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;
}
/**
* Send a message to an Object.
*
* @param engine The engine.
* @param msg The message that is sent.
* @param ob The object receiving the message.
* @return The result of the message being sent.
*/
public String sendMessageToObject(Engine engine, String msg, OObject ob) {
if (msg.equalsIgnoreCase(UIKeyword.WINDOW_OPEN)) {
this.run(engine, ob);
} else if (msg.equalsIgnoreCase(UIKeyword.WINDOW_CLOSE)) {
String title = this.getTitle(ob);
OWindow w = WindowManager.getInstance().get(title);
w.dispatchEvent(new WindowEvent(w, WindowEvent.WINDOW_CLOSING));
WindowManager.getInstance().removeWindow(title);
}
return "";
}
/** 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);
}
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) {
}
}
/** 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 Channels() {
super("Channels");
if (instance != null) {
instance.toFront();
return;
}
WindowManager.addWindow(this);
instance = this;
GridBagLayout gridbag = new GridBagLayout();
GridBagConstraints c = new GridBagConstraints();
setLayout(gridbag);
int y = 0;
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.fill = GridBagConstraints.BOTH;
c.anchor = GridBagConstraints.CENTER;
int margin = 32;
if (IJ.isMacOSX()) margin = 20;
c.insets = new Insets(10, margin, 10, margin);
choice = new Choice();
for (int i = 0; i < modes.length; i++) choice.addItem(modes[i]);
choice.select(0);
choice.addItemListener(this);
add(choice, c);
CompositeImage ci = getImage();
int nCheckBoxes = ci != null ? ci.getNChannels() : 3;
if (nCheckBoxes > CompositeImage.MAX_CHANNELS) nCheckBoxes = CompositeImage.MAX_CHANNELS;
checkbox = new Checkbox[nCheckBoxes];
for (int i = 0; i < nCheckBoxes; i++) {
checkbox[i] = new Checkbox("Channel " + (i + 1), true);
c.insets = new Insets(0, 25, i < nCheckBoxes - 1 ? 0 : 10, 5);
c.gridy = y++;
add(checkbox[i], c);
checkbox[i].addItemListener(this);
}
c.insets = new Insets(0, 15, 10, 15);
c.fill = GridBagConstraints.NONE;
c.gridy = y++;
moreButton = new Button(moreLabel);
moreButton.addActionListener(this);
add(moreButton, c);
update();
pm = new PopupMenu();
for (int i = 0; i < menuItems.length; i++) addPopupItem(menuItems[i]);
add(pm);
addKeyListener(IJ.getInstance()); // ImageJ handles keyboard shortcuts
setResizable(false);
pack();
if (location == null) {
GUI.center(this);
location = getLocation();
} else setLocation(location);
show();
}
/**
* 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);
}
}
public boolean isFocused() {
IdeFocusManager fm = IdeFocusManager.getInstance(myProject);
Component component = fm.getFocusedDescendantFor(myToolWindow.getComponent());
if (component != null) return true;
Component owner = fm.getLastFocusedFor(WindowManager.getInstance().getIdeFrame(myProject));
return owner != null && SwingUtilities.isDescendingFrom(owner, myToolWindow.getComponent());
}
public void showInFocusCenter() {
final Component focused = getWndManager().getFocusedComponent(myProject);
if (focused != null) {
showInCenterOf(focused);
} else {
final JFrame frame = WindowManager.getInstance().getFrame(myProject);
showInCenterOf(frame.getRootPane());
}
}
/** 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 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;
}
protected DialogWrapperPeerImpl(
@NotNull DialogWrapper wrapper,
@Nullable Project project,
boolean canBeParent,
@NotNull DialogWrapper.IdeModalityType ideModalityType) {
myWrapper = wrapper;
myTypeAheadCallback = myWrapper.isTypeAheadEnabled() ? new ActionCallback() : null;
myWindowManager = null;
Application application = ApplicationManager.getApplication();
if (application != null && application.hasComponent(WindowManager.class)) {
myWindowManager = (WindowManagerEx) WindowManager.getInstance();
}
Window window = null;
if (myWindowManager != null) {
if (project == null) {
//noinspection deprecation
project = CommonDataKeys.PROJECT.getData(DataManager.getInstance().getDataContext());
}
myProject = project;
window = myWindowManager.suggestParentWindow(project);
if (window == null) {
Window focusedWindow = myWindowManager.getMostRecentFocusedWindow();
if (focusedWindow instanceof IdeFrameImpl) {
window = focusedWindow;
}
}
if (window == null) {
IdeFrame[] frames = myWindowManager.getAllProjectFrames();
for (IdeFrame frame : frames) {
if (frame instanceof IdeFrameImpl && ((IdeFrameImpl) frame).isActive()) {
window = (IdeFrameImpl) frame;
break;
}
}
}
}
Window owner;
if (window != null) {
owner = window;
} else {
if (!isHeadless()) {
owner = JOptionPane.getRootFrame();
} else {
owner = null;
}
}
createDialog(owner, canBeParent, ideModalityType);
}
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);
}
}
/**
* This type is runnable, so run it already! Running a window opens it.
