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

Example 36 with Node

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

the class ProjectTree method remove.

/**
 * Remove the node, its Thing and the object hold by the thing from the database.
 */
public void remove(DefaultMutableTreeNode node, boolean check, boolean remove_empty_parents, int levels) {
    Object uob = node.getUserObject();
    if (!(uob instanceof ProjectThing))
        return;
    ProjectThing thing = (ProjectThing) uob;
    Display3D.remove(thing);
    ProjectThing parent = (ProjectThing) thing.getParent();
    if (!thing.remove(check))
        return;
    ((DefaultTreeModel) this.getModel()).removeNodeFromParent(node);
    if (remove_empty_parents)
        removeProjectThingLadder(parent, levels);
    this.updateUILater();
}

Example 37 with Node

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

the class ProjectTree method duplicateChild.

/**
 * Implements the "Duplicate, link and send to next/previous layer" functionality. The 'position' can be zero (before) or 1 (after). The profile has no layer assigned.
 */
public Profile duplicateChild(Profile original, int position, Layer layer) {
    Utils.log2("ProjectTree: Called duplicateChild " + System.currentTimeMillis() + " for original id = " + original.getId() + " at position " + position);
    // find the Thing that holds it
    Thing child = project.findProjectThing(original);
    if (null == child) {
        Utils.log("ProjectTree.duplicateChild: node not found for original " + original);
        return null;
    }
    Profile copy = (Profile) original.clone();
    // for the Z ordering
    copy.setLayer(layer);
    ProjectThing new_thing = null;
    try {
        new_thing = new ProjectThing(((ProjectThing) child.getParent()).getChildTemplate(child.getType()), original.getProject(), copy);
    } catch (Exception e) {
        IJError.print(e);
        return null;
    }
    DefaultMutableTreeNode child_node = (DefaultMutableTreeNode) findNode(child, this);
    DefaultMutableTreeNode parent_node = (DefaultMutableTreeNode) child_node.getParent();
    ProjectThing parent_thing = (ProjectThing) parent_node.getUserObject();
    // sanity check:
    if (position < 0)
        position = 0;
    else if (position > 1)
        position = 1;
    int index = parent_node.getIndex(child_node) + position;
    if (index < 0)
        index = 0;
    if (index > parent_node.getChildCount())
        index = parent_node.getChildCount() - 1;
    if (!parent_thing.addChild(new_thing, index))
        return null;
    DefaultMutableTreeNode new_node = new DefaultMutableTreeNode(new_thing);
    ((DefaultTreeModel) this.getModel()).insertNodeInto(new_node, parent_node, index);
    // relist properly the nodes
    updateList(parent_node);
    TreePath treePath = new TreePath(new_node.getPath());
    this.scrollPathToVisible(treePath);
    this.setSelectionPath(treePath);
    return copy;
}

Example 38 with Node

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

the class ProjectTree method sendToSiblingProject.

/**
 * When two or more people work on the same XML file, images may be the same but segmentations and the transformations of the images may diverge.
 *  This function provides the means to send VectorData instances, wrapped in tree nodes, from one project to another,
 *  transforming the VectorData as appropriate to fall onto the same locations on the images.
 *  The ids of the copied objects will be new and unique for the target project.
 *  A dialog opens asking for options.
 */
@SuppressWarnings("unchecked")
public boolean sendToSiblingProject(final DefaultMutableTreeNode node) {
    ArrayList<Project> ps = Project.getProjects();
    if (1 == ps.size()) {
        Utils.log("There aren't any other projects open!");
        return false;
    }
    final ProjectThing pt = (ProjectThing) node.getUserObject();
    if (pt.getTemplate().getType().equals("project")) {
        Utils.log("Cannot transfer the project node.");
        return false;
    }
    final ArrayList<Project> psother = new ArrayList<Project>(ps);
    psother.remove(this.project);
    ps = null;
    // Find all potential landing nodes for this node: those with a TemplateThing type like the parent of node:
    final String parent_type = ((ProjectThing) pt.getParent()).getTemplate().getType();
    final List<ProjectThing> landing_pt = new ArrayList<ProjectThing>(psother.get(0).getRootProjectThing().findChildrenOfTypeR(parent_type));
    final Comparator<ProjectThing> comparator = new Comparator<ProjectThing>() {

