diff --git a/pom.xml b/pom.xml
index faacb112c..800983e01 100644
--- a/pom.xml
+++ b/pom.xml
@@ -105,12 +105,8 @@ like Selective Plane Illumination Microscopy (SPIM) Data.
sign,deploy-to-scijava
- 6.1.0
- 0.13.2
- 1.0.0-beta-17
- 10.4.6
- 1.0.0-beta-32
- 5.0.0
+ 10.4.12
+ 1.0.0-beta-33
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/plugin/Data_Explorer.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/Data_Explorer.java
index 87a45c5dc..6b08e0068 100644
--- 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( 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
index 55278a5d7..ec0736cbd 100644
--- 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
index 6003a8292..5e2bc5a85 100644
--- 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( 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
index 10a754b76..26435afca 100644
--- 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
index 7998a264b..5e0642f8c 100644
--- 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, X extends XmlIoAbstractSpimData< ?, AS >>
+public abstract class FilteredAndGroupedExplorer >
{
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()
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 a84abdb8b..351a31b31 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
@@ -22,6 +22,7 @@
*/
package net.preibisch.mvrecon.fiji.spimdata.explorer;
+import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.util.ArrayList;
@@ -29,8 +30,9 @@
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
-import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JTable;
@@ -40,10 +42,9 @@
import bdv.BigDataViewer;
import bdv.tools.HelpDialog;
import bdv.tools.brightness.ConverterSetup;
-import bdv.tools.transformation.TransformedSource;
import bdv.viewer.DisplayMode;
-import bdv.viewer.VisibilityAndGrouping;
-import bdv.viewer.state.SourceState;
+import bdv.viewer.SourceAndConverter;
+import bdv.viewer.ViewerState;
import mpicbg.spim.data.SpimDataException;
import mpicbg.spim.data.generic.AbstractSpimData;
import mpicbg.spim.data.generic.XmlIoAbstractSpimData;
@@ -62,6 +63,7 @@
import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
import net.preibisch.mvrecon.fiji.spimdata.SpimDataTools;
import net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough;
+import net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVUtils;
import net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup;
import net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ExplorerWindowSetable;
import net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints;
@@ -69,10 +71,10 @@
import net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPoints;
import net.preibisch.mvrecon.process.interestpointregistration.TransformationTools;
-public abstract class FilteredAndGroupedExplorerPanel, X extends XmlIoAbstractSpimData< ?, AS >>
- extends JPanel implements ExplorerWindow< AS, X >, GroupedRowWindow
+public abstract class FilteredAndGroupedExplorerPanel< AS extends AbstractSpimData< ? > >
+ extends JPanel implements ExplorerWindow< AS >, GroupedRowWindow
{
- public static FilteredAndGroupedExplorerPanel< ?, ? > currentInstance = null;
+ public static FilteredAndGroupedExplorerPanel< ? > currentInstance = null;
protected ArrayList< ExplorerWindowSetable > popups;
@@ -81,32 +83,31 @@ public abstract class FilteredAndGroupedExplorerPanel tableModel;
protected ArrayList< SelectedViewDescriptionListener< AS > > listeners;
protected AS data;
- protected FilteredAndGroupedExplorer< AS, X > explorer;
+ protected FilteredAndGroupedExplorer< AS > explorer;
protected final String xml;
- protected final X io;
+ protected final XmlIoAbstractSpimData< ?, AS > io;
protected final boolean isMac;
protected boolean colorMode = false;
-
- final protected HashSet< List> > selectedRows;
- protected BasicViewDescription< ? extends BasicViewSetup > firstSelectedVD;
+ final protected HashSet< List< BasicViewDescription< ? > > > selectedRows;
+ protected BasicViewDescription< ? > firstSelectedVD;
- public FilteredAndGroupedExplorerPanel(final FilteredAndGroupedExplorer< AS, X > explorer, final AS data,
- final String xml, final X io)
+ public FilteredAndGroupedExplorerPanel(final FilteredAndGroupedExplorer< AS > explorer, final AS data,
+ final String xml, final XmlIoAbstractSpimData< ?, AS > io)
{
-
-
-
+
+
+
this.explorer = explorer;
- this.listeners = new ArrayList< SelectedViewDescriptionListener< AS > >();
+ this.listeners = new ArrayList<>();
this.data = data;
// normalize the xml path
@@ -119,9 +120,9 @@ public FilteredAndGroupedExplorerPanel(final FilteredAndGroupedExplorer< AS, X >
this.selectedRows = new HashSet<>();
this.firstSelectedVD = null;
-
+
popups = initPopups();
-
+
// for access to the current BDV
currentInstance = this;
}
@@ -130,8 +131,8 @@ public FilteredAndGroupedExplorerPanel(final FilteredAndGroupedExplorer< AS, X >
public BDVPopup bdvPopup()
{
for ( final ExplorerWindowSetable s : popups )
- if ( BDVPopup.class.isInstance( s ) )
- return ( (BDVPopup) s );
+ if ( s instanceof BDVPopup )
+ return ( BDVPopup ) s;
return null;
}
@@ -143,7 +144,7 @@ public boolean colorMode()
}
@Override
- public BasicViewDescription< ? extends BasicViewSetup > firstSelectedVD()
+ public BasicViewDescription< ? > firstSelectedVD()
{
return firstSelectedVD;
}
@@ -165,20 +166,20 @@ public String xml()
return xml;
}
- public X io()
+ public XmlIoAbstractSpimData< ?, AS > io()
{
return io;
}
- public FilteredAndGroupedExplorer< AS, X > explorer()
+ public FilteredAndGroupedExplorer< AS > explorer()
{
return explorer;
}
- @SuppressWarnings("unchecked")
- public void setSpimData(final Object data)
+ @SuppressWarnings( "unchecked" )
+ public void setSpimData( final Object data )
{
- this.data = (AS) data;
+ this.data = ( AS ) data;
this.getTableModel().updateElements();
}
@@ -191,11 +192,11 @@ public void updateContent()
}
@Override
- public List< BasicViewDescription< ? extends BasicViewSetup > > selectedRows()
+ public List< BasicViewDescription< ? > > selectedRows()
{
// TODO: this will break the grouping of selected Views -> change interface???
- final ArrayList< BasicViewDescription< ? extends BasicViewSetup > > list = new ArrayList< BasicViewDescription< ? extends BasicViewSetup > >();
- for (List> vds : selectedRows)
+ final ArrayList< BasicViewDescription< ? > > list = new ArrayList<>();
+ for ( List< BasicViewDescription< ? > > vds : selectedRows )
list.addAll( vds );
Collections.sort( list );
return list;
@@ -205,13 +206,9 @@ public void updateContent()
public List< ViewId > selectedRowsViewId()
{
// TODO: adding Grouped Views here, not all selected ViewIds individually
- final ArrayList< ViewId > list = new ArrayList< ViewId >();
- for (List> vds : selectedRows)
- {
- ArrayList< ViewId > vids = new ArrayList<>();
- vids.addAll( vds );
- list.add( new GroupedViews( vids ));
- }
+ final ArrayList< ViewId > list = new ArrayList<>();
+ for ( List< BasicViewDescription< ? > > vds : selectedRows )
+ list.add( new GroupedViews( new ArrayList<>( vds ) ) );
Collections.sort( list );
return list;
}
@@ -220,10 +217,7 @@ public void addListener(final SelectedViewDescriptionListener< AS > listener)
{
this.listeners.add( listener );
- List>> selectedList = new ArrayList<>();
- for (List> selectedI : selectedRows)
- selectedList.add( selectedI );
-
+ final List< List< BasicViewDescription< ? > > > selectedList = new ArrayList<>( selectedRows );
listener.selectedViewDescriptions( selectedList );
}
@@ -233,48 +227,43 @@ public ArrayList< SelectedViewDescriptionListener< AS > > getListeners()
}
public abstract void initComponent();
-
- public void updateFilter(Class entityClass, Entity selectedInstance)
+
+ public void updateFilter( Class< ? extends Entity > entityClass, Entity selectedInstance )
{
- ArrayList selectedInstances = new ArrayList<>();
+ ArrayList< Entity > selectedInstances = new ArrayList<>();
selectedInstances.add( selectedInstance );
- tableModel.addFilter( entityClass, selectedInstances );
+ tableModel.addFilter( entityClass, selectedInstances );
}
-
- protected static List getEntityNamesOrIds(List entities)
+
+ protected static List< String > getEntityNamesOrIds( List< ? extends Entity > entities )
{
- ArrayList names = new ArrayList<>();
-
- for (Entity e : entities)
- names.add( NamedEntity.class.isInstance( e ) ? ((NamedEntity)e).getName() : Integer.toString( e.getId()));
-
+ ArrayList< String > names = new ArrayList<>();
+
+ for ( Entity e : entities )
+ names.add( e instanceof NamedEntity ? ( ( NamedEntity ) e ).getName() : Integer.toString( e.getId() ) );
+
return names;
}
-
- public static Entity getInstanceFromNameOrId(AbstractSequenceDescription sd, Class entityClass, String nameOrId)
+
+ public static Entity getInstanceFromNameOrId( AbstractSequenceDescription< ?, ?, ? > sd, Class< ? extends Entity > entityClass, String nameOrId )
{
- for (Entity e : SpimDataTools.getInstancesOfAttribute( sd, entityClass ))
