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

Example 71 with Layer

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

the class Display method adjustProperties.

public void adjustProperties() {
    final GenericDialog gd = new GenericDialog("Properties", Display.this.frame);
    // gd.addNumericField("layer_scroll_step: ", this.scroll_step, 0);
    gd.addSlider("layer_scroll_step: ", 1, layer.getParent().size(), Display.this.scroll_step);
    gd.addChoice("snapshots_mode", LayerSet.snapshot_modes, LayerSet.snapshot_modes[layer.getParent().getSnapshotsMode()]);
    gd.addCheckbox("prefer_snapshots_quality", layer.getParent().snapshotsQuality());
    final Loader lo = getProject().getLoader();
    final boolean using_mipmaps = lo.isMipMapsRegenerationEnabled();
    gd.addCheckbox("enable_mipmaps", using_mipmaps);
    gd.addCheckbox("enable_layer_pixels virtualization", layer.getParent().isPixelsVirtualizationEnabled());
    final double max = layer.getParent().getLayerWidth() < layer.getParent().getLayerHeight() ? layer.getParent().getLayerWidth() : layer.getParent().getLayerHeight();
    gd.addSlider("max_dimension of virtualized layer pixels: ", 0, max, layer.getParent().getPixelsMaxDimension());
    gd.addCheckbox("Show arrow heads in Treeline/AreaTree", layer.getParent().paint_arrows);
    gd.addCheckbox("Show edge confidence boxes in Treeline/AreaTree", layer.getParent().paint_edge_confidence_boxes);
    gd.addSlider("Stroke width (Treeline, AreaTree, Ball)", 1.0, 10.0, DisplayCanvas.DEFAULT_STROKE.getLineWidth());
    gd.addCheckbox("Show color cues", layer.getParent().color_cues);
    gd.addSlider("+/- layers to color cue", 0, 10, layer.getParent().n_layers_color_cue);
    gd.addCheckbox("Show color cues for areas", layer.getParent().area_color_cues);
    gd.addCheckbox("Use red/blue for color cues", layer.getParent().use_color_cue_colors);
    gd.addCheckbox("Prepaint images", layer.getParent().prepaint);
    gd.addSlider("Preload ahead from sections: ", 0, layer.getParent().size(), layer.getParent().preload_ahead);
    // --------
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    // --------
    int sc = (int) gd.getNextNumber();
    if (sc < 1)
        sc = 1;
    Display.this.scroll_step = sc;
    updateInDatabase("scroll_step");
    // 
    layer.getParent().setSnapshotsMode(gd.getNextChoiceIndex());
    layer.getParent().setSnapshotsQuality(gd.getNextBoolean());
    // 
    final boolean using_mipmaps2 = gd.getNextBoolean();
    if (using_mipmaps2 == using_mipmaps) {
    // Nothing changed
    } else if (!using_mipmaps2 && using_mipmaps) {
        // Desactivate mipmaps
        lo.setMipMapsRegeneration(false);
        lo.flushMipMaps(true);
    } else if (using_mipmaps2 && !using_mipmaps) {
        // Reactivate mipmaps
        lo.setMipMapsRegeneration(true);
        lo.generateMipMaps(layer.getParent().getDisplayables(Patch.class));
    }
    // 
    layer.getParent().setPixelsVirtualizationEnabled(gd.getNextBoolean());
    layer.getParent().setPixelsMaxDimension((int) gd.getNextNumber());
    layer.getParent().paint_arrows = gd.getNextBoolean();
    layer.getParent().paint_edge_confidence_boxes = gd.getNextBoolean();
    DisplayCanvas.DEFAULT_STROKE = new BasicStroke((float) Math.max(1, gd.getNextNumber()), BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER);
    layer.getParent().color_cues = gd.getNextBoolean();
    layer.getParent().n_layers_color_cue = (int) gd.getNextNumber();
    layer.getParent().area_color_cues = gd.getNextBoolean();
    layer.getParent().use_color_cue_colors = gd.getNextBoolean();
    layer.getParent().prepaint = gd.getNextBoolean();
    layer.getParent().preload_ahead = (int) Math.min(gd.getNextNumber(), layer.getParent().size());
    Display.repaint(layer.getParent());
}

Example 72 with Layer

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

the class Layer method exportXML.

