T
- assignment-type.public class CompareAnnotations<T extends Assignment<ObjectMask>> extends Task<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T>>
The following outputs are produced:
Output Name | Default? | Description |
---|---|---|
yes | a single CSV file showing summary statistics of matching for all images. | |
yes | a single CSV file showing summary statistics of matching for all groups group of images. | |
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 |
Modifier and Type | Field and Description |
---|---|
static String |
OUTPUT_BY_GROUP |
Constructor and Description |
---|
CompareAnnotations() |
Modifier and Type | Method and 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() |
String |
getBackground()
The name of the stack to use as background to the annotations.
|
ColorScheme |
getColorsUnpaired() |
StackDisplayer |
getDisplayer()
How to convert an image to be displayed to the user.
|
int |
getMaxSplitGroups() |
int |
getNumberLevelsGrouping() |
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() |
void |
setAssigner(AnnotationComparisonAssigner<T> assigner) |
void |
setBackground(String background)
The name of the stack to use as background to the annotations.
|
void |
setColorsUnpaired(ColorScheme colorsUnpaired) |
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) |
void |
setNumberLevelsGrouping(int numberLevelsGrouping) |
void |
setOutlineWidth(int outlineWidth)
How many pixels should the outline be around objects.
|
void |
setReplaceMatchesWithSolids(boolean replaceMatchesWithSolids) |
void |
setSplitIdentifierRegex(String splitIdentifierRegex)
If non-empty, the string (a regular-expression) is used to split the file's identifier into
groups.
|
executeJob, isInputCompatibleWith
checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString
public static final String OUTPUT_BY_GROUP
public ComparisonSharedState<T> beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<AnnotationComparisonInput<ProvidesStackInput>> inputs, ParametersExperiment parameters) throws ExperimentExecutionException
Task
Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>)
.beforeAnyJobIsExecuted
in class Task<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T extends Assignment<ObjectMask>>>
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.Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>)
and to Task.afterAllJobsAreExecuted(S, org.anchoranalysis.io.output.outputter.InputOutputContext)
.ExperimentExecutionException
- if a fatal error occurs executing this step of the
experiment.public void doJobOnInput(InputBound<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T>> input) throws JobExecutionException
Task
doJobOnInput
in class Task<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T extends Assignment<ObjectMask>>>
input
- the input for the job.JobExecutionException
- if an error occurs executing a particular job, that is not
otherwise suppressed.public InputTypesExpected inputTypesExpected()
Task
This is usually the class of T (or sometimes the absolute base class InputFromManager).
inputTypesExpected
in class Task<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T extends Assignment<ObjectMask>>>
public void afterAllJobsAreExecuted(ComparisonSharedState<T> sharedState, InputOutputContext context) throws ExperimentExecutionException
Task
Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>)
.afterAllJobsAreExecuted
in class Task<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T extends Assignment<ObjectMask>>>
sharedState
- the shared-statecontext
- IO-context for experiment (not for an individual job)ExperimentExecutionException
- if a fatal error occurs executing this step of the
experiment.public boolean hasVeryQuickPerInputExecution()
Task
hasVeryQuickPerInputExecution
in class Task<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T extends Assignment<ObjectMask>>>
public OutputEnabledMutable defaultOutputs()
Task
defaultOutputs
in class Task<AnnotationComparisonInput<ProvidesStackInput>,ComparisonSharedState<T extends Assignment<ObjectMask>>>
public String getBackground()
public void setBackground(String background)
public String getSplitIdentifierRegex()
public void setSplitIdentifierRegex(String splitIdentifierRegex)
public int getMaxSplitGroups()
public void setMaxSplitGroups(int maxSplitGroups)
public int getNumberLevelsGrouping()
public void setNumberLevelsGrouping(int numberLevelsGrouping)
public boolean isFlatten()
public void setFlatten(boolean flatten)
public int getOutlineWidth()
public void setOutlineWidth(int outlineWidth)
public AnnotationComparisonAssigner<T> getAssigner()
public void setAssigner(AnnotationComparisonAssigner<T> assigner)
public boolean isReplaceMatchesWithSolids()
public void setReplaceMatchesWithSolids(boolean replaceMatchesWithSolids)
public ColorScheme getColorsUnpaired()
public void setColorsUnpaired(ColorScheme colorsUnpaired)
public StackDisplayer getDisplayer()
public void setDisplayer(StackDisplayer displayer)
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.