Deprecated API

Contents

• Interfaces
• Classes
• Enums
• Methods
• Constructors

Interfaces

Interface	Description
inra.ijpb.binary.geodesic.GeodesicDiameter	since 1.3.5, use inra.ijpb.measure.region2d.GeodesicDiameter instead
inra.ijpb.binary.geodesic.GeodesicDiameter3D	since 1.3.5, use inra.ijpb.measure.region3d.GeodesicDiameter3D instead

Classes

Class	Description
inra.ijpb.binary.ChamferWeights3D.FloatOffset
inra.ijpb.binary.ChamferWeights3D.ShortOffset
inra.ijpb.binary.ConnectedComponents	all methods have been moved to the BinaryImages class
inra.ijpb.binary.distmap.DistanceTransform3D4WeightsFloat	replaced by ChamferDistanceTransform3DFloat (since 1.5.0)
inra.ijpb.binary.distmap.DistanceTransform3D4WeightsShort	replaced by ChamferDistanceTransform3DShort (since 1.5.0)
inra.ijpb.binary.distmap.DistanceTransform3DFloat	replaced by ChamferDistanceTransform3DFloat (since 1.5.0)
inra.ijpb.binary.distmap.DistanceTransform3DShort	replaced by ChamferDistanceTransform3DShort (since 1.5.0)
inra.ijpb.binary.distmap.DistanceTransform3x3Float	replaced by ChamferDistanceTransform2DFloat (since 1.5.0)
inra.ijpb.binary.distmap.DistanceTransform3x3Short	replaced by ChamferDistanceTransform2DShort (since 1.5.0)
inra.ijpb.binary.distmap.DistanceTransform5x5Float	replaced by ChamferDistanceTransform2DFloat (since 1.5.0)
inra.ijpb.binary.distmap.DistanceTransform5x5Short	replaced by ChamferDistanceTransform2DShort (since 1.5.0)
inra.ijpb.binary.geodesic.GeodesicDiameter3DFloat	replaced by inra.ijpb.measure.region3d.GeodesicDiameter3D
inra.ijpb.binary.geodesic.GeodesicDiameterFloat	since 1.3.5, use inra.ijpb.measure.region2d.GeodesicDiameter instead
inra.ijpb.binary.geodesic.GeodesicDiameterShort	since 1.3.5, use inra.ijpb.measure.region2d.GeodesicDiameter instead
inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat5x5	replaced by GeodesicDistanceTransformFloat (since 1.4.4)
inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort5x5	replaced by GeodesicDistanceTransformShort (since 1.5.0)
inra.ijpb.label.distmap.DistanceTransform3DFloat	replaced by ChamferDistanceTransform3DFloat (since 1.4.4)
inra.ijpb.label.distmap.DistanceTransform3DShort	replaced by ChamferDistanceTransform3DShort (since 1.4.4)
inra.ijpb.label.distmap.LabelDilation2DShort	replaced by inra.ijpb.label.filter.ChamferLabelDilation2DShort
inra.ijpb.label.distmap.LabelDilation3D4WShort	replaced by LabelDilation3DShort (since 1.4.4)
inra.ijpb.label.distmap.LabelDilation3DShort	replaced by inra.ijpb.label.filter.ChamferLabelDilation3DShort
inra.ijpb.label.distmap.LabelDilationShort5x5	replaced by LabelDilation2DShort (since 1.5.0)
inra.ijpb.measure.GeometricMeasures2D	use IntrinsicVolumes2D instead
inra.ijpb.measure.GeometricMeasures3D	use IntrinsicVolumes3D instead
inra.ijpb.measure.region2d.InertiaEllipse	Replaced by EquivalentEllipse (since 1.4.2)
inra.ijpb.measure.region3d.InertiaEllipsoid	replaced by EquivalentEllipsoid (since 1.4.1)
inra.ijpb.measure.Vector3d	since 1.3.6, replaced by inra.ijpb.geometry.Vector3D
inra.ijpb.morphology.GeodesicReconstruction	replaced by the Reconstruction class (2017.07.25)
inra.ijpb.morphology.GeodesicReconstruction3D	replaced by the Reconstruction class (2017.07.25)
inra.ijpb.morphology.LabelImages	as from 2014.11.03, replaced by class inra.ijpb.label.LabelImages
inra.ijpb.plugins.GeodesicDistanceMap3D	use GeodesicDistanceMap3DPlugin instead
inra.ijpb.plugins.InertiaEllipsePlugin	replaced by EquivalentEllipsePlugin (since 1.4.2).
inra.ijpb.plugins.InertiaEllipsoidPlugin	replaced by EquivalentEllipsoidPlugin (since 1.4.1)
inra.ijpb.plugins.ParticleAnalysis3DPlugin	replaced by AnalyzeRegions3D
inra.ijpb.plugins.RegionMorphometryPlugin	replaced by AnalyzeRegions
inra.ijpb.util.ColorMaps	use inra.ijpb.color.ColorMaps instead (v1.4.3)

