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Scientific computing and data visualization.

 
 
Fie Pye
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      09-06-2006
Hallo

I would like to have a high class open source tools for scientific computing and powerful 2D and 3D data visualisation. Therefore I chose python, numpy and scipy as a base. Now I am in search for a visualisation tool. I tried matplotlib and py_opendx with OpenDx. OpenDx seems to me very good but the project py_opendx looks like closed. After py_opendx instalation and subsequent testing I got an error that needs discussion with author or an experienced user. Unfortunately a mail to author returned as undeliverable.

Does anybody now about suitable visualisation tool?

Does anybody have an experience with OpenDx and py_opendx instalation?

Thanks for your response.

fiepye



 
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Matteo
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      09-06-2006

Fie Pye wrote:
> Hallo
>
> I would like to have a high class open source tools for scientific computing and powerful 2D and 3D data visualisation. Therefore I chose python, numpy and scipy as a base. Now I am in search for a visualisation tool. I tried matplotlib and py_opendx with OpenDx. OpenDx seems to me very good but the project py_opendx looks like closed. After py_opendx instalation and subsequent testing I got an error that needs discussion with author or an experienced user. Unfortunately a mail to author returned as undeliverable.
>
> Does anybody now about suitable visualisation tool?
>
> Does anybody have an experience with OpenDx and py_opendx instalation?
>
> Thanks for your response.
>
> fiepye


As another poster pointed out below, VTK is a very strong vis tool. It
is actively supported and has bindings to several languages (C++,
Python, Java, and Tcl at last count). I have used the combination of
python and VTK together to produce many scientific visualizations,
including production quality animations (Usually, I use Python/VTK to
generate isosurfaces or the like, and import the resulting geometry
data into Maya or another high-quality renderer)

One hurdle to overcome is transferring array data from Numeric/Numpy
into VTK. I have a sort of ad-hoc method to do that (mainly for volume
data). If anyone knows of any elegant solution, or a module to ease the
pain, I'd like to hear about it.

If you are working with NetCDF files, you may wish to add
ScientificPython (distinct from SciPy) to your toolset. It has a very
nice NetCDF interface. Unfortunately, it is ancient, and you would have
to install Numeric Python (ancestor to NumPy). However, it is easy to
convert Numeric arrays into Numpy arrays:
>>> my_numpy_array=numpy.array(my_numeric_array)



-matt

 
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Fernando Perez
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      09-06-2006
Matteo wrote:

> One hurdle to overcome is transferring array data from Numeric/Numpy
> into VTK. I have a sort of ad-hoc method to do that (mainly for volume
> data). If anyone knows of any elegant solution, or a module to ease the
> pain, I'd like to hear about it.


https://svn.enthought.com/enthought/wiki/TVTK

Much, much, MUCH nicer interface to VTK than the plain bindings that come by
default. And built from the ground up to seamlessly couple numpy with VTK.

Cheers,

f

 
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Robert Kern
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      09-06-2006
Matteo wrote:
> If you are working with NetCDF files, you may wish to add
> ScientificPython (distinct from SciPy) to your toolset. It has a very
> nice NetCDF interface. Unfortunately, it is ancient, and you would have
> to install Numeric Python (ancestor to NumPy). However, it is easy to
> convert Numeric arrays into Numpy arrays:
>>>> my_numpy_array=numpy.array(my_numeric_array)


The NetCDF interface has been ported to numpy and currently resides in the scipy
sandbox.

http://svn.scipy.org/svn/scipy/trunk...andbox/netcdf/

--
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
that is made terrible by our own mad attempt to interpret it as though it had
an underlying truth."
-- Umberto Eco

 
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bernhard.voigt@gmail.com
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      09-07-2006
A commonly used data analysis framework is root (http://root.cern.ch).
It offers a object oriented C++ framework with all kind of things one
needs for plotting and data visualization. It comes along with PyRoot,
an interface making the root objects available to Python.
Take a look at the root manual for examples, it also contains a section
describing the use of PyRoot.

