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 index 89eefedab..ddf4e5bff 100644 --- 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 > void applyToSpimData( - AS data, - List > > viewDescriptions, + AS data, + List > > viewDescriptions, RegularTranslationParameters params, boolean applyToAllTimePoints) { @@ -313,8 +313,8 @@ private static int getRotationAxisFromUnitVector(double[] axis) } private static > 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/spimdata/explorer/FilteredAndGroupedExplorerPanel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java index 1ec7b5413..a3b358b9e 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java +++ b/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; } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedTableModel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedTableModel.java index c6a7dce09..86543af1b 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedTableModel.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedTableModel.java @@ -170,12 +170,12 @@ public FilteredAndGroupedTableModel( final ExplorerWindow< AS > panel ) elements(); } - protected List >> elements() + protected List >> elements() { return elements(false); } - protected List >> elements( boolean forceUpdate ) + protected List >> 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> vds = elements().get( row ); + final List> vds = elements().get( row ); Class c = columnClasses.get(column); final HashSet entries = new HashSet<>(); - - for (BasicViewDescription< ? extends BasicViewSetup > vd : vds) + + for (BasicViewDescription< ? > vd : vds) { if ( c == TimePoint.class ) entries.add(vd.getTimePoint()); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MultiViewTableModelDecorator.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MultiViewTableModelDecorator.java index f24cf1d92..d1d07e7cd 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MultiViewTableModelDecorator.java +++ b/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() ) { diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorerPanel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorerPanel.java index 5a90e4a15..e959dc220 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorerPanel.java +++ b/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>> selectedList = new ArrayList<>(); - for (List> selectedI : selectedRows) + + List>> selectedList = new ArrayList<>(); + for (List> 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 ); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorer.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorer.java index d9fede760..f8481e8d7 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorer.java +++ b/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 ); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorerPanel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorerPanel.java index ba140f75c..ebd8ba096 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorerPanel.java +++ b/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 ); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorer.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorer.java index d5a531754..2dd8f3056 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorer.java +++ b/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 >> viewDescriptions ) + public void selectedViewDescriptions( final List >> viewDescriptions ) { - List> vdsFlat = new ArrayList<>(); - for (List> vdsI : viewDescriptions) + List> vdsFlat = new ArrayList<>(); + for (List> vdsI : viewDescriptions) vdsFlat.addAll( vdsI ); panel.updateViewDescriptions( vdsFlat ); System.out.println( viewDescriptions ); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/DHMImgLoader.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/DHMImgLoader.java index a84867e68..bd43ac29d 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/DHMImgLoader.java +++ b/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 ) ); } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyDHMImgLoader.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyDHMImgLoader.java index b1950fdeb..7ee55a99d 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyDHMImgLoader.java +++ b/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; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyMicroManagerImgLoader.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyMicroManagerImgLoader.java index 78a06fdf3..d3f68cb77 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyMicroManagerImgLoader.java +++ b/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; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/MicroManagerImgLoader.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/MicroManagerImgLoader.java index 8739523e1..77bf3d6be 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/MicroManagerImgLoader.java +++ b/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 ) ); } diff --git a/src/main/java/net/preibisch/mvrecon/process/deconvolution/util/ProcessInputImages.java b/src/main/java/net/preibisch/mvrecon/process/deconvolution/util/ProcessInputImages.java index 004505b33..f8b1702a3 100644 --- a/src/main/java/net/preibisch/mvrecon/process/deconvolution/util/ProcessInputImages.java +++ b/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, diff --git a/src/main/java/net/preibisch/mvrecon/process/fusion/FusionTools.java b/src/main/java/net/preibisch/mvrecon/process/fusion/FusionTools.java index d00cf694c..1cdca1b86 100644 --- a/src/main/java/net/preibisch/mvrecon/process/fusion/FusionTools.java +++ b/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() );