Add documentation for export functions

README.md

@@ -270,6 +270,22 @@ Example: ![sort_lineage_tree_cell_life_cycle_duration.gif](doc/treesmanagement/s
 
 ### Export spot counts per lineage
 
+* Menu Location: `File > Export > Export measurements > 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`
+* 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 lineage lengths
+
+### Export phyloXML for selected spot
+
+* Menu Location: `File > Export > Export phyloXML for selected spot`
+* Export the subtree of the selected spot in phyloXML format.
+* The phyloXML format is a standard for representing phylogenetic trees: [phyloxml.org](http://www.phyloxml.org/)

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

@@ -77,7 +77,7 @@
 @Plugin( type = MamutPlugin.class )
 public class TomancakPlugins extends AbstractContextual implements MamutPlugin
 {
-	private static final String EXPORT_PHYLOXML = "[tomancak] export phyloxml for selection";
+	private static final String EXPORT_PHYLOXML = "[tomancak] export phyloxml for selected spot";
 	private static final String FLIP_DESCENDANTS = "[tomancak] flip lineage descendants";
 	private static final String COPY_TAG = "[tomancak] copy tag";
 	private static final String INTERPOLATE_SPOTS = "[tomancak] interpolate missing spots";
@@ -92,8 +92,10 @@ public class TomancakPlugins extends AbstractContextual implements MamutPlugin
 
 	private static final String REMOVE_ISOLATED_SPOTS = "[tomancak] remove isolated spots";
 	private static final String EXPORTS_LINEAGE_LENGTHS = "[tomancak] export lineage lengths";
-	private static final String EXPORT_SPOTS_COUNTS_PER_LINEAGE = "[tomancak] export spots counts per lineage";
-	private static final String EXPORT_SPOTS_COUNTS_PER_TIMEPOINT = "[tomancak] export spots counts per timepoint";
+
+	private static final String EXPORT_SPOTS_COUNTS_PER_LINEAGE = "[tomancak] export spot counts per lineage";
+
+	private static final String EXPORT_SPOTS_COUNTS_PER_TIMEPOINT = "[tomancak] export spot counts per timepoint";
 
 	private static final String ADD_CENTER_SPOTS = "[tomancak] add center spots";
 	private static final String MIRROR_SPOTS = "[tomancak] mirror spots";
@@ -133,7 +135,7 @@ public class TomancakPlugins extends AbstractContextual implements MamutPlugin
 
 	static
 	{
-		menuTexts.put( EXPORT_PHYLOXML, "Export phyloXML for selection" );
+		menuTexts.put( EXPORT_PHYLOXML, "Export phyloXML for selected spot" );
 		menuTexts.put( FLIP_DESCENDANTS, "Flip descendants" );
 		menuTexts.put( COPY_TAG, "Copy tag" );
 		menuTexts.put( INTERPOLATE_SPOTS, "Interpolate missing spots" );
@@ -147,8 +149,8 @@ public class TomancakPlugins extends AbstractContextual implements MamutPlugin
 		menuTexts.put( LABEL_SPOTS_SYSTEMATICALLY, "Systematically label spots (extern-intern)" );
 		menuTexts.put( REMOVE_ISOLATED_SPOTS, "Remove isolated spots" );
 		menuTexts.put( EXPORTS_LINEAGE_LENGTHS, "Export lineage lengths" );
-		menuTexts.put( EXPORT_SPOTS_COUNTS_PER_LINEAGE, "Export spots counts per lineage" );
-		menuTexts.put( EXPORT_SPOTS_COUNTS_PER_TIMEPOINT, "Export spots counts per timepoint" );
+		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( 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" );

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

@@ -81,9 +81,9 @@ public static void exportSelectedSubtreeToPhyloXmlFile( final ProjectModel appMo
 		{
 			final String message;
 			if ( vertices.isEmpty() )
-				message = "No spot selected. (Please select the root of the subtree to export.)";
+				message = "No spot selected. Please select the root of the subtree to export.";
 			else
-				message = "Too many spots selected. (Please select only the root spot of the subtree to export.)";
+				message = "Too many spots selected. Please select only the root spot of the subtree to export.";
 			JOptionPane.showMessageDialog( null,
 					message,
 					"Warning",