org.rhwlab.dispim.datasource.Segmentation.java Source code

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Here is the source code for org.rhwlab.dispim.datasource.Segmentation.java

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package org.rhwlab.dispim.datasource;

import java.util.ArrayList;
import java.util.List;
import org.apache.commons.math3.linear.RealVector;

/**
 *
 * @author gevirl
 */
public class Segmentation {
    public Segmentation(VoxelDataSource source, double thresh, BoundingBox box) {
        this.source = source;
        this.thresh = thresh;
        segmentIndex = new ArrayList<>();
        mins = new double[source.getD()];
        maxs = new double[source.getD()];
        for (int d = 0; d < source.getD(); ++d) {
            mins[d] = Double.MAX_VALUE;
            maxs[d] = 0.0;
        }

        for (long i = 0; i < source.getN(); ++i) { // process each voxel in the segmented tiff
            Voxel segVox = source.get(i);
            if (segVox.getIntensity() >= thresh && box.isWithin(segVox)) { // do not include the voxel in the segmentation if less than the threshold or outside the bounding box
                for (int d = 0; d < mins.length; ++d) {
                    RealVector v = segVox.coords;
                    double e = v.getEntry(d);
                    if (e < mins[d]) {
                        mins[d] = e;
                    }
                    if (e > maxs[d]) {
                        maxs[d] = e;
                    }
                }
                segmentIndex.add(i);
            }
        }
    }

    public long getVoxelIndex(int segIndex) {
        return segmentIndex.get(segIndex);
    }

    public int getSegmentN() {
        return segmentIndex.size();
    }

    public double[] getMins() {
        return mins;
    }

    public double[] getMaxs() {
        return maxs;
    }

    public double getThreshold() {
        return thresh;
    }

    public double getSegmentationProbability(int segIndex) {
        return ((double) source.get(segmentIndex.get(segIndex)).getIntensity()) / 100.0;
    }

    VoxelDataSource source;
    double thresh;
    double[] mins; // min coordinates of non-background voxels
    double[] maxs; // max coordinates of non-background voxels  
    List<Long> segmentIndex; // list of voxels in the segment    
}