mrcImageShapeOrientation

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mrcImageShapeOrientation is the program that calculates that calculates Orientation Parameter for representation of orientation of particle images(3D also 2D). It performs the purpose of same as mrcImageShapePCA by using another method.

Algorithm

 It determines the shape of the 3D object by using Orientation Parameter.

Orientation parameter

 Orientation Parameter is used when indicating the order of the sequence of molecules in a liquid crystal. Here, it is used for indicating the deviation of the density.

pi = <3cos(anglei)^2 -1 >/2

and, i means axis of x, y, z, anglei means angle from the axis. The axis of image is determined as the vector whose orientation from small one to large one among 2 points whose pixel value is over the threshold (Orientation has no effect in some cases). When calcutaing average, it uses weight that is multiplied the length of vector to the density of 2 points (pixel value - threshold). Consequently, the orientation of vector that has 2 distant points whose density is large takes precedence.
 Thus, it can analysis independent to position of particle.

List of option

Main option

Option Essential/Optional Description Default
-i Essential Input: mrcImage NULL
-o Optional Output: ASCII stdout(Standard output by default)
-thres Optional threshold defining density 0.0
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help  

-m details

Value Description
0 Calculation of Orientation Parameter each direction(x, y, z)


Execution example