Netcdf import error - Netcdf supported formats?

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Netcdf import error - Netcdf supported formats?

lennert.schepers

Dear Geoserver Users list

 

I’m looking for a way to upload our Netcdf files with the Netcdf-plugin to GeoServer (Version 2.11.5).

The plugin works well with with CF and COARDS sample data from https://www.unidata.ucar.edu/software/netcdf/examples/files.html

 

However, when I try to upload our own Netcdf files, I receive an error when saving the store.

Could not list layers for this store, an error occurred retrieving them: Failed to create reader from file:coverages/testLennertS/log.x5.20132013.0103.10001.10001.anl.nc and hints null

 

Ncdump:

netcdf log.x5.20132013.0103.10001.10001.anl {

dimensions:

        lon = 950 ;

        lat = 400 ;

        depth = 1 ;

        time = 1 ;

        nv = 2 ;

variables:

        float lon(lon) ;

                lon:units = "degrees_east" ;

        float lat(lat) ;

                lat:units = "degrees_north" ;

        float depth(depth) ;

                depth:units = "meters" ;

                depth:positive = "down" ;

        float time(time) ;

                time:units = "Days since 2013-01-01" ;

                time:climatology = "climatology_bounds" ;

        float climatology_bounds(time, nv) ;

        float CORRLEN(time, depth) ;

                CORRLEN:long_name = "Correlation Length" ;

                CORRLEN:units = "degrees_north" ;

        float SNR(time, depth) ;

                SNR:long_name = "Signal to Noise" ;

        float VARBACK(time, depth) ;

                VARBACK:long_name = "Background Field Variance" ;

                VARBACK:units = "logab^2" ;

        float log.x5(time, depth, lat, lon) ;

                log.x5:long_name = "log.x5" ;

                log.x5:units = "logab" ;

                log.x5:valid_min = -0.7f ;

                log.x5:valid_max = 5.8f ;

                log.x5:_FillValue = -99.f ;

                log.x5:cell_methods = "timebins" ;

                log.x5:missing_value = -99.f ;

        float log.x5_err(time, depth, lat, lon) ;

                log.x5_err:long_name = "Error standard deviation of log.x5" ;

                log.x5_err:units = "logab" ;

                log.x5_err:valid_min = 0.f ;

                log.x5_err:valid_max = 0.69f ;

                log.x5_err:_FillValue = -99.f ;

                log.x5_err:missing_value = -99.f ;

        float log.x5_L1(time, depth, lat, lon) ;

                log.x5_L1:long_name = "log.x5 masked using relative error threshold 0.3" ;

                log.x5_L1:units = "logab" ;

                log.x5_L1:valid_min = -0.4f ;

                log.x5_L1:valid_max = 5.8f ;

                log.x5_L1:_FillValue = -99.f ;

                log.x5_L1:missing_value = -99.f ;

        float log.x5_L2(time, depth, lat, lon) ;

                log.x5_L2:long_name = "log.x5 masked using relative error threshold 0.5" ;

                log.x5_L2:units = "logab" ;

                log.x5_L2:valid_min = -0.4f ;

                log.x5_L2:valid_max = 5.8f ;

                log.x5_L2:_FillValue = -99.f ;

                log.x5_L2:missing_value = -99.f ;

        float log.x5_relerr(time, depth, lat, lon) ;

                log.x5_relerr:long_name = "Relative error of log.x5" ;

                log.x5_relerr:valid_min = 0.f ;

                log.x5_relerr:valid_max = 1.f ;

                log.x5_relerr:_FillValue = -99.f ;

                log.x5_relerr:missing_value = -99.f ;

        float databins(time, depth, lat, lon) ;

                databins:long_name = "Logarithm10 of number of data in bins" ;

                databins:valid_min = 0.f ;

                databins:valid_max = 0.7f ;

                databins:_FillValue = -99.f ;

                databins:missing_value = -99.f ;

        float outlbins(time, depth, lat, lon) ;

                outlbins:long_name = "Logarithm10 of number of outliers data in bins" ;

                outlbins:valid_min = 0.f ;

                outlbins:valid_max = -99.f ;

                outlbins:_FillValue = -99.f ;

                outlbins:missing_value = -99.f ;

        float CLfield(time, depth, lat, lon) ;

                CLfield:long_name = "Correlation length field" ;

                CLfield:valid_min = 0.f ;

                CLfield:valid_max = 1.5f ;

                CLfield:_FillValue = -99.f ;

