Package | Description |
---|---|
org.anchoranalysis.feature.energy |
A particular stack used in feature-calculations called a
EnergyStack together with related classes. |
org.anchoranalysis.feature.initialization |
Initialization parameters used for beans in
org.anchoranalysis.feature.bean . |
org.anchoranalysis.feature.input |
Base classes providing inputs to feature calculations.
|
org.anchoranalysis.image.feature.bean.evaluator |
Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
|
org.anchoranalysis.image.feature.calculator |
Implementations of
FeatureCalculatorMulti
related to images, especially to create tables of feature-calculations. |
org.anchoranalysis.image.feature.calculator.merged |
A particular implementation of
FeatureCalculatorMulti for feature-calculations based
upon pairs of image-objects. |
org.anchoranalysis.image.feature.input |
Image-related implementations of
FeatureInput . |
org.anchoranalysis.mpp.feature.addcriteria |
Criteria for adding edges during optimization of marked-point-processes.
|
org.anchoranalysis.mpp.feature.bean.mark |
Features calculated on a
Mark . |
org.anchoranalysis.mpp.feature.energy.marks |
Non-bean classes pertaining to calculating energy of {org.anchoranalysis.mpp.mark.Mark}s.
|
org.anchoranalysis.mpp.feature.energy.saved |
Saved snapshots of energy-calculations.
|
org.anchoranalysis.mpp.feature.input |
Inputs to mark-point-processes related
Feature s. |
org.anchoranalysis.mpp.feature.mark |
Non-bean classes for calculating feature-values related to
Mark s. |
org.anchoranalysis.mpp.io.output |
Non-beans for writing data structures related to marked point processes from the file system.
|
org.anchoranalysis.mpp.mark |
Non-bean classes related to
Mark s. |
org.anchoranalysis.mpp.proposer |
Non-bean classes for proposing
Mark s or other data-structures
with particular attributes. |
org.anchoranalysis.mpp.segment.bean.define |
DefineOutputter and its sub-classes. |
org.anchoranalysis.mpp.segment.optimization |
Non-bean classes used in
org.anchoranalysis.mpp.segment.bean.optimization |
org.anchoranalysis.mpp.segment.optimization.kernel |
Non-bean classes used in
org.anchoranalysis.mpp.segment.bean.optimization.kernel |
org.anchoranalysis.plugin.image.feature.bean.object.combine |
Features from combinations of
ObjectMask s. |
org.anchoranalysis.plugin.image.feature.bean.object.single |
Implementations of
FeatureSingleObject . |
org.anchoranalysis.plugin.image.feature.bean.object.single.border |
Implementations of
FeatureSingleObject that determine if an
object lies at the border of an image. |
org.anchoranalysis.plugin.image.feature.bean.object.single.energy |
Implementations of
FeatureSingleObject that reference a
particular Channel in the associated EnergyStack . |
org.anchoranalysis.plugin.image.task.feature |
Non-bean classes pertaining to
Feature s as used in tasks. |
org.anchoranalysis.plugin.image.task.feature.calculator |
Non-beans for calculating
Feature s. |
org.anchoranalysis.plugin.mpp.bean.check |
Implementations of
CheckMark . |
org.anchoranalysis.plugin.mpp.bean.define | |
org.anchoranalysis.test.feature.plugins.objects |
Fixtures for creating object-masks and related feature-inputs.
|
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 |
---|---|
EnergyStack |
EnergyStack.copyChangeDictionary(Dictionary dictionaryToAssign)
Makes a copy of the
EnergyStack but assigns a new Dictionary . |
EnergyStack |
EnergyStack.extractSlice(int z)
Extract a particular z-slice from the
EnergyStack as a new stack. |
Constructor and Description |
---|
FeatureInitialization(EnergyStack energyStack)
Create only with an energy-stack.
|
Modifier and Type | Method and Description |
---|---|
EnergyStack |
FeatureInputEnergy.getEnergyStackRequired()
The associated energy-stack or throws an exception if it isn't present.
|
Modifier and Type | Method and Description |
---|---|
Optional<EnergyStack> |
FeatureInputEnergy.getEnergyStackOptional()
The associated energy-stack.
|
Modifier and Type | Method and Description |
---|---|
void |
FeatureInputEnergy.setEnergyStack(EnergyStack energyStack)
Assigns an
EnergyStack to be associated with the input. |
Modifier and Type | Method and Description |
---|---|
void |
FeatureInputEnergy.setEnergyStack(Optional<EnergyStack> energyStack)
Assigns an optional
EnergyStack to be associated with the input. |
Constructor and Description |
---|
FeatureInputEnergy(Optional<EnergyStack> energyStack) |
Modifier and Type | Method and Description |
---|---|
Optional<EnergyStack> |
FeatureEvaluator.energyStack()
The specified energy stack.
