Package jhd.FloodFill

Class GDT3D

java.lang.Object
jhd.FloodFill.Offsets
jhd.FloodFill.GDT3D
public class GDT3D
extends Offsets
Methods for 2D and 3D Geodesic transform and tortousity
Author:
John H Dunsmuir

  • Nested Class Summary

    Nested classes/interfaces inherited from class jhd.FloodFill.Offsets

    Offsets.PointDesc

  • Constructor Summary

    Constructors
    Constructor Description
    GDT3D()
    Default Constructor

  • Method Summary

    Modifier and Type Method Description
    void gdt2D​(java.lang.Object data, int width, int height, float pixWidth, float pixHeight, java.lang.String mapChoice, java.lang.String seedChoice, int[] xPts, int[] yPts)
    2D Geodesic distance mapper
    void gdt3D​(java.lang.Object[] data, int width, int height, int depth, float pixWidth, float pixHeight, float pixDepth, java.lang.String mapChoice, java.lang.String seedChoice, int[] xPts, int[] yPts, int[] zPts)
    3D Geodesic distance by distance propagation
    java.util.ArrayList<Offsets.PointDesc> getGeoPath2D​(java.lang.Object data, int width, int height, Offsets.PointDesc probePt)
    Finds the shortest path through a 2D GDT image between a probePoint and the GDT origin.
    java.util.ArrayList<Offsets.PointDesc> getGeoPath3D​(java.lang.Object[] data, int width, int height, int depth, Offsets.PointDesc probePt)
    Finds the shortest path through a 2D GDT image between a probePoint and the GDT origin.
    java.util.ArrayList<Offsets.PointDesc>[] getGeoPaths2D​(java.lang.Object data, int width, int height, java.util.ArrayList<Offsets.PointDesc> probePts)
    Finds the shortest path through a 2D GDT image between each probePoint and the GDT origin.
    java.util.ArrayList<Offsets.PointDesc>[] getGeoPaths3D​(java.lang.Object[] data, int width, int height, int depth, java.util.ArrayList<Offsets.PointDesc> probePts)
    Finds the shortest path through a 2D GDT image between each probePoint and the GDT origin.
    java.lang.String[] getMapChoices()
    Used to build Dialogs
    java.lang.String[] getSeedChoices2D()
    Used to build Dialogs
    java.lang.String[] getSeedChoices3D()
    Used to build Dialogs
    void tort2D​(java.lang.Object data, int width, int height, float pixWidth, float pixHeight, java.lang.String floodChoice, java.lang.String seedChoice, int[] xPts, int[] yPts)
    2D Tortuosity mapper
    void tort3D​(java.lang.Object[] data, int width, int height, int depth, float pixWidth, float pixHeight, float pixDepth, java.lang.String floodChoice, java.lang.String seedChoice, int[] xPts, int[] yPts, int[] zPts)
    3D tortuosity map

    Methods inherited from class jhd.FloodFill.Offsets

    get1dOffsets2D, get1dOffsets2D, get1dOffsets3D, get1dOffsets3D, GetConnectivityChoices, GetConnectivityValue, getIndexOffsets2D, getIndexOffsets2D, getIndexOffsets3D, getIndexOffsets3D

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • GDT3D

      public GDT3D()
      Default Constructor

  • Method Details

    • getMapChoices

      public java.lang.String[] getMapChoices()
      Used to build Dialogs
      Returns:
      A map choices: "Map 0","Map !0"

    • getSeedChoices3D

      public java.lang.String[] getSeedChoices3D()
      Used to build Dialogs
      Returns:
      A list of choices for the start of the GDT: "LeftSlice","RightSlice","TopSlice","BottomSlice","FrontSlice","BackSlice","Point(s)"

    • gdt3D

      public void gdt3D​(java.lang.Object[] data, int width, int height, int depth, float pixWidth, float pixHeight, float pixDepth, java.lang.String mapChoice, java.lang.String seedChoice, int[] xPts, int[] yPts, int[] zPts)
      3D Geodesic distance by distance propagation
      Parameters:
      data - Object[] where data[0] instanceof float[], as returned by imageJ imp.getStack().getImageArray(). The image must be 32-bit. The gdt can be performed on the zero or non-zero image pixels.
      width - The image width in pixels
      height - The image height in pixels
      depth - The image depth in pixels
      pixWidth - The pixel width in user units
      pixHeight - The pixel height in user units
      pixDepth - The pixel depth in user units
      mapChoice - A string selecting the region to map; "Map 0" or "Map !0"
      seedChoice - Choices are "LeftEdge","RightEdge","TopEdge","BottomEdge","Point(s)"
      xPts - A zero based array of seedPoint column indices, pass null if not using Point(s) choice
      yPts - A zero based array of seedPoint row indices, pass null if not using Point(s) choice
      zPts - A zero based array of seedPoint slice indices, pass null if not using Point(s) choice