        public int compare(ProjectThing t1, ProjectThing t2) {
            return t1.toString().compareTo(t2.toString());
        }

        public boolean equals(Object o) {
            return this == o;
        }
    };
    Collections.sort(landing_pt, comparator);
    String[] landing = new String[landing_pt.size()];
    int next = 0;
    if (landing_pt.isEmpty()) {
        landing = new String[] { "-- NONE --" };
    } else
        for (ProjectThing t : landing_pt) landing[next++] = t.toString();
    // Suggest the first potential landing node that has the same title
    String parentTitle = pt.getParent().toString();
    int k = 0;
    boolean matched = false;
    // First search for exact match
    for (final String candidate : landing) {
        if (candidate.equals(parentTitle)) {
            matched = true;
            break;
        }
        k += 1;
    }
    // If not matched, find one that contains the string
    if (!matched) {
        k = 0;
        for (final String candidate : landing) {
            if (-1 != candidate.indexOf(parentTitle)) {
                matched = true;
                break;
            }
            k += 1;
        }
    }
    if (!matched) {
        k = 0;
    }
    // Ask:
    GenericDialog gd = new GenericDialog("Send to sibling project");
    gd.addMessage("Transfering node: " + pt);
    final String[] trmode = new String[] { "As is", "Transformed as the images" };
    gd.addChoice("Transfer:", trmode, trmode[0]);
    String[] ptitles = new String[psother.size()];
    for (int i = 0; i < ptitles.length; i++) ptitles[i] = psother.get(i).toString();
    gd.addChoice("Target project:", ptitles, ptitles[0]);
    gd.addChoice("Landing node:", landing, landing[k]);
    final Vector<Choice> vc = (Vector<Choice>) gd.getChoices();
    final Choice choice_project = vc.get(vc.size() - 2);
    final Choice choice_landing = vc.get(vc.size() - 1);
    choice_project.addItemListener(new ItemListener() {

        public void itemStateChanged(ItemEvent ie) {
            landing_pt.clear();
            landing_pt.addAll(psother.get(choice_project.getSelectedIndex()).getRootProjectThing().findChildrenOfTypeR(parent_type));
            Collections.sort(landing_pt, comparator);
            choice_landing.removeAll();
            if (landing_pt.isEmpty()) {
                choice_landing.add("-- NONE --");
            } else
                for (ProjectThing t : landing_pt) choice_landing.add(t.toString());
        }
    });
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    if (choice_landing.getSelectedItem().equals("-- NONE --")) {
        Utils.log("No valid landing nodes!");
        return false;
    }
    final int transfer_mode = gd.getNextChoiceIndex();
    final Project target_project = psother.get(gd.getNextChoiceIndex());
    final ProjectThing landing_parent = landing_pt.get(gd.getNextChoiceIndex());
    return rawSendToSiblingProject(pt, transfer_mode, target_project, landing_parent);
}

Example 39 with Node

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

the class ProjectTree method rawSendToSiblingProject.

