Package qupath.lib.plugins.objects

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:
PathInteractivePlugin<T>, PathPlugin<T>
public class SmoothFeaturesPlugin<T> extends 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.

Author:
Pete Bankhead

  • Constructor Details

    • SmoothFeaturesPlugin

      public SmoothFeaturesPlugin()
      Default constructor.

  • Method Details

    • getName

      public String getName()
      Description copied from interface: PathPlugin
      Get the name of the plugin for display.

      This should be descriptive and, above all, short - as it may be used for menu item names & dialog box titles.

      Returns:

    • getDescription

      public String getDescription()
      Description copied from interface: PathPlugin
      Get a brief description of the plugin's purpose & operation.

      If no description is provided, this may return null.

      Returns:

    • getLastResultsDescription

      public String getLastResultsDescription()
      Description copied from interface: PathPlugin
      (Optional) short one-line description of the results, e.g. to say how many objects detected. GUIs may choose to display this on a label during interactive processing.
      Returns:

    • getSupportedParentObjectClasses

      public Collection<Class<? extends PathObject>> getSupportedParentObjectClasses()
      Description copied from interface: PathInteractivePlugin
      Get a collection of possible parent objects that the plugin could have. This may be used, for example, to specified that analysis may be applied to any/all TMA cores or annotations. If no parent objects are required, PathRootObject.class should be returned in the list.
      Returns:

    • addRunnableTasks

      protected void addRunnableTasks(ImageData<T> imageData, PathObject parentObject, List<Runnable> tasks)
      Description copied from class: AbstractPlugin
      For a specified parent object, generate a task to run. In practice, this method can be overridden to return anything/nothing if getTasks is overridden instead.
      Specified by:
      addRunnableTasks in class AbstractPlugin<T>
      Parameters:
      imageData -
      parentObject -
      tasks -

    • smoothMeasurements

      public static void smoothMeasurements(List<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 ParameterList getDefaultParameterList(ImageData<T> imageData)
      Description copied from class: AbstractInteractivePlugin
      This should return a default ParameterList containing any information that is needed to repeat the task exactly.
      Specified by:
      getDefaultParameterList in interface PathInteractivePlugin<T>
      Specified by:
      getDefaultParameterList in class AbstractInteractivePlugin<T>
      Parameters:
      imageData -
      Returns:

    • getParentObjects

      protected Collection<PathObject> getParentObjects(ImageData<T> imageData)
      Description copied from class: AbstractPlugin
      Get a collection of objects to process, based on the contents of the PluginRunner. This could (for example) return the selected object, the root object, all detection objects... depending upon what the plugin does. Each object this returns will be passed to addRunnableTasks to create a task to run. In practice, this method can be overridden to return anything/nothing if getTasks is overridden instead.
      Specified by:
      getParentObjects in class AbstractPlugin<T>
      Parameters:
      imageData -
      Returns: