private void openDirectory(File f, String path) {
if (path == null) return;
if (!(path.endsWith(File.separator) || path.endsWith("/"))) path += File.separator;
String[] names = f.list();
names = (new FolderOpener()).trimFileList(names);
if (names == null) return;
String msg = "Open all " + names.length + " images in \"" + f.getName() + "\" as a stack?";
GenericDialog gd = new GenericDialog("Open Folder");
gd.setInsets(10, 5, 0);
gd.addMessage(msg);
gd.setInsets(15, 35, 0);
gd.addCheckbox("Convert to RGB", convertToRGB);
gd.setInsets(0, 35, 0);
gd.addCheckbox("Use Virtual Stack", virtualStack);
gd.enableYesNoCancel();
gd.showDialog();
if (gd.wasCanceled()) return;
if (gd.wasOKed()) {
convertToRGB = gd.getNextBoolean();
virtualStack = gd.getNextBoolean();
String options = " sort";
if (convertToRGB) options += " convert_to_rgb";
if (virtualStack) options += " use";
IJ.run("Image Sequence...", "open=[" + path + "]" + options);
DirectoryChooser.setDefaultDirectory(path);
} else {
for (int k = 0; k < names.length; k++) {
IJ.redirectErrorMessages();
if (!names[k].startsWith(".")) (new Opener()).open(path + names[k]);
}
}
IJ.register(DragAndDrop.class);
}
private ImagePlus openImage(String directory, String name, String path) {
Object o = tryOpen(directory, name, path);
// if an image was returned, assume success
if (o instanceof ImagePlus) return (ImagePlus) o;
// try opening the file with LOCI Bio-Formats plugin - always check this last!
// Do not call Bio-Formats if File>Import>Image Sequence is opening this file.
if (o == null
&& (IJ.getVersion().compareTo("1.38j") < 0 || !IJ.redirectingErrorMessages())
&& (new File(path).exists())) {
Object loci = IJ.runPlugIn("loci.plugins.LociImporter", path);
if (loci != null) {
// plugin exists and was launched
try {
// check whether plugin was successful
Class c = loci.getClass();
boolean success = c.getField("success").getBoolean(loci);
boolean canceled = c.getField("canceled").getBoolean(loci);
if (success || canceled) {
width = IMAGE_OPENED;
return null;
}
} catch (Exception exc) {
}
}
}
return null;
} // openImage
/** Called by ImageJ when the user selects Quit. */
public void quit() {
quitMacro = IJ.macroRunning();
Thread thread = new Thread(this, "Quit");
thread.setPriority(Thread.NORM_PRIORITY);
thread.start();
IJ.wait(10);
}
/** 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);
}
}
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;
}
/** Called from io/Opener.java. */
public void run(String path) {
if (path.equals("")) return;
File theFile = new File(path);
String directory = theFile.getParent();
String fileName = theFile.getName();
if (directory == null) directory = "";
// Try and recognise file type and load the file if recognised
ImagePlus imp = openImage(directory, fileName, path);
if (imp == null) {
IJ.showStatus("");
return; // failed to load file or plugin has opened and displayed it
}
ImageStack stack = imp.getStack();
// get the title from the stack (falling back to the fileName)
String title = imp.getTitle().equals("") ? fileName : imp.getTitle();
// set the stack of this HandleExtraFileTypes object
// to that attached to the ImagePlus object returned by openImage()
setStack(title, stack);
// copy over the calibration info since it doesn't come with the ImageProcessor
setCalibration(imp.getCalibration());
// also copy the Show Info field over if it exists
if (imp.getProperty("Info") != null) setProperty("Info", imp.getProperty("Info"));
// copy the FileInfo
setFileInfo(imp.getOriginalFileInfo());