                CLfield:missing_value = -99.f ;

        float log.x5_deepest(time, lat, lon) ;

                log.x5_deepest:long_name = "Deepest values of log.x5" ;

                log.x5_deepest:units = "logab" ;

                log.x5_deepest:valid_min = -0.7f ;

                log.x5_deepest:valid_max = 5.8f ;

                log.x5_deepest:_FillValue = -99.f ;

                log.x5_deepest:missing_value = -99.f ;

        float log.x5_deepest_L1(time, lat, lon) ;

                log.x5_deepest_L1:long_name = "Deepest values of log.x5 masked using relative error threshold 0.3" ;

                log.x5_deepest_L1:units = "logab" ;

                log.x5_deepest_L1:valid_min = -0.4f ;

                log.x5_deepest_L1:valid_max = 5.8f ;

                log.x5_deepest_L1:_FillValue = -99.f ;

                log.x5_deepest_L1:missing_value = -99.f ;

        float log.x5_deepest_L2(time, lat, lon) ;

                log.x5_deepest_L2:long_name = "Deepest values of log.x5 masked using relative error threshold 0.5" ;

                log.x5_deepest_L2:units = "logab" ;

                log.x5_deepest_L2:valid_min = -0.4f ;

                log.x5_deepest_L2:valid_max = 5.8f ;

                log.x5_deepest_L2:_FillValue = -99.f ;

                log.x5_deepest_L2:missing_value = -99.f ;

 

// global attributes:

                :Conventions = "CF-1.0" ;

                :project = "SeaDataNetII" ;

                :institution = "SAHFOS" ;

                :production = "Flanders Marine Institute" ;

                :data_access = "GHER OPENDAB:;

                :WEB_visualisation = "" ;

                :Author_e-mail = "***" ;

                :date = "2015-11-25 04:21:30.00" ;

                :title = "Diva analysis" ;

                :file_name = "../output/3Danalysis/log.x5.20132013.0103.10001.10001.anl.nc" ;

                :source = "SAHFOS" ;

                :comment = "No comment" ;

}

 

Part of the log error:

2018-07-04 17:16:08,825 DEBUG [geoserver.config] - Persisting coverage store log.x5.20132013.0103.10001.10001.anl.nc

2018-07-04 17:16:08,827 DEBUG [geoserver.config] - Persisted com.sun.proxy.$Proxy17 to workspaces/testLennertS/log.x5.20132013.0103.10001.10001.anl.nc/coveragestore.xml

2018-07-04 17:16:08,828 DEBUG [geoserver.config] - Persisted com.sun.proxy.$Proxy22 to global.xml

2018-07-04 17:16:08,834 TRACE [geotools.factory] - ENTRY  (GridCoverageFactory)

2018-07-04 17:16:08,834 TRACE [geotools.factory] - RETURN (GridCoverageFactory): found implementation GridCoverageFactory.

2018-07-04 17:16:08,834 DEBUG [io.netcdf] - Provided URL is a file

2018-07-04 17:16:08,834 DEBUG [imageio.netcdf] - Found a valid FileImageInputStream

2018-07-04 17:16:08,840 DEBUG [imageio.netcdf] - File successfully opened

2018-07-04 17:16:08,851 DEBUG [geotools.jdbc] - CREATE CONNECTION

2018-07-04 17:16:08,948 DEBUG [geotools.jdbc] - CLOSE CONNECTION

2018-07-04 17:16:08,948 DEBUG [geotools.jdbc] - CREATE CONNECTION

2018-07-04 17:16:08,950 DEBUG [geotools.jdbc] - CLOSE CONNECTION

2018-07-04 17:16:08,951 DEBUG [io.catalog] - BBOXFilterExtractor::extractBasicProperties(): Problems when opening the index, no typenames for the schema are defined

2018-07-04 17:16:08,952 WARN [netcdf.NetCDFFormat] - Unable to connect

 

I looked up the documentation for netcdf files and this maillist archive, and tried different things, for example to explicitly add the ‘nv’ dimension as a variable (now ‘nv’ is only a dimension), but without success.

 

Does anyone know what (part) of my netcdf files are currently not supported?

Or where can I find more information?

 

Thanks a lot

Lennert Schepers

 


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Re: Netcdf import error - Netcdf supported formats?

Daniele Romagnoli-3
Dear Lennert,
do you have any chance to share one of these samples? (eventually, even through a private email).
If that's not an option, even a small sample dataset with "fake" values reporting the same problem should be fine for a quick check.

Best Regards,
Daniele



On Thu, Jul 5, 2018 at 5:55 PM, Lennert Schepers <[hidden email]> wrote:

Dear Geoserver Users list

 

I’m looking for a way to upload our Netcdf files with the Netcdf-plugin to GeoServer (Version 2.11.5).

The plugin works well with with CF and COARDS sample data from https://www.unidata.ucar.edu/software/netcdf/examples/files.html

 

However, when I try to upload our own Netcdf files, I receive an error when saving the store.

