Class SmoothFeaturesPlugin<T>

java.lang.Object
qupath.lib.plugins.AbstractPlugin<T>
qupath.lib.plugins.AbstractInteractivePlugin<T>
qupath.lib.plugins.objects.SmoothFeaturesPlugin<T>
Type Parameters:
T -
All Implemented Interfaces:
qupath.lib.plugins.PathInteractivePlugin<T>, qupath.lib.plugins.PathPlugin<T>

public class SmoothFeaturesPlugin<T> extends qupath.lib.plugins.AbstractInteractivePlugin<T>
Plugin to supplement the measurements for detection objects with the weighted sum of measurements from nearby objects, using weights derived from a 2D Gaussian function.

This effectively adds in some contextual information.

  • Constructor Summary

    Constructors
    Constructor
    Description
    Default constructor.
  • Method Summary

    Modifier and Type
    Method
    Description
    protected void
    addRunnableTasks(qupath.lib.images.ImageData<T> imageData, qupath.lib.objects.PathObject parentObject, List<Runnable> tasks)
     
    qupath.lib.plugins.parameters.ParameterList
    getDefaultParameterList(qupath.lib.images.ImageData<T> imageData)
     
     
     
     
    protected Collection<qupath.lib.objects.PathObject>
    getParentObjects(qupath.lib.images.ImageData<T> imageData)
     
    Collection<Class<? extends qupath.lib.objects.PathObject>>
     
    static void
    smoothMeasurements(List<qupath.lib.objects.PathObject> pathObjects, List<String> measurements, double fwhmPixels, String fwhmString, boolean withinClass, boolean useLegacyNames)
    Using the centroids of the ROIs within PathObjects, 'smooth' measurements by summing up the corresponding measurements of nearby objects, weighted by centroid distance.

    Methods inherited from class qupath.lib.plugins.AbstractInteractivePlugin

    alwaysPromptForObjects, getLoggableParameters, getParameterList, parseArgument

    Methods inherited from class qupath.lib.plugins.AbstractPlugin

    addWorkflowStep, getTasks, postprocess, preprocess, rearrangeByStride, requestHierarchyUpdate, runPlugin

    Methods inherited from class java.lang.Object

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

    Methods inherited from interface qupath.lib.plugins.PathPlugin

    runPlugin
  • Constructor Details

    • SmoothFeaturesPlugin

      public SmoothFeaturesPlugin()
      Default constructor.
  • Method Details

    • getName

      public String getName()
    • getDescription

      public String getDescription()
    • getLastResultsDescription

      public String getLastResultsDescription()
    • getSupportedParentObjectClasses

      public Collection<Class<? extends qupath.lib.objects.PathObject>> getSupportedParentObjectClasses()
    • addRunnableTasks

      protected void addRunnableTasks(qupath.lib.images.ImageData<T> imageData, qupath.lib.objects.PathObject parentObject, List<Runnable> tasks)
      Specified by:
      addRunnableTasks in class qupath.lib.plugins.AbstractPlugin<T>
    • smoothMeasurements

      public static void smoothMeasurements(List<qupath.lib.objects.PathObject> pathObjects, List<String> measurements, double fwhmPixels, String fwhmString, boolean withinClass, boolean useLegacyNames)
      Using the centroids of the ROIs within PathObjects, 'smooth' measurements by summing up the corresponding measurements of nearby objects, weighted by centroid distance.
      Parameters:
      pathObjects -
      measurements -
      fwhmPixels -
      fwhmString -
      withinClass -
      useLegacyNames -
    • getDefaultParameterList

      public qupath.lib.plugins.parameters.ParameterList getDefaultParameterList(qupath.lib.images.ImageData<T> imageData)
      Specified by:
      getDefaultParameterList in interface qupath.lib.plugins.PathInteractivePlugin<T>
      Specified by:
      getDefaultParameterList in class qupath.lib.plugins.AbstractInteractivePlugin<T>
    • getParentObjects

      protected Collection<qupath.lib.objects.PathObject> getParentObjects(qupath.lib.images.ImageData<T> imageData)
      Specified by:
      getParentObjects in class qupath.lib.plugins.AbstractPlugin<T>