public void changeLAF(int iLAFIndex) {
try {
// Change LAF
if (iLAFIndex >= marrLaf.length) iLAFIndex = marrLaf.length - 1;
UIManager.setLookAndFeel(
(LookAndFeel) Class.forName(marrLaf[iLAFIndex].getClassName()).newInstance());
// Update UI
((JMenuItem) mvtLAFItem.elementAt(iLAFIndex)).setSelected(true);
SwingUtilities.updateComponentTreeUI(this);
SwingUtilities.updateComponentTreeUI(mnuMain);
WindowManager.updateLookAndField();
// Store config
try {
Hashtable prt = Global.loadHashtable(Global.FILE_CONFIG);
prt.put("LAF", String.valueOf(iLAFIndex));
Global.storeHashtable(prt, Global.FILE_CONFIG);
} catch (Exception e) {
}
} catch (Exception e) {
e.printStackTrace();
MessageBox.showMessageDialog(this, e, Global.APP_NAME, MessageBox.ERROR_MESSAGE);
}
}
/**
* Creates a new GenericDialog with the specified title. Uses the current image image window as
* the parent frame or the ImageJ frame if no image windows are open. Dialog parameters are
* recorded by ImageJ's command recorder but this requires that the first word of each label be
* unique.
*/
public GenericDialog(String title) {
this(
title,
WindowManager.getCurrentImage() != null
? (Frame) WindowManager.getCurrentImage().getWindow()
: IJ.getInstance() != null ? IJ.getInstance() : new Frame());
}
private static Frame getParentFrame() {
Frame parent =
WindowManager.getCurrentImage() != null
? (Frame) WindowManager.getCurrentImage().getWindow()
: IJ.getInstance() != null ? IJ.getInstance() : new Frame();
if (IJ.isMacOSX() && IJ.isJava18()) {
ImageJ ij = IJ.getInstance();
if (ij != null && ij.isActive()) parent = ij;
else parent = null;
}
return parent;
}
/** Quit using a separate thread, hopefully avoiding thread deadlocks. */
public void run() {
quitting = true;
boolean changes = false;
int[] wList = WindowManager.getIDList();
if (wList != null) {
for (int i = 0; i < wList.length; i++) {
ImagePlus imp = WindowManager.getImage(wList[i]);
if (imp != null && imp.changes == true) {
changes = true;
break;
}
}
}
Frame[] frames = WindowManager.getNonImageWindows();
if (frames != null) {
for (int i = 0; i < frames.length; i++) {
if (frames[i] != null && (frames[i] instanceof Editor)) {
if (((Editor) frames[i]).fileChanged()) {
changes = true;
break;
}
}
}
}
if (windowClosed
&& !changes
&& Menus.window.getItemCount() > Menus.WINDOW_MENU_ITEMS
&& !(IJ.macroRunning() && WindowManager.getImageCount() == 0)) {
GenericDialog gd = new GenericDialog("ImageJ", this);
gd.addMessage("Are you sure you want to quit ImageJ?");
gd.showDialog();
quitting = !gd.wasCanceled();
windowClosed = false;
}
if (!quitting) return;
if (!WindowManager.closeAllWindows()) {
quitting = false;
return;
}
// IJ.log("savePreferences");
if (applet == null) {
saveWindowLocations();
Prefs.savePreferences();
}
IJ.cleanup();
// setVisible(false);
// IJ.log("dispose");
dispose();
if (exitWhenQuitting) System.exit(0);
}
/** Handles CheckboxMenuItem state changes. */
public void itemStateChanged(ItemEvent e) {
MenuItem item = (MenuItem) e.getSource();
MenuComponent parent = (MenuComponent) item.getParent();
String cmd = e.getItem().toString();
if ((Menu) parent == Menus.window) WindowManager.activateWindow(cmd, item);
else doCommand(cmd);
}
public Zipper<Map<Integer, MZipper<RoiContainer>>> exec(
Zipper<Map<Integer, MZipper<RoiContainer>>> z, int frame) {
JFileChooser fc = new JFileChooser();
int returnVal = fc.showOpenDialog(WindowManager.getCurrentWindow().getCanvas());
Map<Integer, MZipper<RoiContainer>> newRois;
if (returnVal == JFileChooser.APPROVE_OPTION) {
try {
FileInputStream f = new FileInputStream(fc.getSelectedFile().getCanonicalPath());
MroiLisp parser = new MroiLisp(f);
parser.ReInit(f);
newRois = parser.roiFile();
// z.rights.clear();
// z.rights.add(newRois);
// z = z.right();
// return z;
return z.insertAndStep(newRois);
} catch (IOException e) {
IJ.error("Couldn't open from " + fc.getSelectedFile().getName() + ": " + e.getMessage());
} catch (mroi.ParseException e) {
IJ.error("Failed in parsing: " + e.getMessage());
} catch (Exception e) {
IJ.error("Malformed input file: " + e.getMessage());
}
}
return z;
}
public void changeDictionary(String strLanguage) {
// Change dictionary
MonitorDictionary.setCurrentLanguage(strLanguage);
DefaultDictionary.setCurrentLanguage(strLanguage);
ErrorDictionary.setCurrentLanguage(strLanguage);
// Update UI
updateLanguage();
WindowManager.updateLanguage();
int iIndex = mvtLanguage.indexOf(strLanguage);
if (iIndex >= 0) {
JRadioButtonMenuItem mnu = (JRadioButtonMenuItem) mvtLanguageItem.elementAt(iIndex);
mnu.setSelected(true);
}
// Store config
Hashtable prt = null;
try {
prt = Global.loadHashtable(Global.FILE_CONFIG);
} catch (Exception e) {
prt = new Hashtable();
}
prt.put("Language", strLanguage);
try {
Global.storeHashtable(prt, Global.FILE_CONFIG);
} catch (Exception e) {
}
}
/**
* Adds a checkbox labelled "Preview" for "automatic" preview. The reference to this checkbox can
* be retrieved by getPreviewCheckbox() and it provides the additional method previewRunning for
* optical feedback while preview is prepared. PlugInFilters can have their "run" method
* automatically called for preview under the following conditions: - the PlugInFilter must pass a
* reference to itself (i.e., "this") as an argument to the AddPreviewCheckbox - it must implement
* the DialogListener interface and set the filter parameters in the dialogItemChanged method. -
* it must have DIALOG and PREVIEW set in its flags. A previewCheckbox is always off when the
* filter is started and does not get recorded by the Macro Recorder.
*
* @param pfr A reference to the PlugInFilterRunner calling the PlugInFilter if automatic preview
* is desired, null otherwise.