Could not list layers for this store, an error occurred retrieving them: Failed to create reader from file:coverages/testLennertS/log.x5.20132013.0103.10001.10001.anl.nc and hints null

 

Ncdump:

netcdf log.x5.20132013.0103.10001.10001.anl {

dimensions:

        lon = 950 ;

        lat = 400 ;

        depth = 1 ;

        time = 1 ;

        nv = 2 ;

variables:

        float lon(lon) ;

                lon:units = "degrees_east" ;

        float lat(lat) ;

                lat:units = "degrees_north" ;

        float depth(depth) ;

                depth:units = "meters" ;

                depth:positive = "down" ;

        float time(time) ;

                time:units = "Days since 2013-01-01" ;

                time:climatology = "climatology_bounds" ;

        float climatology_bounds(time, nv) ;

        float CORRLEN(time, depth) ;

                CORRLEN:long_name = "Correlation Length" ;

                CORRLEN:units = "degrees_north" ;

        float SNR(time, depth) ;

                SNR:long_name = "Signal to Noise" ;

        float VARBACK(time, depth) ;

                VARBACK:long_name = "Background Field Variance" ;

                VARBACK:units = "logab^2" ;

        float log.x5(time, depth, lat, lon) ;

                log.x5:long_name = "log.x5" ;

                log.x5:units = "logab" ;

                log.x5:valid_min = -0.7f ;

                log.x5:valid_max = 5.8f ;

                log.x5:_FillValue = -99.f ;

                log.x5:cell_methods = "timebins" ;

                log.x5:missing_value = -99.f ;

        float log.x5_err(time, depth, lat, lon) ;

                log.x5_err:long_name = "Error standard deviation of log.x5" ;

                log.x5_err:units = "logab" ;

                log.x5_err:valid_min = 0.f ;

                log.x5_err:valid_max = 0.69f ;

                log.x5_err:_FillValue = -99.f ;

                log.x5_err:missing_value = -99.f ;

        float log.x5_L1(time, depth, lat, lon) ;

                log.x5_L1:long_name = "log.x5 masked using relative error threshold 0.3" ;

                log.x5_L1:units = "logab" ;

                log.x5_L1:valid_min = -0.4f ;

                log.x5_L1:valid_max = 5.8f ;

                log.x5_L1:_FillValue = -99.f ;

                log.x5_L1:missing_value = -99.f ;

        float log.x5_L2(time, depth, lat, lon) ;

                log.x5_L2:long_name = "log.x5 masked using relative error threshold 0.5" ;

                log.x5_L2:units = "logab" ;

                log.x5_L2:valid_min = -0.4f ;

                log.x5_L2:valid_max = 5.8f ;

                log.x5_L2:_FillValue = -99.f ;

                log.x5_L2:missing_value = -99.f ;

        float log.x5_relerr(time, depth, lat, lon) ;

                log.x5_relerr:long_name = "Relative error of log.x5" ;

                log.x5_relerr:valid_min = 0.f ;

                log.x5_relerr:valid_max = 1.f ;

                log.x5_relerr:_FillValue = -99.f ;

                log.x5_relerr:missing_value = -99.f ;

        float databins(time, depth, lat, lon) ;

                databins:long_name = "Logarithm10 of number of data in bins" ;

                databins:valid_min = 0.f ;

                databins:valid_max = 0.7f ;

                databins:_FillValue = -99.f ;

                databins:missing_value = -99.f ;

        float outlbins(time, depth, lat, lon) ;

                outlbins:long_name = "Logarithm10 of number of outliers data in bins" ;

                outlbins:valid_min = 0.f ;

                outlbins:valid_max = -99.f ;

                outlbins:_FillValue = -99.f ;

                outlbins:missing_value = -99.f ;

        float CLfield(time, depth, lat, lon) ;

                CLfield:long_name = "Correlation length field" ;

                CLfield:valid_min = 0.f ;

                CLfield:valid_max = 1.5f ;

                CLfield:_FillValue = -99.f ;

                CLfield:missing_value = -99.f ;

        float log.x5_deepest(time, lat, lon) ;

                log.x5_deepest:long_name = "Deepest values of log.x5" ;

                log.x5_deepest:units = "logab" ;

                log.x5_deepest:valid_min = -0.7f ;

                log.x5_deepest:valid_max = 5.8f ;

                log.x5_deepest:_FillValue = -99.f ;

                log.x5_deepest:missing_value = -99.f ;

        float log.x5_deepest_L1(time, lat, lon) ;

                log.x5_deepest_L1:long_name = "Deepest values of log.x5 masked using relative error threshold 0.3" ;

                log.x5_deepest_L1:units = "logab" ;

                log.x5_deepest_L1:valid_min = -0.4f ;

                log.x5_deepest_L1:valid_max = 5.8f ;

                log.x5_deepest_L1:_FillValue = -99.f ;

                log.x5_deepest_L1:missing_value = -99.f ;

        float log.x5_deepest_L2(time, lat, lon) ;

                log.x5_deepest_L2:long_name = "Deepest values of log.x5 masked using relative error threshold 0.5" ;

                log.x5_deepest_L2:units = "logab" ;

                log.x5_deepest_L2:valid_min = -0.4f ;

                log.x5_deepest_L2:valid_max = 5.8f ;

                log.x5_deepest_L2:_FillValue = -99.f ;

                log.x5_deepest_L2:missing_value = -99.f ;

 

// global attributes:

                :Conventions = "CF-1.0" ;

                :project = "SeaDataNetII" ;

                :institution = "SAHFOS" ;

                :production = "Flanders Marine Institute" ;

