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====== Visualizing NetCDF Files with Python ======
===== Configuring YT for NetCDF Files =====
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June 1-2, 2014: Donald Willcox

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====== Visualizing NetCDF Files with Python ======
Once you've installed netcdf, you can access data in netcdf files from Python by installing numpy and ScientificPython. You should be able to get these by searching your package manager of choice or visiting their project sites:

  * [[http://www.numpy.org/]]
  * [[https://sourcesup.renater.fr/projects/scientific-py/]]

I go into more detail on building and installing ScientificPython in the following section for adding it to yt if you're interested in using yt to plot your data. Otherwise you can use python to access the netcdf files by referencing the NetCDF/python documentation here: 

  * [[http://gfesuite.noaa.gov/developer/netCDFPythonInterface.html]]

If you aren't using yt but do want to use python and need ScientificPython, follow the procedure in the next section except the ''source'' command for activating yt.

To load the necessary modules in your python script, use the following:

''import Scientific.IO.NetCDF''

''from numpy import *''

''from Scientific.IO.NetCDF import *''

===== Configuring YT for NetCDF Files =====
yt is great for visualizing large multidimensional datasets from astrophysics codes such as FLASH, and it can be obtained from [[yt-project.org]]. yt returned errors in interpreting the netcdf files output by VH-1 when I tried opening them using its ''load'' function, so here's how I added NetCDF support to my yt distribution.

First, make sure you've set the ''NETCDF_PREFIX'' environment variable as in the section on configuring NetCDF: 

[[june_1-2_2014_detailed_installation_steps_for_parallel_vh-1_and_required_libraries|Setting up Parallel VH-1 with NetCDF]] 

I installed the NetCDF libraries so my include and lib directories are as follows:

Include dir: ''/home/dwillcox/local/netcdf/include''

Lib dir: ''/home/dwillcox/local/netcdf/lib''

So I set the following environment variable to point to the netcdf directory:

''export NETCDF_PREFIX=/home/dwillcox/local/netcdf''

I have installed yt to the following location: ''/home/dwillcox/codes/local/yt-x86_64''

To use NetCDF, yt needs numpy and ScientificPython installed, and it already comes with numpy. So the only thing to do is download ScientificPython: 

[[https://sourcesup.renater.fr/frs/download.php/4411/ScientificPython-2.8.1.tar.gz]]

Extract the tarball and ''cd'' into its directory. Activate the yt package by executing:

''source /home/dwillcox/codes/local/yt-x86_64/bin/activate''

Now execute the following:

''python setup.py build''

''python setup.py install''

And ScientificPython should be added to your yt distribution!

For a sample script using NetCDF with yt, see plotnc.py in my github repo: 

[[https://github.com/dwillcox/VH1-solarwind/blob/master/scripts/plotnc.py]]