Package | Description |
---|---|
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.experiment.io |
Interfaces for replacing attributes of an experiment: input, output, task etc.
|
org.anchoranalysis.experiment.task |
Non-bean classes related to a
Task . |
org.anchoranalysis.feature.io.csv |
Metadata for writing feature calculation-results in CSV format.
|
org.anchoranalysis.io.output.outputter |
Classes for outputting to particular directories.
|
org.anchoranalysis.io.output.writer |
Allows a generators to write element(s) to the filesystem.
|
org.anchoranalysis.mpp.io.output |
Non-beans for writing data structures related to marked point processes from the file system.
|
org.anchoranalysis.mpp.segment.bean |
Beans for segmentation algorithms related to marked-point-processes.
|
org.anchoranalysis.mpp.segment.bean.define |
DefineOutputter and its sub-classes. |
org.anchoranalysis.mpp.segment.optimization |
Non-bean classes used in
org.anchoranalysis.mpp.segment.bean.optimization |
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.image.task.labeller |
Non-bean classes about labelling images.
|
org.anchoranalysis.plugin.image.task.stack |
Non-bean classes pertaining to stacks and channels as used in tasks.
|
org.anchoranalysis.plugin.io.bean.task |
Implementations of
Task related to file-system
I/O. |
org.anchoranalysis.plugin.io.shared |
Objects used in shared-state in
Task s in this
plugin. |
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.mpp.segment.shared |
Stared-state for segmentation tasks involving mark-point-processes.
|
org.anchoranalysis.test.image.io |
Utilities for testing-related reading and writing to the filesystem.
|
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 |
---|---|
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 |
---|---|
Outputter |
InitializationContext.getOutputter()
An outputter that writes to the particular output-directory.
|
Modifier and Type | Method and Description |
---|---|
Outputter |
InputBound.getOutputter()
The
Outputter associated with this input, as it is being processed as a job. |
Outputter |
InputOutputContextStateful.getOutputter() |
Outputter |
ParametersExperiment.getOutputter()
An outputter that writes to the particular output-directory.
|
Constructor and Description |
---|
InputOutputContextStateful(ExecutionArguments executionArguments,
Outputter outputter,
ExecutionTimeRecorder executionTimeRecorder,
StatefulMessageLogger logger,
ErrorReporter errorReporter)
Creates with initialization arguments.
|
Modifier and Type | Method and Description |
---|---|
static Optional<FeatureCSVWriter> |
FeatureCSVWriter.create(FeatureCSVMetadata metadata,
Outputter outputter,
boolean visuallyShortenedDecimals)
Maybe creates a
FeatureCSVWriter depending if the output is allowed. |
Modifier and Type | Method and Description |
---|---|
Outputter |
Outputter.deriveSubdirectory(String subdirectoryName,
boolean inheritOutputRulesAndRecording)
|
Outputter |
InputOutputContext.getOutputter()
An outputter that writes to the particular output-directory.
|
Modifier and Type | Method and Description |
---|---|
Optional<Outputter> |
WriterRouterErrors.createSubdirectory(String outputName,
boolean inheritOutputRulesAndRecording)
Maybe creates a subdirectory for writing to.
|
Constructor and Description |
---|
EnergyStackWriter(EnergyStack energyStack,
Outputter outputter) |
Modifier and Type | Method and Description |
---|---|
void |
ExperimentState.outputAfterAllTasksAreExecuted(Outputter outputter) |
void |
ExperimentState.outputBeforeAnyTasksAreExecuted(Outputter outputter) |
Modifier and Type | Method and Description |
---|---|
protected void |
DefineOutputter.outputSharedObjects(SharedObjects sharedObjects,
Optional<EnergyStack> energyStack,
Outputter outputter) |
Modifier and Type | Method and Description |
---|---|
Outputter |
OptimizationContext.getOutputter() |
Modifier and Type | Method and Description |
---|---|
AggregateSharedState |
AggregateAnnotations.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<AnnotationWithStrategy<S>> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
ComparisonSharedState<T> |
CompareAnnotations.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<AnnotationComparisonInput<ProvidesStackInput>> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
MontageSharedState |
Montage.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<StackSequenceInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
FeatureExporter<S> |
ExportFeatures.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<T> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
NoSharedState |
ConvertImageFormat.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<NamedChannelsInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
GroupedSharedState<S,T> |
GroupedStackBase.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<ProvidesStackInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
SharedStateFilteredImageOutput<T> |
ImageAssignLabel.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<ProvidesStackInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
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 |
---|---|
SharedStateSegmentInstance<T> |
SegmentInstanceWithModel.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan plan,
List<StackSequenceInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
SharedStateSelectedSlice |
ExtractSlice.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<NamedChannelsInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
Optional<Outputter> |
SharedStateFilteredImageOutput.getOutputterFor(String groupIdentifier)
groupIdentifierFor should always called at least once before getOutputManagerFor
|
Constructor and Description |
---|
SharedStateFilteredImageOutput(Outputter baseOutputter,
ImageLabeller<T> filter,
String outputNameMapping,
String outputNameImages) |
Constructor and Description |
---|
SharedStateSelectedSlice(Outputter baseOutputter) |
Modifier and Type | Method and Description |
---|---|
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) |
Constructor and Description |
---|
RecordingCounter(Counter counter,
Outputter outputter,
T namingSharedState) |
Modifier and Type | Method and Description |
---|---|
SharedStateRememberConverted<U,S> |
ConvertNamedChannels.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<T> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
CSVWriter |
ExportReportFeatures.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<MultiInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
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 |
---|---|
ExperimentState |
SegmentMarksFromImage.beforeAnyJobIsExecuted(Outputter outputter,
ConcurrencyPlan concurrencyPlan,
List<MultiInput> inputs,
ParametersExperiment parameters) |
Modifier and Type | Method and Description |
---|---|
void |
SegmentMarksState.outputAfterAllTasksAreExecuted(Outputter outputter) |
void |
SegmentMarksState.outputBeforeAnyTasksAreExecuted(Outputter outputter) |
Modifier and Type | Method and Description |
---|---|
static Outputter |
OutputterFixture.outputter(Optional<Path> pathTempDirectory) |
static Outputter |
OutputterFixture.outputter(OutputManager outputManager,
OutputEnabledRules outputsEnabled) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.