Package org.anchoranalysis.plugin.image.task.feature

Class FeatureExporter<S>

Object
org.anchoranalysis.plugin.image.task.feature.FeatureExporter<S>
Type Parameters:
S - a source-of-rows that is duplicated for each new thread (to prevent any concurrency issues)
public class FeatureExporter<S>
extends Object
Shared-state for an ExportFeatures task.
Author:
Owen Feehan

  • Field Summary

    Fields 
    Modifier and Type Field Description
    static String OUTPUT_THUMBNAILS
    The output-name for writing thumbnails.

  • Constructor Summary

    Constructors 
    Constructor Description
    FeatureExporter​(org.anchoranalysis.feature.io.results.FeatureOutputMetadata outputMetadata, Supplier<S> featureSource, Optional<org.anchoranalysis.io.input.grouper.InputGrouper> grouper, FeatureExporterContext context)
    Creates the shared state.

  • Method Summary

    Modifier and Type Method Description
    void closeAndWriteOutputs​(Optional<org.anchoranalysis.feature.store.NamedFeatureStore<org.anchoranalysis.feature.input.FeatureInputResults>> featuresAggregate, boolean includeGroups, Function<org.anchoranalysis.io.output.outputter.InputOutputContext,​org.anchoranalysis.feature.io.csv.results.FeatureCSVWriterFactory> csvWriterCreator, org.anchoranalysis.io.output.outputter.InputOutputContext context)
    Writes all the results that have been collected as a CSV file, and closes open I/O handles and memory structures.
    static <T extends org.anchoranalysis.feature.input.FeatureInput>
    FeatureExporter<org.anchoranalysis.feature.bean.list.FeatureList<T>>    		 create​(List<org.anchoranalysis.bean.NamedBean<org.anchoranalysis.feature.bean.list.FeatureListProvider<T>>> features, org.anchoranalysis.feature.io.csv.metadata.LabelHeaders metadataHeaders, org.anchoranalysis.feature.io.results.FeatureOutputNames outputNames, Optional<org.anchoranalysis.io.input.grouper.InputGrouper> grouper, FeatureExporterContext context)
    Alternative static constructor that creates a shared-state from a list of named FeatureListProviders.
    static <T extends org.anchoranalysis.feature.input.FeatureInput>
    FeatureExporter<org.anchoranalysis.image.feature.calculator.FeatureTableCalculator<T>>    		 create​(org.anchoranalysis.feature.io.results.FeatureOutputNames outputNames, org.anchoranalysis.image.feature.calculator.FeatureTableCalculator<T> features, org.anchoranalysis.feature.io.csv.metadata.LabelHeaders identifierHeaders, Optional<org.anchoranalysis.io.input.grouper.InputGrouper> grouper, FeatureExporterContext context)
    Alternative static constructor that creates a shared-state from a NamedFeatureStore.
    static <T extends org.anchoranalysis.feature.input.FeatureInput>
    FeatureExporter<org.anchoranalysis.feature.bean.list.FeatureList<T>>    		 create​(org.anchoranalysis.feature.store.NamedFeatureStore<T> featureStore, org.anchoranalysis.feature.io.csv.metadata.LabelHeaders metadataHeaders, org.anchoranalysis.feature.io.results.FeatureOutputNames outputNames, Optional<org.anchoranalysis.io.input.grouper.InputGrouper> grouper, FeatureExporterContext context)
    Alternative static constructor that creates a shared-state from a NamedFeatureStore.
    FeatureCalculationContext<S> createCalculationContext​(Optional<String> groupName, org.anchoranalysis.core.time.ExecutionTimeRecorder executionTimeRecorder, org.anchoranalysis.io.output.outputter.InputOutputContext ioContext)
    Creates a FeatureCalculationContext for calculating features to later use this exporter.
    org.anchoranalysis.feature.name.FeatureNameList getFeatureNames()
    The names of the features to be exported.
    Optional<org.anchoranalysis.io.input.grouper.InputGrouper> getGrouper()
    When defined, assigns each input to a group.
    FeatureResultsAndThumbnails getResults()
    Saved store feature calculation results, and writes associated thumbnails.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

  • Constructor Details

    • FeatureExporter

      public FeatureExporter​(org.anchoranalysis.feature.io.results.FeatureOutputMetadata outputMetadata, Supplier<S> featureSource, Optional<org.anchoranalysis.io.input.grouper.InputGrouper> grouper, FeatureExporterContext context) throws org.anchoranalysis.io.output.error.OutputWriteFailedException
      Creates the shared state.
      Parameters:
      outputMetadata - headers and output-name for the feature CSV file that is written.
      featureSource - source of rows in the feature-table (called independently for each thread).
      grouper - when defined, assigns each input to a group.
      context - context for exporting features.
      Throws:
      org.anchoranalysis.io.output.error.OutputWriteFailedException - if there's an error during output writing

