TransformedSource (Fiji Javadocs 0-SNAPSHOT API)

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 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, TransformedSource<?> shareTransform)`

Method Summary

All Methods Instance Methods Concrete Methods
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.
- 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,
                         TransformedSource<?> shareTransform)
```
- 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()
```

Class TransformedSource<T>

Nested Class Summary

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

Field Summary

Fields inherited from interface bdv.viewer.render.MipmapOrdering

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

source

sourceMipmapOrdering

incrementalTransform

fixedTransform

sourceTransform

composed

Constructor Detail

TransformedSource

TransformedSource

Method Detail

doBoundingBoxCulling

setFixedTransform

getFixedTransform

setIncrementalTransform

getIncrementalTransform

getSourceTransform

isPresent

getSource

getInterpolatedSource

getType

getName

getVoxelDimensions

getNumMipmapLevels

getMipmapHints

getWrappedSource