Merge pull request #3 from PreibischLab/master

Merge 3.2.5 changes

pom.xml

@@ -5,13 +5,13 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>36.0.0</version>
+		<version>37.0.0</version>
 		<relativePath />
 	</parent>
 
 	<groupId>net.preibisch</groupId>
 	<artifactId>multiview-reconstruction</artifactId>
-	<version>3.2.4-SNAPSHOT</version>
+	<version>3.2.6-SNAPSHOT</version>
 
 	<name>Multiview Reconstruction</name>
 	<description>Software for the reconstruction of multi-view microscopic acquisitions
@@ -105,12 +105,8 @@ like Selective Plane Illumination Microscopy (SPIM) Data.</description>
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 
-		<imglib2.version>6.1.0</imglib2.version>
-		<imglib2-algorithm.version>0.13.2</imglib2-algorithm.version>
-		<imglib2-cache.version>1.0.0-beta-17</imglib2-cache.version>
-		<bigdataviewer-core.version>10.4.6</bigdataviewer-core.version>
-		<bigdataviewer-vistools.version>1.0.0-beta-32</bigdataviewer-vistools.version>
-		<n5-imglib2.version>5.0.0</n5-imglib2.version>
+		<bigdataviewer-core.version>10.4.12</bigdataviewer-core.version>
+		<bigdataviewer-vistools.version>1.0.0-beta-33</bigdataviewer-vistools.version>
 	</properties>
 
 	<repositories>

src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/grid/RegularTranformHelpers.java

@@ -264,8 +264,8 @@ private static int prod(int ... v)
 	}
 
 	public static <AS extends AbstractSpimData<?> > void applyToSpimData(
-			AS data, 
-			List<? extends Group< ? extends BasicViewDescription< ? extends BasicViewSetup > > > viewDescriptions,
+			AS data,
+			List<? extends Group< ? extends BasicViewDescription< ? > > > viewDescriptions,
 			RegularTranslationParameters params,
 			boolean applyToAllTimePoints)
 	{
@@ -313,8 +313,8 @@ private static int getRotationAxisFromUnitVector(double[] axis)
 	}
 
 	private static <AS extends AbstractSpimData<?> > void applyToSpimDataSingleTP(
-			AS data, 
-			List< ? extends Group< ? extends BasicViewDescription< ? extends BasicViewSetup > > > viewDescriptions,
+			AS data,
+			List< ? extends Group< ? extends BasicViewDescription< ? > > > viewDescriptions,
 			RegularTranslationParameters params,
 			TimePoint tp)
 	{

src/main/java/net/preibisch/mvrecon/fiji/plugin/Data_Explorer.java

@@ -73,7 +73,7 @@ public void actionPerformed(ActionEvent e)
 		final String xml = result.getXMLFileName();
 		final XmlIoSpimData2 io = result.getIO();
 
-		final ViewSetupExplorer< SpimData2, XmlIoSpimData2 > explorer = new ViewSetupExplorer<SpimData2, XmlIoSpimData2 >( data, xml, io );
+		final ViewSetupExplorer< SpimData2 > explorer = new ViewSetupExplorer<>( data, xml, io );
 
 		explorer.getFrame().toFront();
 	}

src/main/java/net/preibisch/mvrecon/fiji/plugin/Interest_Point_Detection.java

@@ -66,7 +66,7 @@ public class Interest_Point_Detection implements PlugIn
 
 	public static boolean defaultGroupTiles = true;
 	public static boolean defaultGroupIllums = true;
-	public static ExplorerWindow< ?, ? > currentPanel;
+	public static ExplorerWindow< ? > currentPanel;
 
 	static
 	{

src/main/java/net/preibisch/mvrecon/fiji/plugin/Split_Views.java

@@ -86,7 +86,7 @@ public static boolean split(
 
 		if ( display )
 		{
-			final ViewSetupExplorer< SpimData2, XmlIoSpimData2 > explorer = new ViewSetupExplorer<SpimData2, XmlIoSpimData2 >( newSD, saveAs, new XmlIoSpimData2( "" ) );
+			final ViewSetupExplorer< SpimData2 > explorer = new ViewSetupExplorer<>( newSD, saveAs, new XmlIoSpimData2( "" ) );
 			explorer.getFrame().toFront();
 		}
 		else

src/main/java/net/preibisch/mvrecon/fiji/plugin/queryXML/GenericLoadParseQueryXML.java

@@ -316,7 +316,7 @@ public boolean queryXML(
 		this.gd = gd;
 
 		gd.addMessage( "" );
-		GUIHelper.addPreibischLabWebsite( gd );
+		GUIHelper.addCredits( gd );
 
 		gd.showDialog();
 

src/main/java/net/preibisch/mvrecon/fiji/plugin/util/GUIHelper.java

@@ -73,13 +73,13 @@ public class GUIHelper
 
 	public static Font staticfont = new Font( Font.MONOSPACED, Font.PLAIN, 12 );
 
