Merge pull request #83 from mastodon-sc/division_counts

Add new command Export Division counts per timepoint

Author: stefanhahmann

README.md

@@ -37,7 +37,7 @@
 * [Export measurements](#export-measurements)
     * [Export spot counts per lineage](#export-spot-counts-per-lineage)
     * [Export spot counts per time point](#export-spot-counts-per-time-point)
-    * [Export lineage lengths](#export-lineage-lengths)
+  * [Export division counts per time point](#export-division-counts-per-time-point)
   * [Export phyloXML for selected spot](#export-phyloxml-for-selected-spot)
 
 ## Documentation of Mastodon
@@ -349,18 +349,25 @@ The plugin allows performing various operations based on the correspondence info
 
 ### Export spot counts per lineage
 
-* Menu Location: `File > Export > Export measurements > Export spot counts per lineage`
+* Menu Location: `File > Export > Export measurements > Spot counts > Export spot counts per lineage`
 * Export spots counts per lineage per time point.
 * If spots are selected, only lineages with selected spots are included, otherwise all lineages are included.
 * Results in one CSV file per lineage.
 * Example: ![export_spot_counts_per_lineage.png](doc/export/export_spot_counts_per_lineage.png)
 
 ### Export spot counts per time point
 
-* Menu Location: `File > Export > Export measurements > Export spot counts per time point`
+* Menu Location: `File > Export > Export measurements > Spot counts > Export spot counts per time point`
 * This command writes the time point and the number of spots at each time point to a single CSV file.
 * Example: ![export_spot_counts_per_time_point.png](doc/export/export_spot_counts_per_time_point.png)
 
+### Export division counts per time point
+
+* Menu Location: `File > Export > Export measurements > Export division counts per time point`
+* This command writes the time point and the number of divisions at each time point to a single CSV file.
+* A division is defined as a spot with more than one outgoing edge.
+* Example: ![export_division_counts_per_time_point.png](doc/export/export_division_counts_per_time_point.png)
+
 ### Export phyloXML for selected spot
 
 * Menu Location: `File > Export > Export phyloXML for selected spot`

doc/export/export_division_counts_per_time_point.png

@@ -47,6 +47,7 @@
 import org.mastodon.mamut.tomancak.compact_lineage.CompactLineageFrame;
 import org.mastodon.mamut.tomancak.divisiontagset.CellDivisionsTagSetCommand;
 import org.mastodon.mamut.tomancak.export.ExportCounts;
+import org.mastodon.mamut.tomancak.export.ExportDivisionCountsPerTimepointCommand;
 import org.mastodon.mamut.tomancak.export.ExportSpotCountsPerTimepointCommand;
 import org.mastodon.mamut.tomancak.export.LineageLengthExporter;
 import org.mastodon.mamut.tomancak.export.MakePhyloXml;
@@ -97,6 +98,8 @@ public class TomancakPlugins extends AbstractContextual implements MamutPlugin
 
 	private static final String EXPORT_SPOTS_COUNTS_PER_TIMEPOINT = "[tomancak] export spot counts per timepoint";
 
+	private static final String EXPORT_DIVISION_COUNTS_PER_TIMEPOINT = "[tomancak] export division counts per timepoint";
+
 	private static final String ADD_CENTER_SPOTS = "[tomancak] add center spots";
 	private static final String MIRROR_SPOTS = "[tomancak] mirror spots";
 	private static final String CREATE_CONFLICT_TAG_SET = "[tomancak] create conflict tag set";
@@ -123,6 +126,8 @@ public class TomancakPlugins extends AbstractContextual implements MamutPlugin
 	private static final String[] EXPORTS_SPOTS_COUNTS_PER_LINEAGE_KEYS = { "not mapped" };
 	private static final String[] EXPORTS_SPOTS_COUNTS_PER_TIMEPOINT_KEYS = { "not mapped" };
 
