protected void runScript(String[] cmd, JTextArea txaMsg) {
String strg = "";
if (cmd == null) return;
Process prcs = null;
try {
Messages.postDebug("Running script: " + cmd[2]);
Runtime rt = Runtime.getRuntime();
prcs = rt.exec(cmd);
if (prcs == null) return;
InputStream istrm = prcs.getInputStream();
if (istrm == null) return;
BufferedReader bfr = new BufferedReader(new InputStreamReader(istrm));
while ((strg = bfr.readLine()) != null) {
// System.out.println(strg);
strg = strg.trim();
// Messages.postDebug(strg);
strg = strg.toLowerCase();
if (txaMsg != null) {
txaMsg.append(strg);
txaMsg.append("\n");
}
}
} catch (Exception e) {
// e.printStackTrace();
Messages.writeStackTrace(e);
Messages.postDebug(e.toString());
} finally {
// It is my understanding that these streams are left
// open sometimes depending on the garbage collector.
// So, close them.
try {
if (prcs != null) {
OutputStream os = prcs.getOutputStream();
if (os != null) os.close();
InputStream is = prcs.getInputStream();
if (is != null) is.close();
is = prcs.getErrorStream();
if (is != null) is.close();
}
} catch (Exception ex) {
Messages.writeStackTrace(ex);
}
}
}
private void onOK() {
try {
InputStream in = new FileInputStream(inputFile);
if (outputFile == null) {
outputFile = new File(inputFile.getAbsolutePath() + "_");
}
OutputStream out = new FileOutputStream(outputFile);
ANSIUnicodeConverter converter = new ANSIUnicodeConverter();
converter.setDirection(ANSIUnicodeConverter.ANSI2UNICODE);
StringBuffer output = new StringBuffer();
final int BUFFER_SIZE = 1024 * 1024; // 1M
byte[] buffer = new byte[BUFFER_SIZE];
int currentPosition = 0;
while (in.available() != 0) {
int currentBufferSize = BUFFER_SIZE;
if (in.available() < BUFFER_SIZE) {
currentBufferSize = in.available();
}
in.read(buffer, currentPosition, currentBufferSize);
currentBufferSize = currentBufferSize + currentBufferSize;
converter.setInput(new String(buffer));
out.write(converter.convert().getBytes());
}
in.close();
out.close();
} catch (Exception e) {
e
.printStackTrace(); // To change body of catch statement use File | Settings | File
// Templates.
}
}
/**
* Loads the drawing. By convention this method is invoked on a worker thread.
*
* @param progress A ProgressIndicator to inform the user about the progress of the operation.
* @return The Drawing that was loaded.
*/
protected Drawing loadDrawing(ProgressIndicator progress) throws IOException {
Drawing drawing = createDrawing();
if (getParameter("datafile") != null) {
URL url = new URL(getDocumentBase(), getParameter("datafile"));
URLConnection uc = url.openConnection();
// Disable caching. This ensures that we always request the
// newest version of the drawing from the server.
// (Note: The server still needs to set the proper HTTP caching
// properties to prevent proxies from caching the drawing).
if (uc instanceof HttpURLConnection) {
((HttpURLConnection) uc).setUseCaches(false);
}
// Read the data into a buffer
int contentLength = uc.getContentLength();
InputStream in = uc.getInputStream();
try {
if (contentLength != -1) {
in = new BoundedRangeInputStream(in);
((BoundedRangeInputStream) in).setMaximum(contentLength + 1);
progress.setProgressModel((BoundedRangeModel) in);
progress.setIndeterminate(false);
}
BufferedInputStream bin = new BufferedInputStream(in);
bin.mark(512);
// Read the data using all supported input formats
// until we succeed
IOException formatException = null;
for (InputFormat format : drawing.getInputFormats()) {
try {
bin.reset();
} catch (IOException e) {
uc = url.openConnection();
in = uc.getInputStream();
in = new BoundedRangeInputStream(in);
((BoundedRangeInputStream) in).setMaximum(contentLength + 1);
progress.setProgressModel((BoundedRangeModel) in);
bin = new BufferedInputStream(in);
bin.mark(512);
}
try {
bin.reset();
format.read(bin, drawing, true);
formatException = null;
break;
} catch (IOException e) {
formatException = e;
}
}
if (formatException != null) {
throw formatException;
}
} finally {
in.close();
}
}
return drawing;
}
// Essentially links an InputStream to the proper channels in the log box.
