void addShortcut(String name) {
int index1 = name.indexOf('[');
if (index1 == -1) return;
int index2 = name.lastIndexOf(']');
if (index2 <= (index1 + 1)) return;
String shortcut = name.substring(index1 + 1, index2);
int len = shortcut.length();
if (len > 1) shortcut = shortcut.toUpperCase(Locale.US);
;
if (len > 3 || (len > 1 && shortcut.charAt(0) != 'F' && shortcut.charAt(0) != 'N')) return;
int code = Menus.convertShortcutToCode(shortcut);
if (code == 0) return;
if (nShortcuts == 0) removeShortcuts();
// One character shortcuts go in a separate hash table to
// avoid conflicts with ImageJ menu shortcuts.
if (len == 1 || shortcut.equals("N+") || shortcut.equals("N-")) {
Hashtable macroShortcuts = Menus.getMacroShortcuts();
macroShortcuts.put(new Integer(code), commandPrefix + name);
nShortcuts++;
return;
}
Hashtable shortcuts = Menus.getShortcuts();
if (shortcuts.get(new Integer(code)) != null) {
if (shortcutsInUse == null) shortcutsInUse = "\n \n";
shortcutsInUse += " " + name + "\n";
inUseCount++;
return;
}
shortcuts.put(new Integer(code), commandPrefix + name);
nShortcuts++;
// IJ.log("addShortcut3: "+name+" "+shortcut+" "+code);
}
void updateMenus() {
if (IJ.debugMode) {
long start = System.currentTimeMillis();
Menus.updateImageJMenus();
IJ.log("Refresh Menus: " + (System.currentTimeMillis() - start) + " ms");
} else Menus.updateImageJMenus();
}
/** Handle menu events. */
public void actionPerformed(ActionEvent e) {
if ((e.getSource() instanceof MenuItem)) {
MenuItem item = (MenuItem) e.getSource();
String cmd = e.getActionCommand();
commandName = cmd;
ImagePlus imp = null;
if (item.getParent() == Menus.getOpenRecentMenu()) {
new RecentOpener(cmd); // open image in separate thread
return;
} else if (item.getParent() == Menus.getPopupMenu()) {
Object parent = Menus.getPopupMenu().getParent();
if (parent instanceof ImageCanvas) imp = ((ImageCanvas) parent).getImage();
}
int flags = e.getModifiers();
hotkey = false;
actionPerformedTime = System.currentTimeMillis();
long ellapsedTime = actionPerformedTime - keyPressedTime;
if (cmd != null && (ellapsedTime >= 200L || !cmd.equals(lastKeyCommand))) {
if ((flags & Event.ALT_MASK) != 0) IJ.setKeyDown(KeyEvent.VK_ALT);
if ((flags & Event.SHIFT_MASK) != 0) IJ.setKeyDown(KeyEvent.VK_SHIFT);
new Executer(cmd, imp);
}
lastKeyCommand = null;
if (IJ.debugMode) IJ.log("actionPerformed: time=" + ellapsedTime + ", " + e);
}
}
void removeShortcuts() {
Menus.getMacroShortcuts().clear();
Hashtable shortcuts = Menus.getShortcuts();
for (Enumeration en = shortcuts.keys(); en.hasMoreElements(); ) {
Integer key = (Integer) en.nextElement();
String value = (String) shortcuts.get(key);
if (value.charAt(0) == commandPrefix) shortcuts.remove(key);
}
}
public int install(String text) {
if (text == null && pgm == null) return 0;
this.text = text;
macrosMenu = Menus.getMacrosMenu();
if (listener != null) macrosMenu.removeActionListener(listener);
macrosMenu.addActionListener(this);
listener = this;
install();
return nShortcuts;
}
String showDialog() {
if (defaultDir == null) defaultDir = Menus.getMacrosPath();
OpenDialog od = new OpenDialog("Install Macros", defaultDir, fileName);
String name = od.getFileName();
if (name == null) return null;
String dir = od.getDirectory();
if (!(name.endsWith(".txt") || name.endsWith(".ijm"))) {
IJ.showMessage("Macro Installer", "File name must end with \".txt\" or \".ijm\" .");
