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README.md

PhysiCell POV-writer (Version 1.0.0)

Copyright (c) Paul Macklin 2019, on behalf of PhysiCell & PhysiCell-Tools
OSI License: BSD-3-Clause (see LICENSE.txt)

This is an adaptation of Paul Macklin's 3-D cancer immune visualizations.

This processes a series of PhysiCell digital snapshots to create POV files for 3-D raytracing.

Note that users will then need to run POV-Ray on the .pov files, and potentially annotate them (e.g., with ImageMagick) and stitch them together into a movie (e.g., via mencocder).

Please see http://mathcancer.org/blog/povwriter for a full tutorial.

Syntax

povwriter		: run povwriter with config file ./config/settings.xml

povwriter FILENAME.xml	: run povwriter with config file FILENAME.xml

povwriter x:y:z		: run povwriter on data in FOLDER with indices from x 
               		  to y in incremenets of z

               		 Example: ./povwriter 0:2:10 processes files: 
               		          ./FOLDER/FILEBASE00000000_physicell_cells.mat
               		          ./FOLDER/FILEBASE00000002_physicell_cells.mat
               		          ...
               		          ./FOLDER/FILEBASE00000010_physicell_cells.mat
               		 (See the config file to set FOLDER and FILEBASE)

povwriter x1,...,xn	: run povwriter on data in FOLDER with indices x1,...,xn 

               		 Example: ./povwriter 1,3,17 processes files: 
               		          ./FOLDER/FILEBASE00000001_physicell_cells.mat
               		          ./FOLDER/FILEBASE00000003_physicell_cells.mat
               		          ./FOLDER/FILEBASE00000017_physicell_cells.mat
               		 (Note that there are no spaces.)
               		 (See the config file to set FOLDER and FILEBASE)
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