/**
 * Assumes that both projects have the same TemplateThing structure,
 * and assumes that the parent of the ({@code source_pt} and the {@code landing_parent}
 * instances are of the same type.
 *
 * @param source_pt The {@link ProjectThing} to be cloned.
 * @param transfer_mode Either 0 ("As is") or 1 ("Transformed with the images").
 * @param target_project The sibling project into which insert a clone of the {@code source_pt}.
 * @param landing_parent The ProjectThing in the sibling project that receives the cloned {@code source_pt}.
 */
public boolean rawSendToSiblingProject(// the source ProjectThing to copy to the target project
final ProjectThing source_pt, final int transfer_mode, final Project target_project, final ProjectThing landing_parent) {
    try {
        // Check that all the Layers used by the objects to transfer also exist in the target project!
        // 1 - Cheap way: check if all layers in the target project exist in the source project, by id
        HashSet<Long> lids = new HashSet<Long>();
        for (final Layer layer : this.project.getRootLayerSet().getLayers()) {
            lids.add(layer.getId());
        }
        HashSet<Long> tgt_lids = new HashSet<Long>(lids);
        for (final Layer layer : target_project.getRootLayerSet().getLayers()) {
            lids.remove(layer.getId());
            tgt_lids.add(layer.getId());
        }
        List<Displayable> original_vdata = null;
        final Set<Long> lids_to_operate = new HashSet<Long>();
        if (0 != lids.size()) {
            original_vdata = new ArrayList<Displayable>();
            // All their layers MUST be in the target project.
            for (final ProjectThing child : source_pt.findChildrenOfTypeR(Displayable.class)) {
                final Displayable d = (Displayable) child.getObject();
                if (!tgt_lids.containsAll(d.getLayerIds())) {
                    Utils.log("CANNOT transfer: not all required layers are present in the target project!\n  First object that couldn't be transfered: \n    " + d);
                    return false;
                }
                if (d instanceof VectorData) {
                    original_vdata.add(d);
                    lids_to_operate.addAll(d.getLayerIds());
                }
            }
        }
        // Deep cloning of the ProjectThing to transfer, then added to the landing_parent in the other tree.
        ProjectThing copy;
        try {
            // new ids, taken from target_project
            copy = source_pt.deepClone(target_project, false);
        } catch (Exception ee) {
            Utils.logAll("Can't send: " + ee.getMessage());
            IJError.print(ee);
            return false;
        }
        if (null == landing_parent.getChildTemplate(copy.getTemplate().getType())) {
            // ensure a copy is there
            landing_parent.getTemplate().addChild(copy.getTemplate().shallowCopy());
        }
        if (!landing_parent.addChild(copy)) {
            Utils.log("Could NOT transfer the node!");
            return false;
        }
        // Get the list of Profile instances in the source Project, in the same order
        // that they will be in the target project:
        final List<Profile> srcProfiles = new ArrayList<Profile>();
        for (final ProjectThing profile_pt : source_pt.findChildrenOfTypeR(Profile.class)) {
            srcProfiles.add((Profile) profile_pt.getObject());
        }
        final List<ProjectThing> copies = copy.findChildrenOfTypeR(Displayable.class);
        final List<Profile> newProfiles = new ArrayList<Profile>();
        // Utils.log2("copies size: " + copies.size());
        final List<Displayable> vdata = new ArrayList<Displayable>();
        final List<ZDisplayable> zd = new ArrayList<ZDisplayable>();
        for (final ProjectThing t : copies) {
            final Displayable d = (Displayable) t.getObject();
            // all should be, this is just future-proof code.
            if (d instanceof VectorData)
                vdata.add(d);
            if (d instanceof ZDisplayable) {
                zd.add((ZDisplayable) d);
            } else {
                // profile: always special
                newProfiles.add((Profile) d);
            }
        }
        // Fix Profile instances: exploit that the order as been conserved when copying.
        int profileIndex = 0;
        for (final Profile newProfile : newProfiles) {
            // Corresponding Profile:
            final Profile srcProfile = srcProfiles.get(profileIndex++);
            // Corresponding layer: layers have the same IDs by definition of what a sibling Project is.
            final Layer newLayer = target_project.getRootLayerSet().getLayer(srcProfile.getLayer().getId());
            newLayer.add(newProfile);
            // Corresponding links
            for (final Displayable srcLinkedProfile : srcProfile.getLinked(Profile.class)) {
                newProfile.link(newProfiles.get(srcProfiles.indexOf(srcLinkedProfile)));
            }
        }
        // add them all in one shot
        target_project.getRootLayerSet().addAll(zd);
        // could have changed
        target_project.getTemplateTree().rebuild();
        // When trying to rebuild just the landing_parent, it doesn't always work. Needs checking TODO
        target_project.getProjectTree().rebuild();
        // Open up the path to the landing parent node
        final TreePath tp = new TreePath(DNDTree.findNode(landing_parent, target_project.getProjectTree()).getPath());
        Utils.invokeLater(new Runnable() {

