Uses of Class
org.anchoranalysis.core.exception.CreateException

Packages that use CreateException

Package	Description
org.anchoranalysis.annotation.io.assignment	A pairing of objects from two collections (bipartite matching).
org.anchoranalysis.annotation.io.bean.comparer	What to compare an annotation (ground truth) against?
org.anchoranalysis.bean.permute	Applying permutations to a bean's fields.
org.anchoranalysis.bean.shared	Utility beans which have a generally broader use than a specific module.
org.anchoranalysis.image.bean.channel	Base classes for performing operations on Channels.
org.anchoranalysis.image.bean.displayer
org.anchoranalysis.image.bean.spatial.direction	Beans to specify a direction.
org.anchoranalysis.image.core.bufferedimage	Conversions and operations involving Java AWT's BufferedImage.
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.object	The key data entity org.anchoranalysis.image.voxel.object and related-classes and operations.
org.anchoranalysis.image.core.object.label	Labelling elements (object-masks or similar) with unique successive integers in a channel.
org.anchoranalysis.image.core.object.scale	Scaling object-collections, or lists of elements with object-representations.
org.anchoranalysis.image.core.points	Operations that extract points from image data entities or vice versa.
org.anchoranalysis.image.core.stack	Defines the key data object, Stack, and related classes.
org.anchoranalysis.image.io.bean.channel	Beans pertaining to reading Channels as input.
org.anchoranalysis.image.io.object.output.rgb	Writing an ObjectCollection to the filesystem as RGB raster-images.
org.anchoranalysis.image.io.stack	Non-bean classes for reading / writing a Stack from and to the filesystem.
org.anchoranalysis.image.voxel	Data-structures to store and manipulate image raster-data or voxels.
org.anchoranalysis.image.voxel.binary	The BinaryVoxels class and related operations.
org.anchoranalysis.image.voxel.convert.bufferedimage	Converts anchor data-structures to the BufferedImage used by Java's AWT.
org.anchoranalysis.image.voxel.datatype	The different data-types that can be used to represent voxels.
org.anchoranalysis.image.voxel.neighborhood	A region in proximity to a voxel, encompassing this voxel as well as others.
org.anchoranalysis.image.voxel.object	The fundamental data class that is an ObjectMask and related structures.
org.anchoranalysis.image.voxel.object.morphological	Morphological operations applied to ObjectMasks.
org.anchoranalysis.io.bioformats	Non-bean classes for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.copyconvert	Converts the byte stream opened by Bioformats into channels of particular data-type.
org.anchoranalysis.io.input.bean.namer	Beans to derive names (compact unique identifiers) from files.
org.anchoranalysis.mpp.bean.mark	Beans generally related to Marks.
org.anchoranalysis.mpp.feature.addcriteria	Criteria for adding edges during optimization of marked-point-processes.
org.anchoranalysis.mpp.feature.bean.energy.scheme	Creating EnergySchemes.
org.anchoranalysis.mpp.feature.energy.scheme	Factorized form of storing the energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.io.input	Non-beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.io.output	Non-beans for writing data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.overlay	Any Overlay related to a Mark.
org.anchoranalysis.overlay	Overlays and related classes involving drawing entities on top of an image.
org.anchoranalysis.overlay.object	An implementation of an Overlay that draws an ObjectMask on an image.
org.anchoranalysis.plugin.annotation.bean.comparison.assigner	Pairs annotations from two different sets, creating an assignment of some type.
org.anchoranalysis.plugin.fiji.bean.mask.provider	Implementations of MaskProvider that use FIJI.
org.anchoranalysis.plugin.image.bean.channel.convert	Implementations of ConvertChannelTo and ConvertChannelToWithHistogram.
org.anchoranalysis.plugin.image.bean.mask.provider	Implementations of MaskProvider.
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.segment	Implementations of MaskProvider where an ObjectCollection is created by segmenting a Channel.
org.anchoranalysis.plugin.image.bean.stack.provider.color	Implementations of StackProvider that color portions of an image.
org.anchoranalysis.plugin.image.bean.thumbnail.stack	Implementations of ThumbnailFromStack.
org.anchoranalysis.plugin.image.feature.bean.object.combine	Features from combinations of ObjectMasks.
org.anchoranalysis.plugin.image.intensity.level	Non-beans for calculating a thresholding level from itensity values.
org.anchoranalysis.plugin.image.task.bean.combine	Combining multiple images together into a single image.
org.anchoranalysis.plugin.image.task.bean.feature.source	Source of rows in feature-tables with FeatureSource and derived classes.
org.anchoranalysis.plugin.image.task.bean.grouped	Tasks that involved stacks (usually each channel from an image) that are somehow grouped-together.
org.anchoranalysis.plugin.image.task.bean.grouped.histogram	Task(s) to export histograms of intensity values.
org.anchoranalysis.plugin.image.task.feature	Non-bean classes pertaining to Features as used in tasks.
org.anchoranalysis.plugin.image.task.labeller	Non-bean classes about labelling images.
org.anchoranalysis.plugin.image.task.segment	Non-bean classes for image-segmentation.
org.anchoranalysis.plugin.image.task.stack	Non-bean classes pertaining to stacks and channels as used in tasks.
org.anchoranalysis.plugin.image.thumbnail	Non-bean classes for thumbnail creation.
org.anchoranalysis.plugin.io.bean.channel.map	Implementations of ChannelMapCreator.
org.anchoranalysis.plugin.io.bean.file.copy.method	Methods for copying files on the file-system.
org.anchoranalysis.plugin.io.bean.file.namer	Implementations of FileNamer.
org.anchoranalysis.plugin.mpp.bean.define	Beans related to Define involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.stack.provider	Implementations of StackProvider involving Mark or related classes.
org.anchoranalysis.plugin.opencv.convert	Conversion to/from OpenCV data-structures.
org.anchoranalysis.plugin.points.bean.fitter	Fitting geometric structures to points.
org.anchoranalysis.plugin.points.calculate.ellipsoid	CalculationPart related to fitting ellipsoids to points by least-squares.
org.anchoranalysis.plugin.points.convexhull	Non-bean convex hull operations.
org.anchoranalysis.test.feature.plugins	Testing utilities and fixtures with no greater downstream dependency than anchor-image-feature or anchor-mpp.

