Converting a NetCDF file to GeoTIFF using GDAL?

Question

I have a NetCDF file which contains data for the number of rain days in the UK. I'd like to convert it to a GeoTIFF, but can't get GDAL correctly georeference it. See dumps from gdalinfo below.

I want a single band TIFF showing the "raindays_tmean_abs" variable. The "lat" and "lon" variables seem to have sensible min/max values to put the data over the UK, but when I convert it with gdal_translate it ends up off the west coast of Africa.

There is a warning about the first dimension not being a "Time or Vertical" dimension. I read that gdal expects the data to be in a certain order, so maybe this is the problem, but I don't know how to modify it.

How do I convert/reproject this data?

gdalinfo NETCDF:RainDays1_1961-1990_LTA_25km.nc

Warning 1: dimension #0 (meaning_period) is not a Time or Vertical dimension.
Driver: netCDF/Network Common Data Format
Files: RainDays1_1961-1990_LTA_25km.nc
 RainDays1_1961-1990_LTA_25km.nc.aux.xml
Size is 39, 52
Coordinate System is `'
Origin = (-17.650008352179277,11.329999312758446)
Pixel Size = (0.219999614514803,-0.219999998807907)
Metadata:
 axis_0#units=
 meaning_period#comment=Meaning periods are all months (12) beginning January, all seasons (4) beginning Winter (DJF) and Annual (1)
 meaning_period#long_name=meaning_period
 meaning_period#units=
 NC_GLOBAL#Conventions=CF-1.0
 NETCDF_DIM_EXTRA={meaning_period}
 NETCDF_DIM_meaning_period_DEF={17,6}
 NETCDF_DIM_meaning_period_VALUES={0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16}
 raindays_tmean_abs#comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 raindays_tmean_abs#coordinates=lon lat
 raindays_tmean_abs#long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 raindays_tmean_abs#missing_value=1e+020
 raindays_tmean_abs#name=rain_days
 raindays_tmean_abs#title=rain_days
 raindays_tmean_abs#units=days
 rlat#axis=Y
 rlat#bounds=bounds_rlat
 rlat#long_name=latitude in rotated pole grid
 rlat#standard_name=grid_latitude
 rlat#units=degrees
 rlon#axis=X
 rlon#bounds=bounds_rlon
 rlon#long_name=longitude in rotated pole grid
 rlon#modulo=360
 rlon#standard_name=grid_longitude
 rlon#topology=circular
 rlon#units=degrees
Subdatasets:
 SUBDATASET_1_NAME=NETCDF:"RainDays1_1961-1990_LTA_25km.nc":bounds_rlat
 SUBDATASET_1_DESC=[52x2] bounds_rlat (64-bit floating-point)
 SUBDATASET_2_NAME=NETCDF:"RainDays1_1961-1990_LTA_25km.nc":bounds_rlon
 SUBDATASET_2_DESC=[39x2] bounds_rlon (64-bit floating-point)
 SUBDATASET_3_NAME=NETCDF:"RainDays1_1961-1990_LTA_25km.nc":lat
 SUBDATASET_3_DESC=[52x39] latitude (32-bit floating-point)
 SUBDATASET_4_NAME=NETCDF:"RainDays1_1961-1990_LTA_25km.nc":lon
 SUBDATASET_4_DESC=[52x39] longitude (32-bit floating-point)
 SUBDATASET_5_NAME=NETCDF:"RainDays1_1961-1990_LTA_25km.nc":raindays_tmean_abs
 SUBDATASET_5_DESC=[17x52x39] raindays_tmean_abs (32-bit floating-point)
Geolocation:
 LINE_OFFSET=0
 LINE_STEP=1
 PIXEL_OFFSET=0
 PIXEL_STEP=1
 SRS=GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],TOWGS84[0,0,0,0,0,0,0],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9108"]],AUTHORITY["EPSG","4326"]]
 X_BAND=1
 X_DATASET=NETCDF:"RainDays1_1961-1990_LTA_25km.nc":lon
 Y_BAND=1
 Y_DATASET=NETCDF:"RainDays1_1961-1990_LTA_25km.nc":lat
Corner Coordinates:
Upper Left ( -17.6500084, 11.3299993) 
Lower Left ( -17.6500084, -0.1100006) 
Upper Right ( -9.0700234, 11.3299993) 
Lower Right ( -9.0700234, -0.1100006) 
Center ( -13.3600159, 5.6099993) 
Band 1 Block=39x1 Type=Float32, ColorInterp=Undefined
 Min=10.658 Max=22.949 
 Minimum=10.658, Maximum=22.949, Mean=15.625, StdDev=3.151
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=0
 NETCDF_VARNAME=raindays_tmean_abs
 STATISTICS_MAXIMUM=22.949373245239
 STATISTICS_MEAN=15.624619410087
 STATISTICS_MINIMUM=10.657625198364
 STATISTICS_STDDEV=3.1508820627895
 title=rain_days
 units=days
Band 2 Block=39x1 Type=Float32, ColorInterp=Undefined
 Min=7.893 Max=17.172 
 Minimum=7.893, Maximum=17.172, Mean=11.591, StdDev=2.282
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=1
 NETCDF_VARNAME=raindays_tmean_abs
 STATISTICS_MAXIMUM=17.172254562378
 STATISTICS_MEAN=11.591275386767
 STATISTICS_MINIMUM=7.8926663398743
 STATISTICS_STDDEV=2.28225356537
 title=rain_days
 units=days
Band 3 Block=39x1 Type=Float32, ColorInterp=Undefined
 Min=9.700 Max=21.762 
 Minimum=9.700, Maximum=21.762, Mean=13.882, StdDev=2.988
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=2
 NETCDF_VARNAME=raindays_tmean_abs
 STATISTICS_MAXIMUM=21.761842727661
 STATISTICS_MEAN=13.88236379732
 STATISTICS_MINIMUM=9.7001943588257
 STATISTICS_STDDEV=2.9875935432638
 title=rain_days
 units=days
Band 4 Block=39x1 Type=Float32, ColorInterp=Undefined
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=3
 NETCDF_VARNAME=raindays_tmean_abs
 title=rain_days
 units=days
Band 5 Block=39x1 Type=Float32, ColorInterp=Undefined
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=4
 NETCDF_VARNAME=raindays_tmean_abs
 title=rain_days
 units=days
Band 6 Block=39x1 Type=Float32, ColorInterp=Undefined
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=5
 NETCDF_VARNAME=raindays_tmean_abs
 title=rain_days
 units=days
Band 7 Block=39x1 Type=Float32, ColorInterp=Undefined
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=6
 NETCDF_VARNAME=raindays_tmean_abs
 title=rain_days
 units=days
Band 8 Block=39x1 Type=Float32, ColorInterp=Undefined
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=7
 NETCDF_VARNAME=raindays_tmean_abs
 title=rain_days
 units=days
Band 9 Block=39x1 Type=Float32, ColorInterp=Undefined
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=8
 NETCDF_VARNAME=raindays_tmean_abs
 title=rain_days
 units=days
Band 10 Block=39x1 Type=Float32, ColorInterp=Undefined
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=9
 NETCDF_VARNAME=raindays_tmean_abs
 title=rain_days
 units=days
Band 11 Block=39x1 Type=Float32, ColorInterp=Undefined
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=10
 NETCDF_VARNAME=raindays_tmean_abs
 title=rain_days
 units=days
Band 12 Block=39x1 Type=Float32, ColorInterp=Undefined
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=11
 NETCDF_VARNAME=raindays_tmean_abs
 title=rain_days
 units=days
Band 13 Block=39x1 Type=Float32, ColorInterp=Undefined
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=12
 NETCDF_VARNAME=raindays_tmean_abs
 title=rain_days
 units=days
Band 14 Block=39x1 Type=Float32, ColorInterp=Undefined
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=13
 NETCDF_VARNAME=raindays_tmean_abs
 title=rain_days
 units=days
Band 15 Block=39x1 Type=Float32, ColorInterp=Undefined
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=14
 NETCDF_VARNAME=raindays_tmean_abs
 title=rain_days
 units=days
Band 16 Block=39x1 Type=Float32, ColorInterp=Undefined
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=15
 NETCDF_VARNAME=raindays_tmean_abs
 title=rain_days
 units=days
Band 17 Block=39x1 Type=Float32, ColorInterp=Undefined
 NoData Value=1.0000000200408773e+020
 Metadata:
 comment=Converted from UKCP09 monthly data to climatologies and then averaged to 25km rotated pole grid.
 coordinates=lon lat
 long_name=Number of days per meaning period having a rainfall >= 1 mm (days)
 missing_value=1e+020
 name=rain_days
 NETCDF_DIM_meaning_period=16
 NETCDF_VARNAME=raindays_tmean_abs
 title=rain_days
 units=days

