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Commit 75e082a6 authored by Tobias Pietzsch's avatar Tobias Pietzsch
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Revise construction of SpimSources, SourceAndConverter, ConverterSetup

parent 9bc71179
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src/main/java/bdv/BigDataViewer.java
+ 78
− 113
View file @ 75e082a6
...@@ -43,6 +43,16 @@ import javax.swing.JMenuBar; ...@@ -43,6 +43,16 @@ import javax.swing.JMenuBar;
import javax.swing.JMenuItem; import javax.swing.JMenuItem;
import javax.swing.filechooser.FileFilter; import javax.swing.filechooser.FileFilter;
import net.imglib2.Volatile;
import net.imglib2.converter.Converter;
import net.imglib2.display.ColorConverter;
import net.imglib2.display.RealARGBColorConverter;
import net.imglib2.display.ScaledARGBConverter;
import net.imglib2.type.numeric.ARGBType;
import net.imglib2.type.numeric.NumericType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.volatiles.VolatileARGBType;
import org.jdom2.Document; import org.jdom2.Document;
import org.jdom2.Element; import org.jdom2.Element;
import org.jdom2.JDOMException; import org.jdom2.JDOMException;
...@@ -85,12 +95,6 @@ import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; ...@@ -85,12 +95,6 @@ import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.generic.sequence.BasicViewSetup; import mpicbg.spim.data.generic.sequence.BasicViewSetup;
import mpicbg.spim.data.sequence.Angle; import mpicbg.spim.data.sequence.Angle;
import mpicbg.spim.data.sequence.Channel; import mpicbg.spim.data.sequence.Channel;
import net.imglib2.Volatile;
import net.imglib2.display.RealARGBColorConverter;
import net.imglib2.display.ScaledARGBConverter;
import net.imglib2.type.numeric.ARGBType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.volatiles.VolatileARGBType;
public class BigDataViewer public class BigDataViewer
{ {
...@@ -162,143 +166,104 @@ public class BigDataViewer ...@@ -162,143 +166,104 @@ public class BigDataViewer
return name; return name;
} }
private static < T extends RealType< T >, V extends Volatile< T > & RealType< V > > void initSetupRealType( @SuppressWarnings( "unchecked" )
final AbstractSpimData< ? > spimData, private static < T > Converter< T, ARGBType > createConverter( final T type )
final BasicViewSetup setup,
final T type,
final List< ConverterSetup > converterSetups,
final List< SourceAndConverter< ? > > sources )
{ {
if ( spimData.getSequenceDescription().getImgLoader() instanceof WrapBasicImgLoader ) if ( type instanceof RealType )
{ {
initSetupRealTypeNonVolatile( spimData, setup, type, converterSetups, sources ); final RealType< ? > t = ( RealType< ? > ) type;
return; final double typeMin = Math.max( 0, Math.min( t.getMinValue(), 65535 ) );
final double typeMax = Math.max( 0, Math.min( t.getMaxValue(), 65535 ) );
return ( Converter< T, ARGBType > ) RealARGBColorConverter.create( t, typeMin, typeMax );
}
else if ( type instanceof ARGBType )
return ( Converter< T, ARGBType > ) new ScaledARGBConverter.ARGB( 0, 255 );
else if ( type instanceof VolatileARGBType )
return ( Converter< T, ARGBType > ) new ScaledARGBConverter.VolatileARGB( 0, 255 );
else
throw new IllegalArgumentException( "ImgLoader of type " + type.getClass() + " not supported." );
} }
final int setupId = setup.getId(); private static ConverterSetup createConverterSetup( final SourceAndConverter< ? > soc, final int setupId )
final V volatileType = ( ( ViewerSetupImgLoader< T, V > ) spimData.getSequenceDescription().getImgLoader().getSetupImgLoader( setupId ) ).getVolatileImageType(); {
final List< ColorConverter > converters = new ArrayList<>();
final double typeMin = Math.max( 0, Math.min( type.getMinValue(), 65535 ) );
final double typeMax = Math.max( 0, Math.min( type.getMaxValue(), 65535 ) );
final RealARGBColorConverter< V > vconverter = RealARGBColorConverter.create( volatileType, typeMin, typeMax );
vconverter.setColor( new ARGBType( 0xffffffff ) );
final RealARGBColorConverter< T > converter = RealARGBColorConverter.create( type, typeMin, typeMax );