private static void printOutput(InputStream in, SimpleAttributeSet set) {
int i = 0;
String s = "";
try {
while ((i = in.read()) != -1) {
s += (char) i;
// print(, set);
}
} catch (IOException io) {
println("Error: IOException when reading InputStream " + in.toString(), progErr);
}
println(s);
}
public void run(String local, String remote, InputStream pin, OutputStream pout) {
try {
microphone = SoundMixerEnumerator.getInputLine(pcmformat, DefaultPhonePCMBlockSize);
} catch (LineUnavailableException lue) {
System.out.println(
"\3b"
+ getClass().getName()
+ ".<init>:\n\tCould not create microphone input stream.\n\t"
+ lue);
}
try {
speaker = SoundMixerEnumerator.getOutputLine(pcmformat, DefaultPhonePCMBlockSize);
} catch (LineUnavailableException lue) {
microphone.close();
System.out.println(
"\3b"
+ getClass().getName()
+ ".<init>:\n\tCould not create speaker output stream.\n\t"
+ lue);
}
if ((speaker == null) || (microphone == null)) {
super.run(local, remote, pin, pout);
return;
}
try {
recorder = new Recorder(pout);
recorder.start();
gui = openMonitorGUI("Remote " + remote + " Local " + local);
pin.skip(pin.available()); // waste whatever we couldn't process in time
super.run(local, remote, new PhoneCallMonitorInputStream(pin), pout);
recorder.interrupt();
gui.dispose();
} catch (Exception e) {
System.out.println("3\b" + getClass().getName() + ".run:\n\t" + e);
e.printStackTrace();
} finally {
deactivate();
microphone.close();
speaker.close();
if (gui != null) {
gui.dispose();
}
}
}
/**
* ** Reads a line from the specified socket's input stream ** @param socket The socket to read a
* line from ** @param maxLen The maximum length of of the line to read ** @param sb The string
* buffer to use ** @throws IOException if an error occurs or the server has stopped
*/
protected static String socketReadLine(Socket socket, int maxLen, StringBuffer sb)
throws IOException {
if (socket != null) {
int dataLen = 0;
StringBuffer data = (sb != null) ? sb : new StringBuffer();
InputStream input = socket.getInputStream();
while ((maxLen < 0) || (maxLen > dataLen)) {
int ch = input.read();
// Print.logInfo("ReadLine char: " + ch);
if (ch < 0) {
// this means that the server has stopped
throw new IOException("End of input");
} else if (ch == LineTerminatorChar) {
// include line terminator in String
data.append((char) ch);
dataLen++;
break;
} else {
// append character
data.append((char) ch);
dataLen++;
}
}
return data.toString();
} else {
return null;
}
}
private final String readMSG(final int len)
throws IOException, InterruptedException, MessagingNetworkException {
if (len > 65000)
ServerConnection.throwProtocolViolated("incoming message is too long: " + len + " bytes");
byte[] b = new byte[len];
InputStream is = getInputStream();
synchronized (is) {
long abortTime =
System.currentTimeMillis() + 1000 * MSNMessagingNetwork.REQPARAM_SOCKET_TIMEOUT_SECONDS;
int ofs = 0;
while (ofs < len) {
if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
int read = is.read(b, ofs, len - ofs);
if (read < 0) read = 0;
ofs += read;
if (System.currentTimeMillis() > abortTime) throw new IOException("connection timed out");
/*
if (len >= buffer.length)
{
...
return ...;
}
int pos = findCRLF();
if (pos != -1) break;
fill(is, abortTime);
*/
}
String msg = new String(b, 0, len, "UTF-8");
return msg;
}
}
private void seticon() {
Image icon;
try {
InputStream data = MainFrame.class.getResourceAsStream("icon.png");
icon = javax.imageio.ImageIO.read(data);
data.close();
} catch (IOException e) {
throw (new Error(e));
}
setIconImage(icon);
}
public final String readCommand(byte[] b)
throws IOException, InterruptedException, MessagingNetworkException {
InputStream is = getInputStream();
synchronized (is) {
long abortTime =
System.currentTimeMillis() + 1000 * MSNMessagingNetwork.REQPARAM_SOCKET_TIMEOUT_SECONDS;
int ofs = 0;
boolean d = false;
for (; ; ) {
if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
int by = is.read();
if (by == -1) throw new IOException("unexpected EOF");
if (by == 10 && d) break;
d = (by == 13);
if (ofs < b.length) {
b[ofs++] = (byte) by;
}
if (System.currentTimeMillis() > abortTime) throw new IOException("connection timed out");
/*
if (len >= buffer.length)
{
...
