mastodon-deep-lineage/src/main/java/org/mastodon/mamut/clustering/ui/ClusterRootNodesView.java at 84c0994ddbdc0cda79a30fcd0f266062a6d83656 · mastodon-sc/mastodon-deep-lineage · GitHub

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/*-
 * #%L
 * mastodon-deep-lineage
 * %%
 * Copyright (C) 2022 - 2023 Stefan Hahmann
 * %%
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 * #L%
 */
package org.mastodon.mamut.clustering.ui;

import org.mastodon.mamut.clustering.ClusterRootNodesController;
import org.mastodon.mamut.clustering.config.ClusteringMethod;
import org.mastodon.mamut.clustering.config.CropCriteria;
import org.mastodon.mamut.clustering.config.SimilarityMeasure;
import org.scijava.ItemVisibility;
import org.scijava.command.InteractiveCommand;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import org.scijava.widget.Button;

@Plugin(type = InteractiveCommand.class, visible = false, label = "Classification of Lineage Trees")
public class ClusterRootNodesView extends InteractiveCommand
{

	private static final int WIDTH = 15;

	private static final int WIDTH_INPUT = 7;


	@SuppressWarnings("unused")
	@Parameter
	private ClusterRootNodesController controller;

	@SuppressWarnings("all")
	@Parameter(visibility = ItemVisibility.MESSAGE, required = false, persist = false)
	private String documentation = "<html>\n"
			+ "<body width=" + WIDTH + "cm align=left>\n"
			+ "<h1>Classification of Lineage Trees</h1>\n"
			+ "<p>This plugin is capable of grouping similar lineage trees together. This is done by creating a tag set an assigning subtrees that are similar to each other with the same tag.</p>\n"
			+ "<p>The similarity between two subtrees is computed based on the Zhang edit distance for unordered trees <a href=\"https://doi.org/10.1007/BF01975866\">(Zhang, K. Algorithmica 15, 205–222, 1996)</a>. The similarity measure uses the attribute the cell lifetime, which is computed as a difference of timepoints between to subsequent divisions. It is possible to apply the <i>absolute difference</i>, <i>average difference</i> or the <i>normalized difference</i> of cell lifetimes.</p>\n"
			+ "<p>The similarity is computed between all possible combinations of subtrees leading to a two-dimensional similarity matrix. This matrix is then used to perform a <a href=\"https://en.wikipedia.org/wiki/Hierarchical_clustering\">agglomerative hierarchical clustering</a> into a specifiable number of classes. For the clustering three different <a href=\"https://en.wikipedia.org/wiki/Hierarchical_clustering#Cluster_Linkage\">linkage methods</a> can be chosen.</p>\n"
			+ "</body>\n"
			+ "</html>\n";

	@SuppressWarnings("all")
	@Parameter(label = "Crop criterion", callback = "update")
	private CropCriteria cropCriterion = CropCriteria.TIMEPOINT;

	@SuppressWarnings("unused")
	@Parameter(label = "Crop start", min = "0", callback = "update")
	private int start;

	@SuppressWarnings("unused")
	@Parameter(label = "Crop end", min = "0", callback = "update")
	private int end;

	@SuppressWarnings("unused")
	@Parameter(label = "Number of classes", min = "2", callback = "update")
	private int numberOfClasses;

	@SuppressWarnings("unused")
	@Parameter(label = "Minimum number of cell divisions", min = "0", description = "Only include lineage trees with at least the number of divisions specified here.", callback = "update")
	private int numberOfCellDivisions;

	@SuppressWarnings("all")
	@Parameter(label = "Similarity measure", callback = "update")
	private SimilarityMeasure similarityMeasure = SimilarityMeasure.NORMALIZED_DIFFERENCE;

	@SuppressWarnings("all")
	@Parameter(label = "Linkage strategy for hierarchical clustering", callback = "update")
	private ClusteringMethod clusteringMethod = ClusteringMethod.AVERAGE_LINKAGE;

	@SuppressWarnings("unused")
	@Parameter(label = "Feature", choices = "Branch duration", callback = "update")
	private String branchDuration;
	// NB: dynamic choices: https://github.com/imagej/tutorials/blob/c78764438d774295d00fc8a4273e4c4f25c8ad46/maven-projects/dynamic-commands/src/main/java/DynamicCallbacks.java

	@SuppressWarnings("unused")
	@Parameter(label = "Show dendrogram of clustering", callback = "update")
	private boolean showDendrogram;

	@SuppressWarnings("unused")
	@Parameter(visibility = ItemVisibility.MESSAGE, required = false, persist = false, label = " ")
	private String paramFeedback;

	@SuppressWarnings("unused")
	@Parameter(visibility = ItemVisibility.MESSAGE, required = false, persist = false, label = " ")
	private String computeFeedback;

	@SuppressWarnings("unused")
	@Parameter(label = "Classify lineage trees", callback = "createTagSet", persist = false)
	private Button createTagSet;

	/**
	 * This method is executed whenever a parameter changes
	 */
	@Override
	public void run()
	{
		// NB: not implemented. Update method is called via callback on each parameter change.
	}

	@SuppressWarnings("unused")
	private void update()
	{
		controller.setInputParams( cropCriterion, start, end, numberOfCellDivisions );
		controller.setComputeParams( similarityMeasure, clusteringMethod, numberOfClasses );
		controller.setShowDendrogram( showDendrogram );

		paramFeedback = "<html><body width=" + WIDTH_INPUT + "cm>";
		if ( controller.isValidParams() )
			paramFeedback += "<font color=green>Parameters are valid.";
		else
		{
			paramFeedback += "<font color=red>" + String.join( "<p>", controller.getFeedback() );
		}
		paramFeedback += "</font></body></html>";
	}

	@SuppressWarnings("unused")
	private void createTagSet()
	{
		update();
		if ( controller.isValidParams() )
		{
			String feedback;
			try
			{
				controller.createTagSet();
				feedback = "Classified lineage trees.<p>";
				feedback += "Tag set created.";
			}
			catch ( IllegalArgumentException e )
			{
				feedback = e.getMessage();
			}
			computeFeedback = "<html><body width=" + WIDTH_INPUT + "cm><font color=\"green\">" + feedback + "</font></body></html>";
		}
	}
}