Uses of CreateException in org.anchoranalysis.annotation.io.assignment

Method parameters in org.anchoranalysis.annotation.io.assignment with type arguments of type CreateException

Modifier and Type	Method	Description
static <T> CostMatrix<T>	CostMatrix.create(List<T> first, List<T> second, boolean symmetric, CheckedToDoubleBiFunction<T,T,CreateException> costCalculator)	Creates by calculating the cost between elements.

Methods in org.anchoranalysis.annotation.io.assignment that throw CreateException

Modifier and Type	Method	Description
static <T> CostMatrix<T>	CostMatrix.create(List<T> first, List<T> second, boolean symmetric, CheckedToDoubleBiFunction<T,T,CreateException> costCalculator)	Creates by calculating the cost between elements.

Uses of CreateException in org.anchoranalysis.annotation.io.bean.comparer

Methods in org.anchoranalysis.annotation.io.bean.comparer that throw CreateException

Modifier and Type	Method	Description
List<NameValue<Stack>>	MultipleComparer.createComparisonStacks(AnnotationWithMarks annotation, DisplayStack background, Path annotationPath, ColorScheme colorScheme, Path modelDirectory, OperationContext context, boolean debugMode)	Creates a Stack illustrating the comparison between annotation and each source in sources.

Uses of CreateException in org.anchoranalysis.bean.permute

Methods in org.anchoranalysis.bean.permute that throw CreateException

Modifier and Type	Method	Description
<S> List<T>	PermutedCopyCreator.createPermutedCopies(List<T> beans, PermuteProperty<S> propertyToPermute, PermutationAssigner setter)	Applies a permutation to a copy of each element in a list of beans, updating the custom name of each bean to reflect the permutation.

Uses of CreateException in org.anchoranalysis.bean.shared

Methods in org.anchoranalysis.bean.shared that throw CreateException

Modifier and Type	Method	Description
Map<String,String>	StringMap.create()	Derives a Map representation for the mapping.

Uses of CreateException in org.anchoranalysis.image.bean.channel

Methods in org.anchoranalysis.image.bean.channel that throw CreateException

Modifier and Type	Method	Description
abstract ChannelConverter<T>	ConvertChannelTo.createConverter()	Creates the converter.

Uses of CreateException in org.anchoranalysis.image.bean.displayer

Methods in org.anchoranalysis.image.bean.displayer that throw CreateException

Modifier and Type	Method	Description
DisplayStack	StackDisplayer.deriveFrom(Channel channel)	Creates from a Channel.
DisplayStack	StackDisplayer.deriveFrom(RGBStack rgbStack)	Derives a DisplayStack from a RGBStack.
DisplayStack	StackDisplayer.deriveFrom(Stack stack)	Derives a DisplayStack from a RGBStack.

Uses of CreateException in org.anchoranalysis.image.bean.spatial.direction

Methods in org.anchoranalysis.image.bean.spatial.direction that throw CreateException

Modifier and Type	Method	Description
DirectionVector	AxisAlignedUnitVector.createVector()
abstract DirectionVector	DirectionVectorBean.createVector()	Creates a vector in a particular direction.

Uses of CreateException in org.anchoranalysis.image.core.bufferedimage

Methods in org.anchoranalysis.image.core.bufferedimage that throw CreateException

Modifier and Type	Method	Description
static BufferedImage	BufferedImageFromStack.create(Stack stack)	Creates a BufferedImage from a Stack.
static BufferedImage	BufferedImageFromStack.createRGB(Voxels<UnsignedByteBuffer> red, Voxels<UnsignedByteBuffer> green, Voxels<UnsignedByteBuffer> blue, Extent extent)	Creates a BufferedImage from three Voxels<UnsignedByteBuffer> representing respectively, red, green, blue color components.

Uses of CreateException in org.anchoranalysis.image.core.channel.factory

Methods in org.anchoranalysis.image.core.channel.factory that throw CreateException

Modifier and Type	Method	Description
Channel	ChannelFactory.createEmptyInitialisedToSupportMaxValue(Dimensions dimensions, long maxIntensityValueNeeded)	Creates an empty initialized channel with discrete type with as minimal as needed data-type to support a maximum value.

Uses of CreateException in org.anchoranalysis.image.core.dimensions

Constructors in org.anchoranalysis.image.core.dimensions that throw CreateException

Modifier	Constructor	Description
	Resolution(double x, double y, double z)	Creates with a resolution from three double values for each dimension.
	Resolution(Tuple3d tuple)	Constructs a resolution from a tuple.

