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)
ComparisonSharedState<T>	beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<AnnotationComparisonInput<ProvidesStackInput>> inputs, ParametersExperiment parameters)
OutputEnabledMutable	defaultOutputs()
void	doJobOnInput(InputBound<AnnotationComparisonInput<ProvidesStackInput>, ComparisonSharedState<T>> 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()
InputTypesExpected	inputTypesExpected()
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

Specified by:

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

Throws:

ExperimentExecutionException

doJobOnInput

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

Specified by:

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

Throws:

JobExecutionException

inputTypesExpected

public InputTypesExpected inputTypesExpected()

Specified by:

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

afterAllJobsAreExecuted

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

Specified by:

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

Throws:

ExperimentExecutionException

hasVeryQuickPerInputExecution

public boolean hasVeryQuickPerInputExecution()

Specified by:

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

defaultOutputs

public OutputEnabledMutable defaultOutputs()

Overrides:

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

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.