Package org.anchoranalysis.annotation.io.bean.comparer

Class MultipleComparer

Object
org.anchoranalysis.bean.AnchorBean<MultipleComparer>
org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
public class MultipleComparer
extends org.anchoranalysis.bean.AnchorBean<MultipleComparer>
Allows comparison of an annotation with multiple other entities.
Author:
Owen Feehan

  • Constructor Summary

    Constructors 
    Constructor Description
    MultipleComparer()  

  • Method Summary

    Modifier and Type Method Description
    List<org.anchoranalysis.core.identifier.name.NameValue<org.anchoranalysis.image.core.stack.Stack>> createComparisonStacks​(AnnotationWithMarks annotation, org.anchoranalysis.image.core.stack.DisplayStack background, Path annotationPath, org.anchoranalysis.bean.shared.color.scheme.ColorScheme colorScheme, Path modelDirectory, org.anchoranalysis.core.time.OperationContext context, boolean debugMode)
    Creates a Stack illustrating the comparison between annotation and each source in sources.
    org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator<org.anchoranalysis.image.feature.input.FeatureInputPairObjects> getFeatureEvaluator()
    Calculates the cost used when making assignments.
    double getMaxCost()
    The maximum cost (as calculated by featureEvaluator) to accept when creating an assignment between objects.
    List<org.anchoranalysis.bean.NamedBean<ComparableSource>> getSources()
    The other entities to compare with the annotation.
    boolean isFlatten()
    If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.
    void setFeatureEvaluator​(org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator<org.anchoranalysis.image.feature.input.FeatureInputPairObjects> featureEvaluator)
    Calculates the cost used when making assignments.
    void setFlatten​(boolean flatten)
    If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.
    void setMaxCost​(double maxCost)
    The maximum cost (as calculated by featureEvaluator) to accept when creating an assignment between objects.
    void setSources​(List<org.anchoranalysis.bean.NamedBean<ComparableSource>> sources)
    The other entities to compare with the annotation.

    Methods inherited from class org.anchoranalysis.bean.AnchorBean

    checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString

    Methods inherited from class java.lang.Object

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

  • Constructor Details

  • Method Details

    • createComparisonStacks

      public List<org.anchoranalysis.core.identifier.name.NameValue<org.anchoranalysis.image.core.stack.Stack>> createComparisonStacks​(AnnotationWithMarks annotation, org.anchoranalysis.image.core.stack.DisplayStack background, Path annotationPath, org.anchoranalysis.bean.shared.color.scheme.ColorScheme colorScheme, Path modelDirectory, org.anchoranalysis.core.time.OperationContext context, boolean debugMode) throws org.anchoranalysis.core.exception.CreateException
      Creates a Stack illustrating the comparison between annotation and each source in sources.
      Parameters:
      annotation - the annotation to compare.
      background - the background to use when comparing.
      annotationPath - the path on the file-system to annotation to use as a reference.
      colorScheme - the color-scheme to use for unpaired objects.
      modelDirectory - a directory in which models reside.
      context - context for reading a stack from the file-system.
      debugMode - whether in debug-mode or not.
      Returns:
      a list of stacks showing the comparisons, with with a corresponding name.
      Throws:
      org.anchoranalysis.core.exception.CreateException - if any one of the stacks cannot be created.

    • getFeatureEvaluator

      public org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator<org.anchoranalysis.image.feature.input.FeatureInputPairObjects> getFeatureEvaluator()
      Calculates the cost used when making assignments.

    • setFeatureEvaluator

      public void setFeatureEvaluator​(org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator<org.anchoranalysis.image.feature.input.FeatureInputPairObjects> featureEvaluator)
      Calculates the cost used when making assignments.

    • getMaxCost

      public double getMaxCost()
      The maximum cost (as calculated by featureEvaluator) to accept when creating an assignment between objects.

    • setMaxCost

      public void setMaxCost​(double maxCost)
      The maximum cost (as calculated by featureEvaluator) to accept when creating an assignment between objects.

    • getSources

      public List<org.anchoranalysis.bean.NamedBean<ComparableSource>> getSources()
      The other entities to compare with the annotation.

    • setSources

      public void setSources​(List<org.anchoranalysis.bean.NamedBean<ComparableSource>> sources)
      The other entities to compare with the annotation.

    • isFlatten

      public boolean isFlatten()
      If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.

    • setFlatten

      public void setFlatten​(boolean flatten)
      If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.