Leginon

Jamie,

While we don't officially support Leginon on a Mac (yet), it should work on any system that can run Python. Craig in our group has installed Leginon on his Mac, so we know it is possible, although I don't know if he has used it to run a session with actual TEM data acquisition.

Some things require compiling from source, but a lot of the python packages, including Leginon, are just python code that you install using python distutils (python setup.py install) and don't require compilation. Python and wxPython have Mac installers, but you can also compile them from scratch.

I'll have Craig respond with the details of what he did.

Jim

So I tried various methods of getting Leginon running on my OS X (10.4.1) machine. An initial problems is that Apple has already included a version of Python (2.3.5) wrapped in their framework (shared library) format in OS X. Leginon will run with this version of Python, but I decided to go with the latest, greatest version of everything when I tried this, so your first decision will be deciding how to install the needed software (Python, wxPython, etc.) I first tried using the DarwingPorts (darwinports.com) and Fink (fink.sourceforge.net) projects to install all the required software. These are both nice since they take care of installing all the required dependencies, and either has their pros and cons. DarwinPorts is perhaps implemented more elegantly but Fink is probably the best choice overall since the packages in the development tree are often more recent and there is a GUI manager (Fink Commander) that makes installing and managing packages much easier. One thing to note when installing using these package managers is that they perform all their installations in their own directories (/opt for DarwinPorts and /sw for Fink) so if you feel like you've messed up and want to undo everything you can often just trash these directories and start over (which is nice). The instructions for installing these utilities are on their respective web sites, and you should note that if you go this route to install wxPython and Python, you will be using Apple's X11 as your display server. I also tried (and preferred) manually installing all the stuff needed by Leginon myself, from source, but I should note I tried this after I got it to succesfully started using Fink. When installed this way you can use the OS X native Python and wxPython windowing display instead of X11. The nice thing about this is that it looks better (and may be more responsive) than using X11, the bad things is there definitely exists a couple of glitches in the interface likely due to differently size widgets and such. I didn't do a full run once I got it finally started up, but I did manage to cycle the presets and grabs images and move the stage about a little using Navigator. With this in mind if you're planning on seriously trying to perform a long run using Leginon on OS X it might be better to go with the X11 display. On last note is that when installing Python you're not going to be overwriting Apple's included version, therefore you'll have to distinguish between them when installing things like the Python modules. This is relatively easy since the pre-installed version of python will go by 'python' in the command line while the version you install will likely go by something like 'python24' or 'python2.4', etc. The python modules built by AMI will install just the same as they would on any computer using the whole 'python setup.py install' lingo, but make sure you call the correct python because the module will only be installed in that python's site-packages directory. I know these instructions aren't probably enough but I'll be looking back on here for a description of what route you'd like to go, (ie Fink, etc.) and can provide you with more help then.

Hi Craig. Thanks for the info. It looks like I'm going to have to wait a while for the apple installation, as we've got to get it installed soon, and the linux version will be easier, even if the computer specs aren't as good. I'll let you know when we get a chance to try it on the apple.

Cheers,

Jamie