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
Feature s 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 Stack s. |
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 |
Modifier and Type | Class and Description |
---|---|
class |
ExecutionTimeRecorderIgnore
An implementation of
ExecutionTimeRecorder that is a simple placeholder that does
nothing. |
Modifier and Type | Method and Description |
---|---|
ExecutionTimeRecorder |
OperationContext.getExecutionTimeRecorder()
Allows for the execution time of certain operations to be recorded.
|
static ExecutionTimeRecorder |
ExecutionTimeRecorderIgnore.instance()
Singleton instance.
|
Constructor and Description |
---|
OperationContext(ExecutionTimeRecorder executionTimeRecorder,
Logger logger) |
Modifier and Type | Method and 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.
|
Constructor and Description |
---|
ExperimentFeedbackContext(StatefulMessageLogger loggerExperiment,
boolean detailedLogging,
ExecutionTimeRecorder executionTimeRecorder) |
InputOutputContextStateful(ExecutionArguments executionArguments,
Outputter outputter,
ExecutionTimeRecorder executionTimeRecorder,
StatefulMessageLogger logger,
ErrorReporter errorReporter)
Creates with initialization arguments.
|
Modifier and Type | Method and 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. |
Modifier and Type | Method and Description |
---|---|
ExecutionTimeRecorder |
ImageInferenceContext.getExecutionTimeRecorder()
Allows execution-time for particular operations to be recorded.
|
Constructor and Description |
---|
ImageInferenceContext(DualScale<Dimensions> dimensions,
ScaleFactor scaleFactor,
Optional<List<String>> classLabels,
VoxelsResizer resizer,
ExecutionTimeRecorder executionTimeRecorder,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
ReductionOutcome<LabelledWithConfidence<ObjectMask>> |
ReduceElementsGreedy.reduce(List<LabelledWithConfidence<ObjectMask>> elements,
Extent extent,
ExecutionTimeRecorder executionTimeRecorder) |
Modifier and Type | Method and Description |
---|---|
SegmentedObjects |
SegmentStackIntoObjectsScaleDecode.segment(Stack stack,
ConcurrentModelPool<S> modelPool,
ExecutionTimeRecorder executionTimeRecorder) |
abstract SegmentedObjects |
SegmentStackIntoObjectsPooled.segment(Stack stack,
ConcurrentModelPool<T> modelPool,
ExecutionTimeRecorder executionTimeRecorder)
Segments a stack to produce an object-collection.
|
SegmentedObjects |
SuppressNonMaximum.segment(Stack stack,
ConcurrentModelPool<T> modelPool,
ExecutionTimeRecorder executionTimeRecorder) |
SegmentedObjects |
SegmentStackIntoObjectsPooled.segment(Stack stack,
ExecutionTimeRecorder executionTimeRecorder)
Segments individually using a pool of size 1 just for one stack.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
SegmentedObjects |
SegmentedObjects.reduce(ReduceElements<ObjectMask> reduce,
boolean separateEachLabel,
ExecutionTimeRecorder executionTimeRecorder)
Reduces the segmented-objects, applying a reduction algorithm separately to each
object-class.
|
Constructor and Description |
---|
SegmentedObjects(List<LabelledWithConfidence<MultiScaleObject>> objects,
SegmentedBackground background,
ExecutionTimeRecorder executionTimeRecorder)
Create for a collection of objects with potentially differing labels.
|
SegmentedObjects(String classLabel,
Collection<WithConfidence<MultiScaleObject>> objects,
SegmentedBackground background,
ExecutionTimeRecorder executionTimeRecorder)
Create for a collection of objects with an identical label.
|
SegmentedObjectsAtScale(List<LabelledWithConfidence<MultiScaleObject>> source,
java.util.function.Function<MultiScaleObject,ObjectMask> extractObject,
Stack background,
StackDisplayer displayer,
ExecutionTimeRecorder executionTimeRecorder,
String executionTimeSuffix) |
Modifier and Type | Method and Description |
---|---|
abstract OpenedImageFile |
StackReaderOrientationCorrection.openFile(Path path,
CalculateOrientationChange orientationCorrection,
ExecutionTimeRecorder executionTimeRecorder)
Opens a file containing one or more images but does not read an image.
|
abstract OpenedImageFile |
StackReader.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder)
Opens a file containing one or more images.
|
Constructor and Description |
---|
VoxelsResizerExecutionTime(VoxelsResizer resizer,
ExecutionTimeRecorder executionTimeRecorder,
String operationIdentifierPrefix)
Creates with an
VoxelsResizer and ExecutionTimeRecorder . |
Modifier and Type | Method and Description |
---|---|
OpenedImageFile |
BioformatsReader.openFile(Path filePath,
CalculateOrientationChange orientationCorrection,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
BioformatsReader.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
Modifier and Type | Method and Description |
---|---|
ExecutionTimeRecorder |
InputManagerParameters.getExecutionTimeRecorder()
Allows for the execution time of certain operations to be recorded.