*/
public void addPreviewCheckbox(PlugInFilterRunner pfr) {
if (previewCheckbox != null) return;
ImagePlus imp = WindowManager.getCurrentImage();
if (imp != null && imp.isComposite() && ((CompositeImage) imp).getMode() == IJ.COMPOSITE)
return;
this.pfr = pfr;
addCheckbox(previewLabel, false, true);
}
public void changePassword() {
try {
DialogChangePassword dlgPass = new DialogChangePassword(this, channel);
if (dlgPass != null) WindowManager.centeredWindow(dlgPass);
} catch (Exception e) {
e.printStackTrace();
MessageBox.showMessageDialog(this, e, Global.APP_NAME, MessageBox.ERROR_MESSAGE);
}
}
/** Sets the color used used for the ROI Manager "Show All" mode. */
public static void setShowAllColor(Color c) {
if (c == null) return;
showAllColor = c;
labelColor = null;
ImagePlus img = WindowManager.getCurrentImage();
if (img != null) {
ImageCanvas ic = img.getCanvas();
if (ic != null && ic.getShowAllROIs()) img.draw();
}
}
private boolean showDialog() {
String[] types = {"RAW", "JPEG", "ZLIB"};
GenericDialog gd = new GenericDialog("Generate Bricks");
gd.addChoice("FileType", types, filetype);
gd.addNumericField("JPEG quality", jpeg_quality, 0);
gd.addNumericField("Max file size (MB)", bdsizelimit, 0);
int[] wlist = WindowManager.getIDList();
if (wlist == null) return false;
String[] titles = new String[wlist.length];
for (int i = 0; i < wlist.length; i++) titles[i] = "";
int tnum = 0;
for (int i = 0; i < wlist.length; i++) {
ImagePlus imp = WindowManager.getImage(wlist[i]);
if (imp != null) {
titles[tnum] = imp.getTitle();
tnum++;
}
}
gd.addChoice("Source image: ", titles, titles[0]);
gd.showDialog();
if (gd.wasCanceled()) return false;
filetype = types[gd.getNextChoiceIndex()];
jpeg_quality = (int) gd.getNextNumber();
if (jpeg_quality > 100) jpeg_quality = 100;
if (jpeg_quality < 0) jpeg_quality = 0;
bdsizelimit = (int) gd.getNextNumber();
int id = gd.getNextChoiceIndex();
lvImgTitle = new ArrayList<String>();
lvImgTitle.add(titles[id]);
Prefs.set("filetype.string", filetype);
Prefs.set("jpeg_quality.int", jpeg_quality);
Prefs.set("bdsizelimit.int", bdsizelimit);
return true;
}
void saveWindowLocations() {
Frame frame = WindowManager.getFrame("B&C");
if (frame != null) Prefs.saveLocation(ContrastAdjuster.LOC_KEY, frame.getLocation());
frame = WindowManager.getFrame("Threshold");
if (frame != null) Prefs.saveLocation(ThresholdAdjuster.LOC_KEY, frame.getLocation());
frame = WindowManager.getFrame("Results");
if (frame != null) {
Prefs.saveLocation(TextWindow.LOC_KEY, frame.getLocation());
Dimension d = frame.getSize();
Prefs.set(TextWindow.WIDTH_KEY, d.width);
Prefs.set(TextWindow.HEIGHT_KEY, d.height);
}
frame = WindowManager.getFrame("Log");
if (frame != null) {
Prefs.saveLocation(TextWindow.LOG_LOC_KEY, frame.getLocation());
Dimension d = frame.getSize();
Prefs.set(TextWindow.LOG_WIDTH_KEY, d.width);
Prefs.set(TextWindow.LOG_HEIGHT_KEY, d.height);
}
}
private boolean checkImage() {
imp = WindowManager.getCurrentImage();
if (imp == null) {
IJ.beep();
IJ.showStatus("No image");
return false;
}
ip = setup(imp);
if (ip == null) return false;
return true;
}
private boolean ignoreArrowKeys(ImagePlus imp) {
Frame frame = WindowManager.getFrontWindow();
String title = frame.getTitle();
if (title != null && title.equals("ROI Manager")) return true;
// Control Panel?
if (frame != null && frame instanceof javax.swing.JFrame) return true;
ImageWindow win = imp.getWindow();
// LOCI Data Browser window?
if (imp.getStackSize() > 1 && win != null && win.getClass().getName().startsWith("loci"))
return true;
return false;
}
public void run(String arg) {
GenericDialog gd = new GenericDialog("Options");
gd.addCheckbox("Add_Titles", true);
gd.addCheckbox("Close Original", false);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
boolean addtitles = gd.getNextBoolean();
boolean closeorig = gd.getNextBoolean();
// first get the table window
Frame[] niframes = WindowManager.getNonImageWindows();
boolean first = true;
TextWindow tw2 = null;
int ncols = 0;
String[] col_labels = null;
for (int i = 0; i < niframes.length; i++) {
if (niframes[i] instanceof TextWindow && !niframes[i].getTitle().equals("Log")) {
TextWindow tw = (TextWindow) niframes[i];
TextPanel tp = tw.getTextPanel();
List<List<String>> listtable = table_tools.table2listtable(tp);
if (listtable.size() == 0) {
col_labels = table_tools.getcollabels(tp);
ncols = col_labels.length;
ArrayList<String> temp = new ArrayList<String>();
for (int j = 0; j < ncols; j++) temp.add("");
listtable.add(temp);
}
if (first) {
col_labels = table_tools.getcollabels(tp);
ncols = col_labels.length;
String headings = tp.getColumnHeadings();
if (addtitles) {
String[] titles = repeated(tw.getTitle(), listtable.size());
table_tools.add_listtable_column(listtable, titles, 0);
headings = "name\t" + headings;
}
tw2 =
new TextWindow(
"Combined Table", headings, table_tools.print_listtable(listtable), 400, 200);
first = false;
} else {
if (addtitles) {
String[] titles = repeated(tw.getTitle(), listtable.size());
table_tools.add_listtable_column(listtable, titles, 0);
}
tw2.append(table_tools.print_listtable(listtable));
}
if (closeorig) tw.close();
}
}
}
void saveWindowLocations() {
Window win = WindowManager.getWindow("B&C");
if (win != null) Prefs.saveLocation(ContrastAdjuster.LOC_KEY, win.getLocation());
win = WindowManager.getWindow("Threshold");
if (win != null) Prefs.saveLocation(ThresholdAdjuster.LOC_KEY, win.getLocation());