converter.setColor( new ARGBType( 0xffffffff ) );
final String setupName = createSetupName( setup );
final VolatileSpimSource< T, V > vs = new VolatileSpimSource<>( spimData, setupId, setupName );
final SpimSource< T > s = vs.nonVolatile();
// Decorate each source with an extra transformation, that can be final Converter< ?, ARGBType > c = soc.getConverter();
// edited manually in this viewer. if ( c instanceof ColorConverter )
final TransformedSource< V > tvs = new TransformedSource<>( vs ); converters.add( ( ColorConverter ) c );
final TransformedSource< T > ts = new TransformedSource<>( s, tvs );
final SourceAndConverter< V > vsoc = new SourceAndConverter<>( tvs, vconverter ); final SourceAndConverter< ? extends Volatile< ? > > vsoc = soc.asVolatile();
final SourceAndConverter< T > soc = new SourceAndConverter<>( ts, converter, vsoc ); if ( vsoc != null )
{
final Converter< ?, ARGBType > vc = vsoc.getConverter();
if ( vc instanceof ColorConverter )
converters.add( ( ColorConverter ) vc );
}
sources.add( soc ); if ( converters.isEmpty() )
converterSetups.add( new RealARGBColorConverterSetup( setupId, converter, vconverter ) ); return null;
else
return new RealARGBColorConverterSetup( setupId, converters );
} }
private static < T extends RealType< T > > void initSetupRealTypeNonVolatile( /**
final AbstractSpimData< ? > spimData, * Decorate source with an extra transformation, that can be edited manually
final BasicViewSetup setup, * in this viewer.
final T type, */
final List< ConverterSetup > converterSetups, private static < T, V extends Volatile< T > > SourceAndConverter< T > wrapWithTransformedSource( final SourceAndConverter< T > soc )
final List< SourceAndConverter< ? > > sources )
{ {
final double typeMin = Math.max( 0, Math.min( type.getMinValue(), 65535 ) ); if ( soc.asVolatile() == null )
final double typeMax = Math.max( 0, Math.min( type.getMaxValue(), 65535 ) ); return new SourceAndConverter<>( new TransformedSource<>( soc.getSpimSource() ), soc.getConverter() );
final RealARGBColorConverter< T > converter = RealARGBColorConverter.create( type, typeMin, typeMax );
converter.setColor( new ARGBType( 0xffffffff ) );
final int setupId = setup.getId();
final String setupName = createSetupName( setup );
final SpimSource< T > s = new SpimSource<>( spimData, setupId, setupName );
// Decorate each source with an extra transformation, that can be
// edited manually in this viewer.
final TransformedSource< T > ts = new TransformedSource<>( s );
final SourceAndConverter< T > soc = new SourceAndConverter<>( ts, converter );
sources.add( soc ); @SuppressWarnings( "unchecked" )
converterSetups.add( new RealARGBColorConverterSetup( setupId, converter ) ); final SourceAndConverter< V > vsoc = ( SourceAndConverter< V > ) soc.asVolatile();
final TransformedSource< T > ts = new TransformedSource<>( soc.getSpimSource() );
final TransformedSource< V > vts = new TransformedSource<>( vsoc.getSpimSource(), ts );
return new SourceAndConverter<>( ts, soc.getConverter(), new SourceAndConverter<>( vts, vsoc.getConverter() ) );
} }
private static void initSetupARGBType( private static < T extends NumericType< T >, V extends Volatile< T > & NumericType< V > > void initSetupNumericType(
final AbstractSpimData< ? > spimData, final AbstractSpimData< ? > spimData,
final BasicViewSetup setup, final BasicViewSetup setup,
final ARGBType type,
final List< ConverterSetup > converterSetups, final List< ConverterSetup > converterSetups,
final List< SourceAndConverter< ? > > sources ) final List< SourceAndConverter< ? > > sources )
{ {
if ( spimData.getSequenceDescription().getImgLoader() instanceof WrapBasicImgLoader )
{
initSetupARGBTypeNonVolatile( spimData, setup, type, converterSetups, sources );
return;
}
final ScaledARGBConverter.VolatileARGB vconverter = new ScaledARGBConverter.VolatileARGB( 0, 255 );
final ScaledARGBConverter.ARGB converter = new ScaledARGBConverter.ARGB( 0, 255 );
final int setupId = setup.getId(); final int setupId = setup.getId();
