Uses of Class
org.anchoranalysis.experiment.ExperimentExecutionException

Packages that use ExperimentExecutionException

Package	Description
org.anchoranalysis.experiment.arguments	Arguments that can further specify an experiment in addition to its bean specification.
org.anchoranalysis.experiment.bean	Beans related to executing an experiment by calling jobs on inputs.
org.anchoranalysis.experiment.bean.io	Generic experiments that handle input and output in structured ways.
org.anchoranalysis.experiment.bean.processor	How a task is executed on multiple inputs.
org.anchoranalysis.experiment.bean.task	Defines a task, which is a set of operations run on an input, that may or may not generate an output.
org.anchoranalysis.launcher.config	Specifies a configuration of the launcher for a particular application.
org.anchoranalysis.launcher.executor	Runs a particular experiment after identifying necessary paths and input files.
org.anchoranalysis.launcher.executor.selectparam	Different methods of selecting a object T that is used as a parameter for an experiment.
org.anchoranalysis.launcher.executor.selectparam.experiment	SelectParams for loading a Experiment.
org.anchoranalysis.launcher.options	A centralized location for all command-line options used by the launcher.
org.anchoranalysis.launcher.options.process	Adding/removing/changing the arguments (input and output) from the experiment via command-line-options.
org.anchoranalysis.plugin.annotation.bean.aggregate	Beans to combine two or more annotations.
org.anchoranalysis.plugin.annotation.bean.comparison	Task to compare a set of annotations to a segmentation or another set of annotations.
org.anchoranalysis.plugin.image.task.bean.combine	Combining multiple images together into a single image.
org.anchoranalysis.plugin.image.task.bean.feature	Tasks pertaining to Features.
org.anchoranalysis.plugin.image.task.bean.format	Tasks for converting image-formats.
org.anchoranalysis.plugin.image.task.bean.grouped	Tasks that involved stacks (usually each channel from an image) that are somehow grouped-together.
org.anchoranalysis.plugin.image.task.bean.labeller	Associating labels with images.
org.anchoranalysis.plugin.image.task.bean.scale	Tasks to scale an image.
org.anchoranalysis.plugin.image.task.bean.segment	Tasks to segment an image.
org.anchoranalysis.plugin.image.task.bean.slice	Tasks that process on one or more slices from a z-stack.
org.anchoranalysis.plugin.io.bean.task	Implementations of Task related to file-system I/O.
org.anchoranalysis.plugin.mpp.bean.convert	Converting from NamedChannelsInput to the input-type expected by a Task.

Uses of ExperimentExecutionException in org.anchoranalysis.experiment.arguments

Methods in org.anchoranalysis.experiment.arguments that throw ExperimentExecutionException

Modifier and Type	Method	Description
void	TaskArguments.assignGroup(String groupRange)	Assigns an index-range to use to form groups, by subsetting components from each input's identifier.
void	TaskArguments.assignMaxNumberProcessors(String numberProcessors)	Assigns a suggested maximum number of processors (CPUs) for a task.
void	TaskArguments.assignSize(String size)	Assign dimensions or scaling factor or size for an image, as may be used by a task.

Uses of ExperimentExecutionException in org.anchoranalysis.experiment.bean

Methods in org.anchoranalysis.experiment.bean that throw ExperimentExecutionException

Modifier and Type	Method	Description
abstract Optional<Path>	Experiment.executeExperiment(ExecutionArguments arguments)	Executes the experiment.

Uses of ExperimentExecutionException in org.anchoranalysis.experiment.bean.io

Methods in org.anchoranalysis.experiment.bean.io that throw ExperimentExecutionException

Modifier and Type	Method	Description
Optional<Path>	OutputExperiment.executeExperiment(ExecutionArguments arguments)	Executes the experiment for given arguments.
protected Optional<TaskStatistics>	InputOutputExperiment.executeExperimentWithParameters(ParametersExperiment parameters)
protected abstract Optional<TaskStatistics>	OutputExperiment.executeExperimentWithParameters(ParametersExperiment parameters)	Executes the experiment for parameters.