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

Methods in org.anchoranalysis.image.core.object that throw CreateException

Modifier and Type	Method	Description
static ObjectMask	ObjectFromPointsFactory.create(Collection<Point3i> points)	Create an ObjectMask from a collection of points.
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.
static Histogram	HistogramFromObjectsFactory.createFrom(Channel channel, Mask mask)	Creates a Histogram of all voxel intensity values in channel corresponding to Mask.

Uses of CreateException in org.anchoranalysis.image.core.object.label

Methods in org.anchoranalysis.image.core.object.label that throw CreateException

Modifier and Type	Method	Description
List<T>	DecodeLabels.create(int smallVolumeThreshold)	Creates a list of elements from voxels that are labelled with unique integers (sequentially increasing).
Map<T,T>	DecodeLabels.create(Map<Integer,T> labelMap, UnaryOperator<T> operationAfterScaling)	Creates a map of elements to other elements that are labelled with unique integers (sequentially increasing) in voxels.
Channel	LabelObjects.createLabelledChannel(BoundedList<T> elements, Optional<Map<Integer,T>> mapLabels)	Creates a channel that contains a unique integer (label) for each element's object-representation.
void	LabelObjects.labelElements(Channel channel, Iterable<T> elements, Optional<Map<Integer,T>> mapLabels)	Replaces the contents of the channel so that all element's voxels are labelled with successive unique integer identifiers 1,2,3 etc. and voxels in no element are 0.

Uses of CreateException in org.anchoranalysis.image.core.object.scale

Constructors in org.anchoranalysis.image.core.object.scale that throw CreateException

Modifier	Constructor	Description
	ScaledElements(List<T> elements, ScaleFactor scaleFactor, ObjectScalingMethod scalingMethod, Optional<UnaryOperator<T>> preOperation, Optional<UnaryOperator<T>> postOperation, AccessObjectMask<T> access)	Creates elements to be scaled.

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

Methods in org.anchoranalysis.image.core.points that throw CreateException

Modifier and Type	Method	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<Point2i>	PointsFromObject.listFrom2i(ObjectMask object)	A list of two-dimensional integer points from the entire object-mask.
static List<Point2i>	PointsFromObject.listFromOutline2i(ObjectMask object)	A list of points as three-dimensional integers from the outline of an object-mask

Uses of CreateException in org.anchoranalysis.image.core.stack

Methods in org.anchoranalysis.image.core.stack that throw CreateException

Modifier and Type	Method	Description
DisplayStack	DisplayStack.extractSlice(int z)	Extract a particular z-slice from the DisplayStack as a new stack, applying any applicable conversion.

Constructors in org.anchoranalysis.image.core.stack that throw CreateException

Modifier	Constructor	Description
	DisplayStack(Stack stack, boolean eventuallyThree, Function<VoxelDataType,ChannelConverterAttached<Channel,UnsignedByteBuffer>> createConverter)	Create for a particular Stack that may needed to be converted.
	Stack(boolean rgb, Channel... channels)	Creates from a varying number of channels, and a flag to indicate if they represent an RGB image or not.
	Stack(Dimensions dimensions, ChannelFactorySingleType factory, int numberChannels, boolean rgb)	Create with a particular number of empty Channels.

Uses of CreateException in org.anchoranalysis.image.io.bean.channel

Methods in org.anchoranalysis.image.io.bean.channel that throw CreateException

Modifier and Type	Method	Description
abstract ChannelMap	ChannelMapCreator.create(OpenedImageFile openedFile, Logger logger)	Creates the ChannelMap.

Uses of CreateException in org.anchoranalysis.image.io.object.output.rgb

Methods in org.anchoranalysis.image.io.object.output.rgb that throw CreateException

Modifier and Type	Method	Description
protected RGBStack	DrawCroppedObjectsGenerator.generateBackgroundRegion(ObjectCollectionWithProperties objects, io.vavr.control.Either<Dimensions,DisplayStack> background)
protected abstract RGBStack	ObjectsAsRGBGenerator.generateBackgroundRegion(ObjectCollectionWithProperties objects, io.vavr.control.Either<Dimensions,DisplayStack> background)	Creates a RGBStack containing the background, without objects being drawn upon it.
protected ObjectCollectionWithProperties	DrawCroppedObjectsGenerator.generateMasks(ObjectCollectionWithProperties objects)
protected abstract ObjectCollectionWithProperties	ObjectsAsRGBGenerator.generateMasks(ObjectCollectionWithProperties objects)	Creates a ObjectCollectionWithProperties indicative of the masks that will be imposed on top of the background-region.

Uses of CreateException in org.anchoranalysis.image.io.stack

Methods in org.anchoranalysis.image.io.stack that throw CreateException

Modifier and Type	Method	Description
static RGBStack	ConvertStackToRGB.convert(Stack stack, StackDisplayer displayer, boolean alwaysNew)	Converts all of a DisplayStack to a RGBStack.