- if (NamedEntity.class.isInstance( e ) && ((NamedEntity)e).getName().equals( nameOrId ) || Integer.toString( e.getId()).equals( nameOrId ))
+ for ( Entity e : SpimDataTools.getInstancesOfAttribute( sd, entityClass ) )
+ if ( e instanceof NamedEntity && ( ( NamedEntity ) e ).getName().equals( nameOrId ) || Integer.toString( e.getId() ).equals( nameOrId ) )
return e;
return null;
}
protected void addHelp()
{
- table.addKeyListener( new KeyListener()
+ table.addKeyListener( new KeyAdapter()
+ {
+ @Override
+ public void keyPressed( KeyEvent e )
{
- public void keyTyped( KeyEvent e ) {}
-
- @Override
- public void keyReleased( KeyEvent e ) {}
-
- @Override
- public void keyPressed( KeyEvent e )
- {
- if ( e.getKeyCode() == 112 )
- new HelpDialog( explorer().getFrame(), this.getClass().getResource( getHelpHtml() ) ).setVisible( true );
- }
- } );
+ if ( e.getKeyCode() == 112 )
+ new HelpDialog( explorer().getFrame(), this.getClass().getResource( getHelpHtml() ) ).setVisible( true );
+ }
+ } );
}
protected abstract String getHelpHtml();
@@ -299,14 +288,15 @@ 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 )
listeners.get( i ).selectedViewDescriptions( selectedList );
-
+
/*
if ( table.getSelectedRowCount() != 1 )
{
@@ -354,48 +344,53 @@ public void valueChanged(final ListSelectionEvent arg0)
*/
if ( b != null && b.bdv != null )
- {
+ {
updateBDV( b.bdv, colorMode, data, firstSelectedVD, selectedRows);
-
+
}
-
-
+
+
}
-
+
};
}
-
-
-
- public static void resetBDVManualTransformations(BigDataViewer bdv)
+ public static void resetBDVManualTransformations( BigDataViewer bdv )
{
if ( bdv == null )
return;
-
+
// reset manual transform for all views
- for (int sourceIdx = 0; sourceIdx s = bdv.getViewer().getVisibilityAndGrouping().getSources().get( sourceIdx );
- ((TransformedSource< ? >)s.getSpimSource()).setFixedTransform( new AffineTransform3D() );
- ((TransformedSource< ? >)s.getSpimSource()).setIncrementalTransform( new AffineTransform3D() );
+ BDVUtils.forEachTransformedSource(
+ state.getSources(),
+ ( soc, source ) -> {
+ source.setFixedTransform( identity );
+ source.setIncrementalTransform( identity );
+ } );
}
}
-
- public static void updateBDV(final BigDataViewer bdv, final boolean colorMode, final AbstractSpimData< ? > data,
- BasicViewDescription< ? extends BasicViewSetup > firstVD,
- final Collection< List< BasicViewDescription< ? extends BasicViewSetup >> > selectedRows)
+
+ public static void updateBDV(
+ final BigDataViewer bdv,
+ final boolean colorMode,
+ final AbstractSpimData< ? > data,
+ BasicViewDescription< ? > firstVD,
+ final Collection< List< BasicViewDescription< ? > > > selectedRows )
{
-
+
// bdv is not open
if ( bdv == null )
return;
-
+
// we always set the fused mode
- //setFusedModeSimple( bdv, data );
-
- //resetBDVManualTransformations( bdv );
+ setFusedModeSimple( bdv, data );
+
+ resetBDVManualTransformations( bdv );
if ( selectedRows == null || selectedRows.size() == 0 )
return;
@@ -403,73 +398,73 @@ public static void updateBDV(final BigDataViewer bdv, final boolean colorMode, f
if ( firstVD == null )
firstVD = selectedRows.iterator().next().get( 0 );
+ final ViewerState state = bdv.getViewer().state();
+
// always use the first timepoint
final TimePoint firstTP = firstVD.getTimePoint();
- if ( bdv.getViewer().getState().getCurrentTimepoint() != getBDVTimePointIndex( firstTP, data ) )
- bdv.getViewer().setTimepoint( getBDVTimePointIndex( firstTP, data ) );
+ state.setCurrentTimepoint( getBDVTimePointIndex( firstTP, data ) );
- final boolean[] active = new boolean[data.getSequenceDescription().getViewSetupsOrdered().size()];
+ final Set< Integer > selectedViewSetupIds = selectedRows.stream()
+ .flatMap( Collection::stream )
+ .filter( vd -> vd.getTimePointId() == firstTP.getId() )
+ .map( ViewId::getViewSetupId )
+ .collect( Collectors.toSet() );
- for ( final List< ? extends BasicViewDescription< ? extends BasicViewSetup > > vds : selectedRows )
- for ( BasicViewDescription< ? > vd : vds){
- if ( vd.getTimePointId() == firstTP.getId() )
- active[getBDVSourceIndex( vd.getViewSetup(), data )] = true;
- }
+ final List< SourceAndConverter< ? > > active = new ArrayList<>();
+ synchronized ( state )
+ {
+ BDVUtils.forEachAbstractSpimSource(
+ state.getSources(),
+ ( soc, source ) -> {
+ if ( selectedViewSetupIds.contains( source.getSetupId() ) )
+ active.add( soc );
+ } );
+ }
+ setVisibleSources( state, active );
// if ( selectedRows.size() > 1 && colorMode )
// colorSources( bdv.getSetupAssignments().getConverterSetups(), data, channelColors);
// else
// whiteSources( bdv.getSetupAssignments().getConverterSetups() );
- setVisibleSources( bdv.getViewer().getVisibilityAndGrouping(), active );
bdv.getViewer().requestRepaint();
}
- public static void setFusedModeSimple(final BigDataViewer bdv, final AbstractSpimData< ? > data)
+ public static void setFusedModeSimple( final BigDataViewer bdv, final AbstractSpimData< ? > data )
{
if ( bdv == null )
return;
-
-
- if ( bdv.getViewer().getVisibilityAndGrouping().getDisplayMode() != DisplayMode.FUSED )
+ final ViewerState state = bdv.getViewer().state();
+ if ( state.getDisplayMode() != DisplayMode.FUSED )
{
- final boolean[] active = new boolean[data.getSequenceDescription().getViewSetupsOrdered().size()];
- active[0] = true;
- setVisibleSources( bdv.getViewer().getVisibilityAndGrouping(), active );
- bdv.getViewer().getVisibilityAndGrouping().setDisplayMode( DisplayMode.FUSED );
- }
- }
-
- public static void colorSources(final List< ConverterSetup > cs, AbstractSpimData< ? > data, Map channelColors)
- {
- for ( int i = 0; i < cs.size(); ++i )
- {
- Channel ch = data.getSequenceDescription().getViewSetups().get(cs.get( i ).getSetupId()).getAttribute( Channel.class );
- cs.get( i ).setColor( channelColors.get( ch ) );
+ setVisibleSources( state, state.getSources().subList( 0, 0 ) );
+ state.setDisplayMode( DisplayMode.FUSED );
}
}
- public static void whiteSources(final List< ConverterSetup > cs)
+ // TODO (TP) This has duplicates in StitchingExplorerPanel and ViewSetupExplorerPanel
+ // Move to common utility class?
+ public static void whiteSources( final List< ConverterSetup > cs )
{
- for ( int i = 0; i < cs.size(); ++i )
- cs.get( i ).setColor( new ARGBType( ARGBType.rgba( 255, 255, 255, 255 ) ) );
+ sameColorSources( cs, 255, 255, 255, 255 );
}
- public static void sameColorSources(final List< ConverterSetup > cs, final int r, final int g, final int b, final int a)
+ public static void sameColorSources( final List< ConverterSetup > cs, final int r, final int g, final int b, final int a )
{
- for ( int i = 0; i < cs.size(); ++i )
- cs.get( i ).setColor( new ARGBType( ARGBType.rgba( r, g, b, a ) ) );
+ final ARGBType color = new ARGBType( ARGBType.rgba( r, g, b, a ) );
+ cs.forEach( c -> c.setColor( color ) );
}
- public static void setVisibleSources(final VisibilityAndGrouping vag, final boolean[] active)
+ public static void setVisibleSources( final ViewerState state, final Collection< ? extends SourceAndConverter< ? > > active )
{
- for ( int i = 0; i < active.length; ++i )
- vag.setSourceActive( i, active[i] );
-
+ final List< SourceAndConverter< ? > > inactive = new ArrayList<>( state.getSources() );
+ inactive.removeAll( active );
+ state.setSourcesActive( inactive, false );
+ state.setSourcesActive( active, true );
}
- public static int getBDVTimePointIndex(final TimePoint t, final AbstractSpimData< ? > data)
+ public static int getBDVTimePointIndex( final TimePoint t, final AbstractSpimData< ? > data )
{
final List< TimePoint > list = data.getSequenceDescription().getTimePoints().getTimePointsOrdered();
@@ -480,7 +475,7 @@ public static int getBDVTimePointIndex(final TimePoint t, final AbstractSpimData
return 0;
}
- public static int getBDVSourceIndex(final BasicViewSetup vs, final AbstractSpimData< ? > data)
+ public static int getBDVSourceIndex( final BasicViewSetup vs, final AbstractSpimData< ? > data )
{
final List< ? extends BasicViewSetup > list = data.getSequenceDescription().getViewSetupsOrdered();
@@ -491,14 +486,14 @@ public static int getBDVSourceIndex(final BasicViewSetup vs, final AbstractSpimD
return 0;
}
- public HashSet< List >> getSelectedRows()
+ public Set< List< BasicViewDescription< ? > > > getSelectedRows()
{
return selectedRows;
}
public void showInfoBox()
{
- new ViewSetupExplorerInfoBox< AS >( data, xml );
+ new ViewSetupExplorerInfoBox<>( data, xml );
}
@Override
@@ -511,9 +506,9 @@ public void saveXML()
for ( final SelectedViewDescriptionListener< AS > l : listeners )
l.save();
- if ( SpimData2.class.isInstance( data ) )
+ if ( data instanceof SpimData2 )
{
- final ViewInterestPoints vip = ( (SpimData2) data ).getViewInterestPoints();
+ final ViewInterestPoints vip = ( ( SpimData2 ) data ).getViewInterestPoints();
for ( final ViewInterestPointLists vipl : vip.getViewInterestPoints().values() )
{
@@ -535,7 +530,7 @@ public void saveXML()
