Package sc.fiji.snt.analysis.detection

Class Detection

java.lang.Object
sc.fiji.snt.analysis.detection.Detection
Direct Known Subclasses:
PeripathDetector.Detection
public class Detection extends Object
One detected feature along or around a traced path (varicosity, spine, bouton, punctum, etc.).
Author:
Tiago Ferreira
See Also:

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    final double
    distanceFromSkeleton
    Distance from the path skeleton at the detection point (physical units)
    final double
    intensity
    Intensity at the detection site
    final int
    labelValue
    Label value from a segmentation/label image associated with this detection, or -1 if not applicable.
    final int
    nodeIndex
    Index of the nearest node on the associated path
    final Path
    path
    The path this detection is associated with
    final double
    x
    X-coordinate of the detection in real-world units
    final double
    y
    Y-coordinate of the detection in real-world units
    final double
    z
    Z-coordinate of the detection in real-world units

  • Constructor Summary

    Constructors
    Constructor
    Description
    Detection(double x, double y, double z, double intensity, Path path, int nodeIndex, double distanceFromSkeleton)
    Creates a new detection.
    Detection(double x, double y, double z, double intensity, Path path, int nodeIndex, double distanceFromSkeleton, int labelValue)
    Creates a new detection with an associated label value.

  • Method Summary

    Modifier and Type
    Method
    Description
    PointInImage
    toSNTPoint()
    Returns this detection as an SNTPoint.
    String
    toString()
     
    double[]
    xyzct()
    Returns the XYZCT coordinates for bookmark/ROI integration.

    Methods inherited from class java.lang.Object

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

  • Field Details

    • x

      public final double x
      X-coordinate of the detection in real-world units

    • y

      public final double y
      Y-coordinate of the detection in real-world units

    • z

      public final double z
      Z-coordinate of the detection in real-world units

    • intensity

      public final double intensity
      Intensity at the detection site

    • path

      public final Path path
      The path this detection is associated with

    • nodeIndex

      public final int nodeIndex
      Index of the nearest node on the associated path

    • distanceFromSkeleton

      public final double distanceFromSkeleton
      Distance from the path skeleton at the detection point (physical units)

    • labelValue

      public final int labelValue
      Label value from a segmentation/label image associated with this detection, or -1 if not applicable. Set by LabelProximityDetector to identify which label surface produced the contact.

  • Constructor Details

    • Detection

      public Detection(double x, double y, double z, double intensity, Path path, int nodeIndex, double distanceFromSkeleton)
      Creates a new detection.
      Parameters:
      x - X-coordinate in real-world units
      y - Y-coordinate in real-world units
      z - Z-coordinate in real-world units
      intensity - intensity at the detection site
      path - associated path
      nodeIndex - index of the nearest node on the path
      distanceFromSkeleton - distance from the skeleton (physical units)

    • Detection

      public Detection(double x, double y, double z, double intensity, Path path, int nodeIndex, double distanceFromSkeleton, int labelValue)
      Creates a new detection with an associated label value.
      Parameters:
      x - X-coordinate in real-world units
      y - Y-coordinate in real-world units
      z - Z-coordinate in real-world units
      intensity - intensity at the detection site
      path - associated path
      nodeIndex - index of the nearest node on the path
      distanceFromSkeleton - distance from the skeleton (physical units)
      labelValue - label-image value associated with this detection, or -1 if not applicable

  • Method Details

    • toSNTPoint

      public PointInImage toSNTPoint()
      Returns this detection as an SNTPoint.
      Returns:
      a new PointInImage at this detection's coordinates

    • xyzct

      public double[] xyzct()
      Returns the XYZCT coordinates for bookmark/ROI integration. X, Y, Z are in pixel (uncalibrated) coordinates; C and T are 1-based indices from the associated path.
      Returns:
      double[5]: {xPixel, yPixel, zPixel, channel, frame}

    • toString

      public String toString()
      Overrides:
      toString in class Object