Index (anchor-plugin-mpp 0.1.0 API)

A B C D E F G H I L O P R S T V
All Classes All Packages

A

addAllOutputNamesTo(OutputEnabledMutable) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: Adds all possible output-names to a OutputEnabledMutable.
addTo(Define) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
afterAllJobsAreExecuted(SharedStateRememberConverted<U, S>, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels

B

beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels

C

ColoredMarks - Class in org.anchoranalysis.plugin.mpp.bean.stack.provider: Draws a colored representation (outline or filled) of an MarkCollection on a background
ColoredMarks() - Constructor for class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
ConvertedInput<U extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.mpp.shared: A converted-input, together with any logged messages associated with it.
ConvertedInput(U, StringBuilder) - Constructor for class org.anchoranalysis.plugin.mpp.shared.ConvertedInput
ConvertNamedChannels<T extends org.anchoranalysis.image.io.channel.input.NamedChannelsInput,S,U extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.mpp.bean.convert: Converts NamedChannelsInput to a variety of others to match a delegate task.
ConvertNamedChannels() - Constructor for class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels
createInitialization(InitializationContext, Optional<SharedObjects>, Optional<Dictionary>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: Creates an ImageInitialization from the given context, shared objects, and dictionary.
createInitialization(InitializationContext, ExportSharedObjects) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: Creates an ImageInitialization from the given context and input.
CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection: Creates a new empty collection of marks
CreateNew() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.CreateNew

D

defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop
DefineOutputter - Class in org.anchoranalysis.plugin.mpp.bean.define: Applies a Define on inputs and outputs produced entities (images, histograms, objects etc.).
DefineOutputter() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter
DefineOutputter.Processor<T> - Interface in org.anchoranalysis.plugin.mpp.bean.define: Functional interface for processing an ImageInitialization.
DefineOutputterWithEnergy - Class in org.anchoranalysis.plugin.mpp.bean.define: Like a Define but outputs also an energy-stack.
DefineOutputterWithEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
DefineOutputterWithEnergy.ProcessWithEnergyStack<T,S> - Interface in org.anchoranalysis.plugin.mpp.bean.define: Functional interface for processing with an energy stack.
Develop - Class in org.anchoranalysis.plugin.mpp.bean.define: Derives various types of outputs (images, histograms etc.) from MultiInputs.
Develop() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.Develop
doJobOnInput(InputBound<MultiInput, NoSharedState>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop
doJobOnInput(InputBound<T, SharedStateRememberConverted<U, S>>) - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels

E

equals(Object) - Method in class org.anchoranalysis.plugin.mpp.shared.ConvertedInput

F

findConvertedInputFor(NamedChannelsInput, MessageLogger) - Method in class org.anchoranalysis.plugin.mpp.shared.SharedStateRememberConverted: Finds a converted-input that has been remembered.
forgetAll() - Method in class org.anchoranalysis.plugin.mpp.shared.SharedStateRememberConverted: Forgets all converted inputs.
FromMarks - Class in org.anchoranalysis.plugin.mpp.bean.object.provider: Creates object-masks from a MarkCollection where (a particular region of) each mark creates an object.
FromMarks() - Constructor for class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
FromSingleMark - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection: Creates a MarkCollection from a single mark provided by a SingleMarkProvider.
FromSingleMark() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark

G

get() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
get() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.CreateNew
get() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark
get() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
get() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
get() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
get() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
getAdd() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
getBackgroundID() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
getConversion() - Method in class org.anchoranalysis.plugin.mpp.shared.ConvertedInput: The converted input.
getDefaultStackReaderForMetadata() - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels: Supplies to the imageMetadataReader to use, if no other reader is specified.
getDefine() - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: The Define to be applied on inputs.
getDefine() - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop: Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
getDictionary() - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy: An optional dictionary provider.
getDictionary() - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop: If non-empty, the identifier for a dictionary that is treated as part of the energy-stack.
getDimensions() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
getFeatureTables() - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop: Specifies a feature-table that can also be outputted.
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference: The ID of the MarkCollection to retrieve from the initialization context.
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
getImageMetadataReader() - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels: How to read the ImageMetadata from the file-system.
getMarkProvider() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark: The provider for a single mark.
getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY: The provider for the MarkCollection to be scaled.
getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
getMessages() - Method in class org.anchoranalysis.plugin.mpp.shared.ConvertedInput: Any messages written to the log during conversion.
getObjects() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects: Provider for the object collection from which to create point marks.
getOutlineWidth() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
getRegionMap() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
getScaleCalculator() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY: The ScaleCalculator used to determine the scaling factor.
getSharedState() - Method in class org.anchoranalysis.plugin.mpp.shared.SharedStateRememberConverted: The shared state.
getStackEnergy() - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy: The stack provider for the energy stack.
getTask() - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels: The underlying task that will be called, perhaps with a different input-type.

