Package net.haesleinhuepf.clij2

Class AbstractCLIJ2Plugin

java.lang.Object

net.haesleinhuepf.clij.macro.AbstractCLIJPlugin

net.haesleinhuepf.clij2.AbstractCLIJ2Plugin

All Implemented Interfaces:

PlugInFilter, net.haesleinhuepf.clij.macro.CLIJMacroPlugin, SciJavaPlugin

Direct Known Subclasses:

Absolute, AbsoluteDifference, AddImageAndScalar, AddImages, AddImagesWeighted, AdjacencyMatrixToTouchMatrix, AffineTransform2D, AffineTransform3D, ApplyVectorField2D, ApplyVectorField3D, ArgMaximumZProjection, AutomaticThreshold, AverageDistanceOfNClosestPoints, AverageDistanceOfNFarOffPoints, AverageDistanceOfTouchingNeighbors, BinaryAnd, BinaryEdgeDetection, BinaryFillHoles, BinaryNot, BinaryOr, BinarySubtract, BinaryXOr, Blur3DSliceBySlice, BottomHatBox, BottomHatSphere, BoundingBox, CenterOfMass, CentroidsOfBackgroundAndLabels, CentroidsOfLabels, Clear, ClInfo, CloseIndexGapsInLabelMap, ClosingBox, ClosingDiamond, CombineHorizontally, CombineVertically, ConcatenateStacks, ConnectedComponentsLabeling, ConvertFloat, ConvertUInt16, ConvertUInt8, Convolve, Copy, CopySlice, CountNonZeroPixels, CountNonZeroPixels2DSphere, CountNonZeroPixelsSliceBySliceSphere, CountNonZeroVoxels3DSphere, CountTouchingNeighbors, Create2D, Create3D, Crop2D, Crop3D, CustomOperation, DepthColorProjection, DetectLabelEdges, DetectMaxima2DBox, DetectMaxima3DBox, DetectMaximaBox, DetectMaximaSliceBySliceBox, DetectMinima2DBox, DetectMinima3DBox, DetectMinimaBox, DetectMinimaSliceBySliceBox, DifferenceOfGaussian2D, DifferenceOfGaussian3D, DilateBox, DilateBoxSliceBySlice, DilateSphere, DilateSphereSliceBySlice, DistanceMap, DistanceMatrixToMesh, DivideImages, Downsample2D, Downsample3D, DownsampleSliceBySliceHalfMedian, DrawBox, DrawLine, DrawSphere, EntropyBox, Equal, EqualConstant, EqualizeMeanIntensitiesOfSlices, ErodeBox, ErodeBoxSliceBySlice, ErodeSphere, ErodeSphereSliceBySlice, ExcludeLabels, ExcludeLabelsOnEdges, ExcludeLabelsOnSurface, ExcludeLabelsSubSurface, ExcludeLabelsWithValuesOutOfRange, ExcludeLabelsWithValuesWithinRange, Exponential, ExtendLabelingViaVoronoi, Flip2D, Flip3D, FloodFillDiamond, GaussianBlur2D, GaussianBlur3D, GenerateBinaryOverlapMatrix, GenerateDistanceMatrix, GenerateJaccardIndexMatrix, GenerateParametricImage, GenerateParametricImageFromResultsTableColumn, GenerateTouchCountMatrix, GenerateTouchMatrix, GetAutomaticThreshold, GetBoundingBox, GetCenterOfMass, GetDimensions, GetGPUProperties, GetJaccardIndex, GetMaximumOfAllPixels, GetMeanOfAllPixels, GetMeanOfMaskedPixels, GetMeanSquaredError, GetMinimumOfAllPixels, GetSize, GetSorensenDiceCoefficient, GetSumOfAllPixels, GetTimeTracing, GPUProperties, GradientX, GradientY, GradientZ, Greater, GreaterConstant, GreaterOrEqual, GreaterOrEqualConstant, Help, Histogram, Image2DToResultsTable, ImageToStack, InvalidateKernelCache, Invert, JaccardIndex, LabelCentroidsToPointList, LabelledSpotsToPointList, LabelSpots, LabelToMask, LabelVoronoiOctagon, LaplaceBox, LaplaceDiamond, ListAvailableGPUs, LocalThreshold, Logarithm, Mask, MaskLabel, MaskStackWithPlane, MatrixEqual, Maximum2DBox, Maximum2DSphere, Maximum3DBox, Maximum3DSphere, MaximumImageAndScalar, MaximumImages, MaximumOctagon, MaximumOfAllPixels, MaximumOfMaskedPixels, MaximumOfTouchingNeighbors, MaximumSliceBySliceSphere, MaximumXProjection, MaximumYProjection, MaximumZProjection, MaximumZProjectionBounded, Mean2DBox, Mean2DSphere, Mean3DBox, Mean3DSphere, MeanClosestSpotDistance, MeanOfAllPixels, MeanOfMaskedPixels, MeanOfPixelsAboveThreshold, MeanOfTouchingNeighbors, MeanSliceBySliceSphere, MeanSquaredError, MeanXProjection, MeanYProjection, MeanZProjection, Median2DBox, Median2DSphere, Median3DBox, Median3DSphere, MedianOfTouchingNeighbors, MedianSliceBySliceBox, MedianSliceBySliceSphere, MedianZProjection, Minimum2DBox, Minimum2DSphere, Minimum3DBox, Minimum3DSphere, MinimumDistanceOfTouchingNeighbors, MinimumImageAndScalar, MinimumImages, MinimumOctagon, MinimumOfAllPixels, MinimumOfMaskedPixels, MinimumOfTouchingNeighbors, MinimumSliceBySliceSphere, MinimumXProjection, MinimumYProjection, MinimumZProjection, MinimumZProjectionBounded, MinimumZProjectionThresholdedBounded, MultiplyImageAndCoordinate, MultiplyImageAndScalar, MultiplyImages, MultiplyImageStackWithScalars, MultiplyMatrix, MultiplyStackWithPlane, NClosestDistances, NClosestPoints, NeighborsOfNeighbors, NonzeroMaximumBox, NonzeroMaximumDiamond, NonzeroMinimumBox, NonzeroMinimumDiamond, NotEqual, NotEqualConstant, OnlyzeroOverwriteMaximumBox, OnlyzeroOverwriteMaximumDiamond, OpeningBox, OpeningDiamond, Paste2D, Paste3D, PointIndexListToMesh, PointlistToLabelledSpots, Power, PowerImages, Print, Pull, PullAsROI, PullBinary, PullLabelsToROIList, PullLabelsToROIManager, PullString, PullToCurrentSlice, PullToCurrentSliceSelection, PullToResultsTable, PullToROIManager, Push, PushArray, PushCurrentSelection, PushCurrentSlice, PushCurrentSliceSelection, PushCurrentZStack, PushResultsTable, PushResultsTableColumn, PushString, ReduceStack, Release, ReplaceIntensities, ReplaceIntensity, ReplacePixelsIfZero, ReportMemory, Resample, ResliceBottom, ResliceLeft, ResliceRadial, ResliceRadialTop, ResliceRight, ResliceTop, ResultsTableColumnToImage, ResultsTableToImage2D, Rotate2D, Rotate3D, RotateClockwise, RotateCounterClockwise, SaveAsTIF, Scale2D, Scale3D, Set, SetColumn, SetImageBorders, SetNonZeroPixelsToPixelIndex, SetPlane, SetRampX, SetRampY, SetRampZ, SetRandom, SetRow, SetWhereXequalsY, SetWhereXgreaterThanY, SetWhereXsmallerThanY, ShortestDistances, Smaller, SmallerConstant, SmallerOrEqual, SmallerOrEqualConstant, Sobel, SorensenDiceCoefficient, SpotsToPointList, SquaredDifference, StandardDeviationOfAllPixels, StandardDeviationOfMaskedPixels, StandardDeviationOfTouchingNeighbors, StandardDeviationZProjection, StartTimeTracing, StatisticsOfBackgroundAndLabelledPixels, StatisticsOfImage, StatisticsOfLabelledPixels, StopTimeTracing, SubtractImageFromScalar, SubtractImages, SumImageSliceBySlice, SumOfAllPixels, SumXProjection, SumYProjection, SumZProjection, Threshold, ThresholdDefault, ThresholdHuang, ThresholdIJ_IsoData, ThresholdIntermodes, ThresholdIsoData, ThresholdLi, ThresholdMaxEntropy, ThresholdMean, ThresholdMinError, ThresholdMinimum, ThresholdMoments, ThresholdOtsu, ThresholdPercentile, ThresholdRenyiEntropy, ThresholdShanbhag, ThresholdTriangle, ThresholdYen, TopHatBox, TopHatSphere, TouchMatrixToAdjacencyMatrix, TouchMatrixToMesh, Translate2D, Translate3D, TransposeXY, TransposeXZ, TransposeYZ, UndefinedToZero, VarianceOfAllPixels, VarianceOfMaskedPixels, VoronoiLabeling, VoronoiOctagon, Watershed, WriteValuesToPositions

