Peter Tuju
2016-Jan-09 11:28 UTC
[R] Extracting point data using longitude and latitude from netcdf file using R
I have data file in netcdf with three dimensions (x, y, t) and I want to extract a variable RAINC and RAINNC using longitude and latitude for a single point location with all the time, but no lucky. The syntax is as follows;; setwd( "/run/media/tuju/0767090047/extract_wrf_txt_file" ) rm( list = ls() )??? ??? ??? ??? ????????????????????????????? library( ncdf4 )???????????????????????????????????? inp_file <- nc_open( "wrfout_d01_2016-01-07.nc" )time <- ncvar_get( inp_file, "Times" )????????????????????? # Reading the time variabledar_lon <- 39.2dar_lat <- -6.866667 RAINC <- ncvar_get( inp_file, varid = "RAINC", start? = c( dar_lon, dar_lat, 1 ), count = c( 1, 1, -1 ) ) RAINNC <- ncvar_get( inp_file, varid = "RAINNC", start? =? c( dar_lon, dar_lat, 1 ), count = c( 1, 1, -1 ) ) RAIN <- RAINC + RAINNCRAIN_TABLE <- cbind( time, RAIN ) write.table( RAIN_TABLE, "Dar_es_Salaam.txt", row.names = FALSE, ???????????? col.names = c( "Valid Forecast Time",? "Rain (mm)", sep = "\t " ) # But no lucky with the red bolded syntax as I end up with the following error message> RAINC <- ncvar_get( inp_file, varid = "RAINC", start? = c( Lon[2], Lat[2], 1 ), count = c( 1, 1, -1 ) ) Error in Rsx_nc4_get_vara_double: NetCDF: Index exceeds dimension bound Var: RAINC? Ndims: 3?? Start: 0,4294967289,38 Count: 17,1,1 Error in ncvar_get_inner(ncid2use, varid2use, nc$var[[li]]$missval, addOffset,? : ? C function R_nc4_get_vara_double returned error However when I cahnge the latitude to postive it works fine. Note latitudes in the file data ranges from -16.71505 to 7.787529 as shown below; head(ncvar_get(inp_file, "XLAT")) [1] -16.71505 -16.71505 -16.71505 -16.71505 -16.71505 -16.71505> tail(ncvar_get(inp_file, "XLAT"))[1] 7.787529 7.787529 7.787529 7.787529 7.787529 7.787529 ## So, how can I get the syntax correct? Please help?_____________ Peter? E. Tuju Dar es Salaam T A N Z A N I A ---------------------- [[alternative HTML version deleted]]
Anthoni, Peter (IMK)
2016-Jan-09 12:14 UTC
[R] Extracting point data using longitude and latitude from netcdf file using R
Hi Peter, the start in nc_varget requires a latitude and longitude index, not the latitude and longitude in double format. So you need to figure out what index your latitude and longitude correspond to, which will depends on what data are in your netCDF. it might have looked like that it worked for a positive latitude, but you got the data from the latitude index 6 or 7, depends on how the double was transformed into an integer. best regards Peter> On 09 Jan 2016, at 12:28, Peter Tuju via R-help <r-help at r-project.org> wrote: > > I have data file in netcdf with three dimensions (x, y, t) and I want to extract a variable RAINC and RAINNC > using longitude and latitude for a single point location with all the time, but no lucky. The syntax is as follows;; > setwd( "/run/media/tuju/0767090047/extract_wrf_txt_file" ) > rm( list = ls() ) > library( ncdf4 ) > inp_file <- nc_open( "wrfout_d01_2016-01-07.nc" )time <- ncvar_get( inp_file, "Times" ) # Reading the time variabledar_lon <- 39.2dar_lat <- -6.866667 > RAINC <- ncvar_get( inp_file, varid = "RAINC", start = c( dar_lon, dar_lat, 1 ), count = c( 1, 1, -1 ) ) > RAINNC <- ncvar_get( inp_file, varid = "RAINNC", start = c( dar_lon, dar_lat, 1 ), count = c( 1, 1, -1 ) ) > RAIN <- RAINC + RAINNCRAIN_TABLE <- cbind( time, RAIN ) > write.table( RAIN_TABLE, "Dar_es_Salaam.txt", row.names = FALSE, > col.names = c( "Valid Forecast Time", "Rain (mm)", sep = "\t " ) > > # But no lucky with the red bolded syntax as I end up with the following