Java Code Examples for ij.io.OpenDialog#getFileName()

/** Ask for the user to provide a template XML file to extract a root TemplateThing. */
public TemplateThing askForXMLTemplate(final Project project) {
	// ask for an .xml file or a .dtd file
	//fd.setFilenameFilter(new XMLFileFilter(XMLFileFilter.BOTH));
	final OpenDialog od = new OpenDialog("Select XML Template",
					OpenDialog.getDefaultDirectory(),
					null);
	final String filename = od.getFileName();
	if (null == filename || filename.toLowerCase().startsWith("null")) return null;
	// if there is a path, read it out if possible
	String dir = od.getDirectory();
	if (null == dir) return null;
	if (IJ.isWindows()) dir = dir.replace('\\', '/');
	if (!dir.endsWith("/")) dir += "/";
	TemplateThing[] roots;
	try {
		roots = DTDParser.extractTemplate(dir + filename);
	} catch (final Exception e) {
		IJError.print(e);
		return null;
	}
	if (null == roots || roots.length < 1) return null;
	if (roots.length > 1) {
		Utils.showMessage("Found more than one root.\nUsing first root only.");
	}
	return roots[0];
}
 

/** Returns the array of AreaList or null if the file dialog is canceled. The xo,yo is the pivot of reference. */
static public Collection<AreaList> importAmiraLabels(Layer first_layer, double xo, double yo, final String default_dir) {
	// open file
	OpenDialog od = new OpenDialog("Choose Amira Labels File", default_dir, "");
	String filename = od.getFileName();
	if (null == filename || 0 == filename.length()) return null;
	String dir = od.getDirectory();
	if (IJ.isWindows()) dir = dir.replace('\\', '/');
	if (!dir.endsWith("/")) dir += "/";
	String path =  dir + filename;
	AmiraMeshDecoder dec = new AmiraMeshDecoder();
	if (!dec.open(path)) {
		YesNoDialog yn = new YesNoDialog("Error", "File was not an Amira labels file.\nChoose another one?");
		if (yn.yesPressed()) return importAmiraLabels(first_layer, xo, yo, default_dir);
		return null;
	}
	ImagePlus imp = null;
	if (dec.isTable()) {
		Utils.showMessage("Select the other file (the labels)!");
		return null;
	} else {
		FileInfo fi = new FileInfo();
		fi.fileName = filename;
		fi.directory = dir;
		imp = new ImagePlus("Amira", dec.getStack());
		dec.parameters.setParameters(imp);
	}
	return extractAmiraLabels(imp, dec.parameters, first_layer, xo, yo);
}
 

/** A dialog to open a stack, making sure there is enough memory for it. */
synchronized public ImagePlus openStack() {
	final OpenDialog od = new OpenDialog("Select stack", OpenDialog.getDefaultDirectory(), null);
	final String file_name = od.getFileName();
	if (null == file_name || file_name.toLowerCase().startsWith("null")) return null;
	String dir = od.getDirectory().replace('\\', '/');
	if (!dir.endsWith("/")) dir += "/";

	final File f = new File(dir + file_name);
	if (!f.exists()) {
		Utils.showMessage("File " + dir + file_name  + " does not exist.");
		return null;
	}
	// avoid opening trakem2 projects
	if (file_name.toLowerCase().endsWith(".xml")) {
		Utils.showMessage("Cannot import " + file_name + " as a stack.");
		return null;
	}
	// estimate file size: assumes an uncompressed tif, or a zipped tif with an average compression ratio of 2.5
	long size = f.length() / 1024; // in megabytes
	if (file_name.length() -4 == file_name.toLowerCase().lastIndexOf(".zip")) {
		size = (long)(size * 2.5); // 2.5 is a reasonable compression ratio estimate based on my experience
	}
	releaseToFit(size);
	ImagePlus imp_stack = null;
	try {
		IJ.redirectErrorMessages();
		imp_stack = openImagePlus(f.getCanonicalPath());
	} catch (final Exception e) {
		IJError.print(e);
		return null;
	}
	if (null == imp_stack) {
		Utils.showMessage("Can't open the stack.");
		return null;
	} else if (1 == imp_stack.getStackSize()) {
		Utils.showMessage("Not a stack!");
		return null;
	}
	return imp_stack; // the open... command
}
 

