Ejemplo n.º 1
0
 /** Quit using a separate thread, hopefully avoiding thread deadlocks. */
 public void run() {
   quitting = true;
   boolean changes = false;
   int[] wList = WindowManager.getIDList();
   if (wList != null) {
     for (int i = 0; i < wList.length; i++) {
       ImagePlus imp = WindowManager.getImage(wList[i]);
       if (imp != null && imp.changes == true) {
         changes = true;
         break;
       }
     }
   }
   Frame[] frames = WindowManager.getNonImageWindows();
   if (frames != null) {
     for (int i = 0; i < frames.length; i++) {
       if (frames[i] != null && (frames[i] instanceof Editor)) {
         if (((Editor) frames[i]).fileChanged()) {
           changes = true;
           break;
         }
       }
     }
   }
   if (windowClosed
       && !changes
       && Menus.window.getItemCount() > Menus.WINDOW_MENU_ITEMS
       && !(IJ.macroRunning() && WindowManager.getImageCount() == 0)) {
     GenericDialog gd = new GenericDialog("ImageJ", this);
     gd.addMessage("Are you sure you want to quit ImageJ?");
     gd.showDialog();
     quitting = !gd.wasCanceled();
     windowClosed = false;
   }
   if (!quitting) return;
   if (!WindowManager.closeAllWindows()) {
     quitting = false;
     return;
   }
   // IJ.log("savePreferences");
   if (applet == null) {
     saveWindowLocations();
     Prefs.savePreferences();
   }
   IJ.cleanup();
   // setVisible(false);
   // IJ.log("dispose");
   dispose();
   if (exitWhenQuitting) System.exit(0);
 }
 public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
   checkc2 = gd.getNextBoolean();
   double[] params = new double[10];
   int[] fixes = new int[10];
   for (int i = 0; i < params.length; i++) {
     params[i] = gd.getNextNumber();
     if (gd.getNextBoolean()) {
       fixes[i] = 1;
     } else {
       fixes[i] = 0;
     }
   }
   gd.getNextBoolean();
   gd.getNextNumber();
   gd.getNextNumber();
   NLLSfit_v2 fitclass = new NLLSfit_v2(this, 0);
   double[] stats = new double[2];
   float[] fit = fitclass.fitdata(params, fixes, null, tempdata, null, stats, true);
   pw.updateSeries(fit, series, false);
   c2 = (float) stats[1];
   return true;
 }
 public void run(String arg) {
   GenericDialog gd = new GenericDialog("Options");
   gd.addCheckbox("Add_Titles", true);
   gd.addCheckbox("Close Original", false);
   gd.showDialog();
   if (gd.wasCanceled()) {
     return;
   }
   boolean addtitles = gd.getNextBoolean();
   boolean closeorig = gd.getNextBoolean();
   // first get the table window
   Frame[] niframes = WindowManager.getNonImageWindows();
   boolean first = true;
   TextWindow tw2 = null;
   int ncols = 0;
   String[] col_labels = null;
   for (int i = 0; i < niframes.length; i++) {
     if (niframes[i] instanceof TextWindow && !niframes[i].getTitle().equals("Log")) {
       TextWindow tw = (TextWindow) niframes[i];
       TextPanel tp = tw.getTextPanel();
       List<List<String>> listtable = table_tools.table2listtable(tp);
       if (listtable.size() == 0) {
         col_labels = table_tools.getcollabels(tp);
         ncols = col_labels.length;
         ArrayList<String> temp = new ArrayList<String>();
         for (int j = 0; j < ncols; j++) temp.add("");
         listtable.add(temp);
       }
       if (first) {
         col_labels = table_tools.getcollabels(tp);
         ncols = col_labels.length;
         String headings = tp.getColumnHeadings();
         if (addtitles) {
           String[] titles = repeated(tw.getTitle(), listtable.size());
           table_tools.add_listtable_column(listtable, titles, 0);
           headings = "name\t" + headings;
         }
         tw2 =
             new TextWindow(
                 "Combined Table", headings, table_tools.print_listtable(listtable), 400, 200);
         first = false;
       } else {
         if (addtitles) {
           String[] titles = repeated(tw.getTitle(), listtable.size());
           table_tools.add_listtable_column(listtable, titles, 0);
         }
         tw2.append(table_tools.print_listtable(listtable));
