Fixes to homogenizeContrast

[trakem2.git] / ini / trakem2 / display / Profile.java

/**

TrakEM2 plugin for ImageJ(C).
Copyright (C) 2005, 2006 Albert Cardona and Rodney Douglas.

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.txt )

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA. 

You may contact Albert Cardona at acardona at ini.phys.ethz.ch
Institute of Neuroinformatics, University of Zurich / ETH, Switzerland.
**/

package ini.trakem2.display;

import ij.measure.Calibration;
import ij.measure.ResultsTable;


import ini.trakem2.Project;
import ini.trakem2.persistence.DBObject;
import ini.trakem2.persistence.Loader;
import ini.trakem2.utils.ProjectToolbar;
import ini.trakem2.utils.Utils;
import ini.trakem2.utils.M;
import ini.trakem2.utils.IJError;
import ini.trakem2.render3d.Perimeter2D;
import ini.trakem2.display.Display3D;
import ini.trakem2.tree.ProjectThing;
import ini.trakem2.tree.Thing;
import ini.trakem2.tree.ProjectThing;
import ini.trakem2.vector.VectorString2D;
import ini.trakem2.vector.SkinMaker;

import java.awt.Color;
import java.awt.Rectangle;
import java.awt.Polygon;
import java.awt.event.MouseEvent;
import java.awt.event.KeyEvent;
import java.awt.geom.Area;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Map;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.awt.geom.AffineTransform;
import java.awt.geom.Point2D;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Composite;
import java.awt.AlphaComposite;

import javax.vecmath.Point3f;


/** A class to be a user-outlined profile over an image, which is painted with a particular color and also holds an associated text label.
 * TODO - label not implemented yet.
 *      - can't paint segments in different colors yet
 *      - the whole curve is updated when only a particular set of points needs readjustment
 *      - also, points are smooth, and options should be given to make them non-smooth.
 */
public class Profile extends Displayable {

        /**The number of points.*/
        protected int n_points;
        /**The array of clicked points.*/
        protected double[][] p;
        /**The array of left control points, one for each clicked point.*/
        protected double[][] p_l;
        /**The array of right control points, one for each clicked point.*/
        protected double[][] p_r;
        /**The array of interpolated points generated from p, p_l and p_r.*/
        protected double[][] p_i;
        /**Paint/behave as open or closed curve.*/
        protected boolean closed = false;

        /** A new user-requested Profile.*/
        public Profile(Project project, String title, double x, double y) {
                super(project, title, x, y);
                n_points = 0;
                p = new double[2][5];
                p_l = new double[2][5];
                p_r = new double[2][5];
                p_i = new double[2][0];
                addToDatabase();
        }

        /**Construct a Bezier Profile object from a set of points mixed in this pattern: PCCPCCPCCPCCP , so, [PCC]n  where P = backbone point and C = control point. This results from a BezierApproximation on a path of points as drawed with the mouse. Keep in mind the control points will NOT have the same tangents, but this may be either left like that or corrected with some smoothing algorithm.*/
        public Profile(Project project, String title, double x, double y, Point2D.Double[] points) {
                super(project, title, x, y);
                //setup arrays
                int size = (points.length / 3) + 1;
                p = new double[2][size];
                p_l =new double[2][size];
                p_r =new double[2][size];
                //first point:
                p[0][0] = points[0].x;
                p[1][0] = points[0].y;
                p_l[0][0] = p[0][0];
                p_l[1][0] = p[1][0];
                p_r[0][0] = points[1].x;
                p_r[1][0] = points[1].y;
                n_points++;
                //all middle points:
                for (int j=1, i=3; i<points.length-3; i+=3, j++) {
                        p[0][j] = points[i].x;
                        p[1][j] = points[i].y;
                        p_l[0][j] = points[i-1].x;
                        p_l[1][j] = points[i-1].y;
                        if (null == points[i+1]) {
                                Utils.log("BezierProfile: points[" + i + " + 1] is null !");
                        }
                        p_r[0][j] = points[i+1].x;
                        p_r[1][j] = points[i+1].y;
                        n_points++;
                }
                //last point:
                int last = points.length-1;
                p[0][n_points] = points[last].x;
                p[1][n_points] = points[last].y;
                p_l[0][n_points] = points[last-1].x;
                p_l[1][n_points] = points[last-1].y;
                p_r[0][n_points] = p[0][n_points];
                p_r[1][n_points] = p[1][n_points];
                n_points++;

                calculateBoundingBox();

                //add to database
                addToDatabase();
                updateInDatabase("points");
        }

        /**Construct a Bezier Profile from the database.*/
        public Profile(Project project, long id, String title, float alpha, boolean visible, Color color, double[][][] bezarr, boolean closed, boolean locked, AffineTransform at) {
                super(project, id, title, locked, at, 0, 0);
                this.visible = visible;
                this.alpha = alpha;
                this.color = color;
                this.closed = closed;
                //make points from the polygon, in which they are stored as LPRLPR ... left control - backbone point - right control point (yes this looks very much like codons, but the important bit is the middle one, not the left one! HaHaHaHa!)
                //// points are fields x,y in PGpoint.
                p_l = bezarr[0];
                p = bezarr[1];
                p_r = bezarr[2];
                n_points = p[0].length;

                //calculate width and height
                calculateBoundingBox(false);
        }

        /** Construct a Bezier Profile from the database, but the points will be loaded later, when actually needed, by calling setupForDisplay(). */
        public Profile(Project project, long id, String title, double width, double height, float alpha, boolean visible, Color color, boolean closed, boolean locked, AffineTransform at) {
                super(project, id, title, locked, at, width, height);
                this.visible = visible;
                this.alpha = alpha;
                this.color = color;
                this.closed = closed;
                this.n_points = -1; //used as a flag to signal "I have points, but unloaded"
        }

        /** Construct a Bezier Profile from an XML entry. */
        public Profile(Project project, long id, HashMap ht, HashMap ht_links) {
                super(project, id, ht, ht_links);
                // parse data
                for (Iterator it = ht.entrySet().iterator(); it.hasNext(); ) {
                        Map.Entry entry = (Map.Entry)it.next();
                        String key = (String)entry.getKey();
                        String data = (String)entry.getValue();
                        if (key.equals("d")) {
                                // parse the SVG points data
                                ArrayList al_p = new ArrayList();
                                ArrayList al_p_r = new ArrayList();
                                ArrayList al_p_l = new ArrayList();// needs shifting, inserting one point at the beginning if not closed.
                                // sequence is: M p[0],p[1] C p_r[0],p_r[1] p_l[0],p_l[1] and repeat without the M, and finishes with the last p[0],p[1]. If closed, appended at the end is p_r[0],p_r[1] p_l[0],p_l[1]
                                // first point:
                                int i_start = data.indexOf('M');
                                int i_end = data.indexOf('C');
                                String point = data.substring(i_start+1, i_end).trim();
                                al_p.add(point);
                                boolean go = true;
                                while (go) {
                                        i_start = i_end;
                                        i_end = data.indexOf('C', i_end+1);
                                        if (-1 == i_end) {
                                                i_end = data.length() -1;
                                                go = false;
                                        }
                                        String txt = data.substring(i_start+1, i_end).trim();
                                        // eliminate double spaces
                                        while (-1 != txt.indexOf("  ")) {
                                                txt = txt.replaceAll("  ", " ");
                                        }
                                        // reduce ", " and " ," to ","
                                        txt = txt.replaceAll(" ,", ",");
                                        txt = txt.replaceAll(", ", ",");
                                        // cut by spaces
                                        String[] points = txt.split(" ");
                                        // debug:
                                        //Utils.log("Profile init: txt=__" + txt + "__ points.length=" + points.length);
                                        if (3 == points.length) {
                                                al_p_r.add(points[0]);
                                                al_p_l.add(points[1]);
                                                al_p.add(points[2]);
                                        } else {
                                                // error
                                                Utils.log("Profile constructor from XML: error at parsing points.");
                                        }
                                        // example: C 34.5,45.6 45.7,23.0 34.8, 78.0 C ..
                                }
                                this.closed = (-1 != data.lastIndexOf('z')); // 'z' must be lowercase to comply with SVG style
                                if (this.closed) {
                                        // prepend last left control point and delete from the end
                                        al_p_l.add(0, al_p_l.remove(al_p_l.size() -1));
                                        // remove last point (duplicated in this SVG format)
                                        al_p.remove(al_p.size() -1); // TODO check that it's really closed by comparing the points, not just by the z, and if not closed, remove the control points.
                                } else {
                                        // prepend a left control point equal to the first point
                                        al_p_l.add(0, al_p.get(0)); // no need to clone, String is final
                                        // and append a right control point equal to the last point
                                        al_p_r.add(al_p.get(al_p.size() -1));
                                }
                                // sanity check:
                                if (!(al_p.size() == al_p_l.size() && al_p_l.size() == al_p_r.size())) {
                                        Utils.log2("Profile XML parsing: Disagreement in the number of points:\n\tp.length=" + al_p.size() + "\n\tp_l.length=" + al_p_l.size() + "\n\tp_r.length=" + al_p_r.size());
                                }
                                // Now parse the points
                                this.n_points = al_p.size();
                                this.p = new double[2][n_points];
                                this.p_l = new double[2][n_points];
                                this.p_r = new double[2][n_points];
                                for (int i=0; i<n_points; i++) {
                                        String[] sp = ((String)al_p.get(i)).split(",");
                                        p[0][i] = Double.parseDouble(sp[0]);
                                        p[1][i] = Double.parseDouble(sp[1]);
                                        sp = ((String)al_p_l.get(i)).split(",");
                                        p_l[0][i] = Double.parseDouble(sp[0]);
                                        p_l[1][i] = Double.parseDouble(sp[1]);
                                        sp = ((String)al_p_r.get(i)).split(",");
                                        p_r[0][i] = Double.parseDouble(sp[0]);
                                        p_r[1][i] = Double.parseDouble(sp[1]);
                                }
                                this.p_i = new double[2][0]; // empty
                                generateInterpolatedPoints(0.05);
                        }
                }
        }

