Package org.anchoranalysis.plugin.mpp.bean.define

Class DefineOutputter

Object

AnchorBean<DefineOutputter>

DefineOutputter

Direct Known Subclasses:

DefineOutputterWithEnergy

public class DefineOutputter
extends AnchorBean<DefineOutputter>

Applies a Define on inputs and outputs produced entities (images, histograms, objects etc.).

The following outputs are produced:

Output Name	Default?	Description
stacks	yes	Image-stacks that are produced.
objects	yes	Collections of ObjectMasks that are produced as HDF5
histograms	yes	Histograms that are produced as CSV.
marks	yes	Collections of Marks that are produced as serialized XML.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	DefineOutputter.Processor<T>	Functional interface for processing an ImageInitialization.

Constructor Summary

Constructors

Constructor	Description
DefineOutputter()

Method Summary

Modifier and Type	Method	Description
void	addAllOutputNamesTo(OutputEnabledMutable outputEnabled)	Adds all possible output-names to a OutputEnabledMutable.
protected ImageInitialization	createInitialization(InitializationContext context, Optional<SharedObjects> sharedObjects, Optional<Dictionary> dictionary)	Creates an ImageInitialization from the given context, shared objects, and dictionary.
protected ImageInitialization	createInitialization(InitializationContext context, ExportSharedObjects input)	Creates an ImageInitialization from the given context and input.
Define	getDefine()	The Define to be applied on inputs.
boolean	isSuppressSubfolders()	If true, suppresses the creation of subfolders for outputs.
protected void	outputSharedObjects(SharedObjects sharedObjects, Optional<EnergyStack> energyStack, Outputter outputter)	Outputs shared objects and optionally an energy stack.
<S> void	process(InputBound<MultiInput,S> input, DefineOutputter.Processor<ImageInitialization> operation)	Processes the input using the provided operation.
void	setDefine(Define define)	The Define to be applied on inputs.
void	setSuppressSubfolders(boolean suppressSubfolders)	If true, suppresses the creation of subfolders for outputs.

Methods inherited from class org.anchoranalysis.bean.AnchorBean

checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

DefineOutputter

public DefineOutputter()

Method Details

addAllOutputNamesTo

public void addAllOutputNamesTo(OutputEnabledMutable outputEnabled)

Adds all possible output-names to a OutputEnabledMutable.

Parameters:

outputEnabled - where to add all possible output-names

process

public <S> void process(InputBound<MultiInput,S> input,
 DefineOutputter.Processor<ImageInitialization> operation)
                 throws OperationFailedException

Processes the input using the provided operation.

Type Parameters:

S - the type of the input

Parameters:

input - the input to process

operation - the operation to apply on the initialization

Throws:

OperationFailedException - if the operation fails

createInitialization

protected ImageInitialization createInitialization(InitializationContext context,
 ExportSharedObjects input)
                                            throws CreateException

Creates an ImageInitialization from the given context and input.

Parameters:

context - the initialization context

input - the input to create the initialization from

Returns:

the created ImageInitialization

Throws:

CreateException - if the initialization creation fails

createInitialization

protected ImageInitialization createInitialization(InitializationContext context,
 Optional<SharedObjects> sharedObjects,
 Optional<Dictionary> dictionary)
                                            throws CreateException

Creates an ImageInitialization from the given context, shared objects, and dictionary.

Parameters:

context - the initialization context

sharedObjects - optional shared objects

dictionary - optional dictionary

Returns:

the created ImageInitialization

Throws:

CreateException - if the initialization creation fails

outputSharedObjects

protected void outputSharedObjects(SharedObjects sharedObjects,
 Optional<EnergyStack> energyStack,
 Outputter outputter)
                            throws OutputWriteFailedException

Outputs shared objects and optionally an energy stack.

Parameters:

sharedObjects - the shared objects to output

energyStack - optional energy stack to output

outputter - the outputter to use

Throws:

OutputWriteFailedException - if the output operation fails

getDefine

public Define getDefine()

The Define to be applied on inputs.

setDefine

public void setDefine(Define define)

The Define to be applied on inputs.

isSuppressSubfolders

public boolean isSuppressSubfolders()

If true, suppresses the creation of subfolders for outputs.

setSuppressSubfolders

public void setSuppressSubfolders(boolean suppressSubfolders)

If true, suppresses the creation of subfolders for outputs.