Module org.bigdataviewer.core

Package bdv.util

Class PlaceHolderSource

java.lang.Object

bdv.util.PlaceHolderSource

All Implemented Interfaces:

Source<Void>

public final class PlaceHolderSource
extends Object
implements Source<Void>

A dummy Source that represents a BdvOverlay.

When a BdvOverlay is shown (with BdvFunctions.showOverlay(BdvOverlay, String, BdvOptions)), a dummy Source and ConverterSetup are added to the BigDataViewer such that the visibility, display range, and color for the overlay can be adjusted by the user, like for a normal Source.

PlaceHolderSource is not present at any time point, so it is never actually visible.

Author:

Tobias Pietzsch

Constructor Summary

Constructors

Constructor	Description
PlaceHolderSource(String name)

Method Summary

Modifier and Type	Method	Description
net.imglib2.RealRandomAccessible<? extends net.imglib2.type.mask.Masked<Void>>	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<Void>	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<Void>>	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<Void>	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.
Void	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

Methods inherited from interface bdv.viewer.Source

doBoundingBoxCulling

Constructor Detail

PlaceHolderSource

public PlaceHolderSource(String name)

Method Detail

getType

public Void getType()

Description copied from interface: Source

Get an instance of the pixel type.

Specified by:

getType in interface Source<Void>

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<Void>

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<Void>

Returns:

voxel size and unit or null.

getNumMipmapLevels

public int getNumMipmapLevels()

Specified by:

getNumMipmapLevels in interface Source<Void>

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<Void>

Parameters:

t - timepoint index

Returns:

true, if there is data for timepoint index t.

getSource

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

Description copied from interface: Source

Get the 3D stack at timepoint index t.

Specified by:

getSource in interface Source<Void>

Parameters:

t - timepoint index

level - mipmap level

Returns:

the stack.

getInterpolatedSource

public net.imglib2.RealRandomAccessible<Void> 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<Void>

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<Void>> 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<Void>

Parameters:

t - timepoint index

level - mipmap level

Returns:

the masked stack

getInterpolatedMaskedSource

public net.imglib2.RealRandomAccessible<? extends net.imglib2.type.mask.Masked<Void>> 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<Void>

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<Void>

Parameters:

t - timepoint index

level - mipmap level

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