Hi all,
I posted a question on GIS StackExchange
https://gis.stackexchange.com/questions/427504/problems-using-wcs-s-rangesubset-parameter-with-netcdf-coverage-views-in-geose
but thought I might reach additional experts here. Sorry if you are
pointed to this issue twice.
Below I pasted the content of the issue.
Thanks for any help and best regards,
Martin
--------------------------------------
*Use case*
My use case is to store environmental data downloaded from the
Copernicus Marine Environment Monitoring Service (CMEMS) as netCDF files
in GeoServer and make them available via Web Coverage Service using
GetCoverage requests. I would like to be able to apply spatial, temporal
and thematic subsetting. While spatial and temporal subsetting work
smoothly (with |subset| parameter), I have trouble using thematic
subsetting (with |rangesubset| parameter). Details are following below
after explaining my setup first.
*Setup*
I use GeoServer 2.18.3 as part of a GeoNode setup, however the problems
occur with GeoServer 2.18.2 and 2.20.3 outside of the GeoNode setup,
too. Along my GeoServer installation I installed the two extensions
netcdf and netcdf-out with the corresponding GeoServer version. In order
to use |scale_factor| correctly I added
|-Dorg.geotools.coverage.io.netcdf.enhance.ScaleMissing=true| to the
|JAVA_OPTS| environment variable.
I have created a netCDF store with an example netCDF file
(global-analysis-forecast-wav-001-027_20220101.nc, ~280 MB). Here is the
output of |ncdump -h|:
|netcdf global-analysis-forecast-wav-001-027_20220101 { dimensions: time
= 8 ; latitude = 2041 ; longitude = 4320 ; variables: short VHM0(time,
latitude, longitude) ; VHM0:_FillValue = -32767s ; VHM0:long_name =
"Spectral significant wave height (Hm0)" ; VHM0:units = "m" ;
VHM0:standard_name = "sea_surface_wave_significant_height" ;
VHM0:cell_methods = "time:point area:mean" ; VHM0:type_of_analysis =
"spectral analysis" ; VHM0:WMO_code = 100LL ; VHM0:_ChunkSizes = 1LL,
681LL, 1440LL ; VHM0:add_offset = 0. ; VHM0:scale_factor = 0.01 ; short
VMDR(time, latitude, longitude) ; VMDR:_FillValue = -32767s ;
VMDR:long_name = "Mean wave direction from (Mdir)" ; VMDR:units =
"degree" ; VMDR:standard_name = "sea_surface_wave_from_direction" ;
VMDR:cell_methods = "time:point area:mean" ; VMDR:type_of_analysis =
"spectral analysis" ; VMDR:WMO_code = 200LL ; VMDR:_ChunkSizes = 1LL,
681LL, 1440LL ; VMDR:add_offset = 180. ; VMDR:scale_factor = 0.01 ;
double longitude(longitude) ; longitude:_FillValue = NaN ;
longitude:standard_name = "longitude" ; longitude:long_name = "longitude
coordinate" ; longitude:units = "degrees_east" ; longitude:axis = "X" ;
longitude:step = 0.08332825 ; longitude:_ChunkSizes = 4320LL ; double
latitude(latitude) ; latitude:_FillValue = NaN ; latitude:standard_name
= "latitude" ; latitude:long_name = "latitude coordinate" ;
latitude:units = "degrees_north" ; latitude:axis = "Y" ; latitude:step =
0.08333588 ; latitude:_ChunkSizes = 2041LL ; double time(time) ;
time:_FillValue = NaN ; time:standard_name = "time" ; time:long_name =
"time" ; time:axis = "T" ; time:step = 3LL ; time:_ChunkSizes = 1LL ;
time:units = "hours since 1950-01-01" ; time:calendar = "standard" ; //
global attributes: :Conventions = "CF-1.6" ; :time_coverage_start =
"20220311-03:00:00" ; :time_coverage_end = "20220312-00:00:00" ;
:date_created = "20220302-07:35:00" ; :product_type = "forecast" ;
:product = "GLOBAL_ANALYSIS_FORECAST_WAV_001_027" ; :product_ref_date =
"20220302-00:00:00" ; :product_range = "D+9" ; :product_user_manual =
"http://marine.copernicus.eu/documents/PUM/CMEMS-GLO-PUM-001-027.pdf"; ;
:quality_information_document = "
http://marine.copernicus.eu/documents/QUID/CMEMS-GLO-QUID-001-027."; ;
:dataset = "global-analysis-forecast-wav-001-027" ; :title = "Mean
fields from global wave model MFWAM of Meteo-France with ECMWF forcing"
; :institution = "METEO-FRANCE" ; :references =
"http://marine.copernicus.eu"; ; :credit = "E.U. Copernicus Marine
Service Information (CMEMS)" ; :licence =
"http://marine.copernicus.eu/services-portfolio/service-commitments-and";
; :contact = "servicedesk.cm...@mercator-ocean.eu" ; :producer = "CMEMS
- Global Monitoring and Forecasting Centre" ; :area = "GLO" ;
:geospatial_lon_min = -180. ; :geospatial_lon_max = 179.9167 ;
:geospatial_lon_step = 0.08332825 ; :geospatial_lon_units = "degree" ;
:geospatial_lat_min = -80. ; :geospatial_lat_max = 90. ;
:geospatial_lat_step = 0.08333588 ; :geospatial_lat_units = "degree" ; } |
On top of this netCDF store I created a Coverage View including the two
variables (in this order: VHM0, VMDR) as bands. Because I would like to
use 10 or more variables in the end, I don’t want to use separate layers
for each variable. In order to serve a long (~several months/years) time
series of data I would like to use an ImageMosaic instead of a netCDF
store later, but as the problems are identical I stick to the simpler
case of a netCDF store in this post.
