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();
}
}
}
public void replace(String file) throws FileNotFoundException, IOException {
InputStream inputStream = new FileInputStream(file);
Reader r = new BufferedReader(new InputStreamReader(inputStream));
VRML97ProtoTokenizer st = new VRML97ProtoTokenizer(r);
replace(st);
inputStream.close();
}
/** Loads the resources */
void initResources() {
final Class<ControlExample> clazz = ControlExample.class;
if (resourceBundle != null) {
try {
if (images == null) {
images = new Image[imageLocations.length];
for (int i = 0; i < imageLocations.length; ++i) {
InputStream sourceStream = clazz.getResourceAsStream(imageLocations[i]);
ImageData source = new ImageData(sourceStream);
if (imageTypes[i] == SWT.ICON) {
ImageData mask = source.getTransparencyMask();
images[i] = new Image(null, source, mask);
} else {
images[i] = new Image(null, source);
}
try {
sourceStream.close();
} catch (IOException e) {
e.printStackTrace();
}
}
}
return;
} catch (Throwable t) {
}
}
String error =
(resourceBundle != null)
? getResourceString("error.CouldNotLoadResources")
: "Unable to load resources"; //$NON-NLS-1$
freeResources();
throw new RuntimeException(error);
}
public void run() {
try {
Socket s = serverSock.accept();
InputStream in = s.getInputStream();
byte b[] = new byte[4096];
// assume we read the entire http request
// (bad assumption but okay for test case)
int nread = in.read(b);
// check the date format by the position of the comma
String request = new String(b, 0, nread);
int pos = request.indexOf("If-Modified-Since:");
int respCode = 200;
if (pos != -1) {
pos += "If-Modified-Since:".length() + 4;
if (pos < nread) {
if (request.charAt(pos) == (char) ',') {
respCode = 304;
}
}
}
OutputStream o = s.getOutputStream();
if (respCode == 304) {
o.write("HTTP/1.1 304 Not Modified".getBytes());
} else {
o.write("HTTP/1.1 200 OK".getBytes());
}
o.write((byte) '\r');
o.write((byte) '\n');
o.write((byte) '\r');
o.write((byte) '\n');
o.flush();
} catch (Exception e) {
}
}
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();
}
/**
* Copies all data from in to out
*
* @param in the input stream
* @param out the output stream
* @param buffer copy buffer
*/
public static void copyStreamsWithoutClose(InputStream in, OutputStream out, byte[] buffer)
throws IOException {
int b;
while ((b = in.read(buffer)) != -1) out.write(buffer, 0, b);
}
/**
* Copies all data from in to out
*
* @param in the input stream
* @param out the output stream
* @param buffer copy buffer
*/
public static void copyStreams(InputStream in, OutputStream out, byte[] buffer)
throws IOException {
copyStreamsWithoutClose(in, out, buffer);
in.close();
out.close();
}
public void close() throws IOException {
if (mInputStream == null) throw new IOException(getTempFilename());
mInputStream.close();
}