/** If base_x or base_y are Double.MAX_VALUE, then those values are asked for in a GenericDialog. */
public Bureaucrat importLabelsAsAreaLists(final Layer first_layer, final String path_, final double base_x_, final double base_y_, final float alpha_, final boolean add_background_) {
	final Worker worker = new Worker("Import labels as arealists") {
		@Override
           public void run() {
			startedWorking();
			try {
				String path = path_;
				if (null == path) {
					final OpenDialog od = new OpenDialog("Select stack", "");
					final String name = od.getFileName();
					if (null == name || 0 == name.length()) {
						return;
					}
					String dir = od.getDirectory().replace('\\', '/');
					if (!dir.endsWith("/")) dir += "/";
					path = dir + name;
				}
				if (path.toLowerCase().endsWith(".xml")) {
					Utils.log("Avoided opening a TrakEM2 project.");
					return;
				}
				double base_x = base_x_;
				double base_y = base_y_;
				float alpha = alpha_;
				boolean add_background = add_background_;
				Layer layer = first_layer;
				if (Double.MAX_VALUE == base_x || Double.MAX_VALUE == base_y || alpha < 0 || alpha > 1) {
					final GenericDialog gd = new GenericDialog("Base x, y");
					Utils.addLayerChoice("First layer:", first_layer, gd);
					gd.addNumericField("Base_X:", 0, 0);
					gd.addNumericField("Base_Y:", 0, 0);
					gd.addSlider("Alpha:", 0, 100, 40);
					gd.addCheckbox("Add background (zero)", false);
					gd.showDialog();
					if (gd.wasCanceled()) {
						return;
					}
					layer = first_layer.getParent().getLayer(gd.getNextChoiceIndex());
					base_x = gd.getNextNumber();
					base_y = gd.getNextNumber();
					if (Double.isNaN(base_x) || Double.isNaN(base_y)) {
						Utils.log("Base x or y is NaN!");
						return;
					}
					alpha = (float)(gd.getNextNumber() / 100);
					add_background = gd.getNextBoolean();
				}
				releaseToFit(new File(path).length() * 3);
				final ImagePlus imp;
				if (path.toLowerCase().endsWith(".am")) {
					final AmiraMeshDecoder decoder = new AmiraMeshDecoder();
					if (decoder.open(path)) imp = new ImagePlus(path, decoder.getStack());
					else imp = null;
				} else {
					imp = openImagePlus(path);
				}
				if (null == imp) {
					Utils.log("Could not open image at " + path);
					return;
				}
				final Map<Float,AreaList> alis = AmiraImporter.extractAreaLists(imp, layer, base_x, base_y, alpha, add_background);
				if (!hasQuitted() && alis.size() > 0) {
					layer.getProject().getProjectTree().insertSegmentations(alis.values());
				}
			} catch (final Exception e) {
				IJError.print(e);
			} finally {
				finishedWorking();
			}
		}
	};
	return Bureaucrat.createAndStart(worker, first_layer.getProject());
}
 

/** Import a new image at the given coordinates; does not puts it into any layer, unless it's a stack -in which case importStack is called with the current front layer of the given project as target. If a path is not provided it will be asked for.*/
public Patch importImage(final Project project, final double x, final double y, String path, final boolean synch_mipmap_generation) {
	if (null == path) {
		final OpenDialog od = new OpenDialog("Import image", "");
		final String name = od.getFileName();
		if (null == name || 0 == name.length()) return null;
		String dir = od.getDirectory().replace('\\', '/');
		if (!dir.endsWith("/")) dir += "/";
		path = dir + name;
	} else {
		path = path.replace('\\', '/');
	}
	// avoid opening trakem2 projects
	if (path.toLowerCase().endsWith(".xml")) {
		Utils.showMessage("Cannot import " + path + " as a stack.");
		return null;
	}
	releaseToFit(new File(path).length() * 3);
	IJ.redirectErrorMessages();
	final ImagePlus imp = openImagePlus(path);
	if (null == imp) return null;
	if (imp.getNSlices() > 1) {
		// a stack!
		final Layer layer = Display.getFrontLayer(project);
		if (null == layer) return null;
		importStack(layer, x, y, imp, true, path, true);
		return null;
	}
	if (0 == imp.getWidth() || 0 == imp.getHeight()) {
		Utils.showMessage("Can't import image of zero width or height.");
		flush(imp);
		return null;
	}
	final Patch p = new Patch(project, imp.getTitle(), x, y, imp);
	addedPatchFrom(path, p);
	last_opened_path = path; // WARNING may be altered concurrently
	if (isMipMapsRegenerationEnabled()) {
		if (synch_mipmap_generation) {
			try {
				regenerateMipMaps(p).get(); // wait
			} catch (final Exception e) {
				IJError.print(e);
			}
		} else regenerateMipMaps(p); // queue for regeneration
	}
	return p;
}