return ...;
}
int pos = findCRLF();
if (pos != -1) break;
fill(is, abortTime);
*/
}
if (b[ofs - 1] == 13) --ofs;
String line = new String(b, 0, ofs, "ASCII");
if (StringUtil.startsWith(line, "MSG")) {
StringTokenizer st = new StringTokenizer(line);
String len_s = null;
while (st.hasMoreTokens()) {
len_s = st.nextToken();
}
if (len_s == null) throw new AssertException("len_s is null");
int len;
try {
len = Integer.parseInt(len_s);
} catch (NumberFormatException ex) {
ServerConnection.throwProtocolViolated("MSG length must be int");
len = 0;
}
String msg = readMSG(len);
line = line + "\r\n" + msg;
}
if (Defines.DEBUG && CAT.isDebugEnabled()) CAT.debug("S: " + line);
return line;
}
}
Ps2RealityControlCenter(String dir) throws IOException {
try {
byte[] abIcon;
InputStream inputstreamIcon = this.getClass().getResourceAsStream("icon.gif");
int iIconSize = inputstreamIcon.available();
abIcon = new byte[iIconSize];
inputstreamIcon.read(abIcon);
this.setIconImage(new ImageIcon(abIcon).getImage());
} catch (Exception ex) {
// the default icon will be used
}
panelChooser = new Ps2RealityFileChooser(dir);
}
public void load(ActionEvent e) {
int returnVal = fc.showOpenDialog(this);
if (returnVal != JFileChooser.APPROVE_OPTION) {
return;
}
file = fc.getSelectedFile();
try {
InputStream in = new BufferedInputStream(new FileInputStream(file));
Properties newWl = new Properties();
newWl.load(in);
in.close();
setWordList(newWl);
} catch (IOException ex) {
handleException(ex);
}
}
public void run() {
try {
final byte[] lBuf = new byte[1024];
int lBytesRead;
while (in.read(lBuf, 0, 1) != -1) {
synchronized (JConsole.this) {
lBytesRead = in.read(lBuf, 1, 1023) + 1;
print(new String(lBuf, 0, lBytesRead), attr);
while (in.available() > 0) {
lBytesRead = in.read(lBuf);
print(new String(lBuf, 0, lBytesRead), attr);
}
}
}
} catch (IOException e) {
e.printStackTrace();
}
}
public void setData(String text) {
if (text != null && text.length() > 0) {
InputStream in = null;
try {
Object result = null;
Drawing drawing = createDrawing();
// Try to read the data using all known input formats.
for (InputFormat fmt : drawing.getInputFormats()) {
try {
fmt.read(in, drawing);
in = new ByteArrayInputStream(text.getBytes("UTF8"));
result = drawing;
break;
} catch (IOException e) {
result = e;
}
}
if (result instanceof IOException) {
throw (IOException) result;
}
setDrawing(drawing);
} catch (Throwable e) {
getDrawing().removeAllChildren();
SVGTextFigure tf = new SVGTextFigure();
tf.setText(e.getMessage());
tf.setBounds(new Point2D.Double(10, 10), new Point2D.Double(100, 100));
getDrawing().add(tf);
e.printStackTrace();
} finally {
if (in != null) {
try {
in.close();
} catch (IOException ex) {
ex.printStackTrace();
}
}
}
}
}
/**
* ** Reads the specified number of bytes from the specifed socket ** @param socket The socket
* from which bytes are read ** @param length The number of bytes to read from the socket
* ** @throws IOException if an error occured or the server has stopped
*/
protected static byte[] socketReadBytes(Socket socket, int length) throws IOException {
if (socket == null) {
return null;
} else if (length <= 0) {
return new byte[0];
} else {
int dataLen = 0;
byte data[] = new byte[length];
InputStream input = socket.getInputStream();
while (dataLen < length) {
int ch = input.read();
if (ch < 0) {
// this means that the server has stopped
throw new IOException("End of input");
} else {
data[dataLen] = (byte) ch;
dataLen++;
}
}
return data;
}
}
private static void copyfile(String srFile, String dtFile) {
try {
File f1 = new File(srFile);
File f2 = new File(dtFile);
InputStream in = new FileInputStream(f1);
// For Overwrite the file.
