Matching (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- process.Matching

```
public class Matching
extends Object
```

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Matching.PeakSort

Nested Classes
Modifier and Type	Class and Description
`static class`	`Matching.PeakSort`

Field Summary

Fields
Modifier and Type Field and Description

static boolean applyScaling

static float factor

protected static PrintWriter outAll

Fields
Modifier and Type	Field and Description
`static boolean`	`applyScaling`
`static float`	`factor`
`protected static PrintWriter`	`outAll`

Constructor Summary

Constructors
Constructor and Description

Matching()

Constructors
Constructor and Description
`Matching()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`addPointMatches(ArrayList<PointMatch> correspondences, Tile<?> tileA, Tile<?> tileB)`
`protected static ArrayList<DifferenceOfGaussianPeak<FloatType>>`	`computeDoG(Image<FloatType> image, float sigma1, float sigma2, boolean lookForMaxima, boolean lookForMinima, float threshold, int localization, int iterations, double[] sigmaGuess, int[] region)`
`static float[]`	`computeMinMax(ij.ImagePlus imp, int channel)`
`protected static String`	`computeRANSAC(ArrayList<PointMatch> candidates, ArrayList<PointMatch> inliers, Model<?> model, float maxEpsilon)`
`static Image<FloatType>`	`convertToFloat(ij.ImagePlus imp, int channel, int timepoint, float[] minmax)` Normalize and make a copy of the `ImagePlus` into an `Image` of FloatType for faster access when copying the slices
`protected static int`	`countMatches(List<ComparePair> pairs)`
`protected static ArrayList<AbstractPointDescriptor>`	`createModelPointDescriptors(KDTree<Particle> tree, ArrayList<Particle> basisPoints, int numNeighbors, Matcher matcher, SimilarityMeasure similarityMeasure, int dimensionality)`
`protected static ArrayList<AbstractPointDescriptor>`	`createSimplePointDescriptors(KDTree<Particle> tree, ArrayList<Particle> basisPoints, int numNeighbors, Matcher matcher, SimilarityMeasure similarityMeasure)`
`static int`	`descriptorBasedRegistration(ij.ImagePlus imp1, ij.ImagePlus imp2, DescriptorParameters params)`
`static ArrayList<InvertibleBoundable>`	`descriptorBasedStackRegistration(ij.ImagePlus imp, DescriptorParameters params)`
`static Vector<ComparePair>`	`descriptorMatching(ArrayList<ArrayList<DifferenceOfGaussianPeak<FloatType>>> peaks, int numImages, DescriptorParameters params, float zStretching)`
`static ArrayList<DifferenceOfGaussianPeak<FloatType>>`	`extractCandidates(ij.ImagePlus imp, int channel, int timepoint, DescriptorParameters params, float[] minmax)`
`protected static ArrayList<DifferenceOfGaussianPeak<FloatType>>`	`filterForROI(Roi roi, ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks)`
`protected static ArrayList<DifferenceOfGaussianPeak<FloatType>>`	`filterForROI(Roi roi, ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks, Model<?> model)`
`protected static ArrayList<PointMatch>`	`findCorrespondingDescriptors(ArrayList<AbstractPointDescriptor> descriptorsA, ArrayList<AbstractPointDescriptor> descriptorsB, float nTimesBetter)`
`protected static Vector<ComparePair>`	`getComparePairs(DescriptorParameters params, int numImages)`
`protected static ArrayList<PointMatch>`	`getCorrespondenceCandidates(double nTimesBetter, Matcher matcher, ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks1, ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks2, Model<?> model, int dimensionality, float zStretching1, float zStretching2, String explanation)`
`static ArrayList<InvertibleBoundable>`	`globalOptimization(Vector<ComparePair> pairs, int numImages, DescriptorParameters params)`
`static void`	`main(String[] args)`
`protected static Model<?>`	`pairwiseMatching(ArrayList<PointMatch> finalInliers, ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks1, ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks2, float zStretching1, float zStretching2, DescriptorParameters params, String explanation)`
`protected static int`	`performIteration(ArrayList<InvertibleBoundable> lastModels, ArrayList<ArrayList<DifferenceOfGaussianPeak<FloatType>>> peaksComplete, int numImages, DescriptorParameters params, float zStretching)` Computes one iteration and updates the lastModels ArrayList with the new models
`protected static int[]`	`removeInvalidAndCollectStatistics(ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks)`
`protected static void`	`setPointRois(ij.ImagePlus imp1, ij.ImagePlus imp2, ArrayList<PointMatch> inliers)`
`protected static void`	`writePoints(ArrayList<PointMatch> finalInliers, DescriptorParameters params, Model<?> finalModel, PrintWriter out)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

applyScaling
```
public static boolean applyScaling
```

factor
```
public static float factor
```

outAll
```
protected static PrintWriter outAll
```

Constructor Detail
- Matching
```
public Matching()
```

Method Detail

descriptorBasedRegistration

public static int descriptorBasedRegistration(ij.ImagePlus imp1,
                                              ij.ImagePlus imp2,
                                              DescriptorParameters params)

Parameters:: imp1 -; imp2 -; params -
Returns:: - the number of inliers

descriptorBasedStackRegistration

public static ArrayList<InvertibleBoundable> descriptorBasedStackRegistration(ij.ImagePlus imp,
                                                                              DescriptorParameters params)

performIteration

protected static int performIteration(ArrayList<InvertibleBoundable> lastModels,
                                      ArrayList<ArrayList<DifferenceOfGaussianPeak<FloatType>>> peaksComplete,
                                      int numImages,
                                      DescriptorParameters params,
                                      float zStretching)

