
                 Help on Analysis_3D
                 
Version 1.3 (14/04/2014)

This plugins have been developed at SIMAP-GPM2 - Grenoble University - CNRS - France by
    Pierre Lhuissier
    Luc Salvo
    Vincent Boulos

When used for scientific communications, 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).


For any information please ask
    pierre.lhuissier@simap.grenoble-inp.fr
    luc.salvo@simap.grenoble-inp.fr



+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 median filter : works only with cubic structural element and 8 bits volume
    Size 1 means a cube of 3x3x3 for a cubic structural element

+Median_fast : 

    3D fast median filter : works only with cubic structural element
    8 bits and 16 bits volumes can be processed
    Due to parallelization, the plugin is memory consuming. 
    We advice to use "Median" plugin in case of memory issue.
    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

+Parameters Filter :

    Filters objects depending on their parameters.
	
    Requires a labeled image and a parameter file.
    Selection can be keeped or excluded.
    Selected objects can be renumbered (change of color on the image) or not.
    A new parameter file and a new stack with the selected objects are generated.


+Interactive_Connected_Grow :
        
    Interactive connected threshold grower (based on im3d connected threshold grower).

    Requires a point selection as seed.


