Uses of Class
org.anchoranalysis.image.core.mask.Mask

Packages that use Mask

Package	Description
org.anchoranalysis.image.bean.nonbean.init	Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
org.anchoranalysis.image.bean.provider	Base classes for providers of different core data entities related to images.
org.anchoranalysis.image.core.contour	Finds outline voxels, the pixels on the contour/edge of the object.
org.anchoranalysis.image.core.mask	An image with only two permissible states.
org.anchoranalysis.image.core.mask.combine	Binary operations involving voxelwise combination of Mask.
org.anchoranalysis.image.core.object	The key data entity org.anchoranalysis.image.voxel.object and related-classes and operations.
org.anchoranalysis.image.core.points	Operations that extract points from image data entities or vice versa.
org.anchoranalysis.image.io.stack.input	Non-bean classes for reading a Stack from the filesystem.
org.anchoranalysis.plugin.fiji.bean.channel.provider.distance	Euclidean Distance Transform implementations via FIJI.
org.anchoranalysis.plugin.fiji.bean.mask.provider	Implementations of MaskProvider that use FIJI.
org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic	Implementations of ChannelProvider that perform arithmetic on voxels in one or more Channels.
org.anchoranalysis.plugin.image.bean.channel.provider.assign	Implementations of ChannelProvider that sets the values of the voxels in a Channel.
org.anchoranalysis.plugin.image.bean.channel.provider.mask	Implementations of ChannelProvider that involve conversion from or application of Masks.
org.anchoranalysis.plugin.image.bean.mask.provider	Implementations of MaskProvider.
org.anchoranalysis.plugin.image.bean.mask.provider.combine	Implementations of MaskProvider that combine existing providers.
org.anchoranalysis.plugin.image.bean.mask.provider.convert	Implementations of MaskProvider that convert providers of other types to ObjectMasks.
org.anchoranalysis.plugin.image.bean.mask.provider.morphological	Implementations of MaskProvider that implement morphological operations.
org.anchoranalysis.plugin.image.bean.mask.provider.predicate	Provides if-else conditions to a MaskProvider.
org.anchoranalysis.plugin.image.bean.mask.provider.segment	Implementations of MaskProvider where an ObjectCollection is created by segmenting a Channel.
org.anchoranalysis.plugin.image.bean.mask.provider.slice	Implementations of MaskProvider that process 3D masks slice-by-slice.
org.anchoranalysis.plugin.image.bean.object.provider.connected	Implementations of ObjectCollectionProvider involving connected-components.
org.anchoranalysis.plugin.image.bean.object.provider.mask	Implementations of ObjectCollectionProvider involving a Mask.
org.anchoranalysis.plugin.image.bean.stack.provider	Implementations of StackProvider.
org.anchoranalysis.plugin.image.channel	Non-beans for operations or calculations relating to Channels.
org.anchoranalysis.plugin.imagej.bean.mask.provider	Implementations of MaskProvider that call ImageJ.
org.anchoranalysis.plugin.mpp.bean.check	Implementations of CheckMark.
org.anchoranalysis.plugin.mpp.bean.contour	Retrieving the contour outline pixels along the exterior outer contour of an ObjectMask.
org.anchoranalysis.plugin.mpp.bean.proposer.points	Implementations of PointsProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.points.contour	Finding a point on the external outer contour of an ObjectMask.
org.anchoranalysis.plugin.points.bean.convexhull	Convex hull operations.
org.anchoranalysis.test.image	Testing utilities and fixtures with no greater downstream dependency than anchor-image-io or anchor-io-bioformats or anchor-imagej.

Uses of Mask in org.anchoranalysis.image.bean.nonbean.init

Methods in org.anchoranalysis.image.bean.nonbean.init that return types with arguments of type Mask

Modifier and Type	Method and Description
NamedProviderStore<Mask>	ImageInitialization.masks() A collection of Masks, indexed by name.