}
}
- protected void addPopupMenu(final JTable table)
+ protected void addPopupMenu( final JTable table )
{
final JPopupMenu popupMenu = new JPopupMenu();
@@ -547,10 +542,10 @@ protected void addPopupMenu(final JTable table)
protected void addColorMode()
{
- table.addKeyListener( new KeyListener()
+ table.addKeyListener( new KeyAdapter()
{
@Override
- public void keyPressed(final KeyEvent arg0)
+ public void keyPressed( final KeyEvent arg0 )
{
if ( arg0.getKeyChar() == 'c' || arg0.getKeyChar() == 'C' )
{
@@ -560,28 +555,18 @@ public void keyPressed(final KeyEvent arg0)
final BDVPopup p = bdvPopup();
if ( p != null && p.bdv != null && p.bdv.getViewerFrame().isVisible() )
- updateBDV( p.bdv, colorMode, data, null, selectedRows);
+ updateBDV( p.bdv, colorMode, data, null, selectedRows );
}
}
-
- @Override
- public void keyReleased(final KeyEvent arg0)
- {
- }
-
- @Override
- public void keyTyped(final KeyEvent arg0)
- {
- }
} );
}
protected void addReCenterShortcut()
{
- table.addKeyListener( new KeyListener()
+ table.addKeyListener( new KeyAdapter()
{
@Override
- public void keyPressed(final KeyEvent arg0)
+ public void keyPressed( final KeyEvent arg0 )
{
if ( arg0.getKeyChar() == 'r' || arg0.getKeyChar() == 'R' )
{
@@ -589,18 +574,13 @@ public void keyPressed(final KeyEvent arg0)
if ( p != null && p.bdv != null && p.bdv.getViewerFrame().isVisible() )
{
TransformationTools.reCenterViews( p.bdv,
- selectedRows.stream().collect(
+ selectedRows.stream().collect(
HashSet< BasicViewDescription< ? > >::new,
- (a, b) -> a.addAll( b ), (a, b) -> a.addAll( b ) ),
- data.getViewRegistrations() );
+ ( a, b ) -> a.addAll( b ), ( a, b ) -> a.addAll( b ) ),
+ data.getViewRegistrations() );
}
}
}
-
- @Override
- public void keyReleased(final KeyEvent arg0){}
- @Override
- public void keyTyped(final KeyEvent arg0){}
} );
}
@@ -611,21 +591,21 @@ protected void addAppleA()
boolean appleKeyDown = false;
@Override
- public void keyTyped(KeyEvent arg0)
+ public void keyTyped( KeyEvent arg0 )
{
if ( appleKeyDown && arg0.getKeyChar() == 'a' )
table.selectAll();
}
@Override
- public void keyReleased(KeyEvent arg0)
+ public void keyReleased( KeyEvent arg0 )
{
if ( arg0.getKeyCode() == 157 )
appleKeyDown = false;
}
@Override
- public void keyPressed(KeyEvent arg0)
+ public void keyPressed( KeyEvent arg0 )
{
if ( arg0.getKeyCode() == 157 )
appleKeyDown = true;
@@ -637,17 +617,17 @@ public void keyPressed(KeyEvent arg0)
protected void addScreenshot()
{
- table.addKeyListener( new KeyListener()
+ table.addKeyListener( new KeyAdapter()
{
@Override
- public void keyPressed(final KeyEvent arg0)
+ public void keyPressed( final KeyEvent arg0 )
{
if ( arg0.getKeyChar() == 'E' )
{
enableFlyThrough = true;
IOFunctions.println( "EASTER EGG activated." );
- IOFunctions.println( "You can now record a fly-through: ");
+ IOFunctions.println( "You can now record a fly-through: " );
IOFunctions.println( " press 'a' to add the current view as keypoint" );
IOFunctions.println( " press 'x' to remove all keypoints" );
IOFunctions.println( " press 'd' to remove last keypoint" );
@@ -672,13 +652,13 @@ public void run()
} ).start();
else
IOFunctions.println("Please open BigDataViewer to record a fly-through or add keypoints.");
-
+
if ( arg0.getKeyChar() == 'a' )
if (bdvRunning)
BDVFlyThrough.addCurrentViewerTransform( bdvPopup().bdv.getViewer() );
else
IOFunctions.println("Please open BigDataViewer to record a fly-through or add keypoints.");
-
+
if ( arg0.getKeyChar() == 'x' )
BDVFlyThrough.clearAllViewerTransform();
@@ -688,39 +668,26 @@ public void run()
if ( arg0.getKeyChar() == 'j' )
BDVFlyThrough.jumpToLastViewerTransform( bdvPopup().bdv.getViewer() );
- if ( arg0.getKeyChar() == 's' ) {
+ if ( arg0.getKeyChar() == 's' )
try { BDVFlyThrough.saveViewerTransforms(); } catch ( Exception e ) { IOFunctions.println( "couldn't save json: " + e ); }
- }
- if ( arg0.getKeyChar() == 'l' ){
+ if ( arg0.getKeyChar() == 'l' )
try { BDVFlyThrough.loadViewerTransforms(); } catch ( Exception e ) { IOFunctions.println( "couldn't load json: " + e ); }
- }
if ( arg0.getKeyChar() == 'R' )
- if (bdvRunning)
- new Thread( new Runnable()
- {
- @Override
- public void run()
- { BDVFlyThrough.renderScreenshot( bdvPopup().bdv.getViewer() ); }
- } ).start();
+ if ( bdvRunning )
+ new Thread( () -> BDVFlyThrough.renderScreenshot( bdvPopup().bdv.getViewer() ) ).start();
else
- IOFunctions.println("Please open BigDataViewer to make a screenshot.");
+ IOFunctions.println( "Please open BigDataViewer to make a screenshot." );
}
}
-
- @Override
- public void keyReleased(final KeyEvent arg0) {}
-
- @Override
- public void keyTyped(final KeyEvent arg0){}
} );
}
public abstract ArrayList< ExplorerWindowSetable > initPopups();
@Override
- public Collection< List< BasicViewDescription< ? extends BasicViewSetup > > > selectedRowsGroups()
+ public Collection< List< BasicViewDescription< ? > > > selectedRowsGroups()
{
return selectedRows;
}
@@ -728,13 +695,9 @@ public void keyTyped(final KeyEvent arg0){}
@Override
public List< List< ViewId > > selectedRowsViewIdGroups()
{
- final ArrayList< List> list = new ArrayList<>();
- for (List> vds : selectedRows)
- {
- ArrayList< ViewId > vids = new ArrayList<>();
- vids.addAll( vds );
- list.add( vids);
- }
+ final ArrayList< List< ViewId > > list = new ArrayList<>();
+ for ( List< BasicViewDescription< ? > > vds : selectedRows )
+ list.add( new ArrayList<>( vds ) );
//Collections.sort( list );
return list;
}
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 7177c5ce8..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
@@ -57,8 +57,8 @@ public class FilteredAndGroupedTableModel < AS extends AbstractSpimData< ? > > e
private static final long serialVersionUID = -6526338840427674269L;
protected List< List< BasicViewDescription< ? > >> elements = null;
-
- final ExplorerWindow< AS, ? > panel;
+
+ final ExplorerWindow< AS > panel;
Set> groupingFactors;
Map, List> filters;
List> columnClasses;
@@ -68,7 +68,7 @@ public class FilteredAndGroupedTableModel < AS extends AbstractSpimData< ? > > e
* @see gui.ISpimDataTableModel#getPanel()
*/
@Override
- public ExplorerWindow< AS, ? > getPanel() {
+ public ExplorerWindow< AS > getPanel() {
return panel;
}
@@ -155,7 +155,7 @@ public static ArrayList> defaultColumnClassesMV()
return res;
}
- public FilteredAndGroupedTableModel( final ExplorerWindow< AS, ? > panel )
+ public FilteredAndGroupedTableModel( final ExplorerWindow< AS > panel )
{
groupingFactors = new HashSet<>();
filters = new HashMap<>();
@@ -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/GroupedRowWindow.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/GroupedRowWindow.java
index 7f9de18d5..d1350f158 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/GroupedRowWindow.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/GroupedRowWindow.java
@@ -31,6 +31,6 @@
public interface GroupedRowWindow
{
- public Collection >> selectedRowsGroups();
+ public Collection< List< BasicViewDescription< ? > > > selectedRowsGroups();
public List> selectedRowsViewIdGroups();
}
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ISpimDataTableModel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ISpimDataTableModel.java
index 205bae6c5..1961958b1 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ISpimDataTableModel.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ISpimDataTableModel.java
@@ -42,9 +42,9 @@ public enum SpecialColumnType{
}
public int getSpecialColumn(SpecialColumnType type);
-
- public ExplorerWindow< AS, ? > getPanel();
-
+
+ public ExplorerWindow< AS > getPanel();
+
public Set> getGroupingFactors();
public void clearSortingFactors();
@@ -61,7 +61,7 @@ public enum SpecialColumnType{
public Map , List> getFilters();
- public List> > getElements();
+ public List< List< BasicViewDescription< ? > > > getElements();
public void updateElements();
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MissingViewsTableModelDecorator.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MissingViewsTableModelDecorator.java
index 98584a621..e5a00ab81 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MissingViewsTableModelDecorator.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MissingViewsTableModelDecorator.java
@@ -117,7 +117,7 @@ public int getSpecialColumn(net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDa
}
@Override
- public ExplorerWindow< AS, ? > getPanel()
+ public ExplorerWindow< AS > getPanel()
{
return decorated.getPanel();
}
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 4ff169e3c..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() )
{
@@ -244,7 +244,7 @@ public void sortByColumn(int column) {
}
@Override
- public ExplorerWindow getPanel() { return decorated.getPanel(); }
+ public ExplorerWindow getPanel() { return decorated.getPanel(); }
@Override
public void setValueAt(Object aValue, int rowIndex, int columnIndex)
