Examples with Layer ini.trakem2.display.Layer used on opensource projects

Example 61 with Layer

use of ini.trakem2.display.Layer in project TrakEM2 by trakem2.

the class AreaList method keyPressed.

@Override
public void keyPressed(final KeyEvent ke) {
    final Object source = ke.getSource();
    if (!(source instanceof DisplayCanvas))
        return;
    final DisplayCanvas dc = (DisplayCanvas) source;
    final Layer layer = dc.getDisplay().getLayer();
    final int keyCode = ke.getKeyCode();
    final long layer_id = layer.getId();
    if (KeyEvent.VK_K == keyCode) {
        final Roi roi = dc.getFakeImagePlus().getRoi();
        if (null == roi)
            return;
        if (!M.isAreaROI(roi)) {
            Utils.log("AreaList only accepts region ROIs, not lines.");
            return;
        }
        final ShapeRoi sroi = new ShapeRoi(roi);
        try {
            final AreaList p = part(layer_id, sroi);
            if (null != p) {
                project.getProjectTree().addSibling(this, p);
            }
            Display.repaint(layer, getBoundingBox(), 5);
            linkPatches();
        } catch (final NoninvertibleTransformException nite) {
            IJError.print(nite);
        }
        ke.consume();
    } else {
        Area a = getArea(layer_id);
        if (null == a) {
            a = new Area();
            ht_areas.put(layer_id, a);
        }
        new AreaWrapper(this, a).keyPressed(ke, dc, layer);
    }
}

Example 62 with Layer

use of ini.trakem2.display.Layer in project TrakEM2 by trakem2.

the class AreaList method getStack.

/**
 * Returns a stack of images representing the pixel data of this LayerSet inside this AreaList.
 */
public ImagePlus getStack(final int type, final double scale) {
    final ImageProcessor ref_ip = Utils.createProcessor(type, 2, 2);
    if (null == ref_ip) {
        Utils.log("AreaList.getStack: Unknown type " + type);
        return null;
    }
    final Rectangle b = getBoundingBox();
    final int w = (int) (0.5 + b.width * scale);
    final int h = (int) (0.5 + b.height * scale);
    final ImageStack stack = new ImageStack(w, h);
    for (final Layer la : getLayerRange()) {
        final Area area = getArea(la);
        final double z = layer.getZ();
        project.getLoader().releaseToFit(w * h * 10);
        final ImageProcessor ip = ref_ip.createProcessor(w, h);
        if (null == area) {
            stack.addSlice(Double.toString(z), ip);
            continue;
        }
        // Create a ROI from the area at Layer la:
        final AffineTransform aff = getAffineTransformCopy();
        aff.translate(-b.x, -b.y);
        aff.scale(scale, scale);
        final ShapeRoi roi = new ShapeRoi(area.createTransformedArea(aff));
        // Create a cropped snapshot of the images at Layer la under the area:
        final ImageProcessor flat = Patch.makeFlatImage(type, la, b, scale, la.getAll(Patch.class), Color.black);
        flat.setRoi(roi);
        final Rectangle rb = roi.getBounds();
        ip.insert(flat.crop(), rb.x, rb.y);
        // Clear the outside
        final ImagePlus bimp = new ImagePlus("", ip);
        bimp.setRoi(roi);
        ip.setValue(0);
        ip.setBackgroundValue(0);
        IJ.run(bimp, "Clear Outside", "");
        stack.addSlice(Double.toString(z), ip);
    }
    final ImagePlus imp = new ImagePlus("AreaList stack for " + this, stack);
    imp.setCalibration(layer_set.getCalibrationCopy());
    return imp;
}

Example 63 with Layer

use of ini.trakem2.display.Layer in project TrakEM2 by trakem2.

the class Project method createLayerTemplates.

private void createLayerTemplates() {
    if (null == layer_template) {
        layer_template = new TemplateThing("layer");
        layer_set_template = new TemplateThing("layer_set");
        layer_set_template.addChild(layer_template);
        // adding a new instance to keep parent/child relationships clean
        layer_template.addChild(layer_set_template);
    // No need, there won't ever be a loop so far WARNING may change in the future.
    }
}

Example 64 with Layer

use of ini.trakem2.display.Layer in project TrakEM2 by trakem2.

the class Project method newFSProject.

