@Deprecated public class GeometricMeasures3D extends Object
Example of code:
ImageStack labelImage = ...
int[] labels = LabelImages.findAllLabels(image);
double[] resol = new double[]{1, 1, 1};
double[][] ellipsoids = GeometricMeasures3D.inertiaEllipsoid(labelImage,
labels, resol);
double[][] elongations = GeometricMeasures3D.computeEllipsoidElongations(ellipsoids);
Modifier and Type | Method and Description |
---|---|
static ij.measure.ResultsTable |
boundingBox(ij.ImageStack labelImage)
Deprecated.
use BoundingBox3D instead
|
static double[][] |
boundingBox(ij.ImageStack labelImage,
int[] labels)
Deprecated.
Computes bounding box of each label in input stack and returns the result
as an array of double for each label.
|
static double[][] |
centroids(ij.ImageStack labelImage,
int[] labels)
Deprecated.
use
Centroid3D.centroids(ImageStack, int[]) instead |
static double[][] |
computeEllipsoidElongations(double[][] ellipsoids)
Deprecated.
use
Ellipsoid.elongations(Ellipsoid[]) instead |
static double[] |
computeSphericity(double[] volumes,
double[] surfaces)
Deprecated.
use IntrinsicVolumes3D instead
|
static double[] |
eulerNumber(ij.ImageStack image,
int[] labels,
int conn)
Deprecated.
|
static ij.measure.ResultsTable |
inertiaEllipsoid(ij.ImageStack image)
Deprecated.
use
InertiaEllipsoid instead |
static ij.measure.ResultsTable |
inertiaEllipsoid(ij.ImageStack image,
double[] resol)
Deprecated.
use
InertiaEllipsoid instead |
static double[][] |
inertiaEllipsoid(ij.ImageStack image,
int[] labels,
double[] resol)
Deprecated.
use
InertiaEllipsoid instead |
static ij.measure.ResultsTable |
maximumInscribedSphere(ij.ImageStack labelImage,
double[] resol)
Deprecated.
use LargestInscribedBall instead
|
static double[][] |
maximumInscribedSphere(ij.ImageStack labelImage,
int[] labels,
double[] resol)
Deprecated.
Radius of maximum inscribed sphere of each particle within a label image.
|
static ij.measure.ResultsTable |
surfaceArea(ij.ImageStack labelImage,
double[] resol,
int nDirs)
Deprecated.
Computes the surface area of each label in the 3D image, using the
specified resolution, and the given number of directions.
|
static double[] |
surfaceAreaCrofton(ij.ImageStack image,
int[] labels,
double[] resol,
int nDirs)
Deprecated.
use IntrinsicVolumes3D instead
|
static double |
surfaceAreaCrofton(ij.ImageStack image,
int label,
double[] resol,
int nDirs)
Deprecated.
use IntrinsicVolumes3D instead
|
static double |
surfaceAreaCroftonD3(ij.ImageStack image,
double[] resol)
Deprecated.
use IntrinsicVolumes3D instead
|
static ij.measure.ResultsTable |
volume(ij.ImageStack labelImage,
double[] resol)
Deprecated.
used IntrinsicVolumes3D instead
|
static double[] |
volume(ij.ImageStack labelImage,
int[] labels,
double[] resol)
Deprecated.