  • Method Details

    • create

      public static <T extends org.anchoranalysis.feature.input.FeatureInput> FeatureExporter<org.anchoranalysis.feature.bean.list.FeatureList<T>> create​(List<org.anchoranalysis.bean.NamedBean<org.anchoranalysis.feature.bean.list.FeatureListProvider<T>>> features, org.anchoranalysis.feature.io.csv.metadata.LabelHeaders metadataHeaders, org.anchoranalysis.feature.io.results.FeatureOutputNames outputNames, Optional<org.anchoranalysis.io.input.grouper.InputGrouper> grouper, FeatureExporterContext context) throws org.anchoranalysis.core.exception.CreateException
      Alternative static constructor that creates a shared-state from a list of named FeatureListProviders.
      Type Parameters:
      T - feature input-type in store
      Parameters:
      features - a list of beans to create the features.
      metadataHeaders - headers to describe any metadata.
      outputNames - customizable output names used by LabelledResultsCollector.
      grouper - when defined, assigns each input to a group.
      context - context.
      Returns:
      a newly created FeatureExporter.
      Throws:
      org.anchoranalysis.core.exception.CreateException - if it cannot be successfully created.

    • create

      public static <T extends org.anchoranalysis.feature.input.FeatureInput> FeatureExporter<org.anchoranalysis.feature.bean.list.FeatureList<T>> create​(org.anchoranalysis.feature.store.NamedFeatureStore<T> featureStore, org.anchoranalysis.feature.io.csv.metadata.LabelHeaders metadataHeaders, org.anchoranalysis.feature.io.results.FeatureOutputNames outputNames, Optional<org.anchoranalysis.io.input.grouper.InputGrouper> grouper, FeatureExporterContext context) throws org.anchoranalysis.core.exception.CreateException
      Alternative static constructor that creates a shared-state from a NamedFeatureStore.
      Type Parameters:
      T - feature input-type in store
      Parameters:
      featureStore - a list of beans to create the features.
      metadataHeaders - headers to describe any metadata.
      outputNames - customizable output names used by LabelledResultsCollector.
      grouper - when defined, assigns each input to a group.
      context - context.
      Returns:
      a newly created FeatureExporter.
      Throws:
      org.anchoranalysis.core.exception.CreateException - if it cannot be successfully created.

    • create

      public static <T extends org.anchoranalysis.feature.input.FeatureInput> FeatureExporter<org.anchoranalysis.image.feature.calculator.FeatureTableCalculator<T>> create​(org.anchoranalysis.feature.io.results.FeatureOutputNames outputNames, org.anchoranalysis.image.feature.calculator.FeatureTableCalculator<T> features, org.anchoranalysis.feature.io.csv.metadata.LabelHeaders identifierHeaders, Optional<org.anchoranalysis.io.input.grouper.InputGrouper> grouper, FeatureExporterContext context) throws org.anchoranalysis.core.exception.CreateException
      Alternative static constructor that creates a shared-state from a NamedFeatureStore.
      Type Parameters:
      T - feature input-type in store
      Parameters:
      outputNames - the names of the feature outputs.
      features - a table calculator for features.
      identifierHeaders - headers to describe the identifier metadata before the feature values.
      grouper - when defined, assigns each input to a group.
      context - context.
      Returns:
      a newly created FeatureExporter.
      Throws:
      org.anchoranalysis.core.exception.CreateException - if it cannot be successfully created.

    • createCalculationContext

      public FeatureCalculationContext<S> createCalculationContext​(Optional<String> groupName, org.anchoranalysis.core.time.ExecutionTimeRecorder executionTimeRecorder, org.anchoranalysis.io.output.outputter.InputOutputContext ioContext)
      Creates a FeatureCalculationContext for calculating features to later use this exporter.
      Parameters:
      groupName - the group to associate with the feature-results when outputted.
      executionTimeRecorder - records execution-times.
      ioContext - IO-context.
      Returns:
      a newly created context.

    • closeAndWriteOutputs

      public void closeAndWriteOutputs​(Optional<org.anchoranalysis.feature.store.NamedFeatureStore<org.anchoranalysis.feature.input.FeatureInputResults>> featuresAggregate, boolean includeGroups, Function<org.anchoranalysis.io.output.outputter.InputOutputContext,​org.anchoranalysis.feature.io.csv.results.FeatureCSVWriterFactory> csvWriterCreator, org.anchoranalysis.io.output.outputter.InputOutputContext context) throws org.anchoranalysis.io.output.error.OutputWriteFailedException
      Writes all the results that have been collected as a CSV file, and closes open I/O handles and memory structures.
      Parameters:
      featuresAggregate - features that can be used for generating additional "aggregated" exports.
      includeGroups - iff true a group-column is included in the CSV file and the group exports occur, otherwise not.
      csvWriterCreator - creates a CSV writer for a particular IO-context.
      context - IO-context.
      Throws:
      org.anchoranalysis.io.output.error.OutputWriteFailedException - if any output cannot be written, or there is an error closing open I/O.

    • getFeatureNames

      public org.anchoranalysis.feature.name.FeatureNameList getFeatureNames()
      The names of the features to be exported.

    • getResults

      public FeatureResultsAndThumbnails getResults()
      Saved store feature calculation results, and writes associated thumbnails.

    • getGrouper

      public Optional<org.anchoranalysis.io.input.grouper.InputGrouper> getGrouper()
      When defined, assigns each input to a group.