@Override
public void exportXML(final StringBuilder sb_body, final String indent, final XMLOptions options) {
    final String in = indent + "\t";
    // 1 - open tag
    sb_body.append(indent).append("<t2_layer oid=\"").append(id).append("\"\n").append(in).append(" thickness=\"").append(thickness).append("\"\n").append(in).append(" z=\"").append(z).append("\"\n");
    // TODO this search is linear!
    final LayerThing lt = project.findLayerThing(this);
    String title;
    if (null == lt)
        title = null;
    else
        title = lt.getTitle();
    if (null == title)
        title = "";
    // TODO 'title' should be a property of the Layer, not the LayerThing. Also, the LayerThing should not exist: LayerSet and Layer should be directly presentable in a tree. They are not Things as in "objects of the sample", but rather, structural necessities such as Patch.
    sb_body.append(in).append(" title=\"").append(title).append("\"\n");
    sb_body.append(indent).append(">\n");
    // 2 - export children
    if (null != al_displayables) {
        for (final Displayable d : al_displayables) {
            d.exportXML(sb_body, in, options);
        }
    }
    // 3 - close tag
    sb_body.append(indent).append("</t2_layer>\n");
}

Example 73 with Layer

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

the class Project method removeAll.

/**
 * Remove any set of Displayable objects from the Layer, LayerSet and Project Tree as necessary.
 *  ASSUMES there aren't any nested LayerSet objects in @param col.
 */
public final boolean removeAll(final Set<Displayable> col, final DefaultMutableTreeNode top_node) {
    // 0. Sort into Displayable and ZDisplayable
    final Set<ZDisplayable> zds = new HashSet<ZDisplayable>();
    final List<Displayable> ds = new ArrayList<Displayable>();
    for (final Displayable d : col) {
        if (d instanceof ZDisplayable) {
            zds.add((ZDisplayable) d);
        } else {
            ds.add(d);
        }
    }
    // Displayable:
    // 1. First the Profile from the Project Tree, one by one,
    // while creating a map of Layer vs Displayable list to remove in that layer:
    final HashMap<Layer, Set<Displayable>> ml = new HashMap<Layer, Set<Displayable>>();
    for (final Iterator<Displayable> it = ds.iterator(); it.hasNext(); ) {
        final Displayable d = it.next();
        if (d.getClass() == Profile.class) {
            if (!project_tree.remove(false, findProjectThing(d), null)) {
                // like Profile.remove2
                Utils.log("Could NOT delete " + d);
                continue;
            }
            // remove the Profile
            it.remove();
            continue;
        }
        // The map of Layer vs Displayable list
        Set<Displayable> l = ml.get(d.getLayer());
        if (null == l) {
            l = new HashSet<Displayable>();
            ml.put(d.getLayer(), l);
        }
        l.add(d);
    }
    // 2. Then the rest, in bulk:
    if (ml.size() > 0) {
        for (final Map.Entry<Layer, Set<Displayable>> e : ml.entrySet()) {
            e.getKey().removeAll(e.getValue());
        }
    }
    // 3. Stacks
    if (zds.size() > 0) {
        final Set<ZDisplayable> stacks = new HashSet<ZDisplayable>();
        for (final Iterator<ZDisplayable> it = zds.iterator(); it.hasNext(); ) {
            final ZDisplayable zd = it.next();
            if (zd.getClass() == Stack.class) {
                it.remove();
                stacks.add(zd);
            }
        }
        layer_set.removeAll(stacks);
    }
    // 4. ZDisplayable: bulk removal
    if (zds.size() > 0) {
        // 1. From the Project Tree:
        Set<Displayable> not_removed = project_tree.remove(zds, top_node);
        // 2. Then only those successfully removed, from the LayerSet:
        zds.removeAll(not_removed);
        layer_set.removeAll(zds);
    }
    // TODO
    return true;
}

Example 74 with Layer

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

the class Project method openDBProject.

