Package org.anchoranalysis.plugin.image.task.bean.grouped.histogram

Class ExportImageHistograms

Object

AnchorBean<Task<ProvidesStackInput,GroupedSharedState<Histogram,Histogram>>>

Task<ProvidesStackInput,GroupedSharedState<Histogram,Histogram>>

GroupedStackBase<Histogram,Histogram>

ExportImageHistograms

public class ExportImageHistograms
extends GroupedStackBase<Histogram,Histogram>

Exports a histogram of voxel intensities as a CSV file for each channel of an image.

Additionally, a histogram with the summation of voxel intensities for all channels in each image is produced.

Optionally, one channel can be used as a mask, to restrict which voxels are included in the histogram.

These steps occur:

1. All files are aggregated into groups.
2. For each image file, a histogram is calculated.
3. The histogram is added to the group histogram.
4. The histograms are written to the filesystem.

The following outputs are produced:

Output Name	Default?	Description
"channels"	yes	A separate CSV histogram for each channel's voxels intensity.
"sum"	yes	A histogram for the sum of each voxel's intensity across all channels.
inherited from Task

Constructor Summary

Constructors

Constructor	Description
ExportImageHistograms()

Method Summary

Modifier and Type	Method	Description
protected CheckedFunction<Channel,Histogram,CreateException>	createChannelDeriver(ChannelSource source)	A function to derive the individual type used for aggregation from a Channel.
protected GroupMapByName<Histogram,Histogram>	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.
String	getChannelMask()	If defined, this is the name of channel used as a mask over the values which are fed into the histogram
int	getMaskValue()	What voxel value to read as "On" in the mask above.
boolean	isCsvIgnoreZeros()	Iff true, bins with zero-counts are not written as a row in the CSV file.
protected String	outputNameForGroups()	The first-level output-name used for determining if groups are written.
protected void	processIndividual(String name, Histogram individual, boolean partOfGroup, CheckedBiConsumer<String,Histogram,OperationFailedException> consumeIndividual, InputOutputContext context)	Processes each derived individual element from a Channel, calling consumeIndividual one or more times.
void	setChannelMask(String channelMask)	If defined, this is the name of channel used as a mask over the values which are fed into the histogram
void	setCsvIgnoreZeros(boolean csvIgnoreZeros)	Iff true, bins with zero-counts are not written as a row in the CSV file.
void	setMaskValue(int maskValue)	What voxel value to read as "On" in the mask above.
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

ExportImageHistograms

public ExportImageHistograms()

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<Histogram,Histogram>>

Returns:

the default rules if they exist.

createGroupMap

protected GroupMapByName<Histogram,Histogram> 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<Histogram,Histogram>

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.

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<Histogram,Histogram>

Returns:

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

createChannelDeriver

protected CheckedFunction<Channel,Histogram,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<Histogram,Histogram>

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.

processIndividual

protected void processIndividual(String name,
 Histogram individual,
 boolean partOfGroup,
 CheckedBiConsumer<String,Histogram,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<Histogram,Histogram>

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.

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<Histogram,Histogram>

Returns:

the output-name.

getChannelMask

public String getChannelMask()

If defined, this is the name of channel used as a mask over the values which are fed into the histogram

setChannelMask

public void setChannelMask(String channelMask)

If defined, this is the name of channel used as a mask over the values which are fed into the histogram

getMaskValue

public int getMaskValue()

What voxel value to read as "On" in the mask above.

setMaskValue

public void setMaskValue(int maskValue)

What voxel value to read as "On" in the mask above.

isCsvIgnoreZeros

public boolean isCsvIgnoreZeros()

Iff true, bins with zero-counts are not written as a row in the CSV file.

setCsvIgnoreZeros

public void setCsvIgnoreZeros(boolean csvIgnoreZeros)

Iff true, bins with zero-counts are not written as a row in the CSV file.