Examples with AmiraMeshDecoder amira.AmiraMeshDecoder used on opensource projects

Example 1 with AmiraMeshDecoder

use of amira.AmiraMeshDecoder in project TrakEM2 by trakem2.

the class AmiraImporter method importAmiraLabels.

/**
 * Returns the array of AreaList or null if the file dialog is canceled. The xo,yo is the pivot of reference.
 */
public static 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);
}

Example 2 with AmiraMeshDecoder

use of amira.AmiraMeshDecoder in project TrakEM2 by trakem2.

the class Loader method importLabelsAsAreaLists.

/**
 * 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());
}