Index (Descriptor based registration 3.0.3 API)

m00 - Static variable in class plugin.Descriptor_based_registration
m01 - Static variable in class plugin.Descriptor_based_registration
m02 - Static variable in class plugin.Descriptor_based_registration
m03 - Static variable in class plugin.Descriptor_based_registration
m10 - Static variable in class plugin.Descriptor_based_registration
m11 - Static variable in class plugin.Descriptor_based_registration
m12 - Static variable in class plugin.Descriptor_based_registration
m13 - Static variable in class plugin.Descriptor_based_registration
m20 - Static variable in class plugin.Descriptor_based_registration
m21 - Static variable in class plugin.Descriptor_based_registration
m22 - Static variable in class plugin.Descriptor_based_registration
m23 - Static variable in class plugin.Descriptor_based_registration
main(String[]) - Static method in class plugin.Manual_Landmark_Selection
main(String[]) - Static method in class process.Matching
Manual_Landmark_Selection - Class in plugin
Manual_Landmark_Selection() - Constructor for class plugin.Manual_Landmark_Selection
Match - Class in selection
Match() - Constructor for class selection.Match
Matching - Class in process
Matching() - Constructor for class process.Matching
Matching.PeakSort - Class in process
max - Static variable in class plugin.DescriptorParameters
max2 - Static variable in class plugin.DescriptorParameters
maxIterations - Static variable in class plugin.DescriptorParameters: if there is a ROI designed, how many iterations
min - Static variable in class plugin.DescriptorParameters
min2 - Static variable in class plugin.DescriptorParameters
minInlierFactor - Static variable in class plugin.DescriptorParameters: How many times more inliers are required than the minimum number of correspondences required for the model.
minmax - Variable in class plugin.DescriptorParameters: The intensity min/max used to normalize the image(s) before DoG detection, resolved once by the dialog so it is not recomputed (e.g. the multi-threaded global computation runs only a single time).
minmax2 - Variable in class plugin.DescriptorParameters: Like DescriptorParameters.minmax, but for the second image of a pairwise (non-series) registration, so the two images can use different intensity ranges.
minMaxChoices - Static variable in class plugin.Descriptor_based_series_registration
minMaxType - Static variable in class plugin.DescriptorParameters: 0 == compute per image (per timepoint/channel individually) 1 == compute global min/max 2 == define min/max
minSimilarity - Static variable in class plugin.DescriptorParameters: How similar two descriptors at least have to be
model - Variable in class plugin.DescriptorParameters
model - Variable in class process.ComparePair
model1 - Variable in class plugin.DescriptorParameters
model2 - Variable in class plugin.DescriptorParameters
mouseClicked(MouseEvent) - Method in class selection.Select_Points
mouseDragged(MouseEvent) - Method in class selection.Select_Points
mouseEntered(MouseEvent) - Method in class selection.Select_Points
mouseExited(MouseEvent) - Method in class selection.Select_Points
mouseMoved(MouseEvent) - Method in class selection.Select_Points
mousePressed(MouseEvent) - Method in class selection.Select_Points
mouseReleased(MouseEvent) - Method in class selection.Select_Points
myURL - Static variable in class plugin.Descriptor_based_series_registration

N

normalizeImage(Image<FloatType>, float[]) - Static method in class process.Matching: Normalizes an imglib1 image in-place to the range [0, 1].
numNeighbors - Variable in class plugin.DescriptorParameters

O

offset - Static variable in class plugin.Descriptor_based_series_registration
oneModelPerChannel - Static variable in class plugin.Descriptor_based_series_registration
optimizeRoi(Roi, ImageProcessor) - Method in class selection.Select_Points
orientation - Static variable in class plugin.Descriptor_based_registration
outAll - Static variable in class process.Matching
OverlayFusion - Class in process
OverlayFusion() - Constructor for class process.OverlayFusion

P

pairwiseMatching(ArrayList<PointMatch>, ArrayList<DifferenceOfGaussianPeak<FloatType>>, ArrayList<DifferenceOfGaussianPeak<FloatType>>, float, float, DescriptorParameters, String) - Static method in class process.Matching
paperURL - Static variable in class plugin.Descriptor_based_series_registration
Particle - Class in process
Particle(int, DifferenceOfGaussianPeak<FloatType>, float) - Constructor for class process.Particle
peak - Variable in class process.Particle
PeakSort(DifferenceOfGaussianPeak<FloatType>) - Constructor for class process.Matching.PeakSort
performIteration(ArrayList<InvertibleBoundable>, ArrayList<ArrayList<DifferenceOfGaussianPeak<FloatType>>>, int, DescriptorParameters, float) - Static method in class process.Matching: Computes one iteration and updates the lastModels ArrayList with the new models
plugin - package plugin
printAllSimilarities - Static variable in class plugin.DescriptorParameters
process - package process

