Deprecated API

Contents

• Deprecated Interfaces
• Deprecated Classes
• Deprecated Enums
• Deprecated Methods
• Deprecated Constructors

Deprecated Interfaces

Interface and 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

Deprecated Classes

Class and Description
inra.ijpb.binary.ChamferWeights3D.FloatOffset
inra.ijpb.binary.ChamferWeights3D.ShortOffset
inra.ijpb.util.ColorMaps use inra.ijpb.color.ColorMaps instead (v1.4.3)
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.label.distmap.DistanceTransform3DFloat replaced by ChamferDistanceTransform3DFloat (since 1.4.4)
inra.ijpb.binary.distmap.DistanceTransform3DShort replaced by ChamferDistanceTransform3DShort (since 1.5.0)
inra.ijpb.label.distmap.DistanceTransform3DShort replaced by ChamferDistanceTransform3DShort (since 1.4.4)
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.plugins.GeodesicDistanceMap3D use GeodesicDistanceMap3DPlugin 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.morphology.GeodesicReconstruction replaced by the Reconstruction class (2017.07.25)
inra.ijpb.morphology.GeodesicReconstruction3D replaced by the Reconstruction class (2017.07.25)
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.plugins.InertiaEllipsePlugin replaced by EquivalentEllipsePlugin (since 1.4.2).
inra.ijpb.measure.region3d.InertiaEllipsoid replaced by EquivalentEllipsoid (since 1.4.1)
inra.ijpb.plugins.InertiaEllipsoidPlugin replaced by EquivalentEllipsoidPlugin (since 1.4.1)
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.morphology.LabelImages as from 2014.11.03, replaced by class inra.ijpb.label.LabelImages
inra.ijpb.plugins.ParticleAnalysis3DPlugin replaced by AnalyzeRegions3D
inra.ijpb.plugins.RegionMorphometryPlugin replaced by AnalyzeRegions
inra.ijpb.measure.Vector3d since 1.3.6, replaced by inra.ijpb.geometry.Vector3D

Deprecated Enums

Enum and 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)

