/*
* LumenDims.java
*
* Created on December 20, 2000, 6:22 AM
*/
package pharynx;
import java.util.*;
/**
* An object that gives the dimensions of the C elegans pharyngeal lumen.
*
* @author leon@eatworms.swmed.edu
* @version 0.1
*/
public class LumenDims {
private double[] diameter;
private double[] isthmusDiameter;
private double[] corpusDiameter;
/*
private ArrayList motion;
private List isthmusMotion;
private List corpusMotion;
*/
private int isthmusP = ISTHMUS_P;
private int isthmusA = ISTHMUS_A;
private int corpusP = CORPUS_P;
private int corpusA = CORPUS_A;
/** Creates new LumenDims object */
public LumenDims() {
init(0);
}
/** Creates new LumenDims object
* @param option Currently ignored.
*/
public LumenDims(int option) {
init(option);
}
/*
* All the diameter access methods make a clone of the array so that user
* can't screw up the original. The motions are all unmodifiable lists, so
* they can be returned directly.
*/
/**
* Get diameter of the pharyngeal lumen
*
* @return an array of lumen diameters from posterior to anterior
*/
public double[] diameter() {
double[] d = new double[diameter.length];
System.arraycopy(diameter, 0, d, 0, d.length);
return d;
}
/**
* Get diameter of the isthmus lumen
*
* @return an array of lumen diameters from posterior to anterior
*/
public double[] isthmusDiameter() {
double[] d = new double[isthmusDiameter.length];
System.arraycopy(isthmusDiameter, 0, d, 0, d.length);
return d;
}
/**
* Get diameter of the corpus lumen
*
* @return an array of lumen diameters from posterior to anterior
*/
public double[] corpusDiameter() {
double[] d = new double[corpusDiameter.length];
System.arraycopy(corpusDiameter, 0, d, 0, d.length);
return d;
}
/**
* Get motions of the pharyngeal lumen
*
* @return a List of Lists of MotionPoints. Each element of the top level
* list corresponds to one location along the anterior/posterior
* axis of the pharynx. Each List of MotionPoints tells how that
* particular section of lumen moves. The MotionPoints are ordered
* by t.
*/
// public List motion() { return new ArrayList(motion); }
/**
* Get motions of the isthmus lumen
*
* @return a List of Lists of MotionPoints. Each element of the top level
* list corresponds to one location along the anterior/posterior
* axis of the pharynx. Each List of MotionPoints tells how that
* particular section of lumen moves. The MotionPoints are ordered
* by t.
*/
// public List isthmusMotion() { return new ArrayList(isthmusMotion); }
/**
* Get motions of the corpus lumen
*
* @return a List of Lists of MotionPoints. Each element of the top level
* list corresponds to one location along the anterior/posterior
* axis of the pharynx. Each List of MotionPoints tells how that
* particular section of lumen moves. The MotionPoints are ordered
* by t.
*/
// public List corpusMotion() { return new ArrayList(corpusMotion); }
/**
* Posterior boundary of the isthmus
*
* The isthmus extends from subscripts isthmusP (inclusive) to isthmusA
* (exclusive).
*/
public int isthmusP() { return(isthmusP); }
/**
* Anterior boundary of the isthmus
*
* The isthmus extends from subscripts isthmusP (inclusive) to isthmusA
* (exclusive).
*/
public int isthmusA() { return(isthmusA); }
/**
* Posterior boundary of the corpus
*
* The corpus extends from subscripts corpusP (inclusive) to corpusA
* (exclusive).
*/
public int corpusP() { return(corpusP); }
/**
* Anterior boundary of the corpus
*
* The corpus extends from subscripts corpusP (inclusive) to corpusA
* (exclusive).