final String setupName = createSetupName( setup ); final ViewerImgLoader imgLoader = ( ViewerImgLoader ) spimData.getSequenceDescription().getImgLoader();
final VolatileSpimSource< ARGBType, VolatileARGBType > vs = new VolatileSpimSource<>( spimData, setupId, setupName ); @SuppressWarnings( "unchecked" )
final SpimSource< ARGBType > s = vs.nonVolatile(); final ViewerSetupImgLoader< T, V > setupImgLoader = ( ViewerSetupImgLoader< T, V > ) imgLoader.getSetupImgLoader( setupId );
final T type = setupImgLoader.getImageType();
final V volatileType = setupImgLoader.getVolatileImageType();
// Decorate each source with an extra transformation, that can be if ( ! ( type instanceof NumericType ) )
// edited manually in this viewer. throw new IllegalArgumentException( "ImgLoader of type " + type.getClass() + " not supported." );
final TransformedSource< VolatileARGBType > tvs = new TransformedSource<>( vs );
final TransformedSource< ARGBType > ts = new TransformedSource<>( s, tvs );
final SourceAndConverter< VolatileARGBType > vsoc = new SourceAndConverter<>( tvs, vconverter );
final SourceAndConverter< ARGBType > soc = new SourceAndConverter<>( ts, converter, vsoc );
sources.add( soc ); final String setupName = createSetupName( setup );
converterSetups.add( new RealARGBColorConverterSetup( setupId, converter, vconverter ) );
}
private static void initSetupARGBTypeNonVolatile( SourceAndConverter< V > vsoc = null;
final AbstractSpimData< ? > spimData, if ( volatileType != null )
final BasicViewSetup setup,
final ARGBType type,
final List< ConverterSetup > converterSetups,
final List< SourceAndConverter< ? > > sources )
{ {
final ScaledARGBConverter.ARGB converter = new ScaledARGBConverter.ARGB( 0, 255 ); final VolatileSpimSource< V > vs = new VolatileSpimSource<>( spimData, setupId, setupName );
vsoc = new SourceAndConverter<>( vs, createConverter( volatileType ) );
final int setupId = setup.getId(); }
final String setupName = createSetupName( setup );
final SpimSource< ARGBType > s = new SpimSource<>( spimData, setupId, setupName );
// Decorate each source with an extra transformation, that can be final SpimSource< T > s = new SpimSource<>( spimData, setupId, setupName );
// edited manually in this viewer. final SourceAndConverter< T > soc = new SourceAndConverter<>( s, createConverter( type ), vsoc );
final TransformedSource< ARGBType > ts = new TransformedSource<>( s ); final SourceAndConverter< T > tsoc = wrapWithTransformedSource( soc );
final SourceAndConverter< ARGBType > soc = new SourceAndConverter<>( ts, converter ); sources.add( tsoc );
sources.add( soc ); final ConverterSetup converterSetup = createConverterSetup( tsoc, setupId );
converterSetups.add( new RealARGBColorConverterSetup( setupId, converter ) ); if ( converterSetup != null )
converterSetups.add( converterSetup );
} }
@SuppressWarnings( { "unchecked", "rawtypes" } )
public static void initSetups( public static void initSetups(
final AbstractSpimData< ? > spimData, final AbstractSpimData< ? > spimData,
final List< ConverterSetup > converterSetups, final List< ConverterSetup > converterSetups,
final List< SourceAndConverter< ? > > sources ) final List< SourceAndConverter< ? > > sources )
{ {
final AbstractSequenceDescription< ?, ?, ? > seq = spimData.getSequenceDescription(); for ( final BasicViewSetup setup : spimData.getSequenceDescription().getViewSetupsOrdered() )
final ViewerImgLoader imgLoader = ( ViewerImgLoader ) seq.getImgLoader(); initSetupNumericType( spimData, setup, converterSetups, sources );
for ( final BasicViewSetup setup : seq.getViewSetupsOrdered() )
{
final int setupId = setup.getId();
final Object type = imgLoader.getSetupImgLoader( setupId ).getImageType();
if ( RealType.class.isInstance( type ) )
initSetupRealType( spimData, setup, ( RealType ) type, converterSetups, sources );
else if ( ARGBType.class.isInstance( type ) )
initSetupARGBType( spimData, setup, ( ARGBType ) type, converterSetups, sources );
else
throw new IllegalArgumentException( "ImgLoader of type " + type.getClass() + " not supported." );
}
} }
/** /**
......
