Package net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap

Class SimpleBoundingBoxOverlap<V extends mpicbg.spim.data.sequence.ViewId>

java.lang.Object

net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap<V>

All Implemented Interfaces:

OverlapDetection<V>

public class SimpleBoundingBoxOverlap<V extends mpicbg.spim.data.sequence.ViewId>
extends Object
implements OverlapDetection<V>

Constructor Summary

Constructors

Constructor	Description
SimpleBoundingBoxOverlap(Map<Integer,? extends mpicbg.spim.data.generic.sequence.BasicViewSetup> viewSetups, Map<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.registration.ViewRegistration> vrs)
SimpleBoundingBoxOverlap(mpicbg.spim.data.generic.AbstractSpimData<? extends mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<? extends mpicbg.spim.data.generic.sequence.BasicViewSetup,?,?>> spimData)
SimpleBoundingBoxOverlap(mpicbg.spim.data.sequence.SequenceDescription sd, mpicbg.spim.data.registration.ViewRegistrations vrs)

Method Summary

Modifier and Type	Method	Description
List<net.imglib2.util.Pair<V,V>>	generateOverlappingPairs(List<V> views, Collection<? extends Group<V>> groups)	Generate overlapping pairs directly without creating all n^2 pairs first.
static BoundingBox	getBoundingBox(mpicbg.spim.data.generic.sequence.BasicViewSetup vs, mpicbg.spim.data.registration.ViewRegistration vr)
static BoundingBox	getBoundingBox(net.imglib2.Dimensions dims, net.imglib2.realtransform.AffineTransform3D transform)
static <V extends mpicbg.spim.data.sequence.ViewId> BoundingBox	getBoundingBox(V view, Map<Integer,? extends mpicbg.spim.data.generic.sequence.BasicViewSetup> vss, mpicbg.spim.data.registration.ViewRegistrations vrs)
static net.imglib2.RealInterval	getBoundingBoxReal(mpicbg.spim.data.generic.sequence.BasicViewSetup vs, mpicbg.spim.data.registration.ViewRegistration vr)
static net.imglib2.RealInterval	getBoundingBoxReal(net.imglib2.Dimensions dims, net.imglib2.realtransform.AffineTransform3D transform)
static <V extends mpicbg.spim.data.sequence.ViewId> net.imglib2.RealInterval	getBoundingBoxReal(V view, Map<Integer,? extends mpicbg.spim.data.generic.sequence.BasicViewSetup> vss, mpicbg.spim.data.registration.ViewRegistrations vrs)
net.imglib2.RealInterval	getOverlapInterval(V view1, V view2)
static boolean	overlaps(BoundingBox bb1, BoundingBox bb2)
boolean	overlaps(V view1, V view2)
Map<V,BoundingBox>	precomputeBoundingBoxes(Collection<V> views)	Pre-compute all bounding boxes for a collection of views in parallel.
ArrayList<net.imglib2.util.Pair<V,V>>	removeNonOverlappingPairsOptimized(List<net.imglib2.util.Pair<V,V>> pairs, Collection<V> views)	Combined method: pre-compute bounding boxes and filter pairs in parallel.
ArrayList<net.imglib2.util.Pair<V,V>>	removeNonOverlappingPairsParallel(List<net.imglib2.util.Pair<V,V>> pairs, Map<V,BoundingBox> boundingBoxes)	Filter overlapping pairs using pre-computed bounding boxes in parallel.

Methods inherited from class java.lang.Object

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

Constructor Details

SimpleBoundingBoxOverlap

public SimpleBoundingBoxOverlap(mpicbg.spim.data.generic.AbstractSpimData<? extends mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<? extends mpicbg.spim.data.generic.sequence.BasicViewSetup,?,?>> spimData)

SimpleBoundingBoxOverlap

public SimpleBoundingBoxOverlap(mpicbg.spim.data.sequence.SequenceDescription sd,
 mpicbg.spim.data.registration.ViewRegistrations vrs)

