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);
}
// tokenizes a string for PBM and PGM headers and plain PBM and PGM data. If oneChar is true,
// then
// rather than parsing a whole string, a single character is read (not including whitespace or
// comments)
static String tokenizeString(InputStream stream, boolean oneChar) throws IOException {
final int EOF = -1;
StringBuilder b = new StringBuilder();
int c;
boolean inComment = false;
while (true) {
c = stream.read();
if (c == EOF)
throw new IOException(
"Stream ended prematurely, before table reading was completed."); // no more tokens
else if (inComment) {
if (c == '\r' || c == '\n') // escape the comment
inComment = false;
else {
} // do nothing
} else if (Character.isWhitespace((char) c)) {
} // do nothing
else if (c == '#') // start of a comment
{
inComment = true;
} else // start of a string
{
b.append((char) c);
break;
}
}
if (oneChar) return b.toString();
// at this point we have a valid string. We read until whitespace or a #
while (true) {
c = stream.read();
if (c == EOF) break;
else if (c == '#') // start of comment, read until a '\n'
{
while (true) {
c = stream.read(); // could hit EOF, which is fine
if (c == EOF) break;
else if (c == '\r' || c == '\n') break;
}
// break; // comments are not delimiters
} else if (Character.isWhitespace((char) c)) break;
else b.append((char) c);
}
return b.toString();
}
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();
}
}
}
private static Clip getClip(String wavFile) {
String soundName = "sound\\" + wavFile + ".wav";
InputStream sound = null;
Clip clip = null;
try {
sound = new FileInputStream(soundName);
} catch (FileNotFoundException ex) {
sound = ClassLoader.getSystemResourceAsStream(soundName);
if (sound == null) {
System.out.println("Cant open file " + soundName);
return null;
}
}
try {
AudioInputStream audioIn = AudioSystem.getAudioInputStream(sound);
clip = AudioSystem.getClip();
clip.open(audioIn);
} catch (Exception ex) {
System.out.println("Error in sound " + wavFile);
System.out.println(ex.getMessage());
if (clip != null) {
clip.close();
return null;
}
try {
sound.close();
} catch (IOException e) {
}
}
return clip;
}
/**
* Take the name of a jar file and extract the plugin.xml file, if possible, to a temporary file.
*
* @param f The jar file to extract from.
* @return a temporary file to which the plugin.xml file has been copied.
*/
public static File unpackPluginXML(File f) {
InputStream in = null;
OutputStream out = null;
try {
JarFile jar = new JarFile(f);
ZipEntry entry = jar.getEntry(PLUGIN_XML_FILE);
if (entry == null) {
return null;
}
File dest = File.createTempFile("jabref_plugin", ".xml");
dest.deleteOnExit();
in = new BufferedInputStream(jar.getInputStream(entry));
out = new BufferedOutputStream(new FileOutputStream(dest));
byte[] buffer = new byte[2048];
for (; ; ) {
int nBytes = in.read(buffer);
if (nBytes <= 0) break;
out.write(buffer, 0, nBytes);
}
out.flush();
return dest;
} catch (IOException ex) {
ex.printStackTrace();
return null;
} finally {
try {
if (out != null) out.close();
if (in != null) in.close();
} catch (IOException ex) {
ex.printStackTrace();
}
}
}
/** execute method之后,取返回的inputstream */
private static ByteArrayInputStream execute4InputStream(HttpClient client) throws Exception {
int statusCode = client.getResponseCode();
if (statusCode != HttpURLConnection.HTTP_OK) {
throw new EnvException("Method failed: " + statusCode);
}
InputStream in = client.getResponseStream();
if (in == null) {
return null;
}
ByteArrayOutputStream out = new ByteArrayOutputStream();
try {
Utils.copyBinaryTo(in, out);
// 看一下传过来的byte[]是不是DesignProcessor.INVALID,如果是的话,就抛Exception
byte[] bytes = out.toByteArray();
// carl：格式一致传中文
String message = new String(bytes, EncodeConstants.ENCODING_UTF_8);
if (ComparatorUtils.equals(message, RemoteDeziConstants.NO_SUCH_RESOURCE)) {
return null;
} else if (ComparatorUtils.equals(message, RemoteDeziConstants.INVALID_USER)) {
throw new EnvException(RemoteDeziConstants.INVALID_USER);
} else if (ComparatorUtils.equals(message, RemoteDeziConstants.FILE_LOCKED)) {
JOptionPane.showMessageDialog(null, Inter.getLocText("FR-Designer_file-is-locked"));
return null;
} else if (message.startsWith(RemoteDeziConstants.RUNTIME_ERROR_PREFIX)) {
}
return new ByteArrayInputStream(bytes);
} finally {
in.close();
out.close();
client.release();
}
}
static int checkAck(InputStream in) throws IOException {
int b = in.read();
// b may be 0 for success,
// 1 for error,
// 2 for fatal error,
// -1
if (b == 0) return b;
if (b == -1) return b;
if (b == 1 || b == 2) {
StringBuffer sb = new StringBuffer();
int c;
do {
c = in.read();
sb.append((char) c);
} while (c != '\n');
if (b == 1) { // error
System.out.print(sb.toString());
}
if (b == 2) { // fatal error
System.out.print(sb.toString());
}
}
return b;
}
@SuppressWarnings({"HardCodedStringLiteral"})