+	private static final String[] EXPORT_DIVISION_COUNTS_PER_TIMEPOINT_KEYS = { "not mapped" };
+
 	private static final String[] ADD_CENTER_SPOTS_KEYS = { "not mapped" };
 	private static final String[] MIRROR_SPOTS_KEYS = { "not mapped" };
 	private static final String[] CREATE_CONFLICT_TAG_SET_KEYS = { "not mapped" };
@@ -151,6 +156,7 @@ public class TomancakPlugins extends AbstractContextual implements MamutPlugin
 		menuTexts.put( EXPORTS_LINEAGE_LENGTHS, "Export lineage lengths" );
 		menuTexts.put( EXPORT_SPOTS_COUNTS_PER_LINEAGE, "Export spot counts per lineage" );
 		menuTexts.put( EXPORT_SPOTS_COUNTS_PER_TIMEPOINT, "Export spot counts per timepoint" );
+		menuTexts.put( EXPORT_DIVISION_COUNTS_PER_TIMEPOINT, "Export division counts per timepoint" );
 		menuTexts.put( ADD_CENTER_SPOTS, "Add center spots" );
 		menuTexts.put( MIRROR_SPOTS, "Mirror spots along X-axis" );
 		menuTexts.put( CREATE_CONFLICT_TAG_SET, "Create conflict tag set" );
@@ -193,6 +199,8 @@ public void getCommandDescriptions( final CommandDescriptions descriptions )
 					"Exports counts of spots into CSV-like files to be imported in data processors. One file per lineage." );
 			descriptions.add( EXPORT_SPOTS_COUNTS_PER_TIMEPOINT, EXPORTS_SPOTS_COUNTS_PER_TIMEPOINT_KEYS,
 					"Exports counts of spots per timepoint into CSV-like files to be imported in data processors. One file." );
+			descriptions.add( EXPORT_DIVISION_COUNTS_PER_TIMEPOINT, EXPORT_DIVISION_COUNTS_PER_TIMEPOINT_KEYS,
+					"Exports counts of divisions per timepoint into CSV-like files to be imported in data processors. One file." );
 			descriptions.add( ADD_CENTER_SPOTS, ADD_CENTER_SPOTS_KEYS, "On each timepoint with selected spots, add a new spot that is in the center (average position)." );
 			descriptions.add( MIRROR_SPOTS, MIRROR_SPOTS_KEYS, "Mirror spots along x-axis." );
 			descriptions.add( CREATE_CONFLICT_TAG_SET, CREATE_CONFLICT_TAG_SET_KEYS, "Search spots that overlap and create a tag set that highlights these conflicts." );
@@ -239,6 +247,8 @@ public void getCommandDescriptions( final CommandDescriptions descriptions )
 
 	private final AbstractNamedAction exportSpotsCountsPerTimepointAction;
 
+	private final AbstractNamedAction exportDivisionCountsPerTimepointAction;
+
 	// private final AbstractNamedAction mergeProjectsAction;
 