OutputStream out = new FileOutputStream(f2);
byte[] buf = new byte[1024];
int len;
while ((len = in.read(buf)) > 0) {
out.write(buf, 0, len);
}
in.close();
out.close();
EIError.debugMsg("File copied " + srFile + " " + dtFile, EIError.ErrorLevel.Notice);
} catch (Exception e) {
EIError.debugMsg(
"Couldn't copy file" + srFile + " " + dtFile + " " + e.getMessage(),
EIError.ErrorLevel.Error);
}
}
public java.util.List<String> readTextFromJar(String s) {
InputStream is = null;
BufferedReader br = null;
String line;
ArrayList<String> list = new ArrayList<String>();
try {
is = getClass().getResourceAsStream(s);
br = new BufferedReader(new InputStreamReader(is));
while (null != (line = br.readLine())) {
list.add(line);
}
} catch (Exception e) {
e.printStackTrace();
} finally {
try {
if (br != null) br.close();
if (is != null) is.close();
} catch (IOException e) {
e.printStackTrace();
}
}
return list;
}
/**
* Copy data from an input stream to an output stream.
*
* @param in Input stream.
* @param out Output stream.
* @throws IOException
*/
public static void copy(InputStream in, OutputStream out) throws IOException {
// Do not allow other threads to read from the
// input or write to the output while copying is
// taking place
synchronized (in) {
synchronized (out) {
byte[] buffer = new byte[1024];
while (true) {
int bytesRead = in.read(buffer);
if (bytesRead == -1) break;
out.write(buffer, 0, bytesRead);
}
}
}
}
/**
* ** Reads the bytes from the specifed socket until an eod-of-stream error occurs, or ** until
* the maximum number of bytes has bee read. ** @param socket The socket from which bytes are read
* ** @param baos The ByteArrayOutputStream to which the bytes are written ** @param maxLength The
* number of bytes to read from the socket ** @return The number of bytes read if no exception has
* occurred ** @throws IOException if an error occured or the server has stopped
*/
protected static int socketReadBytes(Socket socket, ByteArrayOutputStream baos, int maxLength)
throws IOException {
if (socket == null) {
return 0;
} else if (maxLength == 0) {
return 0;
} else {
int dataLen = 0;
InputStream input = socket.getInputStream();
while ((maxLength < 0) || (dataLen < maxLength)) {
int ch = input.read();
if (ch < 0) {
// we've reached the end of input
return dataLen;
} else {
if (baos != null) {
baos.write(ch);
}
dataLen++;
}
}
return dataLen;
}
}
public void ClosePort() {
if (portOpened) {
if (serialPort != null) {
try {
// Close the I/O streams.
out.close();
in.close();
// Close the port.
serialPort.removeEventListener();
serialPort.close();
} catch (IOException e) {
// Don't care
}
}
ClearLog();
portOpened = false;
portConfirmed = false;
previewPane.setConnected(false);
UpdateMenuBar();
}
}
// Deal with something robot has sent.
