Subsetting and saving netcdf in R
0
I am trying to subset 8 netcdf files (one of them is here) in a foor loop according to a shorter period of time and then to save them as a new netcdf file.
I saw that other people already asked on how to subset netcdf files according to different time period (here or here) but once I do it on my netcdf files the "for loop" keeps on running without finishing (not even the first netcdf file) and I can't figure out why.
Here the code I use:
library(raster)
library(netcdf4)
library(lubridate)
#setting wd=indir containing netcdf files
setwd(indir)
files=list.files(pattern="nc")
for (j in seq_along(files)){
#setting wd containing netcdf files in the loop
setwd(indir)
b<-brick(files[j])
nc<-nc_open(files[j])
#variable
varname<-names(nc[['var']][3])
varunits <- ncatt_get(nc,varname,"units")[[2]]
lon<-ncvar_get(nc,"lon")
lat<-ncvar_get(nc,"lat", verbose = F)
time<-ncvar_get(nc, "time")
tunits <- ncatt_get(nc, "time", "units")[[2]]
dlname <- ncatt_get(nc, varname,"long_name")[[2]]
nc_close(nc)
#assigning a crs
proj4string(b)<-"+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"
#setting time as.Date
tm<-ymd(getZ(b))
#setting time to rasterBrick
b<-setZ(b, tm)
# subsetting
b2<-subset(b, which(tm < as.Date('2006-01-01')))
#setting wd where I want to save the "new" netcdf files
setwd(outdir)
writeRaster(b2, filename = paste0(varname, "_1971_2006_Noce.nc"),
format="CDF", varname=varname, varunit=varunits, longname=dlname,
xname="lon", yname="lat", zname="time", zunit=tunits, overwrite=TRUE)
}
Any help on how to get the loop working would be very much appreciated!
r netcdf
edited Nov 22 '18 at 9:20
Bart
4,72132043
asked Nov 21 '18 at 22:53
SteSte
11
add a comment |
0
I am trying to subset 8 netcdf files (one of them is here) in a foor loop according to a shorter period of time and then to save them as a new netcdf file.
I saw that other people already asked on how to subset netcdf files according to different time period (here or here) but once I do it on my netcdf files the "for loop" keeps on running without finishing (not even the first netcdf file) and I can't figure out why.
Here the code I use:
library(raster)
library(netcdf4)
library(lubridate)
#setting wd=indir containing netcdf files
setwd(indir)
files=list.files(pattern="nc")
for (j in seq_along(files)){
#setting wd containing netcdf files in the loop
setwd(indir)
b<-brick(files[j])
nc<-nc_open(files[j])
#variable
varname<-names(nc[['var']][3])
varunits <- ncatt_get(nc,varname,"units")[[2]]
lon<-ncvar_get(nc,"lon")
lat<-ncvar_get(nc,"lat", verbose = F)
time<-ncvar_get(nc, "time")
tunits <- ncatt_get(nc, "time", "units")[[2]]
dlname <- ncatt_get(nc, varname,"long_name")[[2]]
nc_close(nc)
#assigning a crs
proj4string(b)<-"+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"
#setting time as.Date
tm<-ymd(getZ(b))
#setting time to rasterBrick
b<-setZ(b, tm)
# subsetting
b2<-subset(b, which(tm < as.Date('2006-01-01')))
#setting wd where I want to save the "new" netcdf files
setwd(outdir)
writeRaster(b2, filename = paste0(varname, "_1971_2006_Noce.nc"),
format="CDF", varname=varname, varunit=varunits, longname=dlname,
xname="lon", yname="lat", zname="time", zunit=tunits, overwrite=TRUE)
}
Any help on how to get the loop working would be very much appreciated!
r netcdf
edited Nov 22 '18 at 9:20
Bart
4,72132043
asked Nov 21 '18 at 22:53
SteSte
11
1
If your code is indeedfiles=list.files(pattern="nc)then you've missed a"to close out that string.
– shians
Nov 21 '18 at 23:32
Try adding a printed out counter at various points in your code (ieprint(j)orprint(varname)) throughout your loop that might tell you where it is going wrong
– RAB
Nov 22 '18 at 7:57
Thank you shians, but unfortunately this was just a transcription error when I copy pasted the code here. In the code itself I close out that string.
– Ste
Nov 22 '18 at 8:08
thanks, I have added some print(j) and now I get this error: Error in R_nc4_create: Invalid argument (creation mode was 0) Error in ncdf4::nc_create(filename, vardef, force_v4 = force_v4) : Error in nc_create! could you help me understanding why it refers to "nc_create" in writeRaster?
– Ste
Nov 22 '18 at 9:07
hi, your code works well for me. The only thing that I notice is that when you open the subsetted nc file the dates are not well represented. Try to UPDATE your R version and related packages as a start.