Uses of CreateException in org.anchoranalysis.image.voxel

Methods in org.anchoranalysis.image.voxel that throw CreateException

Modifier and Type	Method	Description
BoundedVoxels<T>	BoundedVoxels.region(BoundingBox box, boolean reuseIfPossible)	A (sub-)region of the voxels.
BoundedVoxels<T>	BoundedVoxels.regionIntersecting(BoundingBox box, int voxelValueForRest)	Like BoundedVoxels.region(org.anchoranalysis.spatial.box.BoundingBox, boolean) but only expects a bounding-box that intersects at least partially.
BoundedVoxels<T>	BoundedVoxels.regionZ(int zMin, int zMax, VoxelsFactoryTypeBound<T> factory)	Creates an box with a subrange of the slices.

Uses of CreateException in org.anchoranalysis.image.voxel.binary

Methods in org.anchoranalysis.image.voxel.binary that throw CreateException

Modifier and Type	Method	Description
static BinaryVoxels<?>	BinaryVoxelsFactory.createEmptyOff(Extent extent, VoxelDataType dataType)	Creates an empty binary-voxels of a particular data-type with all voxels initialized to off. (0).

Uses of CreateException in org.anchoranalysis.image.voxel.convert.bufferedimage

Methods in org.anchoranalysis.image.voxel.convert.bufferedimage that throw CreateException

Modifier and Type	Method	Description
static BufferedImage	BufferedImageFromVoxels.createGrayscaleByte(Voxels<UnsignedByteBuffer> voxels)	Creates a BufferedImage from a Voxels<UnsignedByteBuffer>.
static BufferedImage	BufferedImageFromVoxels.createGrayscaleShort(Voxels<UnsignedShortBuffer> voxels)	Creates a BufferedImage from a Voxels<UnsignedShortBuffer>.

Uses of CreateException in org.anchoranalysis.image.voxel.datatype

Methods in org.anchoranalysis.image.voxel.datatype that throw CreateException

Modifier and Type	Method	Description
static VoxelDataType	CombineTypes.combineTypes(VoxelDataType type1, VoxelDataType type2)	What data-type to use to represent voxels of both type1 and type2?

Uses of CreateException in org.anchoranalysis.image.voxel.neighborhood

Methods in org.anchoranalysis.image.voxel.neighborhood that throw CreateException

Modifier and Type	Method	Description
static <V> GraphWithPayload<V,Integer>	NeighborGraph.create(List<V> vertices, Function<V,ObjectMask> vertexToObject, Extent sceneExtent, boolean preventObjectIntersection, boolean do3D)	Like NeighborGraph.create(ObjectCollection, Extent, boolean, boolean) but extracts objects from a list of elements which form the vertices.
static GraphWithPayload<ObjectMask,Integer>	NeighborGraph.create(ObjectCollection objects, Extent sceneExtent, boolean preventObjectIntersection, boolean do3D)	Create the graph with object-masks as vertices, where edges represent the number of neighboring voxels between objects.

Uses of CreateException in org.anchoranalysis.image.voxel.object

Methods in org.anchoranalysis.image.voxel.object that throw CreateException

Modifier and Type	Method	Description
ObjectMask	ObjectMask.region(BoundingBox box, boolean reuseIfPossible)	A (sub-)region of the object-mask.
ObjectMask	ObjectMask.regionIntersecting(BoundingBox box)	Creates an object-mask covering the a bounding-box (that is required to intersect at least partially)
ObjectMask	ObjectMask.regionZ(int zMin, int zMax)	Creates an object-mask with a subrange of the slices.

Uses of CreateException in org.anchoranalysis.image.voxel.object.morphological

Methods in org.anchoranalysis.image.voxel.object.morphological that throw CreateException

Modifier and Type	Method	Description
static BinaryVoxels<UnsignedByteBuffer>	MorphologicalDilation.dilate(BinaryVoxels<UnsignedByteBuffer> voxels, int iterations, DilationContext context)	Performs a morphological dilation operation.
static ObjectMask	MorphologicalDilation.dilate(ObjectMask object, Optional<Extent> extent, boolean useZ, int iterations, boolean bigNeighborhood)	Dilates an ObjectMask, growing the bounding-box as necessary.
static BinaryVoxels<UnsignedByteBuffer>	MorphologicalErosion.erode(BinaryVoxels<UnsignedByteBuffer> voxels, int iterations, boolean useZ, Optional<Predicate<Point3i>> precondition)	Performs a morphological erosion on a BinaryVoxels<UnsignedByteBuffer> voxels.
static ObjectMask	MorphologicalErosion.erode(ObjectMask object, int iterations, boolean useZ)	Performs a morphological erosion on an ObjectMask.
static ObjectMask	MorphologicalErosion.erode(ObjectMask object, int iterations, boolean useZ, Optional<AcceptIterationPredicate> postcondition)	Performs a morphological erosion on an ObjectMask - with a postcondition.

Uses of CreateException in org.anchoranalysis.io.bioformats

Methods in org.anchoranalysis.io.bioformats that throw CreateException

Modifier and Type	Method	Description
Dimensions	DimensionsCreator.apply(loci.formats.IFormatReader reader, ReadOptions readOptions, int seriesIndex)	Infers the dimensions from an image file.

Uses of CreateException in org.anchoranalysis.io.bioformats.copyconvert

Methods in org.anchoranalysis.io.bioformats.copyconvert that throw CreateException

Modifier and Type	Method	Description
static ConvertTo<?>	ConvertToFactory.create(loci.formats.IFormatReader reader, VoxelDataType targetDataType, int effectiveBitsPerPixel)	Creates a ConvertTo to match the desired voxel-type.

