Package org.anchoranalysis.plugin.annotation.bean.comparison

Class CompareAnnotations<T extends Assignment<ObjectMask>>

Object

AnchorBean<Task<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T>>>

Task<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T>>

CompareAnnotations<T>

Type Parameters:

T - assignment-type.

public class CompareAnnotations<T extends Assignment<ObjectMask>>
extends Task<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T>>

Task to compare a set of annotations to a segmentation or another set of annotations.

The following outputs are produced:

Output Name	Default?	Description
"byImage"	yes	a single CSV file showing summary statistics of matching for all images.
"byGroup"<T extends Assignment<ObjectMask>>	yes	a single CSV file showing summary statistics of matching for all groups group of images.
"outline"	yes	a file per image showing a colored representation of which annotations matched (or didn't) for each image.
outputs from the AnnotationComparisonAssigner in assign
	outputs from Task

Author:

Owen Feehan

Field Summary

Fields

Modifier and Type	Field	Description
static final String	OUTPUT_BY_GROUP	Output name for the CSV file containing summary statistics for all groups of images.

Constructor Summary

Constructors

Constructor	Description
CompareAnnotations()

Method Summary

Modifier and Type	Method	Description
void	afterAllJobsAreExecuted(ComparisonSharedState<T> sharedState, InputOutputContext context)	Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
ComparisonSharedState<T>	beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<AnnotationComparisonInput<ProvidesStackInput>> inputs, ParametersExperiment parameters)	Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
OutputEnabledMutable	defaultOutputs()	If specified, default rules for determine which outputs are enabled or not.
void	doJobOnInput(InputBound<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T>> input)	Performs the task on a particular input.
AnnotationComparisonAssigner<T>	getAssigner()	The assigner used for annotation comparison.
String	getBackground()	The name of the stack to use as background to the annotations.
ColorScheme	getColorsUnpaired()	The color scheme for unpaired objects.
StackDisplayer	getDisplayer()	How to convert an image to be displayed to the user.
int	getMaxSplitGroups()	The maximum number of groups to split the identifier into.
int	getNumberLevelsGrouping()	The number of levels for grouping.
int	getOutlineWidth()	How many pixels should the outline be around objects.
String	getSplitIdentifierRegex()	If non-empty, the string (a regular-expression) is used to split the file's identifier into groups.
boolean	hasVeryQuickPerInputExecution()	Is the execution-time of the task per-input expected to be very quick to execute?
InputTypesExpected	inputTypesExpected()	Highest class(es) that will function as a valid input.
boolean	isFlatten()	If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.
boolean	isReplaceMatchesWithSolids()	If true, matched objects are replaced with solid colors.
void	setAssigner(AnnotationComparisonAssigner<T> assigner)	The assigner used for annotation comparison.
void	setBackground(String background)	The name of the stack to use as background to the annotations.
void	setColorsUnpaired(ColorScheme colorsUnpaired)	The color scheme for unpaired objects.
void	setDisplayer(StackDisplayer displayer)	How to convert an image to be displayed to the user.
void	setFlatten(boolean flatten)	If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.
void	setMaxSplitGroups(int maxSplitGroups)	The maximum number of groups to split the identifier into.
void	setNumberLevelsGrouping(int numberLevelsGrouping)	The number of levels for grouping.
void	setOutlineWidth(int outlineWidth)	How many pixels should the outline be around objects.
void	setReplaceMatchesWithSolids(boolean replaceMatchesWithSolids)	If true, matched objects are replaced with solid colors.
void	setSplitIdentifierRegex(String splitIdentifierRegex)	If non-empty, the string (a regular-expression) is used to split the file's identifier into groups.

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

Field Details

OUTPUT_BY_GROUP

public static final String OUTPUT_BY_GROUP

Output name for the CSV file containing summary statistics for all groups of images.

See Also:

• Constant Field Values

Constructor Details

CompareAnnotations

public CompareAnnotations()

Method Details

beforeAnyJobIsExecuted

public ComparisonSharedState<T> beforeAnyJobIsExecuted(Outputter outputter,
 ConcurrencyPlan concurrencyPlan,
 List<AnnotationComparisonInput<ProvidesStackInput>> inputs,
 ParametersExperiment parameters)
                                                throws ExperimentExecutionException

Description copied from class: Task

Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).

