Exemple #1
0
 public boolean getParticlesTableFile() {
   java.lang.String ptable_dir = prefs.get("QuickPALM.ptable_dir", ".");
   java.lang.String ptable_file = prefs.get("QuickPALM.ptable_file", "Particles Table.xls");
   OpenDialog chooser = new OpenDialog("Load Particles Table", ptable_dir, ptable_file);
   ptablefile = chooser.getDirectory() + chooser.getFileName();
   prefs.set("QuickPALM.ptable_dir", chooser.getDirectory());
   prefs.set("QuickPALM.ptable_file", chooser.getFileName());
   return true;
 }
Exemple #2
0
 public boolean getCalibrationFile() {
   java.lang.String cal_dir = prefs.get("QuickPALM.cal_dir", ".");
   java.lang.String cal_file = prefs.get("QuickPALM.cal_file", "Astigmatism calibration.xls");
   OpenDialog chooser = new OpenDialog("Astigmatism calibration", cal_dir, cal_file);
   calfile = chooser.getDirectory() + chooser.getFileName();
   prefs.set("QuickPALM.cal_dir", chooser.getDirectory());
   prefs.set("QuickPALM.cal_file", chooser.getFileName());
   return true;
 }
 public void run(String arg) {
   OpenDialog od = new OpenDialog("Install Plugin, Macro or Script...", arg);
   String directory = od.getDirectory();
   String name = od.getFileName();
   if (name == null) return;
   if (!validExtension(name)) {
     IJ.error("Plugin Installer", errorMessage());
     return;
   }
   String path = directory + name;
   install(path);
 }
 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;
 }
Exemple #5
0
  public void run(String arg) {
    String ijDir = System.getProperty("ij.dir");
    if (!ijDir.endsWith("/")) ijDir += "/";
    if (arg == null || "".equals(arg)) {
      OpenDialog dialog = new OpenDialog("Which Fiji component", ijDir + "plugins", "");
      if (dialog.getDirectory() == null) return;
      arg = dialog.getDirectory() + dialog.getFileName();
    }
    if (arg.startsWith(ijDir)) arg = arg.substring(ijDir.length());

    final JFrame frame = new JFrame("Building " + arg + "...");
    Container panel = frame.getContentPane();
    panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
    JTextArea textArea = new JTextArea("Calling Fiji Build\n", 25, 80);
    textArea.setFont(new Font("Courier", Font.PLAIN, 12));
    textArea.setEditable(false);
    panel.add(new JScrollPane(textArea));
    final JButton okay = new JButton("okay");
    okay.addActionListener(
        new ActionListener() {
          @Override
          public void actionPerformed(ActionEvent e) {
            frame.dispose();
          }
        });
    okay.setEnabled(false);
    okay.setAlignmentX(Component.CENTER_ALIGNMENT);
    panel.add(okay);
    frame.pack();
    frame.setLocationRelativeTo(null);
    okay.requestFocus();
    frame.setVisible(true);

    try {
      Fake fake = new Fake();
      fake.out = fake.err = new PrintStream(new JTextAreaOutputStream(textArea));
      Parser parser = fake.parse(new FileInputStream(ijDir + "/Fakefile"), new File(ijDir));
      final Rule all = parser.parseRules(Arrays.asList(arg.split("\\s+")));
      all.make();
      fake.out.println("Finished.");
      frame.setTitle("Built " + arg);
      okay.setEnabled(true);
    } catch (Exception e) {
      IJ.handleException(e);
    }
  }
Exemple #6
0
 /**
  * Open a file. If it's a directory, ask to open all images as a sequence in a stack or
  * individually.
  */
 public void openFile(File f) {
   if (IJ.debugMode) IJ.log("DragAndDrop.openFile: " + f);
   try {
     if (null == f) return;
     String path = f.getCanonicalPath();
     if (f.exists()) {
       if (f.isDirectory()) openDirectory(f, path);
       else {
         if (openAsVirtualStack && (path.endsWith(".tif") || path.endsWith(".TIF")))
           (new FileInfoVirtualStack()).run(path);
         else (new Opener()).openAndAddToRecent(path);
         OpenDialog.setLastDirectory(f.getParent() + File.separator);
         OpenDialog.setLastName(f.getName());
       }
     } else {
       IJ.log("File not found: " + path);
     }
   } catch (Throwable e) {
     if (!Macro.MACRO_CANCELED.equals(e.getMessage())) IJ.handleException(e);
   }
 }
Exemple #7
0
  public void run(String arg) {
    boolean display = false;
    File test = new File(arg);
    display = !test.exists();
    OpenDialog od = new OpenDialog("Open mkt file...", arg);
    if (od != null) {
      String file = od.getFileName();
      if (file == null) return;
      String directory = od.getDirectory();
      directory = directory.replace('\\', '/'); // Windows safe
      if (!directory.endsWith("/")) directory += "/";
      arg = directory + file;
    }

