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plugin:morphology:analysis_3d:start

Analysis_3D plugin package

Perform 3D operations based on multithreading (Labeling, parameters measure, granulometry, erosion and diatation, median filter).


Author and citation

This plugins have been developed at SIMAP-GPM2 by Pierre Lhuissier, Luc Salvo and Vincent Boulos.

When used for scientific communcations, please cite :

“Investigating performance variations of an optimized GPU-ported granulometry algorithm”, V. Boulos, L. Salvo, V. Fristot, P. Lhuissier, D. Houzet. 18th International European Conference on Parallel and Distributed Computing, Rhodes Island, Greece (2012).

Description

Dilero

3D dilation of erosion using octaedron or cubic structural element

Size 1 means a cube of 3x3x3 for a cubic structural element

Parameters :

  • Erosion / dilation
  • Structural element
  • Number of iteration

Granulometry

3D granulometry using octaedron or cubic structural element

Saves data in a text file with this format : diameter Number_of_voxel volumic_frequency time_to_process

Median

3D fast median filter : works only with cubic structural element

Size 1 means a cube of 3x3x3 for a cubic structural element

Labeling

Search connected components with specified connectivity

  • Initial volume must be 8 bit with only 0 or 255
  • You can eliminate objects with their volume
  • A new volume is generated in 16 bit with objects numbers starting at 1
  • The maximum number of objects is 65500

Parameters :

  • Color to label
  • Minimum volume to label
  • 3D connectivity (6 or 26)

Parameters

Calculate parameters after a labeling treatment.

Calculate several parameters and store them in a text file with space delimiters

Save:

      nb : color of object
      xg : coordinates of center of gravity
      yg : coordinates of center of gravity
      zg : coordinates of center of gravity
      volpix : volume in pixel
      volmarch : volume in marching cubes
      surfacemarch : surface with marching cubes
      surfacemarchnb : surface with marching cubes without taking borders into account
      sphericity :  6*volmarch*Math.sqrt(3.14159265/(surfacemarch^3)) (1 for a sphere, less otherwise)
      I1 : moment of inertia (I1>I2>I3)
      I2 : moment of inertia (I1>I2>I3)
      I3 : moment of inertia (I1>I2>I3)
      vI1x : x direction of I1 in global coordinates	
      vI1y : y direction of I1 in global coordinates
      vI1z : z direction of I1 in global coordinates 
      vI2x : x direction of I2 in global coordinates
      vI2y : y direction of I2 in global coordinates
      vI2z : z direction of I2 in global coordinates 
      vI3x : x direction of I3 in global coordinates
      vI3y : y direction of I3 in global coordinates
      vI3z : z direction of I3 in global coordinates
      a : size of the paralepiped with same inertia matrix
      b : size of the paralepiped with same inertia matrix
      c : size of the paralepiped with same inertia matrix
      Fab : a/b
      Fac : a/c
      Fbc : b/c
      xmin : bounding box in the global coordinates
      xmax : bounding box in the global coordinates
      ymin : bounding box in the global coordinates
      ymax : bounding box in the global coordinates
      zmin : bounding box in the global coordinates
      zmax : bounding box in the global coordinates
      dx : bounding box in the local coordinates from the center of gravity
      dy : bounding box in the local coordinates from the center of gravity
      dz : bounding box in the local coordinates from the center of gravity
      border : 1 if touching the border, 0 otherwise

Installation

Download and copy the jar in your plugins folder.

Download

analysis_3d.jar

Pierre Lhuissier 2012/03/12 17:14

plugin/morphology/analysis_3d/start.txt · Last modified: 2019/04/12 13:13 (external edit)