win = WindowManager.getWindow("Results");
if (win != null) {
Prefs.saveLocation(TextWindow.LOC_KEY, win.getLocation());
Dimension d = win.getSize();
Prefs.set(TextWindow.WIDTH_KEY, d.width);
Prefs.set(TextWindow.HEIGHT_KEY, d.height);
}
win = WindowManager.getWindow("Log");
if (win != null) {
Prefs.saveLocation(TextWindow.LOG_LOC_KEY, win.getLocation());
Dimension d = win.getSize();
Prefs.set(TextWindow.LOG_WIDTH_KEY, d.width);
Prefs.set(TextWindow.LOG_HEIGHT_KEY, d.height);
}
win = WindowManager.getWindow("ROI Manager");
if (win != null) Prefs.saveLocation(RoiManager.LOC_KEY, win.getLocation());
}
private void onClick() {
try {
DialogTabularParameter dlg =
new DialogTabularParameter(cmpCaller, mbModal, mstrTitle, mvtDefinition, mvtValue);
// DialogTableParameter dlg = new
// DialogTableParameter(cmpCaller,mbModal,mstrTitle,mvtDefinition,mvtValue);
WindowManager.centeredWindow(dlg);
cmpCaller.repaint();
setValue(mvtValue);
} catch (Exception e) {
e.printStackTrace();
MessageBox.showMessageDialog(this, e, Global.APP_NAME, MessageBox.ERROR_MESSAGE);
}
}
/** @param context */
public static void showDiagnosticInfo(final Context context) {
try {
DBG.m(" Build.VERSION.SDK_INT: " + Build.VERSION.SDK_INT);
DBG.m(" Build.VERSION.CODENAME: " + Build.VERSION.CODENAME);
DBG.m(" Build.DEVICE: " + android.os.Build.DEVICE);
DBG.m(" Build.MODEL: " + android.os.Build.MODEL);
DBG.m(" Build.PRODUCT: " + android.os.Build.PRODUCT);
final DisplayMetrics displaymetrics = new DisplayMetrics();
final WindowManager windowmanager =
(WindowManager) context.getSystemService(Context.WINDOW_SERVICE);
windowmanager.getDefaultDisplay().getMetrics(displaymetrics);
DBG.m(" DisplayMetrics.density: " + displaymetrics.density);
DBG.m(" DisplayMetrics.densityDpi: " + displaymetrics.densityDpi);
DBG.m(" DisplayMetrics.heightPixels: " + displaymetrics.heightPixels);
DBG.m(" DisplayMetrics.widthPixels: " + displaymetrics.widthPixels);
DBG.m(" DisplayMetrics.scaledDensity: " + displaymetrics.scaledDensity);
DBG.m(" DisplayMetrics.xdpi: " + displaymetrics.xdpi);
DBG.m(" DisplayMetrics.ydpi: " + displaymetrics.ydpi);
} catch (Exception x) {
DBG.m(x);
}
}
public void manageThreads() {
try {
DDTP request = new DDTP();
request.setRequestID(String.valueOf(System.currentTimeMillis()));
DDTP response = channel.sendRequest("ThreadProcessor", "manageThreadsLoad", request);
if (response != null) {
DialogThreadManager dlg =
new DialogThreadManager(this, channel, response.getVector("vtTableData"));
dlg.setComboStartupType(response.getVector("vtStartupType"), "");
WindowManager.centeredWindow(dlg);
}
} catch (Exception e) {
e.printStackTrace();
MessageBox.showMessageDialog(this, e, Global.APP_NAME, MessageBox.ERROR_MESSAGE);
}
}
private synchronized void closeAll() {
try {
// Close all child window
WindowManager.closeAll();
// Remove all child component
pnlThread.setVisible(false);
pnlUser.setVisible(false);
pnlThread.removeAll();
clearAll(txtBoard);
tblUser.setData(new Vector());
Thread.sleep(500);
} catch (Exception e) {
e.printStackTrace();
MessageBox.showMessageDialog(this, e, Global.APP_NAME, MessageBox.ERROR_MESSAGE);
}
}
protected void registerActiveImage() {
ImagePlus activeImage = WindowManager.getCurrentImage();
if (activeImage != null
&& activeImage.getProcessor() != null) { // && activeImage.getImageStackSize() > 1
if (currentImage != null && currentImage.getWindow() != null && currentImage != activeImage) {
// System.out.println("remove listener:"+currentImage.getTitle());
ImageUtils.removeScrollListener(currentImage, this, this);
currentImage.killRoi();
currentImage.updateAndDraw();
currentImage = null;
}
if (currentImage != activeImage) {
// System.out.println("add listener:"+activeImage.getTitle());
ImageUtils.addScrollListener(activeImage, this, this);
this.currentImage = activeImage;
}
}
}
void checkForCalibrationConflict(ImagePlus imp, Calibration cal) {
Calibration gcal = imp.getGlobalCalibration();
if (gcal == null || !showConflictMessage || IJ.isMacro()) return;
if (cal.pixelWidth == gcal.pixelWidth && cal.getUnit().equals(gcal.getUnit())) return;
GenericDialog gd = new GenericDialog(imp.getTitle());
gd.addMessage("The calibration of this image conflicts\nwith the current global calibration.");
gd.addCheckbox("Disable_Global Calibration", true);
gd.addCheckbox("Disable_these Messages", false);
gd.showDialog();
if (gd.wasCanceled()) return;
boolean disable = gd.getNextBoolean();
if (disable) {
imp.setGlobalCalibration(null);
imp.setCalibration(cal);
WindowManager.repaintImageWindows();
}
boolean dontShow = gd.getNextBoolean();
if (dontShow) showConflictMessage = false;
}
public EventGenerator(Simulator sim, RoadMap map, TimeHorizon T, int probPeople, int probParcel) {
this.map = map;
this.T = T;
R = new Random();
r_id = 0;
this.probPeople = probPeople;
this.probParcel = probParcel;
this.sim = sim;
used = new HashMap<Integer, Boolean>();
for (int i = 0; i < sim.lstDepots.size(); i++) {
int v = sim.lstDepots.get(i);
used.put(v, true);
}
for (int i = 0; i < sim.lstParkings.size(); i++) {
Parking p = sim.lstParkings.get(i);
used.put(p.locationID, true);
}
WM = new WindowManager(map);
WM.generateWindows(5, 5);
}
boolean showDialog(ImageProcessor ip) {
String macroOptions = Macro.getOptions();
if (macroOptions != null) {
if (macroOptions.indexOf(" interpolate") != -1)
macroOptions.replaceAll(" interpolate", " interpolation=Bilinear");
