Package org.anchoranalysis.plugin.image.task.bean.slice

Class ExtractSlice

Object
org.anchoranalysis.bean.AnchorBean<org.anchoranalysis.experiment.bean.task.Task<T,​S>>
org.anchoranalysis.experiment.bean.task.Task<org.anchoranalysis.image.io.channel.input.NamedChannelsInput,​SharedStateSelectedSlice>
org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
public class ExtractSlice
extends org.anchoranalysis.experiment.bean.task.Task<org.anchoranalysis.image.io.channel.input.NamedChannelsInput,​SharedStateSelectedSlice>
Reduces a z-stack to a single-slice by taking the optima of a feature calculated for each slice.

Expects a second-level output "stack" to determine which slices are outputted or not.

Author:
Owen Feehan

  • Constructor Summary

    Constructors 
    Constructor Description
    ExtractSlice()  

  • Method Summary

    Modifier and Type Method Description
    void afterAllJobsAreExecuted​(SharedStateSelectedSlice sharedState, org.anchoranalysis.io.output.outputter.InputOutputContext context)  
    SharedStateSelectedSlice beforeAnyJobIsExecuted​(org.anchoranalysis.io.output.outputter.Outputter outputter, org.anchoranalysis.inference.concurrency.ConcurrencyPlan concurrencyPlan, List<org.anchoranalysis.image.io.channel.input.NamedChannelsInput> inputs, org.anchoranalysis.experiment.task.ParametersExperiment parameters)  
    org.anchoranalysis.io.output.enabled.OutputEnabledMutable defaultOutputs()  
    void doJobOnInput​(org.anchoranalysis.experiment.task.InputBound<org.anchoranalysis.image.io.channel.input.NamedChannelsInput,​SharedStateSelectedSlice> input)  
    org.anchoranalysis.feature.bean.list.FeatureListProvider<org.anchoranalysis.image.feature.input.FeatureInputStack> getScoreProvider()  
    org.anchoranalysis.image.bean.provider.stack.StackProvider getStackEnergy()  
    boolean hasVeryQuickPerInputExecution()  
    org.anchoranalysis.experiment.task.InputTypesExpected inputTypesExpected()  
    boolean isFindMaxima()
    If true, the maxima of the score is searched for.
    void setFindMaxima​(boolean findMaxima)
    If true, the maxima of the score is searched for.
    void setScoreProvider​(org.anchoranalysis.feature.bean.list.FeatureListProvider<org.anchoranalysis.image.feature.input.FeatureInputStack> scoreProvider)  
    void setStackEnergy​(org.anchoranalysis.image.bean.provider.stack.StackProvider stackEnergy)  

    Methods inherited from class org.anchoranalysis.experiment.bean.task.Task

    executeJob, isInputCompatibleWith

    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

    • beforeAnyJobIsExecuted

      public SharedStateSelectedSlice beforeAnyJobIsExecuted​(org.anchoranalysis.io.output.outputter.Outputter outputter, org.anchoranalysis.inference.concurrency.ConcurrencyPlan concurrencyPlan, List<org.anchoranalysis.image.io.channel.input.NamedChannelsInput> inputs, org.anchoranalysis.experiment.task.ParametersExperiment parameters) throws org.anchoranalysis.experiment.ExperimentExecutionException
      Specified by:
      beforeAnyJobIsExecuted in class org.anchoranalysis.experiment.bean.task.Task<org.anchoranalysis.image.io.channel.input.NamedChannelsInput,​SharedStateSelectedSlice>
      Throws:
      org.anchoranalysis.experiment.ExperimentExecutionException

    • inputTypesExpected

      public org.anchoranalysis.experiment.task.InputTypesExpected inputTypesExpected()
      Specified by:
      inputTypesExpected in class org.anchoranalysis.experiment.bean.task.Task<org.anchoranalysis.image.io.channel.input.NamedChannelsInput,​SharedStateSelectedSlice>

    • doJobOnInput

      public void doJobOnInput​(org.anchoranalysis.experiment.task.InputBound<org.anchoranalysis.image.io.channel.input.NamedChannelsInput,​SharedStateSelectedSlice> input) throws org.anchoranalysis.experiment.JobExecutionException
      Specified by:
      doJobOnInput in class org.anchoranalysis.experiment.bean.task.Task<org.anchoranalysis.image.io.channel.input.NamedChannelsInput,​SharedStateSelectedSlice>
      Throws:
      org.anchoranalysis.experiment.JobExecutionException

    • afterAllJobsAreExecuted

      public void afterAllJobsAreExecuted​(SharedStateSelectedSlice sharedState, org.anchoranalysis.io.output.outputter.InputOutputContext context) throws org.anchoranalysis.experiment.ExperimentExecutionException
      Specified by:
      afterAllJobsAreExecuted in class org.anchoranalysis.experiment.bean.task.Task<org.anchoranalysis.image.io.channel.input.NamedChannelsInput,​SharedStateSelectedSlice>
      Throws:
      org.anchoranalysis.experiment.ExperimentExecutionException

    • defaultOutputs

      public org.anchoranalysis.io.output.enabled.OutputEnabledMutable defaultOutputs()
      Overrides:
      defaultOutputs in class org.anchoranalysis.experiment.bean.task.Task<org.anchoranalysis.image.io.channel.input.NamedChannelsInput,​SharedStateSelectedSlice>

    • hasVeryQuickPerInputExecution

      public boolean hasVeryQuickPerInputExecution()
      Specified by:
      hasVeryQuickPerInputExecution in class org.anchoranalysis.experiment.bean.task.Task<org.anchoranalysis.image.io.channel.input.NamedChannelsInput,​SharedStateSelectedSlice>

    • getScoreProvider

      public org.anchoranalysis.feature.bean.list.FeatureListProvider<org.anchoranalysis.image.feature.input.FeatureInputStack> getScoreProvider()

    • setScoreProvider

      public void setScoreProvider​(org.anchoranalysis.feature.bean.list.FeatureListProvider<org.anchoranalysis.image.feature.input.FeatureInputStack> scoreProvider)

    • getStackEnergy

      public org.anchoranalysis.image.bean.provider.stack.StackProvider getStackEnergy()

    • setStackEnergy

      public void setStackEnergy​(org.anchoranalysis.image.bean.provider.stack.StackProvider stackEnergy)

    • isFindMaxima

      public boolean isFindMaxima()
      If true, the maxima of the score is searched for. If false, rather the minima.

    • setFindMaxima

      public void setFindMaxima​(boolean findMaxima)
      If true, the maxima of the score is searched for. If false, rather the minima.