        /** A constructor for cloning purposes. */
        private Profile(Project project, String title, double x, double y, double width, double height, float alpha, Color color, int n_points, double[][] p, double[][] p_r, double[][] p_l, double[][] p_i, boolean closed) {
                super(project, title, x, y);
                this.width = width;
                this.height = height;
                this.alpha = alpha;
                this.color = color;
                this.n_points = n_points;
                this.p = p;
                this.p_r = p_r;
                this.p_l = p_l;
                this.p_i = p_i;
                this.closed = closed;
                addToDatabase();
                updateInDatabase("all");
        }

        /**Increase the size of the arrays by 5 points.*/
        protected void enlargeArrays() {
                //catch length
                int length = p[0].length;
                //make copies
                double[][] p_copy = new double[2][length + 5];
                double[][] p_l_copy = new double[2][length + 5];
                double[][] p_r_copy = new double[2][length + 5];
                //copy values
                System.arraycopy(p[0], 0, p_copy[0], 0, length);
                System.arraycopy(p[1], 0, p_copy[1], 0, length);
                System.arraycopy(p_l[0], 0, p_l_copy[0], 0, length);
                System.arraycopy(p_l[1], 0, p_l_copy[1], 0, length);
                System.arraycopy(p_r[0], 0, p_r_copy[0], 0, length);
                System.arraycopy(p_r[1], 0, p_r_copy[1], 0, length);
                //assign them
                this.p = p_copy;
                this.p_l = p_l_copy;
                this.p_r = p_r_copy;
        }

        public boolean isClosed() {
                return this.closed;
        }

        /**Find a point in an array 'a', with a precision dependent on the magnification. */
        protected int findPoint(double[][] a, double x_p, double y_p, double magnification) {
                int index = -1;
                // make parameters local
                double d = (10.0D / magnification);
                if (d < 2) d = 2;
                for (int i=0; i<n_points; i++) {
                        if ((Math.abs(x_p - a[0][i]) + Math.abs(y_p - a[1][i])) <= d) {
                                index = i;
                        }
                }
                return index;
        }

        /**Remove a point from the bezier backbone and its two associated control points.*/
        protected void removePoint(int index) {
                // check preconditions:
                if (index < 0) {
                        return;
                } else if (n_points - 1 == index) {
                        //last point out
                        n_points--;
                } else {
                        //one point out (but not the last)
                        n_points--;
                        // shift all points after 'index' one position to the left:
                        for (int i=index; i<n_points; i++) {
                                p[0][i] = p[0][i+1];            //the +1 doesn't fail ever because the n_points has been adjusted above, but the arrays are still the same size. The case of deleting the last point is taken care above.
                                p[1][i] = p[1][i+1];
                                p_l[0][i] = p_l[0][i+1];
                                p_l[1][i] = p_l[1][i+1];
                                p_r[0][i] = p_r[0][i+1];
                                p_r[1][i] = p_r[1][i+1];
                        }
                }
                // open the curve if necessary
                if (closed && n_points < 2) {
                        closed = false;
                        updateInDatabase("closed");
                }
                //update in database
                updateInDatabase("points");
        }

        /**Calculate distance from one point to another.*/
        protected double distance(double x1, double y1, double x2, double y2) {
                return Math.sqrt((x2-x1)*(x2-x1) + (y2-y1)*(y2-y1));
        }

        /**Move backbone point.*/
        protected void dragPoint(int index, int dx, int dy) {
                p[0][index] += dx;
                p[1][index] += dy;
                p_l[0][index] += dx;
                p_l[1][index] += dy;
                p_r[0][index] += dx;
                p_r[1][index] += dy;
        }

        /**Set the control points to the same value as the backbone point which they control.*/
        protected void resetControlPoints(int index) {
                p_l[0][index] = p[0][index];
                p_l[1][index] = p[1][index];
                p_r[0][index] = p[0][index];
                p_r[1][index] = p[1][index];
        }

        /**Drag a control point and adjust the other, dependent one, in a symmetric way or not.*/
        protected void dragControlPoint(int index, double x_d, double y_d, double[][] p_dragged, double[][] p_adjusted, boolean symmetric) {
                //measure hypothenusa: from p to p control
                double hypothenusa;
                if (symmetric) {
                        //make both points be dragged in parallel, the same distance
                        hypothenusa = distance(p[0][index], p[1][index], p_dragged[0][index], p_dragged[1][index]);
                } else {
                        //make each point be dragged with its own distance
                        hypothenusa = distance(p[0][index], p[1][index], p_adjusted[0][index], p_adjusted[1][index]);
                }
                //measure angle: use the point being dragged
                double angle = Math.atan2(p_dragged[0][index] - p[0][index], p_dragged[1][index] - p[1][index]) + Math.PI;
                //apply
                p_dragged[0][index] = x_d;
                p_dragged[1][index] = y_d;
                p_adjusted[0][index] = p[0][index] + hypothenusa * Math.sin(angle); // it's sin and not cos because of stupid Math.atan2 way of delivering angles
                p_adjusted[1][index] = p[1][index] + hypothenusa * Math.cos(angle);
        }

        /**Add a point either at the end or between two existing points, with accuracy depending on magnification. Does not update the database. x_p,y_p are in the local space. */
        protected int addPoint(double x_p, double y_p, double magnification, double bezier_finess) {
                //lookup closest interpolated point and then get the closest clicked point to it
                int index = findClosestPoint(x_p, y_p, magnification, bezier_finess); // x_p, y_p are already local.
                if (closed && -1 == index) {
                        return -1;
                }
                //check array size
                if (p[0].length == n_points) {
                        enlargeArrays();
                }
                //decide:
                if (0 == n_points || 1 == n_points || -1 == index || index + 1 == n_points) {
                        //append at the end
                        p[0][n_points] = p_l[0][n_points] = p_r[0][n_points] = x_p;
                        p[1][n_points] = p_l[1][n_points] = p_r[1][n_points] = y_p;
                        index = n_points;
                } else {
                        //insert at index:
                        index++; //so it is added after the closest point;
                        // 1 - copy second half of array
                        int sh_length = n_points -index;
                        double[][] p_copy = new double[2][sh_length];
                        double[][] p_l_copy = new double[2][sh_length];
                        double[][] p_r_copy = new double[2][sh_length];
                        System.arraycopy(p[0], index, p_copy[0], 0, sh_length);
                        System.arraycopy(p[1], index, p_copy[1], 0, sh_length);
                        System.arraycopy(p_l[0], index, p_l_copy[0], 0, sh_length);
                        System.arraycopy(p_l[1], index, p_l_copy[1], 0, sh_length);
                        System.arraycopy(p_r[0], index, p_r_copy[0], 0, sh_length);
                        System.arraycopy(p_r[1], index, p_r_copy[1], 0, sh_length);
                        // 2 - insert value into 'p' (the two control arrays get the same value)
                        p[0][index] = p_l[0][index] = p_r[0][index] = x_p;
                        p[1][index] = p_l[1][index] = p_r[1][index] = y_p;
                        // 3 - copy second half into the array
                        System.arraycopy(p_copy[0], 0, p[0], index+1, sh_length);
                        System.arraycopy(p_copy[1], 0, p[1], index+1, sh_length);
                        System.arraycopy(p_l_copy[0], 0, p_l[0], index+1, sh_length);
                        System.arraycopy(p_l_copy[1], 0, p_l[1], index+1, sh_length);
                        System.arraycopy(p_r_copy[0], 0, p_r[0], index+1, sh_length);
                        System.arraycopy(p_r_copy[1], 0, p_r[1], index+1, sh_length);
                }
                //add one up
                this.n_points++;

