JSci.instruments.PTCroquetteCross Maven / Gradle / Ivy

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JSci is a set of open source Java packages. The aim is to encapsulate scientific methods/principles in the most natural way possible. As such they should greatly aid the development of scientific based software. It offers: abstract math interfaces, linear algebra (support for various matrix and vector types), statistics (including probability distributions), wavelets, newtonian mechanics, chart/graph components (AWT and Swing), MathML DOM implementation, ... Note: some packages, like javax.comm, for the astro and instruments package aren't listed as dependencies (not available).

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package JSci.instruments;

import JSci.swing.*;

import java.awt.*;
import java.awt.event.*;
import java.awt.geom.*;
import javax.swing.*;
import javax.swing.text.*;
import javax.swing.event.*;
import java.util.*;
import java.text.*;
import java.awt.image.*;

/** Data about a cross that can be put on an image, follow the
 * center, find the height
*/
public class PTCroquetteCross extends Polygon implements Control {

    private int crossHW=3;
    private int crossL=32;
    private Point2D position = new Point2D.Double();
    private Point intPosition = new Point();
    private double z = 0.0;
    private boolean dragging = true;
    private Rectangle bbox = null;
    private Color color;

    /** 
     * Crates a new cross
     * @param l length of the arm of the cross
     * @param hw half width of the arms of the cross
     * @param p initial center of the cross
     */
    public PTCroquetteCross(int l, int hw, Point p, Color col) {
	super(new int[] {-hw,hw,hw,l,l,hw,hw,-hw,-hw,-l,-l,-hw},
	      new int[] {-l,-l,-hw,-hw,hw,hw,l,l,hw,hw,-hw,-hw},
	      12
	      );
	crossHW=hw;
	crossL=l;
	intPosition.setLocation(p);
	translate(intPosition.x,intPosition.y);
	position.setLocation(p);
	color=col;
	z = 0.0;
	dragging = false;
	calibrating=false;
    }





    private void FFT(double []x,double []y,int d)
    {
	int n,m,l,le,le1,i,j,ip,nv2,nm1,k;
	double ur,ui,wr,wi,tr,ti,sr,si;
	
	n=x.length;
	m=2;
	switch (n) {
	case 4:m=2;break;
	case 8:m=3;break;
	case 16:m=4;break;
	case 32:m=5;break;
	case 64:m=6;break;
	case 128:m=7;break;
	case 256:m=8;break;
	case 512:m=9;break;
	case 1024:m=10;break;
	case 2048:m=11;break;
	}
	le1=n;
	for (l=1;l<=m;l++)
	    {
		le=le1;
		le1=le/2;
		ur=1.0;ui=0.0;
		wr=Math.cos(Math.PI/le1);wi=d*Math.sin(Math.PI/le1);
		for (j=0;j=0) return (int)c; else return (int)(256+c); }

    private Point2D findJNIXY(Image f,int x0,int y0,int l,int w) {
	double t,tx,ty,frp,fip,frm,fim,tr,ti;
	double h[],v[];
	int j,k,mx,my;
	
	h=new double[2*l];
	v=new double[2*l];
	
	for (j=0;j<2*l;j++) h[j]=v[j]=0.0;
	for (k=-w;ktx) { tx=h[j]; mx=j; }
	    if (v[j]>ty) { ty=v[j]; my=j; }
	}
	
	if (mx>=l) mx-=2*l;
	if (my>=l) my-=2*l;
	return new Point2D.Double(mx/2.0+x0,my/2.0+y0);
	
    }


    private double findJNIZ(Image f,int x0,int y0,int l,int w,int n,double []templ) {
	int j,k;
	double msd[],s[],mv,c1,c2;
	int mp;
	s=new double[l];
	for (j=0;j=zNum) return;
	addJNIToTemplate(f,
			 intPosition.x,intPosition.y,
			 crossL,crossHW,
			 calibration,zLevel);
	zLevel=-1;
	notify();
    }

    
    /** Call this when the microscope objective position is right
     * for the calibration. This method returns immediately; to wait for the
     * processing to be done, call calibrationWait()
     * @param zLevel position in the calibration image. Evaluate 
     *    zNum = how many levels are in the calibration image? 
     *    minZ, maxZ = the min and max levels (in micron)
     *    z = where is now the objective? 
     *    So zLevel = (z-minZ)*zNum/(maxZ/minZ)
     * 
     */
    synchronized public void calibrationRequest(int zLevel) {
	this.zLevel = zLevel;
    }


    /** wait that the calibration, requested by calibrationRequest(), has been 
     * completed.
     */
    synchronized public void calibrationWait() {
	while (zLevel>=0) {
	    try { wait(); } catch (InterruptedException e) {}
	}
    }


    /** call this when the calibration has been done
     */
    public void calibrationEnd() {
	double s;
	for (int j=0;j