R

range - Variable in class plugin.DescriptorParameters
ransacParameters - Static variable in class plugin.DescriptorParameters: All RANSAC parameters (max epsilon, min inlier ratio, min num matches, iterations, multi-consensus, max trust, filter-RANSAC).
ransacThreshold - Variable in class plugin.DescriptorParameters
reApply - Variable in class plugin.DescriptorParameters
redundancy - Variable in class plugin.DescriptorParameters
region - Variable in class plugin.DescriptorParameters
regularize - Variable in class plugin.DescriptorParameters
removeBackground(IterableInterval<FloatType>) - Static method in class process.GaussianMaskFit
removeColoredOverlays(ImagePlus, int, Color) - Method in class selection.Select_Points
removeInvalidAndCollectStatistics(ArrayList<DifferenceOfGaussianPeak<FloatType>>) - Static method in class process.Matching
RemoveItemListener - Class in selection
RemoveItemListener(Select_Points, List, List, ArrayList<ExtendedPointMatch>) - Constructor for class selection.RemoveItemListener
resetW() - Method in class process.Particle
restoreBackground(IterableInterval<FloatType>, double) - Static method in class process.GaussianMaskFit
restoreCoordinates() - Method in class process.Particle: Restores the local and global coordinates from the peak that feeded it initially, they might have been changed by applying a model during the optimization
resultChoices - Static variable in class plugin.Descriptor_based_series_registration
roi1 - Variable in class plugin.DescriptorParameters
roi2 - Variable in class plugin.DescriptorParameters
run(String) - Method in class plugin.Descriptor_based_registration
run(String) - Method in class plugin.Descriptor_based_series_registration
run(String) - Method in class plugin.Manual_Landmark_Selection

S

SaveListener - Class in selection
SaveListener(Frame, ArrayList<ExtendedPointMatch>) - Constructor for class selection.SaveListener
Select_Points - Class in selection: This is a template for a generic tool using Fiji's AbstractTool infrastructure.
Select_Points(ImagePlus, ImagePlus) - Constructor for class selection.Select_Points
selection - package selection
set(float, int) - Method in class process.Particle
setDiameter(float) - Method in class process.Particle
setDistance(double) - Method in class process.Particle
setGaussian(IterableInterval<FloatType>, double[], double[]) - Static method in class process.GaussianMaskFit
setPointRois(ImagePlus, ImagePlus, ArrayList<PointMatch>) - Static method in class process.Matching
setPointsRois - Variable in class plugin.DescriptorParameters
setUseW(boolean) - Method in class process.Particle
setW(float[]) - Method in class process.Particle
setWeight(double) - Method in class process.Particle
showOptionDialog() - Method in class selection.Select_Points
sigma - Variable in class plugin.DescriptorParameters
sigma1 - Variable in class plugin.DescriptorParameters
sigma2 - Variable in class plugin.DescriptorParameters
significance - Variable in class plugin.DescriptorParameters
silent - Variable in class plugin.DescriptorParameters
similarOrientation - Variable in class plugin.DescriptorParameters
sliceChanged(ImagePlus) - Method in class selection.Select_Points
storeModels - Variable in class plugin.DescriptorParameters
storePoints - Variable in class plugin.DescriptorParameters
switchZCinXYCZT(ImagePlus) - Static method in class process.OverlayFusion: Rearranges an ImageJ XYCZT Hyperstack into XYZCT without wasting memory for processing 3d images as a chunk, if it is already XYZCT it will shuffle it back to XYCZT
switchZTinXYCZT(ImagePlus) - Static method in class process.OverlayFusion: Rearranges an ImageJ XYCTZ Hyperstack into XYCZT without wasting memory for processing 3d images as a chunk, if it is already XYCTZ it will shuffle it back to XYCZT

T

testRegistrationCompatibility(ImagePlus, ImagePlus) - Static method in class plugin.Descriptor_based_registration
threshold - Variable in class plugin.DescriptorParameters
toolToggled(boolean) - Method in class selection.Select_Points
toString() - Method in class process.Particle
transformationModels2d - Variable in class plugin.Descriptor_based_registration
transformationModels2d - Variable in class plugin.Descriptor_based_series_registration
transformationModels3d - Variable in class plugin.Descriptor_based_registration
transformationModels3d - Variable in class plugin.Descriptor_based_series_registration

U

useSizeOfFirstImage - Static variable in class process.OverlayFusion
useW - Variable in class process.Particle

W

weight - Variable in class process.Particle
writePoints(ArrayList<PointMatch>, DescriptorParameters, Model<?>, PrintWriter) - Static method in class process.Matching

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