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CometAnalyzer.java
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CometAnalyzer.java
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/**
* CometAnalyzer.java
* Created in 2012 by Benjamin Gyori
* National University of Singapore
* e-mail: ben.gyori@gmail.com
*
* When you use this plugin for your work, please cite
* Gyori BM, Venkatachalam G, et al. OpenComet: An automated tool for
* comet assay image analysis
*
* CometAnalyzer.java is the main internal class for comet analysis.
* cometAnalyzerRun takes an image as input. It analyzes the image
* and extracts comets. The comet head and tail are segmented and
* measurements are calculated. The resulting Comet objects are returned.
*
* This plugin is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License version 3
* as published by the Free Software Foundation.
*
* This work 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 plugin; if not, write to the Free Software
* Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
*/
import ij.IJ;
import ij.ImagePlus;
import ij.gui.*;
import ij.plugin.filter.*;
import ij.process.*;
import ij.measure.Measurements;
import java.awt.*;
import java.util.Arrays;
import java.util.Vector;
public class CometAnalyzer {
public static int COMETFIND_BGCORRECT = 1;
public static int HEADFIND_AUTO = 2;
public static int HEADFIND_PROFILE = 4;
public static int HEADFIND_BRIGHTEST = 8;
private int activeChannel;
public Comet[] cometAnalyzerRun(ImagePlus img_orig, int cometOptions) {
// ----- Setting up given image
ImageProcessor ip = img_orig.getProcessor();
// Type of original image
int imgOriginalType = img_orig.getType();
// Make a grayscale template from the imate
ByteProcessor ip_gs_template = getGrayscaleCopy(ip,imgOriginalType);
// Make two copies of the grayscale image
ByteProcessor ip_gs = getGrayscaleCopy(ip_gs_template,ImagePlus.GRAY8);
ByteProcessor ip_gs2 = getGrayscaleCopy(ip_gs_template,ImagePlus.GRAY8);
//-----------------------------
ImagePlus img_gs = new ImagePlus("tmpimg",ip_gs);
//----- Global background correction-----
if((cometOptions & COMETFIND_BGCORRECT)!=0){
RankFilters rf = new RankFilters();
rf.rank(ip_gs, 10.0, RankFilters.MEDIAN);
BackgroundSubtracter bSub = new BackgroundSubtracter();
double radiusRollingBall = Math.min(ip_gs.getHeight(),ip_gs.getWidth())*0.3;
bSub.rollingBallBackground(ip_gs, radiusRollingBall, false,
false, false, false, true);
}
//----------------------------------------
// ----- First round of Comet finding ------------
Vector<Comet> Comets = new Vector<Comet>();
// Threshold finding
ip_gs.setAutoThreshold("Huang", true, ImageProcessor.BLACK_AND_WHITE_LUT);
// Binarization
double threshValue = ip_gs.getMinThreshold();
setThreshold(ip_gs, (int)threshValue);
// Morphology
open_ntimes(ip_gs,3,0);
// Setup particle analyzer
int paopts = ParticleAnalyzer.SHOW_NONE |
ParticleAnalyzer.EXCLUDE_EDGE_PARTICLES |
ParticleAnalyzer.INCLUDE_HOLES;
CometParticleAnalyzer pa =
new CometParticleAnalyzer(paopts,0,null,400,Double.POSITIVE_INFINITY,0,1);
// Run particle finding
pa.analyze(img_gs,ip_gs);
// Get ROIs
Roi[] cometRois = pa.getCometRois();
IJ.log("Number of ROIs found: "+cometRois.length);
// Add ROIs as comets
for(int i=0;i<cometRois.length;i++){
