Random coloring of lineage trees only for vizu enhancement

src/main/java/org/mastodon/mamut/tomancak/LineageRandomColorizer.java

@@ -0,0 +1,178 @@
+/*-
+ * #%L
+ * mastodon-tomancak
+ * %%
+ * Copyright (C) 2023 Vladimir Ulman
+ * %%
+ * 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.tomancak;
+
+import org.mastodon.mamut.model.Spot;
+import org.mastodon.mamut.plugin.MamutPluginAppModel;
+import org.mastodon.mamut.tomancak.util.SpotsIterator;
+import org.mastodon.model.tag.ObjTags;
+import org.mastodon.model.tag.TagSetStructure;
+import org.scijava.command.Command;
+import org.scijava.command.DynamicCommand;
+import org.scijava.log.LogService;
+import org.scijava.log.Logger;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import static org.mastodon.mamut.tomancak.lineage_registration.TagSetUtils.addNewTagSetToModel;
+import static org.mastodon.mamut.tomancak.lineage_registration.TagSetUtils.rgbToValidColor;
+
+@Plugin( type = Command.class, name = "Random colorize lineages" )
+public class LineageRandomColorizer extends DynamicCommand  {
+	@Parameter(persist = false)
+	private MamutPluginAppModel pluginAppModel;
+
+	@Parameter
+	private LogService logService;
+
+	@Parameter(label = "Choose color scheme:", initializer = "readAvailColors", choices = {})
+	private String colorScheme = "Create new tagset";
+
+	final static private String COLORS_16 = "Create and use a new tagset (16 colors)";
+	final static private String COLORS_64 = "Create and use a new tagset (64 colors)";
+
+	// sets up the drop-down box in the dialog with two create-tagset-items
+	// followed by the list of the currently available tagsets
+	private void readAvailColors() {
+		List<String> choices = new ArrayList<>(50);
+
+		pluginAppModel.getAppModel().getModel()
+				.getTagSetModel()
+				.getTagSetStructure()
+				.getTagSets()
+				.forEach( ts -> choices.add( "Use existing "+ts.getName() ) );
+
+		//finally, also allow to create new tag sets (color palettes)
+		choices.add( COLORS_16 );
+		choices.add( COLORS_64 );
+
+		this.getInfo().getMutableInput( "colorScheme", String.class ).setChoices( choices );
+	}
+
+	static final Map<String, Integer> mokolePaletteOf16Colors = new HashMap<>(16);
+	{
+		// used https://mokole.com/palette.html with the settings:
+		// 16 colors, 5% min luminosity, 90% max luminosity, 5000 max loops
+		mokolePaletteOf16Colors.put( "darkslategray", rgbToValidColor(0x2f4f4f) );
+		mokolePaletteOf16Colors.put( "saddlebrown", rgbToValidColor(0x8b4513) );
+		mokolePaletteOf16Colors.put( "darkgreen", rgbToValidColor(0x006400) );
+		mokolePaletteOf16Colors.put( "darkkhaki", rgbToValidColor(0xbdb76b) );
+		mokolePaletteOf16Colors.put( "navy", rgbToValidColor(0x000080) );
+		mokolePaletteOf16Colors.put( "mediumturquoise", rgbToValidColor(0x48d1cc) );
+		mokolePaletteOf16Colors.put( "red", rgbToValidColor(0xff0000) );
+		mokolePaletteOf16Colors.put( "orange", rgbToValidColor(0xffa500) );
+		mokolePaletteOf16Colors.put( "yellow", rgbToValidColor(0xffff00) );
+		mokolePaletteOf16Colors.put( "lime", rgbToValidColor(0x00ff00) );
+		mokolePaletteOf16Colors.put( "mediumspringgreen", rgbToValidColor(0x00fa9a) );
+		mokolePaletteOf16Colors.put( "blue", rgbToValidColor(0x0000ff) );
+		mokolePaletteOf16Colors.put( "orchid", rgbToValidColor(0xda70d6) );
+		mokolePaletteOf16Colors.put( "fuchsia", rgbToValidColor(0xff00ff) );
+		mokolePaletteOf16Colors.put( "dodgerblue", rgbToValidColor(0x1e90ff) );
+		mokolePaletteOf16Colors.put( "lightpink", rgbToValidColor(0xffb6c1) );
+	}
+
+	private TagSetStructure.TagSet createCoolSmallTagSet() {
+		return addNewTagSetToModel( pluginAppModel.getAppModel().getModel(),
+				"Palette of 16 colors", mokolePaletteOf16Colors.entrySet() );
+	}
+
+
+	private TagSetStructure.TagSet createNewTagSet(final int rColors,
+	                                               final int gColors,
+	                                               final int bColors) {
+		final int colorsInTotal = rColors*gColors*bColors;
+		final Map<String, Integer> palette = new HashMap<>(colorsInTotal);
+
+		final int rStep = 256 / rColors; //relying on down-rounding
+		final int gStep = 256 / gColors;
+		final int bStep = 256 / bColors;
+
+		for (int rColor = 0; rColor < rColors; ++rColor)
+			for (int gColor = 0; gColor < gColors; ++gColor)
+				for (int bColor = 0; bColor < bColors; ++bColor) {
+					int color = ((rColor*rStep) << 16) + ((gColor*gStep) << 8) + bColor*bStep;
+					palette.put("RGB "+(rColor*rStep)+","
+							+(gColor*gStep)+","+(bColor*bStep), rgbToValidColor(color) );
+				}
+		return addNewTagSetToModel( pluginAppModel.getAppModel().getModel(),
+				"Palette of "+colorsInTotal+" colors", palette.entrySet() );
+	}
+
+
+	private TagSetStructure.TagSet getChosenTagSet() {
+		TagSetStructure.TagSet chosenTagSet = null;
+
+		if (colorScheme.equals(COLORS_16)) chosenTagSet = createCoolSmallTagSet();
+		else if (colorScheme.equals(COLORS_64)) chosenTagSet = createNewTagSet(4,4,4);
+		else {
+			Optional<TagSetStructure.TagSet> ts = pluginAppModel.getAppModel().getModel()
+					.getTagSetModel()
+					.getTagSetStructure()
+					.getTagSets()
+					.stream()
+					.filter(_ts -> _ts.getName().equals(colorScheme))
+					.findFirst();
+			if (!ts.isPresent())
+				throw new IllegalStateException("Requested tagset '"+colorScheme+"' was not found now.");
+			chosenTagSet = ts.get();
+		}
+
+		return chosenTagSet;
+	}
+
+
+	public void run()
+	{
+		pluginAppModel.getAppModel().getModel().getTagSetModel().pauseListeners();
+
+		final TagSetStructure.TagSet chosenTagSet = getChosenTagSet();
+		AtomicInteger currentColorIdx = new AtomicInteger( 0 );
+
+		final ObjTags<Spot> colorizer = pluginAppModel.getAppModel().getModel().getTagSetModel().getVertexTags();
+		final Logger dedicatedLog = logService.subLogger( "Coloring of lineage trees" );
+
+		final SpotsIterator visitor = new SpotsIterator( pluginAppModel.getAppModel(), dedicatedLog );
+		visitor.visitRootsFromEntireGraph( root -> {
+			TagSetStructure.Tag color = chosenTagSet.getTags().get( currentColorIdx.get() );
+			currentColorIdx.set( (currentColorIdx.get()+1) % chosenTagSet.getTags().size() );
+
+			visitor.visitDownstreamSpots( root, spot -> colorizer.set( spot, color ) );
+		} );
+		dedicatedLog.info("Done with the random coloring.");
+
+		pluginAppModel.getAppModel().getModel().getTagSetModel().resumeListeners();
+	}
+}

