Uses of Class
org.anchoranalysis.core.time.ExecutionTimeRecorder

Packages that use ExecutionTimeRecorder

Package	Description
org.anchoranalysis.core.time	Recording the execution-time of operations for profiling.
org.anchoranalysis.experiment.task	Non-bean classes related to a Task.
org.anchoranalysis.experiment.time	How long particular operations take to execute.
org.anchoranalysis.image.inference	Inference of machine learning models on images.
org.anchoranalysis.image.inference.bean.reduce	Beans to reduce the number of results that are returned from inference, by removing overlaping entities etc.
org.anchoranalysis.image.inference.bean.segment.instance	Instance-segmentation of a Stack.
org.anchoranalysis.image.inference.bean.segment.reduce	Non-bean classes to reduce the number of results that are returned from inference, by removing overlapping entities etc.
org.anchoranalysis.image.inference.segment	Non-beans pertaining to segmentation of images via model inference.
org.anchoranalysis.image.io.bean.stack.reader	Bean classes for reading raster-files from the filesystem.
org.anchoranalysis.image.voxel.resizer	Different interpolator methods to use when scaling voxels.
org.anchoranalysis.io.bioformats.bean	Beans for filesystem I/O using Bioformats.
org.anchoranalysis.io.input.bean	Beans related to collecting inputs from the file-system for an experiment.
org.anchoranalysis.io.output.bean	Beans for the framework around writing files to the file-system.
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.plugin.image.bean.object.segment.reduce	Strategies for reducing the number of elements with a list by merging/removing lower-confidence elements that overlap.
org.anchoranalysis.plugin.image.bean.thumbnail.object	Implementations of ThumbnailFromObjects.
org.anchoranalysis.plugin.image.task.feature	Non-bean classes pertaining to Features as used in tasks.
org.anchoranalysis.plugin.image.task.segment	Non-bean classes for image-segmentation.
org.anchoranalysis.plugin.image.task.slice	Non-bean classes pertaining to combining stacks into a single stack.
org.anchoranalysis.plugin.io.bean.input.stack	Implementations of InputManager that process Stacks.
org.anchoranalysis.plugin.io.bean.stack.reader	Implementations of StackReader.
org.anchoranalysis.plugin.io.multifile	Non-bean classes to help use multiple files to represent a single Stack.
org.anchoranalysis.plugin.opencv.bean.stack	Implementations of StackWriter and StackReader that involve OpenCV.

Uses of ExecutionTimeRecorder in org.anchoranalysis.core.time

Subclasses of ExecutionTimeRecorder in org.anchoranalysis.core.time

Modifier and Type	Class	Description
class	ExecutionTimeRecorderIgnore	An implementation of ExecutionTimeRecorder that is a simple placeholder that does nothing.

Methods in org.anchoranalysis.core.time that return ExecutionTimeRecorder

Modifier and Type	Method	Description
ExecutionTimeRecorder	OperationContext.getExecutionTimeRecorder()	Allows for the execution time of certain operations to be recorded.
static ExecutionTimeRecorder	ExecutionTimeRecorderIgnore.instance()	Singleton instance.

Constructors in org.anchoranalysis.core.time with parameters of type ExecutionTimeRecorder

Modifier	Constructor	Description
	OperationContext(ExecutionTimeRecorder executionTimeRecorder, Logger logger)	Creates a new OperationContext instance.

Uses of ExecutionTimeRecorder in org.anchoranalysis.experiment.task

Methods in org.anchoranalysis.experiment.task that return ExecutionTimeRecorder

Modifier and Type	Method	Description
ExecutionTimeRecorder	ExperimentFeedbackContext.getExecutionTimeRecorder()	Allows execution-time for particular operations to be recorded.
ExecutionTimeRecorder	InputOutputContextStateful.getExecutionTimeRecorder()
ExecutionTimeRecorder	ParametersExperiment.getExecutionTimeRecorder()	Allows execution-time for particular operations to be recorded.

Constructors in org.anchoranalysis.experiment.task with parameters of type ExecutionTimeRecorder

Modifier	Constructor	Description
	ExperimentFeedbackContext(StatefulMessageLogger loggerExperiment, boolean detailedLogging, ExecutionTimeRecorder executionTimeRecorder)	Creates a new ExperimentFeedbackContext instance.
	InputOutputContextStateful(ExecutionArguments executionArguments, Outputter outputter, ExecutionTimeRecorder executionTimeRecorder, StatefulMessageLogger logger, ErrorReporter errorReporter)	Creates with initialization arguments.

