Package net.preibisch.mvrecon.process.fusion.lazy

Class LazyAffineFusion<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>

java.lang.Object

net.preibisch.mvrecon.process.fusion.lazy.LazyAffineFusion<T>

Type Parameters:

T - type of input and output

All Implemented Interfaces:

Consumer<net.imglib2.RandomAccessibleInterval<T>>

public class LazyAffineFusion<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
extends Object
implements Consumer<net.imglib2.RandomAccessibleInterval<T>>

BigStitcher Affine Fusion in blocks

Author:

Stephan Preibisch

Constructor Summary

Constructors

Constructor

Description

LazyAffineFusion(net.imglib2.converter.Converter<net.imglib2.type.numeric.real.FloatType,T> converter, mpicbg.spim.data.generic.sequence.BasicImgLoader imgloader, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, Map<mpicbg.spim.data.sequence.ViewId,? extends net.imglib2.realtransform.AffineTransform3D> viewRegistrations, Map<mpicbg.spim.data.sequence.ViewId,? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> viewDescriptions, FusionGUI.FusionType fusionType, int interpolation, Map<mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments, long[] globalMin, T type)

Creates a consumer that will fill the requested RandomAccessibleInterval single-threaded

Method Summary

Modifier and Type	Method	Description
void	accept(net.imglib2.RandomAccessibleInterval<T> output)
protected static final <T extends net.imglib2.type.numeric.RealType<T>> void	finish(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> fused, net.imglib2.RandomAccessibleInterval<T> output, net.imglib2.converter.Converter<net.imglib2.type.numeric.real.FloatType,T> converter, T type)
static final <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> net.imglib2.RandomAccessibleInterval<T>	init(net.imglib2.converter.Converter<net.imglib2.type.numeric.real.FloatType,T> converter, mpicbg.spim.data.generic.sequence.BasicImgLoader imgloader, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, Map<mpicbg.spim.data.sequence.ViewId,? extends net.imglib2.realtransform.AffineTransform3D> viewRegistrations, Map<mpicbg.spim.data.sequence.ViewId,? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> viewDescriptions, FusionGUI.FusionType fusionType, int interpolation, Map<mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments, net.imglib2.Interval fusionInterval, T type, int[] blockSize)
static void	main(String[] args)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.util.function.Consumer

andThen

Constructor Details

LazyAffineFusion

public LazyAffineFusion(net.imglib2.converter.Converter<net.imglib2.type.numeric.real.FloatType,T> converter,
 mpicbg.spim.data.generic.sequence.BasicImgLoader imgloader,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds,
 Map<mpicbg.spim.data.sequence.ViewId,? extends net.imglib2.realtransform.AffineTransform3D> viewRegistrations,
 Map<mpicbg.spim.data.sequence.ViewId,? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> viewDescriptions,
 FusionGUI.FusionType fusionType,
 int interpolation,
 Map<mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments,
 long[] globalMin,
 T type)

Creates a consumer that will fill the requested RandomAccessibleInterval single-threaded

Parameters:

converter - - if type is FloatType, converter can be null; converting inside the lazy construct makes sense since it often requires to save much less data (8 bit or 16 bit instead of 32-bit float)

imgloader - - the imgloader to fetch raw data

viewIds - - which viewids to fuse

viewRegistrations - - the registrations (must include anisotropy and downsampling if desired)

viewDescriptions - - the viewdescriptions

fusionType - - how to combine pixels

interpolation - - 1==linear, 0==nearest neighbor

intensityAdjustments - - intensity adjustments, can be null

globalMin - - the output RAI typically sits at 0,0...0 because it usually is a CachedCellImage (but the actual interval to process in many blocks sits somewhere else)

type - - which type to fuse

Method Details

accept

public void accept(net.imglib2.RandomAccessibleInterval<T> output)

Specified by:

accept in interface Consumer<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>

finish

protected static final <T extends net.imglib2.type.numeric.RealType<T>>
void finish(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> fused,
 net.imglib2.RandomAccessibleInterval<T> output,
 net.imglib2.converter.Converter<net.imglib2.type.numeric.real.FloatType,T> converter,
 T type)

init

public static final <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
net.imglib2.RandomAccessibleInterval<T> init(net.imglib2.converter.Converter<net.imglib2.type.numeric.real.FloatType,T> converter,
 mpicbg.spim.data.generic.sequence.BasicImgLoader imgloader,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds,
 Map<mpicbg.spim.data.sequence.ViewId,? extends net.imglib2.realtransform.AffineTransform3D> viewRegistrations,
 Map<mpicbg.spim.data.sequence.ViewId,? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> viewDescriptions,
 FusionGUI.FusionType fusionType,
 int interpolation,
 Map<mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments,
 net.imglib2.Interval fusionInterval,
 T type,
 int[] blockSize)

main

public static void main(String[] args)
                 throws mpicbg.spim.data.SpimDataException

Throws:

mpicbg.spim.data.SpimDataException