else if (macroOptions.indexOf(" interpolation=") == -1)
macroOptions = macroOptions + " interpolation=None";
Macro.setOptions(macroOptions);
}
int bitDepth = imp.getBitDepth();
int stackSize = imp.getStackSize();
boolean isStack = stackSize > 1;
oldDepth = stackSize;
if (isStack) {
xstr = "1.0";
ystr = "1.0";
zstr = "1.0";
}
r = ip.getRoi();
int width = newWidth;
if (width == 0) width = r.width;
int height = (int) ((double) width * r.height / r.width);
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
zscale = 1.0;
if (xscale != 0.0 && yscale != 0.0) {
width = (int) (r.width * xscale);
height = (int) (r.height * yscale);
} else {
xstr = "-";
ystr = "-";
}
GenericDialog gd = new GenericDialog("Scale");
gd.addStringField("X Scale:", xstr);
gd.addStringField("Y Scale:", ystr);
if (isStack) gd.addStringField("Z Scale:", zstr);
gd.setInsets(5, 0, 5);
gd.addStringField("Width (pixels):", "" + width);
gd.addStringField("Height (pixels):", "" + height);
if (isStack) {
String label = "Depth (images):";
if (imp.isHyperStack()) {
int slices = imp.getNSlices();
int frames = imp.getNFrames();
if (slices == 1 && frames > 1) {
label = "Depth (frames):";
oldDepth = frames;
} else {
label = "Depth (slices):";
oldDepth = slices;
}
}
gd.addStringField(label, "" + oldDepth);
}
fields = gd.getStringFields();
for (int i = 0; i < fields.size(); i++) {
((TextField) fields.elementAt(i)).addTextListener(this);
((TextField) fields.elementAt(i)).addFocusListener(this);
}
xField = (TextField) fields.elementAt(0);
yField = (TextField) fields.elementAt(1);
if (isStack) {
zField = (TextField) fields.elementAt(2);
widthField = (TextField) fields.elementAt(3);
heightField = (TextField) fields.elementAt(4);
depthField = (TextField) fields.elementAt(5);
} else {
widthField = (TextField) fields.elementAt(2);
heightField = (TextField) fields.elementAt(3);
}
fieldWithFocus = xField;
gd.addChoice("Interpolation:", methods, methods[interpolationMethod]);
if (bitDepth == 8 || bitDepth == 24)
gd.addCheckbox("Fill with background color", fillWithBackground);
gd.addCheckbox("Average when downsizing", averageWhenDownsizing);
boolean hyperstack = imp.isHyperStack() || imp.isComposite();
if (isStack && !hyperstack) gd.addCheckbox("Process entire stack", processStack);
gd.addCheckbox("Create new window", newWindow);
title = WindowManager.getUniqueName(imp.getTitle());
gd.setInsets(10, 0, 0);
gd.addStringField("Title:", title, 12);
gd.showDialog();
if (gd.wasCanceled()) return false;
xstr = gd.getNextString();
ystr = gd.getNextString();
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
if (isStack) {
zstr = gd.getNextString();
zscale = Tools.parseDouble(ystr, 0.0);
}
String wstr = gd.getNextString();
newWidth = (int) Tools.parseDouble(wstr, 0);
newHeight = (int) Tools.parseDouble(gd.getNextString(), 0);
if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0")))
newWidth = (int) (newHeight * (double) r.width / r.height);
if (newWidth == 0 || newHeight == 0) {
IJ.error("Scaler", "Width or height is 0");
return false;
}
if (xscale > 0.0 && yscale > 0.0) {
newWidth = (int) (r.width * xscale);
newHeight = (int) (r.height * yscale);
}
if (isStack) newDepth = (int) Tools.parseDouble(gd.getNextString(), 0);
interpolationMethod = gd.getNextChoiceIndex();
if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean();
averageWhenDownsizing = gd.getNextBoolean();
if (isStack && !hyperstack) processStack = gd.getNextBoolean();
if (hyperstack) processStack = true;
newWindow = gd.getNextBoolean();
if (xscale == 0.0) {
xscale = (double) newWidth / r.width;
yscale = (double) newHeight / r.height;
}
title = gd.getNextString();
if (fillWithBackground) {
Color bgc = Toolbar.getBackgroundColor();
if (bitDepth == 8) bgValue = ip.getBestIndex(bgc);
else if (bitDepth == 24) bgValue = bgc.getRGB();
} else bgValue = 0.0;
return true;
}
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);
}
public void keyPressed(KeyEvent e) {
// if (e.isConsumed()) return;
int keyCode = e.getKeyCode();
IJ.setKeyDown(keyCode);
hotkey = false;
if (keyCode == KeyEvent.VK_CONTROL || keyCode == KeyEvent.VK_SHIFT) return;
char keyChar = e.getKeyChar();
int flags = e.getModifiers();
if (IJ.debugMode)
IJ.log(
"keyPressed: code="
+ keyCode
+ " ("
+ KeyEvent.getKeyText(keyCode)
+ "), char=\""
+ keyChar
+ "\" ("
+ (int) keyChar
+ "), flags="
+ KeyEvent.getKeyModifiersText(flags));
boolean shift = (flags & KeyEvent.SHIFT_MASK) != 0;
boolean control = (flags & KeyEvent.CTRL_MASK) != 0;
boolean alt = (flags & KeyEvent.ALT_MASK) != 0;
boolean meta = (flags & KeyEvent.META_MASK) != 0;
String cmd = null;
ImagePlus imp = WindowManager.getCurrentImage();
boolean isStack = (imp != null) && (imp.getStackSize() > 1);
if (imp != null
&& !control
&& ((keyChar >= 32 && keyChar <= 255) || keyChar == '\b' || keyChar == '\n')) {
Roi roi = imp.getRoi();
if (roi instanceof TextRoi) {
if ((flags & KeyEvent.META_MASK) != 0 && IJ.isMacOSX()) return;
if (alt) {
switch (keyChar) {
case 'u':
case 'm':
keyChar = IJ.micronSymbol;
break;
case 'A':
keyChar = IJ.angstromSymbol;
break;
default:
}
}
((TextRoi) roi).addChar(keyChar);
return;
}
}
// Handle one character macro shortcuts
if (!control && !meta) {
Hashtable macroShortcuts = Menus.getMacroShortcuts();
if (macroShortcuts.size() > 0) {
if (shift) cmd = (String) macroShortcuts.get(new Integer(keyCode + 200));
else cmd = (String) macroShortcuts.get(new Integer(keyCode));
if (cmd != null) {
// MacroInstaller.runMacroCommand(cmd);