Comets.add(new Comet(cometRois[i]));
}
// Calculate comet parameters
for(int i=0; i<Comets.size(); i++){
setCometParams(Comets.get(i),ip_gs2);
}
for(int i=0;i<Comets.size();i++){
Comet comet = Comets.get(i);
IJ.log(comet.convexity+","+comet.centerlineDiff);
}
// Set validity status of each comet based on parameters
int validCount = setValidity(Comets,ip_gs2);
// If there are no valid comets, stop
if(validCount==0){
IJ.log("No valid comets found.");
return null;
}
//---Find more comets-----------------
/*for(int t = (int)threshValue;t<255;t+=10){
IJ.log("Thresh value:"+(int)threshValue+ " t: "+t);
ImageProcessor ipTmp = getGrayscaleCopy(ip,imgOriginalType);
ImagePlus imgTmp = new ImagePlus("imgTmp",ipTmp);
if((cometOptions & COMETFIND_BGCORRECT)!=0){
RankFilters rf = new RankFilters();
rf.rank(ipTmp, 10.0, RankFilters.MEDIAN);
BackgroundSubtracter bSub = new BackgroundSubtracter();
double radiusRollingBall = Math.min(ipTmp.getHeight(),ipTmp.getWidth())*0.3;
bSub.rollingBallBackground(ipTmp, radiusRollingBall, false,
false, false, false, true);
}
setThreshold(ipTmp,t);
ipTmp.invertLut();
open_ntimes(ipTmp, 3, 1);
imgTmp.show();
int paTmpOpts = ParticleAnalyzer.SHOW_NONE | ParticleAnalyzer.EXCLUDE_EDGE_PARTICLES | ParticleAnalyzer.INCLUDE_HOLES;
CometParticleAnalyzer paTmp = new CometParticleAnalyzer(paTmpOpts,0,null,200,Double.POSITIVE_INFINITY,0,1);
paTmp.analyze(imgTmp,ipTmp);
Roi[] cometRoisTmp = paTmp.getCometRois();
IJ.log("Number of ROIs found: "+cometRoisTmp.length);
Vector<Roi> addRois = new Vector<Roi>();
Vector<Integer> addRoisIdx = new Vector<Integer>();
Vector<Comet> removeComets = new Vector<Comet>();
for(int j=0;j<Comets.size();j++){
Comet comet = Comets.get(j);
if(comet.status==Comet.INVALID){
addRoisIdx.clear();
for(int i=0;i<cometRoisTmp.length;i++){
Rectangle br = cometRoisTmp[i].getBounds();
int xc = br.x + br.width/2;
int yc = br.y + br.height/2;
if(comet.cometRoi.contains(xc,yc)){
addRoisIdx.add(i);
}
}
if(addRoisIdx.size()>=2){
removeComets.add(comet);
for(int k=0;k<addRoisIdx.size();k++){
addRois.add(cometRoisTmp[addRoisIdx.get(k)]);
}
}
}
}
for(int i=0;i<removeComets.size();i++){
Comets.remove(removeComets.get(i));
}
for(int i=0;i<addRois.size();i++){
Comet newComet = new Comet(addRois.get(i));
setCometParams(newComet,ip_gs2);
newComet.status = Comet.VALID;
Comets.add(newComet);
}
setValidity(Comets,ip_gs2);
}*/
//------------------------------------
// --- Area and height statistics
double meanArea = 0, stdArea = 0;
double meanHeight = 0, stdHeight = 0;
for(int i=0; i<Comets.size(); i++){
Comet comet = Comets.get(i);
if(comet.status == Comet.VALID){
meanHeight += comet.height;
meanArea += comet.area;
}
}
meanArea /= validCount;
meanHeight /= validCount;
for(int i=0; i<Comets.size(); i++){
Comet comet = Comets.get(i);
if(comet.status == Comet.VALID){
stdArea += Math.pow(comet.area - meanArea,2) / validCount;
stdHeight += Math.pow(comet.height - meanHeight,2) / validCount;
}
}
stdArea = Math.sqrt(stdArea);
stdHeight = Math.sqrt(stdHeight);
// ---------------------------
// Set outlier comets based on statistics
for(int i=0; i<Comets.size(); i++){
Comet comet = Comets.get(i);
if(comet.status == Comet.VALID){
IJ.log("Mean height: " + meanHeight + ", std: " + stdHeight +