src/main/java/bdv/VolatileSpimSource.java
+ 6
− 13
View file @ 75e082a6
...@@ -29,21 +29,20 @@ ...@@ -29,21 +29,20 @@
*/ */
package bdv; package bdv;
import bdv.viewer.render.DefaultMipmapOrdering;
import bdv.viewer.render.MipmapOrdering;
import mpicbg.spim.data.generic.AbstractSpimData;
import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import net.imglib2.RandomAccessibleInterval; import net.imglib2.RandomAccessibleInterval;
import net.imglib2.Volatile; import net.imglib2.Volatile;
import net.imglib2.realtransform.AffineTransform3D; import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.NumericType; import net.imglib2.type.numeric.NumericType;
public class VolatileSpimSource< T extends NumericType< T >, V extends Volatile< T > & NumericType< V > > import bdv.viewer.render.DefaultMipmapOrdering;
import bdv.viewer.render.MipmapOrdering;
import mpicbg.spim.data.generic.AbstractSpimData;
import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
public class VolatileSpimSource< V extends Volatile< ? > & NumericType< V > >
extends AbstractSpimSource< V > extends AbstractSpimSource< V >
implements MipmapOrdering implements MipmapOrdering
{ {
protected final SpimSource< T > nonVolatileSource;
protected final ViewerSetupImgLoader< ?, V > imgLoader; protected final ViewerSetupImgLoader< ?, V > imgLoader;
protected final MipmapOrdering mipmapOrdering; protected final MipmapOrdering mipmapOrdering;
...@@ -52,7 +51,6 @@ public class VolatileSpimSource< T extends NumericType< T >, V extends Volatile< ...@@ -52,7 +51,6 @@ public class VolatileSpimSource< T extends NumericType< T >, V extends Volatile<
public VolatileSpimSource( final AbstractSpimData< ? > spimData, final int setup, final String name ) public VolatileSpimSource( final AbstractSpimData< ? > spimData, final int setup, final String name )
{ {
super( spimData, setup, name ); super( spimData, setup, name );
nonVolatileSource = new SpimSource<>( spimData, setup, name );
final AbstractSequenceDescription< ?, ?, ? > seq = spimData.getSequenceDescription(); final AbstractSequenceDescription< ?, ?, ? > seq = spimData.getSequenceDescription();
imgLoader = ( ViewerSetupImgLoader< ?, V > ) ( ( ViewerImgLoader ) seq.getImgLoader() ).getSetupImgLoader( setup ); imgLoader = ( ViewerSetupImgLoader< ?, V > ) ( ( ViewerImgLoader ) seq.getImgLoader() ).getSetupImgLoader( setup );
if ( MipmapOrdering.class.isInstance( imgLoader ) ) if ( MipmapOrdering.class.isInstance( imgLoader ) )
...@@ -68,11 +66,6 @@ public class VolatileSpimSource< T extends NumericType< T >, V extends Volatile< ...@@ -68,11 +66,6 @@ public class VolatileSpimSource< T extends NumericType< T >, V extends Volatile<
return imgLoader.getVolatileImageType(); return imgLoader.getVolatileImageType();
} }
public SpimSource< T > nonVolatile()
{
return nonVolatileSource;
}
@Override @Override
protected RandomAccessibleInterval< V > getImage( final int timepointId, final int level ) protected RandomAccessibleInterval< V > getImage( final int timepointId, final int level )
{ {
......
src/main/java/bdv/spimdata/WrapBasicImgLoader.java
+ 1
− 1
View file @ 75e082a6
...@@ -159,7 +159,7 @@ public class WrapBasicImgLoader implements ViewerImgLoader ...@@ -159,7 +159,7 @@ public class WrapBasicImgLoader implements ViewerImgLoader
@Override @Override
public V getVolatileImageType() public V getVolatileImageType()
{ {
throw new UnsupportedOperationException(); return null;
} }
@Override @Override
......
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