SimpleBoundingBoxOverlap

public SimpleBoundingBoxOverlap(Map<Integer,? extends mpicbg.spim.data.generic.sequence.BasicViewSetup> viewSetups,
 Map<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.registration.ViewRegistration> vrs)

Method Details

overlaps

public boolean overlaps(V view1,
 V view2)

Specified by:

overlaps in interface OverlapDetection<V extends mpicbg.spim.data.sequence.ViewId>

getOverlapInterval

public net.imglib2.RealInterval getOverlapInterval(V view1,
 V view2)

Specified by:

getOverlapInterval in interface OverlapDetection<V extends mpicbg.spim.data.sequence.ViewId>

overlaps

public static boolean overlaps(BoundingBox bb1,
 BoundingBox bb2)

getBoundingBox

public static <V extends mpicbg.spim.data.sequence.ViewId>
BoundingBox getBoundingBox(V view,
 Map<Integer,? extends mpicbg.spim.data.generic.sequence.BasicViewSetup> vss,
 mpicbg.spim.data.registration.ViewRegistrations vrs)

getBoundingBoxReal

public static <V extends mpicbg.spim.data.sequence.ViewId>
net.imglib2.RealInterval getBoundingBoxReal(V view,
 Map<Integer,? extends mpicbg.spim.data.generic.sequence.BasicViewSetup> vss,
 mpicbg.spim.data.registration.ViewRegistrations vrs)

getBoundingBox

public static BoundingBox getBoundingBox(mpicbg.spim.data.generic.sequence.BasicViewSetup vs,
 mpicbg.spim.data.registration.ViewRegistration vr)

getBoundingBox

public static BoundingBox getBoundingBox(net.imglib2.Dimensions dims,
 net.imglib2.realtransform.AffineTransform3D transform)

getBoundingBoxReal

public static net.imglib2.RealInterval getBoundingBoxReal(mpicbg.spim.data.generic.sequence.BasicViewSetup vs,
 mpicbg.spim.data.registration.ViewRegistration vr)

getBoundingBoxReal

public static net.imglib2.RealInterval getBoundingBoxReal(net.imglib2.Dimensions dims,
 net.imglib2.realtransform.AffineTransform3D transform)

precomputeBoundingBoxes

public Map<V,BoundingBox> precomputeBoundingBoxes(Collection<V> views)

Pre-compute all bounding boxes for a collection of views in parallel. This is much faster than computing bounding boxes on-demand for each pair.

Parameters:

views - - the views to compute bounding boxes for

Returns:

a Map from ViewId to its BoundingBox

removeNonOverlappingPairsParallel

public ArrayList<net.imglib2.util.Pair<V,V>> removeNonOverlappingPairsParallel(List<net.imglib2.util.Pair<V,V>> pairs,
 Map<V,BoundingBox> boundingBoxes)

Filter overlapping pairs using pre-computed bounding boxes in parallel. This removes non-overlapping pairs from the list and returns the removed pairs.

Parameters:

pairs - - the pairs to check (will be modified to contain only overlapping pairs)

boundingBoxes - - pre-computed bounding boxes for all views

Returns:

the list of removed (non-overlapping) pairs

generateOverlappingPairs

public List<net.imglib2.util.Pair<V,V>> generateOverlappingPairs(List<V> views,
 Collection<? extends Group<V>> groups)

Generate overlapping pairs directly without creating all n^2 pairs first. This is MUCH faster for large datasets where most pairs don't overlap.

Parameters:

views - - list of views to generate pairs from

groups - - groups (views in same group are skipped)

Returns:

list of overlapping pairs only

removeNonOverlappingPairsOptimized

public ArrayList<net.imglib2.util.Pair<V,V>> removeNonOverlappingPairsOptimized(List<net.imglib2.util.Pair<V,V>> pairs,
 Collection<V> views)

Combined method: pre-compute bounding boxes and filter pairs in parallel. This is the most efficient approach for large datasets.

Parameters:

pairs - - the pairs to check (will be modified to contain only overlapping pairs)

views - - all views involved (used for pre-computing bounding boxes)

Returns:

the list of removed (non-overlapping) pairs