"this height: " + comet.height);
/*if(comet.height > meanHeight + 2*stdHeight){
comet.status = Comet.INVALID;
IJ.log(i+" too high invalid");
}
if(comet.height < meanHeight - 2*stdHeight){
comet.status = Comet.INVALID;
IJ.log(i+" height too small invalid");
}*/
if(Math.abs(comet.area - meanArea) > 2*stdArea){
if(comet.status == Comet.VALID)
comet.status = Comet.OUTLIER;
IJ.log(i + " Suspected outlier based on area");
}
}
}
// -----------------
// ----- Loop over comets and analyze one-by-one ----------
int idxValid = 0;
for(int i=0; i<Comets.size(); i++){
Comet comet = Comets.get(i);
// Skip invalid cometss
if (comet.status == Comet.INVALID) continue;
// Assign an ID to each not-invalid comet
comet.id = idxValid + 1;
IJ.log("-----------------");
IJ.log("ID: "+ comet.id);
IJ.log(comet.cometRoi.getType()+" type");
comet.oldRoi = (Roi)comet.cometRoi.clone();
// Make polygon ROI
comet.cometRoi = new PolygonRoi(comet.cometRoi.getConvexHull(),
Roi.POLYGON);
// Calculate parameters of polygon
setCometParams(comet, ip_gs2);
// Find head
setupHead(ip_gs2,comet,cometOptions);
// Background correction
correctBackground(ip_gs2, comet);
// -----------------------
// --- Measure comets in grayscale image
// Calculate comet parameters again
setCometParams(comet, ip_gs2);
// Comet properties
comet.cometArea = comet.area;
comet.cometIntensity = comet.mean;
comet.cometLength = comet.width;
comet.cometDNA = comet.area*comet.mean;
// Head properties
ip_gs2.setRoi(comet.headRoi);
ImageStatistics headStats = ImageStatistics.getStatistics(ip_gs2, ij.measure.Measurements.ALL_STATS, null);
comet.headArea = headStats.area;
comet.headIntensity = headStats.mean;
comet.headLength = headStats.roiWidth;
comet.headDNA = comet.headArea*comet.headIntensity;
comet.headDNAPercent = ((100*comet.headDNA)/comet.cometDNA);
comet.headCentroid = getXIntensityCentroid(ip_gs2);
// Tail properties
comet.tailArea = comet.cometArea - comet.headArea;
comet.tailLength = Math.max(comet.cometLength - comet.headLength,0);
comet.tailDNA = comet.cometDNA - comet.headDNA;
comet.tailIntensity =
(comet.tailArea > 0) ? (comet.tailDNA / comet.tailArea) : 0;
comet.tailDNApercent =
comet.tailDNA / comet.cometDNA; // Multiply by 100 later
comet.tailMoment = comet.tailLength * comet.tailDNApercent;
Roi roiTail =
(new ShapeRoi(comet.cometRoi)).not(new ShapeRoi(comet.headRoi));
Rectangle tailBoundRect = roiTail.getBounds();
if(tailBoundRect.width * tailBoundRect.height ==0){
comet.tailCentroid = comet.headCentroid;
}
else {
ip_gs2.setRoi(roiTail);
comet.tailCentroid = getXIntensityCentroid(ip_gs2);
}
comet.tailOliveMoment = comet.tailDNApercent *
Math.abs(comet.tailCentroid - comet.headCentroid);
comet.tailDNApercent *= 100;
//-------------
idxValid++;
}
// Close original image
img_orig.changes = false;
img_orig.close();
// Return comets
return (Comet[])Comets.toArray(new Comet[Comets.size()]);
}
private void correctBackground(ImageProcessor ip, Comet comet){
int bgHeight = (int)Math.max(comet.height/5.0, 10);
Roi bgRoi;
if ((comet.y - bgHeight) >= 0) {
bgRoi = new Roi(comet.x, comet.y - bgHeight, comet.width, bgHeight);
}
else {
bgRoi = new Roi(comet.x, comet.y + comet.height, comet.width, bgHeight);
}
double[] bgAvgSmooth = getSmoothColumnAvg(ip, bgRoi, bgRoi.getBounds());
