#### These Cython/Python scripts associated with paper (manuscript):
Ruben A. Tikidji-Hamburyan , Tarek A. El-Ghazawi , Jason W. Triplett

### Novel Models of Visual Topographic Map Alignment in the Superior Colliculus

To use theses scripts you need python libraries:

1. numpy
2. scipy
3. matplotlib and LaTeX for correct graphical interface
4. cython

Under Ubuntu or any other Debian based Linux, run
sudo apt-get install python-numpy python-scipy python-matplotlib texlive-full cython.

You can use yum or zymm under RadHad or SUSE based Linux distributions.

You may also use sudo pip install numpu scipy matloblib cython in any distribution.

To run simulations with small number of steps Nstep=2000 (requires around 4 hours on a desktop):
./runsimulation.sh

Same simulations but with a progress indicator(requires around 4 hours on a desktop):
INDICATOR=True ./runsimulation.sh

To run simulations with the same number of steps as in the paper (manuscript) Nstep=15000 (requires around 16-20 hours on a desktop):
NSTEP=15000 ./runsimulation.sh

To run simulations with the same number of steps as in the paper (manuscript) and with a progress indicator (requires around 16-20 hours on a desktop):
INDICATOR=True NSTEP=15000 ./runsimulation.sh

Do not simulate but plot graphs from existed database:
NSTEP=0 ./runsimulation.sh

Any command above should show three figures with 6 plots each. Each plot on a figure corresponds to particular model and mice mutant.

|  | Correlational model - Wiled Type | Correlational model - IslEphA/EphA | Correlational model - IslEphA/EphA / β2-/-
|  | Integrational model - Wiled Type | Integrational model - IslEphA/EphA | Integrational model - IslEphA/EphA / β2-/-

The accuracy of connectivity pattern depends on the number of steps. Figures below are examples for Nstep=15000.

Termination points | Density distribution | Density Samples

Files in this directory

EnergyChaser.pyx | Cython main code
EnergyModel.py | Python parameters parser and EnergyChaser wrapper
steup.py | Setup script for the Energy Model and Chaser
2D-View.py | - plots 2D terminal zones
| 1D-DensityView.py | - plots 1D density distribution of terminal zones along an NT or DV axis | runsimulation.sh | - helper script | 20160910104211-402-tot.db.gz | An example of simulation result for Nstep=15000