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/SelectedViewDescriptionListener.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/SelectedViewDescriptionListener.java
index f26043b5b..fffd00801 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/SelectedViewDescriptionListener.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/SelectedViewDescriptionListener.java
@@ -30,7 +30,7 @@
public interface SelectedViewDescriptionListener< AS extends AbstractSpimData< ? > >
{
//public void firstSelectedViewDescriptions( List< BasicViewDescription< ? extends BasicViewSetup > > viewDescriptions );
- public void selectedViewDescriptions( List< List< BasicViewDescription< ? extends BasicViewSetup > > > viewDescriptions );
+ public void selectedViewDescriptions( List< List< BasicViewDescription< ? > > > viewDescriptions );
public void updateContent( final AS data );
public void save();
public void quit();
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorer.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorer.java
index b47734a56..8369fe8c7 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorer.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorer.java
@@ -34,17 +34,17 @@
import mpicbg.spim.data.generic.AbstractSpimData;
import mpicbg.spim.data.generic.XmlIoAbstractSpimData;
-public class ViewSetupExplorer< AS extends AbstractSpimData< ? >, X extends XmlIoAbstractSpimData< ?, AS > > extends FilteredAndGroupedExplorer< AS, X >
+public class ViewSetupExplorer< AS extends AbstractSpimData< ? > > extends FilteredAndGroupedExplorer< AS >
{
public static final double xPos = 0.4;
public static final double yPos = 0.4;
public static final double xPosLog = 0.0;
public static final double yPosLog = 0.8;
- public ViewSetupExplorer( final AS data, final String xml, final X io )
+ public ViewSetupExplorer( final AS data, final String xml, final XmlIoAbstractSpimData< ?, AS > io )
{
frame = new JFrame( "ViewSetup Explorer" );
- panel = new ViewSetupExplorerPanel< AS, X >( this, data, xml, io, true );
+ panel = new ViewSetupExplorerPanel< AS >( this, data, xml, io, true );
frame.add( panel, BorderLayout.CENTER );
frame.setSize( panel.getPreferredSize() );
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 c6c3d6714..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
@@ -111,7 +111,7 @@
import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
-public class ViewSetupExplorerPanel< AS extends AbstractSpimData< ? >, X extends XmlIoAbstractSpimData< ?, AS > > extends FilteredAndGroupedExplorerPanel< AS, X > implements ExplorerWindow< AS, X >
+public class ViewSetupExplorerPanel< AS extends AbstractSpimData< ? > > extends FilteredAndGroupedExplorerPanel< AS > implements ExplorerWindow< AS >
{
private static final long serialVersionUID = -2512096359830259015L;
@@ -145,7 +145,7 @@ public boolean illumsGrouped()
@Override
public boolean channelsGrouped() { return false; }
- public ViewSetupExplorerPanel( final FilteredAndGroupedExplorer< AS, X > explorer, final AS data, final String xml, final X io, boolean requestStartBDV )
+ public ViewSetupExplorerPanel( final FilteredAndGroupedExplorer< AS > explorer, final AS data, final String xml, final XmlIoAbstractSpimData< ?, AS > io, boolean requestStartBDV )
{
super( explorer, data, xml, io );
@@ -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/bdv/BDVUtils.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/bdv/BDVUtils.java
new file mode 100644
index 000000000..a9d61dc8c
--- /dev/null
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/bdv/BDVUtils.java
@@ -0,0 +1,40 @@
+package net.preibisch.mvrecon.fiji.spimdata.explorer.bdv;
+
+import bdv.AbstractSpimSource;
+import bdv.tools.transformation.TransformedSource;
+import bdv.viewer.Source;
+import bdv.viewer.SourceAndConverter;
+import java.util.Collection;
+import java.util.function.BiConsumer;
+
+public class BDVUtils
+{
+ public static void forEachAbstractSpimSource(
+ final Collection< ? extends SourceAndConverter< ? > > sources,
+ final BiConsumer< ? super SourceAndConverter< ? >, ? super AbstractSpimSource< ? > > action )
+ {
+ for ( final SourceAndConverter< ? > soc : sources )
+ {
+ Source< ? > source = soc.getSpimSource();
+
+ if ( source instanceof TransformedSource )
+ source = ( ( TransformedSource< ? > ) source ).getWrappedSource();
+
+ if ( source instanceof AbstractSpimSource )
+ action.accept( soc, ( AbstractSpimSource< ? > ) source );
+ }
+ }
+
+ public static void forEachTransformedSource(
+ final Collection< ? extends SourceAndConverter< ? > > sources,
+ final BiConsumer< ? super SourceAndConverter< ? >, ? super TransformedSource< ? > > action )
+ {
+ for ( final SourceAndConverter< ? > soc : sources )
+ {
+ Source< ? > source = soc.getSpimSource();
+
+ if ( source instanceof TransformedSource )
+ action.accept( soc, ( TransformedSource< ? > ) source );
+ }
+ }
+}
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 ad903fc2f..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
@@ -46,15 +46,15 @@
import net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BasicBDVPopup;
import net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints;
-public class InterestPointExplorer< AS extends SpimData2, X extends XmlIoAbstractSpimData< ?, AS > >
+public class InterestPointExplorer< AS extends SpimData2 >
implements SelectedViewDescriptionListener< AS >
{
final String xml;
final JFrame frame;
final InterestPointExplorerPanel panel;
- final FilteredAndGroupedExplorer< AS, X > viewSetupExplorer;
+ final FilteredAndGroupedExplorer< AS > viewSetupExplorer;
- public InterestPointExplorer( final String xml, final X io, final FilteredAndGroupedExplorer< AS, X > viewSetupExplorer )
+ public InterestPointExplorer( final String xml, final XmlIoAbstractSpimData< ?, AS > io, final FilteredAndGroupedExplorer< AS > viewSetupExplorer )
{
this.xml = xml;
this.viewSetupExplorer = viewSetupExplorer;
@@ -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 5f2252953..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
@@ -63,7 +63,7 @@ public class InterestPointExplorerPanel extends JPanel
{
private static final long serialVersionUID = -3767947754096099774L;
- final FilteredAndGroupedExplorer< ?, ? > viewSetupExplorer;
+ final FilteredAndGroupedExplorer< ? > viewSetupExplorer;
protected JTable table;
protected InterestPointTableModel tableModel;
@@ -73,7 +73,7 @@ public class InterestPointExplorerPanel extends JPanel
//protected ArrayList< Pair< InterestPointList, ViewId > > save;
protected ArrayList< Pair< InterestPoints, ViewId > > delete;
- public InterestPointExplorerPanel( final ViewInterestPoints viewInterestPoints, final FilteredAndGroupedExplorer< ?, ? > viewSetupExplorer )
+ public InterestPointExplorerPanel( final ViewInterestPoints viewInterestPoints, final FilteredAndGroupedExplorer< ? > viewSetupExplorer )
{
//this.save = new ArrayList< Pair< InterestPointList, ViewId > >();
this.delete = new ArrayList< Pair< InterestPoints, ViewId > >();
@@ -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/popup/ApplyTransformationPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ApplyTransformationPopup.java
index 4803b86ee..b11037837 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ApplyTransformationPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ApplyTransformationPopup.java
@@ -39,8 +39,6 @@
import net.preibisch.mvrecon.fiji.spimdata.explorer.GroupedRowWindow;
import mpicbg.spim.data.SpimData;
-import mpicbg.spim.data.generic.AbstractSpimData;
-import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.sequence.ViewDescription;
import mpicbg.spim.data.sequence.ViewId;
@@ -49,7 +47,7 @@ public class ApplyTransformationPopup extends JMenuItem implements ExplorerWindo
private static final long serialVersionUID = 5234649267634013390L;
public static boolean showWarning = true;
- ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel;
+ ExplorerWindow< ? > panel;
public ApplyTransformationPopup()
{
@@ -59,20 +57,20 @@ public ApplyTransformationPopup()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
}
- public static final List< ViewId > getSelectedViews(
- final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel)
+ public static final List< ViewId > getSelectedViews( final ExplorerWindow< ? > panel )
{
return getSelectedViews( panel, true );
}
+
public static final List< ViewId > getSelectedViews(
- final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel,
- final boolean filterMissing)
+ final ExplorerWindow< ? > panel,
+ final boolean filterMissing )
{
final List< ViewId > viewIds = new ArrayList<>();
if (GroupedRowWindow.class.isInstance( panel ))
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java
index 83219fc2f..5ecdffa8f 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java
@@ -9,12 +9,12 @@
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 2 of the
* License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* .