H

hashCode() - Method in class org.anchoranalysis.plugin.mpp.shared.ConvertedInput
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop

I

inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop
isStackBackground() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
isSuppressSubfolders() - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: If true, suppresses the creation of subfolders for outputs.

L

logConversionMessages(MessageLogger) - Method in class org.anchoranalysis.plugin.mpp.shared.ConvertedInput: Logs any messages stored from from conversion.

O

objectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
org.anchoranalysis.plugin.mpp.bean.convert - package org.anchoranalysis.plugin.mpp.bean.convert: Converting from NamedChannelsInput to the input-type expected by a Task.
org.anchoranalysis.plugin.mpp.bean.define - package org.anchoranalysis.plugin.mpp.bean.define: Beans related to Define involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.object.provider - package org.anchoranalysis.plugin.mpp.bean.object.provider: Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.mpp.bean.provider.collection - package org.anchoranalysis.plugin.mpp.bean.provider.collection: Implementation of MarkCollectionProvider.
org.anchoranalysis.plugin.mpp.bean.stack.provider - package org.anchoranalysis.plugin.mpp.bean.stack.provider: Implementations of StackProvider involving Mark or related classes.
org.anchoranalysis.plugin.mpp.shared - package org.anchoranalysis.plugin.mpp.shared: Shared-state use across tasks in this JAR.
outputSharedObjects(SharedObjects, Optional<EnergyStack>, Outputter) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: Outputs shared objects and optionally an energy stack.

P

PointsFromObjects - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection: Creates a MarkCollection of point marks from an ObjectCollection.
PointsFromObjects() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
process(InputBound<MultiInput, S>, DefineOutputter.Processor<ImageInitialization>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: Processes the input using the provided operation.
process(T) - Method in interface org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter.Processor: Processes the initialization.
process(T, EnergyStack) - Method in interface org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy.ProcessWithEnergyStack: Processes the initialization with an energy stack.
processInput(InitializationContext, SharedObjects, Optional<Dictionary>, DefineOutputterWithEnergy.ProcessWithEnergyStack<ImageInitialization, S>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy: Processes the input with an energy stack and shared objects.
processInput(ExportSharedObjects, InitializationContext, DefineOutputterWithEnergy.ProcessWithEnergyStack<ImageInitialization, S>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy: Processes the input with an energy stack.

R

Reference - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection: Provides a MarkCollection by referencing it from the initialization context using an ID.
Reference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
Reference(String) - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
ReferenceOrEmpty - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection: Returns an existing marks-collection or an empty set if it doesn't exist
ReferenceOrEmpty() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
rememberConverted(NamedChannelsInput, U, StringBuilder) - Method in class org.anchoranalysis.plugin.mpp.shared.SharedStateRememberConverted: Remembers a converted input.
replaceTask(Task<U, S>) - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels

S

ScaleXY - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection: Scales the X and Y coordinates of marks in a MarkCollection using a ScaleCalculator.
ScaleXY() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
setAdd(DefineAdderBean) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
setBackgroundID(String) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
setDefaultStackReaderForMetadata(StackReader) - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels: Supplies to the imageMetadataReader to use, if no other reader is specified.
setDefine(Define) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: The Define to be applied on inputs.
setDefine(DefineOutputter) - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop: Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
setDictionary(String) - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop: If non-empty, the identifier for a dictionary that is treated as part of the energy-stack.
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy: An optional dictionary provider.
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
setFeatureTables(List<OutputFeatureTable>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.Develop: Specifies a feature-table that can also be outputted.
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference: The ID of the MarkCollection to retrieve from the initialization context.
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
setImageMetadataReader(ImageMetadataReader) - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels: How to read the ImageMetadata from the file-system.
setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark: The provider for a single mark.
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY: The provider for the MarkCollection to be scaled.
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects: Provider for the object collection from which to create point marks.
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
setRegionMap(RegionMap) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY: The ScaleCalculator used to determine the scaling factor.
setSharedState(S) - Method in class org.anchoranalysis.plugin.mpp.shared.SharedStateRememberConverted: The shared state.
setStackBackground(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy: The stack provider for the energy stack.
setSuppressSubfolders(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputter: If true, suppresses the creation of subfolders for outputs.
setTask(Task<U, S>) - Method in class org.anchoranalysis.plugin.mpp.bean.convert.ConvertNamedChannels: The underlying task that will be called, perhaps with a different input-type.
SharedStateRememberConverted<U extends org.anchoranalysis.io.input.InputFromManager,S> - Class in org.anchoranalysis.plugin.mpp.shared: Shared-state that remembers converted inputs for corresponding unconverted inputs.
SharedStateRememberConverted() - Constructor for class org.anchoranalysis.plugin.mpp.shared.SharedStateRememberConverted

T

toString() - Method in class org.anchoranalysis.plugin.mpp.shared.ConvertedInput

V

VisualizeOnBackground - Class in org.anchoranalysis.plugin.mpp.bean.define: Adds a visualization for all binary-masks and object-collections that are added using a particular background
VisualizeOnBackground() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground

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