Peter J. Lu
23 Feb 2012
http://www.peterlu.org
plu@fas.harvard.edu
Copyright 2013 Peter J. Lu

This document provides instructions on how to test the particle-location code, including the programs:

plu_centerfind2D
plu_link3dt
plu_struct3dt

**If you use this code, please cite in your publications:
Peter J. Lu, Peter A. Sims, Hidekazu Oki, James B. Macarthur, and David A. Weitz, 
"Target-locking acquisition with real-time confocal (TARC) microscopy,"
Optics Express Vol. 15, pp. 8702-8712 (2007).

Information on the details of the algorithm are given in Chapter 6 of: 
Peter J. Lu, "Gelation and Phase Separation of Attractive Colloids,"
Harvard University PhD Thesis (2008).

This directory contains the built executables for Ubuntu 64-bit linux, and several 3D stacks of particle data. 

1. Copy the executable from the /release directories of the Eclipse projects for all code. This should replace the existing executables, which you want to test.

2. Execute the script:

./phi41pct_130210.sh

You must have the Intel IPP and FreeImage libraries installed, as well as the program gnuplot, available as an Ubuntu package.

This will launch a combination of all of the programs, and will create an output file from the 3D radial distribution function g(r). View the file "g_of_r_comparison.eps". The original data, executed on code known to run properly, is the red line. The green plus-signs are generated by the code copied to that directory. The two sets should match exactly, manifest as all of the green plus signs sitting right on 
top of the red line. If this matches completely, the code has been compiled and built properly.

There is a reference to hoki_3dcheck. This program reads the 3D coordinates for particle centers and overlays circles over located particles, with the circles adjusted to be the proper size if ideal spheres were sliced in the same place as the experimental data. If this program does not run on your system, just comment the line out from the script and re-run it.

This is a preliminary draft of these instructions. If things are unclear or do not function as described, please contact me so we can resolve the issues.