// copy dimensions
if (IJ.getVersion().compareTo("1.38s") >= 0)
setDimensions(imp.getNChannels(), imp.getNSlices(), imp.getNFrames());
if (IJ.getVersion().compareTo("1.41o") >= 0) setOpenAsHyperStack(imp.getOpenAsHyperStack());
}
void write16BitStack(OutputStream out, Object[] stack) throws IOException {
showProgressBar = false;
for (int i = 0; i < fi.nImages; i++) {
IJ.showStatus("Writing: " + (i + 1) + "/" + fi.nImages);
write16BitImage(out, (short[]) stack[i]);
IJ.showProgress((double) (i + 1) / fi.nImages);
}
}
public void dragOver(DropTargetDragEvent e) {
if (IJ.debugMode) IJ.log("DragOver: " + e.getLocation());
Point loc = e.getLocation();
int buttonSize = Toolbar.getButtonSize();
int width = IJ.getInstance().getSize().width;
openAsVirtualStack = width - loc.x <= buttonSize;
if (openAsVirtualStack) IJ.showStatus("<<Open as Virtual Stack>>");
else IJ.showStatus("<<Drag and Drop>>");
}
void write16BitVirtualStack(OutputStream out, VirtualStack virtualStack) throws IOException {
showProgressBar = false;
boolean flip = "FlipTheseImages".equals(fi.fileName);
for (int i = 1; i <= fi.nImages; i++) {
IJ.showStatus("Writing: " + i + "/" + fi.nImages);
ImageProcessor ip = virtualStack.getProcessor(i);
if (flip) ip.flipVertical();
short[] pixels = (short[]) ip.getPixels();
write16BitImage(out, pixels);
IJ.showProgress((double) i / fi.nImages);
}
}
/** 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 drop(DropTargetDropEvent dtde) {
dtde.acceptDrop(DnDConstants.ACTION_COPY);
DataFlavor[] flavors = null;
try {
Transferable t = dtde.getTransferable();
iterator = null;
flavors = t.getTransferDataFlavors();
if (IJ.debugMode) IJ.log("DragAndDrop.drop: " + flavors.length + " flavors");
for (int i = 0; i < flavors.length; i++) {
if (IJ.debugMode) IJ.log(" flavor[" + i + "]: " + flavors[i].getMimeType());
if (flavors[i].isFlavorJavaFileListType()) {
Object data = t.getTransferData(DataFlavor.javaFileListFlavor);
iterator = ((List) data).iterator();
break;
} else if (flavors[i].isFlavorTextType()) {
Object ob = t.getTransferData(flavors[i]);
if (!(ob instanceof String)) continue;
String s = ob.toString().trim();
if (IJ.isLinux() && s.length() > 1 && (int) s.charAt(1) == 0) s = fixLinuxString(s);
ArrayList list = new ArrayList();
if (s.indexOf("href=\"") != -1 || s.indexOf("src=\"") != -1) {
s = parseHTML(s);
if (IJ.debugMode) IJ.log(" url: " + s);
list.add(s);
this.iterator = list.iterator();
break;
}
BufferedReader br = new BufferedReader(new StringReader(s));
String tmp;
while (null != (tmp = br.readLine())) {
tmp = java.net.URLDecoder.decode(tmp.replaceAll("\\+", "%2b"), "UTF-8");
if (tmp.startsWith("file://")) tmp = tmp.substring(7);
if (IJ.debugMode) IJ.log(" content: " + tmp);
if (tmp.startsWith("http://")) list.add(s);
else list.add(new File(tmp));
}
this.iterator = list.iterator();
break;
}
}
if (iterator != null) {
Thread thread = new Thread(this, "DrawAndDrop");
thread.setPriority(Math.max(thread.getPriority() - 1, Thread.MIN_PRIORITY));
thread.start();
}
} catch (Exception e) {
dtde.dropComplete(false);
return;
}
dtde.dropComplete(true);
if (flavors == null || flavors.length == 0) {
if (IJ.isMacOSX())
IJ.error(
"First drag and drop ignored. Please try again. You can avoid this\n"
+ "problem by dragging to the toolbar instead of the status bar.");
else IJ.error("Drag and drop failed");
}
}
public void run(String arg) {
ImageJ ij = IJ.getInstance();
ij.setDropTarget(null);
new DropTarget(ij, this);
new DropTarget(Toolbar.getInstance(), this);
