com.actelion.research.orbit.imageAnalysis.mask.OrbitMaskSegmentationModel Maven / Gradle / Ivy
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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 - 2018 Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 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 tileShapeCache = CacheBuilder.
newBuilder().
//recordStats().
maximumSize(Runtime.getRuntime().availableProcessors()).
build(new CacheLoader() {
@Override
public OrbitMaskSegmentation load(MyPoint tile) throws Exception {
double scaleOuter = 1.5d;
double scaleInner = 0.8d;
boolean bin = false;
RecognitionFrame rf = new RecognitionFrame(tile.tip);
List tiles = new ArrayList<>(1);
tiles.add(new Point(tile.x,tile.y));
ObjectSegmentationWorker segmentationWorker = new ObjectSegmentationWorker(null,rf,null,null,tiles);
segmentationWorker.setModel(model);
segmentationWorker.setNumThreads(1);
segmentationWorker.setWithGUI(false);
segmentationWorker.run();
SegmentationResult segmentationResult = segmentationWorker.getSegmentationResult();
List shapeList = segmentationResult.getShapeList();
if (bin && shapeList!=null) {
// scale shape and exclude inner part
List binnedShapes = new ArrayList<>(shapeList.size());
PolygonMetrics pm = new PolygonMetrics(null);
for (Shape shape: shapeList) {
if (shape instanceof PolygonExt) {
PolygonExt pe = (PolygonExt) shape;
pm.setPolygon(pe.clone());
Shape outer = pe.scale(100d * scaleOuter, pm.getCenter());
pm.setPolygon(pe.clone());
Shape inner = pe.scale(100d * scaleInner, pm.getCenter());
ShapeAnnotationList combined = new ShapeAnnotationList(new ArrayList(), Collections.singletonList(inner), outer, outer.getBounds());
binnedShapes.add(combined);
}
}
shapeList = binnedShapes;
}
OrbitMaskSegmentation segMask = new OrbitMaskSegmentation(shapeList);
return segMask;
}
});
public OrbitMaskSegmentationModel(OrbitModel model) {
this.model = model;
}
@Override
public void reconfigure() {
}
@Override
public void initialize(TiledImagePainter tip) {
this.tip = tip;
}
@Override
public int numClasses() {
return 2; // maybe class per object in the future?
}
@Override
public int classNum(int x, int y, Raster raster) throws Exception {
MyPoint tile = new MyPoint(tip.getImage().XToTileX(x),tip.getImage().YToTileY(y), tip);
OrbitMaskSegmentation segMask = tileShapeCache.get(tile);
return segMask.classNum(x,y,raster);
}
@Override
public boolean isIncluded(int x, int y, Raster raster) throws Exception {
return classNum(x,y,raster)>0;
}
@Override
public String className(int classNum) {
return classNum==0? "background": "object";
}
@Override
public int classColor(int classNum) {
return classNum==0? Color.blue.getRGB() : Color.yellow.getRGB();
}
@Override
public OrbitModel getModel() {
return model;
}
@Override
public IOrbitMask clone() {
OrbitMaskSegmentationModel cloned = null;
try {
cloned = (OrbitMaskSegmentationModel) super.clone();
cloned.model = new OrbitModel(this.model);
return cloned;
} catch (CloneNotSupportedException e) {
e.printStackTrace();
return null;
}
}
class MyPoint {
private int x;
private int y;
private TiledImagePainter tip;
public MyPoint(int x, int y, TiledImagePainter tip) {
this.x = x;
this.y = y;
this.tip = tip;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
MyPoint myPoint = (MyPoint) o;
return x == myPoint.x &&
y == myPoint.y;
}
@Override
public int hashCode() {
return Objects.hash(x, y);
}
public int getX() {
return x;
}
public void setX(int x) {
this.x = x;
}
public int getY() {
return y;
}
public void setY(int y) {
this.y = y;
}
public TiledImagePainter getTip() {
return tip;
}
}
}