Package qupath.ext.biop.utils

Class PathUtils

  • public class PathUtils
extends java.lang.Object

    • Constructor Summary

      Constructors 
      Constructor Description
      PathUtils()  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static qupath.lib.objects.PathObject expand​(qupath.lib.objects.PathObject pathObject, double radiusPixels, boolean removeInterior, boolean constrainToParent)
      expand, taken from DilateAnnotationPlugin which returns an PathObject expanded or dilated by the given amount in pixels
      static double getAreaMicrons​(qupath.lib.objects.PathObject object)
      returns the area of the current PathObject in calibrated units.
      static qupath.lib.objects.PathObject getFullImageAnnotation()
      returns a rectangle with the whole dataset as an annotation.
      static java.util.List<qupath.lib.objects.PathDetectionObject> makePieChart​(java.lang.String name, java.util.Map<qupath.lib.objects.classes.PathClass,​java.lang.Double> elements, qupath.lib.objects.PathObject parent)
      Creates a series of detections as pie chart elements that are added to the provided parent object
      static qupath.lib.objects.PathObject merge​(java.util.List<qupath.lib.objects.PathObject> pathObjects)
      Merge all PathObjects into a single PathObject

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • PathUtils

        public PathUtils()

    • Method Detail

      • getFullImageAnnotation

        public static qupath.lib.objects.PathObject getFullImageAnnotation()
        returns a rectangle with the whole dataset as an annotation. It does not add it to the Hierarchy
        Returns:
        an Annotation Object with the whole image

      • getAreaMicrons

        public static double getAreaMicrons​(qupath.lib.objects.PathObject object)
        returns the area of the current PathObject in calibrated units.
        Parameters:
        object - the object to try and compute the area from
        Returns:
        the calibrated area in um2

      • expand

        public static qupath.lib.objects.PathObject expand​(qupath.lib.objects.PathObject pathObject,
                                                   double radiusPixels,
                                                   boolean removeInterior,
                                                   boolean constrainToParent)
        expand, taken from DilateAnnotationPlugin which returns an PathObject expanded or dilated by the given amount in pixels
        Parameters:
        pathObject - the PathObject to dilate or erode
        radiusPixels - the radius of erosion/dilation
        removeInterior - whether to create an annotation from the difference of the two or just a full new annotation (kind of like "make band"
        constrainToParent - limits the expansion to the parent shape. pathObject must be a child of something in the image.
        Returns:
        an Annotation or Detection object of the same class

      • merge

        public static qupath.lib.objects.PathObject merge​(java.util.List<qupath.lib.objects.PathObject> pathObjects)
        Merge all PathObjects into a single PathObject
        Parameters:
        pathObjects - the things to merge. The resulting PathObject will be of the type (Annotation/Detection), color and class of the first PathObject in this list.
        Returns:
        a single object that is the merge of all objects in the list.

      • makePieChart

        public static java.util.List<qupath.lib.objects.PathDetectionObject> makePieChart​(java.lang.String name,
                                                                                  java.util.Map<qupath.lib.objects.classes.PathClass,​java.lang.Double> elements,
                                                                                  qupath.lib.objects.PathObject parent)
        Creates a series of detections as pie chart elements that are added to the provided parent object
        Parameters:
        name - the name of the pie chart, for the measurements
        elements - a map of PathClass > Double that contains the class and value for each piece of the chart
        parent - to which ROI to attach this chart
        Returns:
        the individual quadrants that make up the chart if you need to modify them further