[Paraview] troubles with netCDF reader ?
Aashish Chaudhary
aashish.chaudhary at kitware.com
Tue Aug 8 16:51:05 EDT 2017
Hi Cynthia,
If you could modify the vtkNetCDFCFReader (
https://github.com/Kitware/VTK/blob/master/IO/NetCDF/vtkNetCDFCFReader.cxx) to
work with WRF formats, that would be an awesome addition. I know few folks
that can use this work. Unfortunately we do not have any direct funding to
accomplish this but we will be more than happy to guide or help a little if
needed.
Let us know and we can discuss more offline.
Thanks,
On Tue, Aug 8, 2017 at 4:40 PM Dan Lipsa <dan.lipsa at kitware.com> wrote:
> Hi Cynthia,
> It is possible to change the reader. You'll need to compile ParaView from
> source. The class you need to change is vtkNetCDFCFReader.
> Probably you'll need an extra parameter to the reader that would be the
> time unit. The time unit read from the file should overides this parameter.
>
> You could also submit your changes back to VTK (most readers in ParaView
> are actually part of VTK). This seems like something other people might
> need.
>
> Dan
>
>
>
>
> On Tue, Aug 8, 2017 at 12:43 PM, Hart, Cynthia Joyce - (cyndyb) <
> cyndyb at email.arizona.edu> wrote:
>
>> Hello,
>>
>>
>>
>> To make a long story short, this solution you used below, does not work
>> well for the weather forecasting group here on my campus that I am working
>> with. Is there any possibility of obtaining the source code of the
>> Paraview netCDF reader? If I could edit that source code to accept the
>> non- CF compliant WRF outputs, I could make use of Paraview in an automated
>> script to create animations for our forecasters much, much more readily
>> than manipulating netCDF file headers. The data I’d sent to you was but a
>> very small subset of the hundreds of netCDF files we’d need to change,
>> every time we do a model run, and this is a process we’d like to actually
>> automate daily. I am unable to force the output to be compliant as it is
>> created. Can you help?
>>
>>
>>
>> Sincerely,
>>
>>
>>
>> Cynthia Hart
>>
>>
>>
>>
>>
>> *From: *Dan Lipsa <dan.lipsa at kitware.com>
>> *Date: *Friday, June 23, 2017 at 10:57 AM
>> *To: *Aashish Chaudhary <aashish.chaudhary at kitware.com>
>> *Cc: *"Hart, Cynthia Joyce - (cyndyb)" <cyndyb at email.arizona.edu>, "
>> paraview at paraview.org" <paraview at paraview.org>
>> *Subject: *Re: [Paraview] troubles with netCDF reader ?
>>
>>
>>
>> Cynthia,
>>
>> It seems that the files you send us are not CF compliant.
>>
>> The problem is that the Time dimension does not have a unit.
>>
>>
>>
>>
>>
>> Here are some quotes from the CF Conventions document:
>>
>> - The use of coordinate variables is required for all dimensions that
>> correspond to one dimensional space or time coordinates.
>>
>> - Variables representing time must always explicitly include the units
>> attribute; there is no default value
>>
>>
>>
>> So, to fix one of your files, I did:
>>
>>
>>
>> 1. ncdump ARAD4_test2.ncdf > ARAD4_test2_CF.txt
>>
>>
>>
>> 2. I added a new variable Time with the unit specified to the txt file.
>>
>>
>>
>> float Time(Time) ;
>>
>> Time:units = "minutes since 2016-07-29 12:00:00" ;
>>
>>
>>
>> 3.
>>
>> I generated a new nc file:
>>
>> ncgen ARAD4_test2_CF.txt -o ARAD4_test2_CF.nc
>>
>>
>>
>> This new file is read correctly by ParaView.
>>
>>
>>
>> Best,
>>
>> Dan
>>
>>
>>
>>
>>
>>
>>
>> On Fri, Jun 16, 2017 at 6:31 PM, Aashish Chaudhary <
>> aashish.chaudhary at kitware.com> wrote:
>>
>> Dear Cynthia,
>>
>>
>>
>> Is there any chance that you can send me a sample dataset?
