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ShapeStatsIJ.java
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ShapeStatsIJ.java
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/*-
* #%L
* This file is part of QuPath.
* %%
* Copyright (C) 2014 - 2016 The Queen's University of Belfast, Northern Ireland
* Contact: IP Management (ipmanagement@qub.ac.uk)
* Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
* %%
* QuPath 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.
*
* QuPath 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 QuPath. If not, see <https://www.gnu.org/licenses/>.
* #L%
*/
package qupath.imagej.detect.cells;
import ij.gui.Roi;
import ij.measure.Measurements;
import ij.process.ImageStatistics;
/**
* Class to help with adding shape measurements calculated by ImageJ to PathObjects.
*
* @author Pete Bankhead
*
*/
class ShapeStatsIJ {
public static int SHAPE_MEASUREMENT_OPTIONS = Measurements.AREA | Measurements.PERIMETER | Measurements.SKEWNESS | Measurements.ELLIPSE | Measurements.FERET;
private double area, perimeter, xCentroid, yCentroid, majorAxisLength, minorAxisLength;
private double maxCaliper, minCaliper;
// TODO: Introduce convex area & solidity
public ShapeStatsIJ(Roi roi, ImageStatistics stats) {
// if (roi.isLine())
// this.area = 0;
// else
this.area = stats.area;
this.perimeter = roi.getLength();
this.xCentroid = stats.xCentroid;
this.yCentroid = stats.yCentroid;
this.majorAxisLength = stats.major;
this.minorAxisLength = stats.minor;
double[] feretValues = roi.getFeretValues();
this.maxCaliper = feretValues[0];
this.minCaliper = feretValues[2];
}
public double area() {
return area;
}
public double perimeter() {
return perimeter;
}
public double maxCaliper() {
return maxCaliper;
}
public double minCaliper() {
return minCaliper;
}
public int xCentroidInt() {
return (int)(xCentroid + .5);
}
public int yCentroidInt() {
return (int)(yCentroid + .5);
}
public double xCentroid() {
return xCentroid;
}
public double yCentroid() {
return yCentroid;
}
public double majorAxisLength() {
return majorAxisLength;
}
public double minorAxisLength() {
return minorAxisLength;
}
public double eccentricity() {
double majAxis = majorAxisLength();
double minAxis = minorAxisLength();
return 2*Math.sqrt(((majAxis * majAxis * 0.25) - (minAxis * minAxis * 0.25))) / majAxis;
}
public double aspectRatio() {
return majorAxisLength / minorAxisLength;
}
public double roundness() {
return 1 / aspectRatio();
}
public double circularity() {
return Math.min(4.0 * Math.PI * area / (perimeter * perimeter), 1);
}
}