error message> RAINC <- ncvar_get( inp_file, varid = "RAINC", start = c( Lon[2], Lat[2], 1 ), count = c( 1, 1, -1 ) ) > Error in Rsx_nc4_get_vara_double: NetCDF: Index exceeds dimension bound > Var: RAINC Ndims: 3 Start: 0,4294967289,38 Count: 17,1,1 > Error in ncvar_get_inner(ncid2use, varid2use, nc$var[[li]]$missval, addOffset, : > C function R_nc4_get_vara_double returned error > However when I cahnge the latitude to postive it works fine. Note latitudes in the file data ranges from -16.71505 to 7.787529 as shown below; > head(ncvar_get(inp_file, "XLAT")) > [1] -16.71505 -16.71505 -16.71505 -16.71505 -16.71505 -16.71505 >> tail(ncvar_get(inp_file, "XLAT")) > [1] 7.787529 7.787529 7.787529 7.787529 7.787529 7.787529 > ## So, how can I get the syntax correct? Please help _____________ > Peter E. Tuju > Dar es Salaam > T A N Z A N I A > ---------------------- > > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
Peter Tuju
2016-Jan-09 12:54 UTC
[R] Extracting point data using longitude and latitude from netcdf file using R
Thank you Mr. Anthon for your feedback. So, how can? I extract the data at the
specified? latitude and longitude?Or, How can I get the latitude and longitude
index which corresponds to the following coordinates from the netcdf file?
dar_lon <- 39.2
dar_lat <- -6.866667?_____________
Peter? E. Tuju
Dar es Salaam
T A N Z A N I A
----------------------
From: "Anthoni, Peter (IMK)" <peter.anthoni at kit.edu>
To: Peter Tuju <peterenos at ymail.com>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Sent: Saturday, January 9, 2016 3:14 PM
Subject: Re: [R] Extracting point data using longitude and latitude from netcdf
file using R
Hi Peter,
the start in nc_varget requires a latitude and longitude index, not the latitude
and longitude in double format.
So you need to figure out what index your latitude and longitude correspond to,
which will depends on what data are in your netCDF.
it might have looked like that it worked for a positive latitude, but you got
the data from the latitude index 6 or 7, depends on how the double was
transformed into an integer.
best regards
Peter
> On 09 Jan 2016, at 12:28, Peter Tuju via R-help <r-help at
r-project.org> wrote:
>
> I have data file in netcdf with three dimensions (x, y, t) and I want to
extract a variable RAINC and RAINNC
> using longitude and latitude for a single point location with all the time,
but no lucky. The syntax is as follows;;
> setwd( "/run/media/tuju/0767090047/extract_wrf_txt_file" )
> rm( list = ls() )? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
> library( ncdf4 )? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
> inp_file <- nc_open( "wrfout_d01_2016-01-07.nc" )time <-
ncvar_get( inp_file, "Times" )? ? ? ? ? ? ? ? ? ? ? # Reading the time
variabledar_lon <- 39.2dar_lat <- -6.866667
> RAINC <- ncvar_get( inp_file, varid = "RAINC", start? = c(
dar_lon, dar_lat, 1 ), count = c( 1, 1, -1 ) )
> RAINNC <- ncvar_get( inp_file, varid = "RAINNC", start? =? c(
dar_lon, dar_lat, 1 ), count = c( 1, 1, -1 ) )
> RAIN <- RAINC + RAINNCRAIN_TABLE <- cbind( time, RAIN )
> write.table( RAIN_TABLE, "Dar_es_Salaam.txt", row.names = FALSE,
>? ? ? ? ? ? ? col.names = c( "Valid Forecast Time",? "Rain
(mm)", sep = "\t " )
>
> # But no lucky with the red bolded syntax as I end up with the following
error message> RAINC <- ncvar_get( inp_file, varid = "RAINC",
start? = c( Lon[2], Lat[2], 1 ), count = c( 1, 1, -1 ) )
> Error in Rsx_nc4_get_vara_double: NetCDF: Index exceeds dimension bound
> Var: RAINC? Ndims: 3? Start: 0,4294967289,38 Count: 17,1,1
> Error in ncvar_get_inner(ncid2use, varid2use, nc$var[[li]]$missval,
addOffset,? :
