public class IntrinsicVolumes3D extends Object
IntrinsicVolumes2D
,
IntrinsicVolumesAnalyzer3D
Modifier and Type | Method and Description |
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static double |
eulerNumber(ij.ImageStack image,
int conn)
Measures the Euler number of the region within the binary image, using
the specified connectivity.
|
static double |
eulerNumberDensity(ij.ImageStack image,
ij.measure.Calibration calib,
int conn)
Measures the Euler number density of the foreground region within a
binary image, using the specified connectivity.
|
static double[] |
eulerNumbers(ij.ImageStack image,
int[] labels,
int conn)
Measures the Euler number of each region given in the "labels" argument,
using the specified connectivity.
|
static double |
interfaceSurfaceArea(ij.ImageStack image,
int label1,
int label2,
ij.measure.Calibration calib,
int nDirs)
Measures the surface area of the interface between two regions in a 3D label image.
|
static double |
meanBreadth(ij.ImageStack image,
ij.measure.Calibration calib,
int nDirs,
int conn2d)
Measures the mean breadth of a single region within a 3D binary image.
|
static double |
meanBreadthDensity(ij.ImageStack image,
ij.measure.Calibration calib,
int nDirs,
int conn2d)
Measures the mean breadth density of a single region within a 3D binary image.
|
static double[] |
meanBreadths(ij.ImageStack image,
int[] labels,
ij.measure.Calibration calib,
int nDirs,
int conn2d)
Measures the mean breadth of each region within a label image.
|
static double |
samplingVolume(ij.ImageStack image,
ij.measure.Calibration calib)
Returns the "inner volume" of the 3D image, i.e.
|
static double[] |
sphericity(double[] volumes,
double[] surfaces)
Helper function that computes the sphericity index of 3D particles, based
on the value of volume and surface area.
|
static double |
sphericity(double volume,
double surface)
Helper function that computes the sphericity index of 3D particles, based
on the value of volume and surface area.
|
static double |
surfaceArea(ij.ImageStack image,
ij.measure.Calibration calib,
int nDirs)
Measures the surface area of a single region within a 3D binary image.
|
static double |
surfaceAreaDensity(ij.ImageStack image,
ij.measure.Calibration calib,
int nDirs)
Measures the surface area density of a single region within a 3D binary image.
|
static double[] |
surfaceAreas(ij.ImageStack image,
int[] labels,
ij.measure.Calibration calib,
int nDirs)
Measures the surface area of each region within a label image.
|
static double |
volume(ij.ImageStack image,
ij.measure.Calibration calib)
Measures the volume of a single region within a 3D binary image.
|
static double |
volumeDensity(ij.ImageStack image)
Measures the volume density of a single region within a 3D binary image.
|
static double[] |
volumes(ij.ImageStack labelImage,
int[] labels,
ij.measure.Calibration calib)
Measures the volume of each region within a 3D label image.
|
public static final double volume(ij.ImageStack image, ij.measure.Calibration calib)
image
- the binary image containing the regioncalib
- the spatial calibration of the imageBinaryImages.countForegroundVoxels(ImageStack)
public static final double[] volumes(ij.ImageStack labelImage, int[] labels, ij.measure.Calibration calib)
labelImage
- image containing the label of each regionlabels
- the set of labels for which volume has to be computedcalib
- the spatial calibration of the imagepublic static final double volumeDensity(ij.ImageStack image)
image
- the binary image containing the regionpublic static final double interfaceSurfaceArea(ij.ImageStack image, int label1, int label2, ij.measure.Calibration calib, int nDirs)
image
- the 3D image containing the label of each particlelabel1
- the label of the first regionlabel2
- the label of the second regioncalib
- the spatial calibration of the imagenDirs
- the number of directions to consider, either 3 or 13InterfaceSurfaceArea
public static final double surfaceArea(ij.ImageStack image, ij.measure.Calibration calib, int nDirs)
image
- image containing the label of each particlecalib
- the spatial calibration of the imagenDirs
- the number of directions to consider, either 3 or 13public static final double[] surfaceAreas(ij.ImageStack image, int[] labels, ij.measure.Calibration calib, int nDirs)
image
- image containing the label of each particlelabels
- the set of labels in the imagecalib
- the spatial calibration of the imagenDirs
- the number of directions to consider, either 3 or 13public static final double surfaceAreaDensity(ij.ImageStack image, ij.measure.Calibration calib, int nDirs)
image
- image containing the label of each particlecalib
- the spatial calibration of the imagenDirs
- the number of directions to consider, either 3 or 13public static final double sphericity(double volume, double surface)
sphericity = 36 * PI * V^2 / S^3
A perfect ball would have a sphericity index close to 1, a very complex
particle will present a lower sphericity index.volume
- the volume of a regionsurface
- the surface area of a regionsurfaceAreas(ij.ImageStack, int[], ij.measure.Calibration, int)
,
volumes(ij.ImageStack, int[], ij.measure.Calibration)
public static final double[] sphericity(double[] volumes, double[] surfaces)
sphericity = 36 * PI * V^2 / S^3
A perfect ball would have a sphericity index close to 1, a very complex
particle will present a lower sphericity index.volumes
- the volume of each particlesurfaces
- the surface area of each particlesurfaceAreas(ij.ImageStack, int[], ij.measure.Calibration, int)
,
volumes(ij.ImageStack, int[], ij.measure.Calibration)
public static final double meanBreadth(ij.ImageStack image, ij.measure.Calibration calib, int nDirs, int conn2d)
image
- image containing the label of each particlecalib
- the spatial calibration of the imagenDirs
- the number of directions to consider, either 3 or 13conn2d
- the connectivity to use on planar sections with square tiles (either 4 or 8)public static final double[] meanBreadths(ij.ImageStack image, int[] labels, ij.measure.Calibration calib, int nDirs, int conn2d)
image
- image containing the label of each regionlabels
- the set of labels in the imagecalib
- the spatial calibration of the imagenDirs
- the number of directions to consider, either 3 or 13conn2d
- the connectivity to use on planar sections with square tiles (either 4 or 8)public static final double meanBreadthDensity(ij.ImageStack image, ij.measure.Calibration calib, int nDirs, int conn2d)
image
- image containing a binary regioncalib
- the spatial calibration of the imagenDirs
- the number of directions to consider, either 3 or 13conn2d
- the connectivity to use on planar sections with square tiles (either 4 or 8)public static final double eulerNumber(ij.ImageStack image, int conn)
image
- the input 3D binary imageconn
- the connectivity to use (either 6 or 26)public static final double[] eulerNumbers(ij.ImageStack image, int[] labels, int conn)
image
- the input 3D label image (with labels having integer values)labels
- the set of unique labels in imageconn
- the connectivity to use (either 6 or 26)public static final double eulerNumberDensity(ij.ImageStack image, ij.measure.Calibration calib, int conn)
image
- the input 3D binary imagecalib
- the spatial calibration of the imageconn
- the connectivity to use (either 6 or 26)public static final double samplingVolume(ij.ImageStack image, ij.measure.Calibration calib)
image
- the input 3D imagecalib
- the spatial calibration of the imageCopyright © 2014–2023 INRA-IJPB Modeling and Digital Imaging lab. All rights reserved.