Enums

Enum	Description
inra.ijpb.binary.ChamferWeights	replaced by inra.ijpb.binary.distmap.ChamferMask2D (since 1.5.0)
inra.ijpb.binary.ChamferWeights3D	replaced by inra.ijpb.binary.distmap.ChamferMask2D (since 1.5.0)
inra.ijpb.util.CommonColors	use inra.ijpb.color.CommonColors instead (v1.4.3)

Methods

Method	Description
inra.ijpb.binary.ConnectedComponents.computeLabels(ImagePlus, int, int)	replaced by BinaryImages.componentsLabeling(ImagePlus, int, int)
inra.ijpb.binary.ConnectedComponents.computeLabels(ImageStack, int, int)	replaced by BinaryImages.componentsLabeling(ImageStack, int, int)
inra.ijpb.binary.ConnectedComponents.computeLabels(ImageProcessor, int, int)	replaced by BinaryImages.componentsLabeling(ImageProcessor, int, int)
inra.ijpb.data.image.Images3D.isSameSize(ImageStack, ImageStack)	replaced by ImageUtils.isSameSize(...)
inra.ijpb.data.image.Images3D.isSameType(ImageStack, ImageStack)	replaced by ImageUtils.isSameType(...)
inra.ijpb.data.image.Images3D.print(ImageStack)	replaced by ImageUtils.print(ImageStack)
inra.ijpb.data.image.Images3D.replaceValue(ImagePlus, double, double)	replaced by ImageUtils.replaceValue(ImagePlus, double, double)
inra.ijpb.label.LabelImages.findPositionOfMaxValues(ImageProcessor, ImageProcessor, int[])	use LavelValues.findPositionOfMaxValues instead
inra.ijpb.label.LabelImages.findPositionOfMinValues(ImageProcessor, ImageProcessor, int[])	use LavelValues.findPositionOfMinValues instead
inra.ijpb.measure.GeometricMeasures2D.analyzeRegions(ImageProcessor, double[])
inra.ijpb.measure.GeometricMeasures2D.analyzeRegions(ImageProcessor, double[], int)
inra.ijpb.measure.GeometricMeasures2D.area(ImageProcessor, int[], double[])	use IntrinsicVolumes2D.areas(ImageProcessor, int[], Calibration) instead
inra.ijpb.measure.GeometricMeasures2D.boundingBox(ImageProcessor)	use BoundingBox class instead
inra.ijpb.measure.GeometricMeasures2D.boundingBox(ImageProcessor, int[])	use BoundingBox class instead
inra.ijpb.measure.GeometricMeasures2D.centroids(ImageProcessor, int[])	replaced by Centroid.centroids
inra.ijpb.measure.GeometricMeasures2D.croftonPerimeter(ImageProcessor, double[], int)	use analyzeRegions instead
inra.ijpb.measure.GeometricMeasures2D.croftonPerimeter(ImageProcessor, int[], double[], int)	replaced by IntrinsicVolumes2D
inra.ijpb.measure.GeometricMeasures2D.croftonPerimeterD2(ImageProcessor, int[], double[])	replaced by IntrinsicVolumes2D
inra.ijpb.measure.GeometricMeasures2D.croftonPerimeterD4(ImageProcessor, int[], double[])	replaced by IntrinsicVolumes2D
inra.ijpb.measure.GeometricMeasures2D.inertiaEllipse(ImageProcessor)	use inra.ijpb.measure.region2d.InertiaEllipse instead
inra.ijpb.measure.GeometricMeasures2D.maximumInscribedCircle(ImageProcessor)	use class inra.ijpb.measure.region2d.largestInscribedCircle instead
inra.ijpb.measure.GeometricMeasures2D.maximumInscribedCircle(ImageProcessor, double[])	use class inra.ijpb.measure.region2d.largestInscribedCircle instead
inra.ijpb.measure.GeometricMeasures2D.particleArea(ImageProcessor, int)
inra.ijpb.measure.GeometricMeasures2D.perimeterDensity(ImageProcessor, double[], int)
inra.ijpb.measure.GeometricMeasures3D.boundingBox(ImageStack)	use BoundingBox3D instead
inra.ijpb.measure.GeometricMeasures3D.centroids(ImageStack, int[])	use Centroid3D.centroids(ImageStack, int[]) instead
inra.ijpb.measure.GeometricMeasures3D.computeEllipsoidElongations(double[][])	use Ellipsoid.elongations(Ellipsoid[]) instead
inra.ijpb.measure.GeometricMeasures3D.computeSphericity(double[], double[])	use IntrinsicVolumes3D instead
