Simplify generics

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/spimdata/explorer/FilteredAndGroupedExplorerPanel.java

@@ -32,6 +32,7 @@
 import java.util.List;
 import java.util.Map;
 
+import java.util.Set;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.JTable;
@@ -97,7 +98,7 @@ public abstract class FilteredAndGroupedExplorerPanel< AS extends AbstractSpimDa
 	protected boolean colorMode = false;
 
 	final protected HashSet< List< BasicViewDescription< ? > > > selectedRows;
-	protected BasicViewDescription< ? extends BasicViewSetup > firstSelectedVD;
+	protected BasicViewDescription< ? > firstSelectedVD;
 
 	public FilteredAndGroupedExplorerPanel(final FilteredAndGroupedExplorer< AS > explorer, final AS data,
 			final String xml, final XmlIoAbstractSpimData< ?, AS > io)
@@ -373,7 +374,7 @@ public static void updateBDV(
 			final BigDataViewer bdv,
 			final boolean colorMode,
 			final AbstractSpimData< ? > data,
-			BasicViewDescription< ? extends BasicViewSetup > firstVD,
+			BasicViewDescription< ? > firstVD,
 			final Collection< List< BasicViewDescription< ? > > > selectedRows )
 	{
 
@@ -399,7 +400,7 @@ public static void updateBDV(
 
 		final boolean[] active = new boolean[data.getSequenceDescription().getViewSetupsOrdered().size()];
 
-		for ( final List< ? extends BasicViewDescription< ? extends BasicViewSetup > > vds : selectedRows )
+		for ( final List< ? extends BasicViewDescription< ? > > vds : selectedRows )
 			for ( BasicViewDescription< ? > vd : vds){
 				if ( vd.getTimePointId() == firstTP.getId() )
 					active[getBDVSourceIndex( vd.getViewSetup(), data )] = true;
@@ -477,7 +478,7 @@ public static int getBDVSourceIndex( final BasicViewSetup vs, final AbstractSpim
 		return 0;
 	}
 
-	public HashSet< List< BasicViewDescription< ? extends BasicViewSetup > > > getSelectedRows()
+	public Set< List< BasicViewDescription< ? > > > getSelectedRows()
 	{
 		return selectedRows;
 	}

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

@@ -170,12 +170,12 @@ public FilteredAndGroupedTableModel( final ExplorerWindow< AS > panel )
 		elements();
 	}
 
-	protected List<List< BasicViewDescription< ? extends BasicViewSetup > >> elements()
+	protected List<List< BasicViewDescription< ? > >> elements()
 	{
 		return elements(false);
 	}
 
-	protected List<List< BasicViewDescription< ? extends BasicViewSetup > >> elements( boolean forceUpdate )
+	protected List<List< BasicViewDescription< ? > >> elements( boolean forceUpdate )
 	{
 		if (!forceUpdate && elements != null)
 			return elements;
@@ -235,12 +235,12 @@ public boolean isCellEditable( final int row, final int column )
 	@Override
 	public Object getValueAt( final int row, final int column )
 	{
-		final List<BasicViewDescription< ? extends BasicViewSetup >> vds = elements().get( row );
+		final List<BasicViewDescription< ? >> vds = elements().get( row );
 
 		Class <? extends Entity> c = columnClasses.get(column);
 		final HashSet<Entity> entries = new HashSet<>();
-		
-		for (BasicViewDescription< ? extends BasicViewSetup > vd : vds)
+
+		for (BasicViewDescription< ? > vd : vds)
 		{
 			if ( c == TimePoint.class )
 				entries.add(vd.getTimePoint());

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

@@ -124,7 +124,7 @@ public Object getValueAt(int rowIndex, int columnIndex) {
 
 		if ( vds.size() == 1 )
 		{
-			final BasicViewDescription< ? extends BasicViewSetup > vd = vds.get( 0 );
+			final BasicViewDescription< ? > vd = vds.get( 0 );
 
 			if ( vd.isPresent() )
 			{

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

@@ -344,9 +344,9 @@ public void valueChanged(final ListSelectionEvent arg0)
 
 					selectedRows.add( tableModel.getElements().get( row ) );
 				}
-				
-				List<List<BasicViewDescription< ? extends BasicViewSetup >>> selectedList = new ArrayList<>();
-				for (List<BasicViewDescription< ? extends BasicViewSetup >> selectedI : selectedRows)
+
+				List<List<BasicViewDescription< ? >>> selectedList = new ArrayList<>();
+				for (List<BasicViewDescription< ? >> selectedI : selectedRows)
 					selectedList.add( selectedI );
 
 				for ( int i = 0; i < listeners.size(); ++i )
@@ -415,8 +415,8 @@ public void valueChanged(final ListSelectionEvent arg0)
 	}
 
 	public static void updateBDV(final BigDataViewer bdv, final boolean colorMode, final AbstractSpimData< ? > data,
-			BasicViewDescription< ? extends BasicViewSetup > firstVD,
-			final Collection< List< BasicViewDescription< ? extends BasicViewSetup >> > selectedRows)
+			BasicViewDescription< ? > firstVD,
+			final Collection< List< BasicViewDescription< ? >> > selectedRows)
 	{
 		// we always set the fused mode
 		setFusedModeSimple( bdv, data );

src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorer.java

@@ -91,12 +91,12 @@ public void windowClosing(WindowEvent e)
 	public JFrame frame() { return frame; }
 