commandName = cmd;
MacroInstaller.runMacroShortcut(cmd);
return;
}
}
}
if ((!Prefs.requireControlKey || control || meta) && keyChar != '+') {
Hashtable shortcuts = Menus.getShortcuts();
if (shift) cmd = (String) shortcuts.get(new Integer(keyCode + 200));
else cmd = (String) shortcuts.get(new Integer(keyCode));
}
if (cmd == null) {
switch (keyChar) {
case '<':
case ',':
if (isStack) cmd = "Previous Slice [<]";
break;
case '>':
case '.':
case ';':
if (isStack) cmd = "Next Slice [>]";
break;
case '+':
case '=':
cmd = "In [+]";
break;
case '-':
cmd = "Out [-]";
break;
case '/':
cmd = "Reslice [/]...";
break;
default:
}
}
if (cmd == null) {
switch (keyCode) {
case KeyEvent.VK_TAB:
WindowManager.putBehind();
return;
case KeyEvent.VK_BACK_SPACE: // delete
if (deleteOverlayRoi(imp)) return;
cmd = "Clear";
hotkey = true;
break;
// case KeyEvent.VK_BACK_SLASH: cmd=IJ.altKeyDown()?"Animation Options...":"Start
// Animation"; break;
case KeyEvent.VK_EQUALS:
cmd = "In [+]";
break;
case KeyEvent.VK_MINUS:
cmd = "Out [-]";
break;
case KeyEvent.VK_SLASH:
case 0xbf:
cmd = "Reslice [/]...";
break;
case KeyEvent.VK_COMMA:
case 0xbc:
if (isStack) cmd = "Previous Slice [<]";
break;
case KeyEvent.VK_PERIOD:
case 0xbe:
if (isStack) cmd = "Next Slice [>]";
break;
case KeyEvent.VK_LEFT:
case KeyEvent.VK_RIGHT:
case KeyEvent.VK_UP:
case KeyEvent.VK_DOWN: // arrow keys
if (imp == null) return;
Roi roi = imp.getRoi();
if (IJ.shiftKeyDown() && imp == Orthogonal_Views.getImage()) return;
boolean stackKey = imp.getStackSize() > 1 && (roi == null || IJ.shiftKeyDown());
boolean zoomKey = roi == null || IJ.shiftKeyDown() || IJ.controlKeyDown();
if (stackKey && keyCode == KeyEvent.VK_RIGHT) cmd = "Next Slice [>]";
else if (stackKey && keyCode == KeyEvent.VK_LEFT) cmd = "Previous Slice [<]";
else if (zoomKey
&& keyCode == KeyEvent.VK_DOWN
&& !ignoreArrowKeys(imp)
&& Toolbar.getToolId() < Toolbar.SPARE6) cmd = "Out [-]";
else if (zoomKey
&& keyCode == KeyEvent.VK_UP
&& !ignoreArrowKeys(imp)
&& Toolbar.getToolId() < Toolbar.SPARE6) cmd = "In [+]";
else if (roi != null) {
if ((flags & KeyEvent.ALT_MASK) != 0) roi.nudgeCorner(keyCode);
else roi.nudge(keyCode);
return;
}
break;
case KeyEvent.VK_ESCAPE:
abortPluginOrMacro(imp);
return;
case KeyEvent.VK_ENTER:
WindowManager.toFront(this);
return;
default:
break;
}
}
if (cmd != null && !cmd.equals("")) {
commandName = cmd;
if (cmd.equals("Fill") || cmd.equals("Draw")) hotkey = true;
if (cmd.charAt(0) == MacroInstaller.commandPrefix) MacroInstaller.runMacroShortcut(cmd);
else {
doCommand(cmd);
keyPressedTime = System.currentTimeMillis();
lastKeyCommand = cmd;
}
}
}
public void mousePressed(MouseEvent e) {
Undo.reset();
if (!Prefs.noClickToGC) System.gc();
IJ.showStatus(version() + IJ.freeMemory());
if (IJ.debugMode) IJ.log("Windows: " + WindowManager.getWindowCount());
}
boolean showDialog(ImageProcessor ip) {
int bitDepth = imp.getBitDepth();
boolean isStack = imp.getStackSize() > 1;
r = ip.getRoi();
int width = newWidth;
if (width == 0) width = r.width;
int height = (int) ((double) width * r.height / r.width);
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
if (xscale != 0.0 && yscale != 0.0) {
width = (int) (r.width * xscale);
height = (int) (r.height * yscale);
} else {
xstr = "-";
ystr = "-";
}
GenericDialog gd = new GenericDialog("Scale");
gd.addStringField("X Scale (0.05-25):", xstr);
gd.addStringField("Y Scale (0.05-25):", ystr);
gd.setInsets(5, 0, 5);
gd.addStringField("Width (pixels):", "" + width);
gd.addStringField("Height (pixels):", "" + height);
fields = gd.getStringFields();
for (int i = 0; i < 3; i++) {
((TextField) fields.elementAt(i)).addTextListener(this);
((TextField) fields.elementAt(i)).addFocusListener(this);
}
xField = (TextField) fields.elementAt(0);
yField = (TextField) fields.elementAt(1);
widthField = (TextField) fields.elementAt(2);
heightField = (TextField) fields.elementAt(3);
fieldWithFocus = xField;
gd.addCheckbox("Interpolate", interpolate);
if (bitDepth == 8 || bitDepth == 24)
gd.addCheckbox("Fill with Background Color", fillWithBackground);
if (isStack) gd.addCheckbox("Process Entire Stack", processStack);
gd.addCheckbox("Create New Window", newWindow);
title = WindowManager.getUniqueName(imp.getTitle());
gd.setInsets(10, 0, 0);
gd.addStringField("Title:", title, 12);
gd.showDialog();
if (gd.wasCanceled()) return false;
xstr = gd.getNextString();
ystr = gd.getNextString();
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
String wstr = gd.getNextString();
newWidth = (int) Tools.parseDouble(wstr, 0);
newHeight = (int) Tools.parseDouble(gd.getNextString(), 0);
if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0")))
newWidth = (int) (newHeight * (double) r.width / r.height);
if (newWidth == 0 || newHeight == 0) {
IJ.error("Invalid width or height entered");
return false;
}
if (xscale > 25.0) xscale = 25.0;
if (yscale > 25.0) yscale = 25.0;
if (xscale > 0.0 && yscale > 0.0) {
newWidth = (int) (r.width * xscale);
newHeight = (int) (r.height * yscale);
}
interpolate = gd.getNextBoolean();
if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean();
if (isStack) processStack = gd.getNextBoolean();
newWindow = gd.getNextBoolean();
if (!newWindow && xscale == 0.0) {
xscale = (double) newWidth / r.width;
yscale = (double) newHeight / r.height;
}
title = gd.getNextString();
if (fillWithBackground) {
Color bgc = Toolbar.getBackgroundColor();
if (bitDepth == 8) bgValue = ip.getBestIndex(bgc);
