber();
    rlength = (int) gd.getNextNumber();
    inc = (int) gd.getNextNumber();

    int width = imp.getWidth();
    int xregions = 1 + (int) (((float) width - (float) subsize) / (float) stepsize);
    int newwidth = xregions * subsize;
    int height = imp.getHeight();
    int yregions = 1 + (int) (((float) height - (float) subsize) / (float) stepsize);
    int newheight = yregions * subsize;
    ImageStack stack = imp.getStack();
    int slices = imp.getNSlices();
    int channels = imp.getNChannels();
    int frames = imp.getNFrames();
    if (frames == 1) {
      frames = slices;
      slices = 1;
    }

    Roi roi = imp.getRoi();
    if (roi == null) {
      roi = new Roi(0, 0, width, height);
    }

    STICS_map map = new STICS_map(subsize, stepsize);
    Object[] tseries = jutils.get3DTSeries(stack, 0, 0, frames, slices, channels);
    map.update_STICS_map(tseries, width, height, 0, rlength, roi.getPolygon(), shift);
    FloatProcessor fp =
        map.get_map(scaling, ftime, stepsize, centered, norm, multiplier, stepsize, magthresh);
    ImageStack vector_stack = new ImageStack(fp.getWidth(), fp.getHeight());
    vector_stack.addSlice("", fp);
    float[][] vel = map.get_scaled_velocities(scaling, ftime, stepsize);
    ImageStack velstack = new ImageStack(map.xregions, map.yregions);
    velstack.addSlice("", vel[0]);
    velstack.addSlice("", vel[1]);
    int velframes = 2;
    IJ.showStatus("frame " + 0 + " calculated");
    for (int i = inc; i < (frames - rlength); i += inc) {
      map.update_STICS_map(tseries, width, height, i, rlength, roi.getPolygon(), shift);
      FloatProcessor fp2 =
          map.get_map(scaling, ftime, stepsize, centered, norm, multiplier, stepsize, magthresh);
      vector_stack.addSlice("", fp2);
      vel = map.get_scaled_velocities(scaling, ftime, stepsize);
      velstack.addSlice("", vel[0]);
      velstack.addSlice("", vel[1]);
      velframes += 2;
      IJ.showStatus("frame " + i + " calculated");
    }
    (new ImagePlus("STICS Vectors", vector_stack)).show();
    ImagePlus imp3 = new ImagePlus("Velocities", velstack);
    imp3.setOpenAsHyperStack(true);
    imp3.setDimensions(2, 1, velframes / 2);
    new CompositeImage(imp3, CompositeImage.COLOR).show();
  }