new DropTarget(ij.getStatusBar(), this);
}
void updateMenus() {
if (IJ.debugMode) {
long start = System.currentTimeMillis();
Menus.updateImageJMenus();
IJ.log("Refresh Menus: " + (System.currentTimeMillis() - start) + " ms");
} else Menus.updateImageJMenus();
}
/** Opens a stack of images. */
ImagePlus openStack(ColorModel cm, boolean show) {
ImageStack stack = new ImageStack(fi.width, fi.height, cm);
long skip = fi.getOffset();
Object pixels;
try {
ImageReader reader = new ImageReader(fi);
InputStream is = createInputStream(fi);
if (is == null) return null;
IJ.resetEscape();
for (int i = 1; i <= fi.nImages; i++) {
if (!silentMode) IJ.showStatus("Reading: " + i + "/" + fi.nImages);
if (IJ.escapePressed()) {
IJ.beep();
IJ.showProgress(1.0);
silentMode = false;
return null;
}
pixels = reader.readPixels(is, skip);
if (pixels == null) break;
stack.addSlice(null, pixels);
skip = fi.gapBetweenImages;
if (!silentMode) IJ.showProgress(i, fi.nImages);
}
is.close();
} catch (Exception e) {
IJ.log("" + e);
} catch (OutOfMemoryError e) {
IJ.outOfMemory(fi.fileName);
stack.trim();
}
if (!silentMode) IJ.showProgress(1.0);
if (stack.getSize() == 0) return null;
if (fi.sliceLabels != null && fi.sliceLabels.length <= stack.getSize()) {
for (int i = 0; i < fi.sliceLabels.length; i++) stack.setSliceLabel(fi.sliceLabels[i], i + 1);
}
ImagePlus imp = new ImagePlus(fi.fileName, stack);
if (fi.info != null) imp.setProperty("Info", fi.info);
if (show) imp.show();
imp.setFileInfo(fi);
setCalibration(imp);
ImageProcessor ip = imp.getProcessor();
if (ip.getMin() == ip.getMax()) // find stack min and max if first slice is blank
setStackDisplayRange(imp);
if (!silentMode) IJ.showProgress(1.0);
silentMode = false;
return imp;
}
/**
* Reads the image from a URL and returns the pixel array (byte, short, int or float). Returns
* null if there was an IO exception.
*/
public Object readPixels(String url) {
java.net.URL theURL;
InputStream is;
try {
theURL = new URL(url);
} catch (MalformedURLException e) {
IJ.log("" + e);
return null;
}
try {
is = theURL.openStream();
} catch (IOException e) {
IJ.log("" + e);
return null;
}
return readPixels(is);
}
public FileOpener(FileInfo fi) {
this.fi = fi;
if (fi != null) {
width = fi.width;
height = fi.height;
}
if (IJ.debugMode) IJ.log("FileInfo: " + fi);
}
public String getInfo() {
return version()
+ System.getProperty("os.name")
+ " "
+ System.getProperty("os.version")
+ "; "
+ IJ.freeMemory();
}
byte[] getJar(String address) {
// System.out.println("getJar: "+address);
byte[] data;
try {
URL url = new URL(address);
IJ.showStatus("Connecting to " + IJ.URL);
URLConnection uc = url.openConnection();
int len = uc.getContentLength();
if (IJ.debugMode) IJ.log("Updater (url): " + address + " " + len);
if (len <= 0) return null;
String name = address.contains("wsr") ? "daily build (" : "ij.jar (";
IJ.showStatus("Downloading " + name + IJ.d2s((double) len / 1048576, 1) + "MB)");
InputStream in = uc.getInputStream();
data = new byte[len];
int n = 0;
while (n < len) {
int count = in.read(data, n, len - n);
if (count < 0) throw new EOFException();
n += count;
IJ.showProgress(n, len);
}
in.close();
} catch (IOException e) {
if (IJ.debugMode) IJ.log("" + e);
return null;
}
if (IJ.debugMode) IJ.wait(6000);
return data;
}
private String version() {
return "ImageJ "
+ VERSION
+ BUILD
+ "; "
+ "Java "
+ System.getProperty("java.version")
+ (IJ.is64Bit() ? " [64-bit]; " : " [32-bit]; ");
}
byte[] download(File f) {
if (!f.exists()) {
IJ.error("Plugin Installer", "File not found: " + f);
