Scientific Software Projects

I am a Professor in Physics, and a Canada Research Chair in Biophotonics, member of the Centre d'Optique Photonique et Laser. I am based at the Centre de Recherche Universite Laval Robert Giffard where I focus on live animal imaging for neuroscience pathologies such as multiple sclerosis, chronic pain and nerve injuries.

Group web site: http://www.dcclab.ca/

Before that, I worked as a post-doctoral research fellow at the Wellman Centre for Photomedicine (Massachusetts General Hospital, Harvard Medical School) in Boston with Dr Charles Lin. I also trained as a post-docotoral fellow at the Ontario Cancer Institute in Toronto with I.A. Vitkin and Dr. B. C. Wilson. I originally graduated in laser and condensed matter physics from the University of Toronto. Over the years, I have written software to make my life easier in my research. This web site is here for mostly historical reasons, since a few publications refer to it, and other pages also link to it. It may eventually get folded back into www.dcclab.ca.

• Polarized light propagation in tissue with Monte Carlo
  
  Here you will find a discussion, an article and a computer implementation of the Monte Carlo algorithm for polarized light propagation in tissues.
  
  
• THz propagation article and computer code
  
  I recently wrote an article in the Journal of the Optical Society of America describing a simple plane wave decomposition technique for THz propagation that leads to analytical expressions for describing real-life, experimental THz pulses both in the near- and far-field, including the effects of dispersion, interfaces, diffraction, and that is valid for any radiation source (optical rectification or antennas). The publication might appear daunting at first, but the end result is a few equations that can be computed easily, without any finite difference methods (i.e. it is just a 1D integral and a Fourier transform). You can get the preprint and the computer code here. Feel free to contact me for questions at dccote@novajo.ca.
  
  
• ABCD
  
  A Macintosh program to propagate gaussian laser beams through standard optics based on the ray matrix formalism (also known as ABCD matrices). Register online with Kagi.
  
  
• BiblioTeX
  
  Database for managing BibTeX references. Register online with Kagi.
  
  
• Data Reader
  
  Tired of reading data off a graph with a ruler and a pen ? You have better things to do (so do I). This is why Data Reader was written: it allows you to obtain the data from a graph by clicking on the points and save it into an ASCII file for use in a fitting program, spreadsheet or plotting package. Register online with Kagi.
  
  
• Commented Fast Fourier Transform algorithm:
  
  How does the FFT algorithm actually work ? You have read it over and over, but you can't understand the FFT algorithm implementation. You looked at Numerical Recipes (available online by the way) but since it is a port of the Fortran-style routine, you get confused with the C indices (or vice-versa). You can download the source file fourier.cp as well as the header file fourier.h of a commented FFT routine in C++.
  
  

HOWTO tutorials for Mac OS X

• Firewall on Mac OS X 10
  
  This is very outdated (was done for 10.1.x). The general information is relevant, but now OS X manages the firewall very well by itself.
  
  You might be interested in setting up a firewall on OS X 10 if you have you computer connected to the Internet with a fast connection. You can take a look at how I did it for my own machine with a DSL access.
  
  
• CVS server on Mac OS X 10
  
  This is outdated, and anyway you should use Subversion instead of CVS.
  
  Setting up a CVS (Concurrent Versionning System) server for remote access is not complicated once you know how to do it. If you know you want a CVS server but just can't get yours to work properly, take a look at this page. It is brief, but a good start to get you going.
  
  
• Appleshare IP over PPPoE on Mac OS X 10
  
  Outdated
  
  Appletalk does not work directly on a PPPoE link (DSL). You can still do it on Mac OS X 10.1.x with some work.
  
  
• Pine on Mac OS X 10
  
  Outdated: you should use Macports to install everything, including Subversion.
  
  Sometimes, you might be away from your computer and you only have access to a terminal (not a Macintosh, let alone a Macintosh configured properly to check your email via POP3) but you still want to check your home email. You can set up pine on Mac OS X to remotely check your email via the command line.
  
  
• Using Dynamic IP with EasyDNS Mac OS X
  
  There are several clients for a variety of platforms for dynamic IP update with various systems. EasyDNS did not have one for Mac OS X, therefore I made one. I will eventually add a module to Julien Jalon's DNSUpdate to do the same but in the mean time, this simple script does the job.
  
  
• "Trash" perl script
  
  I wrote a simple trash perl script that can replace the 'rm' command to move stuff to the trash instead of deleting it. Instead of using rm file1, you use trash file1. Take a look here.

Unix Tutorials

• Jobs control
  
  Sometimes you start programs from the command lines and you need to stop, suspend or restart them. Here is how.
  
  

Foire aux questions

"Tout existe sur le web". Dans cet esprit, la page suivante est simplement un ramassis de questions et réponses quelconques qui, je l'espère, se retrouveront dans les engins de recherche lorsque les gens tenteront de touver une solution à leurs problèmes.

email: dccote@novajo.ca

Nice layout

I know nothing about HTML and nice layouts. I obtain the one for this page from http://www.bluerobot.com/web/layouts/