Package | Description |
---|---|
org.anchoranalysis.feature.energy |
A particular stack used in feature-calculations called a
EnergyStack together with related classes. |
org.anchoranalysis.feature.input |
Base classes providing inputs to feature calculations.
|
org.anchoranalysis.image.bean.nonbean.segment |
Non-bean classes relating to image-segmentation.
|
org.anchoranalysis.image.core.channel |
The
Channel core data-class and related operations
and converters. |
org.anchoranalysis.image.core.channel.factory |
Factory classes for creating
Channel for various
voxel data-types. |
org.anchoranalysis.image.core.dimensions |
Classes to describe the size of images or components of images both in voxels and physically.
|
org.anchoranalysis.image.core.mask |
An image with only two permissible states.
|
org.anchoranalysis.image.core.stack |
Defines the key data object,
Stack , and related
classes. |
org.anchoranalysis.image.feature.bean.physical |
Features that convert to/from physical spatial units (e.g.
|
org.anchoranalysis.image.feature.input |
Image-related implementations of
FeatureInput . |
org.anchoranalysis.image.io.object.output.mask |
Writing an
ObjectCollection to the filesystem as
multiple binary singled-channeled images. |
org.anchoranalysis.io.imagej.convert |
Converts to and from ImageJ data-structures for images.
|
org.anchoranalysis.mpp.bean.bound |
Lower and upper limits set around variables.
|
org.anchoranalysis.mpp.bean.bound.rotation |
Bounds on how to rotate an entity in Euclidean space.
|
org.anchoranalysis.mpp.bean.proposer |
Proposing
Mark s or other data-structures with particular
attributes. |
org.anchoranalysis.mpp.feature.bean.mark |
Features calculated on a
Mark . |
org.anchoranalysis.mpp.feature.bean.mark.collection |
Features calculated on a
org.anchoranalysis.mpp.feature.bean.mark.collection . |
org.anchoranalysis.mpp.mark.conic |
Mark s implementing conic sections. |
org.anchoranalysis.plugin.fiji.bean.channel.provider.distance |
Euclidean Distance Transform
implementations via FIJI.
|
org.anchoranalysis.plugin.image.bean.object.provider.merge |
Implementations of
ObjectCollectionProvider
involving merging objects together. |
org.anchoranalysis.plugin.image.feature.bean.physical |
Beans involving physical units for measurement.
|
org.anchoranalysis.plugin.io.bean.stack.reader |
Implementations of
StackReader . |
org.anchoranalysis.plugin.io.xml |
Reading and writing metadata XML.
|
org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler |
The
VisitScheduler and related
classes, as used in TraverseOuterContourOnImage . |
org.anchoranalysis.plugin.mpp.bean.proposer.scalar |
Implementations of
ScalarProposer involving Mark or related classes. |
org.anchoranalysis.plugin.mpp.feature.bean.memo.ind |
Implementations of
FeatureSingleMemo . |
org.anchoranalysis.plugin.mpp.feature.bean.unit |
Beans to convert between units.
|
org.anchoranalysis.test.image |
Testing utilities and fixtures with no greater downstream dependency than anchor-image-io
or anchor-io-bioformats or anchor-imagej.
|
Modifier and Type | Method and Description |
---|---|
Optional<Resolution> |
EnergyStack.resolution()
The image-resolution associated with the energy-stack.
|
Modifier and Type | Method and Description |
---|---|
default Resolution |
FeatureInputWithResolution.getResolutionRequired()
The resolution of the associated image, or an exception if it is not available.
|
Modifier and Type | Method and Description |
---|---|
Optional<Resolution> |
FeatureInputDimensions.getResolutionOptional() |
Optional<Resolution> |
FeatureInputWithResolution.getResolutionOptional()
The resolution of the associated image, if it is available.
|
Optional<Resolution> |
FeatureInputEnergy.getResolutionOptional() |
Modifier and Type | Method and Description |
---|---|
Optional<Resolution> |
BinarySegmentationParameters.getResolution()
A
Resolution associated with the image being segmented. |
Constructor and Description |
---|
BinarySegmentationParameters(Resolution resolution,
Optional<Histogram> intensityHistogram)
Creates with a specific resolution and intensity-histogram.
|
Constructor and Description |
---|
BinarySegmentationParameters(Optional<Histogram> intensityHistogram,
Optional<Resolution> resolution) |
BinarySegmentationParameters(Optional<Resolution> resolution)
Creates with a specific resolution, but no intensity-histogram.
|
Modifier and Type | Method and Description |
---|---|
Optional<Resolution> |
Channel.resolution()
The resolution of the voxel that describes a physical size for each voxel.
|
Modifier and Type | Method and Description |
---|---|
void |
Channel.assignResolution(Optional<Resolution> resolution)
Assigns a new resolution.
|
Constructor and Description |
---|
Channel(Voxels<?> voxels,
Optional<Resolution> resolution)
Creates for particular voxels and resolution.