Uses of ExperimentExecutionException in org.anchoranalysis.experiment.bean.processor

Methods in org.anchoranalysis.experiment.bean.processor that throw ExperimentExecutionException

Modifier and Type	Method	Description
protected TaskStatistics	DebugDependentProcessor.execute(Outputter rootOutputter, List<T> inputs, ParametersExperiment parametersExperiment)
protected abstract TaskStatistics	JobProcessor.execute(Outputter rootOutputter, List<T> inputs, ParametersExperiment parametersExperiment)	Executes the task on all inputs.
protected TaskStatistics	ParallelProcessor.execute(Outputter rootOutputter, List<T> inputs, ParametersExperiment parametersExperiment)
protected TaskStatistics	SequentialProcessor.execute(Outputter rootOutputter, List<T> inputs, ParametersExperiment parametersExperiment)
TaskStatistics	JobProcessor.executeLogStatistics(Outputter rootOutputter, List<T> inputs, ParametersExperiment parametersExperiment)	Executes the task on all inputs and logs statistics about this to the file-systen.

Uses of ExperimentExecutionException in org.anchoranalysis.experiment.bean.task

Methods in org.anchoranalysis.experiment.bean.task that throw ExperimentExecutionException

Modifier and Type	Method	Description
abstract void	Task.afterAllJobsAreExecuted(S sharedState, InputOutputContext context)	Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
final void	TaskWithoutSharedState.afterAllJobsAreExecuted(NoSharedState sharedState, InputOutputContext context)
abstract S	Task.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<T> inputs, ParametersExperiment parameters)	Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
final NoSharedState	TaskWithoutSharedState.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<T> inputs, ParametersExperiment parameters)

Uses of ExperimentExecutionException in org.anchoranalysis.launcher.config

Methods in org.anchoranalysis.launcher.config that throw ExperimentExecutionException

Modifier and Type	Method	Description
abstract ExecutionArguments	LauncherConfig.createArguments(org.apache.commons.cli.CommandLine line)	Creates execution arguments from the command line.
ExperimentExecutor	LauncherConfig.createExperimentExecutor(org.apache.commons.cli.CommandLine line)	Creates an experiment executor from the command line.
abstract void	LauncherConfig.customizeExperimentExecutor(ExperimentExecutor executor, org.apache.commons.cli.CommandLine line)	Customizes the experiment executor with additional configuration.

Uses of ExperimentExecutionException in org.anchoranalysis.launcher.executor

Methods in org.anchoranalysis.launcher.executor that throw ExperimentExecutionException

Modifier and Type	Method	Description
static ExperimentExecutor	ExperimentExecutorFactory.create(org.apache.commons.cli.CommandLine line, Path defaultExperiment, Path configDirectory)	Creates an experiment-executor from a command line that EITHER: uses a default-experiment OR accepts a path passed as the first command-line argument.
void	ExperimentExecutor.executeExperiment(ExecutionArguments executionArguments, boolean alwaysShowExperimentArguments, Logger logger)	Executes an experiment after finding a single experiment XML file, and reading the experiment from this file.

Uses of ExperimentExecutionException in org.anchoranalysis.launcher.executor.selectparam

Methods in org.anchoranalysis.launcher.executor.selectparam that throw ExperimentExecutionException

Modifier and Type	Method	Description
String	SelectParam.describe()	Provides a string that can be displayed to the user to describe this particular SelectParam.
String	UseDefaultManager.describe()
static SelectParam<Path>	SelectParamFactory.experimentSelectParam(org.apache.commons.cli.CommandLine line, Path defaultExperiment)	Creates a SelectParam for experiment selection.
static SelectParam<Optional<Path>>	SelectParamFactory.outputSelectParam(org.apache.commons.cli.CommandLine line)	Creates a SelectParam for output selection.
T	SelectParam.select(ExecutionArguments executionArguments)	Retrieves the parameter.

Uses of ExperimentExecutionException in org.anchoranalysis.launcher.executor.selectparam.experiment

Methods in org.anchoranalysis.launcher.executor.selectparam.experiment that throw ExperimentExecutionException

Modifier and Type	Method	Description
static SelectParam<Path>	ExperimentFactory.defaultExperimentOrCustom(org.apache.commons.cli.CommandLine line, Path defaultExperiment)	Chooses either a path to the default-experiment or a path to a custom experiment.

Uses of ExperimentExecutionException in org.anchoranalysis.launcher.options

Method parameters in org.anchoranalysis.launcher.options with type arguments of type ExperimentExecutionException

Modifier and Type	Method	Description
void	CommandLineExtracter.ifPresentMultiple(String optionName, CheckedConsumer<String[],ExperimentExecutionException> consumer)	Executes a Consumer if an option is present - allowing that option to occur multiple times.
void	CommandLineExtracter.ifPresentSingle(String optionName, CheckedConsumer<String,ExperimentExecutionException> consumer)	Executes a Consumer if an option is present - allowing that option to occur only once.