gdalinfo NETCDF:RainDays1_1961-1990_LTA_25km.nc:lon

Driver: netCDF/Network Common Data Format
Files: RainDays1_1961-1990_LTA_25km.nc
 RainDays1_1961-1990_LTA_25km.nc.aux.xml
Size is 39, 52
Coordinate System is `'
Origin = (-17.650008352179277,11.329999312758446)
Pixel Size = (0.219999614514803,-0.219999998807907)
Metadata:
 axis_0#units=
 lon#long_name=longitude
 lon#missing_value=1e+020
 lon#name=lon
 lon#standard_name=longitude
 lon#units=degrees_east
 meaning_period#comment=Meaning periods are all months (12) beginning January, all seasons (4) beginning Winter (DJF) and Annual (1)
 meaning_period#long_name=meaning_period
 meaning_period#units=
 NC_GLOBAL#Conventions=CF-1.0
 rlat#axis=Y
 rlat#bounds=bounds_rlat
 rlat#long_name=latitude in rotated pole grid
 rlat#standard_name=grid_latitude
 rlat#units=degrees
 rlon#axis=X
 rlon#bounds=bounds_rlon
 rlon#long_name=longitude in rotated pole grid
 rlon#modulo=360
 rlon#standard_name=grid_longitude
 rlon#topology=circular
 rlon#units=degrees
Corner Coordinates:
Upper Left ( -17.6500084, 11.3299993) 
Lower Left ( -17.6500084, -0.1100006) 
Upper Right ( -9.0700234, 11.3299993) 
Lower Right ( -9.0700234, -0.1100006) 
Center ( -13.3600159, 5.6099993) 
Band 1 Block=39x1 Type=Float32, ColorInterp=Undefined
 Min=-15.830 Max=3.672 
 Minimum=-15.830, Maximum=3.672, Mean=-5.246, StdDev=4.393
 NoData Value=1.0000000200408773e+020
 Metadata:
 long_name=longitude
 missing_value=1e+020
 name=lon
 NETCDF_VARNAME=lon
 standard_name=longitude
 STATISTICS_MAXIMUM=3.671746969223
 STATISTICS_MEAN=-5.2457962955782
 STATISTICS_MINIMUM=-15.830010414124
 STATISTICS_STDDEV=4.3927366732513
 units=degrees_east