– aaaaa
Nov 23 '18 at 18:32
add a comment |
0
0
0
I am trying to subset 8 netcdf files (one of them is here) in a foor loop according to a shorter period of time and then to save them as a new netcdf file.
I saw that other people already asked on how to subset netcdf files according to different time period (here or here) but once I do it on my netcdf files the "for loop" keeps on running without finishing (not even the first netcdf file) and I can't figure out why.
Here the code I use:
library(raster)
library(netcdf4)
library(lubridate)
#setting wd=indir containing netcdf files
setwd(indir)
files=list.files(pattern="nc")
for (j in seq_along(files)){
#setting wd containing netcdf files in the loop
setwd(indir)
b<-brick(files[j])
nc<-nc_open(files[j])
#variable
varname<-names(nc[['var']][3])
varunits <- ncatt_get(nc,varname,"units")[[2]]
lon<-ncvar_get(nc,"lon")
lat<-ncvar_get(nc,"lat", verbose = F)
time<-ncvar_get(nc, "time")
tunits <- ncatt_get(nc, "time", "units")[[2]]
dlname <- ncatt_get(nc, varname,"long_name")[[2]]
nc_close(nc)
#assigning a crs
proj4string(b)<-"+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"
#setting time as.Date
tm<-ymd(getZ(b))
#setting time to rasterBrick
b<-setZ(b, tm)
# subsetting
b2<-subset(b, which(tm < as.Date('2006-01-01')))
#setting wd where I want to save the "new" netcdf files
setwd(outdir)
writeRaster(b2, filename = paste0(varname, "_1971_2006_Noce.nc"),
format="CDF", varname=varname, varunit=varunits, longname=dlname,
xname="lon", yname="lat", zname="time", zunit=tunits, overwrite=TRUE)
}
Any help on how to get the loop working would be very much appreciated!
r netcdf
edited Nov 22 '18 at 9:20
Bart
4,72132043
asked Nov 21 '18 at 22:53
SteSte
11
I am trying to subset 8 netcdf files (one of them is here) in a foor loop according to a shorter period of time and then to save them as a new netcdf file.
I saw that other people already asked on how to subset netcdf files according to different time period (here or here) but once I do it on my netcdf files the "for loop" keeps on running without finishing (not even the first netcdf file) and I can't figure out why.
Here the code I use:
library(raster)
library(netcdf4)
library(lubridate)
#setting wd=indir containing netcdf files
setwd(indir)
files=list.files(pattern="nc")
for (j in seq_along(files)){
#setting wd containing netcdf files in the loop
setwd(indir)
b<-brick(files[j])
nc<-nc_open(files[j])
#variable
varname<-names(nc[['var']][3])
varunits <- ncatt_get(nc,varname,"units")[[2]]
lon<-ncvar_get(nc,"lon")
lat<-ncvar_get(nc,"lat", verbose = F)
time<-ncvar_get(nc, "time")
tunits <- ncatt_get(nc, "time", "units")[[2]]
dlname <- ncatt_get(nc, varname,"long_name")[[2]]
nc_close(nc)
#assigning a crs
proj4string(b)<-"+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"
#setting time as.Date
tm<-ymd(getZ(b))
#setting time to rasterBrick
b<-setZ(b, tm)
# subsetting
b2<-subset(b, which(tm < as.Date('2006-01-01')))
#setting wd where I want to save the "new" netcdf files
setwd(outdir)
writeRaster(b2, filename = paste0(varname, "_1971_2006_Noce.nc"),
format="CDF", varname=varname, varunit=varunits, longname=dlname,
xname="lon", yname="lat", zname="time", zunit=tunits, overwrite=TRUE)
}
Any help on how to get the loop working would be very much appreciated!
r netcdf
r netcdf
edited Nov 22 '18 at 9:20
Bart
4,72132043
asked Nov 21 '18 at 22:53
SteSte
11
edited Nov 22 '18 at 9:20
Bart
4,72132043
asked Nov 21 '18 at 22:53
SteSte
11
edited Nov 22 '18 at 9:20
Bart
4,72132043
edited Nov 22 '18 at 9:20
Bart
4,72132043
edited Nov 22 '18 at 9:20
Bart
4,72132043
4,72132043
asked Nov 21 '18 at 22:53
SteSte
11
asked Nov 21 '18 at 22:53
SteSte
11
asked Nov 21 '18 at 22:53
SteSte
11
11
1
If your code is indeedfiles=list.files(pattern="nc)then you've missed a"to close out that string.
– shians
Nov 21 '18 at 23:32
Try adding a printed out counter at various points in your code (ieprint(j)orprint(varname)) throughout your loop that might tell you where it is going wrong
– RAB
Nov 22 '18 at 7:57
Thank you shians, but unfortunately this was just a transcription error when I copy pasted the code here. In the code itself I close out that string.