 	@Override
-	public void selectedViewDescriptions( final List< List< BasicViewDescription< ? extends BasicViewSetup > > > viewDescriptions )
+	public void selectedViewDescriptions( final List< List< BasicViewDescription< ? > > > viewDescriptions )
 	{
-		final ArrayList< BasicViewDescription< ? extends BasicViewSetup > > fullList = new ArrayList<>();
+		final ArrayList< BasicViewDescription< ? > > fullList = new ArrayList<>();
 
-		for ( final List< BasicViewDescription< ? extends BasicViewSetup > > list : viewDescriptions )
-			for ( final BasicViewDescription< ? extends BasicViewSetup > vd : list )
+		for ( final List< BasicViewDescription< ? > > list : viewDescriptions )
+			for ( final BasicViewDescription< ? > vd : list )
 				if ( vd.isPresent() )
 					fullList.add( vd );
 

src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorerPanel.java

@@ -84,12 +84,12 @@ public InterestPointExplorerPanel( final ViewInterestPoints viewInterestPoints,
 
 	public InterestPointTableModel getTableModel() { return tableModel; }
 	public JTable getTable() { return table; }
-	
-	public void updateViewDescription( final List< BasicViewDescription< ? extends BasicViewSetup > > viewDescriptionsUnfiltered )
+
+	public void updateViewDescription( final List< BasicViewDescription< ? > > viewDescriptionsUnfiltered )
 	{
-		final ArrayList< BasicViewDescription< ? extends BasicViewSetup > > viewDescriptions = new ArrayList<>();
+		final ArrayList< BasicViewDescription< ? > > viewDescriptions = new ArrayList<>();
 
-		for ( final BasicViewDescription< ? extends BasicViewSetup > vd : viewDescriptionsUnfiltered )
+		for ( final BasicViewDescription< ? > vd : viewDescriptionsUnfiltered )
 			if ( vd.isPresent() )
 				viewDescriptions.add( vd );
 

src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorer.java

@@ -78,10 +78,10 @@ public RegistrationExplorer( final String xml, final XmlIoAbstractSpimData< ?, A
 	public void save() {}
 
 	@Override
-	public void selectedViewDescriptions( final List<List< BasicViewDescription< ? extends BasicViewSetup > >> viewDescriptions )
+	public void selectedViewDescriptions( final List<List< BasicViewDescription< ? > >> viewDescriptions )
 	{
-		List<BasicViewDescription< ? extends BasicViewSetup >> vdsFlat = new ArrayList<>();
-		for (List<BasicViewDescription< ? extends BasicViewSetup >> vdsI : viewDescriptions)
+		List<BasicViewDescription< ? >> vdsFlat = new ArrayList<>();
+		for (List<BasicViewDescription< ? >> vdsI : viewDescriptions)
 			vdsFlat.addAll( vdsI );
 		panel.updateViewDescriptions( vdsFlat );
 		System.out.println( viewDescriptions );

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/DHMImgLoader.java

@@ -43,7 +43,7 @@ public DHMImgLoader(
 			final String extension,
 			final int ampChannelId,
 			final int phaseChannelId,
-			final AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? > sd )
+			final AbstractSequenceDescription< ?, ?, ? > sd )
 	{
 		super( new LegacyDHMImgLoader( directory, stackDir, amplitudeDir, phaseDir, timepoints, zPlanes, extension, ampChannelId, phaseChannelId, sd ) );
 	}

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyDHMImgLoader.java

@@ -51,7 +51,7 @@
 public class LegacyDHMImgLoader extends AbstractImgLoader
 {
 	final File directory;
-	final AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? > sd;
+	final AbstractSequenceDescription< ?, ?, ? > sd;
 	final List< String > timepoints;
 	final List< String > zPlanes;
 	final String stackDir;
@@ -71,7 +71,7 @@ public LegacyDHMImgLoader(
 			final String extension,
 			final int ampChannelId,
 			final int phaseChannelId,
-			final AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? > sd )
+			final AbstractSequenceDescription< ?, ?, ? > sd )
 	{
 		this.directory = directory;
 		this.stackDir = stackDir;