       }
       if (closeorig) tw.close();
     }
   }
 }
 public double[][] get_constraints(double[] params) {
   // here we populate the constraints
   GenericDialog gd = new GenericDialog("Constraints");
   for (int i = 0; i < 10; i++) {
     if (constraints == null) {
       gd.addNumericField("P" + (i + 1) + "_upper", params[i], 5, 10, null);
       gd.addNumericField("P" + (i + 1) + "_lower", params[i], 5, 10, null);
     } else {
       gd.addNumericField("P" + (i + 1) + "_upper", constraints[1][i], 5, 10, null);
       gd.addNumericField("P" + (i + 1) + "_lower", constraints[0][i], 5, 10, null);
     }
   }
   gd.showDialog();
   if (gd.wasCanceled()) {
     return null;
   }
   double[][] constraints = new double[2][10];
   for (int i = 0; i < 10; i++) {
     constraints[1][i] = gd.getNextNumber();
     constraints[0][i] = gd.getNextNumber();
   }
   return constraints;
 }
 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 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;
 }
 boolean showoptions(double[] params, int[] fixes) {
   // GenericDialog gd=new NonBlockingGenericDialog("Options");
   GenericDialog gd = new GenericDialog("Options");
   gd.addCheckbox("Check Chi Squared", checkc2);
   for (int i = 0; i < 10; i++) {
     gd.addNumericField("P" + (i + 1), params[i], 5, 10, null);
     gd.addCheckbox("Fix?", (fixes[i] == 1));
   }
   gd.addCheckbox("Get_Errors", false);
   gd.addCheckbox("Set_Constraints", false);
   gd.addNumericField("Iterations", iterations, 0, 10, null);
   gd.addNumericField("chi squared", c2, 5, 10, null);
   gd.addDialogListener(this);
   gd.showDialog();
   if (gd.wasCanceled()) {
     return false;
   }
   checkc2 = gd.getNextBoolean();
   for (int i = 0; i < 10; i++) {
     params[i] = gd.getNextNumber();
     if (gd.getNextBoolean()) {
       fixes[i] = 1;
     } else {
       fixes[i] = 0;
     }
   }
   boolean geterrors = gd.getNextBoolean();
   boolean setconstraints = gd.getNextBoolean();
   for (int i = 0; i < 10; i++) {
     if (function.indexOf("P" + (i + 1)) < 0) {
       fixes[i] = 1;
     }
   }
   if (geterrors) {
     if (!get_errors(params, fixes)) {
       return false;
     }
   }
   if (setconstraints) constraints = get_constraints(params);
   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();
  }
  /** Displays a modal options dialog. */
  public boolean showDialog() {
    Calibration cal = imp != null ? imp.getCalibration() : (new Calibration());
    double unitSquared = cal.pixelWidth * cal.pixelHeight;
    if (pixelUnits) unitSquared = 1.0;
    if (Macro.getOptions() != null) {
      boolean oldMacro = updateMacroOptions();
      if (oldMacro) unitSquared = 1.0;
      staticMinSize = 0.0;
      staticMaxSize = DEFAULT_MAX_SIZE;
      staticMinCircularity = 0.0;
      staticMaxCircularity = 1.0;
      staticShowChoice = NOTHING;
    }
    GenericDialog gd = new GenericDialog("Analyze Particles");
    minSize = staticMinSize;
    maxSize = staticMaxSize;
    minCircularity = staticMinCircularity;
    maxCircularity = staticMaxCircularity;
    showChoice = staticShowChoice;
    if (maxSize == 999999) maxSize = DEFAULT_MAX_SIZE;
    options = staticOptions;
    String unit = cal.getUnit();
    boolean scaled = cal.scaled();
    if (unit.equals("inch")) {
      unit = "pixel";
      unitSquared = 1.0;
      scaled = false;
      pixelUnits = true;
    }
    String units = unit + "^2";
    int places = 0;
    double cmin = minSize * unitSquared;
    if ((int) cmin != cmin) places = 2;
    double cmax = maxSize * unitSquared;
    if ((int) cmax != cmax && cmax != DEFAULT_MAX_SIZE) places = 2;
    String minStr = ResultsTable.d2s(cmin, places);
    if (minStr.indexOf("-") != -1) {
      for (int i = places; i <= 6; i++) {
        minStr = ResultsTable.d2s(cmin, i);
        if (minStr.indexOf("-") == -1) break;
      }
    }
    String maxStr = ResultsTable.d2s(cmax, places);
    if (maxStr.indexOf("-") != -1) {
      for (int i = places; i <= 6; i++) {