|
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelFactory.create(Voxels<?> voxels,
Optional<Resolution> resolution)
Create a
Channel from particular voxels. |
Channel |
ChannelFactorySingleType.create(Voxels<?> voxels,
Optional<Resolution> resolution)
Create a
Channel from voxels and a resolution. |
Modifier and Type | Method and Description |
---|---|
static Resolution |
Resolution.createWithXY(double xy)
Creates with only XY resolution, identical in both dimensions.
|
static Resolution |
Resolution.createWithXYAndZ(double xy,
double z)
Creates with XY resolution and Z resolution.
|
abstract Resolution |
OrientationChange.resolution(Resolution resolution)
A
Resolution that describes resolution after the orientation change. |
Resolution |
Resolution.scaleXY(ScaleFactor scaleFactor)
Multiplies the X and Y components of the resolution by a factor.
|
Modifier and Type | Method and Description |
---|---|
Optional<Resolution> |
Dimensions.resolution()
Resolution of voxels to physical measurements.
|
Modifier and Type | Method and Description |
---|---|
abstract Resolution |
OrientationChange.resolution(Resolution resolution)
A
Resolution that describes resolution after the orientation change. |
Modifier and Type | Method and Description |
---|---|
Dimensions |
Dimensions.duplicateChangeResolution(Optional<Resolution> resolutionToAssign)
Deep-copies the current object, but assigns a different
Resolution . |
Constructor and Description |
---|
UnitConverter(Resolution resolution) |
Constructor and Description |
---|
Dimensions(Extent extent,
Optional<Resolution> resolution) |
Modifier and Type | Method and Description |
---|---|
Optional<Resolution> |
Mask.resolution()
Resolution of voxels to physical measurements.
|
Constructor and Description |
---|
Mask(BinaryVoxels<UnsignedByteBuffer> voxels,
Optional<Resolution> resolution)
Creates a mask from an existing binary-voxels and a specific image resolution.
|
Modifier and Type | Method and Description |
---|---|
Optional<Resolution> |
DisplayStack.resolution()
Resolution of voxels to physical measurements.
|
Optional<Resolution> |
Stack.resolution()
Resolution of voxels to physical measurements.
|
Modifier and Type | Method and Description |
---|---|
void |
Stack.assignResolution(Resolution resolution)
Assigns a new resolution.
|
Modifier and Type | Method and Description |
---|---|
protected abstract double |
WithResolutionBase.calculateWithResolution(double value,
Resolution resolution) |
protected double |
FeatureConvertUnits.calculateWithResolution(double value,
Resolution resolution) |
Modifier and Type | Method and Description |
---|---|
Optional<Resolution> |
FeatureInputHistogram.getResolutionOptional() |
Constructor and Description |
---|
FeatureInputHistogram(Histogram histogram,
Optional<Resolution> resolution) |
Constructor and Description |
---|
ObjectAsMaskGenerator(Optional<Resolution> resolution) |
ObjectWithBoundingBoxGenerator(Optional<Resolution> resolution)
Create with a resolution, if it is known.
|
Modifier and Type | Method and Description |
---|---|
static Channel |
ConvertFromImagePlus.toChannel(ij.ImagePlus imagePlus,
Optional<Resolution> resolution)
Converts an
ImagePlus to a Channel . |
Modifier and Type | Method and Description |
---|---|
ResolvedBound |
MarkBounds.calculateMinMax(Optional<Resolution> resolution,
boolean do3D) |
abstract double |
MarkBounds.getMaxResolved(Optional<Resolution> resolution,
boolean do3D) |
double |
BoundUnitless.getMaxResolved(Optional<Resolution> resolution,
boolean do3D) |
double |
BoundPhysicalExtent.getMaxResolved(Optional<Resolution> resolution,
boolean do3D) |
double |
BoundDegrees.getMaxResolved(Optional<Resolution> resolution,
boolean do3D) |
abstract double |
MarkBounds.getMinResolved(Optional<Resolution> resolution,
boolean do3D) |
double |
BoundUnitless.getMinResolved(Optional<Resolution> resolution,
boolean do3D) |
double |
BoundPhysicalExtent.getMinResolved(Optional<Resolution> resolution,
boolean do3D) |
double |
BoundDegrees.getMinResolved(Optional<Resolution> resolution,
boolean do3D) |
ResolvedBound |
Bound.resolve(Optional<Resolution> resolution,
boolean do3D) |
Modifier and Type | Method and Description |
---|---|
abstract Orientation |
BoundRotation.randomOrientation(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
Orientation |
BoundRotation2D.randomOrientation(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
Orientation |
BoundRotation3D.randomOrientation(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
Modifier and Type | Method and Description |
---|---|
abstract double |
ScalarProposer.propose(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
Modifier and Type | Method and Description |
---|---|
Optional<Resolution> |
FeatureInputMark.getResolutionOptional() |
Modifier and Type | Method and Description |
---|---|
Optional<Resolution> |
FeatureInputMarkCollection.getResolutionOptional() |
Modifier and Type | Method and Description |
---|---|
double[] |
Ellipsoid.createRadiiArrayResolved(Optional<Resolution> resolution) |
double[] |
Ellipse.createRadiiArrayResolved(Optional<Resolution> resolution) |
