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Re: How to combine Mathematica graphics and Python code?

• To: mathgroup at smc.vnet.net
• Subject: [mg113377] Re: How to combine Mathematica graphics and Python code?
• From: hrh1818 <hrhan at att.net>
• Date: Tue, 26 Oct 2010 05:33:30 -0400 (EDT)
• References: <ia3mu5$rp2$1@smc.vnet.net>

On Oct 25, 5:42 am, kj <no.em... at please.post> wrote:
> I have been given the task of developing a data visualization system
> for a large academic experimental biology lab.  In this lab they
> generate a lot of specialized high-throughput data, and they need
> a custom system for organizing, analyzing, and visualizing it.
> (Many such systems already exist, of course, but for a wide variety
> of reasons the lab's directors decided to go with a custom, home-grown
> alternative.)
>
> I have decided to develop the system primarily in Python, for a
> couple of reasons.[1]  The big downside of Python, however, is that
> it does not have, in my opinion, a sufficiently good support for
> scientific graphics.[2]
>
> In my experience Mathematica is the gold standard for scientific
> graphics, and wondered if there was some way in which I could
> combine Python code with Mathematica graphics.
>
> The absolute ideal system would be something that looked likei a
> (highly stripped down) Mathematica GUI, but receiving Python code
> instead of Mathematica code.  I.e. basically a cross between the
> standard Python interactive text-based interpreter and a Mathematica
> graphics-enabled GUI.
>
> A less attractive possibility (but still adequate) would be for
> the Python system to generate the necessary Mathematica code on
> the fly, and somehow get Mathematica to generate and display a
> figure for it.
>
> A third alternative would be to build a Python interpreter that
> could be run within Mathematica, but this is pushing beyond my
> level of expertise, both with Python and with Mathematica.
>
> At this stage I'm interested in finding out of similar attempts to
> use Mathematica's graphics capabilities in a non-Mathematica app,
> and perhaps learn from their experience.
>
> Technical issues aside, there are also thorny licensing issues.
> If anyone has any experience with that, I would love to read your
> comments.
>
> TIA!
>
> ~kj
>
> [1] The choice of Python is motivated by two reasons: 1) the lab
> already has a significant code base in Python that I can re-use
> for this project; and 2) I expect that in certain special cases
> not covered by the system's base functionality, its users (most of
> whom have no programming experience at all) may need to write very
> simple scripts, and I find Python is particularly easy to teach to
> people with no programming background.
>
> [2] The best Python for scientific graphics is matplotlib, which
> is loosely based on another system.  matplotlib is adequate for relativ=
ely
> simple graphics tasks, but it is not flexible enough for the type
> of visualization that I think will be needed.  (I think this
> inflexibility is the result of some pretty fundamental design flaws
> in matplotlib.)

If you do a Google search on "Python Mathematica" you will find a few
interesting hits.
PYML a Python Mathematica interface
http://library.wolfram.com/infocenter/MathSource/585/
Pythonika. Enabling Python scripting within Mathematica
http://library.wolfram.com/infocenter/MathSource/6622/
And you can use MathLink to create your own interface to Mathematica
http://reference.wolfram.com/mathematica/guide/MathLinkAPI.html

Howard