public void serialEvent(SerialPortEvent events) {
switch (events.getEventType()) {
case SerialPortEvent.DATA_AVAILABLE:
try {
final byte[] buffer = new byte[1024];
int len = in.read(buffer);
if (len > 0) {
String line2 = new String(buffer, 0, len);
Log("<span style='color:#FFA500'>" + line2.replace("\n", "<br>") + "</span>");
line3 += line2;
// wait for the cue ("> ") to send another command
if (line3.lastIndexOf(cue) != -1) {
if (ConfirmPort()) {
line3 = "";
SendFileCommand();
}
}
}
} catch (IOException e) {
}
break;
}
}
public static boolean showLicensing() {
if (Config.getLicenseResource() == null) return true;
ClassLoader cl = Main.class.getClassLoader();
URL url = cl.getResource(Config.getLicenseResource());
if (url == null) return true;
String license = null;
try {
URLConnection con = url.openConnection();
int size = con.getContentLength();
byte[] content = new byte[size];
InputStream in = new BufferedInputStream(con.getInputStream());
in.read(content);
license = new String(content);
} catch (IOException ioe) {
Config.trace("Got exception when reading " + Config.getLicenseResource() + ": " + ioe);
return false;
}
// Build dialog
JTextArea ta = new JTextArea(license);
ta.setEditable(false);
final JDialog jd = new JDialog(_installerFrame, true);
Container comp = jd.getContentPane();
jd.setTitle(Config.getLicenseDialogTitle());
comp.setLayout(new BorderLayout(10, 10));
comp.add(new JScrollPane(ta), "Center");
Box box = new Box(BoxLayout.X_AXIS);
box.add(box.createHorizontalStrut(10));
box.add(new JLabel(Config.getLicenseDialogQuestionString()));
box.add(box.createHorizontalGlue());
JButton acceptButton = new JButton(Config.getLicenseDialogAcceptString());
JButton exitButton = new JButton(Config.getLicenseDialogExitString());
box.add(acceptButton);
box.add(box.createHorizontalStrut(10));
box.add(exitButton);
box.add(box.createHorizontalStrut(10));
jd.getRootPane().setDefaultButton(acceptButton);
Box box2 = new Box(BoxLayout.Y_AXIS);
box2.add(box);
box2.add(box2.createVerticalStrut(5));
comp.add(box2, "South");
jd.pack();
final boolean accept[] = new boolean[1];
acceptButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
accept[0] = true;
jd.hide();
jd.dispose();
}
});
exitButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
accept[0] = false;
jd.hide();
jd.dispose();
}
});
// Apply any defaults the user may have, constraining to the size
// of the screen, and default (packed) size.
Rectangle size = new Rectangle(0, 0, 500, 300);
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
size.width = Math.min(screenSize.width, size.width);
size.height = Math.min(screenSize.height, size.height);
// Center the window
jd.setBounds(
(screenSize.width - size.width) / 2,
(screenSize.height - size.height) / 2,
size.width,
size.height);
// Show dialog
jd.show();
return accept[0];
}
public void fetchExternalJSLibrary(String targetURLString) {
final URL targetURL;
String targetFile = "";
String s = null;
InputStream is = null;
BufferedReader dis = null;
try {
// ------------------------------------------------------------//
// Step 2: Create the URL. //
// ------------------------------------------------------------//
// Note: Put your real URL here, or better yet, read it as a //
// command-line arg, or read it from a file. //
// ------------------------------------------------------------//
targetURL = new URL(targetURLString);
// ----------------------------------------------//
// Step 3: Open an input stream from the url. //
// ----------------------------------------------//
is = targetURL.openStream();
// -------------------------------------------------------------//
// Step 4: //
// -------------------------------------------------------------//
// Convert the InputStream to BufferedReader //
// -------------------------------------------------------------//
dis = new BufferedReader(new InputStreamReader(is));
// ------------------------------------------------------------//
// Step 5: //
// ------------------------------------------------------------//
// Now just read each record of the input stream, and print //
// it out. Note that it's assumed that this problem is run //
// from a command-line, not from an application or applet. //
// ------------------------------------------------------------//
while ((s = dis.readLine()) != null) {
targetFile = targetFile + "\n" + s;
}
alert(targetFile);
System.out.println(targetFile);
} catch (MalformedURLException mue) {
alert("Ouch - a MalformedURLException happened.");
System.out.println("Ouch - a MalformedURLException happened.");
mue.printStackTrace();
System.exit(1);
} catch (IOException ioe) {
alert("Ouch - an IOException happened.");
System.out.println("Ouch - an IOException happened.");
ioe.printStackTrace();
System.exit(1);
} catch (Exception e) {
alert("Ouch - Something wrong happened.");
alert(e.toString());
alert(e.getMessage());
} finally {
// ---------------------------------//
// Step 6: Close the InputStream //
// ---------------------------------//
try {
is.close();
dis.close();
} catch (IOException ioe) {
// just going to ignore this one
}
} // end of 'finally' clause
}
/** Determine JDK level of an applet. */
private void findAppletJDKLevel(Applet applet) {
// To determine the JDK level of an applet, the
// most reliable way is to check the major version
// of the applet class file.