                :data_access = "GHER OPENDAB:;

                :WEB_visualisation = "" ;

                :Author_e-mail = "***" ;

                :date = "2015-11-25 04:21:30.00" ;

                :title = "Diva analysis" ;

                :file_name = "../output/3Danalysis/log.x5.20132013.0103.10001.10001.anl.nc" ;

                :source = "SAHFOS" ;

                :comment = "No comment" ;

}

 

Part of the log error:

2018-07-04 17:16:08,825 DEBUG [geoserver.config] - Persisting coverage store log.x5.20132013.0103.10001.10001.anl.nc

2018-07-04 17:16:08,827 DEBUG [geoserver.config] - Persisted com.sun.proxy.$Proxy17 to workspaces/testLennertS/log.x5.20132013.0103.10001.10001.anl.nc/coveragestore.xml

2018-07-04 17:16:08,828 DEBUG [geoserver.config] - Persisted com.sun.proxy.$Proxy22 to global.xml

2018-07-04 17:16:08,834 TRACE [geotools.factory] - ENTRY  (GridCoverageFactory)

2018-07-04 17:16:08,834 TRACE [geotools.factory] - RETURN (GridCoverageFactory): found implementation GridCoverageFactory.

2018-07-04 17:16:08,834 DEBUG [io.netcdf] - Provided URL is a file

2018-07-04 17:16:08,834 DEBUG [imageio.netcdf] - Found a valid FileImageInputStream

2018-07-04 17:16:08,840 DEBUG [imageio.netcdf] - File successfully opened

2018-07-04 17:16:08,851 DEBUG [geotools.jdbc] - CREATE CONNECTION

2018-07-04 17:16:08,948 DEBUG [geotools.jdbc] - CLOSE CONNECTION

2018-07-04 17:16:08,948 DEBUG [geotools.jdbc] - CREATE CONNECTION

2018-07-04 17:16:08,950 DEBUG [geotools.jdbc] - CLOSE CONNECTION

2018-07-04 17:16:08,951 DEBUG [io.catalog] - BBOXFilterExtractor::extractBasicProperties(): Problems when opening the index, no typenames for the schema are defined

2018-07-04 17:16:08,952 WARN [netcdf.NetCDFFormat] - Unable to connect

 

I looked up the documentation for netcdf files and this maillist archive, and tried different things, for example to explicitly add the ‘nv’ dimension as a variable (now ‘nv’ is only a dimension), but without success.

 

Does anyone know what (part) of my netcdf files are currently not supported?

Or where can I find more information?

 

Thanks a lot

Lennert Schepers

 


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_______________________________________________
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Please make sure you read the following two resources before posting to this list:
- Earning your support instead of buying it, but Ian Turton: http://www.ianturton.com/talks/foss4g.html#/
- The GeoServer user list posting guidelines: http://geoserver.org/comm/userlist-guidelines.html

If you want to request a feature or an improvement, also see this: https://github.com/geoserver/geoserver/wiki/Successfully-requesting-and-integrating-new-features-and-improvements-in-GeoServer


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--
Regards,
Daniele Romagnoli
==
GeoServer Professional Services from the experts! Visit http://goo.gl/it488V for more information.
==

Ing. Daniele Romagnoli
Senior Software Engineer

GeoSolutions S.A.S.
Via di Montramito 3/A
55054  Massarosa (LU)
Italy
phone: +39 0584 962313
fax:      +39 0584 1660272


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- The GeoServer user list posting guidelines: http://geoserver.org/comm/userlist-guidelines.html

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Re: Netcdf import error - Netcdf supported formats?

lennert.schepers

Hi Daniele

Sure, you can download two files here:

https://drive.google.com/drive/folders/1IKz-KVSmGLfCEsh30J4xg0lEB3kLkpM-?usp=sharing

 

Thanks a lot for your help!

Lennert

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Daniele Romagnoli
Sent: Friday, July 6, 2018 3:35 PM
To: Lennert Schepers <[hidden email]>
Cc: [hidden email]
Subject: Re: [Geoserver-users] Netcdf import error - Netcdf supported formats?

 

Dear Lennert,

do you have any chance to share one of these samples? (eventually, even through a private email).

If that's not an option, even a small sample dataset with "fake" values reporting the same problem should be fine for a quick check.

 

Best Regards,

Daniele

 

 

 

On Thu, Jul 5, 2018 at 5:55 PM, Lennert Schepers <[hidden email]> wrote:

Dear Geoserver Users list

 

I’m looking for a way to upload our Netcdf files with the Netcdf-plugin to GeoServer (Version 2.11.5).

The plugin works well with with CF and COARDS sample data from https://www.unidata.ucar.edu/software/netcdf/examples/files.html

 

However, when I try to upload our own Netcdf files, I receive an error when saving the store.

