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Relax NumericType restriction on AbstractSource and RandomAccessibleSources #10

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Relax NumericType restriction on AbstractSource and RandomAccessibleSources #10

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cba1535
Relax NumericType restriction on AbstractSource and RandomAccessibleS…
nthistle Jul 27, 2017
4c3dae6
Relax NumericType to Type on RAIMipMapSource
nthistle Jul 28, 2017
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21 changes: 13 additions & 8 deletions src/main/java/bdv/util/AbstractSource.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,22 +34,27 @@
import bdv.viewer.Source;
import mpicbg.spim.data.sequence.VoxelDimensions;
import net.imglib2.RealRandomAccessible;
import net.imglib2.interpolation.randomaccess.NearestNeighborInterpolatorFactory;
import net.imglib2.type.Type;
import net.imglib2.type.numeric.NumericType;
import net.imglib2.view.Views;

public abstract class AbstractSource< T extends NumericType< T > > implements Source< T >
public abstract class AbstractSource< T extends Type< T > > implements Source< T >
{
protected final T type;
protected final T extension;

protected final String name;

protected final DefaultInterpolators< T > interpolators;
protected final InterpolationFunction<T> interpolators;

public AbstractSource( final T type, final String name )
public AbstractSource( final T extension, final String name )
{
this.type = type;
this.extension = extension;
this.name = name;
interpolators = new DefaultInterpolators<>();
if(extension instanceof NumericType)
interpolators = new DefaultInterpolators();
else
interpolators = (interpolation -> new NearestNeighborInterpolatorFactory<>());
}

public AbstractSource( final Supplier< T > typeSupplier, final String name )
Expand All @@ -66,13 +71,13 @@ public boolean isPresent( final int t )
@Override
public T getType()
{
return type;
return extension;
}

@Override
public RealRandomAccessible< T > getInterpolatedSource( final int t, final int level, final Interpolation method )
{
return Views.interpolate( Views.extendZero( getSource( t, level ) ), interpolators.get( method ) );
return Views.interpolate( Views.extendValue( getSource( t, level ), extension ), interpolators.apply( method ) );
}

@Override
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11 changes: 2 additions & 9 deletions src/main/java/bdv/util/DefaultInterpolators.java
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Original file line number Diff line number Diff line change
@@ -1,15 +1,13 @@
package bdv.util;

import java.util.function.Function;

import bdv.viewer.Interpolation;
import net.imglib2.RandomAccessible;
import net.imglib2.interpolation.InterpolatorFactory;
import net.imglib2.interpolation.randomaccess.ClampingNLinearInterpolatorFactory;
import net.imglib2.interpolation.randomaccess.NearestNeighborInterpolatorFactory;
import net.imglib2.type.numeric.NumericType;

public class DefaultInterpolators< T extends NumericType< T > > implements Function< Interpolation, InterpolatorFactory< T, RandomAccessible< T > > >
public class DefaultInterpolators< T extends NumericType< T > > implements InterpolationFunction< T >
{
private final InterpolatorFactory< T, RandomAccessible< T > >[] factories;

Expand All @@ -21,6 +19,7 @@ public DefaultInterpolators()
factories[ Interpolation.NLINEAR.ordinal() ] = new ClampingNLinearInterpolatorFactory<>();
}

@Override
public InterpolatorFactory< T, RandomAccessible< T > > get( final Interpolation method )
{
return factories[ method.ordinal() ];
Expand All @@ -30,10 +29,4 @@ public int size()
{
return factories.length;
}

@Override
public InterpolatorFactory< T, RandomAccessible< T > > apply( final Interpolation t )
{
return get( t );
}
}
19 changes: 19 additions & 0 deletions src/main/java/bdv/util/InterpolationFunction.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
package bdv.util;

import java.util.function.Function;

import bdv.viewer.Interpolation;
import net.imglib2.RandomAccessible;
import net.imglib2.interpolation.InterpolatorFactory;
import net.imglib2.type.Type;

public interface InterpolationFunction< T extends Type< T > > extends Function< Interpolation, InterpolatorFactory< T, RandomAccessible< T > > >
{
public abstract InterpolatorFactory< T, RandomAccessible< T > > get( final Interpolation method );

@Override
public default InterpolatorFactory< T, RandomAccessible< T > > apply( final Interpolation t )
{
return get( t );
}
}
3 changes: 2 additions & 1 deletion src/main/java/bdv/util/RandomAccessibleIntervalMipmapSource.java
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Expand Up @@ -35,9 +35,10 @@
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.Volatile;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.Type;
import net.imglib2.type.numeric.NumericType;

public class RandomAccessibleIntervalMipmapSource< T extends NumericType< T > > extends AbstractSource< T >
public class RandomAccessibleIntervalMipmapSource< T extends Type< T > > extends AbstractSource< T >
{
protected final RandomAccessibleInterval< T >[] mipmapSources;

