bdv.util

Class RandomAccessibleSource4D<T extends net.imglib2.type.numeric.NumericType<T>>

java.lang.Object

bdv.util.AbstractSource<T>

bdv.util.RandomAccessibleSource4D<T>

All Implemented Interfaces:

Source<T>

public class RandomAccessibleSource4D<T extends net.imglib2.type.numeric.NumericType<T>>
extends AbstractSource<T>

Field Summary

Fields

Modifier and Type	Field and Description
protected int	currentTimePointIndex

Fields inherited from class bdv.util.AbstractSource

interpolators, name, type, voxelDimensions

Constructor Summary

Constructors

Constructor and Description
RandomAccessibleSource4D(net.imglib2.RandomAccessible<T> img, net.imglib2.Interval interval, T type, net.imglib2.realtransform.AffineTransform3D sourceTransform, String name)
RandomAccessibleSource4D(net.imglib2.RandomAccessible<T> img, net.imglib2.Interval interval, T type, net.imglib2.realtransform.AffineTransform3D sourceTransform, String name, boolean doBoundingBoxCulling)
RandomAccessibleSource4D(net.imglib2.RandomAccessible<T> img, net.imglib2.Interval interval, T type, String name)

Method Summary

Modifier and Type	Method and Description
net.imglib2.RealRandomAccessible<? extends net.imglib2.type.mask.Masked<T>>	getInterpolatedMaskedSource(int t, int level, Interpolation method) Get a Masked version of the 3D stack at timepoint index t, extended to infinity and interpolated.
net.imglib2.RealRandomAccessible<T>	getInterpolatedSource(int t, int level, Interpolation method) Get the 3D stack at timepoint index t, extended to infinity and interpolated.
net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.mask.Masked<T>>	getMaskedSource(int t, int level) Get a Masked version of the 3D stack at timepoint index t.
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, getName, getNumMipmapLevels, getType, getVoxelDimensions

Methods inherited from class java.lang.Object

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

Field Detail

currentTimePointIndex

protected int currentTimePointIndex

Constructor Detail

RandomAccessibleSource4D

public RandomAccessibleSource4D(net.imglib2.RandomAccessible<T> img,
                                net.imglib2.Interval interval,
                                T type,
                                String name)

RandomAccessibleSource4D

public RandomAccessibleSource4D(net.imglib2.RandomAccessible<T> img,
                                net.imglib2.Interval interval,
                                T type,
                                net.imglib2.realtransform.AffineTransform3D sourceTransform,
                                String name)

RandomAccessibleSource4D

public RandomAccessibleSource4D(net.imglib2.RandomAccessible<T> img,
                                net.imglib2.Interval interval,
                                T type,
                                net.imglib2.realtransform.AffineTransform3D sourceTransform,
                                String name,
                                boolean doBoundingBoxCulling)

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.

getMaskedSource

public net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.mask.Masked<T>> getMaskedSource(int t,
                                                                                                       int level)

Description copied from interface: Source

Get a Masked version of the 3D stack at timepoint index t.

By default, this is just Source.getSource(int, int) augmented with a constant mask 1.0.

Specified by:

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

Overrides:

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

Parameters:

t - timepoint index

level - mipmap level

Returns:

the masked 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.

getInterpolatedMaskedSource

public net.imglib2.RealRandomAccessible<? extends net.imglib2.type.mask.Masked<T>> getInterpolatedMaskedSource(int t,
                                                                                                               int level,
                                                                                                               Interpolation method)

Description copied from interface: Source

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

By default, this is just Source.getInterpolatedSource(int, int, bdv.viewer.Interpolation) augmented with a constant mask 1.0.

However, most sources should override this to extend Source.getMaskedSource(int, int) to infinity (with a 0 mask) and interpolate.

Specified by:

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

Overrides:

getInterpolatedMaskedSource 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