                // set the x,y and readjust points
                calculateBoundingBox();

                return index;
        }

        /**Find the closest point to an interpolated point with precision depending upon magnification. The point x_p,y_p is in local coordinates. */
        protected int findClosestPoint(double x_p, double y_p, double magnification, double bezier_finess) {
                if (0 == p_i[0].length) return -1; // when none added yet
                int index = -1;
                double distance_sq = Double.MAX_VALUE;
                double distance_sq_i;
                double max = 12.0D / magnification;
                max = max * max; //squaring it
                for (int i=0; i<p_i[0].length; i++) {
                        //see which point is closer (there's no need to calculate the distance by multiplying squares and so on).
                        distance_sq_i = (p_i[0][i] - x_p)*(p_i[0][i] - x_p) + (p_i[1][i] - y_p)*(p_i[1][i] - y_p);
                        if (distance_sq_i < max && distance_sq_i < distance_sq) {
                                index = i;
                                distance_sq = distance_sq_i;
                        }
                }
                if (-1 != index) {
                        int index_found = (int)((double)index * bezier_finess);
                        if (index < (index_found / bezier_finess)) {
                                index_found--;
                        }
                        index = index_found;
                }
                return index;
        }

        /**Toggle curve closed/open.*/
        public void toggleClosed() {
                if (closed) {
                        closed = false;
                } else {
                        closed = true;
                }
                //update database
                updateInDatabase("closed");
        }

        protected void generateInterpolatedPoints(double bezier_finess) {
                if (0 >= n_points) {
                        return;
                }

                int n = n_points;
                if (closed && n > 1) {
                        //do the loop for one more
                        n++;
                        //enlarge arrays if needed
                        if (p[0].length == n_points) {
                                enlargeArrays();
                        }
                        //add first point to the end (doesn't need to be deleted because n_points hasn't changed)
                        // n_points works as an index here.
                        p[0][n_points] = p[0][0];
                        p[1][n_points] = p[1][0];
                        p_l[0][n_points] = p_l[0][0];
                        p_l[1][n_points] = p_l[1][0];
                        p_r[0][n_points] = p_r[0][0];
                        p_r[1][n_points] = p_r[1][0];
                }

                // case there's only one point
                if (1 == n_points) {
                        p_i = new double[2][1];
                        p_i[0][0] = p[0][0];
                        p_i[1][0] = p[1][0];
                        return;
                }
                // case there's more: interpolate!
                p_i = new double[2][(int)(n * (1.0D/bezier_finess))];
                double t, f0, f1, f2, f3;
                int next = 0;
                for (int i=0; i<n-1; i++) {
                        for (t=0.0D; t<1.0D; t += bezier_finess) {
                                f0 = (1-t)*(1-t)*(1-t);
                                f1 = 3*t*(1-t)*(1-t);
                                f2 = 3*t*t*(1-t);
                                f3 = t*t*t;
                                p_i[0][next] = f0*p[0][i] + f1*p_r[0][i] + f2*p_l[0][i+1] + f3*p[0][i+1];
                                p_i[1][next] = f0*p[1][i] + f1*p_r[1][i] + f2*p_l[1][i+1] + f3*p[1][i+1];
                                next++;
                                //enlarge if needed (when bezier_finess is not 0.05, it's difficult to predict because of int loss of precision.
                                if (p_i[0].length == next) {
                                        double[][] p_i_copy = new double[2][p_i[0].length + 5];
                                        System.arraycopy(p_i[0], 0, p_i_copy[0], 0, p_i[0].length);
                                        System.arraycopy(p_i[1], 0, p_i_copy[1], 0, p_i[1].length);
                                        p_i = p_i_copy;
                                }
                        }
                }
                if (p_i[0].length != next) { // 'next' works as a length here
                        //resize back
                        double[][] p_i_copy = new double[2][next];
                        System.arraycopy(p_i[0], 0, p_i_copy[0], 0, next);
                        System.arraycopy(p_i[1], 0, p_i_copy[1], 0, next);
                        p_i = p_i_copy;
                }
        }


        public void paint(final Graphics2D g, final double magnification, final boolean active, final int channels, final Layer active_layer) {
                if (0 == n_points) return;
                if (-1 == n_points) {
                        // load points from the database
                        setupForDisplay();
                        if (-1 == n_points) {
                                Utils.log2("Profile.paint: Some error ocurred, can't load points from database.");
                                return;
                        }
                }
                //arrange transparency
                Composite original_composite = null;
                if (alpha != 1.0f) {
                        original_composite = g.getComposite();
                        g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, alpha));
                }

                // local pointers, since they may be transformed
                double[][] p = this.p;
                double[][] p_r = this.p_r;
                double[][] p_l = this.p_l;
                double[][] p_i = this.p_i;
                if (!this.at.isIdentity()) {
                        final Object[] ob = getTransformedData();
                        p = (double[][])ob[0];
                        p_l = (double[][])ob[1];
                        p_r = (double[][])ob[2];
                        p_i = (double[][])ob[3];
                }
                if (active) {
                        //draw/fill points
                        final int oval_radius = (int)Math.ceil(4 / magnification);
                        final int oval_corr = (int)Math.ceil(3 / magnification);
                        for (int j=0; j<n_points; j++) {
                                DisplayCanvas.drawHandle(g, (int)p[0][j], (int)p[1][j], magnification);
                                g.setColor(this.color);
                                //fill small ovals at control points
                                g.fillOval((int)p_l[0][j] -oval_corr, (int)p_l[1][j] -oval_corr, oval_radius, oval_radius);
                                g.fillOval((int)p_r[0][j] -oval_corr, (int)p_r[1][j] -oval_corr, oval_radius, oval_radius);
                                //draw lines between backbone and control points
                                g.drawLine((int)p[0][j], (int)p[1][j], (int)p_l[0][j], (int)p_l[1][j]);
                                g.drawLine((int)p[0][j], (int)p[1][j], (int)p_r[0][j], (int)p_r[1][j]);
                        }
                }

                //set color
                g.setColor(this.color);

                //draw lines between any two consecutive interpolated points
                for (int i=0; i<p_i[0].length-1; i++) {
                        g.drawLine((int)p_i[0][i], (int)p_i[1][i], (int)p_i[0][i+1], (int)p_i[1][i+1]);
                }
                //draw last segment between last and first points, only if closed:
                if (closed) {
                        g.drawLine((int)p_i[0][p_i[0].length-1], (int)p_i[1][p_i[0].length-1], (int)p_i[0][0], (int)p_i[1][0]);
                }

                //Transparency: fix alpha composite back to original.
                if (null != original_composite) {
                        g.setComposite(original_composite);
                }
        }

        /**Helper vars for mouse events. It's safe to have them static since only one Profile will be edited at a time.*/
        static private int index = -1;
        static private int index_l = -1;
        static private int index_r = -1;
        static private boolean is_new_point = false;

        /**Execute the mousePressed MouseEvent on this Profile.*/
        public void mousePressed(MouseEvent me, int x_p, int y_p, double mag) {
                // transform the x_p, y_p to the local coordinates
                if (!this.at.isIdentity()) {
                        final Point2D.Double po = inverseTransformPoint(x_p, y_p);
                        x_p = (int)po.x;
                        y_p = (int)po.y;
                }

                final int tool = ProjectToolbar.getToolId();

                // reset helper vars
                is_new_point = false;
                index = index_r = index_l = -1;

                if (ProjectToolbar.PEN == tool) {

                        //collect vars
                        if (Utils.isControlDown(me) && me.isShiftDown()) {
                                index = findNearestPoint(p, n_points, x_p, y_p);
                        } else {
                                index = findPoint(p, x_p, y_p, mag);
                        }

                        if (-1 != index) {
                                if (Utils.isControlDown(me) && me.isShiftDown()) {
                                        //delete point
                                        removePoint(index);
                                        index = index_r = index_l = -1;
                                        generateInterpolatedPoints(0.05);
                                        repaint(false);
                                        return;
                                } else if (me.isAltDown()) {
                                        resetControlPoints(index);
                                        return;
                                } else if (me.isShiftDown()) {
                                        //preconditions: at least 2 points!
                                        if (n_points < 2) {
                                                return;
                                        }
                                        toggleClosed();
                                        generateInterpolatedPoints(0.05);
                                        repaint(false);
                                        return;
                                } else if (0 == index && n_points > 1 && !closed) {
                                        //close curve, reset left control point of the first point and set it up for dragging
                                        closed = true;
                                        updateInDatabase("closed");
                                        p_l[0][0] = p[0][0];
                                        p_l[1][0] = p[1][0];
                                        index = -1;
                                        index_r = -1;
                                        index_l = 0; //the first one
                                        repaint(false);
                                        return;
                                }
                        }