else if (bitDepth == 24) bgValue = bgc.getRGB();
} else {
if (bitDepth == 8) bgValue = ip.isInvertedLut() ? 0.0 : 255.0; // white
else if (bitDepth == 24) bgValue = 0xffffffff; // white
}
return true;
}
public void login() {
mbAutoLogIn = false;
while (!mbAutoLogIn) {
try {
// Confirm logout
if (isOpen()) {
if (MessageBox.showConfirmDialog(
this,
MonitorDictionary.getString("Confirm.Exit"),
Global.APP_NAME,
MessageBox.YES_NO_OPTION)
== MessageBox.NO_OPTION) return;
// Disconnect from server
disconnect();
}
// Login
DialogLogin dlgLogin = new DialogLogin(this);
WindowManager.centeredWindow(dlgLogin);
if (dlgLogin.miReturn == JOptionPane.OK_OPTION) {
// Update UI
SwingUtilities.updateComponentTreeUI(pnlUser);
SwingUtilities.updateComponentTreeUI(pnlThread);
// Request to connect
Socket sck = new Socket(dlgLogin.mstrHost, Integer.parseInt(dlgLogin.mstrPort));
sck.setSoLinger(true, 0);
// Start up a channel thread that reads messages from the server
channel =
new SocketTransmitter(sck) {
public void close() {
if (msckMain != null) {
super.close();
closeAll();
if (mbAutoLogIn) login();
}
}
};
channel.setUserName(dlgLogin.mstrUserName);
channel.setPackage("com.fss.thread.");
channel.start();
// Request to Server
DDTP request = new DDTP();
request.setRequestID(String.valueOf(System.currentTimeMillis()));
request.setString("UserName", dlgLogin.mstrUserName);
request.setString("Password", dlgLogin.mstrPassword);
// Response from Server
DDTP response = channel.sendRequest("ThreadProcessor", "login", request);
mstrThreadAppName = response.getString("strThreadAppName");
mstrThreadAppVersion = response.getString("strThreadAppVersion");
mstrAppName = response.getString("strAppName");
mstrAppVersion = response.getString("strAppVersion");
if (response != null) {
if (response.getString("PasswordExpired") != null) {
DialogChangePassword frm = new DialogChangePassword(this, channel);
WindowManager.centeredWindow(frm);
if (frm.miReturnValue != JOptionPane.OK_OPTION) throw new AppException("FSS-10003");
}
String strLog = StringUtil.nvl(response.getString("strLog"), "");
showResult(txtBoard, strLog);
Vector vtThread = response.getVector("vtThread");
updateTabBar(vtThread);
mstrChannel = response.getString("strChannel");
if (mstrChannel != null) removeUser(mstrChannel);
}
btnRefresh.doClick();
pnlThread.setVisible(true);
pnlUser.setVisible(true);
setResizeWeight(1);
setDividerLocation((int) (getSize().getHeight() - 160));
}
mbAutoLogIn = true;
updateLanguage();
} catch (Exception e) {
e.printStackTrace();
MessageBox.showMessageDialog(this, e, Global.APP_NAME, MessageBox.ERROR_MESSAGE);
// Disconnect from server
mstrChannel = null;
disconnect();
}
}
}
public void build_bricks() {
ImagePlus imp;
ImagePlus orgimp;
ImageStack stack;
FileInfo finfo;
if (lvImgTitle.isEmpty()) return;
orgimp = WindowManager.getImage(lvImgTitle.get(0));
imp = orgimp;
finfo = imp.getFileInfo();
if (finfo == null) return;
int[] dims = imp.getDimensions();
int imageW = dims[0];
int imageH = dims[1];
int nCh = dims[2];
int imageD = dims[3];
int nFrame = dims[4];
int bdepth = imp.getBitDepth();
double xspc = finfo.pixelWidth;
double yspc = finfo.pixelHeight;
double zspc = finfo.pixelDepth;
double z_aspect = Math.max(xspc, yspc) / zspc;
int orgW = imageW;
int orgH = imageH;
int orgD = imageD;
double orgxspc = xspc;
double orgyspc = yspc;
double orgzspc = zspc;
lv = lvImgTitle.size();
if (filetype == "JPEG") {
for (int l = 0; l < lv; l++) {
if (WindowManager.getImage(lvImgTitle.get(l)).getBitDepth() != 8) {
IJ.error("A SOURCE IMAGE MUST BE 8BIT GLAYSCALE");
return;
}
}
}
// calculate levels
/* int baseXY = 256;
int baseZ = 256;
if (z_aspect < 0.5) baseZ = 128;
if (z_aspect > 2.0) baseXY = 128;
if (z_aspect >= 0.5 && z_aspect < 1.0) baseZ = (int)(baseZ*z_aspect);
if (z_aspect > 1.0 && z_aspect <= 2.0) baseXY = (int)(baseXY/z_aspect);
IJ.log("Z_aspect: " + z_aspect);
IJ.log("BaseXY: " + baseXY);
IJ.log("BaseZ: " + baseZ);
*/
int baseXY = 256;
int baseZ = 128;
int dbXY = Math.max(orgW, orgH) / baseXY;
if (Math.max(orgW, orgH) % baseXY > 0) dbXY *= 2;
int dbZ = orgD / baseZ;
if (orgD % baseZ > 0) dbZ *= 2;
lv = Math.max(log2(dbXY), log2(dbZ)) + 1;
int ww = orgW;
int hh = orgH;
int dd = orgD;
for (int l = 0; l < lv; l++) {
int bwnum = ww / baseXY;
if (ww % baseXY > 0) bwnum++;
int bhnum = hh / baseXY;
if (hh % baseXY > 0) bhnum++;
int bdnum = dd / baseZ;
if (dd % baseZ > 0) bdnum++;
if (bwnum % 2 == 0) bwnum++;
if (bhnum % 2 == 0) bhnum++;
if (bdnum % 2 == 0) bdnum++;
int bw = (bwnum <= 1) ? ww : ww / bwnum + 1 + (ww % bwnum > 0 ? 1 : 0);
int bh = (bhnum <= 1) ? hh : hh / bhnum + 1 + (hh % bhnum > 0 ? 1 : 0);
int bd = (bdnum <= 1) ? dd : dd / bdnum + 1 + (dd % bdnum > 0 ? 1 : 0);
bwlist.add(bw);
bhlist.add(bh);
bdlist.add(bd);
IJ.log("LEVEL: " + l);
IJ.log(" width: " + ww);
IJ.log(" hight: " + hh);
IJ.log(" depth: " + dd);
IJ.log(" bw: " + bw);
IJ.log(" bh: " + bh);
IJ.log(" bd: " + bd);
int xyl2 = Math.max(ww, hh) / baseXY;
if (Math.max(ww, hh) % baseXY > 0) xyl2 *= 2;
if (lv - 1 - log2(xyl2) <= l) {
ww /= 2;
hh /= 2;
}
IJ.log(" xyl2: " + (lv - 1 - log2(xyl2)));
int zl2 = dd / baseZ;
if (dd % baseZ > 0) zl2 *= 2;
if (lv - 1 - log2(zl2) <= l) dd /= 2;
IJ.log(" zl2: " + (lv - 1 - log2(zl2)));
if (l < lv - 1) {
lvImgTitle.add(lvImgTitle.get(0) + "_level" + (l + 1));
IJ.selectWindow(lvImgTitle.get(0));
IJ.run(
"Scale...",
"x=- y=- z=- width="
+ ww
+ " height="
+ hh
