Examples with Project ini.trakem2.Project used on opensource projects

Example 91 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class ProjectTree method actionPerformed.

public void actionPerformed(final ActionEvent ae) {
    if (!project.isInputEnabled())
        return;
    super.dispatcher.exec(new Runnable() {

        public void run() {
            try {
                if (null == selected_node)
                    return;
                final Object ob = selected_node.getUserObject();
                if (!(ob instanceof ProjectThing))
                    return;
                final ProjectThing thing = (ProjectThing) ob;
                int i_position = 0;
                String command = ae.getActionCommand();
                final Object obd = thing.getObject();
                if (command.startsWith("new ") || command.equals("Duplicate")) {
                    ProjectThing new_thing = null;
                    if (command.startsWith("new ")) {
                        // if it's a Displayable, it will be added to whatever layer is in the front Display
                        new_thing = thing.createChild(command.substring(4));
                    } else if (command.equals("Duplicate")) {
                        // just to keep myself from screwing in the future
                        if (Project.isBasicType(thing.getType()) && null != thing.getParent()) {
                            new_thing = ((ProjectThing) thing.getParent()).createClonedChild(thing);
                        }
                        // adjust parent
                        selected_node = (DefaultMutableTreeNode) selected_node.getParent();
                    }
                    // add it to the tree
                    if (null != new_thing) {
                        DefaultMutableTreeNode new_node = new DefaultMutableTreeNode(new_thing);
                        ((DefaultTreeModel) ProjectTree.this.getModel()).insertNodeInto(new_node, selected_node, i_position);
                        TreePath treePath = new TreePath(new_node.getPath());
                        ProjectTree.this.scrollPathToVisible(treePath);
                        ProjectTree.this.setSelectionPath(treePath);
                    }
                    // bring the display to front
                    if (new_thing.getObject() instanceof Displayable) {
                        Display.getFront().getFrame().toFront();
                    }
                } else if (command.equals("many...")) {
                    ArrayList<TemplateThing> children = thing.getTemplate().getChildren();
                    if (null == children || 0 == children.size())
                        return;
                    String[] cn = new String[children.size()];
                    int i = 0;
                    for (final TemplateThing child : children) {
                        cn[i] = child.getType();
                        i++;
                    }
                    GenericDialog gd = new GenericDialog("Add many children");
                    gd.addNumericField("Amount: ", 1, 0);
                    gd.addChoice("New child: ", cn, cn[0]);
                    gd.addCheckbox("Recursive", true);
                    gd.showDialog();
                    if (gd.wasCanceled())
                        return;
                    int amount = (int) gd.getNextNumber();
                    if (amount < 1) {
                        Utils.showMessage("Makes no sense to create less than 1 child!");
                        return;
                    }
                    project.getRootLayerSet().addChangeTreesStep();
                    final ArrayList<ProjectThing> nc = thing.createChildren(cn[gd.getNextChoiceIndex()], amount, gd.getNextBoolean());
                    addLeafs(nc, new Runnable() {

                        public void run() {
                            project.getRootLayerSet().addChangeTreesStep();
                        }
                    });
                } else if (command.equals("Unhide")) {
                    thing.setVisible(true);
                } else if (command.equals("Select in display")) {
                    boolean shift_down = 0 != (ae.getModifiers() & ActionEvent.SHIFT_MASK);
                    selectInDisplay(thing, shift_down);
                } else if (command.equals("Show centered in Display")) {
                    if (obd instanceof Displayable) {
                        Displayable displ = (Displayable) obd;
                        Display.showCentered(displ.getLayer(), displ, true, 0 != (ae.getModifiers() & ActionEvent.SHIFT_MASK));
                    }
                } else if (command.equals("Show tabular view")) {
                    ((Tree<?>) obd).createMultiTableView();
                } else if (command.equals("Show in 3D")) {
                    Display3D.showAndResetView(thing);
                } else if (command.equals("Remove from 3D view")) {
                    Display3D.removeFrom3D(thing);
                } else if (command.equals("Hide")) {
                    // find all Thing objects in this subtree starting at Thing and hide their Displayable objects.
                    thing.setVisible(false);
                } else if (command.equals("Delete...")) {
                    // store old state
                    project.getRootLayerSet().addChangeTreesStep();
                    remove(true, thing, selected_node);
                    // store new state
                    project.getRootLayerSet().addChangeTreesStep();
                    return;
                } else if (command.equals("Rename...")) {
                    // if (!Project.isBasicType(thing.getType())) {
                    rename(thing);
                // }
                } else if (command.equals("Measure")) {
                    // block displays while measuring
                    Bureaucrat.createAndStart(new Worker("Measuring") {