/**
 * Open a TrakEM2 project from the database. Queries the database for existing projects and if more than one, asks which one to open.
 */
public static Project openDBProject() {
    if (Utils.wrongImageJVersion())
        return null;
    DBLoader loader = new DBLoader();
    if (!loader.isReady())
        return null;
    // check connection
    if (!loader.isConnected()) {
        Utils.showMessage("Can't talk to database.");
        loader.destroy();
        return null;
    }
    // query the database for existing projects
    Project[] projects = loader.getProjects();
    if (null == projects) {
        Utils.showMessage("Can't talk to database (null list of projects).");
        loader.destroy();
        return null;
    }
    Project project = null;
    if (0 == projects.length) {
        Utils.showMessage("No projects in this database.");
        loader.destroy();
        return null;
    } else if (1 == projects.length) {
        project = projects[0];
    } else {
        // ask to choose one
        String[] titles = new String[projects.length];
        for (int i = 0; i < projects.length; i++) {
            titles[i] = projects[i].title;
        }
        GenericDialog gd = new GenericDialog("Choose");
        gd.addMessage("Choose project to open:");
        gd.addChoice("project: ", titles, titles[titles.length - 1]);
        gd.showDialog();
        if (gd.wasCanceled()) {
            loader.destroy();
            return null;
        }
        project = projects[gd.getNextChoiceIndex()];
    }
    // check if the selected project is open already
    for (final Project p : al_open_projects) {
        if (loader.isIdenticalProjectSource(p.loader) && p.id == project.id && p.title.equals(project.title)) {
            Utils.showMessage("A project with title " + p.title + " and id " + p.id + " from the same database is already open.");
            loader.destroy();
            return null;
        }
    }
    // now, open the selected project
    // assign loader
    project.loader = loader;
    // grab the XML template
    TemplateThing template_root = loader.getTemplateRoot(project);
    if (null == template_root) {
        Utils.showMessage("Failed to retrieve the template tree.");
        project.destroy();
        return null;
    }
    project.template_tree = new TemplateTree(project, template_root);
    synchronized (project.ht_unique_tt) {
        project.ht_unique_tt.clear();
        project.ht_unique_tt.putAll(template_root.getUniqueTypes(new HashMap<String, TemplateThing>()));
    }
    // create the project Thing, to be root of the whole user Thing tree (and load all its objects)
    // to collect all created displayables, and  then reassign to the proper layers.
    HashMap<Long, Displayable> hs_d = new HashMap<Long, Displayable>();
    try {
        // create a template for the project Thing
        TemplateThing project_template = new TemplateThing("project");
        project.ht_unique_tt.put("project", project_template);
        project_template.addChild(template_root);
        project.root_pt = loader.getRootProjectThing(project, template_root, project_template, hs_d);
        // restore parent/child and attribute ownership and values (now that all Things exist)
        project.root_pt.setup();
    } catch (Exception e) {
        Utils.showMessage("Failed to retrieve the Thing tree for the project.");
        IJError.print(e);
        project.destroy();
        return null;
    }
    // create the user objects tree
    project.project_tree = new ProjectTree(project, project.root_pt);
    // restore the expanded state of each node
    loader.restoreNodesExpandedState(project);
    // create the layers templates
    project.createLayerTemplates();
    // fetch the root layer thing and the root layer set (will load all layers and layer sets, with minimal contents of patches; gets the basic objects -profile, pipe, etc.- from the project.root_pt). Will open all existing displays for each layer.
    LayerThing root_layer_thing = null;
    try {
        root_layer_thing = loader.getRootLayerThing(project, project.root_pt, Project.layer_set_template, Project.layer_template);
        if (null == root_layer_thing) {
            project.destroy();
            Utils.showMessage("Could not retrieve the root layer thing.");
            return null;
        }
        // set the child/parent relationships now that everything exists
        root_layer_thing.setup();
        project.layer_set = (LayerSet) root_layer_thing.getObject();
        if (null == project.layer_set) {
            project.destroy();
            Utils.showMessage("Could not retrieve the root layer set.");
            return null;
        }
        // set the active layer to each ZDisplayable
        project.layer_set.setup();
        // debug:
        // Utils.log2("$$$ root_lt: " + root_layer_thing + "   ob: " + root_layer_thing.getObject().getClass().getName() + "\n children: " + ((LayerSet)root_layer_thing.getObject()).getLayers().size());
        project.layer_tree = new LayerTree(project, root_layer_thing);
        project.root_lt = root_layer_thing;
    } catch (Exception e) {
        Utils.showMessage("Failed to retrieve the Layer tree for the project.");
        IJError.print(e);
        project.destroy();
        return null;
    }
    // if all when well, register as open:
    al_open_projects.add(project);
    // create the project control window, containing the trees in a double JSplitPane
    ControlWindow.add(project, project.template_tree, project.project_tree, project.layer_tree);
    // now open the displays that were stored for later, if any:
    Display.openLater();
    return project;
}