                        // find if click is on a left control point
                        index_l = findPoint(p_l, x_p, y_p, mag);
                        index_r = -1;
                        // if not, then try on the set of right control points
                        if (-1 == index_l) {
                                index_r = findPoint(p_r, x_p, y_p, mag);
                        }

                        //if no conditions are met, attempt to add point (won't get added if the curve is closed and the click is too far from the interpolated points).
                        if (-1 == index && -1 == index_l && -1 == index_r && !me.isShiftDown() && !me.isAltDown()) {
                                //add a new point and assign its index to the left control point, so it can be dragged right away. This is copying the way Karbon does for drawing Bezier curves, which is the contrary to Adobe's way, but which I find more useful.
                                index_l = addPoint(x_p, y_p, mag, 0.05);
                                if (-1 != index_l) is_new_point = true;
                                else if (1 == n_points) {
                                        //for the very first point, drag the right control point, not the left.
                                        index_r = index_l;
                                        index_l = -1;
                                }
                                repaint(false);
                                return;
                        }
                }
        }

        /**Execute the mouseDragged MouseEvent on this Profile.*/
        public void mouseDragged(MouseEvent me, int x_p, int y_p, int x_d, int y_d, int x_d_old, int y_d_old) {
                // transform to the local coordinates
                if (!this.at.isIdentity()) {
                        final Point2D.Double p = inverseTransformPoint(x_p, y_p);
                        x_p = (int)p.x;
                        y_p = (int)p.y;
                        final Point2D.Double pd = inverseTransformPoint(x_d, y_d);
                        x_d = (int)pd.x;
                        y_d = (int)pd.y;
                        final Point2D.Double pdo = inverseTransformPoint(x_d_old, y_d_old);
                        x_d_old = (int)pdo.x;
                        y_d_old = (int)pdo.y;
                }

                final int tool = ProjectToolbar.getToolId();

                if (ProjectToolbar.PEN == tool) {

                        //if a point in the backbone is found, then:
                        if (-1 != index) {
                                if (!me.isAltDown()) {
                                        //drag point
                                        dragPoint(index, x_d - x_d_old, y_d - y_d_old);
                                } else {
                                        //drag both control points symmetrically
                                        dragControlPoint(index, x_d, y_d, p_l, p_r, true);
                                }
                                generateInterpolatedPoints(0.05);
                                repaint(false);
                                return;
                        }

                        //if a control point is found, then drag it, adjusting the other control point non-symmetrically
                        if (-1 != index_r) {
                                dragControlPoint(index_r, x_d, y_d, p_r, p_l, is_new_point);
                                generateInterpolatedPoints(0.05);
                                repaint(false);
                                return;
                        }
                        if (-1 != index_l) {
                                dragControlPoint(index_l, x_d, y_d, p_l, p_r, is_new_point);
                                generateInterpolatedPoints(0.05);
                                repaint(false);
                                return;
                        }

                        // no points selected. Drag the whole curve on alt down (without affecting linked curves)
                        if (me.isAltDown()) {
                                int dx = x_d - x_d_old;
                                int dy = y_d - y_d_old;
                                this.at.translate(dx, dy);
                                repaint(false);
                                return;
                        }
                }
        }

        /**Execute the mouseReleased MouseEvent on this Profile.*/
        public void mouseReleased(MouseEvent me, int x_p, int y_p, int x_d, int y_d, int x_r, int y_r) {
                int tool = ProjectToolbar.getToolId();
                if (ProjectToolbar.PEN == tool) {
                        //generate interpolated points
                        generateInterpolatedPoints(0.05);
                        repaint(); //needed at least for the removePoint, and also for repainting the DisplayablePanel and the DisplayNavigator // TODO this may be redundant with below
                }

                //update points in database if there was any change
                if (-1 != index || -1 != index_r || -1 != index_l) {
                        updateInDatabase("points");
                        updateInDatabase("transform+dimensions"); //was: dimensions
                        Display.repaint(layer, this); // the DisplayablePanel
                } else if (x_r != x_p || y_r != y_p) {
                        updateInDatabase("transform+dimensions");
                        Display.repaint(layer, this); // the DisplayablePanel
                }
                // reset helper vars
                is_new_point = false;
                index = index_r = index_l = -1;
        }

        protected void calculateBoundingBox() {
                calculateBoundingBox(true);
        }

        /**Calculate the bounding box of the curve in the shape of a Rectangle defined by x,y,width,height. If adjust_position is true, then points are made local to the minimal x,y. */
        protected void calculateBoundingBox(boolean adjust_position) {
                if (0 == n_points) {
                        this.width = this.height = 0.0D;
                        layer.updateBucket(this);
                        return;
                }
                //go over all points and control points and find the max and min
                //      (there's no need to use the interpolated points because the points and control points define the boxes in which the interpolated points are).
                double min_x = Double.MAX_VALUE;
                double min_y = Double.MAX_VALUE;
                double max_x = 0.0D;
                double max_y = 0.0D;

                for (int i=0; i<n_points; i++) {
                        if (p[0][i] < min_x) min_x = p[0][i];
                        if (p_l[0][i] < min_x) min_x = p_l[0][i];
                        if (p_r[0][i] < min_x) min_x = p_r[0][i];
                        if (p[1][i] < min_y) min_y = p[1][i];
                        if (p_l[1][i] < min_y) min_y = p_l[1][i];
                        if (p_r[1][i] < min_y) min_y = p_r[1][i];
                        if (p[0][i] > max_x) max_x = p[0][i];
                        if (p_l[0][i] > max_x) max_x = p_l[0][i];
                        if (p_r[0][i] > max_x) max_x = p_r[0][i];
                        if (p[1][i] > max_y) max_y = p[1][i];
                        if (p_l[1][i] > max_y) max_y = p_l[1][i];
                        if (p_r[1][i] > max_y) max_y = p_r[1][i];
                }

                this.width = max_x - min_x;
                this.height = max_y - min_y;

                if (adjust_position) {
                        // now readjust points to make min_x,min_y be the x,y
                        for (int i=0; i<n_points; i++) {
                                p[0][i] -= min_x;       p[1][i] -= min_y;
                                p_l[0][i] -= min_x;     p_l[1][i] -= min_y;
                                p_r[0][i] -= min_x;     p_r[1][i] -= min_y;
                        }
                        for (int i=0; i<p_i[0].length; i++) {
                                p_i[0][i] -= min_x;     p_i[1][i] -= min_y;
                        }
                        this.at.translate(min_x, min_y); // not using super.translate(...) because a preConcatenation is not needed; here we deal with the data.
                        updateInDatabase("transform");
                }
                layer.updateBucket(this);
                updateInDatabase("dimensions");
        }


        public void repaint() {
                repaint(true);
        }

        /**Repaints in the given ImageCanvas only the area corresponding to the bounding box of this Profile. */
        public void repaint(boolean repaint_navigator) {
                //TODO: this could be further optimized to repaint the bounding box of the last modified segments, i.e. the previous and next set of interpolated points of any given backbone point. This would be trivial if each segment of the Bezier curve was an object.
                Rectangle box = getBoundingBox(null);
                calculateBoundingBox();
                box.add(getBoundingBox(null));
                Display.repaint(layer, this, box, 5, repaint_navigator);
        }

        /**Check if the given point (usually from a MOUSE_PRESSED MouseEvent) is contained within the boundaries of this object. The point is expected as local coordinates. */
        public boolean containsPoint(final int x_p, final int y_p) {
                // as in getPerimeter():
                int n_i = p_i[0].length;
                int[] intx = new int[n_i];
                int[] inty = new int[n_i];
                for (int i=0; i<n_i; i++) {
                        intx[i] = (int)p_i[0][i];
                        inty[i] = (int)p_i[1][i];
                }
                Polygon polygon = new Polygon(intx, inty, n_i);
                return polygon.contains(x_p, y_p);
        }

        /**Release all memory resources taken by this object.*/
        public void destroy() {
                super.destroy();
                p = null;
                p_l = null;
                p_r = null;
                p_i = null;
        }

        /**Make this object ready to be painted.*/
        private void setupForDisplay() {
                // load points
                if (null == p || null == p_l || null == p_r) {
                        //load points from database
                        double[][][] bezarr = project.getLoader().fetchBezierArrays(this.id);
                        if (null == bezarr) {
                                Utils.log("Profile.setupForDisplay: could not load the bezier points from the database for id=" + this.id);
                                this.p_i = new double[0][0];
                                return;
                        }
                        p_l = bezarr[0];
                        p = bezarr[1];
                        p_r = bezarr[2];
                        n_points = p[0].length;
                        // recreate interpolated points
                        generateInterpolatedPoints(0.05); //TODO the 0.05 bezier finess, read the value from the Project perhaps.
                }
        }

        /**Cache this Profile if needed.*/ //Is there much sense in caching Profile objects? Unless you have thousands ... and that CAN be the case!
        public void cache() {
                //TODO
        }

        /**Release memory resources used by this object: namely the arrays of points, which can be reloaded with a call to setupForDisplay()*/
        public void flush() {
                p = null;
                p_l = null;
                p_r = null;
                p_i = null;
                n_points = -1; // flag that points exist (and need to be reloaded)
        }

        /** The perimeter of this profile, in integer precision. */
        public Polygon getPerimeter() {
                if (-1 == n_points) setupForDisplay();
                if (null == p_i) return null; // has been flushed, incorrect access! This is a patch.