Cheers! Bernhard

 
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Paul F. Kunz
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      09-13-2006
"Fie Pye" <(E-Mail Removed)> writes:

> Hallo
>
> I would like to have a high class open source tools for scientific computing and powerful 2D and 3D data visualisation. Therefore I chose python, numpy and scipy as a base. Now I am in search for a visualisation tool. I tried matplotlib and py_opendx with OpenDx. OpenDx seems to me very good but the project py_opendx looks like closed. After py_opendx instalation and subsequent testing I got an error that needs discussion with author or an experienced user. Unfortunately a mail to author returned as undeliverable.
>
> Does anybody now about suitable visualisation tool?
>

Have you looked at HippoDraw?

http://www.slac.stanford.edu/grk/ek/hippodraw
 
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Claudio Grondi
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      09-13-2006
Paul F. Kunz wrote:
> "Fie Pye" <(E-Mail Removed)> writes:
>
>
>> Hallo
>>
>> I would like to have a high class open source tools for scientific computing and powerful 2D and 3D data visualisation. Therefore I chose python, numpy and scipy as a base. Now I am in search for a visualisation tool. I tried matplotlib and py_opendx with OpenDx. OpenDx seems to me very good but the project py_opendx looks like closed. After py_opendx instalation and subsequent testing I got an error that needs discussion with author or an experienced user. Unfortunately a mail to author returned as undeliverable.
>>
>> Does anybody now about suitable visualisation tool?
>>

>
> Have you looked at HippoDraw?
>
> http://www.slac.stanford.edu/grk/ek/hippodraw

http://www.slac.stanford.edu/grp/ek/hippodraw/

Claudio Grondi
 
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David J. Braden
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      09-14-2006
Fie Pye wrote:
> Hallo
>
> I would like to have a high class open source tools for scientific computing and powerful 2D and 3D data visualisation. Therefore I chose python, numpy and scipy as a base. Now I am in search for a visualisation tool. I tried matplotlib and py_opendx with OpenDx. OpenDx seems to me very good but the project py_opendx looks like closed. After py_opendx instalation and subsequent testing I got an error that needs discussion with author or an experienced user. Unfortunately a mail to author returned as undeliverable.
>
> Does anybody now about suitable visualisation tool?
>
> Does anybody have an experience with OpenDx and py_opendx instalation?
>
> Thanks for your response.
>
> fiepye
>
>
>


What sort of "scientific computing" and visualization do you have in
mind? I enjoy R for much of my work. See http://www.r-project.org/

Plz let us know what you have discovered, and what you have settled on.

Tchuss,
DaveB
 
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Carl Friedrich Bolz
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      10-06-2006
http://www.velocityreviews.com/forums/(E-Mail Removed) wrote:
> A commonly used data analysis framework is root (http://root.cern.ch).
> It offers a object oriented C++ framework with all kind of things one
> needs for plotting and data visualization. It comes along with PyRoot,
> an interface making the root objects available to Python.
> Take a look at the root manual for examples, it also contains a section
> describing the use of PyRoot.


I can definitively second that. ROOT is a bit hard to learn but very,
very powerful and PyRoot is really a pleasure to work with.

Cheers,

Carl Friedrich Bolz

 
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Fabian Braennstroem
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      10-07-2006
Hi,

* Carl Friedrich Bolz <(E-Mail Removed)> wrote:
> (E-Mail Removed) wrote:
>> A commonly used data analysis framework is root (http://root.cern.ch).
>> It offers a object oriented C++ framework with all kind of things one
>> needs for plotting and data visualization. It comes along with PyRoot,
>> an interface making the root objects available to Python.
>> Take a look at the root manual for examples, it also contains a section
>> describing the use of PyRoot.

>
> I can definitively second that. ROOT is a bit hard to learn but very,
> very powerful and PyRoot is really a pleasure to work with.


It sounds interesting. Right now, I use matplotlib for
2D plotting and vtk for 3D. Do you have any experience and
can give some recommendations?

Greetings!
Fabian

 
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