subtractBackground(ip, comet.cometRoi, bgAvgSmooth);
comet.bgProfile = getColumnAvg(ip, bgRoi, bgRoi.getBounds());
comet.cometProfile = getColumnAvg(ip, comet.cometRoi, new Rectangle(comet.x,comet.y,comet.width,comet.height));
comet.headProfile = getColumnAvg(ip, comet.headRoi, new Rectangle(comet.x,comet.y,comet.width,comet.height));
comet.tailProfile = new double[comet.width];
double cometAvgMax = 0;
for(int k = 0; k < comet.width; k++){
comet.tailProfile[k] = comet.cometProfile[k]-comet.headProfile[k];
if (comet.cometProfile[k]>cometAvgMax){
cometAvgMax = comet.cometProfile[k];
}
}
comet.profileMax = cometAvgMax;
}
private void setupHead(ImageProcessor ip,Comet comet,int cometOptions){
// --- Crop the grayscale comet from the original image
// Make a grayscale copy of the original image
ByteProcessor ipComet = (ByteProcessor)ip.duplicate();
// TODO: change this
//int img_orig_type = 4;
// Grayscale
/*if(img_orig_type == 0){
ipComet = (ByteProcessor)ip.duplicate();
}
// RGB
else if(img_orig_type == 4){
ipComet = getCometChannel(ip);
}*/
// Set the comet as ROI
ipComet.setRoi(comet.cometRoi);
// Crop the comet from the image
ipComet = (ByteProcessor)(ipComet.crop());
// -------------------------------------------
// ---- Head finding --------------------------------
ShapeRoi roiHead = null, roi1, roi2;
int headX, headY, headCenterY;
Roi roiHeadCircle;
Rectangle headBoundRect;
boolean headValid = true;
// --- First stage: find brightest part of comet
// Get statistics from the comet
IJ.log(cometOptions + "");
if ((cometOptions & HEADFIND_AUTO)!=0 || (cometOptions & HEADFIND_BRIGHTEST)!=0){
// Find the threshold at top 5% of histogram intensities
int threshbin = getLocalThresh(comet.histogram, 255, 0.95);
IJ.log("Local thresh for " + comet.id + " is " + threshbin);
// Apply threshold (make binary)
setThreshold(ipComet, threshbin);
// Find borders of the brightest area
Rectangle brightestBoundRect = getBinaryBoundRect(ipComet);
IJ.log(brightestBoundRect + "");
if((comet.circularity < 0.9) && (brightestBoundRect.width > brightestBoundRect.height*2)){
IJ.log(comet.id + " head is too long invalid");
headValid = false;
}
//else {
// Get statistics of the brightest region of comet
ImageStatistics brightestStats = ImageStatistics.getStatistics(ipComet,
ij.measure.Measurements.ALL_STATS, null);
// Take center of mass of the brightest region
int xc = (int)brightestStats.xCenterOfMass;
IJ.log("Center of mass x: " + xc);
ip.setRoi(comet.cometRoi);
int headRadius = getHeadHeight(ip, xc)/2;
int headGap = xc - headRadius;
if(headGap > 0){
IJ.log(comet.id + " head is at wrong place invalid");
headValid = false;
}
headX = comet.x;
headCenterY = getFrontCentroid(ip);
headY = (int)(headCenterY - headRadius);
roiHeadCircle = new OvalRoi(headX, headY, 2*headRadius, 2*headRadius );
roi1 = new ShapeRoi(comet.cometRoi);
roi2 = new ShapeRoi(roiHeadCircle);
roiHead = roi2.and(roi1);
// If the comet is elongated, the head should be close to the left hand side
/*if(comet.hratio < 0.9){
if((headBoundRect.x - comet.x) > (double)comet.width*0.1){
IJ.log(comet.id+" head is at wrong place invalid");
headValid = false;
}
}*/
headBoundRect = roiHead.getBounds();
if(headBoundRect.width*headBoundRect.height==0) {
IJ.log(comet.id + " head area zero invalid");
