[Paraview] loading nc formatted data
Simon Su
newsgroup4ssu at gmail.com
Mon Mar 21 15:19:24 EDT 2011
Hi Ken,
Thank you for explaining.
The reader that is being used is vtkNetCDFCFReader. It is defined in
> ParaView/Servers/ServerManager/Resources/readers.xml, although it is not
> obvious.
>
>
Can you (or Andy) point me to documentation more documentation beside
http://www.vtk.org/Wiki/ParaView/Plugin_HowTo ? Andy also metioned
readers.xml file you mentioned. But after going through ParaView/Servers/
ServerManager/Resources/readers.xml, I am still fuzzy about where the file
vtkNetCDFCFReader.cxx ( if any - I would like to know how it is implemented
and maybe start by modifying it in my learning process). The plugin wiki
page on "Adding a Reader" section mentioned CMakeList.txt file
FIND_PACKAGE(ParaView REQUIRED)
INCLUDE(${PARAVIEW_USE_FILE})
ADD_PARAVIEW_PLUGIN(MyReader "1.0"
SERVER_MANAGER_XML MyPNGReader.xml
SERVER_MANAGER_SOURCES vtkMyPNGReader.cxx
GUI_RESOURCE_FILES MyReaderGUI.xml)
but the one on my source tree
ParaView-3.10.0/Examples/Plugins/Reader/CMakeList.txt looks like
ADD_PARAVIEW_PLUGIN(MyPNGReader "1.0"
SERVER_MANAGER_XML readers.xml
GUI_RESOURCE_FILES pqReader.xml
)
note no vtkMyPNGReader.cxx file mention and the file is also not in the
directory. I also did a search on source tree for vtkNetCDFCFReader.cxx
file but can't find it. I think I am missing a big piece of something since
I am not getting the point that I should be getting after looking at
readers.xml. In fact, I can't find any of the netcdf file readers (other
than CF reader). It is also not listed under my Plugin Manager GUI on the
ParaView that I compiled but it is loading the CF convention nc file. Are
they (the *.cxx files) generated on the fly during compile time?
Another thing, besides http://www.paraview.org/Wiki/VisIt_Database_Bridge ,
is there a place that I can find how to use that VisIt bridge in ParaView.
Maybe an example of how to load silo file? I actually have a plugin of my
own in VisIt that can load the climate modeling data that I have. I would
like to see if I can use my VisIt plugin in ParaView and not write another
plugin for ParaView? :)
> As the name implies, this reader reads netCDF files using the CF
> convention. (As the default netCDF reader, it also gracefully handles files
> that do not follow this convention.) With this assumption, I will try to
> explain what it does. It reads arrays as regular 1, 2, or 3D arrays,
> possibly with time. The CF convention also provides a means to assign
> coordinates to each grid point and to identify the coordinates as longitude
> or latitude.
>
>
The published nc files we have do adhere to CF convention we also use CMOR
in one of the pipeline. I noticed Data_tos_O1_2001-2002.nc is at CF-1.0 and
since I am new at CF Convention, I can only speculate that what I see at
ftp://ftp.gfdl.noaa.gov/pub/sms/4ParaView/4.png with what looks like double
grid is due to difference between CF-1.0 and CF-1.4? Will vtkNetCDFCFReader
handle CF-1.4 data?
> Even though coordinates are defined as longitude and latitude, the
> topology of the grid itself is still a grid. Thus, the grid gets wrapped
> around, but still has these seems that you see because topologically the one
> end of the regular grid is not attached to the other. I can't think of any
> filter that will identify and close these seems. In fact, it's not
> straightforward to do at all. If you look at your topology, it is not lain
> out on a simple spherical grid.
>
> The "right" way to solve your problem, which may or may not be in your
> control, is to create netCDF files that specify cell boundaries for a closed
> topology. Your netCDF file must be following at least some parts of the CF
> convention; your data would not show up as a sphere if it were not. The CF
> convention provides a way of defining cells that are not constrained by a
> regular grid topology. It is done through a "bounds" attribute on the
> dimension descriptor variables. You need either 1D or 2D bounds. They are
> described in this section of the CF convention documentation:
> http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.5/cf-conventions.html#cell-boundaries
> .
>
>
Agreed. The hack we have in VisIt loader (replace the last grid value with
the 1st grid value to create a "closed topology" ) is not "generalizable"
and will blow up in my face if I hand it to the user.
