Package | Description |
---|---|
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.results |
Writes feature-calculation results in different formats, also grouped results.
|
org.anchoranalysis.image.io |
Reading and writing of image-related data objects to and from the filesystem.
|
org.anchoranalysis.image.io.bean.object.feature |
Beans to specify the outputting of features into CSV from a
ObjectCollection . |
org.anchoranalysis.io.output.outputter |
Classes for outputting to particular directories.
|
org.anchoranalysis.mpp.segment.bean |
Beans for segmentation algorithms related to marked-point-processes.
|
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.annotation.bean.comparison.assigner |
Pairs annotations from two different sets, creating an assignment of some type.
|
org.anchoranalysis.plugin.image.task.bean |
A parent package for many different kinds of tasks.
|
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.grouped.histogram |
Task(s) to export histograms of intensity values.
|
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.feature |
Non-bean classes pertaining to
Feature s as used in tasks. |
org.anchoranalysis.plugin.image.task.feature.calculator |
Non-beans for calculating
Feature s. |
org.anchoranalysis.plugin.image.task.grouped |
Non-bean classes about grouping channels or other inputs.
|
org.anchoranalysis.plugin.image.task.labeller |
Non-bean classes about labelling images.
|
org.anchoranalysis.plugin.image.task.segment |
Non-bean classes for image-segmentation.
|
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.mpp.segment.bean.marks |
Beans to perform segmentation involving
Mark s and related
classes. |
org.anchoranalysis.test.image |
Testing utilities and fixtures with no greater downstream dependency than anchor-image-io
or anchor-io-bioformats or anchor-imagej.
|
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>) . |
Modifier and Type | Method and Description |
---|---|
InputOutputContext |
InitializationContext.getInputOutput()
The input-output context.
|
Constructor and Description |
---|
InitializationContext(InputOutputContext inputOutputContext)
Create with an
InputOutputContext . |
InitializationContext(InputOutputContext inputOutput,
Optional<ImageSizeSuggestion> suggestedSize) |
Modifier and Type | Class and Description |
---|---|
class |
InputOutputContextStateful
This exists as an implementation of
InputOutputContext that exposes a StatefulMessageLogger . |
Modifier and Type | Method and Description |
---|---|
void |
LabelledResultsCollector.flushAndClose(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate,
boolean includeGroups,
java.util.function.Function<InputOutputContext,FeatureCSVWriterFactory> csvWriterCreator,
FeatureOutputMetadata outputMetadata,
InputOutputContext context)
Writes any queued (but not yet written elements to the file-system), and closes open
file-handles.
|
Modifier and Type | Method and Description |
---|---|
void |
LabelledResultsCollector.flushAndClose(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate,
boolean includeGroups,
java.util.function.Function<InputOutputContext,FeatureCSVWriterFactory> csvWriterCreator,
FeatureOutputMetadata outputMetadata,
InputOutputContext context)
Writes any queued (but not yet written elements to the file-system), and closes open
file-handles.
|
Modifier and Type | Method and Description |
---|---|
static ImageInitialization |
ImageInitializationFactory.create(InputOutputContext context)
Create from an
InputOutputContext - without any suggested size. |
static ImageInitialization |
ImageInitializationFactory.create(InputOutputContext context,
Optional<ImageSizeSuggestion> suggestedSize)
Create from an
InputOutputContext - with a suggested size. |
Modifier and Type | Method and Description |
---|---|
void |
OutputFeatureTable.output(InputOutputContext context)
Outputs the feature-table.
|
Modifier and Type | Method and Description |
---|---|
InputOutputContext |
InputOutputContextSubdirectoryCache.get(Optional<String> subdirectoryName)
Gets (from the cache if it's already there) a context for a subdirectory of given-name
|
default InputOutputContext |
InputOutputContext.maybeSubdirectory(Optional<String> subdirectoryName,
boolean inheritOutputRulesAndRecording)
Optionally creates a new context like with
subdirectory(java.lang.String, boolean) but only if a directory-name
is defined |
default InputOutputContext |
InputOutputContext.subdirectory(String subdirectoryName,
boolean inheritOutputRulesAndRecording)
Creates a new context that writes instead to a subdirectory.