Computes one iteration and updates the lastModels ArrayList with the new models

Parameters:: lastModels - - models from last iteration (or init); peaksComplete - - all peaks for all images; numImages - - how many images are there; params - - the parameters; zStretching - - the zStretching if applicable
Returns:: the number of matches found

countMatches

protected static int countMatches(List<ComparePair> pairs)

descriptorMatching

public static Vector<ComparePair> descriptorMatching(ArrayList<ArrayList<DifferenceOfGaussianPeak<FloatType>>> peaks,
                                                     int numImages,
                                                     DescriptorParameters params,
                                                     float zStretching)

globalOptimization

public static ArrayList<InvertibleBoundable> globalOptimization(Vector<ComparePair> pairs,
                                                                int numImages,
                                                                DescriptorParameters params)

addPointMatches

public static void addPointMatches(ArrayList<PointMatch> correspondences,
                                   Tile<?> tileA,
                                   Tile<?> tileB)

getComparePairs

protected static Vector<ComparePair> getComparePairs(DescriptorParameters params,
                                                     int numImages)

pairwiseMatching

protected static Model<?> pairwiseMatching(ArrayList<PointMatch> finalInliers,
                                           ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks1,
                                           ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks2,
                                           float zStretching1,
                                           float zStretching2,
                                           DescriptorParameters params,
                                           String explanation)

writePoints

protected static void writePoints(ArrayList<PointMatch> finalInliers,
                                  DescriptorParameters params,
                                  Model<?> finalModel,
                                  PrintWriter out)

computeMinMax

public static float[] computeMinMax(ij.ImagePlus imp,
                                    int channel)

extractCandidates

public static ArrayList<DifferenceOfGaussianPeak<FloatType>> extractCandidates(ij.ImagePlus imp,
                                                                               int channel,
                                                                               int timepoint,
                                                                               DescriptorParameters params,
                                                                               float[] minmax)

convertToFloat

public static Image<FloatType> convertToFloat(ij.ImagePlus imp,
                                              int channel,
                                              int timepoint,
                                              float[] minmax)

Normalize and make a copy of the ImagePlus into an Image of FloatType for faster access when copying the slices

Parameters:: imp - - the ImagePlus input image
Returns:: - the normalized copy [0...1]

filterForROI

protected static ArrayList<DifferenceOfGaussianPeak<FloatType>> filterForROI(Roi roi,
                                                                             ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks)

filterForROI

protected static ArrayList<DifferenceOfGaussianPeak<FloatType>> filterForROI(Roi roi,
                                                                             ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks,
                                                                             Model<?> model)

setPointRois

protected static void setPointRois(ij.ImagePlus imp1,
                                   ij.ImagePlus imp2,
                                   ArrayList<PointMatch> inliers)

computeRANSAC

protected static String computeRANSAC(ArrayList<PointMatch> candidates,
                                      ArrayList<PointMatch> inliers,
                                      Model<?> model,
                                      float maxEpsilon)

getCorrespondenceCandidates

protected static ArrayList<PointMatch> getCorrespondenceCandidates(double nTimesBetter,
                                                                   Matcher matcher,
                                                                   ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks1,
                                                                   ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks2,
                                                                   Model<?> model,
                                                                   int dimensionality,
                                                                   float zStretching1,
                                                                   float zStretching2,
                                                                   String explanation)

findCorrespondingDescriptors

protected static final ArrayList<PointMatch> findCorrespondingDescriptors(ArrayList<AbstractPointDescriptor> descriptorsA,
                                                                          ArrayList<AbstractPointDescriptor> descriptorsB,
                                                                          float nTimesBetter)

createSimplePointDescriptors

protected static ArrayList<AbstractPointDescriptor> createSimplePointDescriptors(KDTree<Particle> tree,
                                                                                 ArrayList<Particle> basisPoints,
                                                                                 int numNeighbors,
                                                                                 Matcher matcher,
                                                                                 SimilarityMeasure similarityMeasure)

createModelPointDescriptors

protected static ArrayList<AbstractPointDescriptor> createModelPointDescriptors(KDTree<Particle> tree,
                                                                                ArrayList<Particle> basisPoints,
                                                                                int numNeighbors,
                                                                                Matcher matcher,
                                                                                SimilarityMeasure similarityMeasure,
                                                                                int dimensionality)

computeDoG

protected static ArrayList<DifferenceOfGaussianPeak<FloatType>> computeDoG(Image<FloatType> image,
                                                                           float sigma1,
                                                                           float sigma2,
                                                                           boolean lookForMaxima,
                                                                           boolean lookForMinima,
                                                                           float threshold,
                                                                           int localization,
                                                                           int iterations,
                                                                           double[] sigmaGuess,
                                                                           int[] region)

removeInvalidAndCollectStatistics

protected static int[] removeInvalidAndCollectStatistics(ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks)

main

public static void main(String[] args)
                 throws NotEnoughDataPointsException

Throws:: NotEnoughDataPointsException

Class Matching

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

applyScaling

factor

outAll

Constructor Detail

Matching

Method Detail

descriptorBasedRegistration

descriptorBasedStackRegistration

performIteration

countMatches

descriptorMatching

globalOptimization

addPointMatches

getComparePairs

pairwiseMatching

writePoints

computeMinMax

extractCandidates

convertToFloat

filterForROI

filterForROI

setPointRois

computeRANSAC

getCorrespondenceCandidates

findCorrespondingDescriptors

createSimplePointDescriptors

createModelPointDescriptors

computeDoG

removeInvalidAndCollectStatistics

main