Beispiel #1
0
  /**
   * @return the clipboard content as a String (DataFlavor.stringFlavor) Code snippet adapted from
   *     jEdit (Registers.java), http://www.jedit.org. Returns null if clipboard is empty.
   */
  public static String getClipboardStringContent(Clipboard clipboard) {
    // Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
    try {
      String selection =
          (String) (clipboard.getContents(null).getTransferData(DataFlavor.stringFlavor));
      if (selection == null) return null;

      boolean trailingEOL =
          (selection.endsWith("\n") || selection.endsWith(System.getProperty("line.separator")));

      // Some Java versions return the clipboard contents using the native line separator,
      // so have to convert it here , see jEdit's "registers.java"
      BufferedReader in = new BufferedReader(new StringReader(selection));
      StringBuffer buf = new StringBuffer();
      String line;
      while ((line = in.readLine()) != null) {
        buf.append(line);
        buf.append('\n');
      }
      // remove trailing \n
      if (!trailingEOL) buf.setLength(buf.length() - 1);
      return buf.toString();
    } catch (Exception e) {
      e.printStackTrace();
      return null;
    }
  }
Beispiel #2
0
 // =========================================================
 public String recieve() throws IOException // RECIEVE METHOD
     {
   String recievedString;
   recievedString = buffRdr.readLine();
   System.out.println("RECD<<<< " + id + ": " + recievedString);
   return recievedString;
 }
Beispiel #3
0
 public void drop(DropTargetDropEvent dtde) {
   dtde.acceptDrop(DnDConstants.ACTION_COPY);
   DataFlavor[] flavors = null;
   try {
     Transferable t = dtde.getTransferable();
     iterator = null;
     flavors = t.getTransferDataFlavors();
     if (IJ.debugMode) IJ.log("DragAndDrop.drop: " + flavors.length + " flavors");
     for (int i = 0; i < flavors.length; i++) {
       if (IJ.debugMode) IJ.log("  flavor[" + i + "]: " + flavors[i].getMimeType());
       if (flavors[i].isFlavorJavaFileListType()) {
         Object data = t.getTransferData(DataFlavor.javaFileListFlavor);
         iterator = ((List) data).iterator();
         break;
       } else if (flavors[i].isFlavorTextType()) {
         Object ob = t.getTransferData(flavors[i]);
         if (!(ob instanceof String)) continue;
         String s = ob.toString().trim();
         if (IJ.isLinux() && s.length() > 1 && (int) s.charAt(1) == 0) s = fixLinuxString(s);
         ArrayList list = new ArrayList();
         if (s.indexOf("href=\"") != -1 || s.indexOf("src=\"") != -1) {
           s = parseHTML(s);
           if (IJ.debugMode) IJ.log("  url: " + s);
           list.add(s);
           this.iterator = list.iterator();
           break;
         }
         BufferedReader br = new BufferedReader(new StringReader(s));
         String tmp;
         while (null != (tmp = br.readLine())) {
           tmp = java.net.URLDecoder.decode(tmp.replaceAll("\\+", "%2b"), "UTF-8");
           if (tmp.startsWith("file://")) tmp = tmp.substring(7);
           if (IJ.debugMode) IJ.log("  content: " + tmp);
           if (tmp.startsWith("http://")) list.add(s);
           else list.add(new File(tmp));
         }
         this.iterator = list.iterator();
         break;
       }
     }
     if (iterator != null) {
       Thread thread = new Thread(this, "DrawAndDrop");
       thread.setPriority(Math.max(thread.getPriority() - 1, Thread.MIN_PRIORITY));
       thread.start();
     }
   } catch (Exception e) {
     dtde.dropComplete(false);
     return;
   }
   dtde.dropComplete(true);
   if (flavors == null || flavors.length == 0) {
     if (IJ.isMacOSX())
       IJ.error(
           "First drag and drop ignored. Please try again. You can avoid this\n"
               + "problem by dragging to the toolbar instead of the status bar.");
     else IJ.error("Drag and drop failed");
   }
 }
 /** Execute the system command 'cmd' and fill an ArrayList with the results. */
 public static ArrayList<String> executeSystemCommand(String cmd) {
   if (debug) System.out.println("cmd: " + cmd);
   ArrayList<String> list = new ArrayList<>();
   try (BufferedReader br =
       new BufferedReader(
           new InputStreamReader(RUNTIME.exec(/*comSpec +*/ cmd).getInputStream()))) {
     for (String line = null; (line = br.readLine()) != null; ) {
       if (debug) System.out.println(line);
       list.add(line);
     }
   } catch (IOException e) {
     e.printStackTrace();
   }
   return list;
 }
 public static String ping(String address) {
   String reply = "Request timed out";
   try (BufferedReader br =
       new BufferedReader(
           new InputStreamReader(RUNTIME.exec("ping " + address).getInputStream()))) {
     for (String line = null; (line = br.readLine()) != null; ) {
       if (line.trim().startsWith("Reply ")) {
         reply = line;
         break;
       }
     }
   } catch (IOException e) {
     e.printStackTrace();
   }
   return reply;
 }
 public static Properties getEnvironmentVariables() {
   synchronized (cygstartPath) {
     if (envVars != null) return envVars;
     envVars = new Properties();
     try (BufferedReader br =
         new BufferedReader(
             new InputStreamReader(RUNTIME.exec(comSpec + "env").getInputStream()))) {
       for (String line = null; (line = br.readLine()) != null; ) {
         // if (debug) System.out.println("getEnvironmentVariables(): line=" + line);
         int idx = line.indexOf('=');
         if (idx > 0) envVars.put(line.substring(0, idx), line.substring(idx + 1));
       }
     } catch (IOException e) {
       e.printStackTrace();
     }
     return envVars;
   }
 }
  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();
  }
  /**
   * Paste the contents of the clipboard into the console buffer
   *
   * @return true if clipboard contents pasted
   */
  public boolean paste() throws IOException {
    Clipboard clipboard;
    try { // May throw ugly exception on system without X
      clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
    } catch (Exception e) {
      return false;
    }

    if (clipboard == null) {
      return false;
    }

    Transferable transferable = clipboard.getContents(null);

    if (transferable == null) {
      return false;
    }

    try {
      Object content = transferable.getTransferData(DataFlavor.plainTextFlavor);

