Package net.preibisch.mvrecon.process.boundingbox

Class BoundingBoxReorientation

java.lang.Object

net.preibisch.mvrecon.process.boundingbox.BoundingBoxReorientation

All Implemented Interfaces:

BoundingBoxEstimation

public class BoundingBoxReorientation
extends Object
implements BoundingBoxEstimation

Field Summary

Fields

Modifier and Type	Field	Description
static String	reorientationDescription

Constructor Summary

Constructors

Constructor	Description
BoundingBoxReorientation(SpimData2 spimData, ArrayList<net.imglib2.RealLocalizable> points, double percent, boolean testRotations, List<mpicbg.spim.data.sequence.ViewId> viewIdsToApply)
BoundingBoxReorientation(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsForEstimation, String label, boolean useCorresponding, double percent, boolean testRotations, List<mpicbg.spim.data.sequence.ViewId> viewIdsToApply)
BoundingBoxReorientation(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsForEstimation, HashMap<mpicbg.spim.data.sequence.ViewId,? extends Collection<? extends net.imglib2.RealLocalizable>> points, double percent, boolean testRotations, List<mpicbg.spim.data.sequence.ViewId> viewIdsToApply)

Method Summary

Modifier and Type	Method	Description
protected net.imglib2.util.Pair<net.imglib2.realtransform.AffineTransform3D,double[]>	determineOptimalBoundingBox()
protected net.imglib2.util.Pair<double[],double[]>	determineSizeSimple()
BoundingBox	estimate(String title)
static ArrayList<net.imglib2.RealLocalizable>	extractPoints(String label, boolean useCorresponding, boolean transform, List<mpicbg.spim.data.sequence.ViewId> viewIds, SpimData2 data)	Gets point locations in local or global coordinates
static ArrayList<net.imglib2.RealLocalizable>	extractPoints(HashMap<mpicbg.spim.data.sequence.ViewId,? extends Collection<? extends net.imglib2.RealLocalizable>> pointsIn, List<mpicbg.spim.data.sequence.ViewId> viewIdsForEstimation, SpimData2 spimData)
static Transform3D	getRotation(Vector3d v0, Vector3d v1)	Computes a Transform3D that will rotate vector v0 into the direction of vector v1.
static final double	squareDistance(double p1x, double p1y, double p1z, double p2x, double p2y, double p2z)
protected net.imglib2.util.Pair<Double,double[]>	testAxis(Vector3d v, List<net.imglib2.RealLocalizable> points)	Test one major axis for the minimal bounding box volume required

Methods inherited from class java.lang.Object

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

Field Details

reorientationDescription

public static String reorientationDescription

Constructor Details

BoundingBoxReorientation

public BoundingBoxReorientation(SpimData2 spimData,
 List<mpicbg.spim.data.sequence.ViewId> viewIdsForEstimation,
 HashMap<mpicbg.spim.data.sequence.ViewId,? extends Collection<? extends net.imglib2.RealLocalizable>> points,
 double percent,
 boolean testRotations,
 List<mpicbg.spim.data.sequence.ViewId> viewIdsToApply)

Parameters:

spimData - - the spimdata object

viewIdsForEstimation - - which ViewIds to use for BoundingBox determination

points - - a Map linking a list of locations of points to each ViewId used for estimation

percent - - extend/shrink the computed bounding box by the specified percentage (e.g. 10%, -%5, etc.)

testRotations - - if free rotations should be allowed in order to reorient the sample and minimize the bounding box. Warning: this will preconcatenate another rigid transform to all views listed in viewIdsToApply

viewIdsToApply - - only used if testRotations==true, these are the views the identified rotation minimizing the bounding box size will be applied to

BoundingBoxReorientation

public BoundingBoxReorientation(SpimData2 spimData,
 List<mpicbg.spim.data.sequence.ViewId> viewIdsForEstimation,
 String label,
 boolean useCorresponding,
 double percent,
 boolean testRotations,
 List<mpicbg.spim.data.sequence.ViewId> viewIdsToApply)

BoundingBoxReorientation

public BoundingBoxReorientation(SpimData2 spimData,
 ArrayList<net.imglib2.RealLocalizable> points,
 double percent,
 boolean testRotations,
 List<mpicbg.spim.data.sequence.ViewId> viewIdsToApply)

Method Details

estimate

public BoundingBox estimate(String title)

Specified by:

estimate in interface BoundingBoxEstimation

determineOptimalBoundingBox

protected net.imglib2.util.Pair<net.imglib2.realtransform.AffineTransform3D,double[]> determineOptimalBoundingBox()

testAxis

protected net.imglib2.util.Pair<Double,double[]> testAxis(Vector3d v,
 List<net.imglib2.RealLocalizable> points)

Test one major axis for the minimal bounding box volume required

Parameters:

v - - normalized vector

points - - all points

Returns:

- the volume and minX, minY, minZ, maxX, maxY, maxZ as Pair

getRotation

public static Transform3D getRotation(Vector3d v0,
 Vector3d v1)

Computes a Transform3D that will rotate vector v0 into the direction of vector v1. Note: vectors MUST be normalized for this to work!

Parameters:

v0 - - vector 0

v1 - - vector 1

Returns:

the transform

squareDistance

public static final double squareDistance(double p1x,
 double p1y,
 double p1z,
 double p2x,
 double p2y,
 double p2z)

determineSizeSimple

protected net.imglib2.util.Pair<double[],double[]> determineSizeSimple()

extractPoints

public static ArrayList<net.imglib2.RealLocalizable> extractPoints(String label,
 boolean useCorresponding,
 boolean transform,
 List<mpicbg.spim.data.sequence.ViewId> viewIds,
 SpimData2 data)

Gets point locations in local or global coordinates

Parameters:

label - - which label to use

useCorresponding - - use only corresponding points?

transform - - transform the points? Yes for Bounding box, no for PSF extraction

viewIds - - which viewIds to process

data - - the SpimData object

Returns:

- a list of RealLocalizable objects

extractPoints

public static ArrayList<net.imglib2.RealLocalizable> extractPoints(HashMap<mpicbg.spim.data.sequence.ViewId,? extends Collection<? extends net.imglib2.RealLocalizable>> pointsIn,
 List<mpicbg.spim.data.sequence.ViewId> viewIdsForEstimation,
 SpimData2 spimData)