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8 changes: 3 additions & 5 deletions src/main/java/bdv/util/RandomAccessibleIntervalSource.java
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Expand Up @@ -32,10 +32,10 @@
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.RealRandomAccessible;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.NumericType;
import net.imglib2.type.Type;
import net.imglib2.view.Views;

public class RandomAccessibleIntervalSource< T extends NumericType< T > > extends AbstractSource< T >
public class RandomAccessibleIntervalSource< T extends Type< T > > extends AbstractSource< T >
{
private final RandomAccessibleInterval< T > source;

Expand All @@ -61,10 +61,8 @@ public RandomAccessibleIntervalSource(
this.source = img;
this.sourceTransform = sourceTransform;
interpolatedSources = new RealRandomAccessible[ Interpolation.values().length ];
final T zero = getType().createVariable();
zero.setZero();
for ( final Interpolation method : Interpolation.values() )
interpolatedSources[ method.ordinal() ] = Views.interpolate( Views.extendValue( source, zero ), interpolators.get( method ) );
interpolatedSources[ method.ordinal() ] = Views.interpolate( Views.extendValue( source, extension.copy() ), interpolators.get( method ) );
}

@Override
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8 changes: 3 additions & 5 deletions src/main/java/bdv/util/RandomAccessibleIntervalSource4D.java
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Expand Up @@ -34,10 +34,10 @@
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.RealRandomAccessible;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.NumericType;
import net.imglib2.type.Type;
import net.imglib2.view.Views;

public class RandomAccessibleIntervalSource4D< T extends NumericType< T > > extends AbstractSource< T >
public class RandomAccessibleIntervalSource4D< T extends Type< T > > extends AbstractSource< T >
{
private final RandomAccessibleInterval< T > source;

Expand Down Expand Up @@ -75,11 +75,9 @@ private void loadTimepoint( final int timepointIndex )
currentTimePointIndex = timepointIndex;
if ( isPresent( timepointIndex ) )
{
final T zero = getType().createVariable();
zero.setZero();
currentSource = Views.hyperSlice( source, 3, timepointIndex );
for ( final Interpolation method : Interpolation.values() )
currentInterpolatedSources[ method.ordinal() ] = Views.interpolate( Views.extendValue( currentSource, zero ), interpolators.get( method ) );
currentInterpolatedSources[ method.ordinal() ] = Views.interpolate( Views.extendValue( currentSource, extension.copy() ), interpolators.get( method ) );
}
else
{
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/bdv/util/RandomAccessibleSource.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,10 +34,10 @@
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.RealRandomAccessible;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.NumericType;
import net.imglib2.type.Type;
import net.imglib2.view.Views;

public class RandomAccessibleSource< T extends NumericType< T > > extends AbstractSource< T >
public class RandomAccessibleSource< T extends Type< T > > extends AbstractSource< T >
{
private final RandomAccessible< T > source;

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6 changes: 2 additions & 4 deletions src/main/java/bdv/util/RandomAccessibleSource4D.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,11 +36,11 @@
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.RealRandomAccessible;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.NumericType;
import net.imglib2.type.Type;
import net.imglib2.util.Intervals;
import net.imglib2.view.Views;

public class RandomAccessibleSource4D< T extends NumericType< T > > extends AbstractSource< T >
public class RandomAccessibleSource4D< T extends Type< T > > extends AbstractSource< T >
{
private final RandomAccessible< T > source;

Expand Down Expand Up @@ -88,8 +88,6 @@ private void loadTimepoint( final int timepointIndex )
currentTimePointIndex = timepointIndex;
if ( isPresent( timepointIndex ) )
{
final T zero = getType().createVariable();
zero.setZero();
final RandomAccessible< T > slice = Views.hyperSlice( source, 3, timepointIndex );
currentSource = Views.interval( slice, timeSliceInterval );
for ( final Interpolation method : Interpolation.values() )
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/bdv/util/VolatileRandomAccessibleIntervalMipmapSource.java
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Expand Up @@ -36,9 +36,9 @@
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.Volatile;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.NumericType;
import net.imglib2.type.Type;

public class VolatileRandomAccessibleIntervalMipmapSource< T extends NumericType< T >, V extends Volatile< T > & NumericType< V > > extends AbstractSource< V >
public class VolatileRandomAccessibleIntervalMipmapSource< T extends Type< T >, V extends Volatile< T > & Type< V > > extends AbstractSource< V >
{
private final RandomAccessibleIntervalMipmapSource< T > source;

Expand Down