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

Class ScaleImage<S>

Object
org.anchoranalysis.bean.AnchorBean<org.anchoranalysis.experiment.bean.task.Task<T,​S>>
org.anchoranalysis.experiment.bean.task.Task<org.anchoranalysis.image.io.stack.input.StackSequenceInput,​S>
org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage<S>
Type Parameters:
S - shared-state for task.
Direct Known Subclasses:
ScaleImageCommonSize, ScaleImageIndependently
public abstract class ScaleImage<S>
extends org.anchoranalysis.experiment.bean.task.Task<org.anchoranalysis.image.io.stack.input.StackSequenceInput,​S>
Base class for tasks whose primary aim is to scale (resize) an image.

An RGB image is treated as a single-stack, otherwise each channel is scaled and outputted separately.

Second-level output keys for scaled and/or scaledFlattened additionally determine which stacks get outputted or not.

Any z-dimension present is unaffected by the scaling in scaled.

The following outputs are produced:

Output NameDefault?Description
"scaled"yesA scaled copy of the input image.
"scaledFlattened"noA scaled copy of the maximum-intensity-projection of the input image.
inherited from Task
Author:
Owen Feehan

  • Field Summary

    Fields 
    Modifier and Type Field Description
    protected boolean binary
    Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling ensures only two binary-values are outputted.
    protected org.anchoranalysis.image.bean.spatial.ScaleCalculator scaleCalculator
    Calculates what scale-factor to apply on the image.

  • Constructor Summary

    Constructors 
    Constructor Description
    ScaleImage()  

  • Method Summary

    Modifier and Type Method Description
    void afterAllJobsAreExecuted​(S sharedState, org.anchoranalysis.io.output.outputter.InputOutputContext context)  
    org.anchoranalysis.io.output.enabled.OutputEnabledMutable defaultOutputs()  
    void doJobOnInput​(org.anchoranalysis.experiment.task.InputBound<org.anchoranalysis.image.io.stack.input.StackSequenceInput,​S> input)  
    org.anchoranalysis.image.bean.interpolator.Interpolator getInterpolator()
    The interpolator to use for scaling images.
    org.anchoranalysis.image.bean.spatial.ScaleCalculator getScaleCalculator()
    Calculates what scale-factor to apply on the image.
    boolean hasVeryQuickPerInputExecution()  
    org.anchoranalysis.experiment.task.InputTypesExpected inputTypesExpected()  
    boolean isBinary()
    Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling ensures only two binary-values are outputted.
    protected abstract org.anchoranalysis.image.core.stack.Stack scaleStack​(org.anchoranalysis.image.core.stack.Stack stack, Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion> suggestedSize, org.anchoranalysis.image.voxel.resizer.VoxelsResizer voxelsResizer, S sharedState)
    Produce a scaled version of a Stack, mapping each channel to a scaled version of itself.
    void setBinary​(boolean binary)
    Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling ensures only two binary-values are outputted.
    void setInterpolator​(org.anchoranalysis.image.bean.interpolator.Interpolator interpolator)
    The interpolator to use for scaling images.
    void setScaleCalculator​(org.anchoranalysis.image.bean.spatial.ScaleCalculator scaleCalculator)
    Calculates what scale-factor to apply on the image.

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

    beforeAnyJobIsExecuted, 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

  • Field Details

    • scaleCalculator

      protected org.anchoranalysis.image.bean.spatial.ScaleCalculator scaleCalculator
      Calculates what scale-factor to apply on the image.

    • binary

      protected boolean binary
      Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling ensures only two binary-values are outputted.

  • Constructor Details

  • Method Details

    • inputTypesExpected

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

    • doJobOnInput

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

    • afterAllJobsAreExecuted

      public void afterAllJobsAreExecuted​(S 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.stack.input.StackSequenceInput,​S>
      Throws:
      org.anchoranalysis.experiment.ExperimentExecutionException

    • hasVeryQuickPerInputExecution

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

    • defaultOutputs

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

    • scaleStack

      protected abstract org.anchoranalysis.image.core.stack.Stack scaleStack​(org.anchoranalysis.image.core.stack.Stack stack, Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion> suggestedSize, org.anchoranalysis.image.voxel.resizer.VoxelsResizer voxelsResizer, S sharedState) throws org.anchoranalysis.core.exception.OperationFailedException
      Produce a scaled version of a Stack, mapping each channel to a scaled version of itself.
      Parameters:
      stack - the stack before scaling.
      suggestedSize - the suggested-size that has been passed into the task.
      voxelsResizer - how to resize the voxels in a channel.
      sharedState - the shared-state of the task.
      Returns:
      the scaled version of the stack.
      Throws:
      org.anchoranalysis.core.exception.OperationFailedException - if the scaling operation fails.

    • getScaleCalculator

      public org.anchoranalysis.image.bean.spatial.ScaleCalculator getScaleCalculator()
      Calculates what scale-factor to apply on the image.

    • setScaleCalculator

      public void setScaleCalculator​(org.anchoranalysis.image.bean.spatial.ScaleCalculator scaleCalculator)
      Calculates what scale-factor to apply on the image.

    • isBinary

      public boolean isBinary()
      Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling ensures only two binary-values are outputted.

    • setBinary

      public void setBinary​(boolean binary)
      Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling ensures only two binary-values are outputted.

    • getInterpolator

      public org.anchoranalysis.image.bean.interpolator.Interpolator getInterpolator()
      The interpolator to use for scaling images.

    • setInterpolator

      public void setInterpolator​(org.anchoranalysis.image.bean.interpolator.Interpolator interpolator)
      The interpolator to use for scaling images.