Uses of Mask in org.anchoranalysis.image.bean.provider

Methods in org.anchoranalysis.image.bean.provider that return Mask

Modifier and Type	Method and Description
protected abstract Mask	MaskProviderUnary.createFromMask(Mask mask) Creates a Mask given the entity provided by the delegate.
Mask	MaskProviderUnary.get()

Methods in org.anchoranalysis.image.bean.provider that return types with arguments of type Mask

Modifier and Type	Method and Description
Provider<Mask>	MaskProviderUnary.getMask() The delegate Provider<Mask> that is called.

Methods in org.anchoranalysis.image.bean.provider with parameters of type Mask

Modifier and Type	Method and Description
protected abstract Mask	MaskProviderUnary.createFromMask(Mask mask) Creates a Mask given the entity provided by the delegate.

Method parameters in org.anchoranalysis.image.bean.provider with type arguments of type Mask

Modifier and Type	Method and Description
void	MaskProviderUnary.setMask(Provider<Mask> mask) The delegate Provider<Mask> that is called.

Uses of Mask in org.anchoranalysis.image.core.contour

Methods in org.anchoranalysis.image.core.contour that return Mask

Modifier and Type	Method and Description
static Mask	FindContour.createFrom(Mask mask, int numberErosions, boolean do3D, boolean atImageBoundary) Creates an contour from a Mask at the boundary of depth 1 pixel.
static Mask	FindContour.createFromGuess3D(Mask mask, int numberErosions, boolean force2D, boolean atImageBoundary) Like FindContour.createFrom(Mask, int, boolean, boolean), but guesses whether to do this in 2D or 3D.

Methods in org.anchoranalysis.image.core.contour with parameters of type Mask

Modifier and Type	Method and Description
static Mask	FindContour.createFrom(Mask mask, int numberErosions, boolean do3D, boolean atImageBoundary) Creates an contour from a Mask at the boundary of depth 1 pixel.
static Mask	FindContour.createFromGuess3D(Mask mask, int numberErosions, boolean force2D, boolean atImageBoundary) Like FindContour.createFrom(Mask, int, boolean, boolean), but guesses whether to do this in 2D or 3D.

Uses of Mask in org.anchoranalysis.image.core.mask

Methods in org.anchoranalysis.image.core.mask that return Mask

Modifier and Type	Method and Description
static Mask	MaskFromObjects.createFromNotObjects(ObjectCollection objects, Dimensions dimensions, BinaryValuesInt outValues) Create a Mask corresponding to all off voxels in an ObjectCollection.
static Mask	MaskFromObjects.createFromObjects(ObjectCollection objects, Dimensions dimensions, BinaryValuesInt outValues) Create a Mask corresponding to all on voxels in an ObjectCollection.
static Mask	MaskFactory.createMaskOff(Dimensions dimensions) Creates a binary-mask for specific dimensions with all voxels set to off.
static Mask	MaskFactory.createMaskOff(Dimensions dimensions, BinaryValuesInt binaryValues) Creates a binary-mask for specific dimensions with all voxels set to off.
static Mask	MaskFactory.createMaskOn(Dimensions dimensions) Creates a binary-mask for specific dimensions with all voxels set to on.
static Mask	MaskFactory.createMaskOn(Dimensions dimensions, BinaryValuesInt binaryValues) Creates a binary-mask for specific dimensions with all voxels set to on.
Mask	Mask.duplicate() Deep-copies the object.
Mask	Mask.extractSlice(int z) Creates a new Mask containing only one particular slice.
Mask	Mask.flattenZ() Creates an otherwise identical Mask but a maximum-intensity-projection applied to the z-dimension.
Mask	Mask.scaleXY(ScaleFactor scaleFactor) Creates a new Mask whose X- and Y- dimensions are scaled by scaleFactor.

Methods in org.anchoranalysis.image.core.mask with parameters of type Mask

Modifier and Type	Method and Description
static RunningSum	IterateVoxelsMask.calculateRunningSum(Mask mask, Voxels<UnsignedByteBuffer> voxelsIntensity) Calculates the sum and count across voxels intensity that correspond to on voxels on a mask
static void	MaskInverter.invert(Mask mask) Modifies a mask so that off voxels become on voxels and vice versa.
static <T> void	IterateVoxelsMask.withBuffer(Mask mask, Voxels<T> voxels, ProcessBufferUnary<T> process) Iterate over each voxel in a mask - with an associated buffer for each slice from a voxel-bo