                        public void run() {
                            startedWorking();
                            try {
                                thing.measure();
                            } catch (Throwable e) {
                                IJError.print(e);
                            } finally {
                                finishedWorking();
                            }
                        }
                    }, thing.getProject());
                } else /* else if (command.equals("Export 3D...")) {
				GenericDialog gd = ControlWindow.makeGenericDialog("Export 3D");
				String[] choice = new String[]{".svg [preserves links and hierarchical grouping]", ".shapes [limited to one profile per layer per profile_list]"};
				gd.addChoice("Export to: ", choice, choice[0]);
				gd.addNumericField("Z scaling: ", 1, 2);
				gd.showDialog();
				if (gd.wasCanceled()) return;
				double z_scale = gd.getNextNumber();
				switch (gd.getNextChoiceIndex()) {
					case 0:
						Render.exportSVG(thing, z_scale);
						break;
					case 1:
						new Render(thing).save(z_scale);
						break;
				}
			}*/
                if (command.equals("Export project...") || command.equals("Save as...")) {
                    // "Save as..." is for a FS project
                    Utils.log2("Calling export project at " + System.currentTimeMillis());
                    thing.getProject().getLoader().saveTask(thing.getProject(), "Save as...");
                } else if (command.equals("Save")) {
                    // overwrite the xml file of a FSProject
                    // Just do the same as in "Save as..." but without saving the images and overwritting the XML file without asking.
                    thing.getProject().getLoader().saveTask(thing.getProject(), "Save");
                } else if (command.equals("Info")) {
                    showInfo(thing);
                    return;
                } else if (command.equals("Move up")) {
                    move(selected_node, -1);
                } else if (command.equals("Move down")) {
                    move(selected_node, 1);
                } else if (command.equals("Collapse nodes of children nodes")) {
                    if (null == selected_node)
                        return;
                    Enumeration<?> c = selected_node.children();
                    while (c.hasMoreElements()) {
                        DefaultMutableTreeNode child = (DefaultMutableTreeNode) c.nextElement();
                        if (child.isLeaf())
                            continue;
                        collapsePath(new TreePath(child.getPath()));
                    }
                } else if (command.equals("Sibling project")) {
                    sendToSiblingProjectTask(selected_node);
                } else {
                    Utils.log("ProjectTree.actionPerformed: don't know what to do with the command: " + command);
                    return;
                }
            } catch (Exception e) {
                IJError.print(e);
            }
        }
    });
}

Example 92 with Project

use of ini.trakem2.Project 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 93 with Project

use of ini.trakem2.Project 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 94 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class DBLoader method getChildrenProjectThings.

private ArrayList<ProjectThing> getChildrenProjectThings(Project project, long parent_id, String parent_type, HashMap<String, TemplateThing> hs_tt, HashMap<Long, Displayable> hs_d) throws Exception {
    final ArrayList<ProjectThing> al_children = new ArrayList<ProjectThing>();
    ResultSet r = null;
    if (-1 == parent_id)
        Utils.log("parent_id = -1 for parent_type=" + parent_type);
    if (parent_type.equals("profile_list")) {
        // the project_id field is redundant
        r = connection.prepareStatement("SELECT ab_things.* FROM ab_things,ab_displayables,ab_layers WHERE ab_things.parent_id=" + parent_id + " AND ab_things.object_id=ab_displayables.id AND ab_displayables.layer_id=ab_layers.id ORDER BY ab_layers.z,ab_things.id ASC").executeQuery();
    } else {
        r = connection.prepareStatement("SELECT * FROM ab_things WHERE parent_id=" + parent_id + " ORDER BY id").executeQuery();
    }
    while (r.next()) {
        ProjectThing thing = getProjectThing(r, project, hs_tt, hs_d);
        if (null != thing)
            al_children.add(thing);
    }
    r.close();
    return al_children;
}

Example 95 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class DBLoader method fetchBall.

private Ball fetchBall(Project project, long id) throws Exception {
    // strange query, but can't distinguish between pipes and balls otherwise
    ResultSet r = connection.prepareStatement("SELECT ab_displayables.id, title, ab_displayables.width, height, alpha, visible, color_red, color_green, color_blue, ab_zdisplayables.id, ab_ball_points.ball_id, ab_displayables.locked, m00, m10, m01, m11, m02, m12 FROM ab_zdisplayables, ab_displayables, ab_ball_points WHERE ab_zdisplayables.id=ab_displayables.id AND ab_zdisplayables.id=ab_ball_points.ball_id AND ab_zdisplayables.id=" + id).executeQuery();
    Ball b = null;
    if (r.next()) {
        b = new Ball(project, id, r.getString("title"), (float) r.getDouble("width"), (float) r.getDouble("height"), r.getFloat("alpha"), r.getBoolean("visible"), new Color(r.getInt("color_red"), r.getInt("color_green"), r.getInt("color_blue")), r.getBoolean("locked"), new AffineTransform(r.getDouble("m00"), r.getDouble("m10"), r.getDouble("m01"), r.getDouble("m11"), r.getDouble("m02"), r.getDouble("m12")));
    }
    r.close();
    return b;
}