use IntrinsicVolumes3D instead
|
@Deprecated public static final ij.measure.ResultsTable boundingBox(ij.ImageStack labelImage)
labelImage
- a 3D image containing label of particles or regionspublic static final double[][] boundingBox(ij.ImageStack labelImage, int[] labels)
labelImage
- a 3D image containing label of particles or regionslabels
- the set of labels present in image@Deprecated public static final ij.measure.ResultsTable volume(ij.ImageStack labelImage, double[] resol)
labelImage
- image containing the label of each particleresol
- image resolution, as a double array with 3 elements@Deprecated public static final double[] volume(ij.ImageStack labelImage, int[] labels, double[] resol)
labelImage
- image containing the label of each particlelabels
- the set of labels for which volume has to be computedresol
- image resolution, as a double array with 3 elements@Deprecated public static final double[] computeSphericity(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 particlesurfaceArea(ImageStack, double[], int)
,
volume(ImageStack, int[], double[])
public static final ij.measure.ResultsTable surfaceArea(ij.ImageStack labelImage, double[] resol, int nDirs)
labelImage
- image containing the label of each particleresol
- image resolution, as a double array with 3 elementsnDirs
- the number of directions to consider, either 3 or 13@Deprecated public static final double[] surfaceAreaCrofton(ij.ImageStack image, int[] labels, double[] resol, int nDirs)
image
- image containing the label of each particlelabels
- the set of labels in the imageresol
- image resolution, as a double array with 3 elementsnDirs
- the number of directions to consider, either 3 or 13@Deprecated public static final double surfaceAreaCrofton(ij.ImageStack image, int label, double[] resol, int nDirs)
image
- the input 3D label image (with labels having integer values)label
- the value of the label to measureresol
- the resolution of the image, in each directionnDirs
- the number of directions to consider for computing surface (3
or 13)@Deprecated public static final double surfaceAreaCroftonD3(ij.ImageStack image, double[] resol)
image
- the input 3D label image (with labels having integer values)resol
- the resolution of the image, in each direction@Deprecated public static final double[] eulerNumber(ij.ImageStack image, int[] labels, int conn)
IntrinsicVolumes3D.eulerNumbers(ImageStack, int[], int)
insteadimage
- 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)IntrinsicVolumes3D.eulerNumbers(ImageStack, int[], int)
@Deprecated public static final double[][] centroids(ij.ImageStack labelImage, int[] labels)
Centroid3D.centroids(ImageStack, int[])
insteadlabelImage
- an instance of ImageStack containing region labelslabels
- the set of indices contained in the image@Deprecated public static final ij.measure.ResultsTable inertiaEllipsoid(ij.ImageStack image)
InertiaEllipsoid
insteadimage
- an instance of ImageStack containing region labelsRuntimeException
- if jama package is not found.@Deprecated public static final ij.measure.ResultsTable inertiaEllipsoid(ij.ImageStack image, double[] resol)
InertiaEllipsoid
insteadComputes inertia ellipsoid of each 3D region in input 3D label image.
The result is given as a ResultsTable with as many rows as the number of labels, and 9 columns. Columns correspond to the centroid coordinates (3 values), the radius of the ellipsoid (3 values), and the orientation, given as azimut, elevation, and roll angles, in degrees (3 values).
image
- an instance of ImageStack containing region labelsresol
- the resolution of the image, in each directionRuntimeException
- if jama package is not found.@Deprecated public static final double[][] inertiaEllipsoid(ij.ImageStack image, int[] labels, double[] resol)
InertiaEllipsoid
insteadComputes inertia ellipsoid from input 3D label image for each specified region label.
The result is given as an array of double with as many rows as the number of labels, and 9 columns. Columns correspond to the centroid coordinates (3 values), the radius of the ellipsoid (3 values), and the orientation, given as azimut, elevation, and roll angles, in degrees (3 values).
ImageStack labelImage = ...
int[] labels = LabelImages.findAllLabels(image);
double[] resol = new double[]{1, 1, 1};
double[][] ellipsoids = GeometricMeasures3D.inertiaEllipsoid(labelImage,
labels, resol);
double[][] elongations = GeometricMeasures3D.computeEllipsoidElongations(ellipsoids);
image
- input image containing label of each particlelabels
- the list of labels for which we want to compute inertia
ellipsoidresol
- the spatial resolution, as an array of length 3.RuntimeException
- if jama package is not found.@Deprecated public static final double[][] computeEllipsoidElongations(double[][] ellipsoids)
Ellipsoid.elongations(Ellipsoid[])
instead
ImageStack labelImage = ...
int[] labels = LabelImages.findAllLabels(image);
double[] resol = new double[]{1, 1, 1};
double[][] ellipsoids = GeometricMeasures3D.inertiaEllipsoid(labelImage,
labels, resol);
double[][] elongations = GeometricMeasures3D.computeEllipsoidElongations(ellipsoids);
ellipsoids
- an array of ellipsoids, with radius data given in columns 3,
4, and 5inertiaEllipsoid(ImageStack, double[])
,
inertiaEllipsoid(ImageStack, int[], double[])
@Deprecated public static final ij.measure.ResultsTable maximumInscribedSphere(ij.ImageStack labelImage, double[] resol)
labelImage
- input image containing label of each particleresol
- the spatial resolution, as an array of length 3.public static final double[][] maximumInscribedSphere(ij.ImageStack labelImage, int[] labels, double[] resol)
labelImage
- input image containing label of each particlelabels
- the list of labels for which we want to compute inertia
ellipsoidresol
- the spatial resolution, as an array of length 3.Copyright © 2014–2023 INRA-IJPB Modeling and Digital Imaging lab. All rights reserved.