|
Modifier and Type | Method and Description |
---|---|
OutputWriteContext |
OutputManager.createContextForWriting(Optional<ImageFileFormat> suggestedFormatToWrite,
ExecutionTimeRecorder executionTimeRecorder)
Creates the
OutputWriteContext needed for writing files. |
Modifier and Type | Method and Description |
---|---|
ExecutionTimeRecorder |
OutputWriteContext.getExecutionTimeRecorder()
Records the execution time of particular operations.
|
ExecutionTimeRecorder |
InputOutputContext.getExecutionTimeRecorder()
Allows execution-times to be recorded for particular operations.
|
Constructor and Description |
---|
OutputWriteContext(OutputWriteSettings settings,
Optional<ImageFileFormat> suggestedFormatToWrite,
ExecutionTimeRecorder executionTimeRecorder) |
Modifier and Type | Method and Description |
---|---|
ExecutionTimeRecorder |
ElementOutputter.getExecutionTimeRecorder()
Records the execution time of particular operations.
|
Constructor and Description |
---|
ElementOutputter(OutputterChecked outputter,
ExecutionTimeRecorder executionTimeRecorder,
java.util.function.Supplier<Optional<Logger>> logger) |
Modifier and Type | Method and Description |
---|---|
ReductionOutcome<LabelledWithConfidence<ObjectMask>> |
ThresholdConfidence.reduce(List<LabelledWithConfidence<ObjectMask>> elements,
Extent extent,
ExecutionTimeRecorder executionTimeRecorder) |
Modifier and Type | Method and Description |
---|---|
abstract ThumbnailBatch<ObjectCollection> |
ThumbnailFromObjects.start(ObjectCollection objects,
StreamableCollection<BoundingBox> boundingBoxes,
Optional<Stack> background,
ExecutionTimeRecorder executionTimeRecorder)
Initializes a batch to create thumbnails.
|
ThumbnailBatch<ObjectCollection> |
OutlinePreserveRelativeSize.start(ObjectCollection objects,
StreamableCollection<BoundingBox> boundingBoxes,
Optional<Stack> backgroundSource,
ExecutionTimeRecorder executionTimeRecorder) |
Modifier and Type | Method and Description |
---|---|
ExecutionTimeRecorder |
FeatureCalculationContext.getExecutionTimeRecorder()
Records the execution-time of particular operations.
|
Modifier and Type | Method and Description |
---|---|
FeatureCalculationContext<S> |
FeatureExporter.createCalculationContext(Optional<String> groupName,
ExecutionTimeRecorder executionTimeRecorder,
InputOutputContext ioContext)
Creates a
FeatureCalculationContext for calculating features to later use this
exporter. |
Constructor and Description |
---|
FeatureCalculationContext(FeatureResultsAndThumbnails results,
S rowSource,
FeatureNameList featureNames,
Optional<String> groupGeneratorName,
ExecutionTimeRecorder executionTimeRecorder,
boolean suppressErrors,
InputOutputContext context)
Default constructor.
|
Modifier and Type | Method and Description |
---|---|
FeatureCalculationContext<FeatureTableCalculator<FeatureInputSingleObject>> |
SharedStateSegmentInstance.createCalculationContext(ExecutionTimeRecorder executionTimeRecorder,
InputOutputContext ioContext)
Creates a
FeatureCalculationContext for calculating features to later use this
exporter. |
Constructor and Description |
---|
MontageSharedState(Map<Path,BoundingBoxEnclosed> boxes,
Extent sizeCombined,
VoxelsResizer resizer,
ExecutionTimeRecorder executionTimeRecorder)
Create with a mapping from
Path s to boxes. |
Constructor and Description |
---|
ConvertNamedChannelsInputToStack(NamedChannelsInput input,
ExecutionTimeRecorder executionTimeRecorder)
Create with an input.
|
ConvertNamedChannelsInputToStack(NamedChannelsInput input,
int timeIndex,
Optional<String> channelName,
ExecutionTimeRecorder executionTimeRecorder)
Create with an input.
|
Modifier and Type | Method and Description |
---|---|
OpenedImageFile |
RotateImageToMatchEXIFOrientation.openFile(Path path,
CalculateOrientationChange orientationCorrection,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
BranchExtension.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
FlattenAsChannel.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
RejectIfConditionXYResolution.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
ImposeResolution.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
RotateImageToMatchEXIFOrientation.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
MultiFileReader.openFile(Path filePath,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
ReadVoxelExtentXml.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
Constructor and Description |
---|
OpenedMultiFile(StackReader stackReader,
ParsedFilePathBag fileBag,
ExecutionTimeRecorder executionTimeRecorder) |
Modifier and Type | Method and Description |
---|---|
OpenedImageFile |
OpenCVReader.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.