Hi I have a netCDF file of volumetric soil water content at four different soil layers and want to convert each soil layer in the netCDF file to a GeoTIFF layer. This code converts the netCDF file to one GeoTIFF layer, i.e. unclear which soil depth. file.nc <- "C:/Soil_Weather_data/Agro/VMC21/VMC21.nc" file.tiff <- "C:/Soil_Weather_data/Agro /VMC21/VMC21" importnetcdf <- raster(file.nc)> importnetcdfclass : RasterLayer band : 1 (of 4 bands) #the bands here are the four soil layers dimensions : 16800, 43200, 725760000 (nrow, ncol, ncell) resolution : 0.00833333, 0.00833333 (x, y) extent : -180, 179.9998, -56, 83.99995 (xmin, xmax, ymin, ymax) coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0 data source : C:\FAPSEP_Eucalyptus\FAPSEP\Soil_Weather_data\Agro_IBIS_Eucalipto\VMC21\VMC21.nc names : Volumetric.water.content.at..33.kPa z-value : 4.5 zvar : VMC2 VMC1<-writeRaster(importnetcdf,filename="file.tiff",format="GTiff",overwrite=TRUE,bylayer=TRUE,suffix="1:4") #bylayer=TRUE, did not work.> VMC1class : RasterLayer dimensions : 16800, 43200, 725760000 (nrow, ncol, ncell) resolution : 0.00833333, 0.00833333 (x, y) extent : -180, 179.9998, -56, 83.99995 (xmin, xmax, ymin, ymax) coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0 data source : C:\Users\Ahmed\Documents\file.tif names : file values : 2, 80 (min, max) Any help! Ahmed Attia, Ph.D. Agronomist & Soil Scientist [[alternative HTML version deleted]]
Hi Ahmed, When reading from a ncdf file you can use the 'varname', 'lvar' and 'level' arguments - see the 'Details' section in the docs https://www.rdocumentation.org/packages/raster/versions/2.6-7/topics/raster <https://www.rdocumentation.org/packages/raster/versions/2.6-7/topics/raster> We can't tell what is in the ncdf file from what you report other than it has 4 bands (layers) and that the first is called 'Volumetric.water.content.at..33.kPa' If you want to know more about the what is in the file, then I suggest you use the ncdf4 package to open the file and explore it's contents - you should get a clear picture of it's contents from that. Something like this (untested)... library(ncdf4) x <- nc_open(file.nc) x nc_close(x) While print lots of info about the file. Ben> On Mar 28, 2018, at 10:37 AM, Ahmed Attia <ahmedatia80 at gmail.com> wrote: > > Hi > > I have a netCDF file of volumetric soil water content at four > different soil layers and want to convert each soil layer in the > netCDF file to a GeoTIFF layer. This code converts the netCDF file to > one GeoTIFF layer, i.e. unclear which soil depth. > > file.nc <- "C:/Soil_Weather_data/Agro/VMC21/VMC21.nc" > > file.tiff <- "C:/Soil_Weather_data/Agro /VMC21/VMC21" > > importnetcdf <- raster(file.nc) > >> importnetcdf > class : RasterLayer > band : 1 (of 4 bands) > #the bands here are the four soil layers > dimensions : 16800, 43200, 725760000 (nrow, ncol, ncell) > resolution : 0.00833333, 0.00833333 (x, y) > extent : -180, 179.9998, -56, 83.99995 (xmin, xmax, ymin, ymax) > coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0 > data source : > C:\FAPSEP_Eucalyptus\FAPSEP\Soil_Weather_data\Agro_IBIS_Eucalipto\VMC21\VMC21.nc > names : Volumetric.water.content.at..33.kPa > z-value : 4.5 > zvar : VMC2 > > > > VMC1<-writeRaster(importnetcdf,filename="file.tiff",format="GTiff",overwrite=TRUE,bylayer=TRUE,suffix="1:4") > #bylayer=TRUE, did not work. > >> VMC1 > class : RasterLayer > dimensions : 16800, 43200, 725760000 (nrow, ncol, ncell) > resolution : 0.00833333, 0.00833333 (x, y) > extent : -180, 179.9998, -56, 83.99995 (xmin, xmax, ymin, ymax) > coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 > +towgs84=0,0,0 > data source : C:\Users\Ahmed\Documents\file.tif > names : file > values : 2, 80 (min, max) > > Any help! > > > Ahmed Attia, Ph.D. > Agronomist & Soil Scientist > > [[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. >Ben Tupper Bigelow Laboratory for Ocean Sciences 60 Bigelow Drive, P.O. Box 380 East Boothbay, Maine 04544 http://www.bigelow.org Tick Forecasting: https://eco.bigelow.org/ [[alternative HTML version deleted]]