Uses of CreateException in org.anchoranalysis.io.input.bean.namer

Methods in org.anchoranalysis.io.input.bean.namer that throw CreateException

Modifier and Type	Method	Description
protected abstract String	FileNamerIndependent.deriveName(File file, Optional<Path> inputDirectory, int index)	Derives a unique name for this file.

Uses of CreateException in org.anchoranalysis.mpp.bean.mark

Methods in org.anchoranalysis.mpp.bean.mark that throw CreateException

Modifier and Type	Method	Description
abstract VoxelStatistics	MarkRegion.createStatisticsFor(VoxelizedMarkMemo memo, Dimensions dimensions)	Creates voxel statistics for the mark region based on the given memo and dimensions.

Uses of CreateException in org.anchoranalysis.mpp.feature.addcriteria

Methods in org.anchoranalysis.mpp.feature.addcriteria that throw CreateException

Modifier and Type	Method	Description
Optional<T>	AddCriteria.generateEdge(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, EnergyStack energyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)	Generates an edge between two marks based on the defined criteria.
Optional<EnergyPair>	AddCriteriaEnergyPair.generateEdge(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, EnergyStack energyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)
Optional<T>	AddCriteriaNever.generateEdge(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, EnergyStack energyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)
Optional<MarkPair<Mark>>	AddCriteriaPair.generateEdge(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, EnergyStack energyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)
Optional<FeatureList<FeatureInputPairMemo>>	AddCriteriaEnergyPair.orderedListOfFeatures()
Optional<FeatureList<FeatureInputPairMemo>>	AddCriteriaOr.orderedListOfFeatures()
Optional<FeatureList<T>>	OrderedFeatureList.orderedListOfFeatures()	Retrieves an ordered list of features used to determine the AddCriteria.

Uses of CreateException in org.anchoranalysis.mpp.feature.bean.energy.scheme

Methods in org.anchoranalysis.mpp.feature.bean.energy.scheme that throw CreateException

Modifier and Type	Method	Description
abstract EnergyScheme	EnergySchemeCreator.create()	Creates an EnergyScheme instance.
EnergyScheme	EnergySchemeCreatorByElement.create()

Uses of CreateException in org.anchoranalysis.mpp.feature.energy.scheme

Methods in org.anchoranalysis.mpp.feature.energy.scheme that throw CreateException

Modifier and Type	Method	Description
Dictionary	DictionaryForImageCreator.create(EnergyStackWithoutParameters energyStack)	Creates a dictionary containing calculated image features for a given energy stack.
AddCriteriaEnergyPair	EnergySchemeWithSharedFeatures.createAddCriteria()	Creates an AddCriteriaEnergyPair based on the energy scheme.
Dictionary	EnergyScheme.createDictionary()	Creates and returns the associated Dictionary or an empty dictionary if none is associated.

Constructors in org.anchoranalysis.mpp.feature.energy.scheme that throw CreateException

Modifier	Constructor	Description
	EnergyScheme(FeatureList<FeatureInputSingleMemo> individual, FeatureList<FeatureInputPairMemo> pair, FeatureList<FeatureInputAllMemo> all, RegionMap regionMap, AddCriteriaPair pairAddCriteria)	Creates an energy scheme with the specified features and region map.
	EnergyScheme(FeatureList<FeatureInputSingleMemo> individual, FeatureList<FeatureInputPairMemo> pair, FeatureList<FeatureInputAllMemo> all, RegionMap regionMap, AddCriteriaPair pairAddCriteria, Optional<DictionaryProvider> dictionary, List<NamedBean<Feature<FeatureInputStack>>> listImageFeatures)	Creates an energy scheme with the specified features, region map, and additional options.

Uses of CreateException in org.anchoranalysis.mpp.io.input

Methods in org.anchoranalysis.mpp.io.input that throw CreateException

Modifier and Type	Method	Description
static MarksInitialization	MarksInitializationFactory.create(Optional<? extends ExportSharedObjects> input, InitializationContext context, Optional<Define> define)	Creates a new MarksInitialization instance.
static MarksInitialization	MarksInitializationFactory.createFromExisting(InitializationContext context, Optional<Define> define, Optional<SharedObjects> sharedObjects, Optional<Dictionary> dictionary)	Creates a new MarksInitialization instance from existing shared objects and dictionary.

Uses of CreateException in org.anchoranalysis.mpp.io.output

Methods in org.anchoranalysis.mpp.io.output that throw CreateException

Modifier and Type	Method	Description
static DisplayStack	BackgroundCreator.createBackground(NamedProviderStore<Stack> stackCollection, String backgroundStackName, StackDisplayer displayer)	Creates a background DisplayStack from a named stack in a collection.

Uses of CreateException in org.anchoranalysis.mpp.overlay

Methods in org.anchoranalysis.mpp.overlay that throw CreateException

Modifier and Type	Method	Description
ObjectWithProperties	OverlayMark.createObject(Dimensions dimensionsEntireImage, BinaryValuesByte binaryValuesOut)

Uses of CreateException in org.anchoranalysis.overlay

Methods in org.anchoranalysis.overlay that throw CreateException

Modifier and Type	Method	Description
abstract ObjectWithProperties	Overlay.createObject(Dimensions dimensionsEntireImage, BinaryValuesByte binaryValuesOut)	Derives an object-mask representation of the overlay to be drawn with overlayWriter.