Methods in org.anchoranalysis.launcher.options that throw ExperimentExecutionException

Modifier and Type	Method	Description
void	CommandLineExtracter.ifPresentMultiple(String optionName, CheckedConsumer<String[],ExperimentExecutionException> consumer)	Executes a Consumer if an option is present - allowing that option to occur multiple times.
void	CommandLineExtracter.ifPresentSingle(String optionName, CheckedConsumer<String,ExperimentExecutionException> consumer)	Executes a Consumer if an option is present - allowing that option to occur only once.

Uses of ExperimentExecutionException in org.anchoranalysis.launcher.options.process

Method parameters in org.anchoranalysis.launcher.options.process with type arguments of type ExperimentExecutionException

Modifier and Type	Method	Description
protected void	AddOptionsFromCommandLine.ifPresentMultiple(String optionShort, CheckedConsumer<String[],ExperimentExecutionException> consumer)	Executes consumer if one or more options exists with a single argument.
protected void	AddOptionsFromCommandLine.ifPresentSingle(String optionShort, CheckedConsumer<String,ExperimentExecutionException> consumer)	Executes consumer if maximally one option exists with a single argument - without passing associated.
protected void	AddOptionsFromCommandLine.ifPresentSingleAssociated(String optionShort, CheckedBiConsumer<T,String,ExperimentExecutionException> consumer)	Executes consumer if maximally one option exists with a single argument - passing associated.

Methods in org.anchoranalysis.launcher.options.process that throw ExperimentExecutionException

Modifier and Type	Method	Description
static void	AddInputOptions.addFrom(CommandLineExtracter extract, InputArguments arguments)	Adds options to change the inputs from the command-line.
static void	AddOutputOptions.addFrom(CommandLineExtracter extract, OutputArguments arguments)	Adds options to add/remove change the outputs the inputs from the command-line.
void	AddInputOptions.addOptionsFromCommandLine()
abstract void	AddOptionsFromCommandLine.addOptionsFromCommandLine()	Maybe add options to the arguments from the command-line.
void	AddOutputOptions.addOptionsFromCommandLine()
protected void	AddOptionsFromCommandLine.ifPresentMultiple(String optionShort, CheckedConsumer<String[],ExperimentExecutionException> consumer)	Executes consumer if one or more options exists with a single argument.
protected void	AddOptionsFromCommandLine.ifPresentSingle(String optionShort, CheckedConsumer<String,ExperimentExecutionException> consumer)	Executes consumer if maximally one option exists with a single argument - without passing associated.
protected void	AddOptionsFromCommandLine.ifPresentSingleAssociated(String optionShort, CheckedBiConsumer<T,String,ExperimentExecutionException> consumer)	Executes consumer if maximally one option exists with a single argument - passing associated.

Uses of ExperimentExecutionException in org.anchoranalysis.plugin.annotation.bean.aggregate

Methods in org.anchoranalysis.plugin.annotation.bean.aggregate that throw ExperimentExecutionException

Modifier and Type	Method	Description
void	AggregateAnnotations.afterAllJobsAreExecuted(AggregateSharedState sharedState, InputOutputContext context)
AggregateSharedState	AggregateAnnotations.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<AnnotationWithStrategy<S>> inputs, ParametersExperiment parameters)

Uses of ExperimentExecutionException in org.anchoranalysis.plugin.annotation.bean.comparison

Methods in org.anchoranalysis.plugin.annotation.bean.comparison that throw ExperimentExecutionException

Modifier and Type	Method	Description
void	CompareAnnotations.afterAllJobsAreExecuted(ComparisonSharedState<T> sharedState, InputOutputContext context)
ComparisonSharedState<T>	CompareAnnotations.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<AnnotationComparisonInput<ProvidesStackInput>> inputs, ParametersExperiment parameters)

Uses of ExperimentExecutionException in org.anchoranalysis.plugin.image.task.bean.combine

Methods in org.anchoranalysis.plugin.image.task.bean.combine that throw ExperimentExecutionException

Modifier and Type	Method	Description
void	Montage.afterAllJobsAreExecuted(MontageSharedState sharedState, InputOutputContext context)
MontageSharedState	Montage.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<StackSequenceInput> inputs, ParametersExperiment parameters)

Uses of ExperimentExecutionException in org.anchoranalysis.plugin.image.task.bean.feature

Methods in org.anchoranalysis.plugin.image.task.bean.feature that throw ExperimentExecutionException

Modifier and Type	Method	Description
void	ExportFeatures.afterAllJobsAreExecuted(FeatureExporter<S> sharedState, InputOutputContext context)
FeatureExporter<S>	ExportFeatures.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<T> inputs, ParametersExperiment parameters)

