Uses of Class
org.anchoranalysis.image.bean.provider.MaskProvider

Packages that use MaskProvider

Package	Description
org.anchoranalysis.image.bean.provider	Base classes for providers of different core data entities related to images.
org.anchoranalysis.plugin.fiji.bean.mask.provider	Implementations of MaskProvider that use FIJI.
org.anchoranalysis.plugin.image.bean.channel.provider.mask	Implementations of ChannelProvider that involve conversion from or application of Masks.
org.anchoranalysis.plugin.image.bean.channel.provider.score	Implementations of ChannelProvider that assign a score to particular subregions of a channel.
org.anchoranalysis.plugin.image.bean.histogram.provider	Implementations of HistogramProvider.
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.mask	Implementations of ObjectCollectionProvider involving a Mask.
org.anchoranalysis.plugin.image.bean.object.provider.segment	Implementations of ObjectCollectionProvider involving segmentation.
org.anchoranalysis.plugin.image.bean.stack.provider.color	Implementations of StackProvider that color portions of an image.
org.anchoranalysis.plugin.image.channel	Non-beans for operations or calculations relating to Channels.
org.anchoranalysis.plugin.image.feature.bean.object.single.shared	Implementations of FeatureSingleObject that use SharedObjects for calculations.
org.anchoranalysis.plugin.image.feature.bean.shared.object	Beans involving SharedObjects and ObjectCollection.
org.anchoranalysis.plugin.imagej.bean.mask.provider	Implementations of MaskProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.object.provider	Implementations of ObjectCollectionProvider that call ImageJ.
org.anchoranalysis.plugin.points.bean.convexhull	Convex hull operations.

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

Subclasses of MaskProvider in org.anchoranalysis.image.bean.provider

Modifier and Type	Class	Description
class	MaskProviderUnary	Implementation of MaskProvider that calls a single delegate MaskProvider.

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

Subclasses of MaskProvider in org.anchoranalysis.plugin.fiji.bean.mask.provider

Modifier and Type	Class	Description
class	AutoLocalThreshold	Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin

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

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

Modifier and Type	Method	Description
MaskProvider	FromMaskBase.getMask()	The MaskProvider used to create the binary mask.
MaskProvider	UnaryWithMaskBase.getMask()	The MaskProvider used to create the binary mask.

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

Modifier and Type	Method	Description
void	FromMaskBase.setMask(MaskProvider mask)	The MaskProvider used to create the binary mask.
void	UnaryWithMaskBase.setMask(MaskProvider mask)	The MaskProvider used to create the binary mask.

Uses of MaskProvider in org.anchoranalysis.plugin.image.bean.channel.provider.score

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.score that return MaskProvider

Modifier and Type	Method	Description
MaskProvider	ScoreVoxels.getMask()

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.score with parameters of type MaskProvider

Modifier and Type	Method	Description
void	ScoreVoxels.setMask(MaskProvider mask)

Uses of MaskProvider in org.anchoranalysis.plugin.image.bean.histogram.provider

Methods in org.anchoranalysis.plugin.image.bean.histogram.provider that return MaskProvider

Modifier and Type	Method	Description
MaskProvider	FromChannel.getMask()	An optional mask provider to restrict the histogram creation to specific areas.

Methods in org.anchoranalysis.plugin.image.bean.histogram.provider with parameters of type MaskProvider

Modifier and Type	Method	Description
void	FromChannel.setMask(MaskProvider mask)	An optional mask provider to restrict the histogram creation to specific areas.

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

Subclasses of MaskProvider in org.anchoranalysis.plugin.image.bean.mask.provider

Modifier and Type	Class	Description
class	AllValuesOff	Creates a new mask of particular dimensionality where all values are off.
class	AllValuesOn	Creates a new mask of particular dimensionality where all values are on.
class	Duplicate	A provider that creates a duplicate of a given Mask.
class	FromChannelBase	Base-class for MaskProviders that accept a Channel as input.
class	FromDimensionsBase	Base class for MaskProviders that create a mask based on given dimensions.
class	Invert	Switches on voxels to off and vice-versa.
class	Reference	A provider that references an existing Mask by its identifier.
class	ScaleXY	Scales the mask in XY dimensions, but not in Z dimension.

