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:
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.
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected voidaddRunnableTasks(qupath.lib.images.ImageData<T> imageData, qupath.lib.objects.PathObject parentObject, List<Runnable> tasks) qupath.lib.plugins.parameters.ParameterListgetDefaultParameterList(qupath.lib.images.ImageData<T> imageData) getName()protected Collection<qupath.lib.objects.PathObject> getParentObjects(qupath.lib.images.ImageData<T> imageData) Collection<Class<? extends qupath.lib.objects.PathObject>> static voidsmoothMeasurements(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, parseArgumentMethods inherited from class qupath.lib.plugins.AbstractPlugin
addWorkflowStep, getTasks, postprocess, preprocess, rearrangeByStride, requestHierarchyUpdate, runPluginMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface qupath.lib.plugins.PathPlugin
runPlugin
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Constructor Details
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SmoothFeaturesPlugin
public SmoothFeaturesPlugin()Default constructor.
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Method Details
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getName
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getDescription
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getLastResultsDescription
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getSupportedParentObjectClasses
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addRunnableTasks
protected void addRunnableTasks(qupath.lib.images.ImageData<T> imageData, qupath.lib.objects.PathObject parentObject, List<Runnable> tasks) - Specified by:
addRunnableTasksin classqupath.lib.plugins.AbstractPlugin<T>
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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-
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getDefaultParameterList
public qupath.lib.plugins.parameters.ParameterList getDefaultParameterList(qupath.lib.images.ImageData<T> imageData) -
getParentObjects
protected Collection<qupath.lib.objects.PathObject> getParentObjects(qupath.lib.images.ImageData<T> imageData) - Specified by:
getParentObjectsin classqupath.lib.plugins.AbstractPlugin<T>
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