Package net.preibisch.mvrecon.process.fusion.intensity

Class IntensityCorrection

java.lang.Object

net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection

public class IntensityCorrection
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	IntensityCorrection.SerializableRealInterval

Constructor Summary

Constructors

Constructor	Description
IntensityCorrection()

Method Summary

Modifier and Type	Method	Description
static net.imglib2.RealInterval	getBounds(mpicbg.spim.data.generic.AbstractSpimData<?> spimData, mpicbg.spim.data.sequence.ViewId viewId)
static Map<mpicbg.spim.data.sequence.ViewId,List<mpicbg.spim.data.sequence.ViewId>>	getPotentialBleachers(List<mpicbg.spim.data.sequence.ViewId> views, Map<mpicbg.spim.data.sequence.ViewId,net.imglib2.RealInterval> viewBounds)	Given a list of ViewIds in the order they were acquired (such that views later in the list have been potentially bleached by earlier views), finds for each ViewId the potential "bleachers" (earlier views with overlapping bounds).
static ViewPairCoefficientMatches	matchHistograms(mpicbg.spim.data.generic.AbstractSpimData<?> spimData, mpicbg.spim.data.sequence.ViewId viewId1, List<mpicbg.spim.data.sequence.ViewId> viewId1Bleachers, mpicbg.spim.data.sequence.ViewId viewId2, List<mpicbg.spim.data.sequence.ViewId> viewId2Bleachers, UnbleachFunction unbleachFunction, double renderScale, int[] coefficientsSize, double minIntensity, double maxIntensity, int minNumCandidates)
static ViewPairCoefficientMatches	matchHistograms(mpicbg.spim.data.generic.AbstractSpimData<?> spimData, mpicbg.spim.data.sequence.ViewId viewId1, mpicbg.spim.data.sequence.ViewId viewId2, double renderScale, int[] coefficientsSize, double minIntensity, double maxIntensity, int minNumCandidates)
static ViewPairCoefficientMatches	matchRansac(mpicbg.spim.data.generic.AbstractSpimData<?> spimData, mpicbg.spim.data.sequence.ViewId viewId1, List<mpicbg.spim.data.sequence.ViewId> viewId1Bleachers, mpicbg.spim.data.sequence.ViewId viewId2, List<mpicbg.spim.data.sequence.ViewId> viewId2Bleachers, UnbleachFunction unbleachFunction, double renderScale, int[] coefficientsSize, double minIntensity, double maxIntensity, int minNumCandidates, int iterations, double maxEpsilon, double minInlierRatio, int minNumInliers, double maxTrust)
static ViewPairCoefficientMatches	matchRansac(mpicbg.spim.data.generic.AbstractSpimData<?> spimData, mpicbg.spim.data.sequence.ViewId viewId1, mpicbg.spim.data.sequence.ViewId viewId2, double renderScale, int[] coefficientsSize, double minIntensity, double maxIntensity, int minNumCandidates, int iterations, double maxEpsilon, double minInlierRatio, int minNumInliers, double maxTrust)
static Coefficients	readCoefficients(org.janelia.saalfeldlab.n5.N5Reader n5Reader, String group, String dataset, mpicbg.spim.data.sequence.ViewId viewId)
static Map<mpicbg.spim.data.sequence.ViewId,Coefficients>	solve(int[] coefficientsSize, Collection<ViewPairCoefficientMatches> pairwiseMatches, int iterations)
static void	writeCoefficients(org.janelia.saalfeldlab.n5.N5Writer n5Writer, String group, String dataset, Map<mpicbg.spim.data.sequence.ViewId,Coefficients> coefficients)

Methods inherited from class java.lang.Object

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

Constructor Details

IntensityCorrection

public IntensityCorrection()

Method Details

getBounds

public static net.imglib2.RealInterval getBounds(mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
 mpicbg.spim.data.sequence.ViewId viewId)

getPotentialBleachers

public static Map<mpicbg.spim.data.sequence.ViewId,List<mpicbg.spim.data.sequence.ViewId>> getPotentialBleachers(List<mpicbg.spim.data.sequence.ViewId> views,
 Map<mpicbg.spim.data.sequence.ViewId,net.imglib2.RealInterval> viewBounds)

Given a list of ViewIds in the order they were acquired (such that views later in the list have been potentially bleached by earlier views), finds for each ViewId the potential "bleachers" (earlier views with overlapping bounds).

Parameters:

views - list of all ViewIds in the order they were acquired

viewBounds - maps ViewId to bounding box in world coordinates

Returns:

maps every ViewId to the ViewIds of potential bleachers

matchRansac

public static ViewPairCoefficientMatches matchRansac(mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
 mpicbg.spim.data.sequence.ViewId viewId1,
 mpicbg.spim.data.sequence.ViewId viewId2,
 double renderScale,
 int[] coefficientsSize,
 double minIntensity,
 double maxIntensity,
 int minNumCandidates,
 int iterations,
 double maxEpsilon,
 double minInlierRatio,
 int minNumInliers,
 double maxTrust)

matchRansac

public static ViewPairCoefficientMatches matchRansac(mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
 mpicbg.spim.data.sequence.ViewId viewId1,
 List<mpicbg.spim.data.sequence.ViewId> viewId1Bleachers,
 mpicbg.spim.data.sequence.ViewId viewId2,
 List<mpicbg.spim.data.sequence.ViewId> viewId2Bleachers,
 UnbleachFunction unbleachFunction,
 double renderScale,
 int[] coefficientsSize,
 double minIntensity,
 double maxIntensity,
 int minNumCandidates,
 int iterations,
 double maxEpsilon,
 double minInlierRatio,
 int minNumInliers,
 double maxTrust)

matchHistograms

public static ViewPairCoefficientMatches matchHistograms(mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
 mpicbg.spim.data.sequence.ViewId viewId1,
 mpicbg.spim.data.sequence.ViewId viewId2,
 double renderScale,
 int[] coefficientsSize,
 double minIntensity,
 double maxIntensity,
 int minNumCandidates)

matchHistograms

public static ViewPairCoefficientMatches matchHistograms(mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
 mpicbg.spim.data.sequence.ViewId viewId1,
 List<mpicbg.spim.data.sequence.ViewId> viewId1Bleachers,
 mpicbg.spim.data.sequence.ViewId viewId2,
 List<mpicbg.spim.data.sequence.ViewId> viewId2Bleachers,
 UnbleachFunction unbleachFunction,
 double renderScale,
 int[] coefficientsSize,
 double minIntensity,
 double maxIntensity,
 int minNumCandidates)

solve

public static Map<mpicbg.spim.data.sequence.ViewId,Coefficients> solve(int[] coefficientsSize,
 Collection<ViewPairCoefficientMatches> pairwiseMatches,
 int iterations)

writeCoefficients

public static void writeCoefficients(org.janelia.saalfeldlab.n5.N5Writer n5Writer,
 String group,
 String dataset,
 Map<mpicbg.spim.data.sequence.ViewId,Coefficients> coefficients)

readCoefficients

public static Coefficients readCoefficients(org.janelia.saalfeldlab.n5.N5Reader n5Reader,
 String group,
 String dataset,
 mpicbg.spim.data.sequence.ViewId viewId)