    try {
      FileProjectionSource fileSource = new MKTProjectionSource();

      fileSource.initStream(arg);
      ImagePlusDataSink sink = new ImagePlusDataSink();
      Grid2D imp = fileSource.getNextProjection();
      int i = 0;
      while (imp != null) {
        sink.process(imp, i);
        i++;
        imp = fileSource.getNextProjection();
      }
      sink.close();
      setStack(ImageUtil.wrapGrid3D(sink.getResult(), "").getStack());
      setTitle(new File(arg).getName());
      fileSource.close();
      if (display) show();

    } catch (IOException e) {
      // TODO Auto-generated catch block
      e.printStackTrace();
    } catch (Exception e) {
      // TODO Auto-generated catch block
      e.printStackTrace();
    }
  }
  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();
  }
  /** Create a file chooser configured for image writing, adding a panel for image writer options */
  public JFileChooser createFileChooser() {

    // use bio-formats to obtain file filters for available formats
    FileFilter[] ffs = GUITools.buildFileFilters(new ImageWriter());

    Vector<FileFilter> ffv = new Vector<FileFilter>(ffs.length - 1);

    // remove non-image writers
    if (ffs != null) {
      for (int i = 0; i < ffs.length; i++) {
        if (ffs[i] instanceof ExtensionFileFilter) {
          if (!((ExtensionFileFilter) ffs[i]).getExtension().equals("java")) {
            ffv.add(ffs[i]);
          }
        } else {
          ffv.add(ffs[i]);
        }
      }
    }
    ffs = new FileFilter[ffv.size()];
    ffs = ffv.toArray(ffs);

    // use bio-formats to create a file chooser with a preview panel
    JFileChooser jfc = GUITools.buildFileChooser(ffs, true);

    // set initial directory of the file chooser
    String idir = ALDEnvironmentConfig.getConfigValue("mitobo", null, "savedir");
    if (idir == null) idir = ALDEnvironmentConfig.getConfigValue("mitobo", null, "imagedir");
    if (idir == null) idir = OpenDialog.getLastDirectory();
    if (idir == null) idir = OpenDialog.getDefaultDirectory();

    if (idir != null) jfc.setCurrentDirectory(new File(idir));

    // remove file filter that accepts any file extension
    jfc.setAcceptAllFileFilterUsed(false);

    // install the image writer options panel in the file chooser
    this.iwop = new ImageWriterOptionsPane(jfc);
    if (this.img != null) {
      double dt = ImageIOUtils.toSeconds(this.img.getStepsizeT(), this.img.getUnitT());

      if (dt > 0) this.iwop.setDefaultFps((int) Math.round(1.0 / dt));
    } else if (this.imp != null) {
      if (this.imp.getCalibration() != null) {
        int fps = (int) Math.round(this.imp.getCalibration().fps);
        if (fps > 0) this.iwop.setDefaultFps(fps);
      }
    }

    // listen to changed property of the writer options panel
    this.iwop.addPropertyChangeListener(this);

