bdv.tools.transformation

Class TransformedSource<T>

java.lang.Object

bdv.tools.transformation.TransformedSource<T>

Type Parameters:

T - the type of the original source.

All Implemented Interfaces:

MipmapOrdering, Source<T>

public class TransformedSource<T>
extends Object
implements Source<T>, MipmapOrdering

A Source that wraps another Source and allows to decorate it with an extra AffineTransform3D.

This extra transformation is made to capture manual editing of the actual transform in the SpimViewer.

Author:

Jean-Yves Tinevez - Sept 2013

Nested Class Summary

Nested classes/interfaces inherited from interface bdv.viewer.render.MipmapOrdering

MipmapOrdering.Level, MipmapOrdering.MipmapHints, MipmapOrdering.PrefetchOrderComparator, MipmapOrdering.RenderOrderComparator

Field Summary

Fields

Modifier and Type	Field and Description
protected AffineTransform3D	composed temporary.
protected AffineTransform3D	fixedTransform Fixed part of the extra transformation.
protected AffineTransform3D	incrementalTransform Incremental part of the extra transformation.
protected String	name optional new name.
protected Source<T>	source
protected MipmapOrdering	sourceMipmapOrdering This is either the source itself, if it implements MipmapOrdering, or a DefaultMipmapOrdering.
protected AffineTransform3D	sourceTransform Extra transformation.

Fields inherited from interface bdv.viewer.render.MipmapOrdering

prefetchOrderComparator, renderOrderComparator

Constructor Summary

Constructors

Constructor and Description
TransformedSource(Source<T> source) Instantiates a new TransformedSource wrapping the specified source with the identity transform.
TransformedSource(Source<T> source, String name)
TransformedSource(Source<T> source, TransformedSource<?> shareTransform)
TransformedSource(Source<T> source, TransformedSource<?> shareTransform, String name)

Method Summary

Modifier and Type	Method and Description
boolean	doBoundingBoxCulling() Whether this source participates in bounding box culling.
void	getFixedTransform(AffineTransform3D transform) Get the fixed part of the extra transformation.
void	getIncrementalTransform(AffineTransform3D transform) Get the incremental part of the extra transformation.
RealRandomAccessible<T>	getInterpolatedSource(int t, int level, Interpolation method) Get the 3D stack at timepoint index t, extended to infinity and interpolated.
MipmapOrdering.MipmapHints	getMipmapHints(AffineTransform3D screenTransform, int timepoint, int previousTimepoint) Evaluate mipmap levels such that they can be ordered for rendering and/or prefetching.
String	getName() Get the name of the source.
int	getNumMipmapLevels()
RandomAccessibleInterval<T>	getSource(int t, int level) Get the 3D stack at timepoint index t.
void	getSourceTransform(int t, int level, 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.
VoxelDimensions	getVoxelDimensions() Get voxel size and unit for this source.
Source<T>	getWrappedSource()
boolean	isPresent(int t) Is there a stack at timepoint index t?
void	setFixedTransform(AffineTransform3D transform) Sets the fixed part of the extra transformation to the specified transform.
void	setIncrementalTransform(AffineTransform3D transform) Sets the incremental part of the extra transformation to the specified transform.

Methods inherited from class java.lang.Object

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

Field Detail

source

protected final Source<T> source

sourceMipmapOrdering

protected final MipmapOrdering sourceMipmapOrdering

This is either the source itself, if it implements MipmapOrdering, or a DefaultMipmapOrdering.

incrementalTransform

protected final AffineTransform3D incrementalTransform

Incremental part of the extra transformation.

fixedTransform

protected final AffineTransform3D fixedTransform

Fixed part of the extra transformation.

sourceTransform

protected final AffineTransform3D sourceTransform

Extra transformation. Concatenation of incrementalTransform * fixedTransform.

composed

protected final AffineTransform3D composed

temporary. concatenation of sourceTransform and the transform obtained from the decorated source.

name

protected final String name

optional new name. if null, the name of the original source will be used.

Constructor Detail

TransformedSource

public TransformedSource(Source<T> source)

Instantiates a new TransformedSource wrapping the specified source with the identity transform.

Parameters:

source - the source to wrap.

TransformedSource

public TransformedSource(Source<T> source,
                         String name)

TransformedSource

public TransformedSource(Source<T> source,
                         TransformedSource<?> shareTransform)

TransformedSource

public TransformedSource(Source<T> source,
                         TransformedSource<?> shareTransform,
                         String name)

Method Detail

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>

Returns:

true, if this source participates in bounding box culling.

setFixedTransform

public void setFixedTransform(AffineTransform3D transform)

Sets the fixed part of the extra transformation to the specified transform.

The extra transformation applied by the TransformedSource is a concatenation of an incremental and a fixed transform.

Parameters:

transform - is copied to the fixed transform.

getFixedTransform

public void getFixedTransform(AffineTransform3D transform)

Get the fixed part of the extra transformation.

The extra transformation applied by the TransformedSource is a concatenation of an incremental and this fixed transform.

Parameters:

transform - is set to the fixed transform.

setIncrementalTransform

public void setIncrementalTransform(AffineTransform3D transform)

Sets the incremental part of the extra transformation to the specified transform.

The extra transformation applied by the TransformedSource is a concatenation of an incremental and a fixed transform.

Parameters:

transform - is copied to the incremental transform.

getIncrementalTransform

public void getIncrementalTransform(AffineTransform3D transform)

Get the incremental part of the extra transformation.

The extra transformation applied by the TransformedSource is a concatenation of this incremental transform and a fixed transform.

Parameters:

transform - is set to the incremental transform.

getSourceTransform

public void getSourceTransform(int t,
                               int level,
                               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>

Parameters:

t - timepoint index

level - mipmap level

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

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>

Parameters:

t - timepoint index

Returns:

true, if there is data for timepoint index t.

getSource

public 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>

Parameters:

t - timepoint index

level - mipmap level

Returns:

the stack.

getInterpolatedSource

public 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>

Parameters:

t - timepoint index

level - mipmap level

method - interpolation method to use

Returns:

the extended and interpolated stack.

getType

public T getType()

Description copied from interface: Source

Get an instance of the pixel type.

Specified by:

getType in interface Source<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>

Returns:

the name of the source.

getVoxelDimensions

public 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>

Returns:

voxel size and unit or null.

getNumMipmapLevels

public int getNumMipmapLevels()

Specified by:

getNumMipmapLevels in interface Source<T>

getMipmapHints

public MipmapOrdering.MipmapHints getMipmapHints(AffineTransform3D screenTransform,
                                                 int timepoint,
                                                 int previousTimepoint)

Description copied from interface: MipmapOrdering

Evaluate mipmap levels such that they can be ordered for rendering and/or prefetching.

Specified by:

getMipmapHints in interface MipmapOrdering

Parameters:

screenTransform - transforms screen coordinates to global coordinates.

timepoint - current timepoint index

previousTimepoint - previous timepoint index

getWrappedSource

public Source<T> getWrappedSource()