|
Constructor and Description |
---|
InputOutputContextSubdirectoryCache(InputOutputContext parentContext,
boolean inheritOutputRulesAndRecording) |
Modifier and Type | Method and Description |
---|---|
abstract MarkCollection |
SegmentIntoMarks.segment(SharedObjects sharedObjects,
Optional<Dictionary> dictionary,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
InputOutputContext |
OptimizationContext.getInputOutputContext() |
Constructor and Description |
---|
OptimizationContext(String experimentDescription,
EnergySchemeWithSharedFeatures energyScheme,
DualStack dualStack,
TriggerTerminationCondition triggerTerminationCondition,
InputOutputContext inputOutputContext,
RandomNumberGenerator randomNumberGenerator,
MarkWithIdentifierFactory markFactory) |
Modifier and Type | Method and Description |
---|---|
void |
AggregateAnnotations.afterAllJobsAreExecuted(AggregateSharedState sharedState,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
void |
CompareAnnotations.afterAllJobsAreExecuted(ComparisonSharedState<T> sharedState,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
abstract T |
AnnotationComparisonAssigner.createAssignment(ObjectsToCompare objectsToCompare,
Dimensions dimensions,
boolean useMIP,
InputOutputContext context) |
OverlappingObjects |
FeatureCostAssigner.createAssignment(ObjectsToCompare objectsToCompare,
Dimensions dimensions,
boolean useMIP,
InputOutputContext context) |
ObjectVoxelIntersection |
MaskIntersectionAssigner.createAssignment(ObjectsToCompare objectsToCompare,
Dimensions dimensions,
boolean useMIP,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
protected abstract U |
RasterTask.createSharedStateJob(InputOutputContext context)
Creates a shared-state for the duration of a particular input-job
|
abstract void |
RasterTask.doStack(InputBound<NamedChannelsInput,S> input,
U sharedStateJob,
int seriesIndex,
int numberSeries,
InputOutputContext context)
Processes one stack from a series.
|
abstract void |
RasterTask.endSeries(S sharedStateTask,
U sharedStateJob,
InputOutputContext context)
Ends processing of a series.
|
abstract void |
RasterTask.startSeries(S sharedStateTask,
U sharedStateJob,
InputOutputContext context)
Starts processing of a series.
|
Modifier and Type | Method and Description |
---|---|
void |
Montage.afterAllJobsAreExecuted(MontageSharedState sharedState,
InputOutputContext context) |
protected void |
AggregateChannelTask.processIndividual(String name,
Channel individual,
boolean partOfGroup,
CheckedBiConsumer<String,Channel,OperationFailedException> consumeIndividual,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
protected GroupMapByName<Channel,ChannelAggregator> |
AggregateChannelTask.createGroupMap(ConsistentChannelChecker channelChecker,
Optional<java.util.stream.Stream<String>> groupIdentifiers,
Optional<InputOutputContext> outputContext,
OperationContext operationContext) |
Modifier and Type | Method and Description |
---|---|
void |
ExportFeatures.afterAllJobsAreExecuted(FeatureExporter<S> sharedState,
InputOutputContext context) |
FeatureExporterContext |
ExportFeaturesStyle.deriveContext(InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
void |
ConvertImageFormat.afterAllJobsAreExecuted(NoSharedState sharedState,
InputOutputContext context) |
protected OutputSequenceIndexed<Stack,String> |
ConvertImageFormat.createSharedStateJob(InputOutputContext context)
Sets a new output-sequence for the series.
|
void |
ConvertImageFormat.doStack(InputBound<NamedChannelsInput,NoSharedState> input,
OutputSequenceIndexed<Stack,String> sharedStateJob,
int seriesIndex,
int numberSeries,
InputOutputContext context) |
void |
ConvertImageFormat.endSeries(NoSharedState sharedStateTask,
OutputSequenceIndexed<Stack,String> sharedStateJob,
InputOutputContext context) |
void |
ConvertImageFormat.startSeries(NoSharedState sharedStateTask,
OutputSequenceIndexed<Stack,String> sharedStateJob,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
void |
GroupedStackBase.afterAllJobsAreExecuted(GroupedSharedState<S,T> sharedState,
InputOutputContext context) |
protected abstract void |
GroupedStackBase.processIndividual(String name,
S individual,
boolean partOfGroup,
CheckedBiConsumer<String,S,OperationFailedException> consumeIndividual,
InputOutputContext context)
Processes each derived individual element from a
Channel , calling consumeIndividual one or more times. |
Modifier and Type | Method and Description |
---|---|
protected abstract GroupMapByName<S,T> |
GroupedStackBase.createGroupMap(ConsistentChannelChecker channelChecker,
Optional<java.util.stream.Stream<String>> groupIdentifiers,
Optional<InputOutputContext> outputContext,
OperationContext operationContext)
Creates a map for the storing an aggregate-data-object for each group.
|
Modifier and Type | Method and Description |
---|---|
protected void |
ExportImageHistograms.processIndividual(String name,
Histogram individual,
boolean partOfGroup,
CheckedBiConsumer<String,Histogram,OperationFailedException> consumeIndividual,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
protected GroupMapByName<Histogram,Histogram> |
ExportImageHistograms.createGroupMap(ConsistentChannelChecker channelChecker,
Optional<java.util.stream.Stream<String>> groupIdentifiers,
Optional<InputOutputContext> outputContext,
OperationContext operationContext) |
Modifier and Type | Method and Description |
---|---|
void |
ImageAssignLabel.afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T> sharedState,
InputOutputContext context) |
String |
ImageCSVLabeller.labelFor(ImageCSVLabellerInitialization sharedState,
ProvidesStackInput input,
InputOutputContext context) |
String |
ImageLabellerStringMap.labelFor(ImageLabellerStringMapInitialization<T> sharedState,
ProvidesStackInput input,
InputOutputContext context) |
String |
DescriptiveNameContainsImageLabeller.labelFor(NoSharedState sharedState,
ProvidesStackInput input,
InputOutputContext context) |
String |
BinaryClassifierImageLabeller.labelFor(NoSharedState sharedState,
ProvidesStackInput input,
InputOutputContext context) |
abstract String |
ImageLabeller.labelFor(T sharedState,
ProvidesStackInput input,
InputOutputContext context)
Determines a particular group-identifier for an input
|
Modifier and Type | Method and Description |
---|---|
void |
ScaleImage.afterAllJobsAreExecuted(S sharedState,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
void |
SegmentInstanceWithModel.afterAllJobsAreExecuted(SharedStateSegmentInstance<T> sharedState,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
void |
ExtractSlice.afterAllJobsAreExecuted(SharedStateSelectedSlice sharedState,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
InputOutputContext |
FeatureExporterContext.getContext()
Context for reading from or writing outputs to the file-system.
