SCIEN Software


(Difference between revisions)
Jump to: navigation, search
(Repository Browsing)
Line 79: Line 79:
The see the [ ImageVal Web site] for information about this too.
The see the [ ImageVal Web site] for information about this too.
== Repository Browsing ==
== Repository Browsing ==

Revision as of 07:34, 23 April 2016

We are part of Stanford's Center for Image Systems Engineering. The software we develop for this work is distributed through our github repositories. These are links to those repositories

We also maintain some additional github repositories that are described in specific portions of the documentation.

Here is a local page describing the basic GIT operations.


Scientific methods


We are storing critical data sets for ISETBIO and SCIEN and VISTASOFT on the Archiva server.

We interact with these databases using the RemoteDataToolbox.

Project on scientific transparency (POST)

Running Matlab Remotely

We use Microsoft Remote Desktop to login to servers and run remotely.

Virtual Box

Andy Lin has us running Ubuntu on Windows machines using VirtualBox. This is a free virtual machine system from Oracle.

Install Virtual Box on a Windows machine. Then, download a version of Ubuntu.

You can then create a virtual instance of Ubuntu that will run on the Windows machine. Some suggestions:

  1. Set up the Machine properties for more than 1 processor.
  2. Set an execution cap that is less than 100 percent so the Windows side of your machine can continue to run
  3. Use more RAM (e.g., 4 or 5 GB).
  4. Use a virtual disk of 15-20GB at least.

We will try to make the notes here a little better as more people go through the process. Though it may be that only Andy and Brian have Windows machines.

Writing Matlab Files

When you are writing Matlab scripts or functions, please follow some guidelines in order to allow others to be able to use and understand your code and its outputs. It is important that the code is written in a readable modular fashion so that other people in the lab (now and in the future) may benefit from and work with your code.

At the top of each of your files, please add a header describing what it does. The suggested format for a simple example function appears below:

 function ycbcr = myrgb2ycbcr(rgb)
 % Converts an image using the color conversion used in JPEG
 %     ycbcr=myrgb2ycbcr(rgb)
 % A few sentences about the function there ...
 % ...
 %   rgb:        Double array giving an RGB image with values between 0 and 255
 %               size(rgb)=m x n x 3
 %   ycbcr:      Double array giving a YCbCr image with values between 0 and 255
 %               size(ycbcr)=m x n x 3
 % See also:  Related functions
 % Examples:
 %    Examples go here
 % (c) Copyright notice

Additional comments or notes can be added after the description of the output(s).


The see the ImageVal Web site for information about this too.


Repository Browsing

As far as I know, everything is now on github or the RDT (Maven/Archiva) repository.

I leave these links here just in case we forgot something.

Personal tools