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyMicroManagerImgLoader.java

@@ -53,11 +53,11 @@
 public class LegacyMicroManagerImgLoader extends AbstractImgLoader
 {
 	final File mmFile;
-	final AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? > sequenceDescription;
+	final AbstractSequenceDescription< ?, ?, ? > sequenceDescription;
 
 	public LegacyMicroManagerImgLoader(
 			final File mmFile,
-			final AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? > sequenceDescription )
+			final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
 	{
 		super();
 		this.mmFile = mmFile;

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/MicroManagerImgLoader.java

@@ -34,7 +34,7 @@ public class MicroManagerImgLoader extends LegacyImgLoaderWrapper< UnsignedShort
 {
 	public MicroManagerImgLoader(
 			final File mmFile,
-			final AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? > sequenceDescription )
+			final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
 	{
 		super( new LegacyMicroManagerImgLoader( mmFile, sequenceDescription ) );
 	}

src/main/java/net/preibisch/mvrecon/process/deconvolution/util/ProcessInputImages.java

@@ -66,7 +66,7 @@
 
 public class ProcessInputImages< V extends ViewId >
 {
-	final AbstractSpimData< ? extends AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? extends BasicImgLoader > > spimData;
+	final AbstractSpimData< ? > spimData;
 	final ArrayList< Group< V > > groups;
 	final Interval bb;
 	Interval downsampledBB;
@@ -81,7 +81,7 @@ public class ProcessInputImages< V extends ViewId >
 	final Map< ? extends ViewId, AffineModel1D > intensityAdjustments;
 
 	public ProcessInputImages(
-			final AbstractSpimData< ? extends AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? extends BasicImgLoader > > spimData,
+			final AbstractSpimData< ? > spimData,
 			final Collection< Group< V > > groups,
 			final ExecutorService service,
 			final Interval bb,
@@ -116,7 +116,7 @@ public ProcessInputImages(
 	}
 
 	public ProcessInputImages(
-			final AbstractSpimData< ? extends AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? extends BasicImgLoader > > spimData,
+			final AbstractSpimData< ? > spimData,
 			final Collection< Group< V > > groups,
 			final ExecutorService service,
 			final Interval bb,
@@ -131,7 +131,7 @@ public ProcessInputImages(
 	}
 
 	public ProcessInputImages(
-			final AbstractSpimData< ? extends AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? extends BasicImgLoader > > spimData,
+			final AbstractSpimData< ? > spimData,
 			final Collection< Group< V > > groups,
 			final ExecutorService service,
 			final Interval bb,
@@ -275,7 +275,7 @@ public static < V extends ViewId > void copyRandomAccessibleInterval(
 	}
 
 	public static < V extends ViewId > Interval fuseGroups(
-			final AbstractSpimData< ? extends AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? extends BasicImgLoader > > spimData,
+			final AbstractSpimData< ? > spimData,
 			final HashMap< Group< V >, RandomAccessibleInterval< FloatType > > tImgs,
 			final HashMap< Group< V >, RandomAccessibleInterval< FloatType > > tWeights,
 			final HashMap< V, AffineTransform3D > models,

src/main/java/net/preibisch/mvrecon/process/fusion/FusionTools.java

@@ -662,7 +662,7 @@ else if ( imgType == ImgDataType.PRECOMPUTED )
 	 * @param border - the target blending border, e.g. 0
 	 * @param transformationModel - the transformation model used to map from the (downsampled) input to the output
 	 */
-	public static void adjustBlending( final BasicViewDescription< ? extends BasicViewSetup > vd, final float[] blending, final float[] border, final AffineTransform3D transformationModel )
+	public static void adjustBlending( final BasicViewDescription< ? > vd, final float[] blending, final float[] border, final AffineTransform3D transformationModel )
 	{
 		adjustBlending( vd.getViewSetup().getSize(), Group.pvid( vd ), blending, border, transformationModel );
 	}
@@ -691,7 +691,7 @@ public static void adjustBlending( final Dimensions dim, final String name, fina
 	 * @param sigma2 - the target sigma2 for entropy approximation, e.g. 40
 	 * @param usedDownsampleFactors - the downsampling factors used to load the input image
 	 */
-	public static void adjustContentBased( final BasicViewDescription< ? extends BasicViewSetup > vd, final double[] sigma1, final double[] sigma2, final double[] usedDownsampleFactors )
+	public static void adjustContentBased( final BasicViewDescription< ? > vd, final double[] sigma1, final double[] sigma2, final double[] usedDownsampleFactors )
 	{
 		for ( int d = 0; d < sigma1.length; ++d )
 		{
@@ -700,7 +700,7 @@ public static void adjustContentBased( final BasicViewDescription< ? extends Bas
 		}
 	}
 
-	public static double getMinRes( final BasicViewDescription< ? extends BasicViewSetup > desc )
+	public static double getMinRes( final BasicViewDescription< ? > desc )
 	{
 		final VoxelDimensions size = ViewSetupUtils.getVoxelSize( desc.getViewSetup() );