Could not list layers for this store, an error occurred retrieving them: Failed to create reader from file:coverages/testLennertS/log.x5.20132013.0103.10001.10001.anl.nc and hints null

 

Ncdump:

netcdf log.x5.20132013.0103.10001.10001.anl {

dimensions:

        lon = 950 ;

        lat = 400 ;

        depth = 1 ;

        time = 1 ;

        nv = 2 ;

variables:

        float lon(lon) ;

                lon:units = "degrees_east" ;

        float lat(lat) ;

                lat:units = "degrees_north" ;

        float depth(depth) ;

                depth:units = "meters" ;

                depth:positive = "down" ;

        float time(time) ;

                time:units = "Days since 2013-01-01" ;

                time:climatology = "climatology_bounds" ;

        float climatology_bounds(time, nv) ;

        float CORRLEN(time, depth) ;

                CORRLEN:long_name = "Correlation Length" ;

                CORRLEN:units = "degrees_north" ;

        float SNR(time, depth) ;

                SNR:long_name = "Signal to Noise" ;

        float VARBACK(time, depth) ;

                VARBACK:long_name = "Background Field Variance" ;

                VARBACK:units = "logab^2" ;

        float log.x5(time, depth, lat, lon) ;

                log.x5:long_name = "log.x5" ;

                log.x5:units = "logab" ;

                log.x5:valid_min = -0.7f ;

                log.x5:valid_max = 5.8f ;

                log.x5:_FillValue = -99.f ;

                log.x5:cell_methods = "timebins" ;

                log.x5:missing_value = -99.f ;

        float log.x5_err(time, depth, lat, lon) ;

                log.x5_err:long_name = "Error standard deviation of log.x5" ;

                log.x5_err:units = "logab" ;

                log.x5_err:valid_min = 0.f ;

                log.x5_err:valid_max = 0.69f ;

                log.x5_err:_FillValue = -99.f ;

                log.x5_err:missing_value = -99.f ;

        float log.x5_L1(time, depth, lat, lon) ;

                log.x5_L1:long_name = "log.x5 masked using relative error threshold 0.3" ;

                log.x5_L1:units = "logab" ;

                log.x5_L1:valid_min = -0.4f ;

                log.x5_L1:valid_max = 5.8f ;

                log.x5_L1:_FillValue = -99.f ;

                log.x5_L1:missing_value = -99.f ;

        float log.x5_L2(time, depth, lat, lon) ;

                log.x5_L2:long_name = "log.x5 masked using relative error threshold 0.5" ;

                log.x5_L2:units = "logab" ;

                log.x5_L2:valid_min = -0.4f ;

                log.x5_L2:valid_max = 5.8f ;

                log.x5_L2:_FillValue = -99.f ;

                log.x5_L2:missing_value = -99.f ;

        float log.x5_relerr(time, depth, lat, lon) ;

                log.x5_relerr:long_name = "Relative error of log.x5" ;

                log.x5_relerr:valid_min = 0.f ;

                log.x5_relerr:valid_max = 1.f ;

                log.x5_relerr:_FillValue = -99.f ;

                log.x5_relerr:missing_value = -99.f ;

        float databins(time, depth, lat, lon) ;

                databins:long_name = "Logarithm10 of number of data in bins" ;

                databins:valid_min = 0.f ;

                databins:valid_max = 0.7f ;

                databins:_FillValue = -99.f ;

                databins:missing_value = -99.f ;

        float outlbins(time, depth, lat, lon) ;

                outlbins:long_name = "Logarithm10 of number of outliers data in bins" ;

                outlbins:valid_min = 0.f ;

                outlbins:valid_max = -99.f ;

                outlbins:_FillValue = -99.f ;

                outlbins:missing_value = -99.f ;

        float CLfield(time, depth, lat, lon) ;

                CLfield:long_name = "Correlation length field" ;

                CLfield:valid_min = 0.f ;

                CLfield:valid_max = 1.5f ;

                CLfield:_FillValue = -99.f ;

                CLfield:missing_value = -99.f ;

        float log.x5_deepest(time, lat, lon) ;

                log.x5_deepest:long_name = "Deepest values of log.x5" ;

                log.x5_deepest:units = "logab" ;

                log.x5_deepest:valid_min = -0.7f ;

                log.x5_deepest:valid_max = 5.8f ;

                log.x5_deepest:_FillValue = -99.f ;

                log.x5_deepest:missing_value = -99.f ;

        float log.x5_deepest_L1(time, lat, lon) ;

                log.x5_deepest_L1:long_name = "Deepest values of log.x5 masked using relative error threshold 0.3" ;

                log.x5_deepest_L1:units = "logab" ;

                log.x5_deepest_L1:valid_min = -0.4f ;

                log.x5_deepest_L1:valid_max = 5.8f ;

                log.x5_deepest_L1:_FillValue = -99.f ;

                log.x5_deepest_L1:missing_value = -99.f ;

        float log.x5_deepest_L2(time, lat, lon) ;

                log.x5_deepest_L2:long_name = "Deepest values of log.x5 masked using relative error threshold 0.5" ;

                log.x5_deepest_L2:units = "logab" ;

                log.x5_deepest_L2:valid_min = -0.4f ;

                log.x5_deepest_L2:valid_max = 5.8f ;

                log.x5_deepest_L2:_FillValue = -99.f ;

                log.x5_deepest_L2:missing_value = -99.f ;