Deprecated Methods

Method and Description
inra.ijpb.measure.GeometricMeasures2D.analyzeRegions(ImageProcessor, double[])
inra.ijpb.measure.GeometricMeasures2D.analyzeRegions(ImageProcessor, double[], int)
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.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.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.
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.measure.GeometricMeasures2D.area(ImageProcessor, int[], double[]) use IntrinsicVolumes2D.areas(ImageProcessor, int[], Calibration) instead
inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.areaLut(Calibration) use IntrinsicVolumes2DUtils 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.GeometricMeasures3D.boundingBox(ImageStack) use BoundingBox3D instead
inra.ijpb.measure.GeometricMeasures2D.centroids(ImageProcessor, int[]) replaced by Centroid.centroids
inra.ijpb.measure.GeometricMeasures3D.centroids(ImageStack, int[]) use Centroid3D.centroids(ImageStack, int[]) instead
inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.computeCircularities(IntrinsicVolumesAnalyzer2D.Result[])
inra.ijpb.measure.GeometricMeasures3D.computeEllipsoidElongations(double[][]) use Ellipsoid.elongations(Ellipsoid[]) instead
inra.ijpb.binary.ConnectedComponents.computeLabels(ImagePlus, int, int) replaced by BinaryImages.componentsLabeling(ImagePlus, int, int)
inra.ijpb.binary.ConnectedComponents.computeLabels(ImageProcessor, int, int) replaced by BinaryImages.componentsLabeling(ImageProcessor, int, int)
inra.ijpb.binary.ConnectedComponents.computeLabels(ImageStack, int, int) replaced by BinaryImages.componentsLabeling(ImageStack, int, int)
inra.ijpb.measure.GeometricMeasures3D.computeSphericity(double[], double[]) use IntrinsicVolumes3D instead
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.GeometricMeasures3D.eulerNumber(ImageStack, int[], int) use IntrinsicVolumes3D.eulerNumbers(ImageStack, int[], int) instead
inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.eulerNumberIntLut(int) use IntrinsicVolumes2DUtils instead
inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D.eulerNumberLut(int) use IntrinsicVolumes3DUtils instead
inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.eulerNumberLut(int) use IntrinsicVolumes2DUtils instead
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.MicrostructureAnalysisPlugin.exec(ImagePlus, int) specify porosity
inra.ijpb.plugins.RegionMorphometryPlugin.exec(ImagePlus, int)
inra.ijpb.plugins.MicrostructureAnalysisPlugin.exec(ImagePlus, int, boolean) use process method instead
inra.ijpb.plugins.ExtendBordersPlugin.exec(ImagePlus, int, int, int, int, BorderManager)
inra.ijpb.plugins.MorphologicalFilterPlugin.exec(ImagePlus, Morphology.Operation, Strel) use the process method instead
inra.ijpb.plugins.MaxInscribedCirclePlugin.exec(ImagePlus, short[]) replaced by process method
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.morphology.FloodFill.floodFill(ImageStack, int, int, int, double, 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.floodFill(ImageStack, int, int, int, int, int) use FloodFill3D.floodFill instead.
inra.ijpb.morphology.FloodFill.floodFillFloat(ImageStack, int, int, int, ImageStack, float, int) use FloodFill3D.floodFillFloat instead
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.measure.GeometricMeasures2D.inertiaEllipse(ImageProcessor) use inra.ijpb.measure.region2d.InertiaEllipse 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.data.image.Images3D.isSameSize(ImageStack, ImageStack) replaced by ImageUtils.isSameSize(...)
inra.ijpb.data.image.Images3D.isSameType(ImageStack, ImageStack) replaced by ImageUtils.isSameType(...)
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.GeometricMeasures3D.maximumInscribedSphere(ImageStack, double[]) use LargestInscribedBall instead
inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D.meanBreadthLut(Calibration, int, int) use IntrinsicVolumes3DUtils instead
inra.ijpb.measure.GeometricMeasures2D.particleArea(ImageProcessor, int)
inra.ijpb.measure.GeometricMeasures2D.perimeterDensity(ImageProcessor, double[], int)
inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.perimeterLut(Calibration, int) use IntrinsicVolumes2DUtils instead
inra.ijpb.data.image.Images3D.print(ImageStack) replaced by ImageUtils.print(ImageStack)
inra.ijpb.util.IJUtils.printImage(ImageProcessor) use ImageUtils.print(ImageProcessor) instead
inra.ijpb.plugins.AnalyzeRegions.process(ImagePlus) replaced by static process(ImagePlus, Features) method
inra.ijpb.plugins.GeodesicDistanceMapPlugin.process(ImagePlus, ImagePlus, String, float[], boolean)
inra.ijpb.plugins.GeodesicDistanceMap3DPlugin.process(ImagePlus, ImagePlus, String, float[], boolean)
inra.ijpb.plugins.MaxInscribedCirclePlugin.process(ImagePlus, short[]) use LargestInscribedCircle class instead
inra.ijpb.plugins.GeodesicDistanceMapPlugin.process(ImageProcessor, ImageProcessor, float[], boolean)
inra.ijpb.plugins.ExtendBordersPlugin.process(ImageProcessor, int, int, int, int, BorderManager) replaced by inra.ijpb.data.border.BorderManager.addBorders(...) method
inra.ijpb.plugins.InteractiveGeodesicDistanceMap.process(ImageProcessor, Roi, float[], boolean)
inra.ijpb.plugins.InteractiveGeodesicDistanceMap.process(ImageProcessor, Roi, short[], boolean)
inra.ijpb.plugins.GeodesicDistanceMap3DPlugin.process(ImageStack, ImageStack, float[], boolean)
inra.ijpb.plugins.ExtendBordersPlugin.process(ImageStack, int, int, int, int, int, int, BorderManager3D) replaced by inra.ijpb.data.border.BorderManager3D.addBorders(...) method
inra.ijpb.data.image.Images3D.replaceValue(ImagePlus, double, double) replaced by ImageUtils.replaceValue(ImagePlus, double, double)
inra.ijpb.plugins.MorphologicalSegmentation.segment(String, String, String, String) the priority queue method is now the only one
inra.ijpb.measure.region2d.GeodesicDiameter.setChamferWeights(float[])
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.region3d.IntrinsicVolumesAnalyzer3D.surfaceAreaLut(Calibration, int) use IntrinsicVolumes3DUtils 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.region3d.IntrinsicVolumesAnalyzer3D.volumeLut(Calibration) use IntrinsicVolumes3DUtils instead

Deprecated Constructors

Constructor and Description
inra.ijpb.measure.region2d.GeodesicDiameter(ChamferWeights) ChamferWeights is replaced by ChamferMask2D (since 1.4.4)
inra.ijpb.measure.region2d.GeodesicDiameter(float[])
inra.ijpb.binary.geodesic.GeodesicDiameter3DFloat(ChamferWeights3D) new uses ChamferMask3D (since 1.4.4)
inra.ijpb.binary.geodesic.GeodesicDistanceTransform3DFloat(ChamferWeights3D, boolean)
inra.ijpb.binary.geodesic.GeodesicDistanceTransform3DFloat(float[])
inra.ijpb.binary.geodesic.GeodesicDistanceTransform3DFloat(float[], 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