[Paraview] trouble reading in netCDF file
David E DeMarle
dave.demarle at kitware.com
Mon Apr 26 16:37:19 EDT 2010
Most likely yes, that is the reader's purpose.
David E DeMarle
Kitware, Inc.
R&D Engineer
28 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-371-3971 x109
On Mon, Apr 26, 2010 at 4:05 PM, Joel Culina <joel.culina at acadiau.ca> wrote:
> I have VisIt, for which there is a plugin that reads in the unstructured
> netcdf data of the model I am using (FVCOM). I notice that there is a
> VisItReaderPlugin plugin in paraview. Can this plugin be used to read into
> paraview FVCOM-generated data via VisIt; i.e. can I transfer my VisIt-loaded
> file over to paraview using this plugin?
>
> thanks,
> Joel
>
> -----Original Message-----
> From: Moreland, Kenneth [mailto:kmorel at sandia.gov]
> Sent: Tue 4/20/2010 12:41 PM
> To: Joel Culina; paraview at paraview.org
> Subject: Re: [Paraview] trouble reading in netCDF file
>
> This is odd. Your header states that it follows the CF convention, but your
> description of the data is clearly incompatible with the CF convention.
> Could you send me a sample data set?
>
> -Ken
>
>
> On 4/19/10 7:56 PM, "Joel Culina" <joel.culina at acadiau.ca> wrote:
>
> 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:kmorel at sandia.gov]
> Sent: Mon 4/19/2010 5:20 PM
> To: Joel Culina; paraview at 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.culina at 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:kmorel at sandia.gov]
> Sent: Wed 4/7/2010 11:09 AM
> To: Joel Culina; paraview at 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.culina at 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:kmorel at sandia.gov]
> Sent: Tue 4/6/2010 3:41 PM
> To: Joel Culina; paraview at 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.culina at 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: kmorel at sandia.gov
> ** *** ** phone: (505) 844-8919
> *** web: http://www.cs.unm.edu/~kmorel
>
>
>
>
>
>
>
> **** Kenneth Moreland
> *** Sandia National Laboratories
> ***********
> *** *** *** email: kmorel at sandia.gov
> ** *** ** phone: (505) 844-8919
> *** web: http://www.cs.unm.edu/~kmorel
>
>
>
>
>
>
>
> **** Kenneth Moreland
> *** Sandia National Laboratories
> ***********
> *** *** *** email: kmorel at sandia.gov
> ** *** ** phone: (505) 844-8919
> *** web: http://www.cs.unm.edu/~kmorel
>
>
>
>
>
>
>
> **** Kenneth Moreland
> *** Sandia National Laboratories
> ***********
> *** *** *** email: kmorel at sandia.gov
> ** *** ** phone: (505) 844-8919
> *** web: http://www.cs.unm.edu/~kmorel
>
>
>
>
>
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