bdv.viewer

Interface Source<T>

All Known Implementing Classes:

AbstractSource, AbstractSpimSource, PlaceHolderSource, RandomAccessibleIntervalMipmapSource, RandomAccessibleIntervalMipmapSource4D, RandomAccessibleIntervalSource, RandomAccessibleIntervalSource4D, RandomAccessibleSource, RandomAccessibleSource4D, RealRandomAccessibleIntervalSource, RealRandomAccessibleSource, SpimSource, TransformedSource, VolatileRandomAccessibleIntervalMipmapSource, VolatileSource, VolatileSpimSource

public interface Source<T>

Provides image data for all timepoints of one view setup. Note that (partly for convenience and partly for historical reasons) the time-point index is used here instead of the timepoint id. This timepoint index is an index into the ordered list of timepoints TimePoints.getTimePointsOrdered().

Author:

Tobias Pietzsch

Method Summary

Modifier and Type	Method and Description
default boolean	doBoundingBoxCulling() Whether this source participates in bounding box culling.
default 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<T>	getInterpolatedSource(int t, int level, Interpolation method) Get the 3D stack at timepoint index t, extended to infinity and interpolated.
default 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.
String	getName() Get the name of the source.
int	getNumMipmapLevels()
net.imglib2.RandomAccessibleInterval<T>	getSource(int t, int level) Get the 3D stack at timepoint index t.
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.
T	getType() Get an instance of the pixel type.
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?

Method Detail

isPresent

boolean isPresent(int t)

Is there a stack at timepoint index t?

Parameters:

t - timepoint index

Returns:

true, if there is data for timepoint index t.

getSource

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

Get the 3D stack at timepoint index t.

Parameters:

t - timepoint index

level - mipmap level

Returns:

the stack.

doBoundingBoxCulling

default boolean doBoundingBoxCulling()

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 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.)

Returns:

true, if this source participates in bounding box culling.

getInterpolatedSource

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

Get the 3D stack at timepoint index t, extended to infinity and interpolated.

Parameters:

t - timepoint index

level - mipmap level

method - interpolation method to use

Returns:

the extended and interpolated stack.

getSourceTransform

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.

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

T getType()

Get an instance of the pixel type.

Returns:

instance of pixel type.

getName

String getName()

Get the name of the source.

Returns:

the name of the source.

getVoxelDimensions

mpicbg.spim.data.sequence.VoxelDimensions getVoxelDimensions()

Get voxel size and unit for this source. May return null.

Returns:

voxel size and unit or null.

getNumMipmapLevels

int getNumMipmapLevels()

getMaskedSource

default 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.

By default, this is just getSource(int, int) augmented with a constant mask 1.0.

Parameters:

t - timepoint index

level - mipmap level

Returns:

the masked stack

getInterpolatedMaskedSource

default 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.

By default, this is just getInterpolatedSource(int, int, bdv.viewer.Interpolation) augmented with a constant mask 1.0.

However, most sources should override this to extend getMaskedSource(int, int) to infinity (with a 0 mask) and interpolate.

Parameters:

t - timepoint index

level - mipmap level

method - interpolation method to use

Returns:

the extended and interpolated stack.