return null;
}
fileName = name;
defaultDir = dir;
return dir + name;
}
void installPopupMenu(String name, Program pgm) {
Hashtable h = pgm.getMenus();
if (h == null) return;
String[] commands = (String[]) h.get(name);
if (commands == null) return;
PopupMenu popup = Menus.getPopupMenu();
if (popup == null) return;
popup.removeAll();
for (int i = 0; i < commands.length; i++) {
if (commands[i].equals("-")) popup.addSeparator();
else {
MenuItem mi = new MenuItem(commands[i]);
mi.addActionListener(this);
popup.add(mi);
}
}
}
public void run(String arg) {
if (arg.equals("menus")) {
updateMenus();
return;
}
if (IJ.getApplet() != null) return;
// File file = new File(Prefs.getHomeDir() + File.separator + "ij.jar");
// if (isMac() && !file.exists())
// file = new File(Prefs.getHomeDir() + File.separator +
// "ImageJ.app/Contents/Resources/Java/ij.jar");
URL url = getClass().getResource("/ij/IJ.class");
String ij_jar = url == null ? null : url.toString().replaceAll("%20", " ");
if (ij_jar == null || !ij_jar.startsWith("jar:file:")) {
error("Could not determine location of ij.jar");
return;
}
int exclamation = ij_jar.indexOf('!');
ij_jar = ij_jar.substring(9, exclamation);
if (IJ.debugMode) IJ.log("Updater: " + ij_jar);
File file = new File(ij_jar);
if (!file.exists()) {
error("File not found: " + file.getPath());
return;
}
if (!file.canWrite()) {
String msg = "No write access: " + file.getPath();
if (IJ.isVista()) msg += Prefs.vistaHint;
error(msg);
return;
}
String[] list = openUrlAsList(IJ.URL + "/download/jars/list.txt");
int count = list.length + 2;
String[] versions = new String[count];
String[] urls = new String[count];
String uv = getUpgradeVersion();
if (uv == null) return;
versions[0] = "v" + uv;
urls[0] = IJ.URL + "/upgrade/ij.jar";
if (versions[0] == null) return;
for (int i = 1; i < count - 1; i++) {
String version = list[i - 1];
versions[i] = version.substring(0, version.length() - 1); // remove letter
urls[i] =
IJ.URL + "/download/jars/ij" + version.substring(1, 2) + version.substring(3, 6) + ".jar";
}
versions[count - 1] = "daily build";
urls[count - 1] = IJ.URL + "/ij.jar";
int choice = showDialog(versions);
if (choice == -1) return;
if (!versions[choice].startsWith("daily")
&& versions[choice].compareTo("v1.39") < 0
&& Menus.getCommands().get("ImageJ Updater") == null) {
String msg =
"This command is not available in versions of ImageJ prior\n"
+ "to 1.39 so you will need to install the plugin version at\n"
+ "<"
+ IJ.URL
+ "/plugins/imagej-updater.html>.";
if (!IJ.showMessageWithCancel("Update ImageJ", msg)) return;
}
byte[] jar = getJar(urls[choice]);
// file.renameTo(new File(file.getParent()+File.separator+"ij.bak"));
if (version().compareTo("1.37v") >= 0) Prefs.savePreferences();
// if (!renameJar(file)) return; // doesn't work on Vista
saveJar(file, jar);
if (choice < count - 1) // force macro Function Finder to download fresh list
new File(IJ.getDirectory("macros") + "functions.html").delete();
System.exit(0);
}
public void windowActivated(WindowEvent e) {
if (IJ.isMacintosh() && !quitting) {
IJ.wait(10); // may be needed for Java 1.4 on OS X
setMenuBar(Menus.getMenuBar());
}
}
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;
}
}
}
/**
* If 'applet' is not null, creates a new ImageJ frame that runs as an applet. If 'mode' is
* ImageJ.EMBEDDED and 'applet is null, creates an embedded (non-standalone) version of ImageJ.