 	private final AbstractNamedAction addCenterSpots;
@@ -275,6 +285,8 @@ public TomancakPlugins()
 		exportLineageLengthsAction = new RunnableAction( EXPORTS_LINEAGE_LENGTHS, this::exportLengths );
 		exportSpotsCountsPerLineageAction = new RunnableAction( EXPORT_SPOTS_COUNTS_PER_LINEAGE, this::exportCountsPerLineage );
 		exportSpotsCountsPerTimepointAction = new RunnableAction( EXPORT_SPOTS_COUNTS_PER_TIMEPOINT, this::exportCountsPerTimepoint );
+		exportDivisionCountsPerTimepointAction =
+				new RunnableAction( EXPORT_DIVISION_COUNTS_PER_TIMEPOINT, this::exportDivisionCountsPerTimepoint );
 		addCenterSpots = new RunnableAction( ADD_CENTER_SPOTS, this::addCenterSpots );
 		mirrorSpots = new RunnableAction( MIRROR_SPOTS, this::mirrorSpots );
 		createConflictTagSet = new RunnableAction( CREATE_CONFLICT_TAG_SET, this::createConflictTagSet );
@@ -299,7 +311,8 @@ public List< ViewMenuBuilder.MenuItem > getMenuItems()
 								menu( "Export measurements",
 										menu( "Spot counts",
 												item( EXPORT_SPOTS_COUNTS_PER_LINEAGE ),
-												item( EXPORT_SPOTS_COUNTS_PER_TIMEPOINT ) ) ),
+												item( EXPORT_SPOTS_COUNTS_PER_TIMEPOINT ) ),
+										item( EXPORT_DIVISION_COUNTS_PER_TIMEPOINT ) ),
 								// item( EXPORTS_LINEAGE_LENGTHS ) ), // NB: deactivated for now, since the function is too prototype-y
 								item( EXPORT_PHYLOXML ) ) ),
 				menu( "Plugins",
@@ -356,6 +369,7 @@ public void installGlobalActions( final Actions actions )
 		actions.namedAction( exportLineageLengthsAction, EXPORTS_LINEAGE_LENGTHS_KEYS );
 		actions.namedAction( exportSpotsCountsPerLineageAction, EXPORTS_SPOTS_COUNTS_PER_LINEAGE_KEYS );
 		actions.namedAction( exportSpotsCountsPerTimepointAction, EXPORTS_SPOTS_COUNTS_PER_TIMEPOINT_KEYS );
+		actions.namedAction( exportDivisionCountsPerTimepointAction, EXPORT_DIVISION_COUNTS_PER_TIMEPOINT_KEYS );
 		actions.namedAction( addCenterSpots, ADD_CENTER_SPOTS_KEYS );
 		actions.namedAction( mirrorSpots, MIRROR_SPOTS_KEYS );
 		actions.namedAction( createConflictTagSet, CREATE_CONFLICT_TAG_SET_KEYS );
@@ -449,6 +463,12 @@ private void exportCountsPerTimepoint()
 				"context", projectModel.getContext() );
 	}
 
+	private void exportDivisionCountsPerTimepoint()
+	{
+		commandService.run( ExportDivisionCountsPerTimepointCommand.class, true, "projectModel", projectModel,
+				"context", projectModel.getContext() );
+	}
+
 	private void changeBranchLabels()
 	{
 		RenameBranchLabels.run( projectModel );

