Merge pull request #87 from mastodon-sc/improve-spots-and-divisions

Improve dialog show spots and divisions

Author: stefanhahmann

.github/workflows/build-main.yml

@@ -14,7 +14,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - name: Set up Java
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           java-version: '8'
           distribution: 'zulu'

.github/workflows/build-pr.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - name: Set up Java
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           java-version: '8'
           distribution: 'zulu'

README.md

@@ -354,6 +354,8 @@ The plugin allows performing various operations based on the correspondence info
 * Menu Location: `Plugins > Lineage analysis > Show spot and division counts over time`
 * The command shows a plot of the number of spots and divisions over time.
 * It is possible to set a window size, which is used to compute a sliding average.
+* Colors, visibilities, and sliding average windows size can be set in the plot and are persisted as user preference
+* A context menu allows to export the plot as a PNG/SVG file.
 * A division is defined as a spot with more than one outgoing edge.
 * Example: ![spot_and_division_counts_over_time.png](doc/lineageanalysis/spot_and_division_counts_over_time.png)
 

doc/lineageanalysis/spot_and_division_counts_over_time.png

@@ -45,7 +45,7 @@
 import org.mastodon.mamut.model.Spot;
 import org.mastodon.mamut.plugin.MamutPlugin;
 import org.mastodon.mamut.tomancak.compact_lineage.CompactLineageFrame;
-import org.mastodon.mamut.tomancak.divisioncount.ShowSpotAndDivisionCountsOverTimeCommand;
+import org.mastodon.mamut.tomancak.divisioncount.SpotAndDivisionCountChart;
 import org.mastodon.mamut.tomancak.divisiontagset.CellDivisionsTagSetCommand;
 import org.mastodon.mamut.tomancak.export.ExportCounts;
 import org.mastodon.mamut.tomancak.export.ExportDivisionCountsPerTimepointCommand;
@@ -70,6 +70,7 @@
 import org.scijava.command.CommandService;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
+import org.scijava.prefs.PrefService;
 import org.scijava.ui.behaviour.io.gui.CommandDescriptionProvider;
 import org.scijava.ui.behaviour.io.gui.CommandDescriptions;
 import org.scijava.ui.behaviour.util.AbstractNamedAction;
@@ -225,6 +226,9 @@ public void getCommandDescriptions( final CommandDescriptions descriptions )
 	@Parameter
 	private CommandService commandService;
 
+	@Parameter
+	private PrefService prefService;
+
 	private final AbstractNamedAction exportPhyloXmlAction;
 
 	private final AbstractNamedAction flipDescendantsAction;
@@ -488,7 +492,7 @@ private void exportDivisionCountsPerTimepoint()
 
 	private void showSpotAndDivisionCountsOverTime()
 	{
-		commandService.run( ShowSpotAndDivisionCountsOverTimeCommand.class, true, "projectModel", projectModel );
+		SpotAndDivisionCountChart.show( projectModel, prefService );
 	}
 
 	private void changeBranchLabels()