*/
public ImageJ(java.applet.Applet applet, int mode) {
super("ImageJ");
if ((mode & DEBUG) != 0) IJ.setDebugMode(true);
mode = mode & 255;
if (IJ.debugMode) IJ.log("ImageJ starting in debug mode: " + mode);
embedded = applet == null && (mode == EMBEDDED || mode == NO_SHOW);
this.applet = applet;
String err1 = Prefs.load(this, applet);
setBackground(backgroundColor);
Menus m = new Menus(this, applet);
String err2 = m.addMenuBar();
m.installPopupMenu(this);
setLayout(new BorderLayout());
// Tool bar
toolbar = new Toolbar();
toolbar.addKeyListener(this);
add("Center", toolbar);
// Status bar
statusBar = new Panel();
statusBar.setLayout(new BorderLayout());
statusBar.setForeground(Color.black);
statusBar.setBackground(backgroundColor);
statusLine = new JLabel();
statusLine.setFont(new Font("SansSerif", Font.PLAIN, 13));
statusLine.addKeyListener(this);
statusLine.addMouseListener(this);
statusBar.add("Center", statusLine);
progressBar = new ProgressBar(120, 20);
progressBar.addKeyListener(this);
progressBar.addMouseListener(this);
statusBar.add("East", progressBar);
add("South", statusBar);
IJ.init(this, applet);
addKeyListener(this);
addWindowListener(this);
setFocusTraversalKeysEnabled(false);
m.installStartupMacroSet(); // add custom tools
runStartupMacro();
Point loc = getPreferredLocation();
Dimension tbSize = toolbar.getPreferredSize();
setCursor(Cursor.getDefaultCursor()); // work-around for JDK 1.1.8 bug
if (mode != NO_SHOW) {
if (IJ.isWindows())
try {
setIcon();
} catch (Exception e) {
}
setLocation(loc.x, loc.y);
setResizable(!IJ.isMacOSX());
pack();
setVisible(true);
}
if (err1 != null) IJ.error(err1);
if (err2 != null) {
IJ.error(err2);
IJ.runPlugIn("ij.plugin.ClassChecker", "");
}
if (IJ.isMacintosh() && applet == null) {
Object qh = null;
qh = IJ.runPlugIn("MacAdapter", "");
if (qh == null) IJ.runPlugIn("QuitHandler", "");
}
if (applet == null) IJ.runPlugIn("ij.plugin.DragAndDrop", "");
String str = m.getMacroCount() == 1 ? " macro" : " macros";
IJ.showStatus(version() + m.getPluginCount() + " commands; " + m.getMacroCount() + str);
configureProxy();
if (applet == null) loadCursors();
}
/**
* If 'applet' is not null, creates a new ImageJ frame that runs as an applet. If 'mode' is
* ImageJ.EMBEDDED and 'applet is null, creates an embedded (non-standalone) version of ImageJ.
*/
public ImageJ(java.applet.Applet applet, int mode) {
super("ImageJ");
embedded = applet == null && (mode == EMBEDDED || mode == NO_SHOW);
this.applet = applet;
String err1 = Prefs.load(this, applet);
if (IJ.isLinux()) {
backgroundColor = new Color(240, 240, 240);
setBackground(backgroundColor);
}
Menus m = new Menus(this, applet);
String err2 = m.addMenuBar();
m.installPopupMenu(this);
setLayout(new GridLayout(2, 1));
// Tool bar
toolbar = new Toolbar();
toolbar.addKeyListener(this);
add(toolbar);
// Status bar
statusBar = new Panel();
statusBar.setLayout(new BorderLayout());
statusBar.setForeground(Color.black);
statusBar.setBackground(backgroundColor);
statusLine = new Label();
statusLine.setFont(SansSerif12);
statusLine.addKeyListener(this);
statusLine.addMouseListener(this);
statusBar.add("Center", statusLine);
progressBar = new ProgressBar(120, 20);
progressBar.addKeyListener(this);
progressBar.addMouseListener(this);
statusBar.add("East", progressBar);
statusBar.setSize(toolbar.getPreferredSize());
add(statusBar);
IJ.init(this, applet);
addKeyListener(this);
addWindowListener(this);
