[R] about netcdf files

[lily li]

Hi Jon,

The versions are: raster_2.5-2 sp_1.2-3


On Wed, Jul 27, 2016 at 9:31 AM, Jon Skoien <jon.skoien at jrc.ec.europa.eu>
wrote:

> Hi Lily,
>
> You can ignore the first three lines, they are just for information.
> Which version of raster do you have? I see that the attempt to read the
> crs-variable was not wrapped in a try-call in earlier versions. Upgrading
> might help.
>
> Best,
> Jon
>
>
>
> On 7/27/2016 5:13 PM, lily li wrote:
>
> Hi Jon,
>
> I still have problems. The brick function does not work well and I don't
> know where to check the problem. I put the error message below, thanks.
>
> > pre = brick("~/Downloads/sample_precip_daily.nc")
> [1] "vobjtovarid4: error #F: I could not find the requsted var (or dimvar)
> in the file!"
> [1] "var (or dimvar) name: crs"
> [1] "file name: /.../Downloads/sample_precip_daily.nc"
> Error in vobjtovarid4(nc, varid, allowdimvar = TRUE, verbose = verbose) :
>   Variable not found
>
>
> On Wed, Jul 27, 2016 at 1:10 AM, Jon Skoien <jon.skoien at jrc.ec.europa.eu>
> wrote:
>
>> I think you get the error because you passed the object from nc_open(),
>> you should rather pass the filename of the netCDF, so:
>>
>> pre = brick("sample_precip_daily.nc")
>> From the test-file, this gives you a RasterBrick-object with 5*9 pixels
>> and 7305 layers.
>> Then you can extract data.frames of each layer with:
>> dframe = rasterToPoints(pre[[1]])
>> where 1 is the first layer, or time series with:
>> tseries = pre[3,4]
>> where 3 and 4 are the pixels in x and y-direction.
>>
>> To write dframe to csv:
>> write.csv(dframe, filename = "csvfile.csv")
>> Check the function for more options.
>>
>> Hope this helps you a bit further.
>> Jon
>>
>>
>> On 7/26/2016 9:07 PM, lily li wrote:
>>
>> Thanks for your reply. But it says "Error in (function (classes, fdef,
>> mtable)):
>> unable to find an inherited method for function 'brick' for signature
>> 'ncdf4' "
>>
>> The dataset is attached. It contains daily precipitation data for 20
>> years, within a rectangle, so that there are several grid points. I use the
>> code to open it, but don't know how to get csv files, while each file
>> contains continuous daily precipitation data for each grid cell.
>> pre1 = nc_open('sample_precip_daily.nc')
>> pre1
>> pre1_rd = ncvar_get(pre1, 'precipitation')
>> nc_close(pre1)
>>
>> Thanks for your help.
>>
>> On Tue, Jul 26, 2016 at 4:08 AM, Jon Skoien <
>> <jon.skoien at jrc.ec.europa.eu>jon.skoien at jrc.ec.europa.eu> wrote:
>>
>>> You could try with the brick function from the raster package.
>>>
>>> bvar = brick(netcdfName)
>>>
>>> This uses the ncdf4 functions for opening and reading the netcdf, but
>>> makes it easier to extract data for each day:
>>>
>>> p1 = rasterToPoints(bvar[[1]])
>>> and write p1 to csv.
>>>
>>> Best,
>>> Jon
>>>
>>>
>>>
>>> On 7/26/2016 6:54 AM, lily li wrote:
>>>
>>>> Hi all,
>>>>
>>>> I have a problem in opening netcdf files. If one netcdf file contains
>>>> longitude, latitude, and daily precipitation. How to relate each
>>>> precipitation record to its associated location, and export them as csv
>>>> files? Thanks.
>>>>
>>>> I just use nc_open(), ncvar_get(), but it is not very helpful. Thanks
>>>> for
>>>> any ideas.
>>>>
>>>>         [[alternative HTML version deleted]]
>>>>
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>>>>
>>> --
>>> Jon Olav Skøien
>>> Joint Research Centre - European Commission
>>> Institute for Space, Security & Migration
>>> Disaster Risk Management Unit
>>>
>>> Via E. Fermi 2749, TP 122,  I-21027 Ispra (VA), ITALY
>>>
>>> jon.skoien at jrc.ec.europa.eu
>>> Tel:  +39 0332 789205 <%2B39%200332%20789205>
>>>
>>> Disclaimer: Views expressed in this email are those of the individual
>>> and do not necessarily represent official views of the European Commission.
>>>
>>
>>
>> --
>> Jon Olav Skøien
>> Joint Research Centre - European Commission
>> Institute for Space, Security & Migration
>> Disaster Risk Management Unit
>>
>> Via E. Fermi 2749, TP 122,  I-21027 Ispra (VA), ITALY
>> jon.skoien at jrc.ec.europa.eu
>> Tel:  +39 0332 789205
>>
>> Disclaimer: Views expressed in this email are those of the individual and do not necessarily represent official views of the European Commission.
>>
>>
>
> --
> Jon Olav Skøien
> Joint Research Centre - European Commission
> Institute for Space, Security & Migration
> Disaster Risk Management Unit
>
> Via E. Fermi 2749, TP 122,  I-21027 Ispra (VA), ITALY
> jon.skoien at jrc.ec.europa.eu
> Tel:  +39 0332 789205
>
> Disclaimer: Views expressed in this email are those of the individual and do not necessarily represent official views of the European Commission.
>
>

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