Uses of Mask in org.anchoranalysis.image.core.mask.combine

Methods in org.anchoranalysis.image.core.mask.combine with parameters of type Mask

Modifier and Type	Method and Description
static void	MaskAnd.apply(Mask first, Mask second) Performs a logical and operation on each voxel in two masks, writing the result onto the second mask.
static void	MaskOr.apply(Mask first, Mask second) Performs a logical or operation on each voxel in two masks, writing the result onto the first mask.
static void	MaskXor.apply(Mask first, Mask second) Performs a logical xor (exclusive or) operation on each voxel in two masks, writing the result onto the first mask.

Uses of Mask in org.anchoranalysis.image.core.object

Methods in org.anchoranalysis.image.core.object with parameters of type Mask

Modifier and Type	Method and Description
static Histogram	HistogramFromObjectsFactory.createFrom(Channel channel, Mask mask) Creates a Histogram of all voxel intensity values in channel corresponding to Mask.

Method parameters in org.anchoranalysis.image.core.object with type arguments of type Mask

Modifier and Type	Method and Description
static Histogram	HistogramFromObjectsFactory.createFrom(Channel channel, Optional<Mask> mask) Creates a Histogram of all voxel intensity values in channel, or only those in mask if it is dfined.

Uses of Mask in org.anchoranalysis.image.core.points

Methods in org.anchoranalysis.image.core.points with parameters of type Mask

Modifier and Type	Method and Description
static List<Point2i>	PointsFromMask.listFrom2i(Mask mask) All points that have on state in a Mask as a list with type Point2i.
static List<Point3i>	PointsFromMask.listFrom3i(Mask mask) All points that have on state in a Mask as a list with type Point3i.

Uses of Mask in org.anchoranalysis.image.io.stack.input

Methods in org.anchoranalysis.image.io.stack.input that return Mask

Modifier and Type	Method and Description
static Mask	MaskReader.openMask(StackReader stackReader, Path path, BinaryValuesInt binaryValues, OperationContext context) Utility functions for opening a single-channeled stack as a Mask.

Uses of Mask in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance

Methods in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance with parameters of type Mask

Modifier and Type	Method and Description
protected Channel	DistanceTransform3D.createFromMask(Mask mask)

Uses of Mask in org.anchoranalysis.plugin.fiji.bean.mask.provider

Methods in org.anchoranalysis.plugin.fiji.bean.mask.provider that return Mask

Modifier and Type	Method and Description
protected Mask	AutoLocalThreshold.createFromSource(Channel channel)

Uses of Mask in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic with parameters of type Mask

Modifier and Type	Method and Description
protected Channel	SubtractMean.createFromMaskedChannel(Channel channel, Mask mask)

Uses of Mask in org.anchoranalysis.plugin.image.bean.channel.provider.assign

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.assign with parameters of type Mask

Modifier and Type	Method and Description
protected Channel	AssignValue.createFromMaskedChannel(Channel channel, Mask mask)
protected Channel	AssignFromChannel.createFromMaskedChannel(Channel channel, Mask mask)

Uses of Mask in org.anchoranalysis.plugin.image.bean.channel.provider.mask

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.mask with parameters of type Mask

Modifier and Type	Method and Description
protected abstract Channel	FromMaskBase.createFromMask(Mask mask)
protected Channel	FromMask.createFromMask(Mask mask)
protected abstract Channel	UnaryWithMaskBase.createFromMaskedChannel(Channel channel, Mask mask)
protected Channel	ZeroOutsideMask.createFromMaskedChannel(Channel channel, Mask mask)

Uses of Mask in org.anchoranalysis.plugin.image.bean.mask.provider

Methods in org.anchoranalysis.plugin.image.bean.mask.provider that return Mask

Modifier and Type	Method and Description
protected Mask	AllValuesOff.createFromDimensions(Dimensions dimensions)
protected abstract Mask	FromDimensionsBase.createFromDimensions(Dimensions dimensions)
protected Mask	AllValuesOn.createFromDimensions(Dimensions dimensions)
Mask	ScaleXY.createFromMask(Mask mask)
Mask	Invert.createFromMask(Mask maskToInvert)
Mask	Duplicate.createFromMask(Mask mask)
protected abstract Mask	FromChannelBase.createFromSource(Channel source)
Mask	Reference.get()
Mask	FromDimensionsBase.get()
Mask	FromChannelBase.get()