setFocusTraversalKeysEnabled(false);
Point loc = getPreferredLocation();
Dimension tbSize = toolbar.getPreferredSize();
int ijWidth = tbSize.width + 10;
int ijHeight = 100;
setCursor(Cursor.getDefaultCursor()); // work-around for JDK 1.1.8 bug
if (mode != NO_SHOW) {
if (IJ.isWindows())
try {
setIcon();
} catch (Exception e) {
}
setBounds(loc.x, loc.y, ijWidth, ijHeight); // needed for pack to work
setLocation(loc.x, loc.y);
pack();
setResizable(!(IJ.isMacintosh() || IJ.isWindows())); // make resizable on Linux
show();
}
if (err1 != null) IJ.error(err1);
if (err2 != null) {
IJ.error(err2);
IJ.runPlugIn("ij.plugin.ClassChecker", "");
}
m.installStartupMacroSet();
if (IJ.isMacintosh() && applet == null) {
Object qh = null;
qh = IJ.runPlugIn("MacAdapter", "");
if (qh == null) IJ.runPlugIn("QuitHandler", "");
}
if (applet == null) IJ.runPlugIn("ij.plugin.DragAndDrop", "");
String str = m.getMacroCount() == 1 ? " macro" : " macros";
IJ.showStatus(version() + m.getPluginCount() + " commands; " + m.getMacroCount() + str);
// if (applet==null && !embedded && Prefs.runSocketListener)
// new SocketListener();
configureProxy();
if (applet == null) loadCursors();
}
private Object tryOpen(String directory, String name, String path) {
// set up a stream to read in 132 bytes from the file header
// These can be checked for "magic" values which are diagnostic
// of some image types
InputStream is;
byte[] buf = new byte[132];
try {
if (0 == path.indexOf("http://")) is = new java.net.URL(path).openStream();
else is = new FileInputStream(path);
is.read(buf, 0, 132);
is.close();
} catch (IOException e) {
// couldn't open the file for reading
return null;
}
name = name.toLowerCase();
width = PLUGIN_NOT_FOUND;
// Temporarily suppress "plugin not found" errors if LOCI Bio-Formats plugin is installed
if (Menus.getCommands().get("Bio-Formats Importer") != null
&& IJ.getVersion().compareTo("1.37u") >= 0) IJ.suppressPluginNotFoundError();
// OK now we get to the interesting bit
// GJ: added Biorad PIC confocal file handler
// ------------------------------------------
// These make 12345 if you read them as the right kind of short
// and should have this value in every Biorad PIC file
if (buf[54] == 57 && buf[55] == 48) {
return tryPlugIn("Biorad_Reader", path);
}
// GJ: added Gatan Digital Micrograph DM3 handler
// ----------------------------------------------
// check if the file ends in .DM3 or .dm3,
// and bytes make an int value of 3 which is the DM3 version number
if (name.endsWith(".dm3") && buf[0] == 0 && buf[1] == 0 && buf[2] == 0 && buf[3] == 3) {
return tryPlugIn("DM3_Reader", path);
}
// IPLab file handler
// Little-endian IPLab files start with "iiii" or "mmmm".
if (name.endsWith(".ipl")
|| (buf[0] == 105 && buf[1] == 105 && buf[2] == 105 && buf[3] == 105)
|| (buf[0] == 109 && buf[1] == 109 && buf[2] == 109 && buf[3] == 109)) {
return tryPlugIn("IPLab_Reader", path);
}
// Packard InstantImager format (.img) handler -> check HERE
// before Analyze check below!
// Check extension and signature bytes KAJ_
if (name.endsWith(".img") && buf[0] == 75 && buf[1] == 65 && buf[2] == 74 && buf[3] == 0) {
return tryPlugIn("InstantImager_Reader", path);
}
// Analyze format (.img/.hdr) handler
// Opens the file using the Nifti_Reader if it is installed,
// otherwise the Analyze_Reader is used. Note that
// the Analyze_Reader plugin opens and displays the
// image and does not implement the ImagePlus class.
