[Paraview] netcdf

[Moreland, Kenneth]

Rupert,

As Aashish said, it might be easier to diagnose the issue if you sent us a file. But if your file is not following the CF or COARDS convention, then the reader will simply interpret the arrays in the file as uniform grids with spacing of 1. This is not likely to conform with the coordinates you want.

The official documentation for the CF convention is maintained here: http://cfconventions.org/. In summary, you specify coordinates by using arrays of the same name as the dimension. So for example if you have a 3D array with dimensions named “Z”, “Y”, and “X”, then you also make a 1D variable named “X” on the “X” dimension that has the x coordinate for each grid point in the dimension. Likewise, you have a “Y” variable on the “Y” dimension for y coordinates and a “Z” variable on the “Z” dimension for the z coordinates.

Or, if you don’t want to mess with your file format, you can do as Sam suggested and transform the data once it is loaded into ParaView.

-Ken


From: ParaView <paraview-bounces at paraview.org> on behalf of Aashish Chaudhary <aashish.chaudhary at kitware.com>
Date: Monday, May 15, 2017 at 9:08 AM
To: Rupert Gladstone <rupertgladstone1972 at gmail.com>, "paraview at paraview.org" <paraview at paraview.org>
Subject: [EXTERNAL] Re: [Paraview] netcdf

Rupert,

Would it be possible for you to send us a sample file and what the list of VARS you expect to see in the paraview?

Thanks,

On Mon, May 15, 2017 at 3:37 AM Rupert Gladstone <rupertgladstone1972 at gmail.com<mailto:rupertgladstone1972 at gmail.com>> wrote:

Hi, I have a question about netcdf formats.  I am developing a coupled ice sheet - ocean model.  Currently both models run in the same cartesian coordinate system.  The ice model outputs unstructured .vtu files, which paraview reads just fine.  The ocean model outputs structured netcdf files.  If I naively select the "generic and CF conventions" option when reading the ocean netcdf file then the data display ok, but not to scale.  It seems like the structured fields have been read in just fine, but the coordinate variables have not.  I don't think the netcdf files are CF compliant.  I would like to be able to read in both .vtu files and netcdf files and display the data sets together on the same scale.

Do you know what I need to do to read in the netcdf coordinate vars correctly?  I am hoping that I can simply insert a post-processing step to implement some minor manipulation to the ocean model output files so that Paraview can read them in to scale.  Is it simply a case of renaming the coordinate variables in the netcdf file such that they have the same names as the corresponding dimensions?  Note that this is not in general possible as some of the coordinate variables are two-dimensional variables (in the horizontal plane), though for most of the simulations we plan in the near future I can enforce that the coord vars will have a one to one correspondence to the dimension vars (i.e. I can enforce that coord vars are 1D).

Is the ordering of dimensions important?
Is the ordering of coordinate vars important?
Is the naming of dimensions important?
Is the naming of coord vars important?
Can Paraview cope with 2D coord vars?  If so, how does Paraview know which coordinate var applies to which var?
Thanks very much for your help.
Regards,
Rupert Gladstone
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