headValid = false;
}
//}
}
// ----------------------------------------------
// --- Second stage: find head based on intensity profile
if (((cometOptions & HEADFIND_AUTO)!=0 && headValid==false)
|| (cometOptions & HEADFIND_PROFILE)!=0){
int headEdge = getHeadEdge(ip, comet);
ip.setRoi(comet.cometRoi);
int headRadius = headEdge / 2;
headX = comet.x;
headCenterY = getFrontCentroid(ip);
headY = (int)(headCenterY - headRadius);
roiHeadCircle = new OvalRoi(headX, headY, 2*headRadius, 2*headRadius);
roi1 = new ShapeRoi(comet.cometRoi);
roi2 = new ShapeRoi(roiHeadCircle);
roiHead = roi2.and(roi1);
}
comet.headRoi = (Roi)roiHead.clone();
// ----------------------------------------------
}
private void setCometParams(Comet comet, ImageProcessor ip){
ip.setRoi(comet.cometRoi);
ImageStatistics stats = ImageStatistics.getStatistics(ip, ij.measure.Measurements.ALL_STATS, null);
// Position
comet.x = (int)stats.roiX;
comet.y = (int)stats.roiY;
comet.width = (int)stats.roiWidth;
comet.height = (int)stats.roiHeight;
// Internal parameters
comet.histogram = stats.histogram;
comet.area = stats.area;
comet.mean = stats.mean;
comet.symmetry = ySymmetry(ip);;
comet.perimeter = comet.cometRoi.getLength();
comet.circularity = 4.0*Math.PI*comet.area / (comet.perimeter*comet.perimeter);;
comet.hratio = comet.height / comet.width;
comet.headFrontCenterY = getFrontCentroid(ip);
comet.headRoiCenterY = comet.y+comet.height/2;
comet.centerlineDiff = (double)Math.abs(comet.headFrontCenterY-comet.headRoiCenterY)/(double)comet.height;
PolygonRoi roiConvexHull = new PolygonRoi(comet.cometRoi.getConvexHull(),Roi.POLYGON);
ip.setRoi(roiConvexHull);
comet.areaConvexHull = ImageStatistics.getStatistics(ip, ij.measure.Measurements.AREA, null).area;
comet.convexity = (comet.area / comet.areaConvexHull);
}
private Rectangle getBinaryBoundRect(ImageProcessor ip){
int minX = -1, minY = -1;
int maxX=0, maxY=0;
for(int x=0;x<ip.getWidth();x++){
for(int y=0;y<ip.getHeight();y++){
if(ip.getPixel(x,y) > 0){
if(minX < 0){
minX = x;
}
if(minY < 0){
minY = y;
}
maxX = x;
if(y > maxY){
maxY = y;
}
}
}
}
IJ.log(minX+","+maxX+","+minY+","+maxY);
return new Rectangle(minX,minY,maxX-minX,maxY-minY);
}
private void subtractBackground(ImageProcessor ip, Roi r, double[] bgAvg){
Rectangle boundRect = r.getBounds();
ip.setRoi(r);
ImageProcessor maskp = ip.getMask();
int j = 0;
for(int x = 0; x < boundRect.width; x++){
for(int y = 0; y < boundRect.height; y++){
if(maskp.getPixel(x, y)>0){
int pixVal = ((int)(ip.getPixel(x + boundRect.x,y + boundRect.y) - bgAvg[j]));
pixVal = (pixVal < 0) ? 0 : pixVal;
ip.putPixel(x + boundRect.x, y + boundRect.y, pixVal);
}
}
j++;
}
}
private double[] getColumnAvg(ImageProcessor ip, Roi roi, Rectangle boundRect){
double[] colAvg = new double[boundRect.width];
ip.resetRoi();
ip.setRoi(roi);
ImageProcessor maskp = ip.getMask();
IJ.log(ip.getMask()==null ? "NULL MASK" : "NOT NULL MASK");
boolean hasMask = (maskp != null);
if(hasMask){
IJ.log("Mask: "+ maskp.getWidth()+", "+ maskp.getHeight());
}
Rectangle roiBoundRect = roi.getBounds();
int imgX,imgY,maskX,maskY;
for(int i = 0; i < boundRect.width; i++){
colAvg[i] = 0;
for(int j = 0; j < boundRect.height; j++){
imgX = i + boundRect.x;
imgY = j + boundRect.y;
maskX = i + boundRect.x - roiBoundRect.x;
