gdalwarp needs to stop (or pick one) when input filename has subdatasets

[mdsumner]

Example files here: ftp://eclipse.ncdc.noaa.gov/pub/OI-daily-v2/NetCDF/1981/AVHRR/

gdalwarp will crash if given a file name, rather than a subdataset path - I can't get a useable example with an sds string yet but sds and gdalinfo all good.

[edzer]

Thanks; I updated stuff and now seem to have this working:

library(stars)

st_gdalinfo("avhrr-only-v2.19810901.nc")

st_get_subdatasets("avhrr-only-v2.19810901.nc")
st_gdalinfo("NETCDF:avhrr-only-v2.19810901.nc:anom")

# gdalwarp -t_srs '+proj=utm +zone=11 +datum=WGS84' -overwrite NETCDF:avhrr-only-v2.19810901.nc:anom utm11.tif

st_gdalwarp("NETCDF:avhrr-only-v2.19810901.nc:anom", "utm11.tif")
st_gdalwarp("NETCDF:avhrr-only-v2.19810901.nc:anom", "utm11.tif", c("-t_srs", "+proj=utm +zone=11 +datum=WGS84"))

st_gdalrasterize("nc.gpkg", "nc.tif") # where nc.tif was generated by raster

Output:

> library(stars)
Linking to GDAL 2.1.3, proj.4 4.9.2
> 
> st_gdalinfo("avhrr-only-v2.19810901.nc")
Driver: netCDF/Network Common Data Format
Files: avhrr-only-v2.19810901.nc
Size is 512, 512
Coordinate System is `'
Metadata:
  NC_GLOBAL#Contact=Dick Reynolds, email: Richard.W.Reynolds@noaa.gov & Chunying Liu, email: Chunying.liu@noaa.gov
  NC_GLOBAL#Conventions=CF-1.0
  NC_GLOBAL#creation_date=2011-05-04
  NC_GLOBAL#History=Version 2.0
  NC_GLOBAL#Source=NOAA/National Climatic Data Center
  NC_GLOBAL#title=Daily-OI-V2, final, Data (Ship, Buoy, AVHRR, GSFC-ice)
Subdatasets:
  SUBDATASET_1_NAME=NETCDF:"avhrr-only-v2.19810901.nc":sst
  SUBDATASET_1_DESC=[1x1x720x1440] sst (16-bit integer)
  SUBDATASET_2_NAME=NETCDF:"avhrr-only-v2.19810901.nc":anom
  SUBDATASET_2_DESC=[1x1x720x1440] anom (16-bit integer)
  SUBDATASET_3_NAME=NETCDF:"avhrr-only-v2.19810901.nc":err
  SUBDATASET_3_DESC=[1x1x720x1440] err (16-bit integer)
  SUBDATASET_4_NAME=NETCDF:"avhrr-only-v2.19810901.nc":ice
  SUBDATASET_4_DESC=[1x1x720x1440] ice (16-bit integer)
Corner Coordinates:
Upper Left  (    0.0,    0.0)
Lower Left  (    0.0,  512.0)
Upper Right (  512.0,    0.0)
Lower Right (  512.0,  512.0)
Center      (  256.0,  256.0)
> 
> st_get_subdatasets("avhrr-only-v2.19810901.nc")
$SUBDATASET_1_NAME
[1] "NETCDF:\"avhrr-only-v2.19810901.nc\":sst"

$SUBDATASET_2_NAME
[1] "NETCDF:\"avhrr-only-v2.19810901.nc\":anom"

$SUBDATASET_3_NAME
[1] "NETCDF:\"avhrr-only-v2.19810901.nc\":err"

$SUBDATASET_4_NAME
[1] "NETCDF:\"avhrr-only-v2.19810901.nc\":ice"

> st_gdalinfo("NETCDF:avhrr-only-v2.19810901.nc:anom")
Driver: netCDF/Network Common Data Format
Files: avhrr-only-v2.19810901.nc
Size is 1440, 720
Coordinate System is `'
Origin = (0.000000000000000,90.000000000000000)
Pixel Size = (0.250000000000000,-0.250000000000000)
Metadata:
  anom#add_offset=0
  anom#long_name=Daily sea surface temperature anomalies
  anom#scale_factor=0.0099999998
  anom#units=degrees C
  anom#valid_max=1200
  anom#valid_min=-1200
  anom#_FillValue=-999
  lat#grids=Uniform grid from -89.875 to 89.875 by 0.25
  lat#long_name=Latitude
  lat#units=degrees_north
  lon#grids=Uniform grid from 0.125 to 359.875 by 0.25
  lon#long_name=Longitude
  lon#units=degrees_east
  NC_GLOBAL#Contact=Dick Reynolds, email: Richard.W.Reynolds@noaa.gov & Chunying Liu, email: Chunying.liu@noaa.gov
  NC_GLOBAL#Conventions=CF-1.0
  NC_GLOBAL#creation_date=2011-05-04
  NC_GLOBAL#History=Version 2.0
  NC_GLOBAL#Source=NOAA/National Climatic Data Center
  NC_GLOBAL#title=Daily-OI-V2, final, Data (Ship, Buoy, AVHRR, GSFC-ice)
  NETCDF_DIM_EXTRA={time,zlev}
  NETCDF_DIM_time_DEF={1,5}
  NETCDF_DIM_time_VALUES=1339
  NETCDF_DIM_zlev_DEF={1,5}
  NETCDF_DIM_zlev_VALUES=0
  time#long_name=Center time of the day
  time#units=days since 1978-01-01 00:00:00
  zlev#actual_range=0, 0
  zlev#long_name=Sea surface height
  zlev#units=meters
Corner Coordinates:
Upper Left  (   0.0000000,  90.0000000) 
Lower Left  (   0.0000000, -90.0000000) 
Upper Right (     360.000,      90.000) 
Lower Right (     360.000,     -90.000) 
Center      ( 180.0000000,   0.0000000) 
Band 1 Block=1440x1 Type=Int16, ColorInterp=Undefined
  NoData Value=-999
  Unit Type: degrees C
  Offset: 0,   Scale:0.00999999977648258
  Metadata:
    add_offset=0
    long_name=Daily sea surface temperature anomalies
    NETCDF_DIM_time=1339
    NETCDF_DIM_zlev=0
    NETCDF_VARNAME=anom
    scale_factor=0.0099999998
    units=degrees C
    valid_max=1200
    valid_min=-1200
    _FillValue=-999
> 
> # gdalwarp -t_srs '+proj=utm +zone=11 +datum=WGS84' -overwrite NETCDF:avhrr-only-v2.19810901.nc:anom utm11.tif
> 
> st_gdalwarp("NETCDF:avhrr-only-v2.19810901.nc:anom", "utm11.tif")
> st_gdalwarp("NETCDF:avhrr-only-v2.19810901.nc:anom", "utm11.tif", c("-t_srs", "+proj=utm +zone=11 +datum=WGS84"))
> 
> st_gdalrasterize("nc.gpkg", "nc.tif") # where nc.tif was generated by raster
> 

[mdsumner]

Looks good, cheers