[Paraview] netcdf

Tue May 16 09:39:00 EDT 2017

Rupert,

It has been multiple years since I really took a look at the CF convention, so I don’t remember the details of whether it supports varying coordinates across multiple dimensions or whether the ParaView reader supports that. If the ParaView reader is missing some corner of the CF convention, let us know and we can work on that.

In any case, you can displace a 2D or 3D image by a height value that is stored in a field by simply running the “Warp by Scalar” filter.

-Ken

From: Rupert Gladstone <rupertgladstone1972 at gmail.com>
Date: Tuesday, May 16, 2017 at 12:31 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov>
Cc: Aashish Chaudhary <aashish.chaudhary at kitware.com>, "paraview at paraview.org" <paraview at paraview.org>
Subject: [EXTERNAL] Re: [Paraview] netcdf

Hi all, thanks very much for your replies so far.  I must say I am finding the Paraview community very helpful.
Having considered my data further, I would be able to make a 1D coordinate variable for my x and y dimensions but not for my z dimension.  The ocean model uses a hybrid coordinate which can be transformed into depth, but the resulting depth coordinate will be spatially varying across my data set.  In other words my z coordinate variable will need to be a 3D variable.  From my understanding of COARDS and CF this is allowed.  But I think from your email that Paraview will not be able to associate this 3D z coordinate variable to another variable (e.g. ocean temperature) for the purposes of plotting.  At least, not using the Paraview CF interface.  Is that correct?
I don't currently have a handy netcdf file (I have a rather large one).  I could generate a smaller netcdf file to demonstrate the issue, but I am not sure it is needed here, as the problem is not that Paraview fails to read the file as expected, but rather than I am trying to clarify what I can reasonably expect from Paraview with its current functionality.
Do you have a suggestion for how to read in a (topologically) structured data set on a rectangular cartesian projection in which the the vertical coordinate variable varies across all three dimensions?  Should I ask Paraview to read it in as unstructured data?  I think I saw that Paraview offers some kind of interface for unstructured data in netcdf files.  Are the requirements of this documented somewhere?  Or do you still feel that I need to provide an example netcdf file for you to better understand the problem?
Thanks again for your help.
Regards,
Rupert

On Tue, May 16, 2017 at 6:36 AM, Moreland, Kenneth <kmorel at sandia.gov<mailto:kmorel at sandia.gov>> wrote:
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<mailto:paraview-bounces at paraview.org>> on behalf of Aashish Chaudhary <aashish.chaudhary at kitware.com<mailto:aashish.chaudhary at kitware.com>>
Date: Monday, May 15, 2017 at 9:08 AM
To: Rupert Gladstone <rupertgladstone1972 at gmail.com<mailto:rupertgladstone1972 at gmail.com>>, "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto: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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