|
Modifier and Type | Method and Description |
---|---|
static FeatureInitialization |
InitializationFactory.create(Optional<SharedObjects> sharedObjects,
Optional<EnergyStack> energyStack) |
void |
SingleTableCalculator.start(ImageInitialization initialization,
Optional<EnergyStack> energyStack,
Logger logger) |
void |
FeatureTableCalculator.start(ImageInitialization initialization,
Optional<EnergyStack> energyStack,
Logger logger)
Initializes a feature store that has the same structure as that previously created by
createFeatures() from the same object
|
Modifier and Type | Method and Description |
---|---|
void |
PairsTableCalculator.start(ImageInitialization initializtion,
Optional<EnergyStack> energyStack,
Logger logger) |
Constructor and Description |
---|
FeatureInputPairObjects(ObjectMask first,
ObjectMask second,
EnergyStack energyStack) |
FeatureInputSingleObject(ObjectMask object,
EnergyStack energyStack) |
Constructor and Description |
---|
FeatureInputObjectCollection(ObjectCollection objects,
Optional<EnergyStack> energyStack) |
FeatureInputPairObjects(ObjectMask first,
ObjectMask second,
Optional<EnergyStack> energyStack) |
FeatureInputPairObjects(ObjectMask first,
ObjectMask second,
Optional<EnergyStack> energyStack,
Optional<ObjectMask> merged) |
FeatureInputSingleObject(ObjectMask object,
Optional<EnergyStack> energyStack) |
Modifier and Type | Method and Description |
---|---|
abstract boolean |
CheckMark.check(Mark mark,
RegionMap regionMap,
EnergyStack energyStack)
Checks a mark
|
void |
CheckMark.start(EnergyStack energyStack)
|
Modifier and Type | Method and Description |
---|---|
void |
MarksWithEnergyBreakdown.exchange(EnergyMemoList wrapperInd,
int index,
VoxelizedMarkMemo newMark,
EnergyStack energyStack) |
void |
VoxelizedMarksWithEnergy.exchange(int index,
VoxelizedMarkMemo newMark,
EnergyStack energyStack) |
Constructor and Description |
---|
VoxelizedMarksWithEnergy(MarksWithEnergyBreakdown marks,
EnergyStack energyStack,
SharedFeatures sharedFeatures,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
void |
EnergySavedPairs.initUpdatableMarks(MemoForIndex pxlMarkMemoList,
EnergyStack stack,
Logger logger,
SharedFeatures sharedFeatures) |
Constructor and Description |
---|
FeatureInputAllMemo(EnergyMemoList pxlMarkMemoList,
EnergyStack raster) |
FeatureInputPairMemo(VoxelizedMarkMemo object1,
VoxelizedMarkMemo object2,
EnergyStack energyStack) |
FeatureInputSingleMemo(VoxelizedMarkMemo pxlPartMemo,
EnergyStack energyStack) |
Constructor and Description |
---|
FeatureInputSingleMemo(VoxelizedMarkMemo pxlPartMemo,
Optional<EnergyStack> energyStack) |
Modifier and Type | Method and Description |
---|---|
void |
UpdatableMarksList.initUpdatableMarks(MemoForIndex marks,
EnergyStack stack,
Logger logger,
SharedFeatures sharedFeatures) |
Constructor and Description |
---|
EnergyStackWriter(EnergyStack energyStack,
Outputter outputter) |
Modifier and Type | Method and Description |
---|---|
void |
UpdatableMarks.initUpdatableMarks(MemoForIndex memo,
EnergyStack energyStack,
Logger logger,
SharedFeatures sharedFeatures) |
Modifier and Type | Method and Description |
---|---|
EnergyStack |
ProposerContext.getEnergyStack() |
Constructor and Description |
---|
ProposerContext(RandomNumberGenerator randomNumberGenerator,
EnergyStack energyStack,
RegionMap regionMap,
OperationContext operationContext,
ErrorNode errorNode) |
Modifier and Type | Method and Description |
---|---|
protected void |
DefineOutputter.outputSharedObjects(SharedObjects sharedObjects,
Optional<EnergyStack> energyStack,
Outputter outputter) |
Modifier and Type | Method and Description |
---|---|
EnergyStack |
DualStack.getEnergyStack()
The energy-stack
|
Constructor and Description |
---|
DualStack(EnergyStack energyStack,
DisplayStack background) |
DualStack(EnergyStack energyStack,
StackDisplayer displayer)
Creates to infer a background from the energy-stack.
|
Constructor and Description |
---|
KernelCalculationContext(MarkFactoryContext markFactoryContext,
EnergyStack energyStack,
EnergySchemeWithSharedFeatures energyScheme,
RandomNumberGenerator randomNumberGenerator,
ErrorNode errorNode) |
Modifier and Type | Method and Description |
---|---|
ListWithThumbnails<T,ObjectCollection> |
CombineObjectsForFeatures.deriveInputsStartBatch(ObjectCollection objects,
EnergyStack energyStack,
boolean thumbnailsEnabled,
OperationContext context)
Derives a list of inputs (i.e.
