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

Example 96 with Project

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

the class DBLoader method getRootProjectThing.

/**
 * Get all the Thing objects, recursively, for the root, and their corresponding encapsulated objects. Also, fills in the given ArrayList with all loaded Displayable objects.
 */
public ProjectThing getRootProjectThing(Project project, TemplateThing root_tt, TemplateThing project_tt, HashMap<Long, Displayable> hs_d) {
    synchronized (db_lock) {
        // connect if disconnected
        if (!connectToDatabase()) {
            return null;
        }
        // unpack root_tt (assumes TemplateThing objects have unique types, skips any repeated type to avoid problems in recursive things such as neurite_branch)
        HashMap<String, TemplateThing> hs_tt = new HashMap<String, TemplateThing>();
        unpack(root_tt, hs_tt);
        ProjectThing root = null;
        try {
            // -1 signals root
            ResultSet r = connection.prepareStatement("SELECT * FROM ab_things WHERE project_id=" + project.getId() + " AND type='project' AND parent_id=-1").executeQuery();
            if (r.next()) {
                long id = r.getLong("id");
                root = new ProjectThing(project_tt, project, id, project, getChildrenProjectThings(project, id, project_tt.getType(), hs_tt, hs_d));
            }
            r.close();
            if (null == root) {
                Utils.log("Loader.getRootProjectThing: can't find it for project id=" + project.getId());
                return null;
            }
        } catch (Exception e) {
            IJError.print(e);
            return null;
        }
        return root;
    }
}

Example 97 with Project

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

the class DBLoader method fetchPipe.

private Pipe fetchPipe(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_pipe_points.pipe_id, ab_displayables.locked, m00, m10, m01, m11, m02, m12 FROM ab_zdisplayables, ab_displayables, ab_pipe_points WHERE ab_zdisplayables.id=ab_displayables.id AND ab_zdisplayables.id=ab_pipe_points.pipe_id AND ab_zdisplayables.id=" + id).executeQuery();
    Pipe p = null;
    if (r.next()) {
        p = new Pipe(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 p;
}

Example 98 with Project

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

the class DBLoader method fetchLayer.