>? C function R_nc4_get_vara_double returned error
> However when I cahnge the latitude to postive it works fine. Note latitudes
in the file data ranges from -16.71505 to 7.787529 as shown below;
> head(ncvar_get(inp_file, "XLAT"))
> [1] -16.71505 -16.71505 -16.71505 -16.71505 -16.71505 -16.71505
>> tail(ncvar_get(inp_file, "XLAT"))
> [1] 7.787529 7.787529 7.787529 7.787529 7.787529 7.787529
> ## So, how can I get the syntax correct? Please help _____________
> Peter? E. Tuju
> Dar es Salaam
> T A N Z A N I A
> ----------------------
>
>
>
>
>
> ??? [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
Ben Tupper
2016-Jan-09 13:01 UTC
[R] Extracting point data using longitude and latitude from netcdf file using R
Hi, This post gives more details on how to transform your lat/lon values to row/column indices. The question and answer are specifically about the ncdf package, but the workflow is identical when using the ncfd4 package. https://stat.ethz.ch/pipermail/r-help/2011-March/272641.html Cheers, Ben> On Jan 9, 2016, at 7:14 AM, Anthoni, Peter (IMK) <peter.anthoni at kit.edu> wrote: > > Hi Peter, > > the start in nc_varget requires a latitude and longitude index, not the latitude and longitude in double format. > So you need to figure out what index your latitude and longitude correspond to, which will depends on what data are in your netCDF. > > it might have looked like that it worked for a positive latitude, but you got the data from the latitude index 6 or 7, depends on how the double was transformed into an integer. > > best regards > Peter > >> On 09 Jan 2016, at 12:28, Peter Tuju via R-help <r-help at r-project.org> wrote: >> >> I have data file in netcdf with three dimensions (x, y, t) and I want to extract a variable RAINC and RAINNC >> using longitude and latitude for a single point location with all the time, but no lucky. The syntax is as follows;; >> setwd( "/run/media/tuju/0767090047/extract_wrf_txt_file" ) >> rm( list = ls() ) >> library( ncdf4 ) >> inp_file <- nc_open( "wrfout_d01_2016-01-07.nc" )time <- ncvar_get( inp_file, "Times" ) # Reading the time variabledar_lon <- 39.2dar_lat <- -6.866667 >> RAINC <- ncvar_get( inp_file, varid = "RAINC", start = c( dar_lon, dar_lat, 1 ), count = c( 1, 1, -1 ) ) >> RAINNC <- ncvar_get( inp_file, varid = "RAINNC", start = c( dar_lon, dar_lat, 1 ), count = c( 1, 1, -1 ) ) >> RAIN <- RAINC + RAINNCRAIN_TABLE <- cbind( time, RAIN ) >> write.table( RAIN_TABLE, "Dar_es_Salaam.txt", row.names = FALSE, >> col.names = c( "Valid Forecast Time", "Rain (mm)", sep = "\t " ) >> >> # But no lucky with the red bolded syntax as I end up with the following error message> RAINC <- ncvar_get( inp_file, varid = "RAINC", start = c( Lon[2], Lat[2], 1 ), count = c( 1, 1, -1 ) ) >> Error in Rsx_nc4_get_vara_double: NetCDF: Index exceeds dimension bound >> Var: RAINC Ndims: 3 Start: 0,4294967289,38 Count: 17,1,1 >> Error in ncvar_get_inner(ncid2use, varid2use, nc$var[[li]]$missval, addOffset, : >> C function R_nc4_get_vara_double returned error >> However when I cahnge the latitude to postive it works fine. Note latitudes in the file data ranges from -16.71505 to 7.787529 as shown below; >> head(ncvar_get(inp_file, "XLAT")) >> [1] -16.71505 -16.71505 -16.71505 -16.71505 -16.71505 -16.71505 >>> tail(ncvar_get(inp_file, "XLAT")) >> [1] 7.787529 7.787529 7.787529 7.787529 7.787529 7.787529 >> ## So, how can I get the syntax correct? Please help _____________ >> Peter E. Tuju >> Dar es Salaam >> T A N Z A N I A >> ---------------------- >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.Ben Tupper Bigelow Laboratory for Ocean Sciences 60 Bigelow Drive, P.O. Box 380 East Boothbay, Maine 04544 http://www.bigelow.org