            public void run() {
                target_project.getProjectTree().scrollPathToVisible(tp);
                target_project.getProjectTree().setSelectionPath(tp);
            }
        });
        if (1 == transfer_mode) {
            // Collect original vdata
            if (null == original_vdata) {
                original_vdata = new ArrayList<Displayable>();
                for (final ProjectThing child : source_pt.findChildrenOfTypeR(Displayable.class)) {
                    final Displayable d = (Displayable) child.getObject();
                    if (d instanceof VectorData) {
                        original_vdata.add(d);
                        lids_to_operate.addAll(d.getLayerIds());
                    }
                }
            }
            // Utils.log2("original vdata:", original_vdata);
            // Utils.log2("vdata:", vdata);
            // Transform with images
            AlignTask.transformVectorData(AlignTask.createTransformPropertiesTable(original_vdata, vdata, lids_to_operate), vdata, target_project.getRootLayerSet());
        }
        return true;
    } catch (Exception e) {
        IJError.print(e);
    }
    return false;
}

Example 40 with Node

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

the class Search method executeSearch.

private void executeSearch() {
    final Project project = Project.getProjects().get(projects.getSelectedIndex());
    if (null == project) {
        // Should not happen
        return;
    }
    Bureaucrat.createAndStart(new Worker.Task("Searching") {