public static Project newFSProject(String arg, TemplateThing template_root, String storage_folder, boolean autocreate_one_layer) {
    if (Utils.wrongImageJVersion())
        return null;
    FSLoader loader = null;
    try {
        String dir_project = storage_folder;
        if (null == dir_project || !new File(dir_project).isDirectory()) {
            DirectoryChooser dc = new DirectoryChooser("Select storage folder");
            dir_project = dc.getDirectory();
            // user cancelled dialog
            if (null == dir_project)
                return null;
            if (!Loader.canReadAndWriteTo(dir_project)) {
                Utils.showMessage("Can't read/write to the selected storage folder.\nPlease check folder permissions.");
                return null;
            }
            if (IJ.isWindows())
                dir_project = dir_project.replace('\\', '/');
        }
        loader = new FSLoader(dir_project);
        Project project = createNewProject(loader, !("blank".equals(arg) || "amira".equals(arg)), template_root);
        // help the helpless users:
        if (autocreate_one_layer && null != project && ControlWindow.isGUIEnabled()) {
            Utils.log2("Creating automatic Display.");
            // add a default layer
            Layer layer = new Layer(project, 0, 1, project.layer_set);
            project.layer_set.add(layer);
            project.layer_tree.addLayer(project.layer_set, layer);
            layer.recreateBuckets();
            Display.createDisplay(project, layer);
        }
        try {
            // waiting cheaply for asynchronous swing calls
            Thread.sleep(200);
        } catch (InterruptedException ie) {
            ie.printStackTrace();
        }
        if ("amira".equals(arg) || "stack".equals(arg)) {
            // forks into a task thread
            loader.importStack(project.layer_set.getLayer(0), null, true);
        }
        project.restartAutosaving();
        return project;
    } catch (Exception e) {
        IJError.print(e);
        if (null != loader)
            loader.destroy();
    }
    return null;
}

Example 65 with Layer

use of ini.trakem2.display.Layer in project TrakEM2 by trakem2.

the class Project method adjustProperties.