@@ -22,12 +22,16 @@
*/
package net.preibisch.mvrecon.fiji.spimdata.explorer.popup;
+import bdv.tools.brightness.ConverterSetup;
+import bdv.util.Bounds;
+import bdv.viewer.ConverterSetups;
+import bdv.viewer.SourceAndConverter;
+import bdv.viewer.ViewerFrame;
+import bdv.viewer.ViewerState;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.lang.reflect.Field;
-import java.lang.reflect.Method;
-import java.util.List;
+import java.util.Collection;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
@@ -35,14 +39,10 @@
import bdv.AbstractSpimSource;
import bdv.BigDataViewer;
import bdv.tools.InitializeViewerState;
-import bdv.tools.brightness.MinMaxGroup;
-import bdv.tools.brightness.SetupAssignments;
import bdv.tools.transformation.TransformedSource;
import bdv.viewer.Source;
import bdv.viewer.ViewerOptions;
import bdv.viewer.ViewerPanel;
-import bdv.viewer.state.SourceState;
-import bdv.viewer.state.ViewerState;
import mpicbg.spim.data.generic.AbstractSpimData;
import mpicbg.spim.data.registration.ViewRegistration;
import net.imglib2.Interval;
@@ -52,6 +52,9 @@
import net.imglib2.histogram.Real1dBinMapper;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.RealType;
+import net.imglib2.type.numeric.integer.UnsignedByteType;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
+import net.imglib2.util.Cast;
import net.imglib2.util.LinAlgHelpers;
import net.imglib2.view.Views;
import net.preibisch.legacy.io.IOFunctions;
@@ -67,7 +70,7 @@ public class BDVPopup extends JMenuItem implements ExplorerWindowSetable, BasicB
{
private static final long serialVersionUID = 5234649267634013390L;
- public ExplorerWindow< ?, ? > panel;
+ public ExplorerWindow< ? > panel;
public BigDataViewer bdv = null;
public BDVPopup()
@@ -78,12 +81,13 @@ public BDVPopup()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
}
+ // TODO (TP): replace with method and method reference
public class MyActionListener implements ActionListener
{
@Override
@@ -95,6 +99,7 @@ public void actionPerformed( final ActionEvent e )
return;
}
+ // TODO (TP): replace with lambda
new Thread( new Runnable()
{
@Override
@@ -144,53 +149,36 @@ public void updateBDV()
if ( bdv == null )
return;
- for ( final ViewRegistration r : panel.getSpimData().getViewRegistrations().getViewRegistrationsOrdered() )
- r.updateModel();
+ final Collection< ViewRegistration > regs = panel.getSpimData().getViewRegistrations().getViewRegistrations().values();
+ regs.forEach( ViewRegistration::updateModel );
- final ViewerPanel viewerPanel = bdv.getViewer();
- final ViewerState viewerState = viewerPanel.getState();
- final List< SourceState< ? > > sources = viewerState.getSources();
-
- for ( final SourceState< ? > state : sources )
- {
- Source< ? > source = state.getSpimSource();
-
- while ( TransformedSource.class.isInstance( source ) )
- {
- source = ( ( TransformedSource< ? > ) source ).getWrappedSource();
- }
+ final ViewerPanel viewer = bdv.getViewer();
- if ( AbstractSpimSource.class.isInstance( source ) )
- {
- final AbstractSpimSource< ? > s = ( AbstractSpimSource< ? > ) source;
-
- final int tpi = getCurrentTimePointIndex( s );
- callLoadTimePoint( s, tpi );
-// forceBDVReload( s );
- }
+ final ViewerState state = viewer.state().snapshot();
+ state.getSources().forEach( BDVPopup::reloadTransformFromViewRegistrations );
+ viewer.requestRepaint();
+ }
- if ( state.asVolatile() != null )
- {
- source = state.asVolatile().getSpimSource();
- while ( TransformedSource.class.isInstance( source ) )
- {
- source = ( ( TransformedSource< ? > ) source ).getWrappedSource();
- }
+ /**
+ * Calls {@link AbstractSpimSource#reload} on volatile and non-volatile
+ * versions nested under {@code source}. This reloads transformations from
+ * modified {@code ViewRegistrations}.
+ */
+ private static void reloadTransformFromViewRegistrations( final SourceAndConverter< ? > source )
+ {
+ Source< ? > s = source.getSpimSource();
- if ( AbstractSpimSource.class.isInstance( source ) )
- {
- final AbstractSpimSource< ? > s = ( AbstractSpimSource< ? > ) source;
+ if ( s instanceof TransformedSource )
+ s = ( ( TransformedSource ) s ).getWrappedSource();
- final int tpi = getCurrentTimePointIndex( s );
- callLoadTimePoint( s, tpi );
-// forceBDVReload( s );
- }
- }
- }
+ if ( s instanceof AbstractSpimSource )
+ ( ( AbstractSpimSource< ? > ) s ).reload();
- bdv.getViewer().requestRepaint();
+ if ( source.asVolatile() != null )
+ reloadTransformFromViewRegistrations( source.asVolatile() );
}
+
@Override
public boolean bdvRunning()
{
@@ -198,74 +186,102 @@ public boolean bdvRunning()
return ( p != null && p.getBDV() != null && p.getBDV().getViewerFrame().isVisible() );
}
-
+
public void setBDV(BigDataViewer bdv)
{
// close existing bdv if necessary
if (bdvRunning())
new Thread(() -> {closeBDV();}).start();
-
+
this.bdv = bdv;
ViewSetupExplorerPanel.updateBDV( this.bdv, panel.colorMode(), panel.getSpimData(), panel.firstSelectedVD(), ((GroupedRowWindow)panel).selectedRowsGroups() );
}
-
+
/**
* set BDV brightness by sampling the mid z plane (and 1/4 and 3/4 if z is large enough )
* of the currently selected source (typically the first source) and getting quantiles from intensity histogram
* (slightly modified version of InitializeViewerState.initBrightness)
*
- * @param cumulativeMinCutoff - quantile of min
- * @param cumulativeMaxCutoff - quantile of max
- * @param state - Bdv's ViewerSate
- * @param setupAssignments - Bdv's View assignments
- * @param - type extending RealType
+ * @param cumulativeMinCutoff
+ * fraction of pixels that are allowed to be saturated at the lower end of the range.
+ * @param cumulativeMaxCutoff
+ * fraction of pixels that are allowed to be saturated at the upper end of the range.
+ * @param viewerFrame
+ * the ViewerFrame containing ViewerState and ConverterSetups
*/
- public static > void initBrightness( final double cumulativeMinCutoff, final double cumulativeMaxCutoff, final ViewerState state, final SetupAssignments setupAssignments )
+ public static void initBrightness( final double cumulativeMinCutoff, final double cumulativeMaxCutoff, final ViewerFrame viewerFrame )
{
- final Source< ? > source = state.getSources().get( state.getCurrentSource() ).getSpimSource();
- final int timepoint = state.getCurrentTimepoint();
- if ( !source.isPresent( timepoint ) )
- return;
- if ( !RealType.class.isInstance( source.getType() ) )
- return;
- @SuppressWarnings( "unchecked" )
- final RandomAccessibleInterval< T > img = ( RandomAccessibleInterval< T > ) source.getSource( timepoint, source.getNumMipmapLevels() - 1 );
- final long z = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 2;
-
- final int numBins = 6535;
- final Histogram1d< T > histogram = new Histogram1d< T >( Views.iterable( Views.hyperSlice( img, 2, z ) ), new Real1dBinMapper< T >( 0, 65535, numBins, false ) );
+ initBrightness( cumulativeMinCutoff, cumulativeMaxCutoff, viewerFrame.getViewerPanel().state().snapshot(), viewerFrame.getConverterSetups() );
+ }
- // sample some more planes if we have enough
- if ( (img.max( 2 ) + 1 - img.min( 2 ) ) > 4 )
+ private static void initBrightness( final double cumulativeMinCutoff, final double cumulativeMaxCutoff, final ViewerState state, final ConverterSetups converterSetups )
+ {
+ final SourceAndConverter< ? > current = state.getCurrentSource();
+ if ( current == null )
+ return;
+ final Source< ? > source = current.getSpimSource();
+ final int timepoint = state.getCurrentTimepoint();
+ final Bounds bounds = estimateSourceRange( source, timepoint, cumulativeMinCutoff, cumulativeMaxCutoff );
+ for ( final SourceAndConverter< ? > s : state.getSources() )
{
- final long z14 = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 4;
- final long z34 = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 4 * 3;
- histogram.addData( Views.iterable( Views.hyperSlice( img, 2, z14 ) ) );
- histogram.addData( Views.iterable( Views.hyperSlice( img, 2, z34 ) ) );
+ final ConverterSetup setup = converterSetups.getConverterSetup( s );
+ setup.setDisplayRange( bounds.getMinBound(), bounds.getMaxBound() );
}
+ }
- final DiscreteFrequencyDistribution dfd = histogram.dfd();
- final long[] bin = new long[] { 0 };
- double cumulative = 0;
- int i = 0;
- for ( ; i < numBins && cumulative < cumulativeMinCutoff; ++i )
- {
- bin[ 0 ] = i;
- cumulative += dfd.relativeFrequency( bin );
- }
- final int min = i * 65535 / numBins;
- for ( ; i < numBins && cumulative < cumulativeMaxCutoff; ++i )
+ /**
+ * @param cumulativeMinCutoff
+ * fraction of pixels that are allowed to be saturated at the lower end of the range.
+ * @param cumulativeMaxCutoff
+ * fraction of pixels that are allowed to be saturated at the upper end of the range.
+ */
+ private static < T extends RealType< T > > Bounds estimateSourceRange( final Source< ? > source, final int timepoint, final double cumulativeMinCutoff, final double cumulativeMaxCutoff )
+ {
+ final Object type = source.getType();
+ if ( type instanceof UnsignedShortType && source.isPresent( timepoint ) )
{
- bin[ 0 ] = i;
- cumulative += dfd.relativeFrequency( bin );
+ final RandomAccessibleInterval< T > img = Cast.unchecked( source.getSource( timepoint, source.getNumMipmapLevels() - 1 ) );
+ final double sZ0 = img.min( 2 );
+ final double sZ1 = img.max( 2 );
+ final long z = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 2;
+
+ final int numBins = 6535;
+ final Histogram1d< T > histogram = new Histogram1d<>( Views.hyperSlice( img, 2, z ), new Real1dBinMapper<>( 0, 65535, numBins, false ) );
+
+ // sample some more planes if we have enough
+ if ( img.dimension( 2 ) > 4 )
+ {
+ final long z14 = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 4;
+ final long z34 = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 4 * 3;
+ histogram.addData( Views.hyperSlice( img, 2, z14 ) );
+ histogram.addData( Views.hyperSlice( img, 2, z34 ) );
+ }
+
+ final DiscreteFrequencyDistribution dfd = histogram.dfd();
+ final long[] bin = new long[] { 0 };
+ double cumulative = 0;
+ int i = 0;
+ for ( ; i < numBins && cumulative < cumulativeMinCutoff; ++i )
+ {
+ bin[ 0 ] = i;
+ cumulative += dfd.relativeFrequency( bin );
+ }
+ final int min = i * 65535 / numBins;
+ for ( ; i < numBins && cumulative < cumulativeMaxCutoff; ++i )
+ {
+ bin[ 0 ] = i;
+ cumulative += dfd.relativeFrequency( bin );
+ }
+ final int max = i * 65535 / numBins;
+ return new Bounds( min, max );
}
- final int max = i * 65535 / numBins;
- final MinMaxGroup minmax = setupAssignments.getMinMaxGroups().get( 0 );
- minmax.getMinBoundedValue().setCurrentValue( min );
- minmax.getMaxBoundedValue().setCurrentValue( max );
+ else if ( type instanceof UnsignedByteType )
+ return new Bounds( 0, 255 );
+ else
+ return new Bounds( 0, 65535 );
}
- public static BigDataViewer createBDV( final ExplorerWindow< ?, ? > panel )
+ public static BigDataViewer createBDV( final ExplorerWindow< ? > panel )
{
final BigDataViewer bdv = createBDV( panel.getSpimData(), panel.xml() );
@@ -276,7 +292,7 @@ public static BigDataViewer createBDV( final ExplorerWindow< ?, ? > panel )
return bdv;
}
-
+
public static BigDataViewer createBDV(
final AbstractSpimData< ? > spimData,
final String xml )
@@ -292,12 +308,9 @@ public static BigDataViewer createBDV(
return null;
}
- BigDataViewer bdv = BigDataViewer.open( spimData, xml, IOFunctions.getProgressWriter(), ViewerOptions.options() );
-
-// if ( !bdv.tryLoadSettings( panel.xml() ) ) TODO: this should work, but currently tryLoadSettings is protected. fix that.
