ipnat.skel.SummarizeSkeleton.java Source code

Introduction

Here is the source code for ipnat.skel.SummarizeSkeleton.java

Source

/*
 * #%L
 * hIPNAT plugins for Fiji distribution of ImageJ
 * %%
 * Copyright (C) 2016 Tiago Ferreira
 * %%
 * 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
 * <http://www.gnu.org/licenses/gpl-3.0.html>.
 * #L%
 */
package ipnat.skel;

import java.util.stream.IntStream;

import org.apache.commons.math3.stat.StatUtils;

import ij.IJ;
import ij.ImagePlus;
import ij.measure.ResultsTable;
import ij.plugin.filter.PlugInFilter;
import ij.process.ImageProcessor;
import ipnat.Utils;
import sc.fiji.analyzeSkeleton.AnalyzeSkeleton_;
import sc.fiji.analyzeSkeleton.SkeletonResult;

/**
 * This class implements the ImageJ {@code Summarize Skeleton} plugin. For more
 * information, visit the hIPNAT repository
 * {@literal https://github.com/tferr/hIPNAT}
 *
 * @author Tiago Ferreira
 */
public class SummarizeSkeleton implements PlugInFilter {

    ImagePlus imp;
    String TABLE_TITLE = "Skeleton Stats";

    @Override
    public int setup(final String arg, final ImagePlus imp) {

        this.imp = imp;
        if (!IJ.isJava18()) {
            IJ.error("\"Summarize Skeleton\" requires Java 1.8 or later.");
            return DONE;
        } else if (!Utils.validSkelDependencies()
                && !Utils.classExists("org.apache.commons.math3.stat.StatUtils")) {
            return DONE;
        } else
            return DOES_8G | NO_CHANGES;

    }

    @Override
    public void run(final ImageProcessor ignored) {

        // Analyze skeleton
        final AnalyzeSkeleton_ as = new AnalyzeSkeleton_();
        as.setup("", imp);
        final SkeletonResult sr = as.run();

        // Get key skeleton properties
        final int nTrees = sr.getNumOfTrees();
        final int[] branches = sr.getBranches();
        final int nBranches = IntStream.of(branches).sum();

        if (branches == null || (nBranches == 0 && nTrees <= 1)) {
            Utils.error("Summarize Skeleton", "Image does not seem to be a branched skeleton.", imp);
            return;
        }

        final ResultsTable rt = Utils.getTable(TABLE_TITLE);
        try {

            // Integrate values from all trees
            double sumLength = 0d;
            final double[] avgLengths = sr.getAverageBranchLength();
            for (int i = 0; i < nTrees; i++)
                sumLength += avgLengths[i] * branches[i];

            // Log stats
            rt.incrementCounter();
            rt.addValue("Image", imp.getTitle());
            rt.addValue("Unit", imp.getCalibration().getUnits());
            rt.addValue("Total length", sumLength);
            rt.addValue("Max branch length", StatUtils.max(sr.getMaximumBranchLength()));
            rt.addValue("Mean branch length", StatUtils.mean(avgLengths));
            rt.addValue("# Trees", nTrees);
            rt.addValue("# Branches", nBranches);
            rt.addValue("# Junctions", IntStream.of(sr.getJunctions()).sum());
            rt.addValue("# End-points", IntStream.of(sr.getEndPoints()).sum());
            rt.addValue("# Triple Points", IntStream.of(sr.getTriples()).sum());
            rt.addValue("# Quadruple Points", IntStream.of(sr.getQuadruples()).sum());
            rt.addValue("Sum of voxels", IntStream.of(sr.calculateNumberOfVoxels()).sum());

        } catch (final Exception ignored1) {

            Utils.error("Summarize Skeleton", "Some statistics could not be calculated", imp);

        } finally {

            rt.show(TABLE_TITLE);

        }

    }
}