Specified by:

beforeAnyJobIsExecuted in class Task<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T extends Assignment<ObjectMask>>>

Parameters:

outputter - the output-manager for the experiment (not for an individual job)

concurrencyPlan - available numbers of processors that can call Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>)

inputs - a list of inputs, each will result in at least one call to Task.executeJob(ParametersUnbound).

parameters - the experiment-parameters.

Returns:

the shared-state that is passed to each call to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>) and to Task.afterAllJobsAreExecuted(S, org.anchoranalysis.io.output.outputter.InputOutputContext).

Throws:

ExperimentExecutionException - if a fatal error occurs executing this step of the experiment.

doJobOnInput

public void doJobOnInput(InputBound<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T>> input)
                  throws JobExecutionException

Description copied from class: Task

Performs the task on a particular input.

Specified by:

doJobOnInput in class Task<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T extends Assignment<ObjectMask>>>

Parameters:

input - the input for the job.

Throws:

JobExecutionException - if an error occurs executing a particular job, that is not otherwise suppressed.

inputTypesExpected

public InputTypesExpected inputTypesExpected()

Description copied from class: Task

Highest class(es) that will function as a valid input.

This is usually the class of T (or sometimes the absolute base class InputFromManager).

Specified by:

inputTypesExpected in class Task<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T extends Assignment<ObjectMask>>>

Returns:

the input-types that a task expects.

afterAllJobsAreExecuted

public void afterAllJobsAreExecuted(ComparisonSharedState<T> sharedState,
 InputOutputContext context)
                             throws ExperimentExecutionException

Description copied from class: Task

Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).

Specified by:

afterAllJobsAreExecuted in class Task<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T extends Assignment<ObjectMask>>>

Parameters:

sharedState - the shared-state

context - IO-context for experiment (not for an individual job)

Throws:

ExperimentExecutionException - if a fatal error occurs executing this step of the experiment.

hasVeryQuickPerInputExecution

public boolean hasVeryQuickPerInputExecution()

Description copied from class: Task

Is the execution-time of the task per-input expected to be very quick to execute?

Specified by:

hasVeryQuickPerInputExecution in class Task<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T extends Assignment<ObjectMask>>>

Returns:

true iff the execution is expected to be very quick, false otherwise.

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<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T extends Assignment<ObjectMask>>>

Returns:

the default rules if they exist.

getBackground

public String getBackground()

The name of the stack to use as background to the annotations.

setBackground

public void setBackground(String background)

The name of the stack to use as background to the annotations.

getSplitIdentifierRegex

public String getSplitIdentifierRegex()

If non-empty, the string (a regular-expression) is used to split the file's identifier into groups.

setSplitIdentifierRegex

public void setSplitIdentifierRegex(String splitIdentifierRegex)

If non-empty, the string (a regular-expression) is used to split the file's identifier into groups.

getMaxSplitGroups

public int getMaxSplitGroups()

The maximum number of groups to split the identifier into.

setMaxSplitGroups

public void setMaxSplitGroups(int maxSplitGroups)

The maximum number of groups to split the identifier into.

getNumberLevelsGrouping

public int getNumberLevelsGrouping()

The number of levels for grouping.

setNumberLevelsGrouping

public void setNumberLevelsGrouping(int numberLevelsGrouping)

The number of levels for grouping.

isFlatten

public boolean isFlatten()

If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.

setFlatten

public void setFlatten(boolean flatten)

If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.

getOutlineWidth

public int getOutlineWidth()

How many pixels should the outline be around objects.

setOutlineWidth

public void setOutlineWidth(int outlineWidth)

How many pixels should the outline be around objects.

getAssigner

public AnnotationComparisonAssigner<T> getAssigner()

The assigner used for annotation comparison.

setAssigner

public void setAssigner(AnnotationComparisonAssigner<T> assigner)

The assigner used for annotation comparison.

isReplaceMatchesWithSolids

public boolean isReplaceMatchesWithSolids()

If true, matched objects are replaced with solid colors.

setReplaceMatchesWithSolids

public void setReplaceMatchesWithSolids(boolean replaceMatchesWithSolids)

If true, matched objects are replaced with solid colors.

getColorsUnpaired

public ColorScheme getColorsUnpaired()

The color scheme for unpaired objects.

setColorsUnpaired

public void setColorsUnpaired(ColorScheme colorsUnpaired)

The color scheme for unpaired objects.

getDisplayer

public StackDisplayer getDisplayer()

How to convert an image to be displayed to the user.

setDisplayer

public void setDisplayer(StackDisplayer displayer)

How to convert an image to be displayed to the user.