1. Folder For_Running_SimRoot has the InputFiles and the SimRoot executable file.  Run SimRoot models for all phenotypes based on the inputs for bean and maize in 
	a. Bean_Inputs.txt for bean phenotypes
	b. Maize_Inputs.txt for maize phenotypes

2. Extract data from vtu files.
	Save all vtu files and extract point cloud data from all vtu files by running the code vtutotxt.

3. To obtain 2D projections
   Run code For_2D_Projection_Images - For_2D_Projection_Images.py
   Save all vtu files and extract point cloud data from all vtu files by running the code vtutotxt.

4. Data for metrics of 3D images are given in
	a. Bean_3D_Data.txt
	b. Maize_3D_Data.txt

5. To obtain various metrics:

(5-1)  Total Root Length -sum(rootSegmentLength) of all segments in the output file obtained from running vtutotxt.

(5-2)  Total Root Area - sum(rootSegmentArea)  of all segments in the output file obtained from running vtutotxt.
 
(5-3)  Total Root Volume - sum(rootSegmentVolume)  of all segments in the output file obtained from running vtutotxt.

(5-4)  Maximum Number of Roots - count and sort number of roots along depth in the output file obtained from running vtutotxt 

(5-5)  Median Number of Roots - count and sort number of roots along depth in the output file obtained from running vtutotxt and obtain median number of roots.

(5-6)  Bushiness - ratio of maximum number of roots and median number of roots

(5-7) Volume Distribution - ratio of root volume in one-third depth of root system to volume in below onethird depth of root system. root volume obtained from sum(rootSegmentVolume) in output file from running vtutotxt

(5-8)  Maximum Depth - obtain maximum depth by finding the minimum of depth axis

(5-9) Maximum Width - find maximum width at different depths by using getMinCircle (shotGroups package) function in R and find the maximum width among all depths.

(5-10) Convexhull Volume - run qhull algorithm in R (convhulln function (geometry package)) on the x,y,z corodinates obtained from output of vtutotxt file.

(5-11) Convexhull Area - run qhull algorithm in R on the x,y,z corodinates obtained from output of vtutotxt file.

(5-12) Solidity - ratio of total root volume and convex hull volume

(5-13) Ellipsemajor axis - run Minimum_Volume_Enclosing_Ellipse.R on the x,y,z co-ordinates obtained from output of vtutotxt file.

(5-14) Ellipse minor axis - run Minimum_Volume_Enclosing_Ellipse.R on the x,y,z corodinates obtained from output of vtutotxt file.

(5-15)  Ellipse aspect ratio - ratio of ellipsemajor axis to ellipse minor axis

(5-14)  Fractal Dimension -run FD_Codes.R

(5-15)  Fractal Abundance -run FD_Codes.R