thanks
-simon
> The VTK test data has examples of both 1D bounds (tos_O1_2001-2002.nc)
> and 2D bounds (sampleCurveGrid4.nc). You can get the VTK test data from git
> (http://vtk.org/VTKData.git), or download them directly from the
> gitourious server:
>
>
> http://vtk.org/gitweb?p=VTKData.git;a=blob;f=Data/tos_O1_2001-2002.nc;h=30aa4a9b5e08b9bdf64540f2b144d83b279cca6c;hb=HEAD
>
>
> http://vtk.org/gitweb?p=VTKData.git;a=blob;f=Data/sampleCurveGrid4.nc;h=0ab89c27a25f92c047b58dca8b3057ca8d4df017;hb=HEAD
>
>
> -Ken
>
> **** Kenneth Moreland
> *** Sandia National Laboratories
> ***********
> *** *** *** email: *kmorel at sandia.gov
> *** *** ** phone: (505) 844-8919
> *** web: *http://www.cs.unm.edu/~kmorel*
>
> From: Simon Su <newsgroup4ssu at gmail.com>
> Date: Fri, 18 Mar 2011 16:43:42 -0400
> To: Andy Bauer <andy.bauer at kitware.com>
> Cc: <paraview at paraview.org>
> Subject: Re: [Paraview] loading nc formatted data
>
> Hi Andy,
>
> python trace gave me
>
> zos_Omon_GFDLESM2M_historical_r1i1p1_186101188012_nc = NetCDFReader(
> FileName=['/work/sms/data/cmor-20110128/mon/ocean/zos/r1i1p1/zos_Omon_GFDL-ESM2M_historical_r1i1p1_186101-188012.nc']
> )
>
> and there are tons of netcdf reader in ParaView and it is not in the plugin
> directory
>
> sms:/local/home/build/paraview/ParaView-3.10.0/Plugins> pwd
> /local/home/build/paraview/ParaView-3.10.0/Plugins
> sms:/local/home/build/paraview/ParaView-3.10.0/Plugins> ll
> total 84
> drwxr-xr-x 3 sms t 4096 Mar 10 12:37 AdiosReader/
> drwxr-xr-x 2 sms t 4096 Mar 10 12:37 AnalyzeNIfTIReaderWriter/
> -rw-r--r-- 1 sms t 3261 Mar 9 13:31 CMakeLists.txt
> drwxr-xr-x 3 sms t 4096 Mar 10 12:37 CoProcessingScriptGenerator/
> drwxr-xr-x 2 sms t 4096 Mar 10 12:37 CosmoFilters/
> drwxr-xr-x 4 sms t 4096 Mar 10 12:37 EyeDomeLighting/
> drwxr-xr-x 2 sms t 4096 Mar 10 12:37 ForceTime/
> drwxr-xr-x 3 sms t 4096 Mar 10 12:37 H5PartReader/
> drwxr-xr-x 4 sms t 4096 Mar 10 12:37 Manta/
> drwxr-xr-x 2 sms t 4096 Mar 10 12:37 Moments/
> drwxr-xr-x 2 sms t 4096 Mar 10 12:37 NetDMFReader/
> drwxr-xr-x 6 sms t 4096 Mar 10 12:37 PointSprite/
> drwxr-xr-x 4 sms t 4096 Mar 10 12:37 PrismPlugins/
> drwxr-xr-x 3 sms t 4096 Mar 10 12:37 pvblot/
> drwxr-xr-x 3 sms t 4096 Mar 10 12:37 SierraPlotTools/
> drwxr-xr-x 3 sms t 4096 Mar 10 12:37 SLACTools/
> drwxr-xr-x 4 sms t 4096 Mar 10 12:37 StreamingView/
> drwxr-xr-x 2 sms t 4096 Mar 10 12:37 SurfaceLIC/
> drwxr-xr-x 2 sms t 4096 Mar 10 12:37 Vapor/
> drwxr-xr-x 2 sms t 4096 Mar 10 12:37 VRPN/
> drwxr-xr-x 2 sms t 4096 Mar 9 13:31 VRUI/
> sms:/local/home/build/paraview/ParaView-3.10.0/Plugins>
>
>
> Can you help describe how Netcdf files plugins are done in ParaView. Do
> they have a super class of Netcdf that they all derive from to write the
> different flavors of netcdf readers? If so, where can the code be found?
>
> thanks
> -simon
>
>
>
> On Fri, Mar 18, 2011 at 10:30 AM, Andy Bauer <andy.bauer at kitware.com>wrote:
>
>> Hi Simon,
>>
>> Replies below...
>>
>> On Thu, Mar 17, 2011 at 12:41 PM, Simon Su <newsgroup4ssu at gmail.com>wrote:
>>
>>> Hi All,
>>>
>>> ftp://ftp.gfdl.noaa.gov/pub/sms/4ParaView/1.png
>>> ftp://ftp.gfdl.noaa.gov/pub/sms/4ParaView/2.png
>>> ftp://ftp.gfdl.noaa.gov/pub/sms/4ParaView/3.png
>>>
>>> the above are screen shot from older version of *.nc files that I have
>>> that I loaded up with Paraview 3.10.0 64-bit which I compiled myself. As you
>>> can see, the grid is correctly loaded. But in the data, there is a crack. Is
>>> there a filter that can fix this in ParaView? :)
>>>
>>
>> I'm not aware of any filter that will fix this automatically. Can you
>> describe the grid a bit more? It kind of looks like a multiblock of
>> structured grids.
>>
>>>
>>> ftp://ftp.gfdl.noaa.gov/pub/sms/4ParaView/4.png is the latest nc file
>>> that I have of similar simulation preprocessed output. When I loaded it up,
>>> it is clearly doing making assumption on the grid that is not correct and
>>> hence, the double looking grid.
>>>
>>> The questions now are:
>>>
>>> 1. ParaView has lots of *.nc file loader. How do I know which loader is
>>> ParaView using to load the data? If I pick a type for the Files of type
>>> option in the open File window, will that gurantees that ParaView will be
>>> using that particular file loader?
>>>
>>
>> If there is an ambiguity for which file loader to use (i.e. multiple
>> readers assume the same extension), then the GUI should pop up a dialog for
>> you to specify which one to use. You can use the python trace to figure out
>> exactly what reader is being used to load the file.
>>
>>
>>>
>>> 2. If I know which loader is used, I would like to see if I can modify
>>> the existing loader to create a new type of *.nc file loader to fix the grid
>>> of my data. Where is the code in the source tree of ParaView is the loader
>>> plugin placed?
>>>
>> Based on the name of the name of the reader from the python script, you
>> can look up the actual class name in the
>> ParaView/Servers/ServerManager/Resources/readers.xml file.
>>
>>
>>>
>>> or if there is an easier solution to fix my grid problem that doesn't
>>> involve developing a new data loader plugin that would be better.... :)
>>> please let me know...
>>>
>>> thanks
>>> -simon
>>>
>>>
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>>
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