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

@@ -0,0 +1,119 @@
+/*-
+ * #%L
+ * mastodon-tomancak
+ * %%
+ * Copyright (C) 2018 - 2025 Tobias Pietzsch
+ * %%
+ * 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.export;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Iterator;
+
+import com.opencsv.CSVWriter;
+
+import org.mastodon.mamut.ProjectModel;
+import org.mastodon.mamut.model.Model;
+import org.mastodon.mamut.model.Spot;
+import org.mastodon.util.TreeUtils;
+import org.scijava.Context;
+import org.scijava.ItemVisibility;
+import org.scijava.app.StatusService;
+import org.scijava.command.Command;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+@Plugin( type = Command.class, label = "Export division counts per timepoint" )
+public class ExportDivisionCountsPerTimepointCommand implements Command
+{
+
+	@Parameter( visibility = ItemVisibility.MESSAGE, required = false, persist = false )
+	private String documentation = "<html>\n"
+			+ "<body width=15cm align=left>\n"
+			+ "<h1>Export division counts per timepoint</h1>\n"
+			+ "<p>This command writes the timepoint and the number of divisions at each timepoint to a single CSV file.</p>\n"
+			+ "<p>A division is defined as a spot with more than one outgoing edge.</p>\n"
+			+ "<p>The format is: \"timepoint\", \"divisions\".</p>\n"
+			+ "<p>It is recommended to use '*.csv' as file extension.</p>\n"
+			+ "</body>\n"
+			+ "</html>\n";
+
+	@Parameter( label = "Save to" )
+	private File saveTo;
+
+	@Parameter
+	private ProjectModel projectModel;
+
+	@Parameter
+	private Context context;
+
+	@Override
+	public void run()
+	{
+		try
+		{
+			writeDivisionCountsToFile( projectModel.getModel(), saveTo, context.service( StatusService.class ) );
+		}
+		catch ( IOException e )
+		{
+			System.err.println(
+					"Could not write division counts to file: " + saveTo.getAbsolutePath() + ". Error message: " + e.getMessage() );
+		}
+	}
+
+	/**
+	 * Writes all timepoints and the number of divisions for each timepoint to the given file.
+	 * <ul>
+	 *     <li>The file will be overwritten, if it already exists.</li>
+	 *     <li>The file will be created, if it does not exist.</li>
+	 *     <li>The format is: "timepoint", "divisions".</li>
+	 *     <li>The first line is the header.</li>
+	 * </ul>
+	 */
+	public static void writeDivisionCountsToFile( final Model model, final File file, final StatusService statusService ) throws IOException
+	{
+		if ( file == null )
+			throw new IllegalArgumentException( "Cannot write division counts to file. Given file is null." );
+
+		try (CSVWriter csvWriter = new CSVWriter( new FileWriter( file ) ))
+		{
+			csvWriter.writeNext( new String[] { "timepoint", "divisions" } );
+			int minTimepoint = TreeUtils.getMinTimepoint( model );
+			int maxTimepoint = TreeUtils.getMaxTimepoint( model );
+			for ( int timepoint = minTimepoint; timepoint <= maxTimepoint; timepoint++ )
+			{
+				int divisions = 0;
+				for ( Spot spot : model.getSpatioTemporalIndex().getSpatialIndex( timepoint ) )
+				{
+					if ( spot.outgoingEdges().size() > 1 )
+						divisions++;
+				}
+				csvWriter.writeNext( new String[] { String.valueOf( timepoint ), String.valueOf( divisions ) }, false );
+				statusService.showProgress( timepoint, maxTimepoint );
+			}
+		}
+	}
+}

src/main/java/org/mastodon/mamut/tomancak/export/ExportDivisionCountsPerTimepointCommand.java

@@ -0,0 +1,74 @@
+/*-
+ * #%L
+ * mastodon-tomancak
+ * %%
+ * Copyright (C) 2018 - 2025 Tobias Pietzsch
+ * %%
+ * 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.export;
+
+import static org.junit.Assert.assertEquals;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.apache.commons.io.FileUtils;
+import org.junit.Test;
+import org.mastodon.mamut.feature.branch.exampleGraph.ExampleGraph2;
+import org.mastodon.mamut.model.Model;
+import org.scijava.Context;
+import org.scijava.app.StatusService;
+
+/**
+ * Tests {@link ExportDivisionCountsPerTimepointCommand}
+ */
+public class ExportDivisionCountsPerTimepointCommandTest
+{
+
+	@Test
+	public void testWriteDivisionCountsToFile() throws IOException
+	{
+		try (Context context = new Context())
+		{
+			Model model = new ExampleGraph2().getModel();
+			File outputFile = File.createTempFile( "divisioncounts", ".csv" );
+			outputFile.deleteOnExit();
+			StatusService service = context.service( StatusService.class );
+
+			ExportDivisionCountsPerTimepointCommand.writeDivisionCountsToFile( model, outputFile, service );
+
+			String content = FileUtils.readFileToString( outputFile );
+			String expected = "\"timepoint\",\"divisions\"\n"
+					+ "0,0\n"
+					+ "1,0\n"
+					+ "2,1\n"
+					+ "3,0\n"
+					+ "4,1\n"
+					+ "5,0\n"
+					+ "6,0\n"
+					+ "7,0\n";
+			assertEquals( expected, content );
+		}
+	}
+}