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

Example 21 with Node

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

the class Compare method appendAndFork.

/**
 * Recursive.
 */
private static void appendAndFork(final ProjectThing parent, Chain chain, HashSet<ProjectThing> hs_c_done, final ArrayList<Chain> chains, final LayerSet ls, final Pattern exclude) throws Exception {
    if (null != exclude && exclude.matcher(parent.getTitle()).matches()) {
        Utils.logAll("Excluding node " + parent + " with title " + parent.getTitle() + ", and all its children nodes.");
        return;
    }
    final ArrayList<ProjectThing> children = parent.getChildren();
    if (null == children)
        return;
    if (null == hs_c_done)
        hs_c_done = new HashSet<ProjectThing>();
    for (final ProjectThing child : children) {
        if (hs_c_done.contains(child))
            continue;
        if (null != exclude && exclude.matcher(child.getTitle()).matches()) {
            Utils.log2("Excluding child " + child + " with title " + child.getTitle());
            continue;
        }
        hs_c_done.add(child);
        if (child.getObject() instanceof Line3D) {
            final Line3D pipe = (Line3D) child.getObject();
            // not from the same LayerSet, maybe from a nested one.
            if (!pipe.getLayerSet().equals(ls) || pipe.length() < 2)
                continue;
            if (null == chain) {
                chain = new Chain(pipe);
                chains.add(chain);
            } else {
                chain.append(pipe);
            }
            // find other children in the parent who contain children with child pipes
            boolean first = true;
            final Chain base = chain.duplicate();
            for (final ProjectThing c : children) {
                // already visited
                if (hs_c_done.contains(c))
                    continue;
                // c is at the same tree level as child (which contains a pipe directly)
                final ArrayList<Line3D> child_pipes = c.findChildrenOfType(Line3D.class);
                if (child_pipes.size() > 0) {
                    Chain ca;
                    if (first) {
                        // just append
                        ca = chain;
                        first = false;
                    } else {
                        // otherwise make a copy to branch out
                        // can't duplicate from chain itself, because it would have the previous child added to it.
                        ca = base.duplicate();
                        chains.add(ca);
                    }
                    appendAndFork(c, ca, hs_c_done, chains, ls, exclude);
                }
            }
            // pipe wrapping ProjectThing objects cannot have any children
            continue;
        }
        // if it does not have direct pipe children, cut chain - but keep inspecting
        if (0 == child.findChildrenOfType(Line3D.class).size()) {
            chain = null;
        }
        // inspect others down the unvisited tree nodes
        appendAndFork(child, chain, hs_c_done, chains, ls, exclude);
    }
}

Example 22 with Node

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

the class Project method getParentTitle.

/**
 * Returns the title of the enclosing abstract node in the ProjectTree.
 */
public String getParentTitle(final Displayable d) {
    try {
        ProjectThing thing = findProjectThing(d);
        ProjectThing parent = (ProjectThing) thing.getParent();
        if (d instanceof Profile) {
            // skip the profile_list
            parent = (ProjectThing) parent.getParent();
        }
        if (null == parent)
            Utils.log2("null parent for " + d);
        if (null != parent && null == parent.getObject()) {
            Utils.log2("null ob for parent " + parent + " of " + d);
        }
        // the abstract thing should be enclosing a String object
        return parent.getObject().toString();
    } catch (Exception e) {
        IJError.print(e);
        return null;
    }
}

Example 23 with Node

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

the class Project method getMeaningfulTitle2.

public String getMeaningfulTitle2(final Displayable d) {
    final ProjectThing thing = findProjectThing(d);
    // happens if there is no associated node
    if (null == thing)
        return d.getTitle();
    if (!thing.getType().equals(d.getTitle())) {
        return new StringBuilder(!thing.getType().equals(d.getTitle()) ? d.getTitle() + " [" : "[").append(thing.getType()).append(']').toString();
    }
    // Else, search upstream for a ProjectThing whose name differs from its type
    Thing parent = (ProjectThing) thing.getParent();
    while (null != parent) {
        String type = parent.getType();
        Object ob = parent.getObject();
        if (ob.getClass() == Project.class)
            break;
        if (!ob.equals(type)) {
            return ob.toString() + " [" + thing.getType() + "]";
        }
        parent = parent.getParent();
    }
    if (d.getTitle().equals(thing.getType()))
        return "[" + thing.getType() + "]";
    return d.getTitle() + " [" + thing.getType() + "]";
}

Example 24 with Node

use of ini.trakem2.display.Node 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 25 with Node

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

the class Project method select.

private final void select(final Object ob, final DNDTree tree) {
    // Find the Thing that contains the object
    final Thing root_thing = (Thing) ((DefaultMutableTreeNode) tree.getModel().getRoot()).getUserObject();
    final Thing child_thing = root_thing.findChild(ob);
    // find the node that contains the Thing, and select it
    DNDTree.selectNode(child_thing, tree);
}