/* TODO: sorted */
public static MenuItem installPlugin(String menuPath, String name, String command) {
if (Menus.getCommands().get(name) != null) {
IJ.log("The user plugin " + name + " would override an existing command!");
return null;
}
MenuItem item = null;
if (IJ.getInstance() != null) {
int croc = menuPath.lastIndexOf('>');
Menu menu = getMenu(menuPath);
item = new MenuItem(name);
menu.add(item);
item.addActionListener(IJ.getInstance());
}
Menus.getCommands().put(name, command);
return item;
}
/** Install the plugins now */
public void run(String arg) {
if ("update".equals(arg)) {
Menus.updateImageJMenus();
ClassLoader loader = IJ.getClassLoader();
if (loader != null && (loader instanceof FijiClassLoader)) return;
}
FijiClassLoader classLoader = new FijiClassLoader(true);
try {
classLoader.addPath(path);
} catch (IOException e) {
}
try {
// IJ.setClassLoader(classLoader);
Class ij = Class.forName("ij.IJ");
java.lang.reflect.Method method =
ij.getDeclaredMethod("setClassLoader", new Class[] {ClassLoader.class});
method.setAccessible(true);
method.invoke(null, new Object[] {classLoader});
} catch (Exception e) {
e.printStackTrace();
}
installScripts();
installPlugins(path, ".", menuPath);
/* make sure "Update Menus" runs _this_ plugin */
Menus.getCommands().put("Update Menus", "fiji.User_Plugins(\"update\")");
Menus.getCommands().put("Refresh Menus", "fiji.User_Plugins(\"update\")");
Menus.getCommands().put("Compile and Run...", "fiji.Compile_and_Run");
if (IJ.getInstance() != null) {
Menu help = Menus.getMenuBar().getHelpMenu();
for (int i = help.getItemCount() - 1; i >= 0; i--) {
MenuItem item = help.getItem(i);
String name = item.getLabel();
if (name.equals("Update Menus")) item.setLabel("Refresh Menus");
}
}
// make sure "Edit>Options>Memory & Threads runs Fiji's plugin
Menus.getCommands().put("Memory & Threads...", "fiji.Memory");
SampleImageLoader.install();
Main.installRecentCommands();
}
@Override
public Map<String, Throwable> findPlugins(final List<PluginInfo<?>> plugins) {
final Map<String, MenuPath> menuTable = parseMenus(IJ.getInstance());
final Hashtable<?, ?> commands = Menus.getCommands();
final int startSize = plugins.size();
for (final Object key : commands.keySet()) {
final PluginInfo<Command> pe = createEntry(key, commands, menuTable);
if (pe != null) plugins.add(pe);
}
final int pluginCount = plugins.size() - startSize;
final int ignoredCount = commands.size() - pluginCount;
log.info("Found " + pluginCount + " legacy plugins (plus " + ignoredCount + " ignored).");
return null;
}
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);
}
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;
}
/**
* Run the command associated with a menu label if there is one
*
* @param menuLabel the label of the menu item to run
*/
public static void runPlugIn(String menuLabel) {
String className = (String) Menus.getCommands().get(menuLabel);
if (className != null) IJ.runPlugIn(className, null);
}
static {
Hashtable commands = Menus.getCommands();
bioformats = commands != null && commands.get("Bio-Formats Importer") != null;
}