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

Example 21 with Profile

use of ini.trakem2.display.Profile 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 22 with Profile

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

the class Render method renderObject.

/**
 * Accepts a 'profile_list' Thing and composes a new Ob
 */
private void renderObject(Thing profile_list) {
    // check preconditions
    if (!profile_list.getType().equals("profile_list"))
        return;
    // do not accept an empty profile_list Thing
    final ArrayList<? extends Thing> al = profile_list.getChildren();
    if (null == al || al.size() < 2)
        return;
    // new style: follows profiles links and generates several obs, one per branch, ensuring that there is oly one profile per layer in the generated Ob for the .shapes file.
    // 1 - gather all profiles
    final HashSet<Profile> hs = new HashSet<Profile>();
    for (final Thing child : al) {
        Object ob = child.getObject();
        if (ob instanceof Profile) {
            hs.add((Profile) ob);
        } else {
            Utils.log2("Render: skipping non Profile class child");
        }
    }
    String name = profile_list.getParent().getTitle();
    final ArrayList<String> al_used_names = new ArrayList<String>();
    // make unique object name, since it'll be the group
    String name2 = name;
    int k = 1;
    while (ht_objects.containsKey(name2)) {
        name2 = name + "-" + k;
        k++;
    }
    name = name2;
    al_used_names.add(name);
    // 2 - start at the last found profile with the lowest Z, and recurse until done
    // Utils.log2("Calling renderSubObjects with " + hs.size() + " profiles");
    renderSubObjects(hs, al_used_names);
/* //old style, assumes a single profile per section
		Profile[] profiles = new Profile[al.size()];
		Iterator it = al.iterator();
		int i = 0;
		while (it.hasNext()) {
			Thing child = (Thing)it.next();
			Displayable displ = (Displayable)child.getObject();
			profiles[i] = (Profile)displ; //this cast is safe (as long as I'm the only programmer and I remember that Thing objects added to a 'profile_list' Thing are of class Profile only)
			i++;
		}
		// make unique object name, since it'll be the group
		String name = profile_list.getParent().getTitle();
		String name2 = name;
		int k = 1;
		while (ht_objects.containsKey(name2)) {
			name2 = name + "_" + k;
			k++;
		}
		name = name2;
		// store
		ht_objects.put(name, new Ob(name, profiles));
		*/
}

Example 23 with Profile

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

the class Render method accumulate.

/**
 * Recursive; returns the last added profile.
 */
private Profile accumulate(final HashSet<Profile> hs_done, final ArrayList<Profile> al, final Profile step, int z_trend) {
    final HashSet<Displayable> hs_linked = step.getLinked(Profile.class);
    if (al.size() > 1 && hs_linked.size() > 2) {
        // base found
        return step;
    }
    double step_z = step.getLayer().getZ();
    Profile next_step = null;
    boolean started = false;
    for (final Displayable ob : hs_linked) {
        // loop only one cycle, to move only in one direction
        if (al.contains(ob) || started || hs_done.contains(ob))
            continue;
        started = true;
        next_step = (Profile) ob;
        double next_z = next_step.getLayer().getZ();
        if (0 == z_trend) {
            // define trend
            if (next_z > step_z) {
                z_trend = 1;
            } else {
                z_trend = -1;
            }
            // add!
            al.add(next_step);
        } else {
            // if the z trend is broken, finish
            if ((next_z > step_z && 1 == z_trend) || (next_z < step_z && -1 == z_trend)) {
                // z trend continues
                al.add(next_step);
            } else {
                // z trend broken
                next_step = null;
            }
        }
    }
    Profile last = step;
    // Utils.log2("next_step is " + next_step);
    if (null != next_step) {
        hs_done.add(next_step);
        last = accumulate(hs_done, al, next_step, z_trend);
    }
    // Utils.log2("returning last " + last);
    return last;
}

Example 24 with Profile

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

the class Render method renderSubObjects.

/**
 * Render an object from the given profile, following the chain of links, until reaching a profile that is linked to more than two profiles.
 */
private void renderSubObjects(final HashSet<Profile> hs_all, final ArrayList<String> al_used_names) {
    int size = hs_all.size();
    Profile[] p = new Profile[size];
    hs_all.toArray(p);
    // collect starts and ends
    HashSet<Profile> hs_bases = new HashSet<Profile>();
    HashSet<Profile> hs_done = new HashSet<Profile>();
    do {
        Profile base = null;
        // choose among existing bases
        if (hs_bases.size() > 0) {
            base = (Profile) hs_bases.iterator().next();
        } else {
            // find a new base, simply by taking the lowest Z or remaining profiles
            double min_z = Double.MAX_VALUE;
            for (int i = 0; i < p.length; i++) {
                if (hs_done.contains(p[i]))
                    continue;
                double z = p[i].getLayer().getZ();
                if (z < min_z) {
                    min_z = z;
                    base = p[i];
                }
            }
            // add base
            if (null != base)
                hs_bases.add(base);
        }
        if (null == base) {
            Utils.log2("No more bases.");
            return;
        }
        // crawl list to get a sequence of profiles in increasing or decreasing Z order, but not mixed z trends
        ArrayList<Profile> al_profiles = new ArrayList<Profile>();
        // Utils.log2("Calling accumulate for base " + base);
        al_profiles.add(base);
        Profile last = accumulate(hs_done, al_profiles, base, 0);
        // if the trend was not empty, add it
        if (last != base) {
            // Utils.log2("creating Ob with " + al_profiles.size());
            // count as done
            hs_done.addAll(al_profiles);
            // add new possible base (which may have only 2 links if it was from a broken Z trend)
            hs_bases.add(last);
            // create 3D object from base to base
            Profile[] profiles = new Profile[al_profiles.size()];
            al_profiles.toArray(profiles);
            String name = createName(al_used_names);
            String name2 = name;
            int k = 1;
            while (ht_objects.containsKey(name2)) {
                name2 = name + "_" + k;
            }
            name = name2;
            al_used_names.add(name);
            ht_objects.put(name, new Ob(name, profiles));
            counter++;
            Utils.log("count: " + counter + " vs " + ht_objects.size());
        // Utils.log2("Storing ob with name=[" + name + "] and n=" + profiles.length);
        } else {
            // remove base
            // Utils.log2("Removing base " + base);
            hs_bases.remove(base);
        }
    } while (0 != hs_bases.size());
}

Example 25 with Profile

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

the class Profile method makeTriangles.

/**
 * Make a mesh as a calibrated list of 3D triangles.
 */
private static List<Point3f> makeTriangles(final Profile[] p, final double scale) {
    try {
        final VectorString2D[] sv = new VectorString2D[p.length];
        // dummy initialization
        boolean closed = true;
        final Calibration cal = p[0].getLayerSet().getCalibrationCopy();
        cal.pixelWidth *= scale;
        cal.pixelHeight *= scale;
        for (int i = 0; i < p.length; i++) {
            if (0 == p[i].n_points)
                continue;
            if (0 == i)
                closed = p[i].closed;
            else if (p[i].closed != closed) {
                Utils.log2("All profiles should be either open or closed, not mixed.");
                return null;
            }
            sv[i] = p[i].getPerimeter2D(cal);
        }
        return SkinMaker.generateTriangles(sv, -1, -1, closed);
    } catch (final Exception e) {
        IJError.print(e);
    }
    return null;
}