                // transform
                double[][] p_i = this.p_i;
                if (!this.at.isIdentity()) p_i = transformPoints(this.p_i);

                int n_i = p_i[0].length;
                int[] intx = new int[n_i];
                int[] inty = new int[n_i];
                for (int i=0; i<n_i; i++) {
                        intx[i] = (int)p_i[0][i];
                        inty[i] = (int)p_i[1][i];
                }
                return new Polygon(intx, inty, n_i);
        }

        /** Writes the data of this object as a Bezier object in the .shapes file represented by the 'data' StringBuffer. The z_scale is added to manually correct for sample squashing under the coverslip. */
        public void toShapesFile(StringBuffer data, String group, String color, double z_scale) {
                if (-1 == n_points) setupForDisplay(); // reload
                // local pointers, since they may be transformed
                double[][] p = this.p;
                double[][] p_r = this.p_r;
                double[][] p_l = this.p_l;
                if (!this.at.isIdentity()) {
                        final Object[] ob = getTransformedData();
                        p = (double[][])ob[0];
                        p_l = (double[][])ob[1];
                        p_r = (double[][])ob[2];
                }
                final double z = layer.getZ();
                final char l = '\n';
                data.append("type=bezier").append(l)
                    .append("name=").append(project.getMeaningfulTitle(this)).append(l)
                    .append("group=").append(group).append(l)
                    .append("color=").append(color).append(l)
                    .append("supergroup=").append("null").append(l)
                    .append("supercolor=").append("null").append(l)
                    .append("in slice=").append(z * z_scale).append(l)   // fake, this is now the absolute z coordinate
                    .append("curve_closed=").append(true).append(l) // must!
                    .append("density field=").append(false).append(l) // must!
                ;
                for (int i=0; i<n_points; i++) {
                        data.append("p x=").append(p[0][i]).append(l)
                            .append("p y=").append(p[1][i]).append(l)
                            .append("p_r x=").append(p_r[0][i]).append(l)
                            .append("p_r y=").append(p_r[1][i]).append(l)
                            .append("p_l x=").append(p_l[0][i]).append(l)
                            .append("p_l y=").append(p_l[1][i]).append(l)
                        ;
                }
        }

        public void exportSVG(StringBuffer data, double z_scale, String indent) {
                String in = indent + "\t";
                if (-1 == n_points) setupForDisplay(); // reload
                if (0 == n_points) return;
                String[] RGB = Utils.getHexRGBColor(color);
                final double[] a = new double[6];
                at.getMatrix(a);
                data.append(indent).append("<path\n")
                    .append(in).append("type=\"profile\"\n")
                    .append(in).append("id=\"").append(id).append("\"\n")
                    .append(in).append("transform=\"matrix(").append(a[0]).append(',')
                                                                .append(a[1]).append(',')
                                                                .append(a[2]).append(',')
                                                                .append(a[3]).append(',')
                                                                .append(a[4]).append(',')
                                                                .append(a[5]).append(")\"\n")
                    .append(in).append("style=\"fill:none;stroke-opacity:").append(alpha).append(";stroke:#").append(RGB[0]).append(RGB[1]).append(RGB[2]).append(";stroke-width:1.0px;\"\n")
                    .append(in).append("d=\"M");//.append(p[0][0]).append(',').append(p[1][0]).append(" C ").append(p_r[0][0]).append(',').append(p_r[1][0]);
                for (int i=0; i<n_points-1; i++) {
                        data.append(' ').append(p[0][i]).append(',').append(p[1][i])
                            .append(" C ").append(p_r[0][i]).append(',').append(p_r[1][i])
                            .append(' ').append(p_l[0][i+1]).append(',').append(p_l[1][i+1])
                        ;
                }
                data.append(' ').append(p[0][n_points-1]).append(',').append(p[1][n_points-1]);
                if (closed) {
                        data.append(" C ").append(p_r[0][n_points-1]).append(',').append(p_r[1][n_points-1])
                            .append(' ').append(p_l[0][0]).append(',').append(p_l[1][0])
                            .append(' ').append(p[0][0]).append(',').append(p[1][0])
                            .append(" z")
                        ;
                }
                data.append("\"\n")
                    .append(in).append("z=\"").append(layer.getZ() * z_scale).append("\"\n")
                    .append(in).append("links=\"")
                ;
                if (null != hs_linked && 0 != hs_linked.size()) {
                        int ii = 0;
                        int len = hs_linked.size();
                        for (Iterator it = hs_linked.iterator(); it.hasNext(); ) {
                                Object ob = it.next();
                                data.append(((DBObject)ob).getId());
                                if (ii != len-1) data.append(',');
                                ii++;
                        }
                }
                data.append("\"\n")
                    .append(indent).append("/>\n")
                ;
        }

        /** Returns a triple array, each containing a [2][n_points] array specifiying the x,y of each left control point, backbone point and right control point respectively.*/
        public double[][][] getBezierArrays() {
                //assumes the profile is a Bezier curve.
                //put points and control points into PGpoint objects, as: LPRLPRLPR... (L = left control point, P = backbone point, R = right control point)
                if (-1 == n_points) setupForDisplay(); // reload
                final double[][][] b = new double[3][][];
                b[0] = p_l;
                b[1] = p;
                b[2] = p_r;
                return b;
        }

        public boolean isDeletable() {
                return 0 == n_points;
        }

        /** Returns true if it's linked to at least one patch in the same Layer. Otherwise returns false. */
        public boolean isLinked() {
                if (null == hs_linked || hs_linked.isEmpty()) return false;
                for (Iterator it = hs_linked.iterator(); it.hasNext(); ) {
                        Displayable d = (Displayable)it.next();
                        if (d instanceof Patch && d.layer.equals(this.layer)) return true;
                }
                return false;
        }

        /** Returns false if the target_layer contains a profile that is directly linked to this profile. */
        public boolean canSendTo(Layer target_layer) {
                if (null == hs_linked || hs_linked.isEmpty()) return false;
                for (Iterator it = hs_linked.iterator(); it.hasNext(); ) {
                        Displayable d = (Displayable)it.next();
                        if (d instanceof Profile && d.layer.equals(target_layer)) return false;
                }
                return true;
        }
        
        protected double[][] getFirstPoint()
        {
                if (0 == n_points) return null;
                return new double[][]{{p_l[0][0],p_l[1][0]},{p[0][0],p[1][0]},{p_r[0][0],p_r[1][0]}};
        }
        
        protected double[][] getLastPoint()
        {
                return new double[][]{{p_l[0][n_points-1],p_l[1][n_points-1]},{p[0][n_points-1],p[1][n_points-1]},{p_r[0][n_points-1],p_r[1][n_points-1]}};
        }

        public boolean hasPoints() {
                return 0 != n_points;
        }

        protected void setPoints(double[][] p_l, double[][] p, double[][] p_r) {
                this.p_l = p_l;
                this.p = p;
                this.p_r = p_r;
                this.n_points = p_l[0].length;
                this.generateInterpolatedPoints(0.05);
        }

        public void setPoints(double[][] p_l, double[][] p, double[][] p_r, boolean update) {
                setPoints(p_l, p, p_r);
                calculateBoundingBox();
                if (update) {
                        updateInDatabase("points");
                        repaint(true);
                }
        }

        protected void addPointsAtBegin(double[][] new_p_l, double[][] new_p, double[][] new_p_r) {
                double[][] tmp_p_l = new double[2][p_l[0].length + new_p_l[0].length];
                double[][] tmp_p = new double[2][p[0].length + new_p[0].length];
                double[][] tmp_p_r = new double[2][p_r[0].length + new_p_r[0].length];
                int i = 0;
                for (; i < new_p_l[0].length; i++) {
                        tmp_p_l[0][i] = new_p_l[0][i];
                        tmp_p_l[1][i] = new_p_l[1][i];
                        tmp_p[0][i] = new_p[0][i];
                        tmp_p[1][i] = new_p[1][i];
                        tmp_p_r[0][i] = new_p_r[0][i];
                        tmp_p_r[1][i] = new_p_r[1][i];
                }
                for (int j = 0; j < n_points; j++, i++) {
                        tmp_p_l[0][i] = p_l[0][j];
                        tmp_p_l[1][i] = p_l[1][j];
                        tmp_p[0][i] = p[0][j];
                        tmp_p[1][i] = p[1][j];
                        tmp_p_r[0][i] = p_r[0][j];
                        tmp_p_r[1][i] = p_r[1][j];
                }
                this.n_points += new_p_l[0].length;

