Package sc.fiji.snt.util

package sc.fiji.snt.util
Miscellaneous SNT utilities, including classes defining reconstruction nodes.
Author:
Tiago Ferreira
  • Class
    Description
    BoundingBox
    A BoundingBox contains information (including spatial calibration) of a tracing canvas bounding box, i.e., the minimum bounding cuboid containing all nodes (SNTPoints) of a reconstructed structure.
    CircleCursor3D<T>
    Iterate the pixels of an oriented circle in 3-space using Bresenham's algorithm, where the circle is constructed from the unit normal to the circle plane, the center point, and radius.
    ColorMaps
    Utilities for colormaps and IJ lookup tables
    CrossoverFinder
    Utility to detect crossover locations between paths: spatially close locations between paths that look like intersections in the image but are not topological joins in the traced graph.
    CrossoverFinder.Config
    Immutable configuration with builder-like setters.
    CrossoverFinder.CrossoverEvent
    One detected crossover event.
    DiskCursor3D<T>
    Iterate the pixels of an oriented solid disk in 3-space, where the disk is constructed from the unit normal to the circle plane, the center point, and radius.
    ImgUtils
    Static utilities for handling and manipulation of RandomAccessibleIntervals
    ImgUtils.SliceResult<T extends net.imglib2.type.numeric.RealType<T>>
    Result of a channel/time slice extraction from an ImgPlus.
    ImpUtils
    Static utilities for handling and manipulation of ImagePluss
    LinAlgUtils
    Static methods for linear algebra
    Logger
    The Logger class provides functionality for logging messages with different levels such as info, debug, and warn.
    LSystemsTree
    Lindenmayer systems utilities for rendering fractal trees using L-system rules for generating and visualizing self-similar branching structures.
    PathCursor<T>
    Iterate over the pixels along the defined nodes of a Path
    PointDeduplicator
    Greedy non-maximum suppression (NMS) for scored 3D points.
    PointInCanvas
    Defines a Point in a tracing canvas in pixel coordinates.
    PointInImage
    Defines a Point in an image, a node of a traced Path.
    ShollPoint
    Convenience flavor of PointInImage defining 2D/3D points for Sholl Analysis.
    SigmaUtils
    Utility class for computing default Gaussian blur sigma values based on image properties.
    SNTColor
    A simple class for handling Colors including the ability to map an AWT Color to a SWC type integer tag.
    SNTPoint
    Classes extend this interface implement a point in a 3D space, always using real world coordinates.
    SWCPoint
    Defines a node in an SWC reconstruction.
    TreeToRaster
    Rasterizes a Tree into a 3D image using frustum (truncated-cone) geometry with partial-volume supersampling.
    TreeUtils
    Static utilities for Trees.
    TreeUtils.EndpointClusterAnalysis
    Result of analyzing which endpoint cluster (starts vs ends) is tighter.
    TreeUtils.EndpointMatch
    Result of finding the closest endpoints between two paths.