 

// global attributes:

                :Conventions = "CF-1.0" ;

                :project = "SeaDataNetII" ;

                :institution = "SAHFOS" ;

                :production = "Flanders Marine Institute" ;

                :data_access = "GHER OPENDAB:;

                :WEB_visualisation = "" ;

                :Author_e-mail = "***" ;

                :date = "2015-11-25 04:21:30.00" ;

                :title = "Diva analysis" ;

                :file_name = "../output/3Danalysis/log.x5.20132013.0103.10001.10001.anl.nc" ;

                :source = "SAHFOS" ;

                :comment = "No comment" ;

}

 

Part of the log error:

2018-07-04 17:16:08,825 DEBUG [geoserver.config] - Persisting coverage store log.x5.20132013.0103.10001.10001.anl.nc

2018-07-04 17:16:08,827 DEBUG [geoserver.config] - Persisted com.sun.proxy.$Proxy17 to workspaces/testLennertS/log.x5.20132013.0103.10001.10001.anl.nc/coveragestore.xml

2018-07-04 17:16:08,828 DEBUG [geoserver.config] - Persisted com.sun.proxy.$Proxy22 to global.xml

2018-07-04 17:16:08,834 TRACE [geotools.factory] - ENTRY  (GridCoverageFactory)

2018-07-04 17:16:08,834 TRACE [geotools.factory] - RETURN (GridCoverageFactory): found implementation GridCoverageFactory.

2018-07-04 17:16:08,834 DEBUG [io.netcdf] - Provided URL is a file

2018-07-04 17:16:08,834 DEBUG [imageio.netcdf] - Found a valid FileImageInputStream

2018-07-04 17:16:08,840 DEBUG [imageio.netcdf] - File successfully opened

2018-07-04 17:16:08,851 DEBUG [geotools.jdbc] - CREATE CONNECTION

2018-07-04 17:16:08,948 DEBUG [geotools.jdbc] - CLOSE CONNECTION

2018-07-04 17:16:08,948 DEBUG [geotools.jdbc] - CREATE CONNECTION

2018-07-04 17:16:08,950 DEBUG [geotools.jdbc] - CLOSE CONNECTION

2018-07-04 17:16:08,951 DEBUG [io.catalog] - BBOXFilterExtractor::extractBasicProperties(): Problems when opening the index, no typenames for the schema are defined

2018-07-04 17:16:08,952 WARN [netcdf.NetCDFFormat] - Unable to connect

 

I looked up the documentation for netcdf files and this maillist archive, and tried different things, for example to explicitly add the ‘nv’ dimension as a variable (now ‘nv’ is only a dimension), but without success.

 

Does anyone know what (part) of my netcdf files are currently not supported?

Or where can I find more information?

 

Thanks a lot

Lennert Schepers

 


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Regards,

Daniele Romagnoli

==

GeoServer Professional Services from the experts! Visit http://goo.gl/it488V for more information.

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Ing. Daniele Romagnoli

Senior Software Engineer

 

GeoSolutions S.A.S.

Via di Montramito 3/A

55054  Massarosa (LU)

Italy

phone: +39 0584 962313

fax:      +39 0584 1660272

 

 

-------------------------------------------------------

 

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This email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential or otherwise protected from disclosure. We remind that - as provided by European Regulation 2016/679 “GDPR” - copying, dissemination or use of this e-mail or the information herein by anyone other than the intended recipient is prohibited. If you have received this email by mistake, please notify us immediately by telephone or e-mail.


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Re: Netcdf import error - Netcdf supported formats?

Daniele Romagnoli-3
Dear Lennert,
I did a very quick check on your sample files in order to provide you some quick feedback:
It looks like that the variable names containing dots are raising issues when creating the schema in the index.

So your files contain variables having names as:
log.x5
log.x5_L2
...
log.cal_hel
...

During initialization, a DB is created to index the records, by creating tables having same name of the variable name.
It looks like the variables with a "dot" ( . ) in the name are raising problems. 
The code is parsing it as a namespace prefix + local name when creating the feature type and "bad things happen".

As a very quick workaround you may want to rename those vars by removing the "dot" (ncml can do that quickly).

As an instance: 
  <ncml:variable orgName="log.cal_hel_L1" name="cal_hel_L1" shape="time depth lat lon" type="float">


That should allow to let you proceed with the store configuration.
Not sure if CF Convention allows variables with similar types of chars in the name, I should double check that.

Regards,
Daniele


On Fri, Jul 6, 2018 at 3:59 PM, Lennert Schepers <[hidden email]> wrote:

Hi Daniele

Sure, you can download two files here:

https://drive.google.com/drive/folders/1IKz-KVSmGLfCEsh30J4xg0lEB3kLkpM-?usp=sharing

 

Thanks a lot for your help!