-
- InitializeViewerState.initBrightness( 0.001, 0.999, bdv.getViewer(), bdv.getSetupAssignments() );
- //initBrightness( 0.001, 0.999, bdv.getViewer().getState(), bdv.getSetupAssignments() );
+ final BigDataViewer bdv = BigDataViewer.open( spimData, xml, IOFunctions.getProgressWriter(), ViewerOptions.options() );
+ if ( !bdv.tryLoadSettings( xml ) )
+ InitializeViewerState.initBrightness( 0.001, 0.999, bdv.getViewerFrame() );
// do not rotate BDV view by default
BDVPopup.initTransform( bdv.getViewer() );
@@ -338,21 +351,25 @@ public static BigDataViewer createBDV(
public static void initTransform( final ViewerPanel viewer )
{
- final Dimension dim = viewer.getDisplay().getSize();
- final ViewerState state = viewer.getState();
- final AffineTransform3D viewerTransform = initTransform( dim.width, dim.height, false, state );
- viewer.setCurrentViewerTransform( viewerTransform );
+ final Dimension dim = viewer.getDisplayComponent().getSize();
+ final AffineTransform3D viewerTransform = initTransform( dim.width, dim.height, false, viewer.state().snapshot() );
+ viewer.state().setViewerTransform( viewerTransform );
}
+ // TODO (TP) Add initTransform without rotation to bdv-core
public static AffineTransform3D initTransform( final int viewerWidth, final int viewerHeight, final boolean zoomedIn, final ViewerState state )
{
- final int cX = viewerWidth / 2;
- final int cY = viewerHeight / 2;
+ final AffineTransform3D viewerTransform = new AffineTransform3D();
+ final double cX = viewerWidth / 2.0;
+ final double cY = viewerHeight / 2.0;
- final Source< ? > source = state.getSources().get( state.getCurrentSource() ).getSpimSource();
+ final SourceAndConverter< ? > current = state.getCurrentSource();
+ if ( current == null )
+ return viewerTransform;
+ final Source< ? > source = current.getSpimSource();
final int timepoint = state.getCurrentTimepoint();
if ( !source.isPresent( timepoint ) )
- return new AffineTransform3D();
+ return viewerTransform;
final AffineTransform3D sourceTransform = new AffineTransform3D();
source.getSourceTransform( timepoint, 0, sourceTransform );
@@ -364,9 +381,9 @@ public static AffineTransform3D initTransform( final int viewerWidth, final int
final double sY1 = sourceInterval.max( 1 );
final double sZ0 = sourceInterval.min( 2 );
final double sZ1 = sourceInterval.max( 2 );
- final double sX = ( sX0 + sX1 + 1 ) / 2;
- final double sY = ( sY0 + sY1 + 1 ) / 2;
- final double sZ = ( sZ0 != 0 || sZ1 != 0 ) ? ( sZ0 + sZ1 + 1 ) / 2 : 0;
+ final double sX = ( sX0 + sX1 ) / 2;
+ final double sY = ( sY0 + sY1 ) / 2;
+ final double sZ = Math.round( ( sZ0 + sZ1 ) / 2 ); // z-slice in the middle of a pixel
final double[][] m = new double[ 3 ][ 4 ];
@@ -383,7 +400,6 @@ public static AffineTransform3D initTransform( final int viewerWidth, final int
LinAlgHelpers.scale( translation, -1, translation );
LinAlgHelpers.setCol( 3, translation, m );
- final AffineTransform3D viewerTransform = new AffineTransform3D();
viewerTransform.set( m );
// scale
@@ -402,12 +418,11 @@ public static AffineTransform3D initTransform( final int viewerWidth, final int
viewerTransform.scale( scale );
// window center offset
- viewerTransform.set( viewerTransform.get( 0, 3 ) + cX, 0, 3 );
- viewerTransform.set( viewerTransform.get( 1, 3 ) + cY, 1, 3 );
+ viewerTransform.set( viewerTransform.get( 0, 3 ) + cX - 0.5, 0, 3 );
+ viewerTransform.set( viewerTransform.get( 1, 3 ) + cY - 0.5, 1, 3 );
return viewerTransform;
}
-
/*
This does not work yet, because invalidateAll is not implemented yet.
@@ -457,76 +472,4 @@ private static final void forceBDVReload(final AbstractSpimSource< ? > s)
}
*/
-
- private static final void callLoadTimePoint( final AbstractSpimSource< ? > s, final int timePointIndex )
- {
- try
- {
- Class< ? > clazz = null;
- boolean found = false;
-
- do
- {
- if ( clazz == null )
- clazz = s.getClass();
- else
- clazz = clazz.getSuperclass();
-
- if ( clazz != null )
- for ( final Method method : clazz.getDeclaredMethods() )
- if ( method.getName().equals( "loadTimepoint" ) )
- found = true;
- }
- while ( !found && clazz != null );
-
- if ( !found )
- {
- System.out.println( "Failed to find SpimSource.loadTimepoint method. Quiting." );
- return;
- }
-
- final Method loadTimepoint = clazz.getDeclaredMethod( "loadTimepoint", Integer.TYPE );
- loadTimepoint.setAccessible( true );
- loadTimepoint.invoke( s, timePointIndex );
- }
- catch ( Exception e ) { e.printStackTrace(); }
- }
-
- private static final int getCurrentTimePointIndex( final AbstractSpimSource< ? > s )
- {
- try
- {
- Class< ? > clazz = null;
- Field currentTimePointIndex = null;
-
- do
- {
- if ( clazz == null )
- clazz = s.getClass();
- else
- clazz = clazz.getSuperclass();
-
- if ( clazz != null )
- for ( final Field field : clazz.getDeclaredFields() )
- if ( field.getName().equals( "currentTimePointIndex" ) )
- currentTimePointIndex = field;
- }
- while ( currentTimePointIndex == null && clazz != null );
-
- if ( currentTimePointIndex == null )
- {
- System.out.println( "Failed to find AbstractSpimSource.currentTimePointIndex. Quiting." );
- return -1;
- }
-
- currentTimePointIndex.setAccessible( true );
-
- return currentTimePointIndex.getInt( s );
- }
- catch ( Exception e )
- {
- e.printStackTrace();
- return -1;
- }
- }
}
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BakeManualTransformationPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BakeManualTransformationPopup.java
index ac18e7180..24cbdef7a 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BakeManualTransformationPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BakeManualTransformationPopup.java
@@ -24,7 +24,6 @@
import java.awt.event.ActionEvent;
import java.util.ArrayList;
-import java.util.List;
import javax.swing.JComponent;
import javax.swing.JMenuItem;
@@ -33,8 +32,6 @@
import bdv.tools.transformation.TransformedSource;
import bdv.viewer.state.SourceState;
import bdv.viewer.state.ViewerState;
-import mpicbg.spim.data.generic.AbstractSpimData;
-import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.registration.ViewRegistration;
import mpicbg.spim.data.registration.ViewRegistrations;
import mpicbg.spim.data.registration.ViewTransform;
@@ -44,14 +41,12 @@
import net.preibisch.legacy.io.IOFunctions;
import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
import net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow;
-import net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel;
-import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
public class BakeManualTransformationPopup extends JMenuItem implements ExplorerWindowSetable
{
private static final long serialVersionUID = 4627408819269954486L;
- ExplorerWindow< ?, ? > panel;
+ ExplorerWindow< ? > panel;
public BakeManualTransformationPopup()
{
@@ -61,7 +56,7 @@ public BakeManualTransformationPopup()
}
@Override
- public JComponent setExplorerWindow( ExplorerWindow>, ?> panel )
+ public JComponent setExplorerWindow( ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BoundingBoxPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BoundingBoxPopup.java
index 531194425..41e0f1cae 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BoundingBoxPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BoundingBoxPopup.java
@@ -42,7 +42,7 @@ public class BoundingBoxPopup extends JMenuItem implements ExplorerWindowSetable
{
private static final long serialVersionUID = 5234649267634013390L;
- ExplorerWindow< ?, ? > panel;
+ ExplorerWindow< ? > panel;
public BoundingBoxPopup()
{
@@ -52,7 +52,7 @@ public BoundingBoxPopup()
}
@Override
- public JComponent setExplorerWindow( ExplorerWindow>, ?> panel )
+ public JComponent setExplorerWindow( ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DeconvolutionPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DeconvolutionPopup.java
index b60c50d30..f29674463 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DeconvolutionPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DeconvolutionPopup.java
@@ -39,7 +39,7 @@ public class DeconvolutionPopup extends JMenuItem implements ExplorerWindowSetab
{
private static final long serialVersionUID = 5234649267634013390L;
- ExplorerWindow< ?, ? > panel;
+ ExplorerWindow< ? > panel;
public DeconvolutionPopup()
{
@@ -49,7 +49,7 @@ public DeconvolutionPopup()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DetectInterestPointsPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DetectInterestPointsPopup.java
index 327fca94a..e4c51cc3b 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DetectInterestPointsPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DetectInterestPointsPopup.java
@@ -39,7 +39,7 @@ public class DetectInterestPointsPopup extends JMenuItem implements ExplorerWind
{
private static final long serialVersionUID = 5234649267634013390L;
- ExplorerWindow< ?, ? > panel;
+ ExplorerWindow< ? > panel;
public DetectInterestPointsPopup()
{
@@ -49,7 +49,7 @@ public DetectInterestPointsPopup()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayFusedImagesPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayFusedImagesPopup.java
index 527963979..2e46f2bea 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayFusedImagesPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayFusedImagesPopup.java
@@ -71,7 +71,7 @@ public class DisplayFusedImagesPopup extends JMenu implements ExplorerWindowSeta
private static final long serialVersionUID = -4895470813542722644L;
- ExplorerWindow< ?, ? > panel = null;
+ ExplorerWindow< ? > panel = null;
public DisplayFusedImagesPopup()
{
@@ -162,7 +162,7 @@ public void menuCanceled( MenuEvent e ) {}
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayRawImagesPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayRawImagesPopup.java
index 27c01c300..23b121125 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayRawImagesPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayRawImagesPopup.java
@@ -42,7 +42,7 @@ public class DisplayRawImagesPopup extends JMenu implements ExplorerWindowSetabl
public static final int askWhenMoreThan = 5;
private static final long serialVersionUID = 5234649262342301390L;
- ExplorerWindow< ?, ? > panel = null;
+ ExplorerWindow< ? > panel = null;
public DisplayRawImagesPopup()
{
@@ -59,7 +59,7 @@ public DisplayRawImagesPopup()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ExplorerWindowSetable.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ExplorerWindowSetable.java