*/
public int corpusA() { return(corpusA); }
public int length() { return LENGTH; }
public int width() { return WIDTH; }
// Internal methods
private void init(int option) {
diameter = new double[DIAMETER.length];
isthmusDiameter = new double[ISTHMUS_A - ISTHMUS_P];
corpusDiameter = new double[CORPUS_A - CORPUS_P];
initDiameter();
/*
motion = new ArrayList(DIAMETER.length);
initIsthmusMotion();
initCorpusMotion();
motion.trimToSize();
corpusMotion = motion.subList(CORPUS_P, CORPUS_A);
isthmusMotion = motion.subList(ISTHMUS_P, ISTHMUS_A);
*/
}
// copy DIAMETER to instance diameter
private void initDiameter() {
System.arraycopy(DIAMETER, 0, diameter, 0, diameter.length);
System.arraycopy(diameter, ISTHMUS_P,
isthmusDiameter, 0,
isthmusDiameter.length);
System.arraycopy(diameter, CORPUS_P,
corpusDiameter, 0,
corpusDiameter.length);
}
// copy CORPUS_MOTION to all of corpusMotion
/*
private void initCorpusMotion() {
MotionList cm = new MotionList(CORPUS_MOTION.length);
for(int i = 0; i < CORPUS_MOTION.length; i++) {
cm.add(i,
new MotionPoint(CORPUS_MOTION[i][0], CORPUS_MOTION[i][1]));
}
motion.addAll(CORPUS_P, Collections.nCopies(CORPUS_A - CORPUS_P, cm));
}
// interpolate between ISTHMUS_P_MOTION and ISTHMUS_A_MOTION
private void initIsthmusMotion() {
MotionList imc = new MotionList(ISTHMUS_P_MOTION.length);
MotionList imi = new MotionList(ISTHMUS_P_MOTION.length);
for(int i = 0; i < ISTHMUS_P_MOTION.length; i++) {
imc.add(i, new MotionPoint(
ISTHMUS_P_MOTION[i][0], ISTHMUS_P_MOTION[i][1]
));
imi.add(i, new MotionPoint(
(ISTHMUS_A_MOTION[i][0] - ISTHMUS_P_MOTION[i][0]) /
(ISTHMUS_A - ISTHMUS_P - 1),
(ISTHMUS_A_MOTION[i][1] - ISTHMUS_P_MOTION[i][1]) /
(ISTHMUS_A - ISTHMUS_P - 1)
));
}
for(int j = ISTHMUS_P; j < ISTHMUS_A; j++) {
MotionList imcc = new MotionList(imc.size());
for(int i = 0; i < imc.size(); i++) {
imcc.add(i, new MotionPoint(
imc.getmp(i).t() + (j - ISTHMUS_P) * imi.getmp(i).t(),
imc.getmp(i).r() + (j - ISTHMUS_P) * imi.getmp(i).r()
));
}
motion.add(j, imcc);
}
}
*/
// Isthmus is subscripts [0, 249)
private static final int ISTHMUS_P = 0;
private static final int ISTHMUS_A = 249;
// Corpus is subscripts [249, 862)
private static final int CORPUS_P = 249;
private static final int CORPUS_A = 862;
private static final int LENGTH = 862;
private static final int WIDTH = 39;
// The motions of each part of the pharynx are given as a series of (t, r)
// pairs. t is in milliseconds. r varies from 0 = closed lumen, to
// 1 = fully open.
/*
private static final double[][] CORPUS_MOTION = {
{0, 0},
{167, 1},
{172, 0},
{315, 0}
};
private static final double[][] ISTHMUS_P_MOTION = {
{0, 0},
{100, 0},
{300, 1},
{305, 0},
{315, 0}
};
private static final double[][] ISTHMUS_A_MOTION = {
{0, 0},
{67, 0},
{267, 1},
{272, 0},
{315, 0}
};
*/
/*
* Diameter of the pharyngeal lumen. Units are arbitrary, but are the same
* as the subscripts.
*/
private static final double[] DIAMETER = {
1,
1,
1,
1,
1,
1,
1,
1,
2,
2,
2,
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};
}