Lennert

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Daniele Romagnoli
Sent: Friday, July 6, 2018 3:35 PM
To: Lennert Schepers <[hidden email]>
Cc: [hidden email]
Subject: Re: [Geoserver-users] Netcdf import error - Netcdf supported formats?

 

Dear Lennert,

do you have any chance to share one of these samples? (eventually, even through a private email).

If that's not an option, even a small sample dataset with "fake" values reporting the same problem should be fine for a quick check.

 

Best Regards,

Daniele

 

 

 

On Thu, Jul 5, 2018 at 5:55 PM, Lennert Schepers <[hidden email]> wrote:

Dear Geoserver Users list

 

I’m looking for a way to upload our Netcdf files with the Netcdf-plugin to GeoServer (Version 2.11.5).

The plugin works well with with CF and COARDS sample data from https://www.unidata.ucar.edu/software/netcdf/examples/files.html

 

However, when I try to upload our own Netcdf files, I receive an error when saving the store.

Could not list layers for this store, an error occurred retrieving them: Failed to create reader from file:coverages/testLennertS/log.x5.20132013.0103.10001.10001.anl.nc and hints null

 

Ncdump:

netcdf log.x5.20132013.0103.10001.10001.anl {

dimensions:

        lon = 950 ;

        lat = 400 ;

        depth = 1 ;

        time = 1 ;

        nv = 2 ;

variables:

        float lon(lon) ;

                lon:units = "degrees_east" ;

        float lat(lat) ;

                lat:units = "degrees_north" ;

        float depth(depth) ;

                depth:units = "meters" ;

                depth:positive = "down" ;

        float time(time) ;

                time:units = "Days since 2013-01-01" ;

                time:climatology = "climatology_bounds" ;

        float climatology_bounds(time, nv) ;

        float CORRLEN(time, depth) ;

                CORRLEN:long_name = "Correlation Length" ;

                CORRLEN:units = "degrees_north" ;

        float SNR(time, depth) ;

                SNR:long_name = "Signal to Noise" ;

        float VARBACK(time, depth) ;

                VARBACK:long_name = "Background Field Variance" ;

                VARBACK:units = "logab^2" ;

        float log.x5(time, depth, lat, lon) ;

                log.x5:long_name = "log.x5" ;

                log.x5:units = "logab" ;

                log.x5:valid_min = -0.7f ;

                log.x5:valid_max = 5.8f ;

                log.x5:_FillValue = -99.f ;

                log.x5:cell_methods = "timebins" ;

                log.x5:missing_value = -99.f ;

        float log.x5_err(time, depth, lat, lon) ;

                log.x5_err:long_name = "Error standard deviation of log.x5" ;

                log.x5_err:units = "logab" ;

                log.x5_err:valid_min = 0.f ;

                log.x5_err:valid_max = 0.69f ;

                log.x5_err:_FillValue = -99.f ;

                log.x5_err:missing_value = -99.f ;

        float log.x5_L1(time, depth, lat, lon) ;

                log.x5_L1:long_name = "log.x5 masked using relative error threshold 0.3" ;

                log.x5_L1:units = "logab" ;

                log.x5_L1:valid_min = -0.4f ;

                log.x5_L1:valid_max = 5.8f ;

                log.x5_L1:_FillValue = -99.f ;

                log.x5_L1:missing_value = -99.f ;

        float log.x5_L2(time, depth, lat, lon) ;

                log.x5_L2:long_name = "log.x5 masked using relative error threshold 0.5" ;

                log.x5_L2:units = "logab" ;

                log.x5_L2:valid_min = -0.4f ;

                log.x5_L2:valid_max = 5.8f ;

                log.x5_L2:_FillValue = -99.f ;

                log.x5_L2:missing_value = -99.f ;

        float log.x5_relerr(time, depth, lat, lon) ;

                log.x5_relerr:long_name = "Relative error of log.x5" ;

                log.x5_relerr:valid_min = 0.f ;

                log.x5_relerr:valid_max = 1.f ;

                log.x5_relerr:_FillValue = -99.f ;

                log.x5_relerr:missing_value = -99.f ;

        float databins(time, depth, lat, lon) ;

                databins:long_name = "Logarithm10 of number of data in bins" ;

                databins:valid_min = 0.f ;

                databins:valid_max = 0.7f ;

                databins:_FillValue = -99.f ;

                databins:missing_value = -99.f ;

        float outlbins(time, depth, lat, lon) ;

                outlbins:long_name = "Logarithm10 of number of outliers data in bins" ;

                outlbins:valid_min = 0.f ;

                outlbins:valid_max = -99.f ;

                outlbins:_FillValue = -99.f ;

                outlbins:missing_value = -99.f ;

        float CLfield(time, depth, lat, lon) ;

                CLfield:long_name = "Correlation length field" ;

                CLfield:valid_min = 0.f ;

                CLfield:valid_max = 1.5f ;

                CLfield:_FillValue = -99.f ;