return null;
}
byte[] data = null;
try {
int len = (int) f.length();
InputStream in = new BufferedInputStream(new FileInputStream(f));
DataInputStream dis = new DataInputStream(in);
data = new byte[len];
dis.readFully(data);
dis.close();
} catch (Exception e) {
IJ.error("Plugin Installer", "" + e);
data = null;
}
return data;
}
short[] readCompressed16bitImage(InputStream in) throws IOException {
if (IJ.debugMode) IJ.log("ImageReader.read16bit, offset=" + fi.stripOffsets[0]);
short[] pixels = new short[nPixels];
int base = 0;
short last = 0;
for (int k = 0; k < fi.stripOffsets.length; k++) {
// IJ.log("seek: "+fi.stripOffsets[k]+" "+fi.stripLengths[k]+" "+(in instanceof
// RandomAccessStream));
if (in instanceof RandomAccessStream) ((RandomAccessStream) in).seek(fi.stripOffsets[k]);
else if (k > 0) {
long skip =
(fi.stripOffsets[k] & 0xffffffffL)
- (fi.stripOffsets[k - 1] & 0xffffffffL)
- fi.stripLengths[k - 1];
if (skip > 0L) in.skip(skip);
}
byte[] byteArray = new byte[fi.stripLengths[k]];
int read = 0, left = byteArray.length;
while (left > 0) {
int r = in.read(byteArray, read, left);
if (r == -1) {
eofError();
break;
}
read += r;
left -= r;
}
byteArray = uncompress(byteArray);
int pixelsRead = byteArray.length / bytesPerPixel;
pixelsRead = pixelsRead - (pixelsRead % fi.width);
int pmax = base + pixelsRead;
if (pmax > nPixels) pmax = nPixels;
if (fi.intelByteOrder) {
for (int i = base, j = 0; i < pmax; i++, j += 2)
pixels[i] = (short) (((byteArray[j + 1] & 0xff) << 8) | (byteArray[j] & 0xff));
} else {
for (int i = base, j = 0; i < pmax; i++, j += 2)
pixels[i] = (short) (((byteArray[j] & 0xff) << 8) | (byteArray[j + 1] & 0xff));
}
if (fi.compression == FileInfo.LZW_WITH_DIFFERENCING) {
for (int b = base; b < pmax; b++) {
pixels[b] += last;
last = b % fi.width == fi.width - 1 ? 0 : pixels[b];
}
}
base += pixelsRead;
showProgress(k + 1, fi.stripOffsets.length);
}
if (fi.fileType == FileInfo.GRAY16_SIGNED) {
// convert to unsigned
for (int i = 0; i < nPixels; i++) pixels[i] = (short) (pixels[i] + 32768);
}
return pixels;
}
boolean savePlugin(File f, byte[] data) {
try {
FileOutputStream out = new FileOutputStream(f);
out.write(data, 0, data.length);
out.close();
} catch (IOException e) {
IJ.error("Plugin Installer", "" + e);
return false;
}
return true;
}
String[] openUrlAsList(String address) {
IJ.showStatus("Connecting to " + IJ.URL);
Vector v = new Vector();
try {
URL url = new URL(address);
InputStream in = url.openStream();
BufferedReader br = new BufferedReader(new InputStreamReader(in));
String line;
while (true) {
line = br.readLine();
if (line == null) break;
if (!line.equals("")) v.addElement(line);
}
br.close();
} catch (Exception e) {
}
String[] lines = new String[v.size()];
v.copyInto((String[]) lines);
IJ.showStatus("");
return lines;
}
public void run(String arg) {
OpenDialog od = new OpenDialog("Install Plugin, Macro or Script...", arg);
String directory = od.getDirectory();
String name = od.getFileName();
if (name == null) return;
if (!validExtension(name)) {
IJ.error("Plugin Installer", errorMessage());
return;
}
String path = directory + name;
install(path);
}
void abortPluginOrMacro(ImagePlus imp) {
if (imp != null) {
ImageWindow win = imp.getWindow();
if (win != null) {
win.running = false;
win.running2 = false;
}
}
Macro.abort();
Interpreter.abort();
if (Interpreter.getInstance() != null) IJ.beep();
}
/**
* Open a file. If it's a directory, ask to open all images as a sequence in a stack or
* individually.