Uses of CreateException in org.anchoranalysis.overlay.object

Methods in org.anchoranalysis.overlay.object that throw CreateException

Modifier and Type	Method	Description
ObjectWithProperties	OverlayObjectMask.createObject(Dimensions dimensionsEntireImage, BinaryValuesByte binaryValuesOut)

Uses of CreateException in org.anchoranalysis.plugin.annotation.bean.comparison.assigner

Methods in org.anchoranalysis.plugin.annotation.bean.comparison.assigner that throw CreateException

Modifier and Type	Method	Description
abstract T	AnnotationComparisonAssigner.createAssignment(ObjectsToCompare objectsToCompare, Dimensions dimensions, boolean useMIP, InputOutputContext context)	Creates an assignment based on the objects to compare.
OverlappingObjects	FeatureCostAssigner.createAssignment(ObjectsToCompare objectsToCompare, Dimensions dimensions, boolean useMIP, InputOutputContext context)
ObjectVoxelIntersection	MaskIntersectionAssigner.createAssignment(ObjectsToCompare objectsToCompare, Dimensions dimensions, boolean useMIP, InputOutputContext context)

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

Methods in org.anchoranalysis.plugin.fiji.bean.mask.provider that throw CreateException

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

Uses of CreateException in org.anchoranalysis.plugin.image.bean.channel.convert

Methods in org.anchoranalysis.plugin.image.bean.channel.convert that throw CreateException

Modifier and Type	Method	Description
ChannelConverter<UnsignedByteBuffer>	ScaleByDictionary.createConverter()

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

Methods in org.anchoranalysis.plugin.image.bean.mask.provider that throw CreateException

Modifier and Type	Method	Description
protected abstract Mask	FromChannelBase.createFromSource(Channel source)	Creates a Mask from the source Channel.

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

Methods in org.anchoranalysis.plugin.image.bean.mask.provider.convert that throw CreateException

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

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

Methods in org.anchoranalysis.plugin.image.bean.mask.provider.segment that throw CreateException

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

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

Methods in org.anchoranalysis.plugin.image.bean.stack.provider.color that throw CreateException

Modifier and Type	Method	Description
protected abstract ColoredObjectCollection	ColoredBase.coloredObjectsToDraw(Dimensions backgroundDimensions)	Creates colored-objects to be drawn.
protected ColoredObjectCollection	ColoredBaseWithGenerator.coloredObjectsToDraw(Dimensions backgroundDimensions)
protected ColoredObjectCollection	ColoredMask.coloredObjectsToDraw(Dimensions backgroundDimensions)
protected ColoredObjectCollection	ThreeColoredObjects.coloredObjectsToDraw(Dimensions backgroundDimensions)
protected abstract ObjectCollection	ColoredBaseWithGenerator.objectsToDraw(Dimensions backgroundDimensions)	The objects to draw (without any colors) on the background.
protected ObjectCollection	ColoredObjects.objectsToDraw(Dimensions backgroundDimensions)

Uses of CreateException in org.anchoranalysis.plugin.image.bean.thumbnail.stack

Methods in org.anchoranalysis.plugin.image.bean.thumbnail.stack that throw CreateException

Modifier and Type	Method	Description
DisplayStack	ScaleToSize.thumbnailFor(Stack stack)
abstract DisplayStack	ThumbnailFromStack.thumbnailFor(Stack stack)	Creates a thumbnail for a stack.

Uses of CreateException in org.anchoranalysis.plugin.image.feature.bean.object.combine

Methods in org.anchoranalysis.plugin.image.feature.bean.object.combine that throw CreateException

Modifier and Type	Method	Description
abstract FeatureTableCalculator<T>	CombineObjectsForFeatures.createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> featuresSingleObject, NamedFeatureStoreFactory storeFactory, boolean suppressErrors)	Creates features that will be applied on the objects.
FeatureTableCalculator<FeatureInputSingleObject>	EachObjectIndependently.createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> list, NamedFeatureStoreFactory storeFactory, boolean suppressErrors)
FeatureTableCalculator<FeatureInputPairObjects>	PairNeighbors.createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> list, NamedFeatureStoreFactory storeFactory, boolean suppressErrors)
ListWithThumbnails<T,ObjectCollection>	CombineObjectsForFeatures.deriveInputsStartBatch(ObjectCollection objects, EnergyStack energyStack, boolean thumbnailsEnabled, OperationContext context)	Derives a list of inputs (i.e. rows in a feature table) and starts a batch of related thumbnail generation.
abstract ObjectCollection	CombineObjectsForFeatures.objectsForThumbnail(T input)	Selects objects from an input that will be used for thumbnail generation.
ObjectCollection	EachObjectIndependently.objectsForThumbnail(FeatureInputSingleObject input)
ObjectCollection	PairNeighbors.objectsForThumbnail(FeatureInputPairObjects input)
protected abstract List<T>	CombineObjectsForFeatures.startBatchDeriveInputs(ObjectCollection objects, EnergyStack energyStack, Logger logger)	Derives a list of inputs from an object-collection.
List<FeatureInputSingleObject>	EachObjectIndependently.startBatchDeriveInputs(ObjectCollection objects, EnergyStack energyStack, Logger logger)
List<FeatureInputPairObjects>	PairNeighbors.startBatchDeriveInputs(ObjectCollection objects, EnergyStack energyStack, Logger logger)

Uses of CreateException in org.anchoranalysis.plugin.image.intensity.level

Methods in org.anchoranalysis.plugin.image.intensity.level that throw CreateException

Modifier and Type	Method	Description
static LevelResultCollection	LevelResultCollectionFactory.createCollection(Channel channel, ObjectCollection objects, CalculateLevel calculateLevel, int numberDilations, MessageLogger logger)	Creates a LevelResultCollection from a channel and object collection.

