public void run(ImageProcessor ip) {

    dimz = stack.getSize();
    dimy = stack.getWidth();
    dimx = stack.getHeight();

    SaveDialog sd = new SaveDialog("Save Measurements as Text...", "res", ".dat");
    String name = sd.getFileName();
    if (name == null) return;

    String directory = sd.getDirectory();

    nb = calculnb(stack); // -1;
    IJ.showStatus("Measure parameters for the " + nb + " objects ...");
    if (nb < 1) {
      IJ.showMessage("volume must be labeled");
    } else {
      double[] volume_m = new double[nb];
      int[] volume_p = new int[nb];
      double[] surface = new double[nb];
      double[] surfacenb = new double[nb];
      double[][][] I = new double[3][3][nb];
      double[][] J = new double[3][nb];
      double[][][] dir = new double[3][3][nb];
      double[] xg = new double[nb];
      double[] yg = new double[nb];
      double[] zg = new double[nb];
      byte[] bord = new byte[nb];
      //       		double[] a = new double[nb];
      //       		double[] b = new double[nb];
      //       		double[] c = new double[nb];
      //       		double[] Fab = new double[nb];
      //       		double[] Fac = new double[nb];
      //       		double[] Fbc = new double[nb];
      //       		double[] sp = new double[nb];
      double[][] lmin = new double[nb][3];
      double[][] lmax = new double[nb][3];
      IJ.showStatus("Measure surfaces ...");
      calculmarchsurfstack(stack, nb, surface, volume_m);
      calculmarchsurfstacknb(stack, nb, surfacenb);
      // calculvolumestack(stack,nb,volume_p);
      IJ.showStatus("Measure volumes and inertia ...");
      calculcgstack(stack, nb, volume_p, xg, yg, zg);
      calculinertiestack(stack, nb, xg, yg, zg, I);
      inertie(nb, I, J, dir);
      IJ.showStatus("Measure bounding boxes ...");
      boitestack(stack, nb, xg, yg, zg, dir, lmin, lmax);
      borderstack(stack, nb, bord);
      IJ.showStatus("Save results ...");
      sauvegarde(
          volume_p, volume_m, surface, surfacenb, xg, yg, zg, J, dir, nb, bord, lmin, lmax,
          directory, name);
      volume_m = null;
      volume_p = null;
      surface = null;
      xg = null;
      yg = null;
      zg = null;
    }
  }
 String showDialog() {
   if (defaultDir == null) defaultDir = Menus.getMacrosPath();
   OpenDialog od = new OpenDialog("Install Macros", defaultDir, fileName);
   String name = od.getFileName();
   if (name == null) return null;
   String dir = od.getDirectory();
   if (!(name.endsWith(".txt") || name.endsWith(".ijm"))) {
     IJ.showMessage("Macro Installer", "File name must end with \".txt\" or \".ijm\" .");
     return null;
   }
   fileName = name;
   defaultDir = dir;
   return dir + name;
 }
示例#3
0
 private void showioerror() {
   IJ.showMessage("Error in file io");
 }
示例#4
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#5
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();
   }
 }
 void install() {
   subMenus.clear();
   if (text != null) {
     Tokenizer tok = new Tokenizer();
     pgm = tok.tokenize(text);
   }
   if (macrosMenu != null) IJ.showStatus("");
   int[] code = pgm.getCode();
   Symbol[] symbolTable = pgm.getSymbolTable();
   int count = 0, token, nextToken, address;
   String name;
   Symbol symbol;
   shortcutsInUse = null;
   inUseCount = 0;
   nShortcuts = 0;
   toolCount = 0;
   macroStarts = new int[MAX_MACROS];
   macroNames = new String[MAX_MACROS];
   boolean isPluginsMacrosMenu = false;
   if (macrosMenu != null) {
     int itemCount = macrosMenu.getItemCount();
     isPluginsMacrosMenu = macrosMenu == Menus.getMacrosMenu();
     int baseCount = isPluginsMacrosMenu ? MACROS_MENU_COMMANDS : Editor.MACROS_MENU_ITEMS;
     if (itemCount > baseCount) {
       for (int i = itemCount - 1; i >= baseCount; i--) macrosMenu.remove(i);
     }
   }
   if (pgm.hasVars() && pgm.macroCount() > 0 && pgm.getGlobals() == null)
     new Interpreter().saveGlobals(pgm);
   ArrayList tools = new ArrayList();