src/main/java/org/mastodon/mamut/tomancak/TomancakPlugins.java

@@ -84,6 +84,7 @@ public class TomancakPlugins extends AbstractContextual implements MamutPlugin
 	private static final String EXPORTS_SPOTS_COUNTS = "[tomancak] export spots counts";
 	private static final String MERGE_PROJECTS = "[tomancak] merge projects";
 	private static final String TWEAK_DATASET_PATH = "[tomancak] fix project image path";
+	private static final String RANDOM_COLOR_TREES = "[tomancak] random color trees";
 
 	private static final String[] EXPORT_PHYLOXML_KEYS = { "not mapped" };
 	private static final String[] FLIP_DESCENDANTS_KEYS = { "ctrl E" };
@@ -101,6 +102,7 @@ public class TomancakPlugins extends AbstractContextual implements MamutPlugin
 	private static final String[] EXPORTS_SPOTS_COUNTS_KEYS = { "not mapped" };
 	private static final String[] MERGE_PROJECTS_KEYS = { "not mapped" };
 	private static final String[] TWEAK_DATASET_PATH_KEYS = { "not mapped" };
+	private static final String[] RANDOM_COLOR_TREES_KEYS = { "not mapped" };
 
 	private static Map< String, String > menuTexts = new HashMap<>();
 
@@ -121,6 +123,7 @@ public class TomancakPlugins extends AbstractContextual implements MamutPlugin
 		menuTexts.put( EXPORTS_SPOTS_COUNTS, "Export Spots Counts" );
 		menuTexts.put( MERGE_PROJECTS, "Merge Two Projects" );
 		menuTexts.put( TWEAK_DATASET_PATH, "Fix Image Path" );
+		menuTexts.put( RANDOM_COLOR_TREES, "Random Color Lineages" );
 	}
 
 	/*
@@ -152,6 +155,7 @@ public void getCommandDescriptions( final CommandDescriptions descriptions )
 			descriptions.add( EXPORTS_SPOTS_COUNTS, EXPORTS_SPOTS_COUNTS_KEYS, "Exports counts of spots into CSV-like files to be imported in data processors." );
 			descriptions.add( MERGE_PROJECTS, MERGE_PROJECTS_KEYS, "Merge two Mastodon projects into one." );
 			descriptions.add( TWEAK_DATASET_PATH, TWEAK_DATASET_PATH_KEYS, "Allows to insert new path to the BDV data and whether it is relative or absolute." );
+			descriptions.add( RANDOM_COLOR_TREES, RANDOM_COLOR_TREES_KEYS, "Assign to every lineage tree a randomly chosen color from the selected tag set." );
 		}
 	}
 
