bdv.tools.crop

Class CropImgLoader

java.lang.Object

bdv.tools.crop.CropImgLoader

All Implemented Interfaces:

mpicbg.spim.data.generic.sequence.BasicImgLoader

public class CropImgLoader
extends Object
implements mpicbg.spim.data.generic.sequence.BasicImgLoader

This ImgLoader provides views and transformations into a cropped region of a data-set (provided by list of Sources).

Author:

Tobias Pietzsch

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	CropImgLoader.SetupImgLoader<T>

Constructor Summary

Constructors

Constructor and Description
CropImgLoader(ArrayList<Source<?>> sources, net.imglib2.realtransform.AffineTransform3D globalToCropTransform, net.imglib2.RealInterval cropInterval, Map<Integer,Integer> timepointIdToTimepointIndex, Map<Integer,Integer> setupIdToSourceIndex)

Method Summary

Modifier and Type	Method and Description
static <T> net.imglib2.util.Pair<net.imglib2.RandomAccessibleInterval<T>,net.imglib2.realtransform.AffineTransform3D>	crop(net.imglib2.realtransform.AffineTransform3D globalToCropTransform, net.imglib2.RealInterval interval, Source<T> source, int timepoint) Crop a region from a Source.
net.imglib2.realtransform.AffineTransform3D	getCroppedTransform(mpicbg.spim.data.sequence.ViewId view)
CropImgLoader.SetupImgLoader<?>	getSetupImgLoader(int setupId)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CropImgLoader

public CropImgLoader(ArrayList<Source<?>> sources,
                     net.imglib2.realtransform.AffineTransform3D globalToCropTransform,
                     net.imglib2.RealInterval cropInterval,
                     Map<Integer,Integer> timepointIdToTimepointIndex,
                     Map<Integer,Integer> setupIdToSourceIndex)

Method Detail

getCroppedTransform

public net.imglib2.realtransform.AffineTransform3D getCroppedTransform(mpicbg.spim.data.sequence.ViewId view)

getSetupImgLoader

public CropImgLoader.SetupImgLoader<?> getSetupImgLoader(int setupId)

Specified by:

getSetupImgLoader in interface mpicbg.spim.data.generic.sequence.BasicImgLoader

crop

public static <T> net.imglib2.util.Pair<net.imglib2.RandomAccessibleInterval<T>,net.imglib2.realtransform.AffineTransform3D> crop(net.imglib2.realtransform.AffineTransform3D globalToCropTransform,
                                                                                                                                  net.imglib2.RealInterval interval,
                                                                                                                                  Source<T> source,
                                                                                                                                  int timepoint)

Crop a region from a Source.

Parameters:

globalToCropTransform - transform from global into crop-local coordinates.

interval - the interval (in crop-local space) to crop.

source - which source to crop from.

timepoint - which timepoint to crop from.

Returns:

a zero-min view of the cropped region and a transform from that view into global coordinates.