Well, typing ncdump -h file, I get (note last line):
// global attributes:
:title = "Scotia Fundy Maine (Tidal Power) case
" ;
:institution = "School for Marine Science and Technology" ;
:source = "FVCOM_2.6" ;
:history = "model started at: 25/02/2010 18:29" ;
:references = "http://fvcom.smast.umassd.edu,
http://codfish.smast.umassd.edu"; ;
:Conventions = "CF-1.0" ;
Which file(s) do I edit to create my own reader? The new model I will be
getting outputs netCDF-4 files. Can I import unstructured netCDF-4 files into
paraview with an HDF5 reader?
thanks!
Joel
-----Original Message-----
From: Moreland, Kenneth [mailto:kmo...@sandia.gov]
Sent: Mon 4/19/2010 5:20 PM
To: Joel Culina; paraview@paraview.org
Subject: Re: [Paraview] trouble reading in netCDF file
I don't really understand this description, but I can say with confidence that
the netCDF reader will not read this convention. The CF convention does not
support unstructured triangular grids (or any unstructured grids, for that
matter). The (general) netCDF reader knows how to read 1-, 2-, and 3-D arrays
as regular grids with some conventions on setting coordinates to the points in
the grid.
NetCDF is not a data format description. It is simply an I/O library that
specifies how to read/write arrays with some annotation. Thus, if you have
data in a netCDF file that has a structure more complicated than simple arrays,
you will have to create a reader that understands how to construct the data
format. From your description, it sounds like you will have to create your own
reader.
-Ken
On 4/16/10 4:05 PM, "Joel Culina" <joel.cul...@acadiau.ca> wrote:
Hi,
Thanks Ken.
I'm using 3.8 now, but am have some similar troubles. To recap: I'm using
unstructured triangular grid. The 'dimensions' variables include integer
identifiers for triangle nodes, but NOT lat,long and depth. Rather, these are
included among the 'variables' variables (e.g. lat = lat(node)).
Paraview is reading in the data correctly. But I need it to use the 'variable'
variables lat, long, and depth to serve as the coordinates of the grid. All
other 'variables' variables are of course functions of the 'dimensions'
variables only, but are to be plotted over the 3D space determined by lat, long
and depth.
Can this be done in Paraview?
thanks
Joel
-----Original Message-----
From: Moreland, Kenneth [mailto:kmo...@sandia.gov]
Sent: Wed 4/7/2010 11:09 AM
To: Joel Culina; paraview@paraview.org
Subject: Re: [Paraview] trouble reading in netCDF file
The netCDF reader in version understands the COARDS convention (a common subset
of CF). It sounds like the variable annotation you describe should be
supported. However, one major limitation of the netCDF reader is that it only
supports reading variables of the same dimensions because it puts them all on
the same grid. So if you have selected to load variables with different
dimensions, it will use the dimensions of the first variable and fail to load
the rest. That would explain the behavior you are getting since most netCDF
files I have run into seem to have variables with low dimension listed first.
(There is no particular reason for this. It just seems to be what
people/applications do.) If this is the case, you are probably also getting a
lot of warnings from the netCDF reader about it and the Information panel will
be missing many of your variables. Try turning off all variables in the Object
Inspector and turning on only one variable you are interested in.
If this is the problem, it should go away in version 3.8. Realizing this the
3.6 interface to the netCDF reader really sucks, I changed it to select
dimensions instead of variables. All variables conforming to the selected
dimensions are loaded. It makes using the netCDF reader much easier and
problems like the one I described go away. I also expanded the reader to
understand most of the CF convention.
Unfortunately, don't use the CVS for this just yet. I have recently discovered
that a new netCDF reader that was apparently built for a specific use case but
seems to screw up on most data was added to ParaView and it is overriding the
existing netCDF reader. We are trying to work on a resolution.
-Ken
On 4/6/10 6:02 PM, "Joel Culina" <joel.cul...@acadiau.ca> wrote:
Hi,
Thank you Ken for responding.
I suspect that your diagnosis is correct; the root of the problem, I believe,
is that I am reading in netCDF data that follows the CF convention. In
particular, the grid is an unstructured triangular 2D grid ('poly data' grid in
the venacular of paraview). The 'dimensions' variables include integer
identifiers for triangle nodes, but NOT lat, long, x, y, time etc. Rather,
these are included among the 'variables' variables (e.g. lat = lat(node)).
Is the problem indeed that the paraview netCDF reader cannot understand this
particular netCDF-CF file? Is there a way around this, without having to
change the way the data is outputted (from netCDF-CF to netCDF-COARDS
convention)? Note that I can read into paraview certain variables by filtering
out the 1-dimensional variables (lat, long etc.), but of course these variables
do not have the correct dependencies (they should be dependent on the variables
I filtered out - lat, long etc.)
thanks,
Joel
-----Original Message-----
From: Moreland, Kenneth [mailto:kmo...@sandia.gov]
Sent: Tue 4/6/2010 3:41 PM
To: Joel Culina; paraview@paraview.org
Subject: Re: [Paraview] trouble reading in netCDF file
It sounds like you are reading in an array with 0 or 1 dimensions (not
including time). Although the reader should happily create an image data of
that structure, the standard rendering views only understand image data of 2 or
3 dimensions. Hence you get the error.
If you want to see the data in a plot, try adding the "Plot Data" filter.
-Ken
On 4/6/10 11:36 AM, "Joel Culina" <joel.cul...@acadiau.ca> wrote:
Hi,
I am trying to read in a netCDF file using Paraview 3.6.2. It can 'see' the
netCDF file, but when I attempt to read in the file by pressing 'Apply', I get
the following error message:
ERROR: In
/home/kitware/ParaView3/Utilities/BuildScripts/ParaView-3.6/ParaView3/Servers/Filters/vtkTexturePainter.cxx,
line 280
vtkTexturePainter (0xb8a0000): Incorrect dimensionality.
I'm not sure which netCDF release created the netCDF file. However, I read in
a previous post that paraview 3.6.1 could handle netCDF 4, and since "all
netCDF files ever written can always be read by the latest netCDF release. That
is, we guarantee backward data compatibility" then 3.6.2 should be able to
handle my netCDF file (which wasn't created too recently).
I can read the netCDF file into MATLAB, so it isn't corrupt.
So what's the problem?
thanks
Joel
**** Kenneth Moreland
*** Sandia National Laboratories
***********
*** *** *** email: kmo...@sandia.gov
** *** ** phone: (505) 844-8919
*** web: http://www.cs.unm.edu/~kmorel
**** Kenneth Moreland
*** Sandia National Laboratories
***********
*** *** *** email: kmo...@sandia.gov
** *** ** phone: (505) 844-8919
*** web: http://www.cs.unm.edu/~kmorel
**** Kenneth Moreland
*** Sandia National Laboratories
***********
*** *** *** email: kmo...@sandia.gov
** *** ** phone: (505) 844-8919
*** web: http://www.cs.unm.edu/~kmorel
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