                p_l = tmp_p_l;
                p = tmp_p;
                p_r = tmp_p_r;
                this.generateInterpolatedPoints(0.05);
        }

        protected void addPointsAtEnd(double[][] new_p_l, double[][] new_p, double[][] new_p_r) {
                double[][] tmp_p_l = new double[2][p_l[0].length + new_p_l[0].length];
                double[][] tmp_p = new double[2][p[0].length + new_p[0].length];
                double[][] tmp_p_r = new double[2][p_r[0].length + new_p_r[0].length];
                int i = 0;
                for (; i < n_points;  i++) {
                        tmp_p_l[0][i] = p_l[0][i];
                        tmp_p_l[1][i] = p_l[1][i];
                        tmp_p[0][i] = p[0][i];
                        tmp_p[1][i] = p[1][i];
                        tmp_p_r[0][i] = p_r[0][i];
                        tmp_p_r[1][i] = p_r[1][i];
                }
                
                for (int j = 0; j < new_p_l[0].length; i++,j++) {
                        tmp_p_l[0][i] = new_p_l[0][j];
                        tmp_p_l[1][i] = new_p_l[1][j];
                        tmp_p[0][i] = new_p[0][j];
                        tmp_p[1][i] = new_p[1][j];
                        tmp_p_r[0][i] = new_p_r[0][j];
                        tmp_p_r[1][i] = new_p_r[1][j];
                }
                this.n_points += new_p_l[0].length;

                p_l = tmp_p_l;
                p = tmp_p;
                p_r = tmp_p_r;
                this.generateInterpolatedPoints(0.05);
        }

        public int getNearestPointIndex(double x_p, double y_p) {
                int ret = -1;
                double minDist = Double.POSITIVE_INFINITY;
                for (int i = 0; i < this.n_points; i++) {
                        double dx = this.p[0][i]-x_p;
                        double dy = this.p[1][i]-y_p;
                        double dist = dx*dx+dy*dy;
                        if(dist < minDist)
                        {
                                minDist = dist;
                                ret = i;
                        }
                }
                return ret;
        }

        public void insertBetween(int startIndex, int endIndex, double[][] tmp_p_l, double[][] tmp_p, double[][] tmp_p_r){
                if(endIndex < startIndex)
                {
                        for (int i = 0; i < 2; i++) {
                                for (int j = 0; j < tmp_p[0].length/2; j++) {
                                        double tmppl = tmp_p_l[i][j];
                                        double tmpp = tmp_p[i][j];
                                        double tmppr = tmp_p_r[i][j];
                                        
                                        tmp_p_r[i][j] = tmp_p_l[i][tmp_p_l[0].length -1- j];
                                        tmp_p[i][j] = tmp_p[i][tmp_p[0].length -1- j];
                                        tmp_p_l[i][j] = tmp_p_r[i][tmp_p_r[0].length -1- j];
                                        
                                        tmp_p_r[i][tmp_p_l[0].length -1- j]=tmppl;
                                        tmp_p[i][tmp_p[0].length -1- j]=tmpp;
                                        tmp_p_l[i][tmp_p_r[0].length -1- j]=tmppr;
                                }
                        }

                        int tmp = startIndex;
                        startIndex = endIndex;
                        endIndex = tmp;
                }
                
                
                double[][] beginning_p_l;
                double[][] beginning_p;
                double[][] beginning_p_r;

                double[][] ending_p_l;
                double[][] ending_p;
                double[][] ending_p_r;

                if(endIndex - startIndex < n_points + startIndex - endIndex || closed == false)
                {
                        beginning_p_l = new double [2][startIndex+1];
                        beginning_p = new double [2][startIndex+1];
                        beginning_p_r = new double [2][startIndex+1];

                        ending_p_l = new double [2][n_points- endIndex];
                        ending_p = new double [2][n_points- endIndex];
                        ending_p_r = new double [2][n_points- endIndex];
                        
                        for(int i = 0 ; i <= startIndex ; i++)
                        {
                                for (int j = 0; j < 2; j++) {
                                        beginning_p_l [j][i] = this.p_l[j][i];
                                        beginning_p [j][i] = this.p[j][i];
                                        beginning_p_r [j][i] = this.p_r[j][i];
                                }
                        }
                        for(int i = endIndex ; i < this.n_points ; i++)
                        {
                                for (int j = 0; j < 2; j++) {
                                        ending_p_l [j][i-endIndex] = this.p_l[j][i];
                                        ending_p [j][i-endIndex] = this.p[j][i];
                                        ending_p_r [j][i-endIndex] = this.p_r[j][i];
                                }
                        }
                        System.out.println("1");
                }
                else
                {
                        beginning_p_l = new double [2][endIndex-startIndex + 1];
                        beginning_p = new double [2][ endIndex-startIndex + 1 ];
                        beginning_p_r = new double [2][endIndex-startIndex + 1];

                        ending_p_l = new double [2][0];
                        ending_p = new double [2][0];
                        ending_p_r = new double [2][0];
                        
                        for(int i = startIndex ; i <= endIndex ; i++)
                        {
                                for (int j = 0; j < 2; j++) {
                                        beginning_p_r [j][endIndex - i] = this.p_l[j][i];
                                        beginning_p [j][endIndex - i] = this.p[j][i];
                                        beginning_p_l [j][endIndex - i] = this.p_r[j][i];
                                }
                        }
                        
                        System.out.println("2");

                }
                
                
                
                double[][] new_p_l = new double[2][beginning_p_l[0].length + ending_p_l[0].length + tmp_p_l[0].length];
                double[][] new_p = new double[2][beginning_p[0].length + ending_p[0].length + tmp_p[0].length];
                double[][] new_p_r = new double[2][beginning_p_r[0].length + ending_p_r[0].length + tmp_p_r[0].length];
                
                for (int i = 0; i < beginning_p[0].length; i++) {
                        for (int j = 0; j < 2; j++) {
                                new_p_l[j][i] = beginning_p_l[j][i];
                                new_p[j][i] = beginning_p[j][i];
                                new_p_r[j][i] = beginning_p_r[j][i];
                        }
                }
                for (int i = 0; i < tmp_p[0].length; i++) {
                        for (int j = 0; j < 2; j++) {
                                new_p_l[j][i+beginning_p[0].length] = tmp_p_l[j][i];
                                new_p[j][i+beginning_p[0].length] = tmp_p[j][i];
                                new_p_r[j][i+beginning_p[0].length] = tmp_p_r[j][i];
                        }
                }
                for (int i = 0; i < ending_p[0].length; i++) {
                        for (int j = 0; j < 2; j++) {
                                new_p_l[j][i+beginning_p[0].length+tmp_p[0].length] = ending_p_l[j][i];
                                new_p[j][i+beginning_p[0].length+tmp_p[0].length] = ending_p[j][i];
                                new_p_r[j][i+beginning_p[0].length+tmp_p[0].length] = ending_p_r[j][i];
                        }
                }
                this.n_points = new_p[0].length;
                this.p_l = new_p_l;
                this.p = new_p;
                this.p_r = new_p_r;
                this.calculateBoundingBox();
                this.generateInterpolatedPoints(0.05);
        }
        
        public void printPoints() {
                System.out.println("#####\nw,h: " + width + "," + height);
                for (int i=0; i<n_points; i++) {
                        System.out.println("x,y: " + p[0][i] + " , " + p[1][i]);
                }
                System.out.println("\n");
        }
        