gdalinfo NETCDF:RainDays1_1961-1990_LTA_25km.nc:lat

Driver: netCDF/Network Common Data Format
Files: RainDays1_1961-1990_LTA_25km.nc
 RainDays1_1961-1990_LTA_25km.nc.aux.xml
Size is 39, 52
Coordinate System is `'
Origin = (-17.650008352179277,11.329999312758446)
Pixel Size = (0.219999614514803,-0.219999998807907)
Metadata:
 axis_0#units=
 lat#long_name=latitude
 lat#missing_value=1e+020
 lat#name=lat
 lat#standard_name=latitude
 lat#units=degrees_north
 meaning_period#comment=Meaning periods are all months (12) beginning January, all seasons (4) beginning Winter (DJF) and Annual (1)
 meaning_period#long_name=meaning_period
 meaning_period#units=
 NC_GLOBAL#Conventions=CF-1.0
 rlat#axis=Y
 rlat#bounds=bounds_rlat
 rlat#long_name=latitude in rotated pole grid
 rlat#standard_name=grid_latitude
 rlat#units=degrees
 rlon#axis=X
 rlon#bounds=bounds_rlon
 rlon#long_name=longitude in rotated pole grid
 rlon#modulo=360
 rlon#standard_name=grid_longitude
 rlon#topology=circular
 rlon#units=degrees
Corner Coordinates:
Upper Left ( -17.6500084, 11.3299993) 
Lower Left ( -17.6500084, -0.1100006) 
Upper Right ( -9.0700234, 11.3299993) 
Lower Right ( -9.0700234, -0.1100006) 
Center ( -13.3600159, 5.6099993) 
Band 1 Block=39x1 Type=Float32, ColorInterp=Undefined
 Min=47.594 Max=60.806 
 Minimum=47.594, Maximum=60.806, Mean=54.186, StdDev=3.229
 NoData Value=1.0000000200408773e+020
 Metadata:
 long_name=latitude
 missing_value=1e+020
 name=lat
 NETCDF_VARNAME=lat
 standard_name=latitude
 STATISTICS_MAXIMUM=60.805950164795
 STATISTICS_MEAN=54.185836173138
 STATISTICS_MINIMUM=47.594329833984
 STATISTICS_STDDEV=3.228754901642
 units=degrees_north

Answer 1

Your netcdf uses a rotated pole grid. GDAL is not able to handle that.

There is a ticket for it: http://trac.osgeo.org/gdal/ticket/4285 which gives some workaround.

GMT has a tool called grdrotater which should be able to work with rotated poles, but I have not yet used it.

If you are used to GRASS, you can try this workaround:

http://osgeo-org.1560.x6.nabble.com/NetCDF-rotated-pole-td4634232.html

Answer 2

Try to convert it with gdal_translate.

Normally it should work by using one of the two possibilities:

First solution: extract every subdataset manually

gdal_translate -of VRT NETCDF:"RainDays1_1961-1990_LTA_25km.nc":raindays_tmean_abs output_RD.vrt 
gdal_translate -of VRT NETCDF:"RainDays1_1961-1990_LTA_25km.nc":lat output_lat.vrt 
gdal_translate -of VRT NETCDF:"RainDays1_1961-1990_LTA_25km.nc":lon output_lon.vrt

Second solution: let gdal extract the subdatasets automatically

gdal_translate -of VRT -sds RainDays1_1961-1990_LTA_25km.nc output.vrt

The second solution will extract all subdatasets to separate files.

It may be necessary to include the

-a_srs epsg:4326

flag

Answer 3

Your pixel size is different in your files, GDAL complains about that, see:

• http://lists.osgeo.org/pipermail/gdal-dev/2005-November/007148.html
• http://lists.osgeo.org/pipermail/gdal-dev/2005-November/007149.html
• http://lists.osgeo.org/pipermail/gdal-dev/2005-November/007194.html

Afaik, you need to have an equal pixel size. You would need to resample your grid for that or redo the grid from scratch. GMT is a nice tool for that.