+ " depth="
+ dd
+ " interpolation=Bicubic average process create title="
+ lvImgTitle.get(l + 1));
}
}
for (int l = 0; l < lv; l++) {
IJ.log(lvImgTitle.get(l));
}
Document doc = newXMLDocument();
Element root = doc.createElement("BRK");
root.setAttribute("version", "1.0");
root.setAttribute("nLevel", String.valueOf(lv));
root.setAttribute("nChannel", String.valueOf(nCh));
root.setAttribute("nFrame", String.valueOf(nFrame));
doc.appendChild(root);
for (int l = 0; l < lv; l++) {
IJ.showProgress(0.0);
int[] dims2 = imp.getDimensions();
IJ.log(
"W: "
+ String.valueOf(dims2[0])
+ " H: "
+ String.valueOf(dims2[1])
+ " C: "
+ String.valueOf(dims2[2])
+ " D: "
+ String.valueOf(dims2[3])
+ " T: "
+ String.valueOf(dims2[4])
+ " b: "
+ String.valueOf(bdepth));
bw = bwlist.get(l).intValue();
bh = bhlist.get(l).intValue();
bd = bdlist.get(l).intValue();
boolean force_pow2 = false;
/* if(IsPowerOf2(bw) && IsPowerOf2(bh) && IsPowerOf2(bd)) force_pow2 = true;
if(force_pow2){
//force pow2
if(Pow2(bw) > bw) bw = Pow2(bw)/2;
if(Pow2(bh) > bh) bh = Pow2(bh)/2;
if(Pow2(bd) > bd) bd = Pow2(bd)/2;
}
if(bw > imageW) bw = (Pow2(imageW) == imageW) ? imageW : Pow2(imageW)/2;
if(bh > imageH) bh = (Pow2(imageH) == imageH) ? imageH : Pow2(imageH)/2;
if(bd > imageD) bd = (Pow2(imageD) == imageD) ? imageD : Pow2(imageD)/2;
*/
if (bw > imageW) bw = imageW;
if (bh > imageH) bh = imageH;
if (bd > imageD) bd = imageD;
if (bw <= 1 || bh <= 1 || bd <= 1) break;
if (filetype == "JPEG" && (bw < 8 || bh < 8)) break;
Element lvnode = doc.createElement("Level");
lvnode.setAttribute("lv", String.valueOf(l));
lvnode.setAttribute("imageW", String.valueOf(imageW));
lvnode.setAttribute("imageH", String.valueOf(imageH));
lvnode.setAttribute("imageD", String.valueOf(imageD));
lvnode.setAttribute("xspc", String.valueOf(xspc));
lvnode.setAttribute("yspc", String.valueOf(yspc));
lvnode.setAttribute("zspc", String.valueOf(zspc));
lvnode.setAttribute("bitDepth", String.valueOf(bdepth));
root.appendChild(lvnode);
Element brksnode = doc.createElement("Bricks");
brksnode.setAttribute("brick_baseW", String.valueOf(bw));
brksnode.setAttribute("brick_baseH", String.valueOf(bh));
brksnode.setAttribute("brick_baseD", String.valueOf(bd));
lvnode.appendChild(brksnode);
ArrayList<Brick> bricks = new ArrayList<Brick>();
int mw, mh, md, mw2, mh2, md2;
double tx0, ty0, tz0, tx1, ty1, tz1;
double bx0, by0, bz0, bx1, by1, bz1;
for (int k = 0; k < imageD; k += bd) {
if (k > 0) k--;
for (int j = 0; j < imageH; j += bh) {
if (j > 0) j--;
for (int i = 0; i < imageW; i += bw) {
if (i > 0) i--;
mw = Math.min(bw, imageW - i);
mh = Math.min(bh, imageH - j);
md = Math.min(bd, imageD - k);
if (force_pow2) {
mw2 = Pow2(mw);
mh2 = Pow2(mh);
md2 = Pow2(md);
} else {
mw2 = mw;
mh2 = mh;
md2 = md;
}
if (filetype == "JPEG") {
if (mw2 < 8) mw2 = 8;
if (mh2 < 8) mh2 = 8;
}
tx0 = i == 0 ? 0.0d : ((mw2 - mw + 0.5d) / mw2);
ty0 = j == 0 ? 0.0d : ((mh2 - mh + 0.5d) / mh2);
tz0 = k == 0 ? 0.0d : ((md2 - md + 0.5d) / md2);
tx1 = 1.0d - 0.5d / mw2;
if (mw < bw) tx1 = 1.0d;
if (imageW - i == bw) tx1 = 1.0d;
ty1 = 1.0d - 0.5d / mh2;
if (mh < bh) ty1 = 1.0d;
if (imageH - j == bh) ty1 = 1.0d;
tz1 = 1.0d - 0.5d / md2;
if (md < bd) tz1 = 1.0d;
if (imageD - k == bd) tz1 = 1.0d;
bx0 = i == 0 ? 0.0d : (i + 0.5d) / (double) imageW;
by0 = j == 0 ? 0.0d : (j + 0.5d) / (double) imageH;
bz0 = k == 0 ? 0.0d : (k + 0.5d) / (double) imageD;
bx1 = Math.min((i + bw - 0.5d) / (double) imageW, 1.0d);
if (imageW - i == bw) bx1 = 1.0d;
by1 = Math.min((j + bh - 0.5d) / (double) imageH, 1.0d);
if (imageH - j == bh) by1 = 1.0d;
bz1 = Math.min((k + bd - 0.5d) / (double) imageD, 1.0d);
if (imageD - k == bd) bz1 = 1.0d;
int x, y, z;
x = i - (mw2 - mw);
y = j - (mh2 - mh);
z = k - (md2 - md);
bricks.add(
new Brick(
x, y, z, mw2, mh2, md2, 0, 0, tx0, ty0, tz0, tx1, ty1, tz1, bx0, by0, bz0, bx1,
by1, bz1));
}
}
}
Element fsnode = doc.createElement("Files");
lvnode.appendChild(fsnode);
stack = imp.getStack();
int totalbricknum = nFrame * nCh * bricks.size();
int curbricknum = 0;
for (int f = 0; f < nFrame; f++) {
for (int ch = 0; ch < nCh; ch++) {
int sizelimit = bdsizelimit * 1024 * 1024;
int bytecount = 0;
int filecount = 0;
int pd_bufsize = Math.max(sizelimit, bw * bh * bd * bdepth / 8);
byte[] packed_data = new byte[pd_bufsize];
String base_dataname =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f);
String current_dataname = base_dataname + "_data" + filecount;
Brick b_first = bricks.get(0);
if (b_first.z_ != 0) IJ.log("warning");
int st_z = b_first.z_;
int ed_z = b_first.z_ + b_first.d_;
LinkedList<ImageProcessor> iplist = new LinkedList<ImageProcessor>();
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
// ImagePlus test;
// ImageStack tsst;
// test = NewImage.createByteImage("test", imageW, imageH, imageD,
// NewImage.FILL_BLACK);
// tsst = test.getStack();
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
if (ed_z > b.z_ || st_z < b.z_ + b.d_) {
if (b.z_ > st_z) {
for (int s = 0; s < b.z_ - st_z; s++) iplist.pollFirst();
st_z = b.z_;
} else if (b.z_ < st_z) {
IJ.log("warning");
for (int s = st_z - 1; s > b.z_; s--)
iplist.addFirst(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
st_z = b.z_;
}
if (b.z_ + b.d_ > ed_z) {
for (int s = ed_z; s < b.z_ + b.d_; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
ed_z = b.z_ + b.d_;
} else if (b.z_ + b.d_ < ed_z) {
IJ.log("warning");
for (int s = 0; s < ed_z - (b.z_ + b.d_); s++) iplist.pollLast();