Uses of ExecutionTimeRecorder in org.anchoranalysis.experiment.time

Methods in org.anchoranalysis.experiment.time that return ExecutionTimeRecorder

Modifier and Type	Method	Description
static ExecutionTimeRecorder	ExecutionTimeRecorderFactory.create(boolean executionTimeOutputsEnabled)	Creates either a ExecutionTimeRecorder that records times, or ignores the recording depending on whether any output is enabled that needs the execution-time.

Uses of ExecutionTimeRecorder in org.anchoranalysis.image.inference

Methods in org.anchoranalysis.image.inference that return ExecutionTimeRecorder

Modifier and Type	Method	Description
ExecutionTimeRecorder	ImageInferenceContext.getExecutionTimeRecorder()	Allows execution-time for particular operations to be recorded.

Constructors in org.anchoranalysis.image.inference with parameters of type ExecutionTimeRecorder

Modifier	Constructor	Description
	ImageInferenceContext(DualScale<Dimensions> dimensions, ScaleFactor scaleFactor, Optional<List<String>> classLabels, VoxelsResizer resizer, ExecutionTimeRecorder executionTimeRecorder, Logger logger)	Creates a new ImageInferenceContext instance.

Uses of ExecutionTimeRecorder in org.anchoranalysis.image.inference.bean.reduce

Methods in org.anchoranalysis.image.inference.bean.reduce with parameters of type ExecutionTimeRecorder

Modifier and Type	Method	Description
ReductionOutcome<LabelledWithConfidence<ObjectMask>>	ReduceElementsGreedy.reduce(List<LabelledWithConfidence<ObjectMask>> elements, Extent extent, ExecutionTimeRecorder executionTimeRecorder)

Uses of ExecutionTimeRecorder in org.anchoranalysis.image.inference.bean.segment.instance

Methods in org.anchoranalysis.image.inference.bean.segment.instance with parameters of type ExecutionTimeRecorder

Modifier and Type	Method	Description
SegmentedObjects	SegmentStackIntoObjectsPooled.segment(Stack stack, ExecutionTimeRecorder executionTimeRecorder)	Segments individually using a pool of size 1 just for one stack.
abstract SegmentedObjects	SegmentStackIntoObjectsPooled.segment(Stack stack, ConcurrentModelPool<T> modelPool, ExecutionTimeRecorder executionTimeRecorder)	Segments a stack to produce an object-collection.
SegmentedObjects	SegmentStackIntoObjectsScaleDecode.segment(Stack stack, ConcurrentModelPool<S> modelPool, ExecutionTimeRecorder executionTimeRecorder)
SegmentedObjects	SuppressNonMaximum.segment(Stack stack, ConcurrentModelPool<T> modelPool, ExecutionTimeRecorder executionTimeRecorder)

Uses of ExecutionTimeRecorder in org.anchoranalysis.image.inference.bean.segment.reduce

Methods in org.anchoranalysis.image.inference.bean.segment.reduce with parameters of type ExecutionTimeRecorder

Modifier and Type	Method	Description
abstract ReductionOutcome<LabelledWithConfidence<T>>	ReduceElements.reduce(List<LabelledWithConfidence<T>> elements, Extent extent, ExecutionTimeRecorder executionTimeRecorder)	Reduce a list of elements (each with a confidence score and a label) to a smaller-list.

Uses of ExecutionTimeRecorder in org.anchoranalysis.image.inference.segment

Methods in org.anchoranalysis.image.inference.segment with parameters of type ExecutionTimeRecorder

Modifier and Type	Method	Description
SegmentedObjects	SegmentedObjects.reduce(ReduceElements<ObjectMask> reduce, boolean separateEachLabel, ExecutionTimeRecorder executionTimeRecorder)	Reduces the segmented-objects, applying a reduction algorithm separately to each object-class.

Constructors in org.anchoranalysis.image.inference.segment with parameters of type ExecutionTimeRecorder

Modifier	Constructor	Description
	SegmentedObjects(String classLabel, Collection<WithConfidence<MultiScaleObject>> objects, SegmentedBackground background, ExecutionTimeRecorder executionTimeRecorder)	Create for a collection of objects with an identical label.
	SegmentedObjects(List<LabelledWithConfidence<MultiScaleObject>> objects, SegmentedBackground background, ExecutionTimeRecorder executionTimeRecorder)	Create for a collection of objects with potentially differing labels.
	SegmentedObjectsAtScale(List<LabelledWithConfidence<MultiScaleObject>> source, Function<MultiScaleObject,ObjectMask> extractObject, Stack background, StackDisplayer displayer, ExecutionTimeRecorder executionTimeRecorder, String executionTimeSuffix)	Creates a new SegmentedObjectsAtScale instance.