    // set default/initial file filter to OME-TIFF if possible
    if (ffs != null) {
      for (int i = 0; i < ffs.length; i++) {
        if (ffs[i] instanceof ExtensionFileFilter) {
          if (((ExtensionFileFilter) ffs[i]).getExtension().equals("ome.tif")) {
            jfc.setFileFilter(ffs[i]);
          }
        }
      }
    }

    return jfc;
  }
  @Override
  public void run(ImageProcessor arg0) {

    JFileChooser fc = this.createFileChooser();

    // set image title (without extension) as default file name
    String origtitle = null;
    if (this.img != null) origtitle = this.img.getTitle();
    else if (this.imp != null) origtitle = this.imp.getTitle();
    if (origtitle != null) {
      int dotID = origtitle.indexOf(".");
      if (dotID != -1) {
        String name = origtitle.substring(0, dotID);
        fc.setSelectedFile(new File(name + ".ome.tiff"));
      }
    }

    while (fc.showSaveDialog(null) == JFileChooser.APPROVE_OPTION) {

      File outfile = fc.getSelectedFile();

      if (outfile == null) {
        IJ.error("File save dialog returned 'null'");
        return;
      }

      // if a specific format file filter was chosen, but the selected filename does not
      // match the formats extension, add the extension
      FileFilter ff = fc.getFileFilter();
      if (ff instanceof ExtensionFileFilter) {
        ExtensionFileFilter eff = (ExtensionFileFilter) ff;

        // #TODO: bio-formats release 4.2.2 contains a bug in the ExtensionFileFilter.accept(.)
        // method,
        //  therefore the extensions are matched manually. Substitute the for-loop with
        // accept()-method when
        //  using a new release
        String[] exts = eff.getExtensions();
        boolean extmatch = false;
        for (String ext : exts) {
          if (outfile.getName().endsWith(ext)) {
            extmatch = true;
            break;
          }
        }

        if (!extmatch) {
          outfile = new File(outfile.getAbsolutePath() + "." + eff.getExtension());
        }
      }

      // set initial directory of the file chooser for future call
      if (outfile.getParent() != null) {
        OpenDialog.setLastDirectory(outfile.getParent());
        OpenDialog.setDefaultDirectory(outfile.getParent());
      }

      // determine overwrite flag if file exists
      boolean overwrite = false;
      if (outfile.exists()) {
        int ret =
            JOptionPane.showConfirmDialog(
                null,
                "Do you want to overwrite existing file '" + outfile.getName() + "'?",
                "File exists",
                JOptionPane.YES_NO_OPTION);

        if (ret == JOptionPane.YES_OPTION) overwrite = true;
        else continue;
      }

      // create a MiToBo image writer instance
      ImageWriterMTB writer = null;

      try {
        if (this.img != null) {
          writer = new ImageWriterMTB(this.img, outfile.getAbsolutePath());
        } else {
          writer = new ImageWriterMTB(this.imp, outfile.getAbsolutePath());
        }
      } catch (ALDOperatorException e) {
        IJ.error("Image writer instantiation failed: " + e.getMessage());
      }

      if (writer != null) {

        // listener for status and progress bar update
        writer.addStatusListener(this);

        // configure and run the writer
        try {
          writer.setOverwrite(overwrite);

          if (this.compression != null) {
            writer.setCompression(this.compression);
          }
          if (this.fps > 0) {
            writer.setFps(this.fps);
          }
          if (this.quality != -1) {
            writer.setQuality(this.quality);
          }
          if (this.codec != -1) {
            writer.setCodec(this.codec);
          }

          writer.runOp(null);

        } catch (ALDOperatorException e) {
          IJ.error("Writing of file '" + outfile.getName() + "' failed: " + e.getMessage());
          e.printStackTrace();
        } catch (FormatException e) {
          IJ.error("Writing of file '" + outfile.getName() + "' failed: " + e.getMessage());
          e.printStackTrace();
        } catch (ALDProcessingDAGException e) {
          IJ.error("Writing of file '" + outfile.getName() + "' failed: " + e.getMessage());
          e.printStackTrace();
        }
      }

      return;
    }
  }
 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();
   }
 }