Re: syntax of reading netCDF4 files with groups

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 ("X.nc" , "r") ; could also have ccm, grb or hdf suffux
>>>> gNames = getfilegrpnames (f) ; get names of all groups on file
>>>>
>>>> nNames = dimsizes (gNames) ; number of groups on the file
>>>>
>>>> print (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(v) ; dimension size of the group
>>>> rank = dimsizes(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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>>>
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>
>

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Received on Mon Jan 7 09:00:08 2013