index 70829c5e0..dc633deca 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ExplorerWindowSetable.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ExplorerWindowSetable.java
@@ -31,6 +31,6 @@
public interface ExplorerWindowSetable
{
- public JComponent setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel );
+ public JComponent setExplorerWindow( final ExplorerWindow< ? > panel );
}
// AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FlatFieldCorrectionPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FlatFieldCorrectionPopup.java
index 6f85b60a8..d169de4e4 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FlatFieldCorrectionPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FlatFieldCorrectionPopup.java
@@ -35,8 +35,6 @@
import javax.swing.JMenuItem;
import fiji.util.gui.GenericDialogPlus;
-import mpicbg.spim.data.generic.AbstractSpimData;
-import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.sequence.Channel;
import mpicbg.spim.data.sequence.Illumination;
import mpicbg.spim.data.sequence.ImgLoader;
@@ -54,7 +52,7 @@ public class FlatFieldCorrectionPopup extends JMenuItem implements ExplorerWindo
{
private static final long serialVersionUID = 950277697000203629L;
- private ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel;
+ private ExplorerWindow< ? > panel;
public FlatFieldCorrectionPopup()
{
@@ -63,8 +61,7 @@ public FlatFieldCorrectionPopup()
}
@Override
- public JComponent setExplorerWindow(
- ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel)
+ public JComponent setExplorerWindow( ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FusionPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FusionPopup.java
index 55c008f47..020170cca 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FusionPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FusionPopup.java
@@ -39,7 +39,7 @@ public class FusionPopup extends JMenuItem implements ExplorerWindowSetable
{
private static final long serialVersionUID = 5234649267634013390L;
- ExplorerWindow< ?, ? > panel;
+ ExplorerWindow< ? > panel;
public FusionPopup()
{
@@ -49,7 +49,7 @@ public FusionPopup()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/IntensityAdjustmentPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/IntensityAdjustmentPopup.java
index 96d9b6a6f..924919307 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/IntensityAdjustmentPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/IntensityAdjustmentPopup.java
@@ -43,7 +43,7 @@ public class IntensityAdjustmentPopup extends JMenu implements ExplorerWindowSet
{
private static final long serialVersionUID = 1L;
- ExplorerWindow< ?, ? > panel;
+ ExplorerWindow< ? > panel;
protected static String[] types = new String[]{ "Compute ...", "List all", "Remove" };
@@ -65,7 +65,7 @@ public IntensityAdjustmentPopup()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/InterestPointsExplorerPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/InterestPointsExplorerPopup.java
index 76ca00198..054b40992 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/InterestPointsExplorerPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/InterestPointsExplorerPopup.java
@@ -40,8 +40,8 @@ public class InterestPointsExplorerPopup extends JMenuItem implements ExplorerWi
{
private static final long serialVersionUID = 5234649267634013390L;
- ViewSetupExplorerPanel< ?, ? > panel;
- InterestPointExplorer< ?, ? > ipe = null;
+ ViewSetupExplorerPanel< ? > panel;
+ InterestPointExplorer< ? > ipe = null;
public InterestPointsExplorerPopup()
{
@@ -52,9 +52,9 @@ public InterestPointsExplorerPopup()
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
- this.panel = (ViewSetupExplorerPanel< ?, ? >)panel;
+ this.panel = (ViewSetupExplorerPanel< ? >)panel;
return this;
}
@@ -94,8 +94,8 @@ public void run()
}
}
- private static final < AS extends SpimData2, X extends XmlIoAbstractSpimData< ?, AS > > InterestPointExplorer< AS, X > instanceFor( final FilteredAndGroupedExplorerPanel< AS, X > panel )
+ private static < AS extends SpimData2 > InterestPointExplorer< AS > instanceFor( final FilteredAndGroupedExplorerPanel< AS > panel )
{
- return new InterestPointExplorer< AS, X >( panel.xml(), panel.io(), panel.explorer() );
+ return new InterestPointExplorer<>( panel.xml(), panel.io(), panel.explorer() );
}
}
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/LabelPopUp.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/LabelPopUp.java
index 8fc502a8b..90cb8ac6d 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/LabelPopUp.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/LabelPopUp.java
@@ -41,7 +41,7 @@ public LabelPopUp( final String text )
}
@Override
- public JLabel setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JLabel setExplorerWindow( final ExplorerWindow< ? > panel )
{
return this;
}
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/MaxProjectPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/MaxProjectPopup.java
index 7481aa420..fe3572aca 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/MaxProjectPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/MaxProjectPopup.java
@@ -44,7 +44,7 @@ public class MaxProjectPopup extends JMenuItem implements ExplorerWindowSetable
private static final long serialVersionUID = 5234649267634013390L;
public static boolean showWarning = true;
- ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel;
+ ExplorerWindow< ? > panel;
public MaxProjectPopup()
{
@@ -54,7 +54,7 @@ public MaxProjectPopup()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/PointSpreadFunctionsPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/PointSpreadFunctionsPopup.java
index f97763264..e90f1514a 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/PointSpreadFunctionsPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/PointSpreadFunctionsPopup.java
@@ -50,10 +50,10 @@ public class PointSpreadFunctionsPopup extends JMenu implements ExplorerWindowSe
{
private static final long serialVersionUID = 1L;
- ExplorerWindow< ?, ? > panel = null;
+ ExplorerWindow< ? > panel = null;
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/QualityPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/QualityPopup.java
index 8dae96d7c..b0d28224d 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/QualityPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/QualityPopup.java
@@ -40,7 +40,7 @@ public class QualityPopup extends JMenuItem implements ExplorerWindowSetable
{
private static final long serialVersionUID = 5234649267634013390L;
- ExplorerWindow< ?, ? > panel;
+ ExplorerWindow< ? > panel;
public QualityPopup()
{
@@ -50,7 +50,7 @@ public QualityPopup()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegisterInterestPointsPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegisterInterestPointsPopup.java
index 243dcbdf1..e255a36a7 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegisterInterestPointsPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegisterInterestPointsPopup.java
@@ -39,7 +39,7 @@ public class RegisterInterestPointsPopup extends JMenuItem implements ExplorerWi
{
private static final long serialVersionUID = 5234649267634013390L;
- ExplorerWindow< ?, ? > panel;
+ ExplorerWindow< ? > panel;
public RegisterInterestPointsPopup()
{
@@ -49,7 +49,7 @@ public RegisterInterestPointsPopup()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegistrationExplorerPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegistrationExplorerPopup.java
index d6b4cfa1e..8002c2279 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegistrationExplorerPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegistrationExplorerPopup.java
@@ -41,8 +41,8 @@ public class RegistrationExplorerPopup extends JMenuItem implements ExplorerWind
{
private static final long serialVersionUID = 5234649267634013390L;
- FilteredAndGroupedExplorerPanel< ?, ? > panel;
- RegistrationExplorer< ?, ? > re = null;
+ FilteredAndGroupedExplorerPanel< ? > panel;
+ RegistrationExplorer< ? > re = null;
public RegistrationExplorerPopup()
{
@@ -52,9 +52,9 @@ public RegistrationExplorerPopup()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
- this.panel = (FilteredAndGroupedExplorerPanel< ?, ? >)panel;
+ this.panel = ( FilteredAndGroupedExplorerPanel< ? > ) panel;
return this;
}
@@ -88,8 +88,8 @@ public void run()
}
}
- private static final < AS extends AbstractSpimData< ? >, X extends XmlIoAbstractSpimData< ?, AS > > RegistrationExplorer< AS, X > instanceFor( final FilteredAndGroupedExplorerPanel< AS, X > panel )
+ private static < AS extends AbstractSpimData< ? > > RegistrationExplorer< AS > instanceFor( final FilteredAndGroupedExplorerPanel< AS > panel )
{
- return new RegistrationExplorer< AS, X >( panel.xml(), panel.io(), panel.explorer() );
+ return new RegistrationExplorer<>( panel.xml(), panel.io(), panel.explorer() );
}
}
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveDetectionsPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveDetectionsPopup.java
index 4417c075f..9db5f6b16 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveDetectionsPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveDetectionsPopup.java
@@ -57,7 +57,7 @@ public class RemoveDetectionsPopup extends JMenu implements ExplorerWindowSetabl
{
private static final long serialVersionUID = 1L;
- ExplorerWindow< ?, ? > panel = null;
+ ExplorerWindow< ? > panel = null;
public static int defaultLabel = 0;
public static String defaultNewLabel = "Manually removed";
@@ -141,7 +141,7 @@ public void menuCanceled( MenuEvent e ) {}
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveTransformationPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveTransformationPopup.java
index 1907f54ab..4eabbe4c0 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveTransformationPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveTransformationPopup.java
@@ -42,7 +42,7 @@ public class RemoveTransformationPopup extends JMenu implements ExplorerWindowSe
public static final int askWhenMoreThan = 5;
private static final long serialVersionUID = 5234649267634013390L;
- ExplorerWindow< ?, ? > panel;
+ ExplorerWindow< ? > panel;
protected static String[] types = new String[]{ "Latest/Newest Transformation", "First/Oldest Transformation" };
@@ -61,7 +61,7 @@ public RemoveTransformationPopup()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ReorientSamplePopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ReorientSamplePopup.java
