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();
}
public void onCreate() {
int flags, screenLightVal = 1;
Sensor mSensor;
List<Sensor> sensors;
if (scanData == null) return; // no ScanData, not possible to run correctly...
PowerManager pm = (PowerManager) getSystemService(POWER_SERVICE);
SP = PreferenceManager.getDefaultSharedPreferences(getBaseContext());
try {
screenLightVal = Integer.parseInt(SP.getString("screenLight", "2"));
} catch (NumberFormatException nfe) {
}
if (screenLightVal == 1) flags = PowerManager.PARTIAL_WAKE_LOCK;
else if (screenLightVal == 3) flags = PowerManager.FULL_WAKE_LOCK;
else flags = PowerManager.SCREEN_DIM_WAKE_LOCK;
wl = pm.newWakeLock(flags, "OpenWLANMap");
wl.acquire();
while (myWLocate == null) {
try {
myWLocate = new MyWLocate(this);
break;
} catch (IllegalArgumentException iae) {
myWLocate = null;
}
try {
Thread.sleep(100);
} catch (InterruptedException ie) {
}
}
try {
scanData.setUploadThres(Integer.parseInt(SP.getString("autoUpload", "0")));
} catch (NumberFormatException nfe) {
}
try {
scanData.setNoGPSExitInterval(
Integer.parseInt(SP.getString("noGPSExitInterval", "0")) * 60 * 1000);
} catch (NumberFormatException nfe) {
}
Intent intent = new Intent(this, OWMapAtAndroid.class);
intent.setFlags(Intent.FLAG_ACTIVITY_CLEAR_TOP | Intent.FLAG_ACTIVITY_SINGLE_TOP);
PendingIntent pendIntent = PendingIntent.getActivity(this, 0, intent, 0);
notification =
new NotificationCompat.Builder(this)
.setSmallIcon(R.drawable.icon)
.setContentTitle(getResources().getText(R.string.app_name))
.setContentText("")
.setContentIntent(pendIntent)
.build();
notification.flags |= Notification.FLAG_NO_CLEAR;
notification.flags |= Notification.FLAG_ONGOING_EVENT;
startForeground(1703, notification);
getScanData().setService(this);
getScanData().setmView(new HUDView(this));
getScanData().getmView().setValue(getScanData().incStoredValues());
WindowManager.LayoutParams params =
new WindowManager.LayoutParams(
WindowManager.LayoutParams.TYPE_SYSTEM_OVERLAY,
WindowManager.LayoutParams.FLAG_NOT_TOUCHABLE
| WindowManager.LayoutParams.FLAG_NOT_FOCUSABLE,
PixelFormat.TRANSLUCENT);
params.gravity = Gravity.LEFT | Gravity.BOTTOM;
params.setTitle("Load Average");
WindowManager wm = (WindowManager) getSystemService(WINDOW_SERVICE);
wm.addView(getScanData().getmView(), params);
sensorManager = (SensorManager) getSystemService(SENSOR_SERVICE);
sensorManager.registerListener(
this,
sensorManager.getDefaultSensor(Sensor.TYPE_ACCELEROMETER),
SensorManager.SENSOR_DELAY_GAME);
sensorManager.registerListener(
this,
sensorManager.getDefaultSensor(Sensor.TYPE_ORIENTATION),
SensorManager.SENSOR_DELAY_GAME);
sensors = sensorManager.getSensorList(Sensor.TYPE_ACCELEROMETER);
mSensor = sensors.get(0);
getScanData().getTelemetryData().setAccelMax(mSensor.getMaximumRange());
telemetryDir = Environment.getExternalStorageDirectory().getPath() + "/telemetry/";
File dir = new File(telemetryDir);
dir.mkdir();
connManager = (ConnectivityManager) getSystemService(CONNECTIVITY_SERVICE);
}