/**
 * Load all objects into the Layer: Profile and Pipe from the hs_pt (full of ProjectThing wrapping them), and Patch, LayerSet, DLabel, etc from the database.
 */
private Layer fetchLayer(Project project, long id, HashMap hs_pt) throws Exception {
    ResultSet r = connection.prepareStatement("SELECT * FROM ab_layers WHERE id=" + id).executeQuery();
    Layer layer = null;
    if (r.next()) {
        long layer_id = r.getLong("id");
        layer = new Layer(project, layer_id, r.getDouble("z"), r.getDouble("thickness"));
        // find the Layer's parent
        long parent_id = r.getLong("layer_set_id");
        Object set = hs_pt.get(new Long(parent_id));
        if (null != set) {
            ((LayerSet) set).addSilently(layer);
        } else {
            Utils.log("Loader.fetchLayer: WARNING no parent for layer " + layer);
        }
        // add the displayables from hs_pt that correspond to this layer (and all other objects that belong to the layer)
        HashMap hs_d = new HashMap();
        ResultSet rd = connection.prepareStatement("SELECT ab_displayables.id, ab_profiles.id, layer_id, stack_index FROM ab_displayables,ab_profiles WHERE ab_displayables.id=ab_profiles.id AND layer_id=" + layer_id).executeQuery();
        while (rd.next()) {
            Long idd = new Long(rd.getLong("id"));
            Object ob = hs_pt.get(idd);
            // Utils.log("Found profile with id=" + idd + " and ob = " + ob);
            if (null != ob) {
                hs_d.put(new Integer(rd.getInt("stack_index")), ob);
            }
        }
        rd.close();
        // fetch LayerSet objects (which are also Displayable), and put them in the hs_pt (this is hackerous)
        ResultSet rls = connection.prepareStatement("SELECT * FROM ab_layer_sets, ab_displayables WHERE ab_layer_sets.id=ab_displayables.id AND ab_layer_sets.parent_layer_id=" + id).executeQuery();
        while (rls.next()) {
            long ls_id = rls.getLong("id");
            LayerSet layer_set = new LayerSet(project, ls_id, rls.getString("title"), (float) rls.getDouble("width"), (float) rls.getDouble("height"), rls.getDouble("rot_x"), rls.getDouble("rot_y"), rls.getDouble("rot_z"), (float) rls.getDouble("layer_width"), (float) rls.getDouble("layer_height"), rls.getBoolean("locked"), rls.getInt("snapshots_mode"), new AffineTransform(rls.getDouble("m00"), rls.getDouble("m10"), rls.getDouble("m01"), rls.getDouble("m11"), rls.getDouble("m02"), rls.getDouble("m12")));
            hs_pt.put(new Long(ls_id), layer_set);
            hs_d.put(new Integer(rls.getInt("stack_index")), layer_set);
            layer_set.setLayer(layer, false);
            // find the pipes (or other possible ZDisplayable objects) in the hs_pt that belong to this LayerSet and add them silently
            ResultSet rpi = connection.prepareStatement("SELECT ab_displayables.id, ab_zdisplayables.id, layer_id, layer_set_id, stack_index FROM ab_displayables,ab_zdisplayables WHERE ab_displayables.id=ab_zdisplayables.id AND layer_set_id=" + ls_id + " ORDER BY stack_index ASC").executeQuery();
            while (rpi.next()) {
                Long idd = new Long(rpi.getLong("id"));
                Object ob = hs_pt.get(idd);
                if (null != ob && ob instanceof ZDisplayable) {
                    layer_set.addSilently((ZDisplayable) ob);
                } else {
                    Utils.log("fetchLayer: failed to add a ZDisplayable to the layer_set. zdispl id = " + idd);
                }
            }
            rpi.close();
        }
        rls.close();
        // add Patch objects from ab_patches joint-called with ab_displayables
        ResultSet rp = connection.prepareStatement("SELECT ab_patches.id, ab_displayables.id, layer_id, title, width, height, stack_index, imp_type, locked, min, max, m00, m10, m01, m11, m02, m12 FROM ab_patches,ab_displayables WHERE ab_patches.id=ab_displayables.id AND ab_displayables.layer_id=" + layer_id).executeQuery();
        while (rp.next()) {
            long patch_id = rp.getLong("id");
            Patch patch = new Patch(project, patch_id, rp.getString("title"), (float) rp.getDouble("width"), (float) rp.getDouble("height"), rp.getInt("o_width"), rp.getInt("o_height"), rp.getInt("imp_type"), rp.getBoolean("locked"), rp.getDouble("min"), rp.getDouble("max"), new AffineTransform(rp.getDouble("m00"), rp.getDouble("m10"), rp.getDouble("m01"), rp.getDouble("m11"), rp.getDouble("m02"), rp.getDouble("m12")));
            // collecting all Displayable objects to reconstruct links
            hs_pt.put(new Long(patch_id), patch);
            hs_d.put(new Integer(rp.getInt("stack_index")), patch);
        }
        rp.close();
        // add DLabel objects
        ResultSet rl = connection.prepareStatement("SELECT ab_labels.id, ab_displayables.id, layer_id, title, width, height, m00, m10, m01, m11, m02, m12, stack_index, font_name, font_style, font_size, ab_labels.type, locked FROM ab_labels,ab_displayables WHERE ab_labels.id=ab_displayables.id AND ab_displayables.layer_id=" + layer_id).executeQuery();
        while (rl.next()) {
            long label_id = rl.getLong("id");
            DLabel label = new DLabel(project, label_id, rl.getString("title"), (float) rl.getDouble("width"), (float) rl.getDouble("height"), rl.getInt("type"), rl.getString("font_name"), rl.getInt("font_style"), rl.getInt("font_size"), rl.getBoolean("locked"), new AffineTransform(rl.getDouble("m00"), rl.getDouble("m10"), rl.getDouble("m01"), rl.getDouble("m11"), rl.getDouble("m02"), rl.getDouble("m12")));
            // collecting all Displayable objects to reconstruct links
            hs_pt.put(new Long(label_id), label);
            hs_d.put(new Integer(rl.getInt("stack_index")), label);
        }
        rl.close();
        // Add silently to the Layer ordered by stack index
        Set e = hs_d.keySet();
        Object[] si = new Object[hs_d.size()];
        si = e.toArray(si);
        // will it sort an array of integers correctly? Who knows!
        Arrays.sort(si);
        for (int i = 0; i < si.length; i++) {
            // Utils.log("Loader layer.addSilently: adding " + (DBObject)hs_d.get(si[i]));
            layer.addSilently((DBObject) hs_d.get(si[i]));
        }
        // find displays and open later, when fully loaded.
        ResultSet rdi = connection.prepareStatement("SELECT * FROM ab_displays WHERE layer_id=" + layer.getId()).executeQuery();
        while (rdi.next()) {
            fetchDisplay(rdi, layer);
        }
        rdi.close();
    }
    r.close();
    return layer;
}

Example 99 with Project

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

the class DBLoader method restoreNodesExpandedState.

/**
 * Affects only those set to true; the rest are left untouched.
 */
public void restoreNodesExpandedState(final Project project) {
    // connect if disconnected
    if (!connectToDatabase()) {
        return;
    }
    try {
        final ProjectTree ptree = project.getProjectTree();
        final ResultSet r = connection.prepareStatement("SELECT id,expanded from ab_things where project_id=" + project.getId()).executeQuery();
        while (r.next()) {
            // "expanded");
            boolean expanded = r.getBoolean(2);
            if (expanded) {
                // DNDTree.findNode(id, ptree);
                Thing thing = project.find(r.getLong(1));
                if (null != thing)
                    ptree.setExpandedSilently(thing, true);
            }
        }
        ptree.updateUILater();
    } catch (Exception e) {
        IJError.print(e);
    }
}

Example 100 with Project

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

the class DBLoader method getTemplateRoot.

/**
 * Fetch the root of the TemplateThing tree from the database-stored hierarchy of TemplateThing objects defined in the original XML file .
 */
public TemplateThing getTemplateRoot(Project project) {
    // connect if disconnected
    if (!connectToDatabase()) {
        return null;
    }
    TemplateThing root = null;
    synchronized (db_lock) {
        // New way: TemplateThing instances are saved in the ab_things table
        try {
            // fetch TemplateThings, which have no stored object.
            // signature of the root TemplateThing is parent_id=-1 and object_id=-1
            ResultSet r = connection.prepareStatement("SELECT * FROM ab_things WHERE project_id=" + project.getId() + " AND parent_id=-1 AND object_id=-1").executeQuery();
            if (r.next()) {
                long id = r.getLong("id");
                String type = r.getString("type");
                root = new TemplateThing(type, project, id);
                root.setup(getChildrenTemplateThings(project, id));
            }
            r.close();
        } catch (Exception e) {
            IJError.print(e);
            return null;
        }
    }
    return root;
}