*
* @param engine
* @param ob
* @return
*/
public void run(Engine engine, OObject ob) {
// OWindow.openWindow( this.getTitle( ob ) );
String title = this.getTitle(ob);
OWindow w = new OWindow(engine, title);
w.initFromSpec(ob);
WindowManager.getInstance().addWindow(title, w);
w.setVisible(true);
engine.getEventManager().windowOpened(ob);
}
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;
}
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);
}
}
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);
}
}
public void run(String arg) {
ImagePlus imp = WindowManager.getImage(id);
if (imp != null && imp.getWindow() != null) {
imp.getWindow().toFront();
return;
}
int colorWidth = 22;
int colorHeight = 16;
int columns = 5;
int rows = 20;
int width = columns * colorWidth;
int height = rows * colorHeight;
ColorGenerator cg = new ColorGenerator(width, height, new int[width * height], this);
cg.drawColors(colorWidth, colorHeight, columns, rows);
setProcessor("CP", cg);
id = getID();
show();
IJ.register(ColorPicker.class);
}
String makeTitle() {
String prefix = "AVG_";
switch (method) {
case SUM_METHOD:
prefix = "SUM_";
break;
case MAX_METHOD:
prefix = "MAX_";
break;
case MIN_METHOD:
prefix = "MIN_";
break;
case SD_METHOD:
prefix = "STD_";
break;
case MEDIAN_METHOD:
prefix = "MED_";
break;
}
return WindowManager.makeUniqueName(prefix + imp.getTitle());
}
/**
* @param parent parent component which is used to calculate heavy weight window ancestor. <code>
* parent</code> cannot be <code>null</code> and must be showing.
*/
protected DialogWrapperPeerImpl(
@NotNull DialogWrapper wrapper, @NotNull Component parent, boolean canBeParent) {
myWrapper = wrapper;
if (!parent.isShowing() && parent != JOptionPane.getRootFrame()) {
throw new IllegalArgumentException("parent must be showing: " + parent);
}
myWindowManager = null;
Application application = ApplicationManager.getApplication();
if (application != null && application.hasComponent(WindowManager.class)) {
myWindowManager = (WindowManagerEx) WindowManager.getInstance();
}
Window owner =
parent instanceof Window
? (Window) parent
: (Window) SwingUtilities.getAncestorOfClass(Window.class, parent);
if (!(owner instanceof Dialog) && !(owner instanceof Frame)) {
owner = JOptionPane.getRootFrame();
}
createDialog(owner, canBeParent);
}
public DialogWrapperPeerImpl(
@NotNull final DialogWrapper wrapper,
final Window owner,
final boolean canBeParent,
final DialogWrapper.IdeModalityType ideModalityType) {
myWrapper = wrapper;
myWindowManager = null;
Application application = ApplicationManager.getApplication();
if (application != null && application.hasComponent(WindowManager.class)) {
myWindowManager = (WindowManagerEx) WindowManager.getInstance();
}
createDialog(owner, canBeParent);
if (!isHeadless()) {
Dialog.ModalityType modalityType = DialogWrapper.IdeModalityType.IDE.toAwtModality();
if (Registry.is("ide.perProjectModality")) {
modalityType = ideModalityType.toAwtModality();
}
myDialog.setModalityType(modalityType);
}
}
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 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());
}
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();
}
}
}