|
List<FeatureInputPairObjects> |
PairNeighbors.startBatchDeriveInputs(ObjectCollection objects,
EnergyStack energyStack,
Logger logger) |
List<FeatureInputSingleObject> |
EachObjectIndependently.startBatchDeriveInputs(ObjectCollection objects,
EnergyStack energyStack,
Logger logger) |
protected abstract List<T> |
CombineObjectsForFeatures.startBatchDeriveInputs(ObjectCollection objects,
EnergyStack energyStack,
Logger logger)
Derives a list of inputs from an object-collection.
|
Modifier and Type | Method and Description |
---|---|
protected abstract double |
OutlineKernelBase.calculateWithParameters(ObjectMask object,
KernelApplicationParameters parameters,
CheckedSupplier<EnergyStack,FeatureCalculationException> energyStack) |
Modifier and Type | Method and Description |
---|---|
protected double |
NumberVoxelsAtBorder.calculateWithParameters(ObjectMask object,
KernelApplicationParameters parameters,
CheckedSupplier<EnergyStack,FeatureCalculationException> energyStack) |
Modifier and Type | Method and Description |
---|---|
protected double |
NumberNeighboringVoxels.calculateWithParameters(ObjectMask object,
KernelApplicationParameters parameters,
CheckedSupplier<EnergyStack,FeatureCalculationException> energyStack) |
Modifier and Type | Method and Description |
---|---|
EnergyStack |
InitializationWithEnergyStack.getEnergyStack() |
Constructor and Description |
---|
InitializationWithEnergyStack(EnergyStack energyStack,
InitializationContext context) |
InitializationWithEnergyStack(ImageInitialization image,
EnergyStack energyStack) |
Modifier and Type | Method and Description |
---|---|
static EnergyStack |
FeatureCalculatorRepeated.extractStack(ProvidesStackInput input,
StackProvider stackEnergy,
InputOutputContext context) |
EnergyStack |
FeatureCalculatorFromProvider.getEnergyStack() |
Modifier and Type | Method and Description |
---|---|
void |
CalculateFeaturesForObjects.calculateForObjects(ObjectCollection objects,
EnergyStack energyStack,
LabelsForInput labelsForInput)
Calculates the feature-results for
objects , and stores the results. |
Modifier and Type | Method and Description |
---|---|
boolean |
AndList.check(Mark mark,
RegionMap regionMap,
EnergyStack energyStack) |
boolean |
RadiiMinRatio.check(Mark mark,
RegionMap regionMap,
EnergyStack energyStack) |
boolean |
VolumeMin.check(Mark mark,
RegionMap regionMap,
EnergyStack energyStack) |
boolean |
AnySliceCenterOnMask.check(Mark mark,
RegionMap regionMap,
EnergyStack energyStack) |
boolean |
Not.check(Mark mark,
RegionMap regionMap,
EnergyStack energyStack) |
boolean |
CenterOnMask.check(Mark mark,
RegionMap regionMap,
EnergyStack energyStack) |
boolean |
FeatureValueCheckMark.check(Mark mark,
RegionMap regionMap,
EnergyStack energyStack) |
protected FeatureInputSingleMemo |
FeatureValueIndividualEnergyGreaterThan.createFeatureInput(Mark mark,
RegionMap regionMap,
EnergyStack energyStack) |
protected FeatureInputMark |
FeatureValueMarkGreaterEqualThan.createFeatureInput(Mark mark,
RegionMap regionMap,
EnergyStack energyStack) |
protected abstract T |
FeatureValueCheckMark.createFeatureInput(Mark mark,
RegionMap regionMap,
EnergyStack energyStack) |
protected boolean |
CheckMarkWithMask.isPointOnMask(Point3d point,
EnergyStack energyStack,
java.util.function.Function<Point3d,Point3i> deriveFunc) |
void |
AndList.start(EnergyStack energyStack) |
void |
FeatureValueCheckMark.start(EnergyStack energyStack) |
Modifier and Type | Method and Description |
---|---|
S |
DefineOutputterWithEnergy.ProcessWithEnergyStack.process(T initialization,
EnergyStack energyStack) |
Modifier and Type | Method and Description |
---|---|
static EnergyStack |
CircleObjectFixture.energyStack() |
Modifier and Type | Method and Description |
---|---|
static EnergyStack |
EnergyStackFixture.create(boolean big,
boolean do3D)
Creates the energy-stack to use.
|
static EnergyStack |
EnergyStackFixture.create(boolean big,
boolean do3D,
boolean singleChannel,
boolean includeResolution)
Creates the energy-stack to use.
|
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.