|
InputOutputContext |
FeatureCalculationContext.getContext() |
Modifier and Type | Method and Description |
---|---|
void |
FeatureExporter.closeAndWriteOutputs(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate,
boolean includeGroups,
java.util.function.Function<InputOutputContext,FeatureCSVWriterFactory> csvWriterCreator,
InputOutputContext context)
Writes all the results that have been collected as a CSV file, and closes open I/O handles
and memory structures.
|
FeatureCalculationContext<S> |
FeatureExporter.createCalculationContext(Optional<String> groupName,
ExecutionTimeRecorder executionTimeRecorder,
InputOutputContext ioContext)
Creates a
FeatureCalculationContext for calculating features to later use this
exporter. |
void |
FeatureResultsAndThumbnails.writeGroupedResults(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate,
boolean includeGroups,
java.util.function.Function<InputOutputContext,FeatureCSVWriterFactory> csvWriterCreator,
InputOutputContext context)
Writes all the results that have been collected as a CSV file.
|
Modifier and Type | Method and Description |
---|---|
void |
FeatureExporter.closeAndWriteOutputs(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate,
boolean includeGroups,
java.util.function.Function<InputOutputContext,FeatureCSVWriterFactory> csvWriterCreator,
InputOutputContext context)
Writes all the results that have been collected as a CSV file, and closes open I/O handles
and memory structures.
|
void |
FeatureResultsAndThumbnails.writeGroupedResults(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate,
boolean includeGroups,
java.util.function.Function<InputOutputContext,FeatureCSVWriterFactory> csvWriterCreator,
InputOutputContext context)
Writes all the results that have been collected as a CSV file.
|
Constructor and Description |
---|
FeatureCalculationContext(FeatureResultsAndThumbnails results,
S rowSource,
FeatureNameList featureNames,
Optional<String> groupGeneratorName,
ExecutionTimeRecorder executionTimeRecorder,
boolean suppressErrors,
InputOutputContext context)
Default constructor.
|
FeatureExporterContext(InputOutputContext context,
boolean removeNaNColumns,
boolean visuallyShortenDecimals,
boolean suppressErrors) |
Modifier and Type | Method and Description |
---|---|
static EnergyStack |
FeatureCalculatorRepeated.extractStack(ProvidesStackInput input,
StackProvider stackEnergy,
InputOutputContext context) |
Constructor and Description |
---|
FeatureCalculatorFromProvider(ProvidesStackInput stackInput,
Optional<StackProvider> stackEnergy,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
protected abstract void |
GroupMapByName.outputGroupIntoSubdirectory(Collection<Map.Entry<String,T>> namedAggregators,
java.util.function.Function<Boolean,InputOutputContext> createContext,
Optional<String> outputNameSingle)
Output a particular group into a subdirectory.
|
Constructor and Description |
---|
GroupMapByName(String nounT,
Optional<java.util.stream.Stream<String>> groupIdentifiers,
Optional<InputOutputContext> outputContext,
java.util.function.Supplier<T> createAggregator,
CheckedBiConsumer<S,T,OperationFailedException> addSingleToAggregator)
Creates a group-map.
|
Modifier and Type | Method and Description |
---|---|
String |
SharedStateFilteredImageOutput.labelFor(ProvidesStackInput input,
InputOutputContext context)
Determines a particular group-identifier for an input
|
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. |
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) |
Modifier and Type | Method and Description |
---|---|
void |
ConvertNamedChannels.afterAllJobsAreExecuted(SharedStateRememberConverted<U,S> sharedState,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
void |
ExportReportFeatures.afterAllJobsAreExecuted(CSVWriter writer,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
void |
ExportObjectsFromCSV.afterAllJobsAreExecuted(FromCSVSharedState sharedState,
InputOutputContext context) |
void |
ExportObjectsAsCroppedImages.afterAllJobsAreExecuted(NoSharedState sharedState,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
void |
SegmentMarksFromImage.afterAllJobsAreExecuted(ExperimentState sharedState,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
MarkCollection |
SegmentWithMarkedPointProcess.segment(SharedObjects sharedObjects,
Optional<Dictionary> dictionary,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
static InputOutputContext |
InputOutputContextFixture.withLogger(Logger logger) |
static InputOutputContext |
InputOutputContextFixture.withSuppressedLogger() |
static InputOutputContext |
InputOutputContextFixture.withSuppressedLogger(Path modelDir) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.