   for (int i = 0; i < code.length; i++) {
     token = code[i] & TOK_MASK;
     if (token == MACRO) {
       nextToken = code[i + 1] & TOK_MASK;
       if (nextToken == STRING_CONSTANT) {
         if (count == MAX_MACROS) {
           if (isPluginsMacrosMenu)
             IJ.error("Macro Installer", "Macro sets are limited to " + MAX_MACROS + " macros.");
           break;
         }
         address = code[i + 1] >> TOK_SHIFT;
         symbol = symbolTable[address];
         name = symbol.str;
         macroStarts[count] = i + 2;
         macroNames[count] = name;
         if (name.indexOf('-') != -1
             && (name.indexOf("Tool") != -1 || name.indexOf("tool") != -1)) {
           tools.add(name);
           toolCount++;
         } else if (name.startsWith("AutoRun")) {
           if (autoRunCount == 0 && !openingStartupMacrosInEditor) {
             new MacroRunner(pgm, macroStarts[count], name, (String) null);
             if (name.equals("AutoRunAndHide")) autoRunAndHideCount++;
           }
           autoRunCount++;
           count--;
         } else if (name.equals("Popup Menu")) installPopupMenu(name, pgm);
         else if (!name.endsWith("Tool Selected")) {
           if (macrosMenu != null) {
             addShortcut(name);
             int pos = name.indexOf(">");
             boolean inSubMenu = name.startsWith("<") && (pos > 1);
             if (inSubMenu) {
               Menu parent = macrosMenu;
               Menu subMenu = null;
               String parentStr = name.substring(1, pos).trim();
               String childStr = name.substring(pos + 1).trim();
               MenuItem mnuItem = new MenuItem();
               mnuItem.setActionCommand(name);
               mnuItem.setLabel(childStr);
               for (int jj = 0; jj < subMenus.size(); jj++) {
                 String aName = subMenus.get(jj).getName();
                 if (aName.equals(parentStr)) subMenu = subMenus.get(jj);
               }
               if (subMenu == null) {
                 subMenu = new Menu(parentStr);
                 subMenu.setName(parentStr);
                 subMenu.addActionListener(this);
                 subMenus.add(subMenu);
                 parent.add(subMenu);
               }
               subMenu.add(mnuItem);
             } else macrosMenu.add(new MenuItem(name));
           }
         }
         // IJ.log(count+" "+name+" "+macroStarts[count]);
         count++;
       }
     } else if (token == EOF) break;
   }
   nMacros = count;
   if (toolCount > 0 && (isPluginsMacrosMenu || macrosMenu == null) && installTools) {
     Toolbar tb = Toolbar.getInstance();
     if (toolCount == 1) tb.addMacroTool((String) tools.get(0), this);
     else {
       for (int i = 0; i < tools.size(); i++) {
         String toolName = (String) tools.get(i);
         if (toolName.startsWith("Abort Macro or Plugin") && toolCount > 6)
           toolName = "Unused " + toolName;
         tb.addMacroTool(toolName, this, i);
       }
     }
     if (toolCount > 1 && Toolbar.getToolId() >= Toolbar.CUSTOM1) tb.setTool(Toolbar.RECTANGLE);
     tb.repaint();
   }
   if (macrosMenu != null) this.instance = this;
   if (shortcutsInUse != null && text != null)
     IJ.showMessage(
         "Install Macros",
         (inUseCount == 1 ? "This keyboard shortcut is" : "These keyboard shortcuts are")
             + " already in use:"
             + shortcutsInUse);
   if (nMacros == 0 && fileName != null) {
     if (text == null || text.length() == 0) return;
     int dotIndex = fileName.lastIndexOf('.');
     if (dotIndex > 0) anonymousName = fileName.substring(0, dotIndex);
     else anonymousName = fileName;
     if (macrosMenu != null) macrosMenu.add(new MenuItem(anonymousName));
     macroNames[0] = anonymousName;
     nMacros = 1;
   }
   String word = nMacros == 1 ? " macro" : " macros";
   if (isPluginsMacrosMenu) IJ.showStatus(nMacros + word + " installed");
 }