Merge pull request #49 from tpietzsch/upgrade-bdv

Update to more recent bigdataviewer-core API (WIP)
PreibischLab · Nov 16, 2023 · 2d8a6dd · 2d8a6dd
2 parents e10dc99 + 3c1433e
commit 2d8a6dd
Show file tree

Hide file tree

Showing 56 changed files with 481 additions and 574 deletions.
diff --git a/pom.xml b/pom.xml
@@ -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>

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/grid/RegularTranformHelpers.java b/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)
 	{

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/Data_Explorer.java b/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();
 	}

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/Interest_Point_Detection.java b/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
 	{

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/Split_Views.java b/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

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ExplorerWindow.java b/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();
 }
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorer.java b/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()