Uses of ExperimentExecutionException in org.anchoranalysis.plugin.image.task.bean.format

Methods in org.anchoranalysis.plugin.image.task.bean.format that throw ExperimentExecutionException

Modifier and Type	Method	Description
void	ConvertImageFormat.afterAllJobsAreExecuted(NoSharedState sharedState, InputOutputContext context)
NoSharedState	ConvertImageFormat.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<NamedChannelsInput> inputs, ParametersExperiment parameters)

Uses of ExperimentExecutionException in org.anchoranalysis.plugin.image.task.bean.grouped

Methods in org.anchoranalysis.plugin.image.task.bean.grouped that throw ExperimentExecutionException

Modifier and Type	Method	Description
void	GroupedStackBase.afterAllJobsAreExecuted(GroupedSharedState<S,T> sharedState, InputOutputContext context)
GroupedSharedState<S,T>	GroupedStackBase.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<ProvidesStackInput> inputs, ParametersExperiment parameters)

Uses of ExperimentExecutionException in org.anchoranalysis.plugin.image.task.bean.labeller

Methods in org.anchoranalysis.plugin.image.task.bean.labeller that throw ExperimentExecutionException

Modifier and Type	Method	Description
void	ImageAssignLabel.afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T> sharedState, InputOutputContext context)
SharedStateFilteredImageOutput<T>	ImageAssignLabel.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<ProvidesStackInput> inputs, ParametersExperiment parameters)

Uses of ExperimentExecutionException in org.anchoranalysis.plugin.image.task.bean.scale

Methods in org.anchoranalysis.plugin.image.task.bean.scale that throw ExperimentExecutionException

Modifier and Type	Method	Description
void	ScaleImage.afterAllJobsAreExecuted(S sharedState, InputOutputContext context)
CommonSize	ScaleImageCommonSize.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<StackSequenceInput> inputs, ParametersExperiment parameters)
NoSharedState	ScaleImageIndependently.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<StackSequenceInput> inputs, ParametersExperiment parameters)

Uses of ExperimentExecutionException in org.anchoranalysis.plugin.image.task.bean.segment

Methods in org.anchoranalysis.plugin.image.task.bean.segment that throw ExperimentExecutionException

Modifier and Type	Method	Description
void	SegmentInstanceWithModel.afterAllJobsAreExecuted(SharedStateSegmentInstance<T> sharedState, InputOutputContext context)
SharedStateSegmentInstance<T>	SegmentInstanceWithModel.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan plan, List<StackSequenceInput> inputs, ParametersExperiment parameters)

Uses of ExperimentExecutionException in org.anchoranalysis.plugin.image.task.bean.slice

Methods in org.anchoranalysis.plugin.image.task.bean.slice that throw ExperimentExecutionException

Modifier and Type	Method	Description
void	ExtractSlice.afterAllJobsAreExecuted(SharedStateSelectedSlice sharedState, InputOutputContext context)
SharedStateSelectedSlice	ExtractSlice.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<NamedChannelsInput> inputs, ParametersExperiment parameters)

Uses of ExperimentExecutionException in org.anchoranalysis.plugin.io.bean.task

Methods in org.anchoranalysis.plugin.io.bean.task that throw ExperimentExecutionException

Modifier and Type	Method	Description
void	CombineCSV.afterAllJobsAreExecuted(CSVWriter writer, InputOutputContext context)
void	CopyFiles.afterAllJobsAreExecuted(RecordingCounter<T> sharedState, InputOutputContext context)
void	SummarizeBase.afterAllJobsAreExecuted(Summarizer<S> sharedState, InputOutputContext context)
CSVWriter	CombineCSV.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<FileInput> inputs, ParametersExperiment parameters)
RecordingCounter<T>	CopyFiles.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<FileWithDirectoryInput> inputs, ParametersExperiment parameters)
Summarizer<S>	SummarizeBase.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<T> inputs, ParametersExperiment parameters)

Uses of ExperimentExecutionException in org.anchoranalysis.plugin.mpp.bean.convert

Methods in org.anchoranalysis.plugin.mpp.bean.convert that throw ExperimentExecutionException

Modifier and Type	Method	Description
void	ConvertNamedChannels.afterAllJobsAreExecuted(SharedStateRememberConverted<U,S> sharedState, InputOutputContext context)
SharedStateRememberConverted<U,S>	ConvertNamedChannels.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<T> inputs, ParametersExperiment parameters)