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

Example 31 with LayerSet

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

the class Graph method extractAndShowGraph.

/**
 * Shows a dialog to pick which classes is one interested in.
 */
public static final void extractAndShowGraph(final LayerSet ls) {
    GenericDialog gd = new GenericDialog("Graph elements");
    Class<Displayable>[] c = new Class[] { AreaList.class, AreaTree.class, Ball.class, Connector.class, Patch.class, Pipe.class, Polyline.class, Profile.class, DLabel.class, Treeline.class };
    String[] types = new String[] { "AreaList", "AreaTree", "Ball", "Connector", "Image", "Pipe", "Polyline", "Profile", "Text", "Treeline" };
    boolean[] states = new boolean[] { true, true, false, false, false, false, true, true, false, true };
    assert (c.length == types.length && types.length == states.length);
    for (int i = 0; i < c.length; i++) {
        if (ZDisplayable.class.isAssignableFrom(c[i])) {
            if (!ls.contains(c[i]))
                states[i] = false;
        } else if (!ls.containsDisplayable(c[i]))
            states[i] = false;
    }
    gd.addCheckboxGroup(types.length, 1, types, states, new String[] { "Include only:" });
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    HashSet<Class<Displayable>> only = new HashSet<Class<Displayable>>();
    for (int i = 0; i < types.length; i++) {
        if (gd.getNextBoolean())
            only.add(c[i]);
    }
    Graph.extractAndShowGraph(ls, only);
}

Example 32 with LayerSet

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

the class Graph method extractGraph.

public static final <T extends Displayable> Map<String, StringBuilder> extractGraph(final LayerSet ls, final Set<Class<T>> only) {
    final StringBuilder sif = new StringBuilder(4096), xml = new StringBuilder(4096).append("<graph>\n"), names = new StringBuilder(4096);
    final Set<Displayable> seen = new HashSet<Displayable>();
    for (final Connector con : ls.getAll(Connector.class)) {
        Set<Displayable> origins = con.getOrigins();
        if (origins.isEmpty()) {
            Utils.log("Graph: ignoring connector without origins: #" + con.getId());
            continue;
        }
        List<Set<Displayable>> target_lists = con.getTargets();
        if (target_lists.isEmpty()) {
            Utils.log("Graph: ignoring connector without targets: #" + con.getId());
            continue;
        }
        for (final Displayable origin : origins) {
            if (Thread.currentThread().isInterrupted())
                return null;
            if (null != only && !only.contains(origin.getClass()))
                continue;
            seen.add(origin);
            for (final Set<Displayable> targets : target_lists) {
                for (final Displayable target : targets) {
                    if (null != only && !only.contains(target.getClass()))
                        continue;
                    sif.append(origin.getId()).append(" pd ").append(target.getId()).append('\n');
                    xml.append('\t').append("<edge cid=\"").append(con.getId()).append("\" origin=\"").append(origin.getId()).append("\" target=\"").append(target.getId()).append("\" />\n");
                    seen.add(target);
                }
            }
        }
    }
    xml.append("</graph>\n");
    for (final Displayable d : seen) {
        names.append(d.getId()).append('\t').append(d.getProject().getMeaningfulTitle(d)).append('\n');
    }
    final Map<String, StringBuilder> m = new HashMap<String, StringBuilder>();
    m.put("sif", sif);
    m.put("xml", xml);
    m.put("names", names);
    return m;
}

Example 33 with LayerSet

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

the class Display3D method getProfileContent.

/**
 * Checks if the given Displayable is a Profile, and tries to find a possible Content object in the Image3DUniverse of its LayerSet according to the title as created from its profile_list ProjectThing.
 */
public static Content getProfileContent(final Displayable d) {
    if (null == d)
        return null;
    if (d.getClass() != Profile.class)
        return null;
    final Display3D d3d = get(d.getLayer().getParent());
    if (null == d3d)
        return null;
    ProjectThing pt = d.getProject().findProjectThing(d);
    if (null == pt)
        return null;
    pt = (ProjectThing) pt.getParent();
    return d3d.universe.getContent(new StringBuilder(pt.toString()).append(" #").append(pt.getId()).toString());
}

Example 34 with LayerSet

use of ini.trakem2.display.LayerSet 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 35 with LayerSet

use of ini.trakem2.display.LayerSet 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;
}