Uses of ExecutionTimeRecorder in org.anchoranalysis.image.io.bean.stack.reader

Methods in org.anchoranalysis.image.io.bean.stack.reader with parameters of type ExecutionTimeRecorder

Modifier and Type	Method	Description
abstract OpenedImageFile	StackReader.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)	Opens a file containing one or more images.
abstract OpenedImageFile	StackReaderOrientationCorrection.openFile(Path path, CalculateOrientationChange orientationCorrection, ExecutionTimeRecorder executionTimeRecorder)	Opens a file containing one or more images but does not read an image.

Uses of ExecutionTimeRecorder in org.anchoranalysis.image.voxel.resizer

Constructors in org.anchoranalysis.image.voxel.resizer with parameters of type ExecutionTimeRecorder

Modifier	Constructor	Description
	VoxelsResizerExecutionTime(VoxelsResizer resizer, ExecutionTimeRecorder executionTimeRecorder, String operationIdentifierPrefix)	Creates with an VoxelsResizer and ExecutionTimeRecorder.

Uses of ExecutionTimeRecorder in org.anchoranalysis.io.bioformats.bean

Methods in org.anchoranalysis.io.bioformats.bean with parameters of type ExecutionTimeRecorder

Modifier and Type	Method	Description
OpenedImageFile	BioformatsReader.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	BioformatsReader.openFile(Path filePath, CalculateOrientationChange orientationCorrection, ExecutionTimeRecorder executionTimeRecorder)

Uses of ExecutionTimeRecorder in org.anchoranalysis.io.input.bean

Methods in org.anchoranalysis.io.input.bean that return ExecutionTimeRecorder

Modifier and Type	Method	Description
ExecutionTimeRecorder	InputManagerParameters.getExecutionTimeRecorder()	Allows for the execution time of certain operations to be recorded.

Uses of ExecutionTimeRecorder in org.anchoranalysis.io.output.bean

Methods in org.anchoranalysis.io.output.bean with parameters of type ExecutionTimeRecorder

Modifier and Type	Method	Description
OutputWriteContext	OutputManager.createContextForWriting(Optional<ImageFileFormat> suggestedFormatToWrite, ExecutionTimeRecorder executionTimeRecorder)	Creates the OutputWriteContext needed for writing files.

Uses of ExecutionTimeRecorder in org.anchoranalysis.io.output.outputter

Methods in org.anchoranalysis.io.output.outputter that return ExecutionTimeRecorder

Modifier and Type	Method	Description
ExecutionTimeRecorder	InputOutputContext.getExecutionTimeRecorder()	Allows execution-times to be recorded for particular operations.
ExecutionTimeRecorder	OutputWriteContext.getExecutionTimeRecorder()	Records the execution time of particular operations.

Constructors in org.anchoranalysis.io.output.outputter with parameters of type ExecutionTimeRecorder

Modifier	Constructor	Description
	OutputWriteContext(OutputWriteSettings settings, Optional<ImageFileFormat> suggestedFormatToWrite, ExecutionTimeRecorder executionTimeRecorder)	Creates a new OutputWriteContext instance.

Uses of ExecutionTimeRecorder in org.anchoranalysis.io.output.writer

Methods in org.anchoranalysis.io.output.writer that return ExecutionTimeRecorder

Modifier and Type	Method	Description
ExecutionTimeRecorder	ElementOutputter.getExecutionTimeRecorder()	Records the execution time of particular operations.

Constructors in org.anchoranalysis.io.output.writer with parameters of type ExecutionTimeRecorder

Modifier	Constructor	Description
	ElementOutputter(OutputterChecked outputter, ExecutionTimeRecorder executionTimeRecorder, Supplier<Optional<Logger>> logger)	Creates a new ElementOutputter instance.

Uses of ExecutionTimeRecorder in org.anchoranalysis.plugin.image.bean.object.segment.reduce

Methods in org.anchoranalysis.plugin.image.bean.object.segment.reduce with parameters of type ExecutionTimeRecorder

Modifier and Type	Method	Description
ReductionOutcome<LabelledWithConfidence<ObjectMask>>	ThresholdConfidence.reduce(List<LabelledWithConfidence<ObjectMask>> elements, Extent extent, ExecutionTimeRecorder executionTimeRecorder)

Uses of ExecutionTimeRecorder in org.anchoranalysis.plugin.image.bean.thumbnail.object

Methods in org.anchoranalysis.plugin.image.bean.thumbnail.object with parameters of type ExecutionTimeRecorder

Modifier and Type	Method	Description
ThumbnailBatch<ObjectCollection>	OutlinePreserveRelativeSize.start(ObjectCollection objects, StreamableCollection<BoundingBox> boundingBoxes, Optional<Stack> backgroundSource, ExecutionTimeRecorder executionTimeRecorder)
abstract ThumbnailBatch<ObjectCollection>	ThumbnailFromObjects.start(ObjectCollection objects, StreamableCollection<BoundingBox> boundingBoxes, Optional<Stack> background, ExecutionTimeRecorder executionTimeRecorder)	Initializes a batch to create thumbnails.