maskY = j + boundRect.y - roiBoundRect.y;
if(!hasMask || (maskp.getPixel(maskX,maskY)>0)){
colAvg[i] += ip.getPixel(imgX,imgY);
}
}
colAvg[i] /= boundRect.height;
}
IJ.log("Col average: ");
printArray(colAvg);
return colAvg;
}
private double[] getSmoothColumnAvg(ImageProcessor ip, Roi r, Rectangle boundRect){
//Rectangle boundRect = r.getBounds();
int nCol = boundRect.width;
double[] colAvgSmooth = new double[nCol];
double[] colAvg = getColumnAvg(ip, r, boundRect);
for(int i=0; i < nCol; i++){
colAvgSmooth[i] = 0;
int cnt = 0;
for (int j=Math.max(i-2,0); j <= Math.min(i+2, nCol-1); j++){
colAvgSmooth[i] += colAvg[j];
cnt++;
}
colAvgSmooth[i] /= cnt;
}
return colAvgSmooth;
}
private void setThreshold(ImageProcessor ip, int minInt){
Rectangle roi = ip.getRoi();
Rectangle br = roi.getBounds();
double pix;
for(int y=br.y; y<(br.y+br.height); y++){
for(int x=br.x; x<(br.x+br.width); x++){
pix = ip.getPixelValue(x,y);
if(pix >= minInt){
ip.putPixelValue(x,y,255);
}
else {
ip.putPixelValue(x,y,0);
}
}
}
}
/*private void drawComet(ImageProcessor ip, Comet comet){
if(comet.status == Comet.INVALID){
ip.setColor(cometInvalidColor);
comet.cometRoi.drawPixels(ip);
}
else if (comet.status == Comet.OUTLIER){
// Draw comet outline on output image, add label
ip.setColor(cometOutlierColor);
ip.setRoi(comet.cometRoi);
comet.cometRoi.drawPixels(ip);
ip.setRoi(comet.headRoi);
comet.headRoi.drawPixels(ip);
TextRoi textRoi = new TextRoi(comet.x+comet.width,
comet.y, ""+comet.id, new Font("Arial", Font.BOLD, 22));
textRoi.drawPixels(ip);
}
else if(comet.status ==Comet.VALID){
// Draw comet outline on output image, add label
ip.setColor(cometValidColor);
ip.setRoi(comet.cometRoi);
comet.cometRoi.drawPixels(ip);
ip.setRoi(comet.headRoi);
comet.headRoi.drawPixels(ip);
TextRoi textRoi = new TextRoi(comet.x+comet.width,
comet.y, ""+comet.id, new Font("Arial", Font.BOLD, 22));
textRoi.drawPixels(ip);
}
}*/
private int setValidity(Vector<Comet> Comets, ImageProcessor ip){
int validCount = 0;
for(int i=0;i<Comets.size();i++){
Comet comet = Comets.get(i);
// Comet should be convex
if (comet.convexity < 0.85) {
comet.status = Comet.INVALID;
IJ.log(i+" convexity invalid ("+ comet.convexity + ")");
}
// Comet shouldn't be too asymmetrical
if (comet.symmetry > 0.5){
comet.status = Comet.INVALID;
IJ.log(i+" symmetry invalid");
}
// Comet shouldn't be higher than wide
if(comet.hratio > 1.05){
comet.status = Comet.INVALID;
IJ.log(i+" hratio invalid");
}
// Comet shouldn't be on border
if(isOnEdge(ip,comet.cometRoi)){
comet.status = Comet.INVALID;
IJ.log(i+" is on edge invalid");
}
if(comet.centerlineDiff > 0.15){
if(comet.status==Comet.VALID) comet.status = Comet.OUTLIER;
IJ.log(i+" centerline diff too big outlier");
}
if(comet.centerlineDiff > 0.2){
comet.status = Comet.INVALID;
IJ.log(i+" centerline diff too big invalid");
}
if(comet.status == Comet.VALID) validCount++;
}
return validCount;
}
private boolean isOnEdge(ImageProcessor ip, Roi r){
Rectangle br = r.getBounds();
if(br.x <= 1){
return true;
}
if(br.y <= 1){
return true;
}
if((br.x + br.width) >= (ip.getWidth()-1)){
return true;
}
if((br.y + br.height) >= (ip.getHeight()-1)){
return true;
}
return false;
}
// private void yMoments(ImageProcessor ip){
// double sumpix = 0.0;
// double sumy1 = 0.0;
