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
void createSelectionFromMask(ImagePlus imp) {
ImageProcessor ip = imp.getProcessor();
if (ip.getMinThreshold() != ImageProcessor.NO_THRESHOLD) {
IJ.runPlugIn("ij.plugin.filter.ThresholdToSelection", "");
return;
}
if (!ip.isBinary()) {
IJ.error(
"Create Selection",
"This command creates a composite selection from\n"
+ "a mask (8-bit binary image with white background)\n"
+ "or from an image that has been thresholded using\n"
+ "the Image>Adjust>Threshold tool. The current\n"
+ "image is not a mask and has not been thresholded.");
return;
}
int threshold = ip.isInvertedLut() ? 255 : 0;
ip.setThreshold(threshold, threshold, ImageProcessor.NO_LUT_UPDATE);
IJ.runPlugIn("ij.plugin.filter.ThresholdToSelection", "");
}
/**
* 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;
}
/** Restores original disk or network version of image. */
public void revertToSaved(ImagePlus imp) {
Image img;
ProgressBar pb = IJ.getInstance().getProgressBar();
ImageProcessor ip;
String path = fi.directory + fi.fileName;
if (fi.fileFormat == fi.GIF_OR_JPG) {
// restore gif or jpg
img = Toolkit.getDefaultToolkit().createImage(path);
imp.setImage(img);
if (imp.getType() == ImagePlus.COLOR_RGB) Opener.convertGrayJpegTo8Bits(imp);
return;
}
if (fi.fileFormat == fi.DICOM) {
// restore DICOM
ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.DICOM", path);
if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
return;
}
if (fi.fileFormat == fi.BMP) {
// restore BMP
ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.BMP_Reader", path);
if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
return;
}
if (fi.fileFormat == fi.PGM) {
// restore PGM
ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.PGM_Reader", path);
if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
return;
}
if (fi.fileFormat == fi.ZIP_ARCHIVE) {
// restore ".zip" file
ImagePlus imp2 = (new Opener()).openZip(path);
if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
return;
}
// restore PNG or another image opened using ImageIO
if (fi.fileFormat == fi.IMAGEIO) {
ImagePlus imp2 = (new Opener()).openUsingImageIO(path);
if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
return;
}
if (fi.nImages > 1) return;
ColorModel cm;
if (fi.url == null || fi.url.equals("")) IJ.showStatus("Loading: " + path);
else IJ.showStatus("Loading: " + fi.url + fi.fileName);
Object pixels = readPixels(fi);
if (pixels == null) return;
cm = createColorModel(fi);
switch (fi.fileType) {
case FileInfo.GRAY8:
case FileInfo.COLOR8:
case FileInfo.BITMAP:
ip = new ByteProcessor(width, height, (byte[]) pixels, cm);
imp.setProcessor(null, ip);
break;
case FileInfo.GRAY16_SIGNED:
case FileInfo.GRAY16_UNSIGNED:
case FileInfo.GRAY12_UNSIGNED:
ip = new ShortProcessor(width, height, (short[]) pixels, cm);
imp.setProcessor(null, ip);
break;
case FileInfo.GRAY32_INT:
case FileInfo.GRAY32_FLOAT:
ip = new FloatProcessor(width, height, (float[]) pixels, cm);
imp.setProcessor(null, ip);
break;
case FileInfo.RGB:
case FileInfo.BGR:
case FileInfo.ARGB:
case FileInfo.ABGR:
case FileInfo.RGB_PLANAR:
img =
Toolkit.getDefaultToolkit()
.createImage(new MemoryImageSource(width, height, (int[]) pixels, 0, width));
imp.setImage(img);
break;
}
}
/**
* 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();
}
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;
}