bdv.util

Class RandomAccessibleIntervalMipmapSource4D<T extends net.imglib2.type.numeric.NumericType<T>>

java.lang.Object

bdv.util.AbstractSource<T>

bdv.util.RandomAccessibleIntervalMipmapSource4D<T>

All Implemented Interfaces:

Source<T>

public class RandomAccessibleIntervalMipmapSource4D<T extends net.imglib2.type.numeric.NumericType<T>>
extends AbstractSource<T>

Field Summary

Fields

Modifier and Type	Field and Description
protected int	currentTimePointIndex
protected long	maxT
protected long	minT
protected net.imglib2.RandomAccessibleInterval<T>[]	mipmapSources
protected net.imglib2.realtransform.AffineTransform3D[]	mipmapTransforms

Fields inherited from class bdv.util.AbstractSource

interpolators, name, type, voxelDimensions

Constructor Summary

Constructors

Constructor and Description
RandomAccessibleIntervalMipmapSource4D(net.imglib2.RandomAccessibleInterval<T>[] imgs, T type, net.imglib2.realtransform.AffineTransform3D[] mipmapTransforms, mpicbg.spim.data.sequence.VoxelDimensions voxelDimensions, String name, boolean doBoundingBoxCulling)
RandomAccessibleIntervalMipmapSource4D(net.imglib2.RandomAccessibleInterval<T>[] imgs, T type, double[][] mipmapScales, mpicbg.spim.data.sequence.VoxelDimensions voxelDimensions, net.imglib2.realtransform.AffineTransform3D sourceTransform, String name)
RandomAccessibleIntervalMipmapSource4D(net.imglib2.RandomAccessibleInterval<T>[] imgs, T type, double[][] mipmapScales, mpicbg.spim.data.sequence.VoxelDimensions voxelDimensions, net.imglib2.realtransform.AffineTransform3D sourceTransform, String name, boolean doBoundingBoxCulling)
RandomAccessibleIntervalMipmapSource4D(net.imglib2.RandomAccessibleInterval<T>[] imgs, T type, double[][] mipmapScales, mpicbg.spim.data.sequence.VoxelDimensions voxelDimensions, String name)

Method Summary

Modifier and Type	Method and Description
<V extends net.imglib2.Volatile<T> & net.imglib2.type.numeric.NumericType<V>> VolatileSource<T,V>	asVolatile(SharedQueue queue)
<V extends net.imglib2.Volatile<T> & net.imglib2.type.numeric.NumericType<V>> VolatileSource<T,V>	asVolatile(Supplier<V> vTypeSupplier, SharedQueue queue)
<V extends net.imglib2.Volatile<T> & net.imglib2.type.numeric.NumericType<V>> VolatileSource<T,V>	asVolatile(V vType, SharedQueue queue)
net.imglib2.RealRandomAccessible<T>	getInterpolatedSource(int t, int level, Interpolation method) Get the 3D stack at timepoint index t, extended to infinity and interpolated.
int	getNumMipmapLevels()
net.imglib2.RandomAccessibleInterval<T>	getSource(int t, int level) Get the 3D stack at timepoint index t.
void	getSourceTransform(int t, int level, net.imglib2.realtransform.AffineTransform3D transform) Get the transform from the source at the given timepoint index and mipmap level into the global coordinate system.
boolean	isPresent(int t) Is there a stack at timepoint index t?

Methods inherited from class bdv.util.AbstractSource

doBoundingBoxCulling, getInterpolatedMaskedSource, getMaskedSource, getName, getType, getVoxelDimensions

Methods inherited from class java.lang.Object

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

Field Detail

mipmapSources

protected final net.imglib2.RandomAccessibleInterval<T extends net.imglib2.type.numeric.NumericType<T>>[] mipmapSources

minT

protected final long minT

maxT

protected final long maxT

currentTimePointIndex

protected int currentTimePointIndex

mipmapTransforms

protected final net.imglib2.realtransform.AffineTransform3D[] mipmapTransforms

Constructor Detail

RandomAccessibleIntervalMipmapSource4D

public RandomAccessibleIntervalMipmapSource4D(net.imglib2.RandomAccessibleInterval<T>[] imgs,
                                              T type,
                                              net.imglib2.realtransform.AffineTransform3D[] mipmapTransforms,
                                              mpicbg.spim.data.sequence.VoxelDimensions voxelDimensions,
                                              String name,
                                              boolean doBoundingBoxCulling)