@Nullable
public static String getPropertyFromLaxFile(
@NotNull final File file, @NotNull final String propertyName) {
if (file.getName().endsWith(".properties")) {
try {
PropertyResourceBundle bundle;
InputStream fis = new BufferedInputStream(new FileInputStream(file));
try {
bundle = new PropertyResourceBundle(fis);
} finally {
fis.close();
}
if (bundle.containsKey(propertyName)) {
return bundle.getString(propertyName);
}
return null;
} catch (IOException e) {
return null;
}
}
final String fileContent = getContent(file);
// try to find custom config path
final String propertyValue = findProperty(propertyName, fileContent);
if (!StringUtil.isEmpty(propertyValue)) {
return propertyValue;
}
return null;
}
// Loads raw PGM files after the first-line header is stripped
static int[][] loadRawPGM(InputStream stream) throws IOException {
int width = tokenizeInt(stream);
int height = tokenizeInt(stream);
int maxVal = tokenizeInt(stream);
if (width < 0) throw new IOException("Invalid width: " + width);
if (height < 0) throw new IOException("Invalid height: " + height);
if (maxVal <= 0) throw new IOException("Invalid maximum value: " + maxVal);
// this single whitespace character will have likely already been consumed by reading maxVal
// stream.read(); // must be a whitespace
int[][] field = new int[width][height];
for (int i = 0; i < height; i++)
for (int j = 0; j < width; j++) {
if (maxVal < 256) // one byte
field[j][i] = stream.read();
else if (maxVal < 65536) // two bytes
field[j][i] =
(stream.read() << 8) & stream.read(); // two bytes, most significant byte first
else if (maxVal < 16777216) // three bytes -- this is nonstandard
field[j][i] =
(stream.read() << 16)
& (stream.read() << 8)
& stream.read(); // three bytes, most significant byte first
else // four bytes -- this is nonstandard
field[j][i] =
(stream.read() << 24)
& (stream.read() << 16)
& (stream.read() << 8)
& stream.read(); // three bytes, most significant byte first
}
return field;
}
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 static boolean hashMatch(InputStream is, byte[] hash) throws IOException {
boolean correct = true;
for (int i = 0; i < hash.length; i++) {
if (hash[i] != (byte) is.read()) correct = false;
}
return correct;
}
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);
}
}
// Loads raw PBM files after the first-line header is stripped
static int[][] loadRawPBM(InputStream stream) throws IOException {
int width = tokenizeInt(stream);
int height = tokenizeInt(stream);
if (width < 0) throw new IOException("Invalid width in PBM: " + width);
if (height < 0) throw new IOException("Invalid height in PBM: " + height);
// this single whitespace character will have likely already been consumed by reading height
// stream.read(); // must be a whitespace
int[][] field = new int[width][height];
for (int i = 0; i < height; i++) {
int data = 0;
int count = 0;
for (int j = 0; j < width; j++) {
if (count == 0) {
data = stream.read();
count = 8;
}
count--;
field[j][i] = (data >> count) & 0x1;
}
}
return field;
}
/**
* Loads an image from a given image identifier.
*
* @param imageID The identifier of the image.
* @return The image for the given identifier.
*/
@Override
public byte[] getImageInBytes(String imageID) {
InputStream in = getImageInputStream(imageID);
if (in == null) return null;
byte[] image = null;
try {
image = new byte[in.available()];
in.read(image);
} catch (IOException e) {
logger.error("Failed to load image:" + imageID, e);
}
return image;
}
// wonder if throwing error on end of stream f***s over other implementations? :P
public static long readInteger(InputStream is) throws IOException {
byte[] isr = new byte[8];
for (int b = 0; b < isr.length; b++) {
int r = is.read();
if (r == -1) throw new IOException("readInt failed at end of stream");
isr[b] = (byte) r;
}
ByteBuffer bb = ByteBuffer.wrap(isr);
return bb.getLong();
}
public synchronized void loadProperties() {
if (dataDir != null) {
propertyFile = new File(dataDir, USER_FILENAME);
// load font properties from last invocation
if (propertyFile.exists()) {
try {
InputStream in = new FileInputStream(propertyFile);
try {
fontProps.load(in);
fontManager.setFontProperties(fontProps);
} finally {
in.close();
}
} catch (IOException ex) {
// check to make sure the storage relate dialogs can be shown
if (getBoolean("application.showLocalStorageDialogs", true)) {
Resources.showMessageDialog(
null,
JOptionPane.ERROR_MESSAGE,
messageBundle,
"fontManager.properties.title",
"manager.properties.session.readError",
ex);
}
// log the error
if (logger.isLoggable(Level.WARNING)) {
logger.log(Level.WARNING, "Error loading font properties cache", ex);
}
} catch (IllegalArgumentException e) {
// propblem parsing fontProps, reread teh file
setupDefaultProperties();
saveProperties();
}
}
// If no font data, then read font data and save the new file.