        /** x,y is the cursor position in offscreen coordinates. */ // COPIED from the Pipe
        public void snapTo(int cx, int cy, int x_p, int y_p) { // WARNING: DisplayCanvas is locking at mouseDragged when the cursor is outside the DisplayCanvas Component, so this is useless or even harmful at the moment. 
                if (-1 != index) {
                        // #$#@$%#$%!!! TODO this doesn't work, although it *should*. The index_l and index_r work, and the mouseEntered coordinates are fine too. Plus it messes up the x,y position or something, for then on reload the pipe is streched or displaced (not clear).
                        /*
                        double dx = p_l[0][index] - p[0][index];
                        double dy = p_l[1][index] - p[1][index];
                        p_l[0][index] = cx + dx;
                        p_l[1][index] = cy + dy;
                        dx = p_r[0][index] - p[0][index];
                        dy = p_r[1][index] - p[1][index];
                        p_r[0][index] = cx + dx;
                        p_r[1][index] = cy + dy;
                        p[0][index] = cx;
                        p[1][index] = cy;
                        */
                } else if (-1 != index_l) {
                        p_l[0][index_l] = cx;
                        p_l[1][index_l] = cy;
                } else if (-1 != index_r) {
                        p_r[0][index_r] = cx;
                        p_r[1][index_r] = cy;
                } else {
                        // drag the whole pipe
                        // CONCEPTUALLY WRONG, what happens when not dragging the pipe, on mouseEntered? Disaster!
                        //drag(cx - x_p, cy - y_p);
                }
        }

        public void exportXML(StringBuffer sb_body, String indent, Object any) {
                sb_body.append(indent).append("<t2_profile\n");
                String in = indent + "\t";
                super.exportXML(sb_body, in, any);
                if (-1 == n_points) setupForDisplay(); // reload
                String[] RGB = Utils.getHexRGBColor(color);
                sb_body.append(in).append("style=\"fill:none;stroke-opacity:").append(alpha).append(";stroke:#").append(RGB[0]).append(RGB[1]).append(RGB[2]).append(";stroke-width:1.0px;\"\n");
                if (n_points > 0) {
                        sb_body.append(in).append("d=\"M");
                        for (int i=0; i<n_points-1; i++) {
                                sb_body.append(' ').append(p[0][i]).append(',').append(p[1][i])
                                    .append(" C ").append(p_r[0][i]).append(',').append(p_r[1][i])
                                    .append(' ').append(p_l[0][i+1]).append(',').append(p_l[1][i+1])
                                ;
                        }
                        sb_body.append(' ').append(p[0][n_points-1]).append(',').append(p[1][n_points-1]);
                        if (closed) {
                                sb_body.append(" C ").append(p_r[0][n_points-1]).append(',').append(p_r[1][n_points-1])
                                    .append(' ').append(p_l[0][0]).append(',').append(p_l[1][0])
                                    .append(' ').append(p[0][0]).append(',').append(p[1][0])
                                    .append(" z")
                                ;
                        }
                        sb_body.append("\"\n");
                }
                sb_body.append(indent).append(">\n");
                super.restXML(sb_body, in, any);
                sb_body.append(indent).append("</t2_profile>\n");
        }

        static public void exportDTD(StringBuffer sb_header, HashSet hs, String indent) {
                String type = "t2_profile";
                if (hs.contains(type)) return;
                hs.add(type);
                sb_header.append(indent).append("<!ELEMENT t2_profile (").append(Displayable.commonDTDChildren()).append(")>\n");
                Displayable.exportDTD(type, sb_header, hs, indent);
                sb_header.append(indent).append(TAG_ATTR1).append(type).append(" d").append(TAG_ATTR2)
                ;
        }

        /** Returns the interpolated points as a Perimeter2D. */
        public Perimeter2D getPerimeter2D() {
                if (-1 == n_points) setupForDisplay(); // reload
                if (0 == n_points) return null;
                if (0 == p_i[0].length) generateInterpolatedPoints(0.05);
                double[] x = new double[p_i[0].length];
                double[] y = new double[x.length];
                System.arraycopy(p_i[0], 0, x, 0, x.length);
                System.arraycopy(p_i[1], 0, y, 0, x.length); // breaking symmetry in purpose, same result
                return new Perimeter2D(x, y, layer.getZ(), this.closed);
        }

        public void keyPressed(KeyEvent ke) {
                super.keyPressed(ke);
                if (ke.isConsumed()) return;
                int key_code = ke.getKeyCode();
                Rectangle box = null;
                switch(key_code) {
                case KeyEvent.VK_X: // remove all points
                        if (0 == ke.getModifiers() && (ProjectToolbar.getToolId() == ProjectToolbar.PEN || ProjectToolbar.getToolId() == ProjectToolbar.PENCIL)) {
                                box = getBoundingBox(box);
                                n_points = 0;
                                this.p_i = new double[2][0];
                                calculateBoundingBox(true);
                                ke.consume();
                                if (closed) toggleClosed();
                                updateInDatabase("points");
                        }
                        break;
                }
                if (ke.isConsumed()) {
                        Display.repaint(this.layer, box, 5);
                }
        }

        public void setColor(Color c) {
                // propagate to al linked profiles within the same profile_list
                setColor(c, new HashSet());
        }

        /** Exploits the fact that Profile instances among the directly linked as returned by getLinked(Profile.class) will be members of the same profile_list. */
        private void setColor(Color c, HashSet hs_done) {
                if (hs_done.contains(this)) return;
                hs_done.add(this);
                super.setColor(c);
                HashSet hs = getLinked(Profile.class);
                for (Iterator it = hs.iterator(); it.hasNext(); ) {
                        Profile p = (Profile)it.next();
                        p.setColor(c, hs_done);
                }
        }

        /** Performs a deep copy of this object, unlocked and visible. */
        public Displayable clone(final Project pr, final boolean copy_id) {
                final long nid = copy_id ? this.id : pr.getLoader().getNextId();
                final Profile copy = new Profile(pr, nid, null != title ? title.toString() : null, width, height, alpha, this.visible, new Color(color.getRed(), color.getGreen(), color.getBlue()), closed, this.locked, (AffineTransform)this.at.clone());
                // The data:
                if (-1 == n_points) setupForDisplay(); // load data
                copy.n_points = n_points;
                copy.p = new double[][]{(double[])this.p[0].clone(), (double[])this.p[1].clone()};
                copy.p_l = new double[][]{(double[])this.p_l[0].clone(), (double[])this.p_l[1].clone()};
                copy.p_r = new double[][]{(double[])this.p_r[0].clone(), (double[])this.p_r[1].clone()};
                copy.p_i = new double[][]{(double[])this.p_i[0].clone(), (double[])this.p_i[1].clone()};
                // add
                copy.addToDatabase();

                return copy;
        }

        private Object[] getTransformedData() {
                final double[][] p = transformPoints(this.p);
                final double[][] p_l = transformPoints(this.p_l);
                final double[][] p_r = transformPoints(this.p_r);
                final double[][] p_i = transformPoints(this.p_i);
                return new Object[]{p, p_l, p_r, p_i};
        }

        /** Takes a profile_list, scans for its Profile children, makes sublists of continuous profiles (if they happen to be branched), and then creates triangles for them using weighted vector strings. */
        static public List generateTriangles(final ProjectThing pt, final double scale) {
                if (!pt.getType().equals("profile_list")) {
                        Utils.log2("Profile: ignoring unhandable ProjectThing type.");
                        return null;
                }
                ArrayList al = pt.getChildren(); // should be sorted by Z already
                if (al.size() < 2) {
                        Utils.log("profile_list " + pt + " has less than two profiles: can't render in 3D.");
                        return null;
                }
                // collect all Profile
                final HashSet hs = new HashSet();
                for (Iterator it = al.iterator(); it.hasNext(); ) {
                        Thing child = (Thing)it.next();
                        Object ob = child.getObject();
                        if (ob instanceof Profile) {
                                hs.add(ob);
                        } else {
                                Utils.log2("Render: skipping non Profile class child");
                        }
                }
                // Create sublists of profiles, following the chain of links.
                final Profile[] p = new Profile[hs.size()];
                hs.toArray(p);
                // find if at least one is visible
                boolean hidden = true;
                for (int i=0; i<p.length; i++) {
                        if (p[i].visible) {
                                hidden = false;
                                break;
                        }
                }
                if (hidden) return null;
                // collect starts and ends
                final HashSet hs_bases = new HashSet();
                final HashSet hs_done = new HashSet();
                final List triangles = new ArrayList();
                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.");
                                break;
                        }
                        // crawl list to get a sequence of profiles in increasing or decreasing Z order, but not mixed z trends
                        final ArrayList al_profiles = new ArrayList();
                        //Utils.log2("Calling accumulate for base " + base);
                        al_profiles.add(base);
                        final Profile last = accumulate(hs_done, al_profiles, base, 0);
                        // if the trend was not empty, add it
                        if (last != base) {
                                // 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
                                final Profile[] profiles = new Profile[al_profiles.size()];
                                al_profiles.toArray(profiles);
                                List tri = makeTriangles(profiles, scale);
                                if (null != tri) triangles.addAll(tri);
                        } else {
                                // remove base
                                hs_bases.remove(base);
                        }
                } while (0 != hs_bases.size());

                return triangles;
        }

        /** Recursive; returns the last added profile. */
        static private Profile accumulate(final HashSet hs_done, final ArrayList al, final Profile step, int z_trend) {
                final HashSet 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 (Iterator it = hs_linked.iterator(); it.hasNext(); ) {
                        Object ob = it.next();
                        // 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;
                if (null != next_step) {
                        hs_done.add(next_step);
                        last = accumulate(hs_done, al, next_step, z_trend);
                }
                return last;
        }

