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Example 6 with LayerThing

use of ini.trakem2.tree.LayerThing in project TrakEM2 by trakem2.

the class Project method createNewProject.

private static Project createNewProject(Loader loader, boolean ask_for_template, TemplateThing template_root, boolean clone_ids) {
    Project project = new Project(loader);
    // Utils.log2("ask_for_template: " + ask_for_template);
    if (ask_for_template)
        template_root = project.loader.askForXMLTemplate(project);
    if (null == template_root) {
        template_root = new TemplateThing("anything");
    } else if (clone_ids) {
        // the given template_root belongs to another project from which we are cloning
        template_root = template_root.clone(project, true);
    }
    // else, use the given template_root as is.
    // create tree
    project.template_tree = new TemplateTree(project, template_root);
    project.root_tt = template_root;
    // collect unique TemplateThing instances
    synchronized (project.ht_unique_tt) {
        project.ht_unique_tt.clear();
        project.ht_unique_tt.putAll(template_root.getUniqueTypes(new HashMap<String, TemplateThing>()));
    }
    // add all TemplateThing objects to the database, recursively
    if (!clone_ids)
        template_root.addToDatabase(project);
    // else already done when cloning the root_tt
    // create a non-database bound template for the project Thing
    TemplateThing project_template = new TemplateThing("project");
    project.ht_unique_tt.put("project", project_template);
    project_template.addChild(template_root);
    // create the project Thing, to be root of the whole project thing tree
    try {
        project.root_pt = new ProjectThing(project_template, project, project);
    } catch (Exception e) {
        IJError.print(e);
    }
    // create the user objects tree
    project.project_tree = new ProjectTree(project, project.root_pt);
    // create the layer's tree
    project.createLayerTemplates();
    // initialized with default values, and null parent to signal 'root'
    project.layer_set = new LayerSet(project, "Top Level", 0, 0, null, 2048, 2048);
    try {
        project.root_lt = new LayerThing(Project.layer_set_template, project, project.layer_set);
        project.layer_tree = new LayerTree(project, project.root_lt);
    } catch (Exception e) {
        project.remove();
        IJError.print(e);
    }
    // create the project control window, containing the trees in a double JSplitPane
    // beware that this call is asynchronous, dispatched by the SwingUtilities.invokeLater to avoid havok with Swing components.
    ControlWindow.add(project, project.template_tree, project.project_tree, project.layer_tree);
    // register
    al_open_projects.add(project);
    return project;
}
Also used : ProjectTree(ini.trakem2.tree.ProjectTree) LayerTree(ini.trakem2.tree.LayerTree) HashMap(java.util.HashMap) LayerSet(ini.trakem2.display.LayerSet) LayerThing(ini.trakem2.tree.LayerThing) TemplateThing(ini.trakem2.tree.TemplateThing) TemplateTree(ini.trakem2.tree.TemplateTree) ProjectThing(ini.trakem2.tree.ProjectThing)

Example 7 with LayerThing

use of ini.trakem2.tree.LayerThing 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");
}
Also used : LayerThing(ini.trakem2.tree.LayerThing)

Example 8 with LayerThing

use of ini.trakem2.tree.LayerThing in project TrakEM2 by trakem2.

the class Layer method getPrintableTitle.

/**
 * Returns a title such as 018__4-K4_2__z1.67 , which is [layer_set index]__[title]__[z coord] . The ordinal number starts at 1 and finishes at parent's length, inclusive.
 */
public String getPrintableTitle() {
    final LayerThing lt = project.findLayerThing(this);
    if (null == lt)
        return toString();
    String title = lt.getTitle();
    if (null == title)
        title = "";
    else
        title = title.replace(' ', '_');
    final StringBuilder sb = new StringBuilder().append(parent.indexOf(this) + 1);
    final int s_size = Integer.toString(parent.size()).length();
    while (sb.length() < s_size) {
        sb.insert(0, '0');
    }
    sb.append('_').append('_').append(title).append('_').append('_').append('z').append(Utils.cutNumber(this.z, 3, true));
    return sb.toString();
}
Also used : LayerThing(ini.trakem2.tree.LayerThing)

Example 9 with LayerThing

use of ini.trakem2.tree.LayerThing 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;
}
Also used : Displayable(ini.trakem2.display.Displayable) ZDisplayable(ini.trakem2.display.ZDisplayable) HashMap(java.util.HashMap) LayerThing(ini.trakem2.tree.LayerThing) TemplateTree(ini.trakem2.tree.TemplateTree) ProjectTree(ini.trakem2.tree.ProjectTree) LayerTree(ini.trakem2.tree.LayerTree) DBLoader(ini.trakem2.persistence.DBLoader) GenericDialog(ij.gui.GenericDialog) TemplateThing(ini.trakem2.tree.TemplateThing)

Example 10 with LayerThing

use of ini.trakem2.tree.LayerThing 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;
}
Also used : FSLoader(ini.trakem2.persistence.FSLoader) LayerTree(ini.trakem2.tree.LayerTree) ProjectTree(ini.trakem2.tree.ProjectTree) HashMap(java.util.HashMap) LayerThing(ini.trakem2.tree.LayerThing) TemplateTree(ini.trakem2.tree.TemplateTree) TemplateThing(ini.trakem2.tree.TemplateThing) Patch(ini.trakem2.display.Patch)

Aggregations

LayerThing (ini.trakem2.tree.LayerThing)13 Layer (ini.trakem2.display.Layer)8 HashMap (java.util.HashMap)8 LayerSet (ini.trakem2.display.LayerSet)7 TemplateThing (ini.trakem2.tree.TemplateThing)7 ProjectThing (ini.trakem2.tree.ProjectThing)5 DBObject (ini.trakem2.persistence.DBObject)4 LayerTree (ini.trakem2.tree.LayerTree)4 ProjectTree (ini.trakem2.tree.ProjectTree)4 TemplateTree (ini.trakem2.tree.TemplateTree)4 ArrayList (java.util.ArrayList)4 TreePath (javax.swing.tree.TreePath)4 Displayable (ini.trakem2.display.Displayable)3 Patch (ini.trakem2.display.Patch)3 DefaultMutableTreeNode (javax.swing.tree.DefaultMutableTreeNode)3 GenericDialog (ij.gui.GenericDialog)2 Project (ini.trakem2.Project)2 AreaTree (ini.trakem2.display.AreaTree)2 DLabel (ini.trakem2.display.DLabel)2 Display (ini.trakem2.display.Display)2