public void adjustProperties() {
    // should be more generic, but for now it'll do
    GenericDialog gd = new GenericDialog("Properties");
    gd.addMessage("Ignore image linking for:");
    boolean link_labels = addBox(gd, DLabel.class);
    boolean nolink_segmentations = "true".equals(ht_props.get("segmentations_nolinks"));
    gd.addCheckbox("Segmentations", nolink_segmentations);
    gd.addMessage("Currently linked objects will remain so\nunless explicitly unlinked.");
    boolean dissector_zoom = "true".equals(ht_props.get("dissector_zoom"));
    gd.addCheckbox("Zoom-invariant markers for Dissector", dissector_zoom);
    gd.addChoice("Image_resizing_mode: ", Loader.MIPMAP_MODES.values().toArray(new String[Loader.MIPMAP_MODES.size()]), Loader.getMipMapModeName(mipmaps_mode));
    gd.addChoice("mipmaps format:", FSLoader.MIPMAP_FORMATS, FSLoader.MIPMAP_FORMATS[loader.getMipMapFormat()]);
    gd.addNumericField("Save mipmap images from level", this.first_mipmap_level_saved, 0);
    boolean layer_mipmaps = "true".equals(ht_props.get("layer_mipmaps"));
    gd.addCheckbox("Layer_mipmaps", layer_mipmaps);
    boolean keep_mipmaps = "true".equals(ht_props.get("keep_mipmaps"));
    // coping with the fact that thee is no Action context ... there should be one in the Worker thread.
    gd.addCheckbox("Keep_mipmaps_when_deleting_images", keep_mipmaps);
    int bucket_side = (int) getProperty("bucket_side", Bucket.MIN_BUCKET_SIZE);
    gd.addNumericField("Bucket side length: ", bucket_side, 0, 6, "pixels");
    boolean no_shutdown_hook = "true".equals(ht_props.get("no_shutdown_hook"));
    gd.addCheckbox("No_shutdown_hook to save the project", no_shutdown_hook);
    int n_undo_steps = getProperty("n_undo_steps", 32);
    gd.addSlider("Undo steps", 32, 200, n_undo_steps);
    boolean flood_fill_to_image_edge = "true".equals(ht_props.get("flood_fill_to_image_edge"));
    gd.addCheckbox("AreaList_flood_fill_to_image_edges", flood_fill_to_image_edge);
    int look_ahead_cache = (int) getProperty("look_ahead_cache", 0);
    gd.addNumericField("Look_ahead_cache:", look_ahead_cache, 0, 6, "layers");
    // default: every 10 minutes
    int autosaving_interval = getProperty("autosaving_interval", 10);
    gd.addNumericField("Autosave every:", autosaving_interval, 0, 6, "minutes");
    int n_mipmap_threads = getProperty("n_mipmap_threads", 1);
    gd.addSlider("Number of threads for mipmaps", 1, n_mipmap_threads, n_mipmap_threads);
    int meshResolution = getProperty("mesh_resolution", 32);
    gd.addSlider("Default mesh resolution for images", 1, 512, meshResolution);
    // 
    gd.showDialog();
    // 
    if (gd.wasCanceled())
        return;
    setLinkProp(link_labels, gd.getNextBoolean(), DLabel.class);
    boolean nolink_segmentations2 = gd.getNextBoolean();
    if (nolink_segmentations) {
        if (!nolink_segmentations2)
            ht_props.remove("segmentations_nolinks");
    } else if (nolink_segmentations2)
        ht_props.put("segmentations_nolinks", "true");
    if (adjustProp("dissector_zoom", dissector_zoom, gd.getNextBoolean())) {
        // TODO: should repaint nested LayerSets as well
        Display.repaint(layer_set);
    }
    this.mipmaps_mode = Loader.getMipMapModeIndex(gd.getNextChoice());
    final int new_mipmap_format = gd.getNextChoiceIndex();
    final int old_mipmap_format = loader.getMipMapFormat();
    if (new_mipmap_format != old_mipmap_format) {
        YesNoDialog yn = new YesNoDialog("MipMaps format", "Changing mipmaps format to '" + FSLoader.MIPMAP_FORMATS[new_mipmap_format] + "'requires regenerating all mipmaps. Proceed?");
        if (yn.yesPressed()) {
            if (loader.setMipMapFormat(new_mipmap_format)) {
                loader.updateMipMapsFormat(old_mipmap_format, new_mipmap_format);
            }
        }
    }
    setFirstMipMapLevelSaved(gd.getNextNumber());
    boolean layer_mipmaps2 = gd.getNextBoolean();
    if (adjustProp("layer_mipmaps", layer_mipmaps, layer_mipmaps2)) {
        if (layer_mipmaps && !layer_mipmaps2) {
        // TODO
        // 1 - ask first
        // 2 - remove all existing images from layer.mipmaps folder
        } else if (!layer_mipmaps && layer_mipmaps2) {
        // TODO
        // 1 - ask first
        // 2 - create de novo all layer mipmaps in a background task
        }
    }
    adjustProp("keep_mipmaps", keep_mipmaps, gd.getNextBoolean());
    Utils.log2("keep_mipmaps: " + getBooleanProperty("keep_mipmaps"));
    // 
    bucket_side = (int) gd.getNextNumber();
    if (bucket_side > Bucket.MIN_BUCKET_SIZE) {
        setProperty("bucket_side", Integer.toString(bucket_side));
        layer_set.recreateBuckets(true);
    }
    adjustProp("no_shutdown_hook", no_shutdown_hook, gd.getNextBoolean());
    n_undo_steps = (int) gd.getNextNumber();
    if (n_undo_steps < 0)
        n_undo_steps = 0;
    setProperty("n_undo_steps", Integer.toString(n_undo_steps));
    adjustProp("flood_fill_to_image_edge", flood_fill_to_image_edge, gd.getNextBoolean());
    double d_look_ahead_cache = gd.getNextNumber();
    if (!Double.isNaN(d_look_ahead_cache) && d_look_ahead_cache >= 0) {
        setProperty("look_ahead_cache", Integer.toString((int) d_look_ahead_cache));
        if (0 == d_look_ahead_cache) {
            Display.clearColumnScreenshots(this.layer_set);
        } else {
            Utils.logAll("WARNING: look-ahead cache is incomplete.\n  Expect issues when editing objects, adding new ones, and the like.\n  Use \"Project - Flush image cache\" to fix any lack of refreshing issues you encounter.");
        }
    } else {
        Utils.log2("Ignoring invalid 'look ahead cache' value " + d_look_ahead_cache);
    }
    double autosaving_interval2 = gd.getNextNumber();
    if (((int) (autosaving_interval2)) == autosaving_interval) {
    // do nothing
    } else if (autosaving_interval2 < 0 || Double.isNaN(autosaving_interval)) {
        Utils.log("IGNORING invalid autosaving interval: " + autosaving_interval2);
    } else {
        setProperty("autosaving_interval", Integer.toString((int) autosaving_interval2));
        restartAutosaving();
    }
    int n_mipmap_threads2 = (int) Math.max(1, gd.getNextNumber());
    if (n_mipmap_threads != n_mipmap_threads2) {
        setProperty("n_mipmap_threads", Integer.toString(n_mipmap_threads2));
        // WARNING: this does it for a static service, affecting all projects!
        FSLoader.restartMipMapThreads(n_mipmap_threads2);
    }
    int meshResolution2 = (int) gd.getNextNumber();
    if (meshResolution != meshResolution2) {
        if (meshResolution2 > 0) {
            setProperty("mesh_resolution", Integer.toString(meshResolution2));
        } else {
            Utils.log("WARNING: ignoring invalid mesh resolution value " + meshResolution2);
        }
    }
}