    • tort3D

      public void tort3D​(java.lang.Object[] data, int width, int height, int depth, float pixWidth, float pixHeight, float pixDepth, java.lang.String floodChoice, java.lang.String seedChoice, int[] xPts, int[] yPts, int[] zPts)
      3D tortuosity map
      Parameters:
      data - Object[] where data[0] instanceof float[], as returned by imageJ imp.getStack().getImageArray(). The image must be 32-bit. The gdt can be performed on the zero or non-zero image pixels.
      width - The image width in pixels
      height - The height width in pixels
      depth - The depth or number of slices in the 3D image
      pixWidth - The pixel width in user units
      pixHeight - The pixel height in user units
      pixDepth - The pixel depth in user units
      floodChoice - Choices are "Map 0" and "Map !0"
      seedChoice - Choices are "FrontSlice","BackSlice","LeftSlice","RightSlice","TopSlice","BottomSlice","Point(s)"
      xPts - An array of seedPoint column indices, pass null if not using Point(s) choice
      yPts - An array of seedPoint row indices
      zPts - An array of seedPoint slice indices

    • getGeoPaths3D

      public java.util.ArrayList<Offsets.PointDesc>[] getGeoPaths3D​(java.lang.Object[] data, int width, int height, int depth, java.util.ArrayList<Offsets.PointDesc> probePts)
      Finds the shortest path through a 2D GDT image between each probePoint and the GDT origin.
      Parameters:
      data - Object[] where data[0] instanceof float[], as returned by imageJ imp.getStack().getImageArray(). The image must be 32-bit. The gdt can be performed on the zero or non-zero image pixels.
      width - The image width in pixels
      height - The image height in pixels
      depth - The image depth in pixels
      probePts - a list of the starting points for the path to the 0 GDT destination
      Returns:
      An Array of lists of the points along the shortest path between each probe point and the 0 GDT destination

    • getGeoPath3D

      public java.util.ArrayList<Offsets.PointDesc> getGeoPath3D​(java.lang.Object[] data, int width, int height, int depth, Offsets.PointDesc probePt)
      Finds the shortest path through a 2D GDT image between a probePoint and the GDT origin.
      Parameters:
      data - Object[] where data[0] instanceof float[], as returned by imageJ imp.getStack().getImageArray(). The image must be 32-bit. The gdt can be performed on the zero or non-zero image pixels.
      width - The image width in pixels
      height - The image height in pixels
      depth - The image depth in pixels
      probePt - an probe point, the starting point for the path to the 0 GDT destination
      Returns:
      A list of the points along the shortest path between the probe point and the 0 GDT destination

    • getSeedChoices2D

      public java.lang.String[] getSeedChoices2D()
      Used to build Dialogs
      Returns:
      A list of choices for the start of the GDT: "LeftEdge","RightEdge","TopEdge","BottomEdge","Point(s)"

    • gdt2D

      public void gdt2D​(java.lang.Object data, int width, int height, float pixWidth, float pixHeight, java.lang.String mapChoice, java.lang.String seedChoice, int[] xPts, int[] yPts)
      2D Geodesic distance mapper
      Parameters:
      data - Object instanceof float[], A row major 1D representation of floating point 32-bit 3D image
      width - The image width in pixels
      height - The height width in pixels
      pixWidth - The pixel width in user units
      pixHeight - The pixel height in user units
      mapChoice - A string selecting the region to map; "Map 0" or "Map !0"
      seedChoice - Choices are "LeftEdge","RightEdge","TopEdge","BottomEdge","Point(s)"
      xPts - An array of seedPoint column indices, pass null if not using Point(s) choice
      yPts - An array of seedPoint row indices, pass null if not using Point(s) choice

    • tort2D

      public void tort2D​(java.lang.Object data, int width, int height, float pixWidth, float pixHeight, java.lang.String floodChoice, java.lang.String seedChoice, int[] xPts, int[] yPts)
      2D Tortuosity mapper
      Parameters:
      data - Object instanceof float[], A row major 1D representation of floating point 32-bit 3D image
      width - The image width in pixels
      height - The image height in pixels
      pixWidth - The pixel width width in user units
      pixHeight - The pixel height height in user units
      floodChoice - Choices are "Map 0" and "Map !0"
      seedChoice - Choices are "LeftEdge","RightEdge","TopEdge","BottomEdge","Point(s)"
      xPts - An array of seedPoint column indices, pass null if not using Point(s) choice
      yPts - An array of seedPoint row indices

    • getGeoPaths2D

      public java.util.ArrayList<Offsets.PointDesc>[] getGeoPaths2D​(java.lang.Object data, int width, int height, java.util.ArrayList<Offsets.PointDesc> probePts)
      Finds the shortest path through a 2D GDT image between each probePoint and the GDT origin.
      Parameters:
      data - Object instance of float[], a row major 1D representation of a 2D image
      width - The image width in pixels
      height - The image height in pixels
      probePts - a list of the starting points for the path to the 0 GDT destination
      Returns:
      An Array of lists of the points along the shortest path between each probe point and the 0 GDT destination

    • getGeoPath2D

      public java.util.ArrayList<Offsets.PointDesc> getGeoPath2D​(java.lang.Object data, int width, int height, Offsets.PointDesc probePt)
      Finds the shortest path through a 2D GDT image between a probePoint and the GDT origin.
      Parameters:
      data - Object instance of float[], a row major 1D representation of a 2D image
      width - The image width in pixels
      height - The image height in pixels
      probePt - the starting point for the path to the 0 GDT destination
      Returns:
      A list of the points along the shortest path between each probe point and the 0 GDT destination