else {
setupDefaultProperties();
saveProperties();
}
}
}
public static void hashpipe(InputStream is, OutputStream os, long len, MessageDigest md)
throws IOException {
byte[] buf = new byte[SMALL_BUFF];
long read = 0;
while (read < len) {
int thisRead = is.read(buf, 0, (int) Math.min(SMALL_BUFF, len - read));
read += thisRead;
os.write(buf, 0, thisRead);
md.update(buf, 0, thisRead);
}
}
static byte[] readStream(InputStream input) throws IOException {
ByteArrayOutputStream bytes = new ByteArrayOutputStream();
int read;
byte[] buffer = new byte[256];
while ((read = input.read(buffer, 0, 256)) != -1) {
bytes.write(buffer, 0, read);
}
return bytes.toByteArray();
}
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();
}
}
}
}
}
public static void copyFolder(File src, File dest, JLabel updatelbl, JLabel updatelbl2)
throws IOException {
if (src.isDirectory()) {
if (!dest.exists()) {
dest.mkdir();
updatelbl.setText("Directory copied from " + src + " to " + dest);
}
String files[] = src.list();
for (String file : files) {
File srcFile = new File(src, file);
File destFile = new File(dest, file);
// recursive copy
copyFolder(srcFile, destFile, updatelbl, updatelbl2);
}
} else {
InputStream in = new FileInputStream(src);
OutputStream out = new FileOutputStream(dest);
byte[] buffer = new byte[1024];
int length;
while ((length = in.read(buffer)) > 0) {
out.write(buffer, 0, length);
}
in.close();
out.close();
updatelbl.setText("File copied from " + src);
updatelbl2.setText(" to " + dest);
}
}
private static void copyFileFromJar(String sourceFileName, File target) {
try {
JarFile jar = new JarFile(privateInstance.getHome());
ZipEntry entry = jar.getEntry(sourceFileName);
InputStream inputStream = new BufferedInputStream(jar.getInputStream(entry));
OutputStream outputStream = new BufferedOutputStream(new FileOutputStream(target));
byte[] buffer = new byte[4096];
for (; ; ) {
int nBytes = inputStream.read(buffer);
if (nBytes <= 0) break;
outputStream.write(buffer, 0, nBytes);
}
outputStream.flush();
outputStream.close();
inputStream.close();
} catch (FileNotFoundException e) {
JOptionPane.showMessageDialog(null, e);
} catch (IOException e) {
JOptionPane.showMessageDialog(null, e);
}
}
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;
}
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 void main(String[] args) {
// read filename and N 2 parameters
String fileName = args[0];
N = Integer.parseInt(args[1]);
// output two images, one original image at left, the other result image at right
BufferedImage imgOriginal =
new BufferedImage(IMAGE_WIDTH, IMAGE_HEIGHT, BufferedImage.TYPE_INT_RGB);
BufferedImage img = new BufferedImage(IMAGE_WIDTH, IMAGE_HEIGHT, BufferedImage.TYPE_INT_RGB);
try {
File file = new File(fileName);
InputStream is = new FileInputStream(file);
long len = file.length();
byte[] bytes = new byte[(int) len];
int offset = 0;
int numRead = 0;
while (offset < bytes.length
&& (numRead = is.read(bytes, offset, bytes.length - offset)) >= 0) {
offset += numRead;
}
int ind = 0;
for (int y = 0; y < IMAGE_HEIGHT; y++) {
for (int x = 0; x < IMAGE_WIDTH; x++) {
// for reading .raw image to show as a rgb image
byte r = bytes[ind];
byte g = bytes[ind];
byte b = bytes[ind];
// set pixel for display original image
int pixOriginal = 0xff000000 | ((r & 0xff) << 16) | ((g & 0xff) << 8) | (b & 0xff);
imgOriginal.setRGB(x, y, pixOriginal);
ind++;
}
}
is.close();
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
int[] vectorSpace = calculateVectorSpace(imgOriginal);
// quantization
for (int y = 0; y < IMAGE_HEIGHT; y++) {
for (int x = 0; x < IMAGE_WIDTH; x++) {
int clusterId = vectorSpace[IMAGE_WIDTH * y + x];
img.setRGB(x, y, clusters[clusterId].getPixel());
}
}
// Use a panel and label to display the image
JPanel panel = new JPanel();
panel.add(new JLabel(new ImageIcon(imgOriginal)));
panel.add(new JLabel(new ImageIcon(img)));
JFrame frame = new JFrame("Display images");
frame.getContentPane().add(panel);
frame.pack();
frame.setVisible(true);
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
}
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();
}