inra.ijpb.measure.GeometricMeasures3D.eulerNumber(ImageStack, int[], int)	use IntrinsicVolumes3D.eulerNumbers(ImageStack, int[], int) instead
inra.ijpb.measure.GeometricMeasures3D.inertiaEllipsoid(ImageStack)	use InertiaEllipsoid instead
inra.ijpb.measure.GeometricMeasures3D.inertiaEllipsoid(ImageStack, double[])	use InertiaEllipsoid instead
inra.ijpb.measure.GeometricMeasures3D.inertiaEllipsoid(ImageStack, int[], double[])	use InertiaEllipsoid instead
inra.ijpb.measure.GeometricMeasures3D.maximumInscribedSphere(ImageStack, double[])	use LargestInscribedBall instead
inra.ijpb.measure.GeometricMeasures3D.surfaceAreaCrofton(ImageStack, int[], double[], int)	use IntrinsicVolumes3D instead
inra.ijpb.measure.GeometricMeasures3D.surfaceAreaCrofton(ImageStack, int, double[], int)	use IntrinsicVolumes3D instead
inra.ijpb.measure.GeometricMeasures3D.surfaceAreaCroftonD3(ImageStack, double[])	use IntrinsicVolumes3D instead
inra.ijpb.measure.GeometricMeasures3D.volume(ImageStack, double[])	used IntrinsicVolumes3D instead
inra.ijpb.measure.GeometricMeasures3D.volume(ImageStack, int[], double[])	use IntrinsicVolumes3D instead
inra.ijpb.measure.region2d.GeodesicDiameter.setChamferWeights(float[])
inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.areaLut(Calibration)	use IntrinsicVolumes2DUtils instead
inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.computeCircularities(IntrinsicVolumesAnalyzer2D.Result[])
inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.eulerNumberIntLut(int)	use IntrinsicVolumes2DUtils instead
inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.eulerNumberLut(int)	use IntrinsicVolumes2DUtils instead
inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.perimeterLut(Calibration, int)	use IntrinsicVolumes2DUtils instead
inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D.eulerNumberLut(int)	use IntrinsicVolumes3DUtils instead
inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D.meanBreadthLut(Calibration, int, int)	use IntrinsicVolumes3DUtils instead
inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D.surfaceAreaLut(Calibration, int)	use IntrinsicVolumes3DUtils instead
inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D.volumeLut(Calibration)	use IntrinsicVolumes3DUtils instead
inra.ijpb.morphology.FloodFill.floodFill(ImageStack, int, int, int, double, int)	use FLoodFill3D.floodFill instead
inra.ijpb.morphology.FloodFill.floodFill(ImageStack, int, int, int, int, int)	use FloodFill3D.floodFill instead.
inra.ijpb.morphology.FloodFill.floodFill(ImageStack, int, int, int, ImageStack, int, int)	use FloodFill3D.floodFill instead
inra.ijpb.morphology.FloodFill.floodFillFloat(ImageStack, int, int, int, ImageStack, float, int)	use FloodFill3D.floodFillFloat instead
inra.ijpb.plugins.AnalyzeRegions.process(ImagePlus)	replaced by static process(ImagePlus, Features) method
inra.ijpb.plugins.ExtendBordersPlugin.exec(ImagePlus, int, int, int, int, BorderManager)
inra.ijpb.plugins.ExtendBordersPlugin.process(ImageStack, int, int, int, int, int, int, BorderManager3D)	replaced by inra.ijpb.data.border.BorderManager3D.addBorders(...) method
inra.ijpb.plugins.ExtendBordersPlugin.process(ImageProcessor, int, int, int, int, BorderManager)	replaced by inra.ijpb.data.border.BorderManager.addBorders(...) method
inra.ijpb.plugins.GeodesicDistanceMap3DPlugin.process(ImagePlus, ImagePlus, String, float[], boolean)
inra.ijpb.plugins.GeodesicDistanceMap3DPlugin.process(ImageStack, ImageStack, float[], boolean)
inra.ijpb.plugins.GeodesicDistanceMapPlugin.exec(ImagePlus, ImagePlus, String, float[])
inra.ijpb.plugins.GeodesicDistanceMapPlugin.exec(ImagePlus, ImagePlus, String, float[], boolean)	use process method instead
