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Orbit, a versatile image analysis software for biological image-based quantification
/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2017 Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland.
*
* 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, either version 3 of the License, or
* (at your option) any later version.
*
* 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, see Process(BufferedImage input, int bgColor) {
backgroundColor = bgColor;
_input = input;
_width = input.getWidth();
_height = input.getHeight();
_board = new int[_width][];
for (int i = 0; i < _width; i++)
_board[i] = new int[_height];
Map> patterns = Find();
Map images = new HashMap();
inputGD = _input.getGraphics();
inputGD.setColor(Color.BLUE);
for (Integer id : patterns.keySet()) {
BufferedImage bmp = CreateBitmap(patterns.get(id));
images.put(id, bmp);
}
inputGD.dispose();
return images;
}
protected boolean CheckIsBackGround(Pixel currentPixel) {
// check if pixel color is backgroundColor (white).
//return currentPixel.color.getAlpha() == 255 && currentPixel.color.getRed() == 255 && currentPixel.color.getGreen() == 255 && currentPixel.color.getBlue() == 255;
return currentPixel.color == backgroundColor;
}
private static int Min(List neighboringLabels, Map allLabels) {
if (neighboringLabels.isEmpty())
return 0; // TODO: is 0 appropriate for empty list
int ret = allLabels.get(neighboringLabels.get(0)).GetRoot().name;
for (Integer n : neighboringLabels) {
int curVal = allLabels.get(n).GetRoot().name;
ret = (ret < curVal ? ret : curVal);
}
return ret;
}
private static int Min(List pattern, boolean xOrY) {
if (pattern.isEmpty())
return 0; // TODO: is 0 appropriate for empty list
int ret = (xOrY ? pattern.get(0).x : pattern.get(0).y);
for (Pixel p : pattern) {
int curVal = (xOrY ? p.x : p.y);
ret = (ret < curVal ? ret : curVal);
}
return ret;
}
private static int Max(List pattern, boolean xOrY) {
if (pattern.isEmpty())
return 0; // TODO: is 0 appropriate for empty list
int ret = (xOrY ? pattern.get(0).x : pattern.get(0).y);
for (Pixel p : pattern) {
int curVal = (xOrY ? p.x : p.y);
ret = (ret > curVal ? ret : curVal);
}
return ret;
}
private Map> Find() {
int labelCount = 1;
Map allLabels = new HashMap();
for (int i = 0; i < _height; i++) {
for (int j = 0; j < _width; j++) {
Pixel currentPixel = new Pixel(j, i, _input.getRGB(j, i));
if (CheckIsBackGround(currentPixel)) {
continue;
}
List neighboringLabels = GetNeighboringLabels(currentPixel);
int currentLabel;
if (neighboringLabels.isEmpty()) {
currentLabel = labelCount;
allLabels.put(currentLabel, new Label(currentLabel));
labelCount++;
} else {
currentLabel = Min(neighboringLabels, allLabels);
Label root = allLabels.get(currentLabel).GetRoot();
for (Integer neighbor : neighboringLabels) {
if (root.name != allLabels.get(neighbor).GetRoot().name) {
allLabels.get(neighbor).Join(allLabels.get(currentLabel));
}
}
}
_board[j][i] = currentLabel;
}
}
Map> patterns = AggregatePatterns(allLabels);
return patterns;
}
private List GetNeighboringLabels(Pixel pix) {
List neighboringLabels = new ArrayList();
for (int i = pix.y - 1; i <= pix.y + 2 && i < _height - 1; i++) {
for (int j = pix.x - 1; j <= pix.x + 2 && j < _width - 1; j++) {
if (i > -1 && j > -1 && _board[j][i] != 0) {
neighboringLabels.add(_board[j][i]);
}
}
}
return neighboringLabels;
}
private Map> AggregatePatterns(Map allLabels) {
Map> patterns = new HashMap>();
for (int i = 0; i < _height; i++) {
for (int j = 0; j < _width; j++) {
int patternNumber = _board[j][i];
if (patternNumber != 0) {
patternNumber = allLabels.get(patternNumber).GetRoot().name;
if (!patterns.containsKey(patternNumber)) {
patterns.put(patternNumber, new ArrayList());
}
patterns.get(patternNumber).add(new Pixel(j, i, _input.getRGB(j, i)));
}
}
}
return patterns;
}
private BufferedImage CreateBitmap(List pattern) {
int minX = Min(pattern, true);
int maxX = Max(pattern, true);
int minY = Min(pattern, false);
int maxY = Max(pattern, false);
int width = maxX + 1 - minX;
int height = maxY + 1 - minY;
BufferedImage bmp = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
for (Pixel pix : pattern) {
bmp.setRGB(pix.x - minX, pix.y - minY, pix.color); //shift position by minX and minY
}
inputGD.drawRect(minX, minY, maxX - minX, maxY - minY);
return bmp;
}
public static String getBaseFileName(String fileName) {
return fileName.substring(0, fileName.indexOf('.'));
}
public static String getFileNameExtension(String fileName) {
return fileName.substring(fileName.indexOf('.') + 1);
}
public BufferedImage getProcessedImage() {
return _input;
}
protected class Pixel {
public int x;
public int y;
public int color;
public Pixel(int x, int y, int color) {
this.x = x;
this.y = y;
this.color = color;
}
}
protected class Label {
public int name;
public Label Root;
public int Rank;
public Label(int Name) {
this.name = Name;
this.Root = this;
this.Rank = 0;
}
public int getName() {
return name;
}
public void setName(int name) {
this.name = name;
}
public Label getRoot() {
return Root;
}
public void setRoot(Label root) {
Root = root;
}
public int getRank() {
return Rank;
}
public void setRank(int rank) {
Rank = rank;
}
Label GetRoot() {
if (this.Root != this) {
this.Root = this.Root.GetRoot();
}
return this.Root;
}
void Join(Label root2) {
if (root2.Rank < this.Rank)//is the rank of Root2 less than that of Root1 ?
{
root2.Root = this;//yes! then Root1 is the parent of Root2 (since it has the higher rank)
} else //rank of Root2 is greater than or equal to that of Root1
{
this.Root = root2;//make Root2 the parent
if (this.Rank == root2.Rank)//both ranks are equal ?
{
root2.Rank++;//increment Root2, we need to reach a single root for the whole tree
}
}
}
}
// Sample usage:
// java org.ml.ccl.CCL images/one.png
// java org.ml.ccl.CCL images/two.png -5000269
public static void main(String[] args) {
if (args.length == 0) {
System.err.println("Usage: CCL imageFile [bgColor]");
return;
}
CCL ccl = new CCL();
try {
int bgColor = 0xFFFFFFFF; // white default background color
if (args.length == 2) {
bgColor = Integer.decode(args[1]);
}
BufferedImage img = ImageIO.read(new File(args[0]));
// TODO: Obtain background color.
// An attempt to obtain bg color automatically: Center of image.
System.out.println("image bg color: " + img.getRGB(img.getWidth() / 2, img.getHeight() / 2));
Map components = ccl.Process(img, bgColor);
String format = getFileNameExtension(args[0]);
for (Integer c : components.keySet()) {
//ImageIO.write(components.get(c), format, new File(getBaseFileName(args[0]) + "-component-" + c + "." + format));
}
ImageIO.write(ccl.getProcessedImage(), format, new File(getBaseFileName(args[0]) + "-processed" + "." + format));
} catch (Exception ex) {
ex.printStackTrace();
}
}
}