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

Modifier and Type	Method	Description
MaskProvider	Invert.getRestrictTo()	If set, the inversion only occurs on a particular region of the mask, as determined by this mask

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

Modifier and Type	Method	Description
void	Invert.setRestrictTo(MaskProvider restrictTo)	If set, the inversion only occurs on a particular region of the mask, as determined by this mask

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

Subclasses of MaskProvider in org.anchoranalysis.plugin.image.bean.mask.provider.combine

Modifier and Type	Class	Description
class	And	Outputs the logical operation and voxelwise on both masks, modifying {mask} with the result.
class	CombineBase	Base class for combining two masks.
class	IfHighLow	Outputs the logical operation iff first==HIGH and second==LOW then LOW voxelwise on both masks, modifying {mask} with the result.
class	Or	Outputs the logical operation or voxelwise on both masks, modifying {mask} with the result.
class	Xor	Outputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask} with the result.

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

Modifier and Type	Method	Description
MaskProvider	CombineBase.getReceive()	The MaskProvider for the second mask to be combined.

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

Modifier and Type	Method	Description
void	CombineBase.setReceive(MaskProvider receive)	The MaskProvider for the second mask to be combined.

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

Subclasses of MaskProvider in org.anchoranalysis.plugin.image.bean.mask.provider.convert

Modifier and Type	Class	Description
class	FromChannel	Creates a mask from an existing channel, reusing the channel's buffer and considering all 0 values as off, and 255 values as on.
class	FromObjects	Creates a Mask from a collection of object-masks.
class	FromStackChannel	Creates a Mask from a specific channel in a stack.

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

Subclasses of MaskProvider in org.anchoranalysis.plugin.image.bean.mask.provider.morphological

Modifier and Type	Class	Description
class	Box	Creates a Mask where all pixels are on within a box region.
class	Dilate	Performs a dilation morphological operation on BinaryVoxels.
class	Erode	Performs an erosion morphological operation on BinaryVoxels.
class	ExteriorContour	Finds the exterior outer contour for a Mask that forms its outline.
class	FitBoxToOnVoxels	Fits a box around the on voxels.
class	MorphologicalOperatorBase	Base class for performing morphological operations on BinaryVoxels.

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

Subclasses of MaskProvider in org.anchoranalysis.plugin.image.bean.mask.provider.predicate

Modifier and Type	Class	Description
class	IfKeyValueCondition	The current mask is returned if a condition on key-values is satisfied otherwise maskElse is returned.
class	IfNotEmpty	The current mask is returned if it's non-empty (at least one on voxel) otherwise maskElse is returned.
class	IfObjectFilter	The current mask is returned if the mask (treated as an object) passed an object-filter, otherwise maskElse is returned.
class	IfPredicateBase	Base class which multiplexes between the current mask and an alternative depending if a condition is met.
class	IfStackExists	The current mask is a particular stack exists (at least one on voxel) otherwise maskElse is returned.

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

Modifier and Type	Method	Description
MaskProvider	IfPredicateBase.getMaskElse()	Returned instead of mask if the predicate is not satisfied.

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

Modifier and Type	Method	Description
void	IfPredicateBase.setMaskElse(MaskProvider maskElse)	Returned instead of mask if the predicate is not satisfied.

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

Subclasses of MaskProvider in org.anchoranalysis.plugin.image.bean.mask.provider.segment

Modifier and Type	Class	Description
class	SegmentChannel	Applies a BinarySegmentation algorithm to derive a mask from a channel
class	Threshold	Thresholds a channel to produce a mask, reusing (and modifying) the input-buffers of the channel if possible.