inra.ijpb.plugins.GeodesicDistanceMapPlugin.exec(ImagePlus, ImagePlus, String, short[], boolean)	use process method instead
inra.ijpb.plugins.GeodesicDistanceMapPlugin.process(ImagePlus, ImagePlus, String, float[], boolean)
inra.ijpb.plugins.GeodesicDistanceMapPlugin.process(ImageProcessor, ImageProcessor, float[], boolean)
inra.ijpb.plugins.InteractiveGeodesicDistanceMap.process(ImageProcessor, Roi, float[], boolean)
inra.ijpb.plugins.InteractiveGeodesicDistanceMap.process(ImageProcessor, Roi, short[], boolean)
inra.ijpb.plugins.MaxInscribedCirclePlugin.exec(ImagePlus, short[])	replaced by process method
inra.ijpb.plugins.MaxInscribedCirclePlugin.process(ImagePlus, short[])	use LargestInscribedCircle class instead
inra.ijpb.plugins.MicrostructureAnalysisPlugin.exec(ImagePlus, int)	specify porosity
inra.ijpb.plugins.MicrostructureAnalysisPlugin.exec(ImagePlus, int, boolean)	use process method instead
inra.ijpb.plugins.MorphologicalFilterPlugin.exec(ImagePlus, Morphology.Operation, Strel)	use the process method instead
inra.ijpb.plugins.MorphologicalSegmentation.segment(String, String, String, String)	the priority queue method is now the only one
inra.ijpb.plugins.RegionMorphometryPlugin.exec(ImagePlus, int)
inra.ijpb.util.IJUtils.printImage(ImageProcessor)	use ImageUtils.print(ImageProcessor) instead
inra.ijpb.watershed.MarkerControlledWatershedTransform2D.applyWithSortedList()	The algorithm with a sorted list does not visit the pixels based on their h value and proximity to markers so it is not a true watershed method.
inra.ijpb.watershed.MarkerControlledWatershedTransform2D.applyWithSortedListAndDams()	The algorithm with a sorted list does not visit the pixels based on their h value and proximity to markers so it is not a true watershed method.
inra.ijpb.watershed.MarkerControlledWatershedTransform2D.getAnimationSortedList()	The algorithm with a sorted list does not visit the pixels based on their h value and proximity to markers so it is not a true watershed method.
inra.ijpb.watershed.MarkerControlledWatershedTransform2D.getAnimationSortedListAndDams()	The algorithm with a sorted list does not visit the pixels based on their h value and proximity to markers so it is not a true watershed method.
inra.ijpb.watershed.MarkerControlledWatershedTransform3D.applyWithSortedList()	The algorithm with a sorted list does not visit the voxels based on their h value and proximity to markers so it is not a true watershed method.
inra.ijpb.watershed.MarkerControlledWatershedTransform3D.applyWithSortedListAndDams()	The algorithm with a sorted list does not visit the voxels based on their h value and proximity to markers so it is not a true watershed method.

Constructors

Constructor	Description
inra.ijpb.binary.geodesic.GeodesicDiameter3DFloat(ChamferWeights3D)	new uses ChamferMask3D (since 1.4.4)
inra.ijpb.binary.geodesic.GeodesicDistanceTransform3DFloat(float[])
inra.ijpb.binary.geodesic.GeodesicDistanceTransform3DFloat(float[], boolean)
inra.ijpb.binary.geodesic.GeodesicDistanceTransform3DFloat(ChamferWeights3D, boolean)
inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat(float[])
inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat(float[], boolean)
inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort(short[])	should use an instance of ChamferMask2D at construction
inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort(short[], boolean)	should use an instance of ChamferMask2D at construction
inra.ijpb.measure.region2d.GeodesicDiameter(float[])
inra.ijpb.measure.region2d.GeodesicDiameter(ChamferWeights)	ChamferWeights is replaced by ChamferMask2D (since 1.4.4)