*/
public void openFile(File f) {
if (IJ.debugMode) IJ.log("DragAndDrop.openFile: " + f);
try {
if (null == f) return;
String path = f.getCanonicalPath();
if (f.exists()) {
if (f.isDirectory()) openDirectory(f, path);
else {
if (openAsVirtualStack && (path.endsWith(".tif") || path.endsWith(".TIF")))
(new FileInfoVirtualStack()).run(path);
else (new Opener()).openAndAddToRecent(path);
OpenDialog.setLastDirectory(f.getParent() + File.separator);
OpenDialog.setLastName(f.getName());
}
} else {
IJ.log("File not found: " + path);
}
} catch (Throwable e) {
if (!Macro.MACRO_CANCELED.equals(e.getMessage())) IJ.handleException(e);
}
}
public void run(String arg) {
if (IJ.versionLessThan("1.49d")) return;
if (!showDialog()) return;
SaveDialog sd = new SaveDialog("Save as Bricks...", "", "");
basename = sd.getFileName();
directory = sd.getDirectory();
if (basename == null || directory == null) return;
build_bricks();
}
public void run(ImageProcessor ip) {
dimz = stack.getSize();
dimy = stack.getWidth();
dimx = stack.getHeight();
SaveDialog sd = new SaveDialog("Save Measurements as Text...", "res", ".dat");
String name = sd.getFileName();
if (name == null) return;
String directory = sd.getDirectory();
nb = calculnb(stack); // -1;
IJ.showStatus("Measure parameters for the " + nb + " objects ...");
if (nb < 1) {
IJ.showMessage("volume must be labeled");
} else {
double[] volume_m = new double[nb];
int[] volume_p = new int[nb];
double[] surface = new double[nb];
double[] surfacenb = new double[nb];
double[][][] I = new double[3][3][nb];
double[][] J = new double[3][nb];
double[][][] dir = new double[3][3][nb];
double[] xg = new double[nb];
double[] yg = new double[nb];
double[] zg = new double[nb];
byte[] bord = new byte[nb];
// double[] a = new double[nb];
// double[] b = new double[nb];
// double[] c = new double[nb];
// double[] Fab = new double[nb];
// double[] Fac = new double[nb];
// double[] Fbc = new double[nb];
// double[] sp = new double[nb];
double[][] lmin = new double[nb][3];
double[][] lmax = new double[nb][3];
IJ.showStatus("Measure surfaces ...");
calculmarchsurfstack(stack, nb, surface, volume_m);
calculmarchsurfstacknb(stack, nb, surfacenb);
// calculvolumestack(stack,nb,volume_p);
IJ.showStatus("Measure volumes and inertia ...");
calculcgstack(stack, nb, volume_p, xg, yg, zg);
calculinertiestack(stack, nb, xg, yg, zg, I);
inertie(nb, I, J, dir);
IJ.showStatus("Measure bounding boxes ...");
boitestack(stack, nb, xg, yg, zg, dir, lmin, lmax);
borderstack(stack, nb, bord);
IJ.showStatus("Save results ...");
sauvegarde(
volume_p, volume_m, surface, surfacenb, xg, yg, zg, J, dir, nb, bord, lmin, lmax,
directory, name);
volume_m = null;
volume_p = null;
surface = null;
xg = null;
yg = null;
zg = null;
}
}
/**
* Attempts to open the specified path with the given plugin. If the plugin extends the ImagePlus
* class (e.g., BioRad_Reader), set extendsImagePlus to true, otherwise (e.g., LSM_Reader) set it
* to false.
*
* @return A reference to the plugin, if it was successful.
*/
private Object tryPlugIn(String className, String path) {
Object o = IJ.runPlugIn(className, path);
if (o instanceof ImagePlus) {
// plugin extends ImagePlus class
ImagePlus imp = (ImagePlus) o;
if (imp.getWidth() == 0) o = null; // invalid image
else width = IMAGE_OPENED; // success
} else {
// plugin does not extend ImagePlus; assume success
width = IMAGE_OPENED;
}
return o;
}
private String parseHTML(String s) {
if (IJ.debugMode) IJ.log("parseHTML:\n" + s);
int index1 = s.indexOf("src=\"");
if (index1 >= 0) {
int index2 = s.indexOf("\"", index1 + 5);
if (index2 > 0) return s.substring(index1 + 5, index2);
}
index1 = s.indexOf("href=\"");
if (index1 >= 0) {
int index2 = s.indexOf("\"", index1 + 6);
if (index2 > 0) return s.substring(index1 + 6, index2);
}
return s;
}