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

Modifier and Type	Method	Description
MaskProvider	SegmentChannel.getMask()	An optional mask which restricts the algorithm to only parts of the channel where the mask has an on voxel

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

Modifier and Type	Method	Description
void	SegmentChannel.setMask(MaskProvider mask)	An optional mask which restricts the algorithm to only parts of the channel where the mask has an on voxel

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

Subclasses of MaskProvider in org.anchoranalysis.plugin.image.bean.mask.provider.slice

Modifier and Type	Class	Description
class	FlattenZ	Flattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
class	RepeatSlice	Creates a new mask with specific dimensions that repeatedly duplicates a slice from an existing mask

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

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

Modifier and Type	Method	Description
MaskProvider	AndObjectsWithMasks.getMask()

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

Modifier and Type	Method	Description
void	AndObjectsWithMasks.setMask(MaskProvider mask)

Uses of MaskProvider in org.anchoranalysis.plugin.image.bean.object.provider.segment

Methods in org.anchoranalysis.plugin.image.bean.object.provider.segment that return MaskProvider

Modifier and Type	Method	Description
MaskProvider	SegmentChannel.getMask()	Optional mask to restrict the segmentation area.

Methods in org.anchoranalysis.plugin.image.bean.object.provider.segment with parameters of type MaskProvider

Modifier and Type	Method	Description
void	SegmentChannel.setMask(MaskProvider mask)	Optional mask to restrict the segmentation area.

Uses of MaskProvider in org.anchoranalysis.plugin.image.bean.stack.provider.color

Methods in org.anchoranalysis.plugin.image.bean.stack.provider.color that return MaskProvider

Modifier and Type	Method	Description
MaskProvider	ColoredMask.getMask()

Methods in org.anchoranalysis.plugin.image.bean.stack.provider.color with parameters of type MaskProvider

Modifier and Type	Method	Description
void	ColoredMask.setMask(MaskProvider mask)

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

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

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

Uses of MaskProvider in org.anchoranalysis.plugin.image.feature.bean.object.single.shared

Methods in org.anchoranalysis.plugin.image.feature.bean.object.single.shared that return MaskProvider

Modifier and Type	Method	Description
MaskProvider	PairedWithMask.getMask()

Methods in org.anchoranalysis.plugin.image.feature.bean.object.single.shared with parameters of type MaskProvider

Modifier and Type	Method	Description
void	PairedWithMask.setMask(MaskProvider mask)

Uses of MaskProvider in org.anchoranalysis.plugin.image.feature.bean.shared.object

Methods in org.anchoranalysis.plugin.image.feature.bean.shared.object that return MaskProvider

Modifier and Type	Method	Description
MaskProvider	MaskAsSingleObject.getMask()	The provider for the mask to be treated as a single object.

Methods in org.anchoranalysis.plugin.image.feature.bean.shared.object with parameters of type MaskProvider

Modifier and Type	Method	Description
void	MaskAsSingleObject.setMask(MaskProvider mask)	The provider for the mask to be treated as a single object.

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

Subclasses of MaskProvider in org.anchoranalysis.plugin.imagej.bean.mask.provider

Modifier and Type	Class	Description
class	FillHoles	Fills holes in a mask, with options to skip holes touching the border or exceeding a maximum volume.
class	MorphologicalOperation	Applies an ImageJ (2D) morphological operation to each slice

Uses of MaskProvider in org.anchoranalysis.plugin.imagej.bean.object.provider

Methods in org.anchoranalysis.plugin.imagej.bean.object.provider that return MaskProvider

Modifier and Type	Method	Description
MaskProvider	FillHoles.getMask()

Methods in org.anchoranalysis.plugin.imagej.bean.object.provider with parameters of type MaskProvider

Modifier and Type	Method	Description
void	FillHoles.setMask(MaskProvider mask)

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

Subclasses of MaskProvider in org.anchoranalysis.plugin.points.bean.convexhull

Modifier and Type	Class	Description
class	ConvexHull2D	Sets particular voxels to high only if they exist on the convex-hull of the outline of a mask.
class	ConvexHull3D	Calculates a 3D convex hull from a binary mask.
class	ConvexHullBase	Base class for convex hull implementations.