Uses of CreateException in org.anchoranalysis.plugin.image.task.bean.combine

Methods in org.anchoranalysis.plugin.image.task.bean.combine that return types with arguments of type CreateException

Modifier and Type	Method	Description
protected CheckedFunction<Channel,Channel,CreateException>	AggregateChannelTask.createChannelDeriver(ChannelSource source)

Uses of CreateException in org.anchoranalysis.plugin.image.task.bean.feature.source

Methods in org.anchoranalysis.plugin.image.task.bean.feature.source that throw CreateException

Modifier and Type	Method	Description
abstract FeatureExporter<S>	FeatureSource.createExporter(LabelHeaders metadataHeaders, List<NamedBean<FeatureListProvider<U>>> features, FeatureOutputNames outputNames, Optional<InputGrouper> grouper, FeatureExporterContext context)	Creates the FeatureExporter to be used for calculating and exporting feature-results.
FeatureExporter<FeatureList<S>>	SingleRowPerInput.createExporter(LabelHeaders metadataHeaders, List<NamedBean<FeatureListProvider<S>>> features, FeatureOutputNames outputNames, Optional<InputGrouper> grouper, FeatureExporterContext context)

Uses of CreateException in org.anchoranalysis.plugin.image.task.bean.grouped

Methods in org.anchoranalysis.plugin.image.task.bean.grouped that return types with arguments of type CreateException

Modifier and Type	Method	Description
protected abstract CheckedFunction<Channel,S,CreateException>	GroupedStackBase.createChannelDeriver(ChannelSource source)	A function to derive the individual type used for aggregation from a Channel.

Uses of CreateException in org.anchoranalysis.plugin.image.task.bean.grouped.histogram

Methods in org.anchoranalysis.plugin.image.task.bean.grouped.histogram that return types with arguments of type CreateException

Modifier and Type	Method	Description
protected CheckedFunction<Channel,Histogram,CreateException>	ExportImageHistograms.createChannelDeriver(ChannelSource source)

Uses of CreateException in org.anchoranalysis.plugin.image.task.feature

Methods in org.anchoranalysis.plugin.image.task.feature that throw CreateException

Modifier and Type	Method	Description
static <T extends FeatureInput> FeatureExporter<FeatureList<T>>	FeatureExporter.create(List<NamedBean<FeatureListProvider<T>>> features, LabelHeaders metadataHeaders, FeatureOutputNames outputNames, Optional<InputGrouper> grouper, FeatureExporterContext context)	Alternative static constructor that creates a shared-state from a list of named FeatureListProviders.
static <T extends FeatureInput> FeatureExporter<FeatureTableCalculator<T>>	FeatureExporter.create(FeatureOutputNames outputNames, FeatureTableCalculator<T> features, LabelHeaders identifierHeaders, Optional<InputGrouper> grouper, FeatureExporterContext context)	Alternative static constructor that creates a shared-state from a NamedFeatureStore.
static <T extends FeatureInput> FeatureExporter<FeatureList<T>>	FeatureExporter.create(NamedFeatureStore<T> featureStore, LabelHeaders metadataHeaders, FeatureOutputNames outputNames, Optional<InputGrouper> grouper, FeatureExporterContext context)	Alternative static constructor that creates a shared-state from a NamedFeatureStore.

Uses of CreateException in org.anchoranalysis.plugin.image.task.labeller

Constructors in org.anchoranalysis.plugin.image.task.labeller that throw CreateException

Modifier	Constructor	Description
	SharedStateFilteredImageOutput(Outputter baseOutputter, ImageLabeller<T> filter, String outputNameMapping, String outputNameImages)	Creates a new SharedStateFilteredImageOutput.

Uses of CreateException in org.anchoranalysis.plugin.image.task.segment

Constructors in org.anchoranalysis.plugin.image.task.segment that throw CreateException

Modifier	Constructor	Description
	SharedStateSegmentInstance(ConcurrentModelPool<T> modelPool, FeatureTableCalculator<FeatureInputSingleObject> featureTable, LabelHeaders identifierHeaders, String outputNameFeatures, FeatureExporterContext context)	Creates a new instance of SharedStateSegmentInstance.

Uses of CreateException in org.anchoranalysis.plugin.image.task.stack

Constructors in org.anchoranalysis.plugin.image.task.stack that throw CreateException

Modifier	Constructor	Description
	SharedStateSelectedSlice(Outputter baseOutputter)	Creates a new instance of SharedStateSelectedSlice.

Uses of CreateException in org.anchoranalysis.plugin.image.thumbnail

Methods in org.anchoranalysis.plugin.image.thumbnail that throw CreateException

Modifier and Type	Method	Description
DisplayStack	ThumbnailBatch.thumbnailFor(T element)	Creates a thumbnail for an element in the batch.

