RealRandomAccessibleSource (Fiji Javadocs 0-SNAPSHOT API)

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 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 RealRandomAccessible<T>`	`accessible`
`protected boolean`	`doBoundingBoxIntersectionCheck`
`protected String`	`name`
`protected T`	`type`
`protected VoxelDimensions`	`voxelDimensions`

Constructor Summary

Constructors
Constructor and Description
`RealRandomAccessibleSource(RealRandomAccessible<T> accessible, T type, String name)`
`RealRandomAccessibleSource(RealRandomAccessible<T> accessible, T type, String name, VoxelDimensions voxelDimensions)`
`RealRandomAccessibleSource(RealRandomAccessible<T> accessible, T type, String name, VoxelDimensions voxelDimensions, boolean doBoundingBoxIntersectionCheck)`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`doBoundingBoxCulling()` Whether this source participates in bounding box culling.
`RealRandomAccessible<T>`	`getInterpolatedSource(int t, int level, Interpolation method)` Get the 3D stack at timepoint index t, extended to infinity and interpolated.
`abstract Interval`	`getInterval(int t, int level)` Return the interval which should be used to bound the wrapped (unbounded) `RealRandomAccessible` for `getSource(int, int)`.
`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.
`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 RealRandomAccessible<T extends Type<T>> accessible
```
  - type
```
protected final T extends Type<T> type
```
  - name
```
protected final String name
```
  - voxelDimensions
```
protected final VoxelDimensions voxelDimensions
```
  - doBoundingBoxIntersectionCheck
```
protected final boolean doBoundingBoxIntersectionCheck
```
- Constructor Detail
  - RealRandomAccessibleSource
```
public RealRandomAccessibleSource(RealRandomAccessible<T> accessible,
                                  T type,
                                  String name)
```
  - RealRandomAccessibleSource
```
public RealRandomAccessibleSource(RealRandomAccessible<T> accessible,
                                  T type,
                                  String name,
                                  VoxelDimensions voxelDimensions)
```
  - RealRandomAccessibleSource
```
public RealRandomAccessibleSource(RealRandomAccessible<T> accessible,
                                  T type,
                                  String name,
                                  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 Type<T>>
    
    Parameters:
    
    t - timepoint index
    
    Returns:
    
    true, if there is data for timepoint index t.
  - getInterval
```
public abstract 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 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 Type<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 extends 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,
                               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 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 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 Type<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 extends Type<T>>
    
    Returns:
    
    voxel size and unit or null.
  - getNumMipmapLevels
```
public int getNumMipmapLevels()
```
    Specified by:
    
    getNumMipmapLevels in interface Source<T extends 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 Type<T>>
    
    Returns:
    
    true, if this source participates in bounding box culling.

Class RealRandomAccessibleSource<T extends Type<T>>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

accessible

type

name

voxelDimensions

doBoundingBoxIntersectionCheck

Constructor Detail

RealRandomAccessibleSource

RealRandomAccessibleSource

RealRandomAccessibleSource

Method Detail

isPresent

getInterval

getSource

getInterpolatedSource

getSourceTransform

getType

getName

getVoxelDimensions

getNumMipmapLevels

doBoundingBoxCulling