*Problem(s)*
If I use the Coverage View to make the following GetCoverage request
http://localhost/geoserver/geonode/wcs?service=WCS&version=2.0.1&request=GetCoverage&coverageid=geonode%3Aglobal-analysis-forecast-wav-001-027_20220101&rangesubset=VMDR&subset=Lat(40,50)&subset=Long(-10,0)&srs=EPSG%3A4326&format=application/x-netcdf4
I get a |java.lang.NullPointerException|:
|geoserver_n52_geonode | 30 Mar 13:53:39 INFO
[org.vfny.geoserver.servlets] - OutputStream was successfully aborted.
geoserver_n52_geonode | 30 Mar 13:53:39 ERROR [org.geoserver.ows] -
geoserver_n52_geonode | java.lang.NullPointerException
geoserver_n52_geonode | at
com.sun.media.jai.iterator.RandomIterFallback.makeCurrent(RandomIterFallback.java:110)
geoserver_n52_geonode | at
com.sun.media.jai.iterator.RandomIterFallback.getSampleDouble(RandomIterFallback.java:133)
geoserver_n52_geonode | at
org.geoserver.wcs.responses.AbstractNetCDFEncoder.setPixel(AbstractNetCDFEncoder.java:642)
geoserver_n52_geonode | at
org.geoserver.wcs.responses.DefaultNetCDFEncoder.writeDataValues(DefaultNetCDFEncoder.java:423)
geoserver_n52_geonode | at
org.geoserver.wcs.responses.AbstractNetCDFEncoder.write(AbstractNetCDFEncoder.java:482)
|
The full log with logging profile GEOTOOLS_DEVELOPER_LOGGING.properties
applied can be found here:
https://gist.github.com/MartinPontius/bd4ac2c6db4ac80f863c5bc298ba37ec
Interestingly with only the first band (VHM0) the server returns data
correctly (apart from some minor naming/metadata issues). Making a
request with both bands - i.e. using |&rangesubset=VMDR,VHM0| - returns
a netCDF file but only including one variable (always the first variable
in the |rangesubset| list). I would expect to get a netCDF file
containing both variables.
If I work with a different netCDF file
(https://github.com/GeoNode/geoserver-restconfig/blob/master/test/data/polyphemus_20120401.nc)
that is shown in some of the online examples (see
https://geoserver.geo-solutions.it/multidim/multidim/netcdf/netcdf_config.html
or
https://geoserver.geo-solutions.it/multidim/multidim/imagemosaic/mosaic_indexer.html,
actual file name is slightly different but should be very similar), the
server returns data for separate bands correctly (same minor
naming/metadata issues) - i.e. |&rangesubset=N02| or |&rangesubset=O3|.
However, if both bands are chosen - i.e. |&rangesubset=N02,O3| - it only
returns the first band again like with the other file.
Additional observations:
* Using separate layers for each variable instead of a single Coverage
View works
* In the Layer preview with OpenLayers, GetFeatureInfo shows the
correct values for both bands
* Increasing the memory that GeoServer and JAI are allowed to use and
removing WCS resource consumption limits didn’t help
* Changing netCDF version from 4 to 3 didn’t help
Is there a known limitation in using |rangesubset| parameter with netCDF
Coverage Views? Or do you have any idea what might be wrong with my
installation and/or configuration?
--
Martin Pontius
52°North Spatial Information Research GmbH
Martin-Luther-King-Weg 24
48155 Muenster, Germany
E-Mail:m.pont...@52north.org
Fon: +49-(0)-251/396371-41
Fax: +49-(0)-251/396371-11
https://52north.org/
Twitter: @FiveTwoN
Managing Directors: Dr. Benedikt Gräler, Dr. Simon Jirka, Matthes Rieke
Local Court Muenster HRB 10849
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