// double sumy2 = 0.0;
// double sumy3 = 0.0;
// double sumy4 = 0.0;
// double xc, yc;
// double ymean, yvar;
// double yskew, ykurt;
// Rectangle roi = ip.getRoi();
// byte[] mask = ip.getMaskArray();
// Rectangle br = roi.getBounds();
// double pix;
// int cnt1=0;
// int counter = 0;
// for(int y=br.y; y<(br.y+br.height); y++){
// for(int x=br.x; x<(br.x+br.width); x++){
// if(mask[counter++]!=0){
// pix = ip.getPixelValue(x,y);
// xc = x+0.5;
// yc = y+0.5;
// sumpix += pix;
// sumy1 += pix*yc;
// cnt1++;
// }
// }
// }
// ymean = sumy1/sumpix;
// IJ.log("Cnt all: "+counter);
// IJ.log("Cnt no mask: "+cnt1);
// counter = 0;
// for(int y=br.y; y<(br.y+br.height); y++){
// for(int x=br.x; x<(br.x+br.width); x++){
// if(mask[counter++]!=0){
// pix = ip.getPixelValue(x,y);
// xc = x+0.5;
// yc = y+0.5;
// sumpix += pix;
// sumy2 += pix*Math.pow((yc-ymean),2);
// sumy3 += pix*Math.pow((yc-ymean),3);
// sumy4 += pix*Math.pow((yc-ymean),4);
// }
// }
// }
// yvar = sumy2 / sumpix;
// yskew = sumy3 / (sumpix * Math.pow(yvar,1.5));
// ykurt = sumy4 / (sumpix * Math.pow(yvar,2)) - 3.0;
//IJ.log(ymean + "\t" + yvar + "\t" + yskew + "\t" + ykurt);
// }
private int getXIntensityCentroid(ImageProcessor ip){
Rectangle roi = ip.getRoi();
byte[] mask = ip.getMaskArray();
Rectangle br = roi.getBounds();
int maskidx;
ImageStatistics stats = ImageStatistics.getStatistics(ip, ij.measure.Measurements.ALL_STATS, null);
double fullIntensityHalf = (stats.mean * stats.area)/2.0;
double sumIntensity = 0.0;
int x;
for(x=br.x; x<(br.x+br.width); x++){
for(int y=br.y; y<(br.y+br.height); y++){
maskidx = ((y-br.y)*br.width) + (x-br.x);
if(mask[maskidx]!=0){
sumIntensity += ip.getPixelValue(x,y);
}
}
if(sumIntensity > fullIntensityHalf) break;
}
IJ.log("Fullhalf: "+fullIntensityHalf + " Sum intensity: "+ sumIntensity + " x: "+x);
IJ.log(br+"");
return x;
}
private int getFrontCentroid(ImageProcessor ip){
double yFrontCentroid = 0.0;
int cnt = 0;
Rectangle roi = ip.getRoi();
byte[] mask = ip.getMaskArray();
Rectangle br = roi.getBounds();
int maskidx;
for(int x=br.x; x<(br.x+br.width*0.1); x++){
for(int y=br.y; y<(br.y+br.height); y++){
maskidx = ((y-br.y)*br.width) + (x-br.x);
if(mask[maskidx]!=0){
yFrontCentroid += y;
cnt++;
}
}
}
yFrontCentroid /= cnt;
return (int)yFrontCentroid;
}
private double ySymmetry(ImageProcessor ip){
//int counter = 0;
Rectangle roi = ip.getRoi();
byte[] mask = ip.getMaskArray();
Rectangle br = roi.getBounds();
//double pix;
int sum1, sum2;
double absdy = 0.0;
int cnt1=0;
int maskidx;
int yFrontCentroid = getFrontCentroid(ip);
for(int x=br.x; x<(br.x+br.width); x++){
sum1=0;sum2=0;
cnt1 = 0;
for(int y=br.y; y<(br.y+br.height); y++){
maskidx = ((y-br.y)*br.width) + (x-br.x);
if(mask[maskidx]!=0){
//if(y < (br.y+ (br.height/2))){
if(y < yFrontCentroid){
sum1++;
}
else {
sum2++;
}
cnt1++;
}
}
absdy += Math.abs(sum2-sum1) / (double)cnt1;
}
absdy = absdy / br.width;
return absdy;
}
/*private double xCenterOfMass(ImageProcessor ip){
double sumpix = 0.0;
double sumx1 = 0.0;
double xc, yc;
double xmean;
Rectangle roi = ip.getRoi();
//byte[] mask = ip.getMaskArray();
Rectangle br = roi.getBounds();
double pix;
int cnt1=0, cnt0=0;
int counter = 0;
for(int y=br.y; y<(br.y+br.height); y++){
for(int x=br.x; x<(br.x+br.width); x++){