if (name.endsWith(".img") || name.endsWith(".hdr")) {
if (Menus.getCommands().get("NIfTI-Analyze") != null) return tryPlugIn("Nifti_Reader", path);
else return tryPlugIn("Analyze_Reader", path);
}
// NIFTI format (.nii) handler
if (name.endsWith(".nii") || name.endsWith(".nii.gz") || name.endsWith(".nii.z")) {
return tryPlugIn("Nifti_Reader", path);
}
// Image Cytometry Standard (.ics) handler
// http://valelab.ucsf.edu/~nico/IJplugins/Ics_Opener.html
if (name.endsWith(".ics")) {
return tryPlugIn("Ics_Opener", path);
}
// Princeton Instruments SPE image file (.spe) handler
// http://rsb.info.nih.gov/ij/plugins/spe.html
if (name.endsWith(".spe")) {
return tryPlugIn("OpenSPE_", path);
}
// Zeiss Confocal LSM 510 image file (.lsm) handler
// http://rsb.info.nih.gov/ij/plugins/lsm-reader.html
if (name.endsWith(".lsm")) {
Object obj = tryPlugIn("LSM_Reader", path);
if (obj == null && Menus.getCommands().get("Show LSMToolbox") != null)
obj = tryPlugIn("LSM_Toolbox", "file=" + path);
return obj;
}
// BM: added Bruker file handler 29.07.04
if (name.equals("ser")
|| name.equals("fid")
|| name.equals("2rr")
|| name.equals("2ii")
|| name.equals("3rrr")
|| name.equals("3iii")
|| name.equals("2dseq")) {
ij.IJ.showStatus("Opening Bruker " + name + " File");
return tryPlugIn("BrukerOpener", name + "|" + path);
}
// AVI: open AVI files using AVI_Reader plugin
if (name.endsWith(".avi")) {
return tryPlugIn("AVI_Reader", path);
}
// QuickTime: open .mov and .pict files using QT_Movie_Opener plugin
if (name.endsWith(".mov") || name.endsWith(".pict")) {
return tryPlugIn("QT_Movie_Opener", path);
}
// ZVI file handler
// Little-endian ZVI and Thumbs.db files start with d0 cf 11 e0
// so we can only look at the extension.
if (name.endsWith(".zvi")) {
return tryPlugIn("ZVI_Reader", path);
}
// University of North Carolina (UNC) file format handler
// 'magic' numbers are (int) offsets to data structures and
// may change in future releases.
if (name.endsWith(".unc")
|| (buf[3] == 117 && buf[7] == -127 && buf[11] == 36 && buf[14] == 32 && buf[15] == -127)) {
return tryPlugIn("UNC_Reader", path);
}
// Amira file handler
// http://wbgn013.biozentrum.uni-wuerzburg.de/ImageJ/amira-io.html
if (buf[0] == 0x23
&& buf[1] == 0x20
&& buf[2] == 0x41
&& buf[3] == 0x6d
&& buf[4] == 0x69
&& buf[5] == 0x72
&& buf[6] == 0x61
&& buf[7] == 0x4d
&& buf[8] == 0x65
&& buf[9] == 0x73
&& buf[10] == 0x68
&& buf[11] == 0x20) {
return tryPlugIn("AmiraMeshReader_", path);
}
// Deltavision file handler
// Open DV files generated on Applied Precision DeltaVision systems
if (name.endsWith(".dv") || name.endsWith(".r3d")) {
return tryPlugIn("Deltavision_Opener", path);
}
// Albert Cardona: read .mrc files (little endian).
// Documentation at: http://ami.scripps.edu/prtl_data/mrc_specification.htm.
// The parsing of the header is a bare minimum of what could be done.
if (name.endsWith(".mrc")) {
return tryPlugIn("Open_MRC_Leginon", path);
}
// Albert Cardona: read .dat files from the EMMENU software
if (name.endsWith(".dat") && 1 == buf[1] && 0 == buf[2]) { // 'new format' only
return tryPlugIn("Open_DAT_EMMENU", path);
}
// Timo Rantalainen and Michael Doube: read Stratec pQCT files.
// File name is IDDDDDDD.MHH, where D is decimal and H is hex.