Example 75 with Layer

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

the class Project method createSubproject.

/**
 * Create a new subproject for the given layer range and ROI.
 *   Create a new Project using the given project as template. This means the DTD of the given project is copied, as well as the storage and mipmaps folders; everything else is empty in the new project.
 */
public Project createSubproject(final Rectangle roi, final Layer first, final Layer last, final boolean ignore_hidden_patches) {
    try {
        // The order matters.
        final Project pr = new Project(new FSLoader(this.getLoader().getStorageFolder()));
        pr.id = this.id;
        // copy properties
        pr.title = this.title;
        pr.ht_props.putAll(this.ht_props);
        // copy template
        pr.root_tt = this.root_tt.clone(pr, true);
        pr.template_tree = new TemplateTree(pr, pr.root_tt);
        synchronized (pr.ht_unique_tt) {
            pr.ht_unique_tt.clear();
            pr.ht_unique_tt.putAll(root_tt.getUniqueTypes(new HashMap<String, TemplateThing>()));
        }
        TemplateThing project_template = new TemplateThing("project");
        project_template.addChild(pr.root_tt);
        pr.ht_unique_tt.put("project", project_template);
        // create the layers templates
        pr.createLayerTemplates();
        // copy LayerSet and all involved Displayable objects
        // (A two-step process to provide the layer_set pointer and all Layer pointers to the ZDisplayable to copy and crop.)
        pr.layer_set = (LayerSet) this.layer_set.clone(pr, first, last, roi, false, true, ignore_hidden_patches);
        LayerSet.cloneInto(this.layer_set, first, last, pr, pr.layer_set, roi, true);
        // create layer tree
        pr.root_lt = new LayerThing(Project.layer_set_template, pr, pr.layer_set);
        pr.layer_tree = new LayerTree(pr, pr.root_lt);
        // add layer nodes to the layer tree (solving chicken-and-egg problem)
        pr.layer_set.updateLayerTree();
        // copy project tree
        pr.root_pt = this.root_pt.subclone(pr);
        pr.project_tree = new ProjectTree(pr, pr.root_pt);
        // not copying node expanded state.
        // register
        al_open_projects.add(pr);
        // add to gui:
        ControlWindow.add(pr, pr.template_tree, pr.project_tree, pr.layer_tree);
        // Above, the id of each object is preserved from this project into the subproject.
        // The abstract structure should be copied in full regardless, without the basic objects
        // included if they intersect the roi.
        // Regenerate mipmaps (blocks GUI from interaction other than navigation)
        pr.loader.regenerateMipMaps(pr.layer_set.getDisplayables(Patch.class));
        pr.restartAutosaving();
        return pr;
    } catch (Exception e) {
        e.printStackTrace();
    }
    return null;
}