Uses of CreateException in org.anchoranalysis.plugin.io.bean.channel.map

Methods in org.anchoranalysis.plugin.io.bean.channel.map that throw CreateException

Modifier and Type	Method	Description
ChannelMap	Autoname.create(OpenedImageFile openedFile, Logger logger)
ChannelMap	FromMetadata.create(OpenedImageFile openedFile, Logger logger)
ChannelMap	SingleChannel.create(OpenedImageFile openedFile, Logger logger)

Uses of CreateException in org.anchoranalysis.plugin.io.bean.file.copy.method

Methods in org.anchoranalysis.plugin.io.bean.file.copy.method that throw CreateException

Modifier and Type	Method	Description
void	CopyFilesMethod.makeCopy(Path source, Path destination)	Makes a copy of the file at source at destination.
void	Bytewise.makeCopyWithDirectory(Path source, Path destination)
void	CompressAnyTIFF.makeCopyWithDirectory(Path source, Path destination)
protected abstract void	CopyFilesMethod.makeCopyWithDirectory(Path source, Path destination)	Like CopyFilesMethod.makeCopy(Path,Path) but after any necessary directories are created so destination can be written.

Uses of CreateException in org.anchoranalysis.plugin.io.bean.file.namer

Methods in org.anchoranalysis.plugin.io.bean.file.namer that throw CreateException

Modifier and Type	Method	Description
protected String	NormalizedPath.deriveName(File file, Optional<Path> inputDirectory, int index)
protected String	RelativeToDirectory.deriveName(File file, Optional<Path> inputDirectory, int index)

Uses of CreateException in org.anchoranalysis.plugin.mpp.bean.define

Methods in org.anchoranalysis.plugin.mpp.bean.define that throw CreateException

Modifier and Type	Method	Description
protected ImageInitialization	DefineOutputter.createInitialization(InitializationContext context, Optional<SharedObjects> sharedObjects, Optional<Dictionary> dictionary)	Creates an ImageInitialization from the given context, shared objects, and dictionary.
protected ImageInitialization	DefineOutputter.createInitialization(InitializationContext context, ExportSharedObjects input)	Creates an ImageInitialization from the given context and input.

Uses of CreateException in org.anchoranalysis.plugin.mpp.bean.stack.provider

Methods in org.anchoranalysis.plugin.mpp.bean.stack.provider that throw CreateException

Modifier and Type	Method	Description
protected ObjectCollection	ColoredMarks.objectsToDraw(Dimensions backgroundDimensions)

Uses of CreateException in org.anchoranalysis.plugin.opencv.convert

Methods in org.anchoranalysis.plugin.opencv.convert that throw CreateException

Modifier and Type	Method	Description
static org.opencv.core.Mat	ConvertToMat.fromObject(ObjectMask object)	Convert a ObjectMask to a Mat.
static org.opencv.core.Mat	ConvertToMat.fromStack(Stack stack)	Converts a Stack to a Mat.
static org.opencv.core.Mat	ConvertToMat.makeRGBStack(Stack stack, boolean swapRedBlueChannels)	Derives a Mat representing an RGB stack.

Uses of CreateException in org.anchoranalysis.plugin.points.bean.fitter

Constructors in org.anchoranalysis.plugin.points.bean.fitter that throw CreateException

Modifier	Constructor	Description
	EllipseStandardFormConverter(cern.colt.matrix.DoubleMatrix1D matrix)	Creates a new EllipseStandardFormConverter and performs the conversion.

Uses of CreateException in org.anchoranalysis.plugin.points.calculate.ellipsoid

Method parameters in org.anchoranalysis.plugin.points.calculate.ellipsoid with type arguments of type CreateException

Modifier and Type	Method	Description
static Ellipsoid	EllipsoidFactory.createMarkEllipsoidLeastSquares(CheckedSupplier<List<Point3i>,CreateException> opPoints, Dimensions dimensions, boolean suppressZCovariance, double shell)	Creates a Ellipsoid using least-squares fitting to a supplied list of points.

Methods in org.anchoranalysis.plugin.points.calculate.ellipsoid that throw CreateException

Modifier and Type	Method	Description
static Ellipsoid	EllipsoidFactory.createMarkEllipsoidLeastSquares(CheckedSupplier<List<Point3i>,CreateException> opPoints, Dimensions dimensions, boolean suppressZCovariance, double shell)	Creates a Ellipsoid using least-squares fitting to a supplied list of points.
static Ellipsoid	EllipsoidFactory.createMarkEllipsoidLeastSquares(ObjectMask object, Dimensions dimensions, boolean suppressZCovariance, double shell)	Creates a Ellipsoid using least-squares fitting to the points on the outline of an ObjectMask.

Uses of CreateException in org.anchoranalysis.plugin.points.convexhull

Methods in org.anchoranalysis.plugin.points.convexhull that throw CreateException

Modifier and Type	Method	Description
static List<Point2i>	ConvexHullUtilities.pointsOnOutline(ObjectMask object)	Get points on the outline of a single object.

Uses of CreateException in org.anchoranalysis.test.feature.plugins

Methods in org.anchoranalysis.test.feature.plugins that throw CreateException

Modifier and Type	Method	Description
static <T extends FeatureInput> FeatureList<T>	FeaturesFromXMLFixture.createFeatureList(String xmlPath, TestLoader loader)	Creates a feature list from an XML file.
static <T extends FeatureInput> List<NamedBean<FeatureListProvider<T>>>	FeaturesFromXMLFixture.createNamedFeatureProviders(String xmlPath, TestLoader loader)	Creates a list of named feature list providers from an XML file.