RandomAccessibleIntervalMipmapSource4D

public RandomAccessibleIntervalMipmapSource4D(net.imglib2.RandomAccessibleInterval<T>[] imgs,
                                              T type,
                                              double[][] mipmapScales,
                                              mpicbg.spim.data.sequence.VoxelDimensions voxelDimensions,
                                              net.imglib2.realtransform.AffineTransform3D sourceTransform,
                                              String name,
                                              boolean doBoundingBoxCulling)

RandomAccessibleIntervalMipmapSource4D

public RandomAccessibleIntervalMipmapSource4D(net.imglib2.RandomAccessibleInterval<T>[] imgs,
                                              T type,
                                              double[][] mipmapScales,
                                              mpicbg.spim.data.sequence.VoxelDimensions voxelDimensions,
                                              net.imglib2.realtransform.AffineTransform3D sourceTransform,
                                              String name)

RandomAccessibleIntervalMipmapSource4D

public RandomAccessibleIntervalMipmapSource4D(net.imglib2.RandomAccessibleInterval<T>[] imgs,
                                              T type,
                                              double[][] mipmapScales,
                                              mpicbg.spim.data.sequence.VoxelDimensions voxelDimensions,
                                              String name)

Method Detail

isPresent

public boolean isPresent(int t)

Description copied from interface: Source

Is there a stack at timepoint index t?

Specified by:

isPresent in interface Source<T extends net.imglib2.type.numeric.NumericType<T>>

Overrides:

isPresent in class AbstractSource<T extends net.imglib2.type.numeric.NumericType<T>>

Parameters:

t - timepoint index

Returns:

true, if there is data for timepoint index t.

getSource

public net.imglib2.RandomAccessibleInterval<T> getSource(int t,
                                                         int level)

Description copied from interface: Source

Get the 3D stack at timepoint index t.

Parameters:

t - timepoint index

level - mipmap level

Returns:

the stack.

getInterpolatedSource

public net.imglib2.RealRandomAccessible<T> getInterpolatedSource(int t,
                                                                 int level,
                                                                 Interpolation method)

Description copied from interface: Source

Get the 3D stack at timepoint index t, extended to infinity and interpolated.

Specified by:

getInterpolatedSource in interface Source<T extends net.imglib2.type.numeric.NumericType<T>>

Overrides:

getInterpolatedSource in class AbstractSource<T extends net.imglib2.type.numeric.NumericType<T>>

Parameters:

t - timepoint index

level - mipmap level

method - interpolation method to use

Returns:

the extended and interpolated stack.

getSourceTransform

public void getSourceTransform(int t,
                               int level,
                               net.imglib2.realtransform.AffineTransform3D transform)

Description copied from interface: Source

Get the transform from the source at the given timepoint index and mipmap level into the global coordinate system.

Parameters:

t - timepoint index

level - mipmap level

transform - is set to the source-to-global transform, that transforms source coordinates into the global coordinates

getNumMipmapLevels

public int getNumMipmapLevels()

Specified by:

getNumMipmapLevels in interface Source<T extends net.imglib2.type.numeric.NumericType<T>>

Overrides:

getNumMipmapLevels in class AbstractSource<T extends net.imglib2.type.numeric.NumericType<T>>

asVolatile

public <V extends net.imglib2.Volatile<T> & net.imglib2.type.numeric.NumericType<V>> VolatileSource<T,V> asVolatile(V vType,
                                                                                                                    SharedQueue queue)

asVolatile

public <V extends net.imglib2.Volatile<T> & net.imglib2.type.numeric.NumericType<V>> VolatileSource<T,V> asVolatile(Supplier<V> vTypeSupplier,
                                                                                                                    SharedQueue queue)

asVolatile

public <V extends net.imglib2.Volatile<T> & net.imglib2.type.numeric.NumericType<V>> VolatileSource<T,V> asVolatile(SharedQueue queue)