Package org.anchoranalysis.plugin.image.task.bean.combine

Class AggregateChannelTask

Object

AnchorBean<Task<ProvidesStackInput,GroupedSharedState<Channel,ChannelAggregator>>>

Task<ProvidesStackInput,GroupedSharedState<Channel,ChannelAggregator>>

GroupedStackBase<Channel,ChannelAggregator>

AggregateChannelTask

public class AggregateChannelTask
extends GroupedStackBase<Channel,ChannelAggregator>

Creates a an aggregated-image for each group, where each voxel-value is aggregated across each channel in each image in the group.

Each channel is processed independently.

2D images are added in their entirety as one unit.

3D images are treated differently, depending on resizeTo. When not set, they are also added in their entirety. When set, they are projected to 2D via a maximum-intensity-projection and then added (unless slicewise==true.

When a particular input image is errored, it is omitted from the aggregation. The aggregation is still nevertheless produced, if possible from other successful inputs.

The following outputs are produced:

Output Name	Default?	Description
outputName	yes	An image with the aggregated voxel value for each corresponding voxel.
inherited from AggregateChannelTask

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
AggregateChannelTask()

Method Summary

Modifier and Type	Method	Description
protected CheckedFunction<Channel,Channel,CreateException>	createChannelDeriver(ChannelSource source)	A function to derive the individual type used for aggregation from a Channel.
protected GroupMapByName<Channel,ChannelAggregator>	createGroupMap(ConsistentChannelChecker channelChecker, Optional<Stream<String>> groupIdentifiers, Optional<InputOutputContext> outputContext, OperationContext operationContext)	Creates a map for the storing an aggregate-data-object for each group.
OutputEnabledMutable	defaultOutputs()	If specified, default rules for determine which outputs are enabled or not.
ChannelAggregator	getAggregator()	How to aggregate the Channels.
String	getOutputName()	How to name the aggregated channel in the output.
boolean	isSlicewise()	When true, a 3D image is added slice-by-slice to the aggregation, treating each slice as a separate image.
protected String	outputNameForGroups()	The first-level output-name used for determining if groups are written.
protected void	processIndividual(String name, Channel individual, boolean partOfGroup, CheckedBiConsumer<String,Channel,OperationFailedException> consumeIndividual, InputOutputContext context)	Processes each derived individual element from a Channel, calling consumeIndividual one or more times.
void	setAggregator(ChannelAggregator aggregator)	How to aggregate the Channels.
void	setOutputName(String outputName)	How to name the aggregated channel in the output.
void	setSlicewise(boolean slicewise)	When true, a 3D image is added slice-by-slice to the aggregation, treating each slice as a separate image.
protected Optional<String>	subdirectoryForGroupOutputs()	An optional subdirectory where the group outputs are placed.

Methods inherited from class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase

afterAllJobsAreExecuted, beforeAnyJobIsExecuted, doJobOnInput, getGroup, getInterpolator, getResizeTo, getSelectChannels, hasVeryQuickPerInputExecution, inputTypesExpected, setGroup, setInterpolator, setResizeTo, setSelectChannels

Methods inherited from class org.anchoranalysis.experiment.bean.task.Task

executeJob, isInputCompatibleWith

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

AggregateChannelTask

public AggregateChannelTask()

Method Details

defaultOutputs

public OutputEnabledMutable defaultOutputs()

Description copied from class: Task

If specified, default rules for determine which outputs are enabled or not.

Overrides:

defaultOutputs in class Task<ProvidesStackInput,GroupedSharedState<Channel,ChannelAggregator>>

Returns:

the default rules if they exist.

subdirectoryForGroupOutputs

protected Optional<String> subdirectoryForGroupOutputs()

Description copied from class: GroupedStackBase

An optional subdirectory where the group outputs are placed.

Specified by:

subdirectoryForGroupOutputs in class GroupedStackBase<Channel,ChannelAggregator>

Returns:

an Optional containing the subdirectory name as a String, or Optional.empty() if no subdirectory is specified.

outputNameForGroups

protected String outputNameForGroups()

Description copied from class: GroupedStackBase

The first-level output-name used for determining if groups are written.

Second-level matches against this, and will determine which specific groups may or may not be written.

Specified by:

outputNameForGroups in class GroupedStackBase<Channel,ChannelAggregator>

Returns:

the output-name.

createGroupMap

protected GroupMapByName<Channel,ChannelAggregator> createGroupMap(ConsistentChannelChecker channelChecker,
 Optional<Stream<String>> groupIdentifiers,
 Optional<InputOutputContext> outputContext,
 OperationContext operationContext)

Description copied from class: GroupedStackBase

Creates a map for the storing an aggregate-data-object for each group.

Specified by:

createGroupMap in class GroupedStackBase<Channel,ChannelAggregator>

Parameters:

channelChecker - checks that the channels of all relevant stacks have the same size and data-type.

groupIdentifiers - a stream with each group-identifier that should be added to the map.

outputContext - where to write results to when a group is processed.

operationContext - supporting entities for the operation.

Returns:

a newly created map.

processIndividual

protected void processIndividual(String name,
 Channel individual,
 boolean partOfGroup,
 CheckedBiConsumer<String,Channel,OperationFailedException> consumeIndividual,
 InputOutputContext context)
                          throws OperationFailedException

Description copied from class: GroupedStackBase

Processes each derived individual element from a Channel, calling consumeIndividual one or more times.

Specified by:

processIndividual in class GroupedStackBase<Channel,ChannelAggregator>

Parameters:

name - the name of the channel.

individual - the derived-individual element.

partOfGroup - true when the item is part of a group, false otherwise.

consumeIndividual - a function that should be called one or more times for the individual element, or sub-elements of it.

context - supporting entities for the operation.

Throws:

OperationFailedException - if anything goes wrong during processing.

createChannelDeriver

protected CheckedFunction<Channel,Channel,CreateException> createChannelDeriver(ChannelSource source)
                                                                         throws OperationFailedException

Description copied from class: GroupedStackBase

A function to derive the individual type used for aggregation from a Channel.

Specified by:

createChannelDeriver in class GroupedStackBase<Channel,ChannelAggregator>

Parameters:

source - how to retrieve a Channel, appropriately-sized.

Returns:

a function, that given a Channel will return an individual element of type T.

Throws:

OperationFailedException - if the channel-deriver cannot be successfully created.

isSlicewise

public boolean isSlicewise()

When true, a 3D image is added slice-by-slice to the aggregation, treating each slice as a separate image.

setSlicewise

public void setSlicewise(boolean slicewise)

When true, a 3D image is added slice-by-slice to the aggregation, treating each slice as a separate image.

getAggregator

public ChannelAggregator getAggregator()

How to aggregate the Channels.

setAggregator

public void setAggregator(ChannelAggregator aggregator)

How to aggregate the Channels.

getOutputName

public String getOutputName()

How to name the aggregated channel in the output.

setOutputName

public void setOutputName(String outputName)

How to name the aggregated channel in the output.