>>
>>
>>
>> - Aashish
>>
>>
>>
>> On Fri, Jun 16, 2017 at 6:15 PM Hart, Cynthia Joyce - (cyndyb) <
>> cyndyb at email.arizona.edu> wrote:
>>
>> Folks –
>>
>>
>>
>> I am struggling with using the netCDF reader, with a bunch of timeseries
>> of WRF data output (weather prediction modeling). I am a visualizer, NOT a
>> meteorologist, and so, my full understanding of the model’s output is shaky
>> at best. The researcher I am trying to assist is currently on vacation,
>> and I’m trying to animate the output of his WRF model.
>>
>>
>>
>> So! I have been viewing some of the output using the built in reader in
>> Paraview (the ‘generic and cf’ reader) and it works for some variables, not
>> for others. I am using NCO tools to extract some of the variables of
>> interest into their own CDF file, to try and isolate the problem Paraview
>> has, reading some variables.. but that doesn’t help. I am particularly
>> trying to read a variable for radar data, “REFL_10CM”. Here is the
>> relevant bit of the file header from ncdump, below:
>>
>>
>>
>> netcdf ARAD4_test2 {
>>
>> dimensions:
>>
>> Time = UNLIMITED ; // (1 currently)
>>
>> south_north = 393 ;
>>
>> west_east = 639 ;
>>
>> bottom_top = 37 ;
>>
>> variables:
>>
>> float REFD_MAX(Time, south_north, west_east) ;
>>
>> REFD_MAX:FieldType = 104 ;
>>
>> REFD_MAX:MemoryOrder = "XY " ;
>>
>> REFD_MAX:description = "MAX DERIVED RADAR
>> REFL" ;
>>
>> REFD_MAX:units = "dbZ" ;
>>
>> REFD_MAX:stagger = "" ;
>>
>> REFD_MAX:coordinates = "XLONG XLAT XTIME"
>> ;
>>
>> float REFL_10CM(Time, bottom_top, south_north, west_east)
>> ;
>>
>> REFL_10CM:FieldType = 104 ;
>>
>> REFL_10CM:MemoryOrder = "XYZ" ;
>>
>> REFL_10CM:description = "Radar
>> reflectivity (lamda = 10 cm)" ;
>>
>> REFL_10CM:units = "dBZ" ;
>>
>> REFL_10CM:stagger = "" ;
>>
>> REFL_10CM:coordinates = "XLONG XLAT
>> XTIME" ;
>>
>> float XLAT(Time, south_north, west_east) ;
>>
>> XLAT:FieldType = 104 ;
>>
>> XLAT:MemoryOrder = "XY " ;
>>
>> XLAT:description = "LATITUDE, SOUTH IS
>> NEGATIVE" ;
>>
>> XLAT:units = "degree_north" ;
>>
>> XLAT:stagger = "" ;
>>
>> XLAT:coordinates = "XLONG XLAT" ;
>>
>> float XLONG(Time, south_north, west_east) ;
>>
>> XLONG:FieldType = 104 ;
>>
>> XLONG:MemoryOrder = "XY " ;
>>
>> XLONG:description = "LONGITUDE, WEST IS
>> NEGATIVE" ;
>>
>> XLONG:units = "degree_east" ;
>>
>> XLONG:stagger = "" ;
>>
>> XLONG:coordinates = "XLONG XLAT" ;
>>
>> float XTIME(Time) ;
>>
>> XTIME:FieldType = 104 ;
>>
>> XTIME:MemoryOrder = "0 " ;
>>
>> XTIME:description = "minutes since
>> 2016-07-29 12:00:00" ;
>>
>> XTIME:units = "minutes since 2016-07-29
>> 12:00:00" ;
>>
>> XTIME:stagger = "" ;
>>
>>
>>
>> Paraview complains that it cannot read a variable with more than three
>> dimensions without time. But there appears to ‘be’ time (I’m very unclear
>> what “UNLIMITED” time , as seen in the header, refers to in this context).
>> Is there any way I can work around this? Most frustrating. I can
>> actually read this variable into QGIS, but I’d rather use the strengths of
>> Paraview to visualize this data.
>>
>>
>>
>> Thanks in advance.
>>
>>
>>
>>
>>
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