pix = (ip.getPixelValue(x,y))>0 ? 1:0;
xc = x+0.5;
yc = y+0.5;
sumpix += pix;
sumx1 += pix*xc;
if (pix==255)
cnt1++;
else
cnt0++;
}
}
xmean = sumx1/sumpix;
//IJ.log("Cnt 0: "+ cnt0 + " Cnt 1: "+ cnt1);
//IJ.log("Cnt no mask: "+cnt1);
return xmean;
}*/
/*private void printCenterLine(ImageProcessor ip){
int w = ip.getWidth();
int h = ip.getHeight();
int[] center_data = new int[w];
IJ.log("H: "+h+" W: " +w+ "\n");
ip.getRow(0,(int)(h/2),center_data,w);
//IJ.log(center_data);
String s = "";
for(int i:center_data) s += i + "\t";
IJ.log(s);
}*/
private int getHeadHeight(ImageProcessor ip, int xcenter){
int height = 0;
ImageProcessor maskp = ip.getMask();
for(int y=0;y<maskp.getHeight();y++){
if(maskp.getPixel(xcenter, y)>0){
height++;
}
}
return height;
}
private void printArray(double[] arr){
String s = "";
for(int i=0;i<arr.length;i++){
s += arr[i];
if(i<arr.length-1) s+=",";
}
IJ.log(s);
}
private void open_ntimes(ImageProcessor ip, int n, int dark){
if(dark==0){
for(int i=0;i<n;i++){
ip.dilate();
}
for(int i=0;i<n;i++){
ip.erode();
}
}
else
{
for(int i=0;i<n;i++){
ip.erode();
}
for(int i=0;i<n;i++){
ip.dilate();
}
}
}
private int getHeadEdge(ImageProcessor ip, Comet comet){
ip.setRoi(comet.cometRoi);
Rectangle boundRect = comet.cometRoi.getBounds();
int yc = getFrontCentroid(ip);
Rectangle profileRect;
if(comet.circularity < 0.9){
profileRect = new Rectangle(boundRect.x, yc-5, boundRect.width, 10);
}
else {
profileRect = new Rectangle(boundRect);
}
double[] cometProfile = getColumnAvg(ip, comet.cometRoi, profileRect);
printArray(cometProfile);
int kernelWidth = (int)boundRect.width/10;
double[] smoothKernel = new double[kernelWidth];
Arrays.fill(smoothKernel, 1.0/kernelWidth);
double[] diffKernel = {-1.0,1.0};
// Smooth comet profile
double[] y1 = convFilter(cometProfile,smoothKernel,true);
printArray(y1);
// Differentiate comet profile
double[] y2 = convFilter(y1,diffKernel,false);
printArray(y2);
// Smooth differential
double[] y3 = convFilter(y2,smoothKernel,true);
printArray(y3);
// Differentiate again
double[] y4 = convFilter(y3,diffKernel,false);
printArray(y4);
// Smooth again
double[] ddCometProfile = convFilter(y4,smoothKernel,true);
IJ.log("Kernel width: "+kernelWidth);
/*printArray(ddCometProfile);
int edge = 0;
for(int i=0; i < ddCometProfile.length-1; i++){
if((ddCometProfile[i+1] > 0) && (ddCometProfile[i] < 0)){
IJ.log("Transition at "+i);
edge = i + 5;
break;
}
}
return edge;*/
int zcross = 0;
for(int i=0; i < ddCometProfile.length-1; i++){
if((ddCometProfile[i+1] > 0) && (ddCometProfile[i] < 0)){
IJ.log("Transition at "+i);
zcross = i;
break;
}
}
int ddmax = 0;
for(int i=1; i < ddCometProfile.length-1; i++){
if(i<zcross) continue;
if(ddCometProfile[i+1] <= ddCometProfile[i] &&
ddCometProfile[i-1] <= ddCometProfile[i]){
ddmax = i;
IJ.log("Head edge at "+i);
break;
}
}
if(ddmax==0){
ddmax = boundRect.width;
}
return ddmax;
}
private double[] convFilter(double[] x, double[] kernel, boolean pad){
int outLen;
if(pad){
outLen = x.length;
}
else {
outLen = x.length + 1 - kernel.length;
}
double[] y = new double[outLen];
int kernRadius = (int)Math.floor(kernel.length / 2.0);
int kernStart;
for(int i = 0; i < outLen; i++){
y[i] = 0.0;
if(pad){
kernStart = i - kernRadius;
}
else {
kernStart = i;
}