if (name.matches("[iI]\\d{7}\\.[mM]\\p{XDigit}{2}")) {
return tryPlugIn("org.doube.bonej.pqct.Read_Stratec_File", path);
}
// Michael Doube: read Scanco ISQ files
// File name is ADDDDDDD.ISQ;D where D is a decimal and A is a letter
try {
String isqMagic = new String(buf, 0, 16, "UTF-8");
if (name.matches("[a-z]\\d{7}.isq;\\d+") || isqMagic.equals("CTDATA-HEADER_V1"))
return tryPlugIn("org.bonej.io.ISQReader", path);
} catch (Exception e) {
}
// David Mills: read Queen Mary MCD files
if (name.endsWith(".mcd")) {
return tryPlugIn("mcdReader", path);
}
// David Mills: read Queen Mary TOM files
if (name.endsWith(".tom")) {
return tryPlugIn("tomReader", path);
}
// ****************** MODIFY HERE ******************
// do what ever you have to do to recognise your own file type
// and then call appropriate plugin using the above as models
// e.g.:
/*
// A. Dent: Added XYZ handler
// ----------------------------------------------
// check if the file ends in .xyz, and bytes 0 and 1 equal 42
if (name.endsWith(".xyz") && buf[0]==42 && buf[1]==42) {
// Ok we've identified the file type - now load it
return tryPlugIn("XYZ_Reader", path);
}
*/
return null;
}
public boolean install(String path) {
boolean isURL = path.contains("://");
String lcPath = path.toLowerCase();
if (isURL) path = Opener.updateUrl(path);
boolean isTool =
lcPath.endsWith("tool.ijm")
|| lcPath.endsWith("tool.txt")
|| lcPath.endsWith("tool.class")
|| lcPath.endsWith("tool.jar");
boolean isMacro = lcPath.endsWith(".txt") || lcPath.endsWith(".ijm");
byte[] data = null;
String name = path;
if (isURL) {
int index = path.lastIndexOf("/");
if (index != -1 && index <= path.length() - 1) name = path.substring(index + 1);
data = download(path, name);
} else {
File f = new File(path);
name = f.getName();
data = download(f);
}
if (data == null) return false;
if (name.endsWith(".txt") && !name.contains("_"))
name = name.substring(0, name.length() - 4) + ".ijm";
if (name.endsWith(".zip")) {
if (!name.contains("_")) {
IJ.error("Plugin Installer", "No underscore in file name:\n \n " + name);
return false;
}
name = name.substring(0, name.length() - 4) + ".jar";
}
String dir = null;
boolean isLibrary = name.endsWith(".jar") && !name.contains("_");
if (isLibrary) {
dir = Menus.getPlugInsPath() + "jars";
File f = new File(dir);
if (!f.exists()) {
boolean ok = f.mkdir();
if (!ok) dir = Menus.getPlugInsPath();
}
}
if (isTool) {
dir = Menus.getPlugInsPath() + "Tools" + File.separator;
File f = new File(dir);
if (!f.exists()) {
boolean ok = f.mkdir();
if (!ok) dir = null;
}
if (dir != null && isMacro) {
String name2 = getToolName(data);
if (name2 != null) name = name2;
}
}
if (dir == null) {
SaveDialog sd =
new SaveDialog("Save Plugin, Macro or Script...", Menus.getPlugInsPath(), name, null);
String name2 = sd.getFileName();
if (name2 == null) return false;
dir = sd.getDirectory();
}
// IJ.log(dir+" "+Menus.getPlugInsPath());
if (!savePlugin(new File(dir, name), data)) return false;
if (name.endsWith(".java")) IJ.runPlugIn("ij.plugin.Compiler", dir + name);
Menus.updateImageJMenus();
if (isTool) {
if (isMacro) IJ.runPlugIn("ij.plugin.Macro_Runner", "Tools/" + name);
else if (name.endsWith(".class")) {
name = name.replaceAll("_", " ");
name = name.substring(0, name.length() - 6);
IJ.run(name);
}
}
return true;
}
void install() {
subMenus.clear();
if (text != null) {
Tokenizer tok = new Tokenizer();
pgm = tok.tokenize(text);
}
if (macrosMenu != null) IJ.showStatus("");
int[] code = pgm.getCode();
Symbol[] symbolTable = pgm.getSymbolTable();
int count = 0, token, nextToken, address;
String name;
Symbol symbol;
shortcutsInUse = null;
inUseCount = 0;