abstract double[] |
ConicBase.createRadiiArrayResolved(Optional<Resolution> resolution) |
static double[] |
EllipsoidUtilities.normalisedRadii(Ellipsoid mark,
Optional<Resolution> resolution) |
double[] |
ConicBase.radiiOrderedResolved(Optional<Resolution> resolution) |
static Point3d |
RadiiRandomizer.randomizeRadii(Bound bound,
RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution,
boolean do3D) |
Modifier and Type | Method and Description |
---|---|
Voxels<UnsignedByteBuffer> |
DistanceTransform3D.createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer> voxels,
Optional<Resolution> resolution,
float multiplyByZRes) |
Modifier and Type | Method and Description |
---|---|
protected Resolution |
MergeBase.resolutionRequired() |
Modifier and Type | Method and Description |
---|---|
protected double |
UnitsWithinRange.calculateWithResolution(double value,
Resolution resolution) |
Modifier and Type | Method and Description |
---|---|
static Optional<Resolution> |
ReadVoxelExtentXml.readMetadata(Path filePath,
boolean acceptNoResolution)
Looks for a metadata file describing the resolution
|
Modifier and Type | Method and Description |
---|---|
static Resolution |
ResolutionAsXml.readResolutionXml(File file)
Retrieves resolution from a XML file previously written by
ResolutionAsXml.writeResolutionXml(Resolution, Path) . |
Modifier and Type | Method and Description |
---|---|
static void |
ResolutionAsXml.writeResolutionXml(Resolution resolution,
Path path)
Writes a XML metadata file describing the image-resolution.
|
Modifier and Type | Method and Description |
---|---|
abstract void |
VisitScheduler.afterCreateObject(Point3i root,
Optional<Resolution> resolution,
RandomNumberGenerator randomNumberGenerator) |
void |
VisitSchedulerMaxDistanceAlongContour.afterCreateObject(Point3i root,
Optional<Resolution> resolution,
RandomNumberGenerator randomNumberGenerator) |
void |
VisitSchedulerUniformSample.afterCreateObject(Point3i root,
Optional<Resolution> resolution,
RandomNumberGenerator randomNumberGenerator) |
void |
VisitSchedulerAnd.afterCreateObject(Point3i root,
Optional<Resolution> resolution,
RandomNumberGenerator randomNumberGenerator) |
void |
VisitSchedulerConvexAboutRoot.afterCreateObject(Point3i root,
Optional<Resolution> resolution,
RandomNumberGenerator randomNumberGenerator) |
abstract void |
VisitScheduler.beforeCreateObject(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
void |
VisitSchedulerMaxDistanceAlongContour.beforeCreateObject(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
void |
VisitSchedulerUniformSample.beforeCreateObject(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
void |
VisitSchedulerAnd.beforeCreateObject(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
void |
VisitSchedulerConvexAboutRoot.beforeCreateObject(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
abstract Optional<Tuple3i> |
VisitScheduler.maxDistanceFromRootPoint(Optional<Resolution> resolution) |
Optional<Tuple3i> |
VisitSchedulerMaxDistanceAlongContour.maxDistanceFromRootPoint(Optional<Resolution> resolution) |
Optional<Tuple3i> |
VisitSchedulerUniformSample.maxDistanceFromRootPoint(Optional<Resolution> resolution) |
Optional<Tuple3i> |
VisitSchedulerAnd.maxDistanceFromRootPoint(Optional<Resolution> resolution) |
Optional<Tuple3i> |
VisitSchedulerConvexAboutRoot.maxDistanceFromRootPoint(Optional<Resolution> resolution) |
Modifier and Type | Method and Description |
---|---|
double |
Constant.propose(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
double |
GaussianSampler.propose(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
double |
Scale.propose(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
double |
FromUnitValueDistance.propose(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
double |
MaxWithConstant.propose(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
Modifier and Type | Method and Description |
---|---|
protected double |
FeatureSingleMemoRegion.resolveArea(double value,
Optional<Resolution> res) |
protected double |
FeatureSingleMemoRegion.resolveVolume(double value,
Optional<Resolution> res) |
Modifier and Type | Method and Description |
---|---|
double |
UnitConverter.resolveArea(double value,
Optional<Resolution> resolution)
Convert area into another unit representation
|
double |
UnitConverter.resolveDistance(double value,
Optional<Resolution> resolution,
DirectionVector direction)
Convert distance into another unit representation
|
double |
UnitConverter.resolveVolume(double value,
Optional<Resolution> resolution)
Convert volume into another unit representation
|
Modifier and Type | Field and Description |
---|---|
static Resolution |
ResolutionFixture.INSTANCE |
Modifier and Type | Method and Description |
---|---|
static Mask |
MaskFixture.create(boolean do3D,
Optional<Resolution> resolution)
Creates the
Mask with the default corner and a particular resolution. |
static Mask |
MaskFixture.create(Point3i corner,
boolean do3D,
Optional<Resolution> resolution)
Creates the
Mask with a particular corner and a particular resolution. |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.