index 2b2221382..df981c131 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ReorientSamplePopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ReorientSamplePopup.java
@@ -31,8 +31,6 @@
import bdv.BigDataViewer;
import mpicbg.spim.data.SpimData;
-import mpicbg.spim.data.generic.AbstractSpimData;
-import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.sequence.ViewDescription;
import mpicbg.spim.data.sequence.ViewId;
import net.imglib2.realtransform.AffineTransform3D;
@@ -48,7 +46,7 @@ public class ReorientSamplePopup extends JMenuItem implements ExplorerWindowSeta
private static final long serialVersionUID = 5234649267634013390L;
public static boolean showWarning = true;
- ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel;
+ ExplorerWindow< ? > panel;
public ReorientSamplePopup()
{
@@ -58,7 +56,7 @@ public ReorientSamplePopup()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java
index 7950f2616..05d98dd08 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java
@@ -25,10 +25,7 @@
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.File;
-import java.io.IOException;
import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
import java.util.Date;
import java.util.List;
import java.util.Map;
@@ -38,22 +35,11 @@
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
-import org.janelia.saalfeldlab.n5.GzipCompression;
-
import bdv.export.ExportMipmapInfo;
import bdv.export.ProgressWriter;
-import bdv.export.ProposeMipmaps;
-import bdv.export.WriteSequenceToHdf5;
-import bdv.export.ExportScalePyramid;
-import bdv.export.n5.WriteSequenceToN5;
import bdv.img.n5.N5ImageLoader;
-import mpicbg.spim.data.generic.AbstractSpimData;
-import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.sequence.ViewId;
import mpicbg.spim.data.sequence.ViewSetup;
-import net.imglib2.img.array.ArrayImgFactory;
-import net.imglib2.img.cell.CellImgFactory;
-import net.imglib2.type.numeric.real.FloatType;
import net.preibisch.legacy.io.IOFunctions;
import net.preibisch.mvrecon.fiji.ImgLib2Temp.Pair;
import net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5;
@@ -66,15 +52,13 @@
import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
import net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow;
import net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel;
-import net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgFactoryImgLoader;
-import net.preibisch.mvrecon.fiji.spimdata.imgloaders.MicroManagerImgLoader;
public class ResavePopup extends JMenu implements ExplorerWindowSetable
{
public static final int askWhenMoreThan = 5;
private static final long serialVersionUID = 5234649267634013390L;
- FilteredAndGroupedExplorerPanel< ?, ? > panel;
+ FilteredAndGroupedExplorerPanel< ? > panel;
protected static String[] types = new String[]{ "As TIFF ...", "As compressed TIFF ...", "As HDF5 ...", "As compressed HDF5 ...", "As compressed N5 ..." };
@@ -102,9 +86,9 @@ public ResavePopup()
}
@Override
- public JMenuItem setExplorerWindow(ExplorerWindow>, ?> panel )
+ public JMenuItem setExplorerWindow( ExplorerWindow< ? > panel )
{
- this.panel = (FilteredAndGroupedExplorerPanel< ?, ? >)panel;
+ this.panel = ( FilteredAndGroupedExplorerPanel< ? > ) panel;
return this;
}
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/Separator.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/Separator.java
index c6049aca3..2db7e1615 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/Separator.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/Separator.java
@@ -31,7 +31,7 @@ public class Separator extends JSeparator implements ExplorerWindowSetable
private static final long serialVersionUID = 5234649267634013390L;
@Override
- public JSeparator setExplorerWindow( final ExplorerWindow< ?, ? > panel )
+ public JSeparator setExplorerWindow( final ExplorerWindow< ? > panel )
{
return this;
}
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SimpleHyperlinkPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SimpleHyperlinkPopup.java
index 77cc021ce..78d3a2412 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SimpleHyperlinkPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SimpleHyperlinkPopup.java
@@ -34,10 +34,7 @@
import javax.swing.JLabel;
import javax.swing.JMenuItem;
-import mpicbg.spim.data.generic.AbstractSpimData;
-import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow;
-import net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ExplorerWindowSetable;
public class SimpleHyperlinkPopup extends JMenuItem implements ExplorerWindowSetable
{
@@ -55,8 +52,7 @@ public SimpleHyperlinkPopup(String title, URI uri)
}
@Override
- public JComponent setExplorerWindow(
- ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel)
+ public JComponent setExplorerWindow( ExplorerWindow< ? > panel )
{
return this;
}
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SpecifyCalibrationPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SpecifyCalibrationPopup.java
index 6ef51d2db..d3d0c1f22 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SpecifyCalibrationPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SpecifyCalibrationPopup.java
@@ -45,7 +45,7 @@ public class SpecifyCalibrationPopup extends JMenuItem implements ExplorerWindow
private static final long serialVersionUID = 5234649267634013390L;
public static boolean showWarning = true;
- ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel;
+ ExplorerWindow< ? > panel;
public SpecifyCalibrationPopup()
{
@@ -55,7 +55,7 @@ public SpecifyCalibrationPopup()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeDetectionsPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeDetectionsPopup.java
index 2fa4892e4..3e9c905e9 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeDetectionsPopup.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeDetectionsPopup.java
@@ -34,15 +34,13 @@
import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
import net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow;
-import mpicbg.spim.data.generic.AbstractSpimData;
-import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.sequence.ViewId;
public class VisualizeDetectionsPopup extends JMenuItem implements ExplorerWindowSetable
{
private static final long serialVersionUID = 5234649267634013390L;
- ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel;
+ ExplorerWindow< ? > panel;
public VisualizeDetectionsPopup()
{
@@ -52,7 +50,7 @@ public VisualizeDetectionsPopup()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeNonRigid.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeNonRigid.java
index 8c1a36704..9e40e8828 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeNonRigid.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeNonRigid.java
@@ -69,7 +69,7 @@ public class VisualizeNonRigid extends JMenuItem implements ExplorerWindowSetabl
{
private static final long serialVersionUID = -4858927229313796971L;
- ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel;
+ ExplorerWindow< ? > panel;
final private static String[] displayOptions = new String[] {
"Overlay all views affine vs. non-rigid",
@@ -87,7 +87,7 @@ public VisualizeNonRigid()
}
@Override
- public JMenuItem setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel )
+ public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel )
{
this.panel = panel;
return this;
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 18eaa839c..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
@@ -40,15 +40,15 @@
import mpicbg.spim.data.generic.sequence.BasicViewDescription;
import mpicbg.spim.data.generic.sequence.BasicViewSetup;
-public class RegistrationExplorer< AS extends AbstractSpimData< ? >, X extends XmlIoAbstractSpimData< ?, AS > >
+public class RegistrationExplorer< AS extends AbstractSpimData< ? > >
implements SelectedViewDescriptionListener< AS >
{
final String xml;
final JFrame frame;
final RegistrationExplorerPanel panel;
- final FilteredAndGroupedExplorer< AS, X > viewSetupExplorer;
-
- public RegistrationExplorer( final String xml, final X io, final FilteredAndGroupedExplorer< AS, X > viewSetupExplorer )
+ final FilteredAndGroupedExplorer< AS > viewSetupExplorer;
+
+ public RegistrationExplorer( final String xml, final XmlIoAbstractSpimData< ?, AS > io, final FilteredAndGroupedExplorer< AS > viewSetupExplorer )
{
this.xml = xml;
this.viewSetupExplorer = viewSetupExplorer;
@@ -78,10 +78,10 @@ public RegistrationExplorer( final String xml, final X io, final FilteredAndGrou
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/explorer/registration/RegistrationExplorerPanel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorerPanel.java
index 99c51f36a..3a6ef3ac2 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorerPanel.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorerPanel.java
@@ -77,9 +77,9 @@
public class RegistrationExplorerPanel extends JPanel
{
private static final long serialVersionUID = -3767947754096099774L;
-
- final RegistrationExplorer< ?, ? > explorer;
-
+
+ final RegistrationExplorer< ? > explorer;
+
protected JTable table;
protected RegistrationTableModel tableModel;
protected JLabel label;
@@ -89,8 +89,8 @@ public class RegistrationExplorerPanel extends JPanel
protected List> lastSelectedVDs;
protected ArrayList< ViewTransform > cache;
-
- public RegistrationExplorerPanel( final ViewRegistrations viewRegistrations, final RegistrationExplorer< ?, ? > explorer )
+
+ public RegistrationExplorerPanel( final ViewRegistrations viewRegistrations, final RegistrationExplorer< ? > explorer )
{
this.cache = new ArrayList< ViewTransform >();
this.explorer = explorer;
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/headless/splitting/TestSplitting.java b/src/main/java/net/preibisch/mvrecon/headless/splitting/TestSplitting.java
index d973cb432..70787f324 100644
--- a/src/main/java/net/preibisch/mvrecon/headless/splitting/TestSplitting.java
+++ b/src/main/java/net/preibisch/mvrecon/headless/splitting/TestSplitting.java
@@ -60,7 +60,7 @@ public static void main( String[] args ) throws SpimDataException
SpimData2 newSD = SplittingTools.splitImages( spimData, new long[] { 30, 30, 10 }, new long[] { 200, 200, 40 } );
// drosophila with 1000 views
- final ViewSetupExplorer< SpimData2, XmlIoSpimData2 > explorer = new ViewSetupExplorer( newSD, fileOut, new XmlIoSpimData2( "" ) );
+ final ViewSetupExplorer< SpimData2 > explorer = new ViewSetupExplorer<>( newSD, fileOut, new XmlIoSpimData2( "" ) );
explorer.getFrame().toFront();
}
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() );