– Ste
Nov 22 '18 at 8:08
thanks, I have added some print(j) and now I get this error: Error in R_nc4_create: Invalid argument (creation mode was 0) Error in ncdf4::nc_create(filename, vardef, force_v4 = force_v4) : Error in nc_create! could you help me understanding why it refers to "nc_create" in writeRaster?
– Ste
Nov 22 '18 at 9:07
hi, your code works well for me. The only thing that I notice is that when you open the subsetted nc file the dates are not well represented. Try to UPDATE your R version and related packages as a start.
– aaaaa
Nov 23 '18 at 18:32
add a comment |
1
If your code is indeedfiles=list.files(pattern="nc)then you've missed a"to close out that string.
– shians
Nov 21 '18 at 23:32
Try adding a printed out counter at various points in your code (ieprint(j)orprint(varname)) throughout your loop that might tell you where it is going wrong
– RAB
Nov 22 '18 at 7:57
Thank you shians, but unfortunately this was just a transcription error when I copy pasted the code here. In the code itself I close out that string.
– Ste
Nov 22 '18 at 8:08
thanks, I have added some print(j) and now I get this error: Error in R_nc4_create: Invalid argument (creation mode was 0) Error in ncdf4::nc_create(filename, vardef, force_v4 = force_v4) : Error in nc_create! could you help me understanding why it refers to "nc_create" in writeRaster?
– Ste
Nov 22 '18 at 9:07
hi, your code works well for me. The only thing that I notice is that when you open the subsetted nc file the dates are not well represented. Try to UPDATE your R version and related packages as a start.
– aaaaa
Nov 23 '18 at 18:32
1
1
If your code is indeed
files=list.files(pattern="nc) then you've missed a " to close out that string.– shians
Nov 21 '18 at 23:32
If your code is indeed
files=list.files(pattern="nc) then you've missed a " to close out that string.– shians
Nov 21 '18 at 23:32
Try adding a printed out counter at various points in your code (ie
print(j) or print(varname)) throughout your loop that might tell you where it is going wrong– RAB
Nov 22 '18 at 7:57
Try adding a printed out counter at various points in your code (ie
print(j) or print(varname)) throughout your loop that might tell you where it is going wrong– RAB
Nov 22 '18 at 7:57
Thank you shians, but unfortunately this was just a transcription error when I copy pasted the code here. In the code itself I close out that string.
– Ste
Nov 22 '18 at 8:08
Thank you shians, but unfortunately this was just a transcription error when I copy pasted the code here. In the code itself I close out that string.
– Ste
Nov 22 '18 at 8:08
thanks, I have added some print(j) and now I get this error: Error in R_nc4_create: Invalid argument (creation mode was 0) Error in ncdf4::nc_create(filename, vardef, force_v4 = force_v4) : Error in nc_create! could you help me understanding why it refers to "nc_create" in writeRaster?
– Ste
Nov 22 '18 at 9:07
thanks, I have added some print(j) and now I get this error: Error in R_nc4_create: Invalid argument (creation mode was 0) Error in ncdf4::nc_create(filename, vardef, force_v4 = force_v4) : Error in nc_create! could you help me understanding why it refers to "nc_create" in writeRaster?
– Ste
Nov 22 '18 at 9:07
hi, your code works well for me. The only thing that I notice is that when you open the subsetted nc file the dates are not well represented. Try to UPDATE your R version and related packages as a start.
– aaaaa
Nov 23 '18 at 18:32
hi, your code works well for me. The only thing that I notice is that when you open the subsetted nc file the dates are not well represented. Try to UPDATE your R version and related packages as a start.
– aaaaa
Nov 23 '18 at 18:32
add a comment |
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1
If your code is indeed
files=list.files(pattern="nc)then you've missed a"to close out that string.– shians
Nov 21 '18 at 23:32
Try adding a printed out counter at various points in your code (ie
print(j)orprint(varname)) throughout your loop that might tell you where it is going wrong– RAB
Nov 22 '18 at 7:57
Thank you shians, but unfortunately this was just a transcription error when I copy pasted the code here. In the code itself I close out that string.
– Ste
Nov 22 '18 at 8:08
thanks, I have added some print(j) and now I get this error: Error in R_nc4_create: Invalid argument (creation mode was 0) Error in ncdf4::nc_create(filename, vardef, force_v4 = force_v4) : Error in nc_create! could you help me understanding why it refers to "nc_create" in writeRaster?
– Ste
Nov 22 '18 at 9:07
hi, your code works well for me. The only thing that I notice is that when you open the subsetted nc file the dates are not well represented. Try to UPDATE your R version and related packages as a start.
– aaaaa
Nov 23 '18 at 18:32