/** 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());
}
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);
}
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;
}
/** Returns an InputStream for the image described by this FileInfo. */
public InputStream createInputStream(FileInfo fi) throws IOException, MalformedURLException {
InputStream is = null;
boolean gzip =
fi.fileName != null && (fi.fileName.endsWith(".gz") || fi.fileName.endsWith(".GZ"));
if (fi.inputStream != null) is = fi.inputStream;
else if (fi.url != null && !fi.url.equals("")) is = new URL(fi.url + fi.fileName).openStream();
else {
if (fi.directory.length() > 0 && !fi.directory.endsWith(Prefs.separator))
fi.directory += Prefs.separator;
File f = new File(fi.directory + fi.fileName);
if (gzip) fi.compression = FileInfo.COMPRESSION_UNKNOWN;
if (f == null || f.isDirectory() || !validateFileInfo(f, fi)) is = null;
else is = new FileInputStream(f);
}
if (is != null) {
if (fi.compression >= FileInfo.LZW) is = new RandomAccessStream(is);
else if (gzip) is = new GZIPInputStream(is, 50000);
}
return is;
}
/**
* 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);
}
}
static boolean validateFileInfo(File f, FileInfo fi) {
long offset = fi.getOffset();
long length = 0;
if (fi.width <= 0 || fi.height < 0) {
error("Width or height <= 0.", fi, offset, length);
return false;
}
if (offset >= 0 && offset < 1000L) return true;
if (offset < 0L) {
error("Offset is negative.", fi, offset, length);
return false;
}
if (fi.fileType == FileInfo.BITMAP || fi.compression != FileInfo.COMPRESSION_NONE) return true;
length = f.length();
long size = fi.width * fi.height * fi.getBytesPerPixel();
size = fi.nImages > 1 ? size : size / 4;
if (fi.height == 1) size = 0; // allows plugins to read info of unknown length at end of file
if (offset + size > length) {
error("Offset + image size > file length.", fi, offset, length);
return false;
}
return true;
}
public void run(String arg) {
if (arg.equals("menus")) {
updateMenus();
return;
}
if (IJ.getApplet() != null) return;
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 (jar loc): " + 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();
error(msg);
return;
}
String[] list = openUrlAsList(IJ.URL + "/download/jars/list.txt");
int count = list.length + 3;
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 - 2; 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 - 2] = "daily build";
urls[count - 2] = IJ.URL + "/ij.jar";
versions[count - 1] = "previous";
urls[count - 1] = IJ.URL + "/upgrade/ij2.jar";
int choice = showDialog(versions);
if (choice == -1 || !Commands.closeAll()) return;
// System.out.println("choice: "+choice);
// for (int i=0; i<urls.length; i++) System.out.println(" "+i+" "+urls[i]);
byte[] jar = null;
if ("daily build".equals(versions[choice]) && notes != null && notes.contains(" </title>"))
jar = getJar("http://wsr.imagej.net/download/daily-build/ij.jar");
if (jar == null) jar = getJar(urls[choice]);
if (jar == null) {
error("Unable to download ij.jar from " + urls[choice]);
return;
}
Prefs.savePreferences();
// System.out.println("saveJar: "+file);
saveJar(file, jar);
if (choice < count - 2) // force macro Function Finder to download fresh list
new File(IJ.getDirectory("macros") + "functions.html").delete();
System.exit(0);
}
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 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;
}