public abstract class AbstractCLIJ2Plugin
extends net.haesleinhuepf.clij.macro.AbstractCLIJPlugin

Field Summary

Fields inherited from class net.haesleinhuepf.clij.macro.AbstractCLIJPlugin

args, clij, default_values, name

Fields inherited from interface ij.plugin.filter.PlugInFilter

CONVERT_TO_FLOAT, DOES_16, DOES_32, DOES_8C, DOES_8G, DOES_ALL, DOES_RGB, DOES_STACKS, DONE, FINAL_PROCESSING, KEEP_THRESHOLD, NO_CHANGES, NO_IMAGE_REQUIRED, NO_UNDO, NO_UNDO_RESET, PARALLELIZE_IMAGES, PARALLELIZE_STACKS, ROI_REQUIRED, SNAPSHOT, STACK_REQUIRED, SUPPORTS_MASKING

Constructor Summary

Constructors

Constructor	Description
AbstractCLIJ2Plugin()

Method Summary

Modifier and Type	Method	Description
CLIJ2	getCLIJ2()
void	setClij(net.haesleinhuepf.clij.CLIJ clij)
void	setCLIJ2(CLIJ2 clij2)

Methods inherited from class net.haesleinhuepf.clij.macro.AbstractCLIJPlugin

asBoolean, asFloat, asInteger, containsCLBufferArguments, containsCLImageArguments, createOutputBufferFromSource, getDefaultValues, getImageVariableName, getName, imageJ2Args, imageJArgs, openCLBufferArgs, openCLImageArgs, releaseBuffers, releaseImages, run, setArgs, setup

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.haesleinhuepf.clij.macro.CLIJMacroPlugin

getParameterHelpText

Constructor Detail

AbstractCLIJ2Plugin

public AbstractCLIJ2Plugin()

Method Detail

setClij

public void setClij(net.haesleinhuepf.clij.CLIJ clij)

Specified by:

setClij in interface net.haesleinhuepf.clij.macro.CLIJMacroPlugin

Overrides:

setClij in class net.haesleinhuepf.clij.macro.AbstractCLIJPlugin

setCLIJ2

public void setCLIJ2(CLIJ2 clij2)

getCLIJ2

public CLIJ2 getCLIJ2()