Methods in org.anchoranalysis.plugin.image.bean.mask.provider with parameters of type Mask

Modifier and Type	Method and Description
Mask	ScaleXY.createFromMask(Mask mask)
Mask	Invert.createFromMask(Mask maskToInvert)
Mask	Duplicate.createFromMask(Mask mask)

Uses of Mask in org.anchoranalysis.plugin.image.bean.mask.provider.combine

Methods in org.anchoranalysis.plugin.image.bean.mask.provider.combine that return Mask

Modifier and Type	Method and Description
Mask	CombineBase.createFromMask(Mask mask)
protected Mask	And.createFromTwoMasks(Mask maskToModify, Mask maskOther)
protected Mask	IfHighLow.createFromTwoMasks(Mask maskToModify, Mask maskReceiver)
protected abstract Mask	CombineBase.createFromTwoMasks(Mask maskToModify, Mask maskOther) Creates masks from some combination of two masks
protected Mask	Or.createFromTwoMasks(Mask maskToModify, Mask maskOther)
protected Mask	Xor.createFromTwoMasks(Mask maskToModify, Mask maskOther)

Methods in org.anchoranalysis.plugin.image.bean.mask.provider.combine with parameters of type Mask

Modifier and Type	Method and Description
Mask	CombineBase.createFromMask(Mask mask)
protected Mask	And.createFromTwoMasks(Mask maskToModify, Mask maskOther)
protected Mask	IfHighLow.createFromTwoMasks(Mask maskToModify, Mask maskReceiver)
protected abstract Mask	CombineBase.createFromTwoMasks(Mask maskToModify, Mask maskOther) Creates masks from some combination of two masks
protected Mask	Or.createFromTwoMasks(Mask maskToModify, Mask maskOther)
protected Mask	Xor.createFromTwoMasks(Mask maskToModify, Mask maskOther)

Uses of Mask in org.anchoranalysis.plugin.image.bean.mask.provider.convert

Methods in org.anchoranalysis.plugin.image.bean.mask.provider.convert that return Mask

Modifier and Type	Method and Description
protected Mask	FromObjects.createFromDimensions(Dimensions dimensions)
protected Mask	FromChannel.createFromSource(Channel source)
Mask	FromStackChannel.get()

Uses of Mask in org.anchoranalysis.plugin.image.bean.mask.provider.morphological

Methods in org.anchoranalysis.plugin.image.bean.mask.provider.morphological that return Mask

Modifier and Type	Method and Description
protected Mask	Box.createFromDimensions(Dimensions dimensions)
Mask	ExteriorContour.createFromMask(Mask mask)
Mask	FitBoxToOnVoxels.createFromMask(Mask mask)
Mask	MorphologicalOperatorBase.createFromMask(Mask mask)

Methods in org.anchoranalysis.plugin.image.bean.mask.provider.morphological with parameters of type Mask

Modifier and Type	Method and Description
protected void	Dilate.applyMorphologicalOperation(Mask source, boolean do3D)
protected void	Erode.applyMorphologicalOperation(Mask source, boolean do3D)
protected abstract void	MorphologicalOperatorBase.applyMorphologicalOperation(Mask source, boolean do3D)
Mask	ExteriorContour.createFromMask(Mask mask)
Mask	FitBoxToOnVoxels.createFromMask(Mask mask)
Mask	MorphologicalOperatorBase.createFromMask(Mask mask)

Uses of Mask in org.anchoranalysis.plugin.image.bean.mask.provider.predicate

Methods in org.anchoranalysis.plugin.image.bean.mask.provider.predicate that return Mask

Modifier and Type	Method and Description
protected Mask	IfPredicateBase.createFromMask(Mask mask)

Methods in org.anchoranalysis.plugin.image.bean.mask.provider.predicate with parameters of type Mask