        maxStr = ResultsTable.d2s(cmax, i);
        if (maxStr.indexOf("-") == -1) break;
      }
    }
    if (scaled) gd.setInsets(5, 0, 0);
    gd.addStringField("Size (" + units + "):", minStr + "-" + maxStr, 12);
    if (scaled) {
      gd.setInsets(0, 40, 5);
      gd.addCheckbox("Pixel units", pixelUnits);
    }
    gd.addStringField("Circularity:", IJ.d2s(minCircularity) + "-" + IJ.d2s(maxCircularity), 12);
    gd.addChoice("Show:", showStrings, showStrings[showChoice]);
    String[] labels = new String[8];
    boolean[] states = new boolean[8];
    labels[0] = "Display results";
    states[0] = (options & SHOW_RESULTS) != 0;
    labels[1] = "Exclude on edges";
    states[1] = (options & EXCLUDE_EDGE_PARTICLES) != 0;
    labels[2] = "Clear results";
    states[2] = (options & CLEAR_WORKSHEET) != 0;
    labels[3] = "Include holes";
    states[3] = (options & INCLUDE_HOLES) != 0;
    labels[4] = "Summarize";
    states[4] = (options & DISPLAY_SUMMARY) != 0;
    labels[5] = "Record starts";
    states[5] = (options & RECORD_STARTS) != 0;
    labels[6] = "Add to Manager";
    states[6] = (options & ADD_TO_MANAGER) != 0;
    labels[7] = "In_situ Show";
    states[7] = (options & IN_SITU_SHOW) != 0;
    gd.addCheckboxGroup(4, 2, labels, states);
    gd.addHelp(IJ.URL + "/docs/menus/analyze.html#ap");
    gd.showDialog();
    if (gd.wasCanceled()) return false;

    String size = gd.getNextString(); // min-max size
    if (scaled) pixelUnits = gd.getNextBoolean();
    if (pixelUnits) unitSquared = 1.0;
    else unitSquared = cal.pixelWidth * cal.pixelHeight;
    String[] minAndMax = Tools.split(size, " -");
    double mins = gd.parseDouble(minAndMax[0]);
    double maxs = minAndMax.length == 2 ? gd.parseDouble(minAndMax[1]) : Double.NaN;
    minSize = Double.isNaN(mins) ? DEFAULT_MIN_SIZE : mins / unitSquared;
    maxSize = Double.isNaN(maxs) ? DEFAULT_MAX_SIZE : maxs / unitSquared;
    if (minSize < DEFAULT_MIN_SIZE) minSize = DEFAULT_MIN_SIZE;
    if (maxSize < minSize) maxSize = DEFAULT_MAX_SIZE;
    staticMinSize = minSize;
    staticMaxSize = maxSize;

    minAndMax = Tools.split(gd.getNextString(), " -"); // min-max circularity
    double minc = gd.parseDouble(minAndMax[0]);
    double maxc = minAndMax.length == 2 ? gd.parseDouble(minAndMax[1]) : Double.NaN;
    minCircularity = Double.isNaN(minc) ? 0.0 : minc;
    maxCircularity = Double.isNaN(maxc) ? 1.0 : maxc;
    if (minCircularity < 0.0 || minCircularity > 1.0) minCircularity = 0.0;
    if (maxCircularity < minCircularity || maxCircularity > 1.0) maxCircularity = 1.0;
    if (minCircularity == 1.0 && maxCircularity == 1.0) minCircularity = 0.0;
    staticMinCircularity = minCircularity;
    staticMaxCircularity = maxCircularity;

    if (gd.invalidNumber()) {
      IJ.error("Bins invalid.");
      canceled = true;
      return false;
    }
    showChoice = gd.getNextChoiceIndex();
    staticShowChoice = showChoice;
    if (gd.getNextBoolean()) options |= SHOW_RESULTS;
    else options &= ~SHOW_RESULTS;
    if (gd.getNextBoolean()) options |= EXCLUDE_EDGE_PARTICLES;
    else options &= ~EXCLUDE_EDGE_PARTICLES;
    if (gd.getNextBoolean()) options |= CLEAR_WORKSHEET;
    else options &= ~CLEAR_WORKSHEET;
    if (gd.getNextBoolean()) options |= INCLUDE_HOLES;
    else options &= ~INCLUDE_HOLES;
    if (gd.getNextBoolean()) options |= DISPLAY_SUMMARY;
    else options &= ~DISPLAY_SUMMARY;
    if (gd.getNextBoolean()) options |= RECORD_STARTS;
    else options &= ~RECORD_STARTS;
    if (gd.getNextBoolean()) options |= ADD_TO_MANAGER;
    else options &= ~ADD_TO_MANAGER;
    if (gd.getNextBoolean()) options |= IN_SITU_SHOW;
    else options &= ~IN_SITU_SHOW;
    staticOptions = options;
    options |= SHOW_PROGRESS;
    if ((options & DISPLAY_SUMMARY) != 0)
      Analyzer.setMeasurements(Analyzer.getMeasurements() | AREA);
    return true;
  }
Ejemplo n.º 10
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();
   }
 }
Ejemplo n.º 11
0
  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();
  }