Uses of ExecutionTimeRecorder in org.anchoranalysis.plugin.image.task.feature

Methods in org.anchoranalysis.plugin.image.task.feature that return ExecutionTimeRecorder

Modifier and Type	Method	Description
ExecutionTimeRecorder	FeatureCalculationContext.getExecutionTimeRecorder()	Records the execution-time of particular operations.

Methods in org.anchoranalysis.plugin.image.task.feature with parameters of type ExecutionTimeRecorder

Modifier and Type	Method	Description
FeatureCalculationContext<S>	FeatureExporter.createCalculationContext(Optional<String> groupName, ExecutionTimeRecorder executionTimeRecorder, InputOutputContext ioContext)	Creates a FeatureCalculationContext for calculating features to later use this exporter.

Constructors in org.anchoranalysis.plugin.image.task.feature with parameters of type ExecutionTimeRecorder

Modifier	Constructor	Description
	FeatureCalculationContext(FeatureResultsAndThumbnails results, S rowSource, FeatureNameList featureNames, Optional<String> groupGeneratorName, ExecutionTimeRecorder executionTimeRecorder, boolean suppressErrors, InputOutputContext context)	Creates a new FeatureCalculationContext.

Uses of ExecutionTimeRecorder in org.anchoranalysis.plugin.image.task.segment

Methods in org.anchoranalysis.plugin.image.task.segment with parameters of type ExecutionTimeRecorder

Modifier and Type	Method	Description
FeatureCalculationContext<FeatureTableCalculator<FeatureInputSingleObject>>	SharedStateSegmentInstance.createCalculationContext(ExecutionTimeRecorder executionTimeRecorder, InputOutputContext ioContext)	Creates a FeatureCalculationContext for calculating features to later use this exporter.

Uses of ExecutionTimeRecorder in org.anchoranalysis.plugin.image.task.slice

Constructors in org.anchoranalysis.plugin.image.task.slice with parameters of type ExecutionTimeRecorder

Modifier	Constructor	Description
	MontageSharedState(Map<Path,BoundingBoxEnclosed> boxes, Extent sizeCombined, VoxelsResizer resizer, ExecutionTimeRecorder executionTimeRecorder)	Create with a mapping from Paths to boxes.

Uses of ExecutionTimeRecorder in org.anchoranalysis.plugin.io.bean.input.stack

Constructors in org.anchoranalysis.plugin.io.bean.input.stack with parameters of type ExecutionTimeRecorder

Modifier	Constructor	Description
	ConvertNamedChannelsInputToStack(NamedChannelsInput input, int timeIndex, Optional<String> channelName, ExecutionTimeRecorder executionTimeRecorder)	Create with an input.
	ConvertNamedChannelsInputToStack(NamedChannelsInput input, ExecutionTimeRecorder executionTimeRecorder)	Create with an input.

Uses of ExecutionTimeRecorder in org.anchoranalysis.plugin.io.bean.stack.reader

Methods in org.anchoranalysis.plugin.io.bean.stack.reader with parameters of type ExecutionTimeRecorder

Modifier and Type	Method	Description
OpenedImageFile	BranchExtension.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	FlattenAsChannel.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	ImposeResolution.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	MultiFileReader.openFile(Path filePath, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	ReadVoxelExtentXml.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	RejectIfConditionXYResolution.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	RotateImageToMatchEXIFOrientation.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)
OpenedImageFile	RotateImageToMatchEXIFOrientation.openFile(Path path, CalculateOrientationChange orientationCorrection, ExecutionTimeRecorder executionTimeRecorder)

Uses of ExecutionTimeRecorder in org.anchoranalysis.plugin.io.multifile

Constructors in org.anchoranalysis.plugin.io.multifile with parameters of type ExecutionTimeRecorder

Modifier	Constructor	Description
	OpenedMultiFile(StackReader stackReader, ParsedFilePathBag fileBag, ExecutionTimeRecorder executionTimeRecorder)

Uses of ExecutionTimeRecorder in org.anchoranalysis.plugin.opencv.bean.stack

Methods in org.anchoranalysis.plugin.opencv.bean.stack with parameters of type ExecutionTimeRecorder

Modifier and Type	Method	Description
OpenedImageFile	OpenCVReader.openFile(Path path, ExecutionTimeRecorder executionTimeRecorder)