// synchronized on applet class object, so calling from
// different instances of the same applet will be
// serialized.
Class<?> appletClass = applet.getClass();
synchronized (appletClass) {
// Determine if the JDK level of an applet has been
// checked before.
Boolean jdk11Target = loader.isJDK11Target(appletClass);
Boolean jdk12Target = loader.isJDK12Target(appletClass);
// if applet JDK level has been checked before, retrieve
// value and return.
if (jdk11Target != null || jdk12Target != null) {
jdk11Applet = (jdk11Target == null) ? false : jdk11Target.booleanValue();
jdk12Applet = (jdk12Target == null) ? false : jdk12Target.booleanValue();
return;
}
String name = appletClass.getName();
// first convert any '.' to '/'
name = name.replace('.', '/');
// append .class
final String resourceName = name + ".class";
byte[] classHeader = new byte[8];
try (InputStream is =
AccessController.doPrivileged(
(PrivilegedAction<InputStream>) () -> loader.getResourceAsStream(resourceName))) {
// Read the first 8 bytes of the class file
int byteRead = is.read(classHeader, 0, 8);
// return if the header is not read in entirely
// for some reasons.
if (byteRead != 8) return;
} catch (IOException e) {
return;
}
// Check major version in class file header
int major_version = readShort(classHeader, 6);
// Major version in class file is as follows:
// 45 - JDK 1.1
// 46 - JDK 1.2
// 47 - JDK 1.3
// 48 - JDK 1.4
// 49 - JDK 1.5
if (major_version < 46) jdk11Applet = true;
else if (major_version == 46) jdk12Applet = true;
// Store applet JDK level in AppContext for later lookup,
// e.g. page switch.
loader.setJDK11Target(appletClass, jdk11Applet);
loader.setJDK12Target(appletClass, jdk12Applet);
}
}
/** Unpacks a resource to a temp. file */
public static File unpackInstaller(String resourceName) {
// Array to hold all results (this code is slightly more
// generally that it needs to be)
File[] results = new File[1];
URL[] urls = new URL[1];
// Determine size of download
ClassLoader cl = Main.class.getClassLoader();
urls[0] = cl.getResource(Config.getInstallerResource());
if (urls[0] == null) {
Config.trace("Could not find resource: " + Config.getInstallerResource());
return null;
}
int totalSize = 0;
int totalRead = 0;
for (int i = 0; i < urls.length; i++) {
if (urls[i] != null) {
try {
URLConnection connection = urls[i].openConnection();
totalSize += connection.getContentLength();
} catch (IOException ioe) {
Config.trace("Got exception: " + ioe);
return null;
}
}
}
// Unpack each file
for (int i = 0; i < urls.length; i++) {
if (urls[i] != null) {
// Create temp. file to store unpacked file in
InputStream in = null;
OutputStream out = null;
try {
// Use extension from URL (important for dll files)
String extension = new File(urls[i].getFile()).getName();
int lastdotidx = (extension != null) ? extension.lastIndexOf('.') : -1;
if (lastdotidx == -1) {
extension = ".dat";
} else {
extension = extension.substring(lastdotidx);
}
// Create output stream
results[i] = File.createTempFile("jre", extension);
results[i].deleteOnExit();
out = new FileOutputStream(results[i]);
// Create inputstream
URLConnection connection = urls[i].openConnection();
in = connection.getInputStream();
int read = 0;
byte[] buf = new byte[BUFFER_SIZE];
while ((read = in.read(buf)) != -1) {
out.write(buf, 0, read);
// Notify delegate
totalRead += read;
if (totalRead > totalSize && totalSize != 0) totalSize = totalRead;
// Update UI
if (totalSize != 0) {
int percent = (100 * totalRead) / totalSize;
setStepText(STEP_UNPACK, Config.getWindowStepProgress(STEP_UNPACK, percent));
}
}
} catch (IOException ie) {
Config.trace("Got exception while downloading resource: " + ie);
for (int j = 0; j < results.length; j++) {
if (results[j] != null) results[j].delete();
}
return null;
} finally {
try {
if (in != null) in.close();
if (out != null) out.close();
} catch (IOException io) {
/* ignore */
}
}
}
}
setStepText(STEP_UNPACK, Config.getWindowStep(STEP_UNPACK));
return results[0];
}
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();
}