      /*
       * This fix was suggested in bug #1060649 at
       * http://sourceforge.net/tracker/index.php?func=detail&aid=1060649&group_id=64033&atid=506056
       * to get around the deprecated DataFlavor.plainTextFlavor, but it
       * raises a UnsupportedFlavorException on Mac OS X
       */
      if (content == null) {
        try {
          content = new DataFlavor().getReaderForText(transferable);
        } catch (Exception e) {
        }
      }

      if (content == null) {
        return false;
      }

      String value;

      if (content instanceof Reader) {
        // TODO: we might want instead connect to the input stream
        // so we can interpret individual lines
        value = "";

        String line = null;

        for (BufferedReader read = new BufferedReader((Reader) content);
            (line = read.readLine()) != null; ) {
          if (value.length() > 0) {
            value += "\n";
          }

          value += line;
        }
      } else {
        value = content.toString();
      }

      if (value == null) {
        return true;
      }

      putString(value);

      return true;
    } catch (UnsupportedFlavorException ufe) {
      if (debugger != null) debug(ufe + "");

      return false;
    }
  }
  /**
   * Try to determine whether this application is running under Windows or some other platform by
   * examining the "os.name" property.
   */
  static {
    String os = System.getProperty("os.name");
    // String version = System.getProperty("os.version"); // for Win7, reports "6.0" on JDK7, should
    // be "6.1"; for Win8, reports "6.2" as of JDK7u17

    if (SystemUtils.startsWithIgnoreCase(os, "windows 7"))
      isWin7 = true; // reports "Windows Vista" on JDK7
    else if (SystemUtils.startsWithIgnoreCase(os, "windows 8"))
      isWin7 = true; // reports "Windows 8" as of JDK7u17
    else if (SystemUtils.startsWithIgnoreCase(os, "windows vista")) isVista = true;
    else if (SystemUtils.startsWithIgnoreCase(os, "windows xp")) isWinXP = true;
    else if (SystemUtils.startsWithIgnoreCase(os, "windows 2000")) isWin2k = true;
    else if (SystemUtils.startsWithIgnoreCase(os, "windows nt")) isWinNT = true;
    else if (SystemUtils.startsWithIgnoreCase(os, "windows"))
      isWin9X = true; // win95 or win98 (what about WinME?)
    else if (SystemUtils.startsWithIgnoreCase(os, "mac")) isMac = true;
    else if (SystemUtils.startsWithIgnoreCase(os, "so")) isSolaris = true; // sunos or solaris
    else if (os.equalsIgnoreCase("linux")) isLinux = true;
    else isUnix = true; // assume UNIX, e.g. AIX, HP-UX, IRIX

    String osarch = System.getProperty("os.arch");
    String arch = (osarch != null && osarch.contains("64")) ? "_x64" /* eg. 'amd64' */ : "_x32";
    String syslib = SYSLIB + arch;

    try { // loading a native lib in a static initializer ensures that it is available before any
          // method in this class is called:
      System.loadLibrary(syslib);
      System.out.println(
          "Done loading '" + System.mapLibraryName(syslib) + "', PID=" + getProcessID());
    } catch (Error e) {
      System.err.println(
          "Native library '"
              + System.mapLibraryName(syslib)
              + "' not found in 'java.library.path': "
              + System.getProperty("java.library.path"));
      throw e; // re-throw
    }

    if (isWinPlatform()) {
      System.setProperty(
          "line.separator", "\n"); // so we won't have to mess with DOS line endings ever again
      comSpec =
          getEnv(
              "comSpec"); // use native method here since getEnvironmentVariable() needs to know
                          // comSpec
      comSpec = (comSpec != null) ? comSpec + " /c " : "";

      try (BufferedReader br =
          new BufferedReader(
              new InputStreamReader(
                  RUNTIME.exec(comSpec + "ver").getInputStream()))) { // fix for Win7,8
        for (String line = null; (line = br.readLine()) != null; ) {
          if (isVista && (line.contains("6.1" /*Win7*/) || line.contains("6.2" /*Win8*/))) {
            isVista = false;
            isWin7 = true;
          }
        }
      } catch (IOException e) {
        e.printStackTrace();
      }

      String cygdir = getEnv("cygdir"); // this is set during CygWin install to "?:/cygwin/bin"
      isCygWin = (cygdir != null && !cygdir.equals("%cygdir%"));
      cygstartPath = cygdir + "/cygstart.exe"; // path to CygWin's cygutils' "cygstart" binary

      if (getDebug() && Desktop.isDesktopSupported()) {
        Desktop desktop = Desktop.getDesktop();
        for (Desktop.Action action : Desktop.Action.values())
          System.out.println(
              "Desktop action " + action + " supported?  " + desktop.isSupported(action));
      }
    }
  }