Re: syntax of reading netCDF4 files with groups

Dear Dr. Huang,

Thank you very much!
It works great now!

Hope everything goes well with version 6.1.1!

Best,
Wenshan

On Mon, Jan 7, 2013 at 7:59 AM, Wei Huang <huangwei@ucar.edu> wrote:

> Wenshan,
>
> We will fix that issue in the 6.1.1 release.
>
> Meanwhile, you may try:
>
> vn1 = "/snd_LImon_CCSM4_historical_all-ens_GN_monthly_anomaly/snd"
> dd1 = fin->$vn1$
>
> vn2 = "/snd_LImon_CSIRO-Mk3-6-0_historical_all-ens_GN_monthly_anomaly/snd"
> dd2 = fin->$vn2$
>
> Which allows you to read variable directly from a file.
>
> Thanks,
>
> Wei
>
> huangwei@ucar.edu
> VETS/CISL
> National Center for Atmospheric Research
> P.O. Box 3000 (1850 Table Mesa Dr.)
> Boulder, CO 80307-3000 USA
> (303) 497-8924
>
>
>
>
>
>
> On Jan 5, 2013, at 1:11 PM, Wenshan Wang wrote:
>
> Dear Dr. Huang and friends,
>
> I found that if I only read one group from one file. It will be OK using
> Dr. Huang's scripts.
> But if I tried to read the second group of the file. The message
> "fatal:NclNetCDF4: Could not reopen the file
> (~/data/cmip5/output/4plot/snd_LImon_all-model_historical_all-ens_GN_monthly-anomaly.nc)
> for reading" will show again.
>
> NCL version: 6.1.0;
> Sample file has been uploaded to the ftp:
> incoming/snd_LImon_all-model_historical_all-ens_GN_monthly-anomaly.nc
>
> The script I used is as follow:
> dir = "~/data/cmip5/output/4plot/"
> fn = "snd_LImon_all-model_historical_all-ens_GN_monthly-anomaly.nc"
> fin = addfile(dir+fn,"r")
>
> gn1 = "snd_LImon_CCSM4_historical_all-ens_GN_monthly_anomaly"
> gg1 = fin=>$gn1$
> dd1 = gg1->snd
> printVarSummary(dd1)
> printMinMax(dd1,True)
> print(dd1)
>
> gn2 = "snd_LImon_CSIRO-Mk3-6-0_historical_all-ens_GN_monthly_anomaly"
> gg2 = fin=>$gn2$
> dd2 = gg2->snd
> printVarSummary(dd2)
> printMinMax(dd2,True)
> print(dd2)
>
> ================================================================
> Moreover, it seems the content of variable is not the same as that ncdump
> gives me.
> Much smaller.
> I used 'ncdump -v snd
> snd_LImon_all-model_historical_all-ens_GN_monthly-anomaly.nc'.
>
>
>
> ================================================================
> When i use 'ncl_filedump -v snd
> snd_LImon_all-model_historical_all-ens_GN_monthly-anomaly.nc', it will be
> "Segmentation fault (core dumped)".
>
>
> Thank you!
>
> Best,
> Wenshan
>
>
> On Fri, Jan 4, 2013 at 8:09 PM, Wei Huang <huangwei@ucar.edu> wrote:
>
>> Wenshan,
>>
>> We have fixed the problem.
>> The fixes will be in the new release (6.1.1, coming soon).
>>
>> Thanks,
>>
>> Wei
>>
>> huangwei@ucar.edu
>> VETS/CISL
>> National Center for Atmospheric Research
>> P.O. Box 3000 (1850 Table Mesa Dr.)
>> Boulder, CO 80307-3000 USA
>> (303) 497-8924
>>
>>
>>
>>
>>
>>
>> On Jan 4, 2013, at 8:23 PM, Wei Huang wrote:
>>
>> Wenshan,
>>
>> There is a problem with getfilegrpnames, otherwise, the second script
>> below will work.
>>
>> Mean while, you can use "ncl_filedump X.nc | grep group" to get the group
>> names.
>>
>> Then use script:
>> f = addfile ("X.nc" , "r") ; could also have ccm, grb or hdf suffux
>>
>> ;(0) snd_LImon_ACCESS1-0_historical_all-ens_GN_monthly_anomaly
>> ;(1) snd_LImon_CCSM4_historical_all-ens_GN_monthly_anomaly
>> ;(2) snd_LImon_CESM1-CAM5_historical_all-ens_GN_monthly_anomaly
>> ;(3) snd_LImon_CESM1-FASTCHEM_historical_all-ens_GN_monthly_anomaly
>> ;(4) snd_LImon_CESM1-WACCM_historical_all-ens_GN_monthly_anomaly
>> ;(5) snd_LImon_CMCC-CM_historical_all-ens_GN_monthly_anomaly
>> ;(6) snd_LImon_CMCC-CMS_historical_all-ens_GN_monthly_anomaly
>> ;(7) snd_LImon_CSIRO-Mk3-6-0_historical_all-ens_GN_monthly_anomaly
>>
>> gn = "snd_LImon_ACCESS1-0_historical_all-ens_GN_monthly_anomaly"
>>
>> g = f=>$gn$ ; read the group to memory
>>
>> printVarSummary(g)
>>
>> vNames = getfilevarnames (g) ; get names of all groups on file
>> nvNames = dimsizes (vNames) ; number of vars in the group
>>
>> print (nvNames) ; print number of variables in group
>> print (vNames) ; print variable name in group
>>
>> do m=0,nvNames-1
