AbstractSpimSource (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- bdv.AbstractSpimSource<T>

All Implemented Interfaces:: Source<T>

Direct Known Subclasses:: SpimSource, VolatileSpimSource

public abstract class AbstractSpimSource<T extends NumericType<T>>
extends Object
implements Source<T>

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

protected static class AbstractSpimSource.ImgKey

Nested Classes
Modifier and Type	Class and Description
`protected static class`	`AbstractSpimSource.ImgKey`

Field Summary

Fields
Modifier and Type	Field and Description
`protected UncheckedCache<AbstractSpimSource.ImgKey,RealRandomAccessible<T>>`	`cachedInterpolatedSources`
`protected UncheckedCache<AbstractSpimSource.ImgKey,RandomAccessibleInterval<T>>`	`cachedSources`
`protected AffineTransform3D[]`	`currentSourceTransforms`
`protected int`	`currentTimePointIndex`
`protected boolean`	`currentTimePointIsPresent`
`protected static int`	`iNearestNeighborMethod`
`protected static int`	`iNLinearMethod`
`protected InterpolatorFactory<T,RandomAccessible<T>>[]`	`interpolatorFactories`
`protected Set<ViewId>`	`missingViews`
`protected String`	`name`
`protected static int`	`numInterpolationMethods`
`protected int`	`numMipmapLevels`
`protected int`	`setupId`
`protected List<TimePoint>`	`timePointsOrdered`
`protected Map<ViewId,ViewRegistration>`	`viewRegistrations`
`protected VoxelDimensions`	`voxelDimensions`

Constructor Summary

Constructors
Constructor and Description

AbstractSpimSource(AbstractSpimData<?> spimData, int setupId, String name)

Constructors
Constructor and Description
`AbstractSpimSource(AbstractSpimData<?> spimData, int setupId, String name)`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`protected abstract RandomAccessibleInterval<T>`	`getImage(int timepointId, int level)`
`RealRandomAccessible<T>`	`getInterpolatedSource(int t, int level, Interpolation method)` Get the 3D stack at timepoint index t, extended to infinity and interpolated.
`RealRandomAccessible<T>`	`getInterpolatedSource(int t, int level, Interpolation method, ThreadGroup threadGroup)`
`protected abstract AffineTransform3D[]`	`getMipmapTransforms()`
`String`	`getName()` Get the name of the source.
`int`	`getNumMipmapLevels()`
`int`	`getSetupId()`
`RandomAccessibleInterval<T>`	`getSource(int t, int level)` Get the 3D stack at timepoint index t.
`RandomAccessibleInterval<T>`	`getSource(int t, int level, ThreadGroup threadGroup)`
`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.
`VoxelDimensions`	`getVoxelDimensions()` Get voxel size and unit for this source.
`boolean`	`isPresent(int t)` Is there a stack at timepoint index t?
`protected void`	`loadTimepoint(int timepointIndex)`

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, getType

Field Detail

currentTimePointIndex
```
protected int currentTimePointIndex
```

currentTimePointIsPresent

protected boolean currentTimePointIsPresent

currentSourceTransforms

protected final AffineTransform3D[] currentSourceTransforms

setupId
```
protected final int setupId
```

name
```
protected final String name
```

timePointsOrdered

protected final List<TimePoint> timePointsOrdered

viewRegistrations

protected final Map<ViewId,ViewRegistration> viewRegistrations

missingViews

protected final Set<ViewId> missingViews

voxelDimensions

protected final VoxelDimensions voxelDimensions

numMipmapLevels
```
protected final int numMipmapLevels
```

numInterpolationMethods
```
protected static final int numInterpolationMethods
```
See Also:

Constant Field Values

iNearestNeighborMethod
```
protected static final int iNearestNeighborMethod
```
See Also:

Constant Field Values

iNLinearMethod
```
protected static final int iNLinearMethod
```
See Also:

Constant Field Values

interpolatorFactories

protected final InterpolatorFactory<T extends NumericType<T>,RandomAccessible<T extends NumericType<T>>>[] interpolatorFactories

cachedSources

protected final UncheckedCache<AbstractSpimSource.ImgKey,RandomAccessibleInterval<T extends NumericType<T>>> cachedSources

cachedInterpolatedSources

protected final UncheckedCache<AbstractSpimSource.ImgKey,RealRandomAccessible<T extends NumericType<T>>> cachedInterpolatedSources

Constructor Detail

AbstractSpimSource

public AbstractSpimSource(AbstractSpimData<?> spimData,
                          int setupId,
                          String name)

Method Detail
- loadTimepoint
```
protected void loadTimepoint(int timepointIndex)
```
- getMipmapTransforms
```
protected abstract AffineTransform3D[] getMipmapTransforms()
```
- getImage
```
protected abstract RandomAccessibleInterval<T> getImage(int timepointId,
                                                        int level)
```
- 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 NumericType<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 extends NumericType<T>>
  
  Parameters:
  
  t - timepoint index
  
  level - mipmap level
  
  Returns:
  
  the stack.
- getSource
```
public RandomAccessibleInterval<T> getSource(int t,
                                             int level,
                                             ThreadGroup threadGroup)
```
- 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 NumericType<T>>
  
  Parameters:
  
  t - timepoint index
  
  level - mipmap level
  
  method - interpolation method to use
  
  Returns:
  
  the extended and interpolated stack.
- getInterpolatedSource
```
public RealRandomAccessible<T> getInterpolatedSource(int t,
                                                     int level,
                                                     Interpolation method,
                                                     ThreadGroup threadGroup)
```
- 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 NumericType<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
- getName
```
public String getName()
```
  Description copied from interface: Source
  
  Get the name of the source.
  
  Specified by:
  
  getName in interface Source<T extends NumericType<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 NumericType<T>>
  
  Returns:
  
  voxel size and unit or null.
- getNumMipmapLevels
```
public int getNumMipmapLevels()
```
  Specified by:
  
  getNumMipmapLevels in interface Source<T extends NumericType<T>>
- getSetupId
```
public int getSetupId()
```

Class AbstractSpimSource<T extends NumericType<T>>

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface bdv.viewer.Source

Field Detail

currentTimePointIndex

currentTimePointIsPresent

currentSourceTransforms

setupId

name

timePointsOrdered

viewRegistrations

missingViews

voxelDimensions

numMipmapLevels

numInterpolationMethods

iNearestNeighborMethod

iNLinearMethod

interpolatorFactories

cachedSources

cachedInterpolatedSources

Constructor Detail

AbstractSpimSource

Method Detail

loadTimepoint

getMipmapTransforms

getImage

isPresent

getSource

getSource

getInterpolatedSource

getInterpolatedSource

getSourceTransform

getName

getVoxelDimensions

getNumMipmapLevels

getSetupId