How to read netcdf files containing string arrays?
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I have a netCDF file which consists of a float array and a string array as verified by ncdump. In Matlab, I am able to load the float array, but I fail in loading the string array.
In particular, ncread produces an error:
ncread('string_test.nc','StringArray')
Error using netcdf.getVar (line 130)
12 is not a recognized netCDF datatype.
"12" is the code for NC_STRING and it seems like Matlab can not handle that.
The .nc file I'm trying to load can be downloaded from http://piotr.majdak.com/temp/netcdf/ where also more description is available.
I'm using Matlab 2011b - any ideas what I can do?
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per isakson
le 5 Mar 2013
Modifié(e) : per isakson
le 5 Mar 2013
I use R2012a.
ncdisp says: Datatype: UNSUPPORTED DATATYPE. See below. Why not accept that? What is the source of string_test.nc?
>> ncdisp( 'string_test.nc')
Source:
h:\m\cssm\string_test.nc
Format:
netcdf4
Dimensions:
test = 4
Variables:
FloatArray
Size: 4x1
Dimensions: test
Datatype: single
StringArray
Size: 4x1
Dimensions: test
Datatype: UNSUPPORTED DATATYPE
>> str = h5read( 'h:\m\cssm\string_test.nc', '/StringArray' )
str =
'NH10'
'CI03'
'HI17'
'NH11'
>>
>> h5disp( 'h:\m\cssm\string_test.nc', '/StringArray' )
HDF5 string_test.nc
Dataset 'StringArray'
Size: 4
MaxSize: 4
Datatype: H5T_STRING
String Length: variable
Padding: H5T_STR_NULLTERM
Character Set: H5T_CSET_ASCII
Character Type: H5T_C_S1
ChunkSize: []
Filters: none
Attributes:
'DIMENSION_LIST': H5T_VLEN
3 commentaires
per isakson
le 5 Mar 2013
Modifié(e) : per isakson
le 5 Mar 2013
I think:
- strings can be stored in more than one way (format).
- Matlab is often slow to adapt to new versions of supported software.
- When there is a high and a low-level set of functions in Matlab some functionality is typically missing in the high-level functions. I easily believe that Matlab's high-level support is limited. However, I often find it difficult to spot the critical statements (supported or not supported) in the documentation.
- in this context one should avoid the word "must"
My guess:
- ncread (R2012a) doesn't support variable length strings
Plus de réponses (3)
Peter Kuma
le 20 Août 2018
Just to let others know, I have submitted a new bug report (since I could not find the one submitted by Erik). The answer was:
As you correctly pointed out, this is a current limitation of the
netCDF implementation. It is being actively investigated for
enhacement.
The workaround is to utilize the fact that netCDF4 formats are a
subset of the HDF5 format and we can utilize the HDF5 functionality
to read the data
Workaround:
Instead of ncdisp, ncread utilize h5disp, h5read
I hope the above workaround solves your issue. If you have any
further queries, please reach out to me.
1 commentaire
Anna Weeks
le 21 Août 2018
The ability to write a mapped array section of values into a netCDF variable (i.e the 'NF_PUT_VARM_ type' functionality) would be highly desirable.
Maxime Hervo
le 31 Mar 2017
Is there any update for this issue ? I still have the same problem with MATLAB R2016b !
0 commentaires
liu jibao
le 31 Jan 2018
Is there any update for this issue ? I still have the same problem with MATLAB R2017b !
3 commentaires
Natalie Perlin
le 24 Juil 2019
Thank you for filing the report, I wonder if anything has been done since then!
I have the same problem with Matlab not being able to read string variables in R2017a, R2018b.
chidi
le 23 Jan 2023
I've tried using the h5read and hdf5read function but I'm not getting desired results
For ref. VX= h5read('d20220602.nc','.............../current velocity down')
Output comes out as [15532×1 single] . . .[15532×1 single]
The expected output are water current data and its 56x1 array
How can I resolve this issue
Thanks
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