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 |
SelectParam s 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
Feature s. |
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.experiment.bean.convert |
Converting from
NamedChannelsInput to the
input-type expected by a Task . |
org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task |
Tasks that calculate and export
ReportFeature s. |
org.anchoranalysis.plugin.mpp.experiment.bean.objects |
Tasks involving
ObjectMask s. |
org.anchoranalysis.plugin.mpp.experiment.bean.segment |
Tasks that segment an image to produce a
MarkCollection . |
org.anchoranalysis.plugin.quick.bean.experiment |
Quickly defining experiments via several assumptions, including particular file-paths.
|
org.anchoranalysis.plugin.quick.bean.structure |
Specifying a structure of subdirectories and filenames when quickly defining an experiment.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
abstract Optional<Path> |
Experiment.executeExperiment(ExecutionArguments arguments)
Executes the experiment.
|
Modifier and Type | Method and Description |
---|---|
Optional<Path> |
OutputExperiment.executeExperiment(ExecutionArguments arguments)
Executes the experiment for given arguments.
|
protected abstract Optional<TaskStatistics> |
OutputExperiment.executeExperimentWithParameters(ParametersExperiment parameters)
Executes the experiment for parameters.
|
protected Optional<TaskStatistics> |
InputOutputExperiment.executeExperimentWithParameters(ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
protected TaskStatistics |
ParallelProcessor.execute(Outputter rootOutputter,
List<T> inputs,
ParametersExperiment parametersExperiment) |
protected TaskStatistics |
DebugDependentProcessor.execute(Outputter rootOutputter,
List<T> inputs,
ParametersExperiment parametersExperiment) |
protected TaskStatistics |
SequentialProcessor.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 . |
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. |
Modifier and Type | Method and Description |
---|---|
void |
TaskWithoutSharedState.afterAllJobsAreExecuted(NoSharedState sharedState,
InputOutputContext context) |
abstract void |
Task.afterAllJobsAreExecuted(S sharedState,
InputOutputContext context)
Called once after all calls to
Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>) . |
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>) . |
NoSharedState |
TaskWithoutSharedState.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<T> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
abstract ExecutionArguments |
LauncherConfig.createArguments(org.apache.commons.cli.CommandLine line) |
ExperimentExecutor |
LauncherConfig.createExperimentExecutor(org.apache.commons.cli.CommandLine line) |
abstract void |
LauncherConfig.customizeExperimentExecutor(ExperimentExecutor executor,
org.apache.commons.cli.CommandLine line) |
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
String |
UseDefaultManager.describe() |
String |
SelectParam.describe()
A string that can be displayed to the user to describe this particular
SelectParam . |
static SelectParam<Path> |
SelectParamFactory.experimentSelectParam(org.apache.commons.cli.CommandLine line,
Path defaultExperiment)
Can point to either:
a path ending in .xml, assumed to BeanXML for an experiment
nothing, then default experiment is used
|
static SelectParam<Optional<Path>> |
SelectParamFactory.outputSelectParam(org.apache.commons.cli.CommandLine line)
Can point to either:
a path ending in .xml, assumed to BeanXML for an output manager
a directory, set as the outputDirectory in the input-context
|
T |
SelectParam.select(ExecutionArguments executionArguments)
Retrieves the parameter.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and 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. |
Modifier and Type | Method and 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. |
Modifier and Type | Method and 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 . |
Modifier and Type | Method and 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.
|
abstract void |
AddOptionsFromCommandLine.addOptionsFromCommandLine()
Maybe add options to the arguments from the command-line.
|
void |
AddOutputOptions.addOptionsFromCommandLine() |
void |
AddInputOptions.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 . |
Modifier and Type | Method and Description |
---|---|
void |
AggregateAnnotations.afterAllJobsAreExecuted(AggregateSharedState sharedState,
InputOutputContext context) |
AggregateSharedState |
AggregateAnnotations.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<AnnotationWithStrategy<S>> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
void |
CompareAnnotations.afterAllJobsAreExecuted(ComparisonSharedState<T> sharedState,
InputOutputContext context) |
ComparisonSharedState<T> |
CompareAnnotations.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<AnnotationComparisonInput<ProvidesStackInput>> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
void |
Montage.afterAllJobsAreExecuted(MontageSharedState sharedState,
InputOutputContext context) |
MontageSharedState |
Montage.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<StackSequenceInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
void |
ExportFeatures.afterAllJobsAreExecuted(FeatureExporter<S> sharedState,
InputOutputContext context) |
FeatureExporter<S> |
ExportFeatures.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<T> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
void |
ConvertImageFormat.afterAllJobsAreExecuted(NoSharedState sharedState,
InputOutputContext context) |
NoSharedState |
ConvertImageFormat.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<NamedChannelsInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
void |
GroupedStackBase.afterAllJobsAreExecuted(GroupedSharedState<S,T> sharedState,
InputOutputContext context) |
GroupedSharedState<S,T> |
GroupedStackBase.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<ProvidesStackInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
void |
ImageAssignLabel.afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T> sharedState,
InputOutputContext context) |
SharedStateFilteredImageOutput<T> |
ImageAssignLabel.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<ProvidesStackInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
void |
ScaleImage.afterAllJobsAreExecuted(S sharedState,
InputOutputContext context) |
NoSharedState |
ScaleImageIndependently.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<StackSequenceInput> inputs,
ParametersExperiment parameters) |
CommonSize |
ScaleImageCommonSize.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<StackSequenceInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
void |
SegmentInstanceWithModel.afterAllJobsAreExecuted(SharedStateSegmentInstance<T> sharedState,
InputOutputContext context) |
SharedStateSegmentInstance<T> |
SegmentInstanceWithModel.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan plan,
List<StackSequenceInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
void |
ExtractSlice.afterAllJobsAreExecuted(SharedStateSelectedSlice sharedState,
InputOutputContext context) |
SharedStateSelectedSlice |
ExtractSlice.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<NamedChannelsInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and 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) |
Modifier and Type | Method and Description |
---|---|
void |
ConvertNamedChannels.afterAllJobsAreExecuted(SharedStateRememberConverted<U,S> sharedState,
InputOutputContext context) |
SharedStateRememberConverted<U,S> |
ConvertNamedChannels.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<T> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
void |
ExportReportFeatures.afterAllJobsAreExecuted(CSVWriter writer,
InputOutputContext context) |
CSVWriter |
ExportReportFeatures.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<MultiInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
void |
ExportObjectsFromCSV.afterAllJobsAreExecuted(FromCSVSharedState sharedState,
InputOutputContext context) |
void |
ExportObjectsAsCroppedImages.afterAllJobsAreExecuted(NoSharedState sharedState,
InputOutputContext context) |
FromCSVSharedState |
ExportObjectsFromCSV.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<FromCSVInput> inputs,
ParametersExperiment parameters) |
NoSharedState |
ExportObjectsAsCroppedImages.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<MultiInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
void |
SegmentMarksFromImage.afterAllJobsAreExecuted(ExperimentState sharedState,
InputOutputContext context) |
ExperimentState |
SegmentMarksFromImage.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<MultiInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
Optional<Path> |
QuickExperiment.executeExperiment(ExecutionArguments arguments) |
Optional<Path> |
QuickMultiDatasetExperiment.executeExperiment(ExecutionArguments arguments) |
Modifier and Type | Method and Description |
---|---|
Optional<Path> |
QuickMultiDatasetStructuredExperiment.executeExperiment(ExecutionArguments arguments) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.