@@ -185,6 +189,8 @@ public void getCommandDescriptions( final CommandDescriptions descriptions )
 
 	private final AbstractNamedAction tweakDatasetPathAction;
 
+	private final AbstractNamedAction randomColorTreesAction;
+
 	private MamutPluginAppModel pluginAppModel;
 
 	public TomancakPlugins()
@@ -204,6 +210,7 @@ public TomancakPlugins()
 		exportSpotsCountsAction = new RunnableAction( EXPORTS_SPOTS_COUNTS, this::exportCounts );
 		mergeProjectsAction = new RunnableAction( MERGE_PROJECTS, this::mergeProjects );
 		tweakDatasetPathAction = new RunnableAction( TWEAK_DATASET_PATH, this::tweakDatasetPath );
+		randomColorTreesAction = new RunnableAction( RANDOM_COLOR_TREES, this::randomColorTrees );
 		updateEnabledActions();
 	}
 
@@ -220,6 +227,7 @@ public List< ViewMenuBuilder.MenuItem > getMenuItems()
 		return Arrays.asList(
 				menu( "Plugins",
 						item( COPY_TAG ),
+						item( RANDOM_COLOR_TREES ),
 						menu( "Auxiliary Displays",
 								item( COMPACT_LINEAGE_VIEW )),
 						menu( "Trees Management",
@@ -264,6 +272,7 @@ public void installGlobalActions( final Actions actions )
 		actions.namedAction( exportSpotsCountsAction, EXPORTS_SPOTS_COUNTS_KEYS );
 		actions.namedAction( mergeProjectsAction, MERGE_PROJECTS_KEYS );
 		actions.namedAction( tweakDatasetPathAction, TWEAK_DATASET_PATH_KEYS );
+		actions.namedAction( randomColorTreesAction, RANDOM_COLOR_TREES_KEYS );
 	}
 
 	private void updateEnabledActions()
@@ -283,6 +292,7 @@ private void updateEnabledActions()
 		exportSpotsCountsAction.setEnabled( appModel != null );
 		mergeProjectsAction.setEnabled( appModel != null );
 		tweakDatasetPathAction.setEnabled( appModel != null );
+		randomColorTreesAction.setEnabled( appModel != null );
 	}
 
 	private void exportPhyloXml()
@@ -413,4 +423,11 @@ private void labelSpotsSystematically()
 			LabelSpotsSystematicallyDialog.showDialog( pluginAppModel.getAppModel() );
 		}
 	}
+
+	private void randomColorTrees()
+	{
+		this.getContext().getService(CommandService.class).run(
+				LineageRandomColorizer.class, true,
+				"pluginAppModel", pluginAppModel);
+	}
 }

src/main/java/org/mastodon/mamut/tomancak/lineage_registration/TagSetUtils.java

@@ -19,6 +19,44 @@ private TagSetUtils()
 		// prevent instantiation of utility class
 	}
 
+	/**
+	 * Help creating a visible color value by adding
+	 * a (full opacity) alpha channel.
+	 * @param rgbAsBottom24bits The encoded RGB triplet.
+	 * @return The int value of the RGB color, ready to use
+	 *         with {@link org.mastodon.model.tag.TagSetStructure.Tag}.
+	 */
+	static public int rgbToValidColor(final int rgbAsBottom24bits) {
+		return 0xFF000000 | rgbAsBottom24bits;
+	}
+
+	/**
+	 * Help creating a visible color value by adding
+	 * a (full opacity) alpha channel.
+	 * @param r 0-255 valued red channel.
+	 * @param g 0-255 valued green channel.
+	 * @param b 0-255 valued blue channel.
+	 * @return The int value of the RGB color, ready to use
+	 *         with {@link org.mastodon.model.tag.TagSetStructure.Tag}.
+	 */
+	static public int rgbToValidColor(final int r, final int g, final int b) {
+		return 0xFF000000 | ((r & 0xFF) << 16) | ((g & 0xFF) << 8) | (b & 0xFF);
+	}
+
+	/**
+	 * Help creating a fully-described color value.
+	 * @param r 0-255 valued red channel.
+	 * @param g 0-255 valued green channel.
+	 * @param b 0-255 valued blue channel.
+	 * @param alpha 0-255 valued opacity (alpha) channel,
+	 *              0 - fully transparent, 255 - fully opaque.
+	 * @return The int value of the RGB color, ready to use
+	 *         with {@link org.mastodon.model.tag.TagSetStructure.Tag}.
+	 */
+	static public int rgbaToValidColor(final int r, final int g, final int b, final int alpha) {
+		return ((alpha & 0xFF) << 24) | ((r & 0xFF) << 16) | ((g & 0xFF) << 8) | (b & 0xFF);
+	}
+
 	/**
 	 * Add a new tag set to the given model.
 	 * @param model The model that will contain the new tag set.