[GIS] Converting netCDF to geotiff file

gdalnetcdf

NetCDF files downloaded from NASA ocean color website could not be converted to geotiff using gdaltranslate command below:

 gdal_translate -ot float32 -unscale -CO COMPRESS=deflate NETCDF:"A2006001170000.L2_LAC_OC.x.nc":chlor_a fulldisk.tif

The error message is the following:

Warning 1: NetCDF driver detected file type=5, but libnetcdf detected type=3
Warning 1: NETCDF:A2006001170000.L2_LAC_OC.x.nc:chlor_a is a netCDF file, but chlor_a is not a variable.
ERROR 4: `NETCDF:A2006001170000.L2_LAC_OC.x.nc:chlor_a' does not exist in the file system, and is not recognized as a supported dataset name.

Is there any way of fixing the issue?

Best Answer

Try

gdal_translate -ot float32 -unscale -CO COMPRESS=deflate HDF5:"A2006001170000.L2_LAC_OC.nc"://geophysical_data/chlor_a fulldisk.tif

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[GIS] Converting a NetCDF file to GeoTIFF using GDAL

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

[GIS] Converting Sentinel-3 data (netcdf) to GeoTIFF

it's a bit old but here I am. Unfortunately GDAL does not fully support the NetCDF standard and Sentinel 3 netcdf are one of those unfortunate case.

The following is a simple script written in kotlin unsing the java bindings:

    println(" * Converting $prodName...")
    val wgs84 = SpatialReference()
    wgs84.ImportFromEPSG(4326)

    val lst = gdal.Open("NETCDF:$prodName/LST_in.nc:LST")
    val map = mapOf(
            "LINE_OFFSET" to "1", "LINE_STEP" to "1",
            "PIXEL_OFFSET" to "1", "PIXEL_STEP" to "1",
            "X_BAND" to "1", "X_DATASET" to "NETCDF:$prodName/geodetic_in.nc:longitude_in",
            "Y_BAND" to "1", "Y_DATASET" to "NETCDF:$prodName/geodetic_in.nc:latitude_in"
    )

    lst.SetMetadata(Hashtable(map), "GEOLOCATION")

    val warp = gdal.AutoCreateWarpedVRT(lst, wgs84.ExportToWkt())

    gdal.Translate("$prodName/lst.tif", warp, TranslateOptions( gdal.ParseCommandLine("-of gtiff -oo COMPRESS=LZW ") ) )

    println(" * Complete")

this perfectly works with Sentinel 1 OCN products, but with Sentinel 3 GDAL gives some strange errors while parsing the file:

Warning 1: NetCDF driver detected file type=5, but libnetcdf detected type=3
Warning 1: No UNIDATA NC_GLOBAL:Conventions attribute
Warning 1: NetCDF driver detected file type=5, but libnetcdf detected type=3
Warning 1: No UNIDATA NC_GLOBAL:Conventions attribute
Warning 1: NetCDF driver detected file type=5, but libnetcdf detected type=3
Warning 1: No UNIDATA NC_GLOBAL:Conventions attribute
ERROR 1: Too many points (441 out of 441) failed to transform, unable to compute output bounds.
ERROR 1: IReadBlock failed at X offset 2, Y offset 0
ERROR 1: GetBlockRef failed at X block offset 2, Y block offset 0

After some throubleshooting it seems that it does not automatically apply the scale factor and offset of each variable, and so he have to deal with raw lat-lon coordinates and he does not know what to do with it.

I hope this will get fixed soon

Best Answer

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[GIS] Converting a NetCDF file to GeoTIFF using GDAL

[GIS] Converting Sentinel-3 data (netcdf) to GeoTIFF

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