====== Analysis_3D plugin package ======

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

{{:plugin:morphology:analysis_3d:analysis_3d.jar|}}


 --- //[[:users:lhuissier|Pierre Lhuissier]] 2012/03/12 17:14//