Package inra.ijpb.watershed

Class WatershedTransform3D

java.lang.Object
inra.ijpb.watershed.WatershedTransform3D
Direct Known Subclasses:
MarkerControlledWatershedTransform3D
public class WatershedTransform3D
extends java.lang.Object
Class to apply the watershed algorithm in 3D to an image. It allows specifying a binary mask to restrict the regions of interest.
Author:
Ignacio Arganda-Carreras

  • Constructor Summary

    Constructors
    Constructor Description
    WatershedTransform3D​(ij.ImagePlus input, ij.ImagePlus mask)
    Construct a watershed transform
    WatershedTransform3D​(ij.ImagePlus input, ij.ImagePlus mask, int connectivity)
    Construct a watershed transform

  • Method Summary

    Modifier and Type Method Description
    ij.ImagePlus apply()
    Apply fast watersheds using flooding simulations, as described by Soille, Pierre, and Luc M.
    ij.ImagePlus apply​(double hMin, double hMax)
    Apply fast watersheds using flooding simulations, as described by Soille, Pierre, and Luc M.
    java.util.ArrayList<VoxelRecord> extractVoxelValues​(ij.ImageStack inputStack, double hMin, double hMax)
    Extract voxel values from input image such that they have value h, hMin <= h <= hMax.
    int getConnectivity()
    Get the voxel connectivity (6 or 26)
    void setConnectivity​(int conn)
    Set the voxel connectivity (6 or 26)
    void setVerbose​(boolean verbose)
    Set verbose flag

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • WatershedTransform3D

      public WatershedTransform3D​(ij.ImagePlus input, ij.ImagePlus mask)
      Construct a watershed transform
      Parameters:
      input - input image (usually a gradient image)
      mask - binary mask to restrict the region of interest (null to use whole input image)

    • WatershedTransform3D

      public WatershedTransform3D​(ij.ImagePlus input, ij.ImagePlus mask, int connectivity)
      Construct a watershed transform
      Parameters:
      input - grayscale image (usually a gradient image)
      mask - binary mask to restrict the region of interest (null to use whole input image)
      connectivity - voxel connectivity (6 or 26)

  • Method Details

    • getConnectivity

      public int getConnectivity()
      Get the voxel connectivity (6 or 26)
      Returns:
      voxel connectivity

    • setConnectivity

      public void setConnectivity​(int conn)
      Set the voxel connectivity (6 or 26)
      Parameters:
      conn - voxel connectivity

    • setVerbose

      public void setVerbose​(boolean verbose)
      Set verbose flag
      Parameters:
      verbose - new verbose flag

    • apply

      public ij.ImagePlus apply()
      Apply fast watersheds using flooding simulations, as described by Soille, Pierre, and Luc M. Vincent. "Determining watersheds in digital pictures via flooding simulations." Lausanne-DL tentative. International Society for Optics and Photonics, 1990.
      Returns:
      image of labeled catchment basins (with dams)

    • apply

      public ij.ImagePlus apply​(double hMin, double hMax)
      Apply fast watersheds using flooding simulations, as described by Soille, Pierre, and Luc M. Vincent. "Determining watersheds in digital pictures via flooding simulations." Lausanne-DL tentative. International Society for Optics and Photonics, 1990.
      Parameters:
      hMin - the minimum value for dynamic
      hMax - the maximum value for dynamic
      Returns:
      image of labeled catchment basins (with dams)

    • extractVoxelValues

      public java.util.ArrayList<VoxelRecord> extractVoxelValues​(ij.ImageStack inputStack, double hMin, double hMax)
      Extract voxel values from input image such that they have value h, hMin <= h <= hMax. A binary mask is used if it exists.
      Parameters:
      inputStack - input stack
      hMin - minimum grayscale height value
      hMax - maximum grayscale height value
      Returns:
      list of input voxel values