nShortcuts = 0;
toolCount = 0;
macroStarts = new int[MAX_MACROS];
macroNames = new String[MAX_MACROS];
boolean isPluginsMacrosMenu = false;
if (macrosMenu != null) {
int itemCount = macrosMenu.getItemCount();
isPluginsMacrosMenu = macrosMenu == Menus.getMacrosMenu();
int baseCount = isPluginsMacrosMenu ? MACROS_MENU_COMMANDS : Editor.MACROS_MENU_ITEMS;
if (itemCount > baseCount) {
for (int i = itemCount - 1; i >= baseCount; i--) macrosMenu.remove(i);
}
}
if (pgm.hasVars() && pgm.macroCount() > 0 && pgm.getGlobals() == null)
new Interpreter().saveGlobals(pgm);
ArrayList tools = new ArrayList();
for (int i = 0; i < code.length; i++) {
token = code[i] & TOK_MASK;
if (token == MACRO) {
nextToken = code[i + 1] & TOK_MASK;
if (nextToken == STRING_CONSTANT) {
if (count == MAX_MACROS) {
if (isPluginsMacrosMenu)
IJ.error("Macro Installer", "Macro sets are limited to " + MAX_MACROS + " macros.");
break;
}
address = code[i + 1] >> TOK_SHIFT;
symbol = symbolTable[address];
name = symbol.str;
macroStarts[count] = i + 2;
macroNames[count] = name;
if (name.indexOf('-') != -1
&& (name.indexOf("Tool") != -1 || name.indexOf("tool") != -1)) {
tools.add(name);
toolCount++;
} else if (name.startsWith("AutoRun")) {
if (autoRunCount == 0 && !openingStartupMacrosInEditor) {
new MacroRunner(pgm, macroStarts[count], name, (String) null);
if (name.equals("AutoRunAndHide")) autoRunAndHideCount++;
}
autoRunCount++;
count--;
} else if (name.equals("Popup Menu")) installPopupMenu(name, pgm);
else if (!name.endsWith("Tool Selected")) {
if (macrosMenu != null) {
addShortcut(name);
int pos = name.indexOf(">");
boolean inSubMenu = name.startsWith("<") && (pos > 1);
if (inSubMenu) {
Menu parent = macrosMenu;
Menu subMenu = null;
String parentStr = name.substring(1, pos).trim();
String childStr = name.substring(pos + 1).trim();
MenuItem mnuItem = new MenuItem();
mnuItem.setActionCommand(name);
mnuItem.setLabel(childStr);
for (int jj = 0; jj < subMenus.size(); jj++) {
String aName = subMenus.get(jj).getName();
if (aName.equals(parentStr)) subMenu = subMenus.get(jj);
}
if (subMenu == null) {
subMenu = new Menu(parentStr);
subMenu.setName(parentStr);
subMenu.addActionListener(this);
subMenus.add(subMenu);
parent.add(subMenu);
}
subMenu.add(mnuItem);
} else macrosMenu.add(new MenuItem(name));
}
}
// IJ.log(count+" "+name+" "+macroStarts[count]);
count++;
}
} else if (token == EOF) break;
}
nMacros = count;
if (toolCount > 0 && (isPluginsMacrosMenu || macrosMenu == null) && installTools) {
Toolbar tb = Toolbar.getInstance();
if (toolCount == 1) tb.addMacroTool((String) tools.get(0), this);
else {
for (int i = 0; i < tools.size(); i++) {
String toolName = (String) tools.get(i);
if (toolName.startsWith("Abort Macro or Plugin") && toolCount > 6)
toolName = "Unused " + toolName;
tb.addMacroTool(toolName, this, i);
}
}
if (toolCount > 1 && Toolbar.getToolId() >= Toolbar.CUSTOM1) tb.setTool(Toolbar.RECTANGLE);
tb.repaint();
}
if (macrosMenu != null) this.instance = this;
if (shortcutsInUse != null && text != null)
IJ.showMessage(
"Install Macros",
(inUseCount == 1 ? "This keyboard shortcut is" : "These keyboard shortcuts are")
+ " already in use:"
+ shortcutsInUse);
if (nMacros == 0 && fileName != null) {
if (text == null || text.length() == 0) return;
int dotIndex = fileName.lastIndexOf('.');
if (dotIndex > 0) anonymousName = fileName.substring(0, dotIndex);
else anonymousName = fileName;
if (macrosMenu != null) macrosMenu.add(new MenuItem(anonymousName));
macroNames[0] = anonymousName;
nMacros = 1;
}
String word = nMacros == 1 ? " macro" : " macros";
if (isPluginsMacrosMenu) IJ.showStatus(nMacros + word + " installed");
}