ed_z = b.z_ + b.d_;
}
} else {
IJ.log("warning");
iplist.clear();
st_z = b.z_;
ed_z = b.z_ + b.d_;
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
}
if (iplist.size() != b.d_) {
IJ.log("Stack Error");
return;
}
// int zz = st_z;
int bsize = 0;
byte[] bdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Iterator<ImageProcessor> ipite = iplist.iterator();
while (ipite.hasNext()) {
// ImageProcessor tsip = tsst.getProcessor(zz+1);
ImageProcessor ip = ipite.next();
ip.setRoi(b.x_, b.y_, b.w_, b.h_);
if (bdepth == 8) {
byte[] data = (byte[]) ip.crop().getPixels();
System.arraycopy(data, 0, bdata, bsize, data.length);
bsize += data.length;
} else if (bdepth == 16) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
short[] data = (short[]) ip.crop().getPixels();
for (short e : data) buffer.putShort(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
} else if (bdepth == 32) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
float[] data = (float[]) ip.crop().getPixels();
for (float e : data) buffer.putFloat(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
}
}
String filename =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f)
+ "_ID"
+ String.valueOf(i);
int offset = bytecount;
int datasize = bdata.length;
if (filetype == "RAW") {
int dummy = -1;
// do nothing
}
if (filetype == "JPEG" && bdepth == 8) {
try {
DataBufferByte db = new DataBufferByte(bdata, datasize);
Raster raster = Raster.createPackedRaster(db, b.w_, b.h_ * b.d_, 8, null);
BufferedImage img =
new BufferedImage(b.w_, b.h_ * b.d_, BufferedImage.TYPE_BYTE_GRAY);
img.setData(raster);
ByteArrayOutputStream baos = new ByteArrayOutputStream();
ImageOutputStream ios = ImageIO.createImageOutputStream(baos);
String format = "jpg";
Iterator<javax.imageio.ImageWriter> iter =
ImageIO.getImageWritersByFormatName("jpeg");
javax.imageio.ImageWriter writer = iter.next();
ImageWriteParam iwp = writer.getDefaultWriteParam();
iwp.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
iwp.setCompressionQuality((float) jpeg_quality * 0.01f);
writer.setOutput(ios);
writer.write(null, new IIOImage(img, null, null), iwp);
// ImageIO.write(img, format, baos);
bdata = baos.toByteArray();
datasize = bdata.length;
} catch (IOException e) {
e.printStackTrace();
return;
}
}
if (filetype == "ZLIB") {
byte[] tmpdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Deflater compresser = new Deflater();
compresser.setInput(bdata);
compresser.setLevel(Deflater.DEFAULT_COMPRESSION);
compresser.setStrategy(Deflater.DEFAULT_STRATEGY);
compresser.finish();
datasize = compresser.deflate(tmpdata);
bdata = tmpdata;
compresser.end();
}
if (bytecount + datasize > sizelimit && bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
filecount++;
current_dataname = base_dataname + "_data" + filecount;
bytecount = 0;
offset = 0;
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
} else {
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
}
Element filenode = doc.createElement("File");
filenode.setAttribute("filename", current_dataname);
filenode.setAttribute("channel", String.valueOf(ch));
filenode.setAttribute("frame", String.valueOf(f));
filenode.setAttribute("brickID", String.valueOf(i));
filenode.setAttribute("offset", String.valueOf(offset));
filenode.setAttribute("datasize", String.valueOf(datasize));
filenode.setAttribute("filetype", String.valueOf(filetype));
fsnode.appendChild(filenode);
curbricknum++;
IJ.showProgress((double) (curbricknum) / (double) (totalbricknum));
}
if (bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
}
}
}
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
Element bricknode = doc.createElement("Brick");
bricknode.setAttribute("id", String.valueOf(i));
bricknode.setAttribute("st_x", String.valueOf(b.x_));
bricknode.setAttribute("st_y", String.valueOf(b.y_));
bricknode.setAttribute("st_z", String.valueOf(b.z_));
bricknode.setAttribute("width", String.valueOf(b.w_));
bricknode.setAttribute("height", String.valueOf(b.h_));
bricknode.setAttribute("depth", String.valueOf(b.d_));
brksnode.appendChild(bricknode);
Element tboxnode = doc.createElement("tbox");
tboxnode.setAttribute("x0", String.valueOf(b.tx0_));
tboxnode.setAttribute("y0", String.valueOf(b.ty0_));
tboxnode.setAttribute("z0", String.valueOf(b.tz0_));
tboxnode.setAttribute("x1", String.valueOf(b.tx1_));
tboxnode.setAttribute("y1", String.valueOf(b.ty1_));
tboxnode.setAttribute("z1", String.valueOf(b.tz1_));
bricknode.appendChild(tboxnode);
Element bboxnode = doc.createElement("bbox");
bboxnode.setAttribute("x0", String.valueOf(b.bx0_));
bboxnode.setAttribute("y0", String.valueOf(b.by0_));
bboxnode.setAttribute("z0", String.valueOf(b.bz0_));
bboxnode.setAttribute("x1", String.valueOf(b.bx1_));
bboxnode.setAttribute("y1", String.valueOf(b.by1_));
bboxnode.setAttribute("z1", String.valueOf(b.bz1_));
bricknode.appendChild(bboxnode);
}
if (l < lv - 1) {
imp = WindowManager.getImage(lvImgTitle.get(l + 1));
int[] newdims = imp.getDimensions();
imageW = newdims[0];
imageH = newdims[1];
imageD = newdims[3];
xspc = orgxspc * ((double) orgW / (double) imageW);
yspc = orgyspc * ((double) orgH / (double) imageH);
zspc = orgzspc * ((double) orgD / (double) imageD);
bdepth = imp.getBitDepth();
}
}
File newXMLfile = new File(directory + basename + ".vvd");
writeXML(newXMLfile, doc);
for (int l = 1; l < lv; l++) {
imp = WindowManager.getImage(lvImgTitle.get(l));
imp.changes = false;
imp.close();
}
}