        /** Make a mesh as a calibrated list of 3D triangles.*/
        static private List<Point3f> makeTriangles(final Profile[] p, final double scale) {
                try {
                        final VectorString2D[] sv = new VectorString2D[p.length];
                        boolean closed = true; // dummy initialization
                        final Calibration cal = p[0].getLayerSet().getCalibration();
                        for (int i=0; i<p.length; i++) {
                                if (-1 == p[i].n_points) p[i].setupForDisplay();
                                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;
                                }
                                double[][] pi = p[i].transformPoints(p[i].p_i);
                                final double[] x = (double[])pi[0].clone();
                                final double[] y = (double[])pi[1].clone();
                                pi = null;
                                if (1 != scale) {
                                        for (int k=0; k<x.length; k++) {
                                                x[k] *= scale;
                                                y[k] *= scale;
                                        }
                                }
                                sv[i] = new VectorString2D(x, y, p[i].layer.getZ(), p[i].closed);
                                sv[i].calibrate(cal);
                        }
                        return SkinMaker.generateTriangles(sv, -1, -1, closed);
                } catch (Exception e) {
                        IJError.print(e);
                }
                return null;
        }

        protected boolean remove2(boolean check) {
                return project.getProjectTree().remove(check, project.findProjectThing(this), null); // will call remove(check) here
        }

        /** Calibrated for pixel width only (that is, it assumes pixel aspect ratio 1:1), in units as specified at getLayerSet().getCalibration().getUnit() */
        public double computeLength() {
                if (-1 == n_points || 0 == this.p_i[0].length) setupForDisplay();
                if (this.p_i[0].length < 2) return 0;
                final double[][] p_i = transformPoints(this.p_i);
                double len = 0;
                for (int i=1; i<p_i[0].length; i++) {
                        len += Math.sqrt(Math.pow(p_i[0][i] - p_i[0][i-1], 2) + Math.pow(p_i[1][i] - p_i[1][i-1], 2));
                }
                if (closed) {
                        int last = p[0].length -1;
                        len += Math.sqrt(Math.pow(p_i[0][last] - p_i[0][0], 2) + Math.pow(p_i[1][last] - p_i[1][0], 2));
                }
                // to calibrate for pixelWidth and pixelHeight, I'd have to multiply each x,y values above separately
                return len * getLayerSet().getCalibration().pixelWidth;
        }

        /** Calibrated, in units as specified at getLayerSet().getCalibration().getUnit() -- returns zero if this profile is not closed. */
        public double computeArea() {
                if (-1 == n_points) setupForDisplay();
                if (n_points < 2) return 0;
                if (!closed) return 0;
                if (0 == p_i[0].length) generateInterpolatedPoints(0.05);
                Calibration cal = getLayerSet().getCalibration();
                return M.measureArea(new Area(getPerimeter()), getProject().getLoader()) * cal.pixelWidth * cal.pixelHeight;
        }

        /** Measures the calibrated length, the lateral surface as the length times the layer thickness, and the volume (if closed) as the area times the layer thickness. */
        public ResultsTable measure(ResultsTable rt) {
                if (null == rt) rt = Utils.createResultsTable("Profile results", new String[]{"id", "length", "side surface: length x thickness", "volume: area x thickness", "name-id"});
                if (-1 == n_points) setupForDisplay();
                if (n_points < 2) return null;
                if (0 == p_i[0].length) generateInterpolatedPoints(0.05);
                final Calibration cal = getLayerSet().getCalibration();
                // computeLength returns a calibrated length, so only calibrate the layer thickness:
                final double len = computeLength();
                final double surface_flat = len * layer.getThickness() * cal.pixelWidth;
                rt.incrementCounter();
                rt.addLabel("units", cal.getUnit());
                rt.addValue(0, id);
                rt.addValue(1, len);
                rt.addValue(2, surface_flat);
                final double volume = closed ? computeArea() * layer.getThickness() * cal.pixelWidth : 0;
                rt.addValue(3, volume);
                rt.addValue(4, getNameId());
                return rt;
        }

        /** Assumes Z-coord sorted list of profiles, as stored in a "profile_list" ProjectThing type. . */
        static public ResultsTable measure(final Profile[] profiles, ResultsTable rt, final long profile_list_id) {
                Utils.log2("profiles.length" + profiles.length);
                if (null == profiles || 0 == profiles.length) return null;
                if (1 == profiles.length) {
                        // don't measure if there is only one
                        return rt;
                }
                if (null == rt) rt = Utils.createResultsTable("Profile list results", new String[]{"id", "interpolated surface", "surface: sum of length x thickness", "volume", "name-id"});
                Calibration cal = profiles[0].getLayerSet().getCalibration();
                // else, interpolate skin and measure each triangle
                List<Point3f> tri = makeTriangles(profiles, 1.0); // already calibrated
                final int n_tri = tri.size();
                if (0 != n_tri % 3) {
                        Utils.log("Profile.measure error: triangle verts list not a multiple of 3 for profile list id " + profile_list_id);
                        return rt;
                }
                // Surface: calibrated sum of the area of all triangles in the mesh.
                double surface = 0;
                for (int i=2; i<n_tri; i+=3) {
                        surface += M.measureArea(tri.get(i-2), tri.get(i-1), tri.get(i));
                }
                // add capping ends
                double area_first = profiles[0].computeArea();
                double area_last = profiles[profiles.length-1].computeArea();
                if (profiles[0].closed) surface += area_first;
                if (profiles[profiles.length-1].closed) surface += area_last;

                // calibrate surface measurement
                surface *= Math.pow(cal.pixelWidth, 3);

                // Surface flat: sum of the perimeter lengths times the layer thickness
                double surface_flat = 0;
                for (int i=0; i<profiles.length; i++) {
                        if (0 == profiles[i].p_i[0].length) profiles[i].generateInterpolatedPoints(0.05);
                        surface_flat += profiles[i].computeLength() * profiles[i].layer.getThickness() * cal.pixelWidth;
                }

                // Volume: area times layer thickness
                double volume = area_first * profiles[0].layer.getThickness();
                for (int i=1; i<profiles.length-1; i++) {
                        volume += profiles[i].computeArea() * profiles[i].layer.getThickness();
                }
                volume += area_last * profiles[profiles.length-1].layer.getThickness();

                // calibrate volume: the Z is still in pixels
                volume *= cal.pixelWidth;

                rt.incrementCounter();
                rt.addLabel("units", cal.getUnit());
                rt.addValue(0, profile_list_id);
                rt.addValue(1, surface);
                rt.addValue(2, surface_flat);
                rt.addValue(3, volume);
                double nameid = 0;
                try {
                        nameid = Double.parseDouble(profiles[0].project.findProjectThing(profiles[0]).getParent().getTitle());
                } catch (NumberFormatException nfe) {}
                rt.addValue(4, nameid);
                return rt;
        }

        @Override
        final Class getInternalDataPackageClass() {
                return DPProfile.class;
        }

        @Override
        synchronized Object getDataPackage() {
                return new DPProfile(this);
        }

        static private final class DPProfile extends Displayable.DataPackage {
                final double[][] p, p_l, p_r, p_i;
                final boolean closed;

                DPProfile(final Profile profile) {
                        super(profile);
                        // store copies of all arrays
                        this.p = new double[][]{Utils.copy(profile.p[0], profile.n_points), Utils.copy(profile.p[1], profile.n_points)};
                        this.p_r = new double[][]{Utils.copy(profile.p_r[0], profile.n_points), Utils.copy(profile.p_r[1], profile.n_points)};
                        this.p_l = new double[][]{Utils.copy(profile.p_l[0], profile.n_points), Utils.copy(profile.p_l[1], profile.n_points)};
                        this.p_i = new double[][]{Utils.copy(profile.p_i[0], profile.p_i[0].length), Utils.copy(profile.p_i[1], profile.p_i[0].length)};
                        this.closed = profile.closed;
                }
                @Override
                final boolean to2(final Displayable d) {
                        super.to1(d);
                        final Profile profile = (Profile)d;
                        final int len = p[0].length; // == n_points, since it was cropped on copy
                        profile.p = new double[][]{Utils.copy(p[0], len), Utils.copy(p[1], len)};
                        profile.n_points = p[0].length;
                        profile.p_r = new double[][]{Utils.copy(p_r[0], len), Utils.copy(p_r[1], len)};
                        profile.p_l = new double[][]{Utils.copy(p_l[0], len), Utils.copy(p_l[1], len)};
                        profile.p_i = new double[][]{Utils.copy(p_i[0], p_i[0].length), Utils.copy(p_i[1], p_i[1].length)};
                        profile.closed = closed;
                        return true;
                }
        }
}