bdv

Class AbstractSpimSource<T extends net.imglib2.type.numeric.NumericType<T>>

java.lang.Object

bdv.AbstractSpimSource<T>

All Implemented Interfaces:

Source<T>

Direct Known Subclasses:

SpimSource, VolatileSpimSource

public abstract class AbstractSpimSource<T extends net.imglib2.type.numeric.NumericType<T>>
extends Object
implements Source<T>

Constructor Summary

Constructors

Constructor and Description
AbstractSpimSource(mpicbg.spim.data.generic.AbstractSpimData<?> spimData, int setupId, String name)

Method Summary

Modifier and Type	Method and Description
net.imglib2.RealRandomAccessible<? extends net.imglib2.type.mask.Masked<T>>	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<? extends net.imglib2.type.mask.Masked<T>>	getInterpolatedMaskedSource(int t, int level, Interpolation method, ThreadGroup threadGroup)
net.imglib2.RealRandomAccessible<T>	getInterpolatedSource(int t, int level, Interpolation method) Get the 3D stack at timepoint index t, extended to infinity and interpolated.
net.imglib2.RealRandomAccessible<T>	getInterpolatedSource(int t, int level, Interpolation method, ThreadGroup threadGroup)
net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.mask.Masked<T>>	getMaskedSource(int t, int level) Get a Masked version of the 3D stack at timepoint index t.
net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.mask.Masked<T>>	getMaskedSource(int t, int level, ThreadGroup threadGroup)
String	getName() Get the name of the source.
int	getNumMipmapLevels()
int	getSetupId()
net.imglib2.RandomAccessibleInterval<T>	getSource(int t, int level) Get the 3D stack at timepoint index t.
net.imglib2.RandomAccessibleInterval<T>	getSource(int t, int level, ThreadGroup threadGroup)
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.
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?
void	reload() Invalidate cached source transformations, triggering a reload from SpimData.

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

Constructor Detail

AbstractSpimSource

public AbstractSpimSource(mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
                          int setupId,
                          String name)

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 net.imglib2.type.numeric.NumericType<T>>

Parameters:

t - timepoint index

Returns:

true, if there is data for timepoint index t.

getSource

public net.imglib2.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 net.imglib2.type.numeric.NumericType<T>>

Parameters:

t - timepoint index

level - mipmap level

Returns:

the stack.

getSource

public net.imglib2.RandomAccessibleInterval<T> getSource(int t,
                                                         int level,
                                                         ThreadGroup threadGroup)

getInterpolatedSource

public net.imglib2.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 net.imglib2.type.numeric.NumericType<T>>

Parameters:

t - timepoint index

level - mipmap level

method - interpolation method to use

Returns:

the extended and interpolated stack.

getInterpolatedSource

public net.imglib2.RealRandomAccessible<T> getInterpolatedSource(int t,
                                                                 int level,
                                                                 Interpolation method,
                                                                 ThreadGroup threadGroup)

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<T extends net.imglib2.type.numeric.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 net.imglib2.type.numeric.NumericType<T>>

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<T extends net.imglib2.type.numeric.NumericType<T>>

Returns:

voxel size and unit or null.

getNumMipmapLevels

public int getNumMipmapLevels()

Specified by:

getNumMipmapLevels in interface Source<T extends net.imglib2.type.numeric.NumericType<T>>

getSetupId

public int getSetupId()

reload

public void reload()

Invalidate cached source transformations, triggering a reload from SpimData.

Implementation Note: This method was added so that BigStitcher can trigger reloading source transforms from ViewRegistrations. It doesn't currently trigger update of anything else (MissingViews, available timepoints, etc.) However, if the need for these arises, this method would be a good place to put it.

getMaskedSource

public net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.mask.Masked<T>> 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<T extends net.imglib2.type.numeric.NumericType<T>>

Parameters:

t - timepoint index

level - mipmap level

Returns:

the masked stack

getMaskedSource

public net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.mask.Masked<T>> getMaskedSource(int t,
                                                                                                       int level,
                                                                                                       ThreadGroup threadGroup)

getInterpolatedMaskedSource

public net.imglib2.RealRandomAccessible<? extends net.imglib2.type.mask.Masked<T>> 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<T extends net.imglib2.type.numeric.NumericType<T>>

Parameters:

t - timepoint index

level - mipmap level

method - interpolation method to use

Returns:

the extended and interpolated stack.

getInterpolatedMaskedSource

public net.imglib2.RealRandomAccessible<? extends net.imglib2.type.mask.Masked<T>> getInterpolatedMaskedSource(int t,
                                                                                                               int level,
                                                                                                               Interpolation method,
                                                                                                               ThreadGroup threadGroup)