Examples with DBLoader ini.trakem2.persistence.DBLoader used on opensource projects

Example 1 with DBLoader

use of ini.trakem2.persistence.DBLoader in project TrakEM2 by trakem2.

the class DBLoader method updateInDatabase.

/**
 * The ImagePlus, if updated, is saved in the 'tiff_working' column always.
 */
private void updateInDatabase(Patch patch, String key) throws Exception {
    if (key.equals("tiff_snapshot")) {
        /* // DEPRECATED, now using mipmaps
			InputStream i_stream = null;
			try {
				ImagePlus imp = new ImagePlus("s", snaps.get(patch.getId())); // not calling fetchSnapshot because old code could end in a loop.
				if (null == imp) {
					Utils.log2("DBLoader: snapshot ImagePlus is null!");
					stmt_update_snap.setNull(1, java.sql.Types.BINARY);
				} else {
					i_stream = createZippedStream(imp);
					stmt_update_snap.setBinaryStream(1, i_stream, i_stream.available());
					flush(imp);
				}
				stmt_update_snap.setLong(2, patch.getId());
				stmt_update_snap.executeUpdate();
			} catch (Exception e) {
				IJError.print(e);
			} finally {
				if (null != i_stream) try { i_stream.close(); } catch (Exception e1) { IJError.print(e1); }
			}
			*/
        return;
    }
    StringBuffer sb = new StringBuffer("UPDATE ab_patches SET ");
    boolean update_imp = false;
    if (key.equals("tiff_working")) {
        sb.append("imp_type=").append(patch.getType()).append(", tiff_working=?");
        update_imp = true;
    } else if (key.equals("remove_tiff_working")) {
        sb.append("tiff_working=NULL");
    } else if (key.equals("min_and_max")) {
        sb.append("min=").append(patch.getMin()).append(", max=").append(patch.getMax());
    } else {
        // try the Displayable level
        updateInDatabase((Displayable) patch, key);
        return;
    }
    PreparedStatement st = connection.prepareStatement(sb.append(" WHERE id=").append(patch.getId()).toString());
    int i = 1;
    InputStream i_stream2 = null;
    try {
        if (update_imp) {
            // WARNING if the cache is very small relative to the size of the images, this strategy may fail
            ImagePlus imp = mawts.get(patch.getId());
            i_stream2 = createZippedStream(imp);
            st.setBinaryStream(i, i_stream2, i_stream2.available());
            // defensive programming: if later I add any other ..
            i++;
        }
        st.executeUpdate();
        if (null != i_stream2)
            i_stream2.close();
    } catch (Exception e) {
        IJError.print(e);
        if (null != i_stream2)
            try {
                i_stream2.close();
            } catch (Exception e2) {
                IJError.print(e2);
            }
    }
}

Example 2 with DBLoader

use of ini.trakem2.persistence.DBLoader in project TrakEM2 by trakem2.

the class Project method destroy.

public boolean destroy() {
    if (null == loader) {
        return true;
    }
    if (loader.hasChanges() && !getBooleanProperty("no_shutdown_hook")) {
        // DBLoader always returns false
        if (ControlWindow.isGUIEnabled()) {
            final YesNoDialog yn = ControlWindow.makeYesNoDialog("TrakEM2", "There are unsaved changes in project " + title + ". Save them?");
            if (yn.yesPressed()) {
                save();
            }
        } else {
            Utils.log2("WARNING: closing project '" + title + "' with unsaved changes.");
        }
    }
    try {
        if (null != autosaving)
            autosaving.cancel(true);
    } catch (Throwable t) {
    }
    al_open_projects.remove(this);
    // flush all memory
    if (null != loader) {
        // the last project is destroyed twice for some reason, if several are open. This is a PATCH
        // and disconnect
        loader.destroy();
        loader = null;
    }
    if (null != layer_set)
        layer_set.destroy();
    // AFTER loader.destroy() call.
    ControlWindow.remove(this);
    if (null != template_tree)
        template_tree.destroy();
    if (null != project_tree)
        project_tree.destroy();
    if (null != layer_tree)
        layer_tree.destroy();
    Polyline.flushTraceCache(this);
    // flag to mean: we're closing
    this.template_tree = null;
    // close all open Displays
    Display.close(this);
    Search.removeTabs(this);
    synchronized (ptcache) {
        ptcache.clear();
    }
    return true;
}

Example 3 with DBLoader

use of ini.trakem2.persistence.DBLoader 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 4 with DBLoader

use of ini.trakem2.persistence.DBLoader in project TrakEM2 by trakem2.

the class ProjectThing method getPopupItems.

public JMenuItem[] getPopupItems(final ActionListener listener) {
    JMenuItem item = null;
    ArrayList<JMenuItem> al_items = new ArrayList<JMenuItem>();
    JMenu menu = new JMenu("Add...");
    // call the project unique type
    final ArrayList<TemplateThing> tc = project.getTemplateThing(template.getType()).getChildren();
    if (null != tc) {
        for (final TemplateThing tt : tc) {
            item = new JMenuItem("new " + tt.getType());
            item.addActionListener(listener);
            menu.add(item);
        }
        item = new JMenuItem("many...");
        item.addActionListener(listener);
        menu.add(item);
    }
    if (0 != menu.getItemCount()) {
        if (template.getType().equals("profile_list") && null != al_children && al_children.size() > 0) {
            // can't add a new profile unless linked to another one.
            item.setEnabled(false);
        }
        al_items.add(menu);
    }
    // generic for all:
    // a 'Show' command on a non-basic type is a render preview.
    addPopupItem("Unhide", listener, al_items).setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_H, Event.ALT_MASK, true));
    addPopupItem("Hide", listener, al_items).setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_H, 0, true));
    addPopupItem("Info", listener, al_items);
    addPopupItem("Rename...", listener, al_items).setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F2, 0, true));
    // enable duplicating for basic types only
    if (Project.isBasicType(getType())) {
        addPopupItem("Duplicate", listener, al_items);
    }
    addPopupItem("Select in display", listener, al_items).setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_A, 0, true));
    if (null != object && object instanceof Displayable) {
        addPopupItem("Show centered in Display", listener, al_items);
    }
    if (null != object && object instanceof Tree<?>) {
        addPopupItem("Show tabular view", listener, al_items);
    }
    // plugins
    JMenuItem plugin_menu = Utils.addPlugIns("Project Tree", project, new Callable<Displayable>() {

        public Displayable call() {
            if (object instanceof Displayable)
                return (Displayable) object;
            return null;
        }
    });
    if (null != plugin_menu)
        al_items.add(plugin_menu);
    addPopupItem("Measure", listener, al_items);
    addPopupItem("Show in 3D", listener, al_items).setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_3, 0, true));
    addPopupItem("Remove from 3D view", listener, al_items);
    if (template.getType().equals("project")) {
        if (project.getLoader() instanceof DBLoader) {
            addPopupItem("Export project...", listener, al_items);
        } else if (project.getLoader() instanceof FSLoader) {
            addPopupItem("Save", listener, al_items).setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_S, 0, true));
            addPopupItem("Save as...", listener, al_items);
        }
    }
    if (!(template.getType().equals("project") && project.getLoader() instanceof FSLoader)) {
        addPopupItem("Delete...", listener, al_items);
    }
    JMenuItem[] items = new JMenuItem[al_items.size()];
    al_items.toArray(items);
    return items;
}