        public void exec() {
            String pattern = search_field.getText();
            if (null == pattern || 0 == pattern.length()) {
                return;
            }
            // fix pattern
            final String typed_pattern = pattern;
            // I hate java
            final StringBuilder sb = new StringBuilder();
            if (!pattern.startsWith("^"))
                sb.append("^.*");
            for (int i = 0; i < pattern.length(); i++) {
                sb.append(pattern.charAt(i));
            }
            if (!pattern.endsWith("$"))
                sb.append(".*$");
            pattern = sb.toString();
            final Pattern pat = Pattern.compile(pattern, Pattern.CASE_INSENSITIVE | Pattern.MULTILINE | Pattern.DOTALL);
            // Utils.log2("pattern after: " + pattern);
            final ArrayList<DBObject> al = new ArrayList<DBObject>();
            // Utils.log("types[pulldown] = " +
            // types[pulldown.getSelectedIndex()]);
            find(project.getRootLayerSet(), al, types[pulldown.getSelectedIndex()]);
            // Utils.log2("found labels: " + al.size());
            if (0 == al.size())
                return;
            final Vector<DBObject> v_obs = new Vector<DBObject>();
            final Vector<String> v_txt = new Vector<String>();
            final Vector<Coordinate<?>> v_co = new Vector<Coordinate<?>>();
            Coordinate<?> co = null;
            for (final DBObject dbo : al) {
                if (Thread.currentThread().isInterrupted()) {
                    return;
                }
                boolean matched = false;
                // Search in its title
                Displayable d = null;
                if (dbo instanceof Displayable) {
                    d = (Displayable) dbo;
                }
                String txt;
                String meaningful_title = null;
                if (null == d || Patch.class == d.getClass())
                    txt = dbo.getTitle();
                else {
                    txt = meaningful_title = dbo.getProject().getMeaningfulTitle(d);
                }
                if (null == txt || 0 == txt.trim().length())
                    continue;
                matched = pat.matcher(txt).matches();
                if (!matched && null != d) {
                    // Search also in its annotation
                    txt = d.getAnnotation();
                    if (null != txt)
                        matched = pat.matcher(txt).matches();
                }
                if (!matched) {
                    // Search also in its toString()
                    txt = dbo.toString();
                    matched = pat.matcher(txt).matches();
                }
                if (!matched) {
                    // Search also in its id
                    txt = Long.toString(dbo.getId());
                    matched = pat.matcher(txt).matches();
                    if (matched)
                        txt = "id: #" + txt;
                }
                if (!matched && null != d) {
                    // Search also in its properties
                    Map<String, String> props = d.getProperties();
                    if (null != props) {
                        for (final Map.Entry<String, String> e : props.entrySet()) {
                            if (pat.matcher(e.getKey()).matches() || pat.matcher(e.getValue()).matches()) {
                                matched = true;
                                txt = e.getKey() + " => " + e.getValue() + " [property]";
                                break;
                            }
                        }
                    }
                    if (!matched) {
                        Map<Displayable, Map<String, String>> linked_props = ((Displayable) dbo).getLinkedProperties();
                        if (null != linked_props) {
                            for (final Map.Entry<Displayable, Map<String, String>> e : linked_props.entrySet()) {
                                for (final Map.Entry<String, String> ee : e.getValue().entrySet()) {
                                    if (pat.matcher(ee.getKey()).matches() || pat.matcher(ee.getValue()).matches()) {
                                        matched = true;
                                        txt = ee.getKey() + " => " + e.getValue() + " [linked property]";
                                        break;
                                    }
                                }
                            }
                        }
                    }
                }
                if (!matched && dbo instanceof Tree<?>) {
                    // search Node tags
                    Node<?> root = ((Tree<?>) dbo).getRoot();
                    if (null == root)
                        continue;
                    for (final Node<?> nd : root.getSubtreeNodes()) {
                        Set<Tag> tags = nd.getTags();
                        if (null == tags)
                            continue;
                        for (final Tag tag : tags) {
                            if (pat.matcher(tag.toString()).matches()) {
                                v_obs.add(dbo);
                                v_txt.add(new StringBuilder(tag.toString()).append(" (").append(null == meaningful_title ? dbo.toString() : meaningful_title).append(')').toString());
                                v_co.add(createCoordinate((Tree<?>) dbo, nd));
                            }
                        }
                    }
                    // all added if any
                    continue;
                }
                if (!matched)
                    continue;
                // txt = txt.length() > 30 ? txt.substring(0, 27) + "..." :
                // txt;
                v_obs.add(dbo);
                v_txt.add(txt);
                v_co.add(co);
            }
            if (0 == v_obs.size()) {
                Utils.showMessage("Nothing found.");
                return;
            }
            final JPanel result = new JPanel();
            GridBagLayout gb = new GridBagLayout();
            result.setLayout(gb);
            GridBagConstraints c = new GridBagConstraints();
            c.anchor = GridBagConstraints.NORTHWEST;
            c.fill = GridBagConstraints.HORIZONTAL;
            c.insets = new Insets(5, 10, 5, 10);
            String xml = "";
            if (project.getLoader() instanceof FSLoader) {
                String path = ((FSLoader) project.getLoader()).getProjectXMLPath();
                if (null != path) {
                    xml = " [" + new File(path).getName() + "]";
                }
            }
            JLabel projectTitle = new JLabel(project.getTitle() + xml);
            gb.setConstraints(projectTitle, c);
            result.add(projectTitle);
            c.insets = new Insets(0, 0, 0, 0);
            JPanel padding = new JPanel();
            c.weightx = 1;
            gb.setConstraints(padding, c);
            result.add(padding);
            c.gridy = 1;
            c.gridwidth = 2;
            c.fill = GridBagConstraints.BOTH;
            c.weighty = 1;
            JScrollPane jsp = makeTable(new DisplayableTableModel(v_obs, v_txt, v_co), project);
            gb.setConstraints(jsp, c);
            result.add(jsp);
            search_tabs.addTab(typed_pattern, result);
            search_tabs.setSelectedComponent(result);
            synchronized (tabMap) {
                List<JPanel> cs = tabMap.get(project);
                if (null == cs) {
                    cs = new ArrayList<JPanel>();
                    tabMap.put(project, cs);
                }
                cs.add(result);
            }
        }
    }, project);
}