Hi Ben, Adding 'band' to raster provided what I want; importnetcdf <- raster(file.nc,band=4) writeRaster(importnetcdf,file.tiff,"GTiff",overwrite=FALSE) Thanks for your help. Ahmed Ahmed Attia, Ph.D. Agronomist & Soil Scientist On Wed, Mar 28, 2018 at 11:53 AM, Ben Tupper <btupper at bigelow.org> wrote:> Hi Ahmed, > > When reading from a ncdf file you can use the 'varname', 'lvar' and > 'level' arguments - see the 'Details' section in the docs > > https://www.rdocumentation.org/packages/raster/versions/2.6- > 7/topics/raster > > We can't tell what is in the ncdf file from what you report other than it > has 4 bands (layers) and that the first is called ' > Volumetric.water.content.at..33.kPa' If you want to know more about the > what is in the file, then I suggest you use the ncdf4 package to open the > file and explore it's contents - you should get a clear picture of it's > contents from that. Something like this (untested)... > > library(ncdf4) > x <- nc_open(file.nc) > x > nc_close(x) > > While print lots of info about the file. > > Ben > > On Mar 28, 2018, at 10:37 AM, Ahmed Attia <ahmedatia80 at gmail.com> wrote: > > Hi > > I have a netCDF file of volumetric soil water content at four > different soil layers and want to convert each soil layer in the > netCDF file to a GeoTIFF layer. This code converts the netCDF file to > one GeoTIFF layer, i.e. unclear which soil depth. > > file.nc <- "C:/Soil_Weather_data/Agro/VMC21/VMC21.nc" > > file.tiff <- "C:/Soil_Weather_data/Agro /VMC21/VMC21" > > importnetcdf <- raster(file.nc) > > importnetcdf > > class : RasterLayer > band : 1 (of 4 bands) > #the bands here are the four soil layers > dimensions : 16800, 43200, 725760000 (nrow, ncol, ncell) > resolution : 0.00833333, 0.00833333 (x, y) > extent : -180, 179.9998, -56, 83.99995 (xmin, xmax, ymin, ymax) > coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0 > data source : > C:\FAPSEP_Eucalyptus\FAPSEP\Soil_Weather_data\Agro_IBIS_Euca > lipto\VMC21\VMC21.nc > names : Volumetric.water.content.at..33.kPa > z-value : 4.5 > zvar : VMC2 > > > > VMC1<-writeRaster(importnetcdf,filename="file.tiff",format=" > GTiff",overwrite=TRUE,bylayer=TRUE,suffix="1:4") > #bylayer=TRUE, did not work. > > VMC1 > > class : RasterLayer > dimensions : 16800, 43200, 725760000 (nrow, ncol, ncell) > resolution : 0.00833333, 0.00833333 (x, y) > extent : -180, 179.9998, -56, 83.99995 (xmin, xmax, ymin, ymax) > coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 > +towgs84=0,0,0 > data source : C:\Users\Ahmed\Documents\file.tif > names : file > values : 2, 80 (min, max) > > Any help! > > > Ahmed Attia, Ph.D. > Agronomist & Soil Scientist > > [[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/posti > ng-guide.html > and provide commented, minimal, self-contained, reproducible code. > > > Ben Tupper > Bigelow Laboratory for Ocean Sciences > 60 Bigelow Drive > <https://maps.google.com/?q=60+Bigelow+Drive&entry=gmail&source=g>, P.O. > Box 380 > East Boothbay, Maine 04544 > http://www.bigelow.org > > Tick Forecasting: https://eco.bigelow.org/ > > > > >[[alternative HTML version deleted]]