bdv.util

Class RealRandomAccessibleSource<T extends net.imglib2.type.Type<T>>

java.lang.Object

bdv.util.RealRandomAccessibleSource<T>

Type Parameters:

T -

All Implemented Interfaces:

Source<T>

Direct Known Subclasses:

RealRandomAccessibleIntervalSource

public abstract class RealRandomAccessibleSource<T extends net.imglib2.type.Type<T>>
extends Object
implements Source<T>

A Source wrapping some RealRandomAccessible. Derived concrete classes must implement getInterval(int, int) to specify which interval to use for getSource(int, int).

Author:

Tobias Pietzsch

Field Summary

Fields

Modifier and Type	Field and Description
protected net.imglib2.RealRandomAccessible<T>	accessible
protected boolean	doBoundingBoxIntersectionCheck
protected String	name
protected T	type
protected mpicbg.spim.data.sequence.VoxelDimensions	voxelDimensions

Constructor Summary

Constructors

Constructor and Description
RealRandomAccessibleSource(net.imglib2.RealRandomAccessible<T> accessible, T type, String name)
RealRandomAccessibleSource(net.imglib2.RealRandomAccessible<T> accessible, T type, String name, mpicbg.spim.data.sequence.VoxelDimensions voxelDimensions)
RealRandomAccessibleSource(net.imglib2.RealRandomAccessible<T> accessible, T type, String name, mpicbg.spim.data.sequence.VoxelDimensions voxelDimensions, boolean doBoundingBoxIntersectionCheck)

Method Summary

Modifier and Type	Method and Description
boolean	doBoundingBoxCulling() Whether this source participates in bounding box culling.
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.
abstract net.imglib2.Interval	getInterval(int t, int level) Return the interval which should be used to bound the wrapped (unbounded) RealRandomAccessible for getSource(int, int).
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.
String	getName() Get the name of the source.
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.
T	getType() Get an instance of the pixel type.
mpicbg.spim.data.sequence.VoxelDimensions	getVoxelDimensions() Get voxel size and unit for this source.
boolean	isPresent(int t) Is there a stack at timepoint index t?

Methods inherited from class java.lang.Object

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

Field Detail

accessible

protected net.imglib2.RealRandomAccessible<T extends net.imglib2.type.Type<T>> accessible

type

protected final T extends net.imglib2.type.Type<T> type

name

protected final String name

voxelDimensions

protected final mpicbg.spim.data.sequence.VoxelDimensions voxelDimensions

doBoundingBoxIntersectionCheck

protected final boolean doBoundingBoxIntersectionCheck

Constructor Detail

RealRandomAccessibleSource

public RealRandomAccessibleSource(net.imglib2.RealRandomAccessible<T> accessible,
                                  T type,
                                  String name)

RealRandomAccessibleSource

public RealRandomAccessibleSource(net.imglib2.RealRandomAccessible<T> accessible,
                                  T type,
                                  String name,
                                  mpicbg.spim.data.sequence.VoxelDimensions voxelDimensions)

RealRandomAccessibleSource

public RealRandomAccessibleSource(net.imglib2.RealRandomAccessible<T> accessible,
                                  T type,
                                  String name,
                                  mpicbg.spim.data.sequence.VoxelDimensions voxelDimensions,
                                  boolean doBoundingBoxIntersectionCheck)

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.Type<T>>

Parameters:

t - timepoint index

Returns:

true, if there is data for timepoint index t.

getInterval

public abstract net.imglib2.Interval getInterval(int t,
                                                 int level)

Return the interval which should be used to bound the wrapped (unbounded) RealRandomAccessible for getSource(int, int).

Returns:

image interval

getSource

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

Description copied from interface: Source

Get the 3D stack at timepoint index t.

Specified by:

getSource in interface Source<T extends net.imglib2.type.Type<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.Type<T>>

Parameters:

t - timepoint index

level - mipmap level

method - interpolation method to use

Returns:

the extended and interpolated 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.Type<T>>

Parameters:

t - timepoint index

level - mipmap level

Returns:

the masked 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.Type<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.

Specified by:

getSourceTransform in interface Source<T extends net.imglib2.type.Type<T>>

Parameters:

t - timepoint index

level - mipmap level

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

getType

public T getType()

Description copied from interface: Source

Get an instance of the pixel type.

Specified by:

getType in interface Source<T extends net.imglib2.type.Type<T>>

Returns:

instance of pixel type.

getName

public String getName()

Description copied from interface: Source

Get the name of the source.

Specified by:

getName in interface Source<T extends net.imglib2.type.Type<T>>

Returns:

the name of the source.

getVoxelDimensions

public mpicbg.spim.data.sequence.VoxelDimensions getVoxelDimensions()

Description copied from interface: Source

Get voxel size and unit for this source. May return null.

Specified by:

getVoxelDimensions in interface Source<T extends net.imglib2.type.Type<T>>

Returns:

voxel size and unit or null.

getNumMipmapLevels

public int getNumMipmapLevels()

Specified by:

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

doBoundingBoxCulling

public boolean doBoundingBoxCulling()

Description copied from interface: Source

Whether this source participates in bounding box culling.

If true, then this source will only be rendered if its bounding box, i.e., the interval of Source.getSource(int, int), intersects the current screen area (when transformed to viewer coordinates).

If false, then this source will be always rendered (if it is set to be visible.)

Specified by:

doBoundingBoxCulling in interface Source<T extends net.imglib2.type.Type<T>>

Returns:

true, if this source participates in bounding box culling.