>>
>> print("===========================================================")
>> print("Variable Number: " + m)
>> v = g->$vNames(m)$ ; read the variable to memory
>> printVarSummary(v)
>> delete(v)
>> end do
>>
>> to read variables.
>>
>> We are working on getfilegrpnames, and hope to fix it soon.
>>
>> Regards,
>>
>> Wei
>>
>>
>> huangwei@ucar.edu
>> VETS/CISL
>> National Center for Atmospheric Research
>> P.O. Box 3000 (1850 Table Mesa Dr.)
>> Boulder, CO 80307-3000 USA
>> (303) 497-8924
>>
>>
>> -------------
>> f = addfile ("X.nc" , "r") ; could also have ccm, grb or hdf suffux
>>
>> ;print(f)
>>
>> gNames = getfilegrpnames (f) ; get names of all groups on file
>> ngNames = dimsizes (gNames) ; number of groups on the file
>>
>> print (ngNames) ; print number of group names on file
>> print (gNames) ; print group names on file
>>
>> do n=0,ngNames-1 ; loop thru each group
>> print("--------------------------------------------------------")
>> print("Group Number: " + n)
>>
>> g = f=>$gNames(n)$ ; read the group to memory
>>
>> printVarSummary(g)
>>
>> vNames = getfilevarnames (g) ; get names of all groups on file
>> nvNames = dimsizes (vNames) ; number of vars in the group
>>
>> print (nvNames) ; print number of variables in group
>> print (vNames) ; print variable name in group
>>
>> do m=0,nvNames-1
>>
>> print("===========================================================")
>> print("Variable Number: " + m)
>> v = g->$vNames(m)$ ; read the variable to memory
>> printVarSummary(v)
>> delete(v)
>> end do
>>
>> ;[SNIP]
>>
>> delete(g)
>> end do
>>
>>
>>
>>
>> On Jan 4, 2013, at 4:38 PM, Wei Huang wrote:
>>
>> Wenshan,
>>
>> I'll check and get back to you.
>>
>> Thanks,
>>
>> Wei
>>
>> huangwei@ucar.edu
>> VETS/CISL
>> National Center for Atmospheric Research
>> P.O. Box 3000 (1850 Table Mesa Dr.)
>> Boulder, CO 80307-3000 USA
>> (303) 497-8924
>>
>>
>>
>>
>>
>>
>> On Jan 4, 2013, at 4:32 PM, Wenshan Wang wrote:
>>
>> The version of NCL I am using is: 6.1.0-08Oct2012_1119
>>
>> I've put my sample file on the ftp:
>> incoming/snd_LImon_all-model_historical_all-ens_GN_monthly-anomaly.nc
>>
>> Thank you!
>>
>> Best,
>> Wenshan
>>
>>
>> On Fri, Jan 4, 2013 at 3:15 PM, Wenshan Wang <wenshanw@uci.edu> wrote:
>>
>>> Dear all,
>>>
>>> I am trying to read netCDF4 files with groups, following the example
>>> given on the page of 'getfilegrpnames'.
>>> Here it is:
>>>
>>> f = *addfile* <http://www.ncl.ucar.edu/Document/Functions/Built-in/addfile.shtml> ("X.nc" , "r") ; could also have ccm, grb or hdf suffux
>>> gNames = *getfilegrpnames* (f) ; get names of all groups on file
>>>
>>> nNames = *dimsizes* <http://www.ncl.ucar.edu/Document/Functions/Built-in/dimsizes.shtml> (gNames) ; number of groups on the file
>>>
>>> *print* <http://www.ncl.ucar.edu/Document/Functions/Built-in/print.shtml> (nNames) ; print all group names on file
>>>
>>> do n=0,nNames-1 ; loop thru each group
>>> v = f->$gNames(n)$ ; read the group to memory
>>>
>>> dimv = *dimsizes* <http://www.ncl.ucar.edu/Document/Functions/Built-in/dimsizes.shtml>(v) ; dimension size of the group
>>> rank = *dimsizes* <http://www.ncl.ucar.edu/Document/Functions/Built-in/dimsizes.shtml>(dimv) ; rank [ie: number of dimensions]
>>>
>>> [SNIP]
>>>
>>> delete (v)
>>> delete (rank)
>>> end do
>>>
>>>
>>> However, if I followed the example and use:
>>>
>>> v = f->$gNames(n)$
>>>
>>> It will result in:
>>> fatal:["Execute.c":5709]:variable
>>> (snc_LImon_bcc-csm1-1_historical_all-ens_clm) is not in file (fin)
>>>
>>> Instead, if I use:
>>> gg = fin=>$gn(j)$
>>> dd = gg->$var(i)$
>>> It can read what I want, but there is an error message:
>>> fatal:NclNetCDF4: Could not reopen the file
>>> (~/data/cmip5/output/4plot/snd_LImon_all-model_historical_all-ens_clm.nc)
>>> for reading
>>>
>>> So, what syntax should I use to read variables in groups?
>>>
>>> Thank you very much!
>>> Happy New Year!
>>>
>>> Best,
>>> Wenshan
>>>
>>
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Received on Mon Jan 7 13:58:08 2013