Modifier and Type	Method and Description
protected Mask	IfPredicateBase.createFromMask(Mask mask)
protected boolean	IfNotEmpty.predicate(Mask mask)
protected boolean	IfObjectFilter.predicate(Mask mask)
protected boolean	IfStackExists.predicate(Mask mask)
protected boolean	IfKeyValueCondition.predicate(Mask mask)
protected abstract boolean	IfPredicateBase.predicate(Mask mask) If this evaluates true, the mask will be returned as-is, otherwise maskElse is returned

Uses of Mask in org.anchoranalysis.plugin.image.bean.mask.provider.segment

Methods in org.anchoranalysis.plugin.image.bean.mask.provider.segment that return Mask

Modifier and Type	Method and Description
protected Mask	SegmentChannel.createFromSource(Channel source)
protected Mask	Threshold.createFromSource(Channel source)

Uses of Mask in org.anchoranalysis.plugin.image.bean.mask.provider.slice

Methods in org.anchoranalysis.plugin.image.bean.mask.provider.slice that return Mask

Modifier and Type	Method and Description
Mask	FlattenZ.createFromMask(Mask mask)
Mask	RepeatSlice.createFromMask(Mask mask)

Methods in org.anchoranalysis.plugin.image.bean.mask.provider.slice with parameters of type Mask

Modifier and Type	Method and Description
Mask	FlattenZ.createFromMask(Mask mask)
Mask	RepeatSlice.createFromMask(Mask mask)

Uses of Mask in org.anchoranalysis.plugin.image.bean.object.provider.connected

Methods in org.anchoranalysis.plugin.image.bean.object.provider.connected that return types with arguments of type Mask

Modifier and Type	Method and Description
Provider<Mask>	ConnectedComponentsFromMask.getMask()

Method parameters in org.anchoranalysis.plugin.image.bean.object.provider.connected with type arguments of type Mask

Modifier and Type	Method and Description
void	ConnectedComponentsFromMask.setMask(Provider<Mask> mask)

Uses of Mask in org.anchoranalysis.plugin.image.bean.object.provider.mask

Methods in org.anchoranalysis.plugin.image.bean.object.provider.mask that return types with arguments of type Mask

Modifier and Type	Method and Description
Provider<Mask>	FromMask.getMask()

Method parameters in org.anchoranalysis.plugin.image.bean.object.provider.mask with type arguments of type Mask

Modifier and Type	Method and Description
void	FromMask.setMask(Provider<Mask> mask)

Uses of Mask in org.anchoranalysis.plugin.image.bean.stack.provider

Methods in org.anchoranalysis.plugin.image.bean.stack.provider that return types with arguments of type Mask

Modifier and Type	Method and Description
Provider<Mask>	FromChannelOrMask.getMask() A mask that is provided to the stack.

Method parameters in org.anchoranalysis.plugin.image.bean.stack.provider with type arguments of type Mask

Modifier and Type	Method and Description
void	FromChannelOrMask.setMask(Provider<Mask> mask) A mask that is provided to the stack.

Uses of Mask in org.anchoranalysis.plugin.image.channel

Methods in org.anchoranalysis.plugin.image.channel that return Mask

Modifier and Type	Method and Description
static Mask	DimensionsChecker.createSameSize(MaskProvider provider, String providerName, Channel channelSameSize) Creates a new channel from a provider, making sure it's the same size as an an existing channel

Methods in org.anchoranalysis.plugin.image.channel with parameters of type Mask

Modifier and Type	Method and Description
static void	DimensionsChecker.check(Channel channel, Mask mask)
static void	DimensionsChecker.check(Mask maskToCheck, String channelToCheckName, Dimensions dimensionsFromChannel) Checks a channel to make sure it's the same size as an an existing channel

Uses of Mask in org.anchoranalysis.plugin.imagej.bean.mask.provider

Methods in org.anchoranalysis.plugin.imagej.bean.mask.provider that return Mask

Modifier and Type	Method and Description
Mask	MorphologicalOperation.createFromMask(Mask mask)
Mask	FillHoles.createFromMask(Mask mask)

Methods in org.anchoranalysis.plugin.imagej.bean.mask.provider with parameters of type Mask