-	final public static String myURL = "http://preibischlab.mdc-berlin.de/";
-	final public static String paperURL = "http://www.nature.com/nmeth/journal/v7/n6/full/nmeth0610-418.html";
-	final public static String messagePaper = "Please note that the SPIM Registration is based on a publication.\n" +
+	final public static String myURL = "https://www.janelia.org/open-science/overview/open-science-software-initiative-ossi";
+	final public static String paperURL = "https://www.nature.com/articles/s41592-019-0501-0";
+	final public static String messagePaper = "Please note that BigStitcher is based on a publication.\n" +
 											  "If you use it successfully for your research please be so kind to cite our work:\n" +
-											  "Preibisch et al., Nature Methods (2010), 7(6):418-419\n";
+											  "Nature Methods 16: 870–874 (2019)\n";
 
-	final public static String messageWebsite = "This plugin is written and maintained by the Preibisch Lab (click for webpage)\n";
+	final public static String messageWebsite = "This plugin was written by the Preibisch Lab is now supported by the HHMI Janelia Open Science Software initative\n";
 
 	public static void addNatMethBeadsPaper( final GenericDialog gd ) { addNatMethBeadsPaper( gd, messagePaper ); }
 	public static void addNatMethBeadsPaper( final GenericDialog gd, final String msg )  { addHyperLink( gd, msg, paperURL ); }
@@ -94,11 +94,11 @@ public static final void addHyperLink( final GenericDialog gd, final String msg,
 		GUIHelper.addHyperLinkListener( text, url );
 	}
 
-	public static final void addPreibischLabWebsite( final GenericDialog gd )
+	public static final void addCredits( final GenericDialog gd )
 	{
-		gd.addMessage( "This software is developed by the Preibisch Lab in collaboration with the ImgLib2 and Fiji team\nhttp://preibischlab.mdc-berlin.de/", new Font( Font.SANS_SERIF, Font.BOLD, 12 ) );
+		gd.addMessage( "This software was developed by the Preibisch Lab (MDC Berlin) and is now supported by the\nHHMI Janelia Open Science Software initative in collaboration with the ImgLib2 and Fiji team", new Font( Font.SANS_SERIF, Font.BOLD, 12 ) );
 		MultiLineLabel text =  (MultiLineLabel) gd.getMessage();
-		GUIHelper.addHyperLinkListener( text, "http://preibischlab.github.io/preibisch-labsite" );
+		GUIHelper.addHyperLinkListener( text, "https://www.janelia.org/open-science/overview/open-science-software-initiative-ossi" );
 	}
 
 	public static void displayRegistrationNames( final GenericDialog gd, final HashMap< String, Integer > names )

src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ExplorerWindow.java

@@ -32,9 +32,9 @@
 import mpicbg.spim.data.generic.sequence.BasicViewSetup;
 import mpicbg.spim.data.sequence.ViewId;
 
-public interface ExplorerWindow< AS extends AbstractSpimData< ? >, X extends XmlIoAbstractSpimData< ?, AS > >
+public interface ExplorerWindow< AS extends AbstractSpimData< ? > >
 {
-	public List< BasicViewDescription< ? extends BasicViewSetup > > selectedRows();
+	public List< BasicViewDescription< ? > > selectedRows();
 	public List< ViewId > selectedRowsViewId();
 	public AS getSpimData();
 	public void updateContent();
@@ -48,5 +48,5 @@ public interface ExplorerWindow< AS extends AbstractSpimData< ? >, X extends Xml
 	// BDV-specific
 	public BasicBDVPopup bdvPopup();
 	public boolean colorMode();
-	public BasicViewDescription< ? extends BasicViewSetup > firstSelectedVD();
+	public BasicViewDescription< ? > firstSelectedVD();
 }

src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorer.java

@@ -27,19 +27,18 @@
 import javax.swing.JFrame;
 
 import mpicbg.spim.data.generic.AbstractSpimData;
-import mpicbg.spim.data.generic.XmlIoAbstractSpimData;
 
-public abstract class FilteredAndGroupedExplorer<AS extends AbstractSpimData< ? >, X extends XmlIoAbstractSpimData< ?, AS >>
+public abstract class FilteredAndGroupedExplorer<AS extends AbstractSpimData< ? > >
 {
 
 	protected JFrame frame;
-	protected FilteredAndGroupedExplorerPanel< AS, X > panel;
+	protected FilteredAndGroupedExplorerPanel< AS > panel;
 
 
 	public AS getSpimData()
 	{ return panel.getSpimData(); }
 
-	public FilteredAndGroupedExplorerPanel< AS, X > getPanel()
+	public FilteredAndGroupedExplorerPanel< AS > getPanel()
 	{ return panel; }
 
 	public JFrame getFrame()