Modifier and Type	Method and Description
Mask	MorphologicalOperation.createFromMask(Mask mask)
Mask	FillHoles.createFromMask(Mask mask)

Uses of Mask in org.anchoranalysis.plugin.mpp.bean.check

Methods in org.anchoranalysis.plugin.mpp.bean.check that return Mask

Modifier and Type	Method and Description
protected Mask	CheckMarkWithMask.createChannel()

Methods in org.anchoranalysis.plugin.mpp.bean.check that return types with arguments of type Mask

Modifier and Type	Method and Description
Provider<Mask>	CheckMarkWithMask.getMask()

Method parameters in org.anchoranalysis.plugin.mpp.bean.check with type arguments of type Mask

Modifier and Type	Method and Description
void	CheckMarkWithMask.setMask(Provider<Mask> mask)

Uses of Mask in org.anchoranalysis.plugin.mpp.bean.contour

Methods in org.anchoranalysis.plugin.mpp.bean.contour that return types with arguments of type Mask

Modifier and Type	Method and Description
Provider<Mask>	TraverseOuterContourOnImage.getMaskContour()
Provider<Mask>	TraverseOuterContourOnImage.getMaskFilled()

Method parameters in org.anchoranalysis.plugin.mpp.bean.contour with type arguments of type Mask

Modifier and Type	Method and Description
void	TraverseOuterContourOnImage.setMaskContour(Provider<Mask> maskContour)
void	TraverseOuterContourOnImage.setMaskFilled(Provider<Mask> maskFilled)

Uses of Mask in org.anchoranalysis.plugin.mpp.bean.proposer.points

Methods in org.anchoranalysis.plugin.mpp.bean.proposer.points that return types with arguments of type Mask

Modifier and Type	Method and Description
Provider<Mask>	XYOrientationExtendToZ.getMask()
Provider<Mask>	XYOrientationExtendToZ.getMaskFilled()

Method parameters in org.anchoranalysis.plugin.mpp.bean.proposer.points with type arguments of type Mask

Modifier and Type	Method and Description
void	XYOrientationExtendToZ.setMask(Provider<Mask> mask)
void	XYOrientationExtendToZ.setMaskFilled(Provider<Mask> maskFilled)

Uses of Mask in org.anchoranalysis.plugin.mpp.bean.proposer.points.contour

Methods in org.anchoranalysis.plugin.mpp.bean.proposer.points.contour that return types with arguments of type Mask

Modifier and Type	Method and Description
Provider<Mask>	FindPointOnContourWalk.getMask()

Method parameters in org.anchoranalysis.plugin.mpp.bean.proposer.points.contour with type arguments of type Mask

Modifier and Type	Method and Description
void	FindPointOnContourWalk.setMask(Provider<Mask> mask)

Uses of Mask in org.anchoranalysis.plugin.points.bean.convexhull

Methods in org.anchoranalysis.plugin.points.bean.convexhull that return Mask

Modifier and Type	Method and Description
Mask	ConvexHullBase.createFromMask(Mask mask)
protected abstract Mask	ConvexHullBase.createFromMask(Mask mask, Mask outline)
protected Mask	ConvexHull3D.createFromMask(Mask maskIn, Mask outline)
protected Mask	ConvexHull2D.createFromMask(Mask mask, Mask outline)

Methods in org.anchoranalysis.plugin.points.bean.convexhull with parameters of type Mask

Modifier and Type	Method and Description
Mask	ConvexHullBase.createFromMask(Mask mask)
protected abstract Mask	ConvexHullBase.createFromMask(Mask mask, Mask outline)
protected Mask	ConvexHull3D.createFromMask(Mask maskIn, Mask outline)
protected Mask	ConvexHull2D.createFromMask(Mask mask, Mask outline)

Uses of Mask in org.anchoranalysis.test.image

Methods in org.anchoranalysis.test.image that return Mask

Modifier and Type	Method and Description
static Mask	MaskFixture.create(boolean do3D) Creates the Mask with the default corner and no assigned resolution.
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) Creates the Mask with a particular corner and no assigned resolution.
static Mask	MaskFixture.create(Point3i corner, boolean do3D, Optional<Resolution> resolution) Creates the Mask with a particular corner and a particular resolution.