                CLfield:missing_value = -99.f ;

        float log.x5_deepest(time, lat, lon) ;

                log.x5_deepest:long_name = "Deepest values of log.x5" ;

                log.x5_deepest:units = "logab" ;

                log.x5_deepest:valid_min = -0.7f ;

                log.x5_deepest:valid_max = 5.8f ;

                log.x5_deepest:_FillValue = -99.f ;

                log.x5_deepest:missing_value = -99.f ;

        float log.x5_deepest_L1(time, lat, lon) ;

                log.x5_deepest_L1:long_name = "Deepest values of log.x5 masked using relative error threshold 0.3" ;

                log.x5_deepest_L1:units = "logab" ;

                log.x5_deepest_L1:valid_min = -0.4f ;

                log.x5_deepest_L1:valid_max = 5.8f ;

                log.x5_deepest_L1:_FillValue = -99.f ;

                log.x5_deepest_L1:missing_value = -99.f ;

        float log.x5_deepest_L2(time, lat, lon) ;

                log.x5_deepest_L2:long_name = "Deepest values of log.x5 masked using relative error threshold 0.5" ;

                log.x5_deepest_L2:units = "logab" ;

                log.x5_deepest_L2:valid_min = -0.4f ;

                log.x5_deepest_L2:valid_max = 5.8f ;

                log.x5_deepest_L2:_FillValue = -99.f ;

                log.x5_deepest_L2:missing_value = -99.f ;

 

// global attributes:

                :Conventions = "CF-1.0" ;

                :project = "SeaDataNetII" ;

                :institution = "SAHFOS" ;

                :production = "Flanders Marine Institute" ;

                :data_access = "GHER OPENDAB:;

                :WEB_visualisation = "" ;

                :Author_e-mail = "***" ;

                :date = "2015-11-25 04:21:30.00" ;

                :title = "Diva analysis" ;

                :file_name = "../output/3Danalysis/log.x5.20132013.0103.10001.10001.anl.nc" ;

                :source = "SAHFOS" ;

                :comment = "No comment" ;

}

 

Part of the log error:

2018-07-04 17:16:08,825 DEBUG [geoserver.config] - Persisting coverage store log.x5.20132013.0103.10001.10001.anl.nc

2018-07-04 17:16:08,827 DEBUG [geoserver.config] - Persisted com.sun.proxy.$Proxy17 to workspaces/testLennertS/log.x5.20132013.0103.10001.10001.anl.nc/coveragestore.xml

2018-07-04 17:16:08,828 DEBUG [geoserver.config] - Persisted com.sun.proxy.$Proxy22 to global.xml

2018-07-04 17:16:08,834 TRACE [geotools.factory] - ENTRY  (GridCoverageFactory)

2018-07-04 17:16:08,834 TRACE [geotools.factory] - RETURN (GridCoverageFactory): found implementation GridCoverageFactory.

2018-07-04 17:16:08,834 DEBUG [io.netcdf] - Provided URL is a file

2018-07-04 17:16:08,834 DEBUG [imageio.netcdf] - Found a valid FileImageInputStream

2018-07-04 17:16:08,840 DEBUG [imageio.netcdf] - File successfully opened

2018-07-04 17:16:08,851 DEBUG [geotools.jdbc] - CREATE CONNECTION

2018-07-04 17:16:08,948 DEBUG [geotools.jdbc] - CLOSE CONNECTION

2018-07-04 17:16:08,948 DEBUG [geotools.jdbc] - CREATE CONNECTION

2018-07-04 17:16:08,950 DEBUG [geotools.jdbc] - CLOSE CONNECTION

2018-07-04 17:16:08,951 DEBUG [io.catalog] - BBOXFilterExtractor::extractBasicProperties(): Problems when opening the index, no typenames for the schema are defined

2018-07-04 17:16:08,952 WARN [netcdf.NetCDFFormat] - Unable to connect

 

I looked up the documentation for netcdf files and this maillist archive, and tried different things, for example to explicitly add the ‘nv’ dimension as a variable (now ‘nv’ is only a dimension), but without success.

 

Does anyone know what (part) of my netcdf files are currently not supported?

Or where can I find more information?

 

Thanks a lot

Lennert Schepers

 


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--

Regards,

Daniele Romagnoli

==

GeoServer Professional Services from the experts! Visit http://goo.gl/it488V for more information.

==

 

Ing. Daniele Romagnoli

Senior Software Engineer

 

GeoSolutions S.A.S.

Italy

phone: +39 0584 962313

fax:      +39 0584 1660272

 

 

-------------------------------------------------------

 

Con riferimento alla normativa sul trattamento dei dati personali (Reg. UE 2016/679 - Regolamento generale sulla protezione dei dati “GDPR”), si precisa che ogni circostanza inerente alla presente email (il suo contenuto, gli eventuali allegati, etc.) è un dato la cui conoscenza è riservata al/i solo/i destinatario/i indicati dallo scrivente. Se il messaggio Le è giunto per errore, è tenuta/o a cancellarlo, ogni altra operazione è illecita. Le sarei comunque grato se potesse darmene notizia.

 

This email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential or otherwise protected from disclosure. We remind that - as provided by European Regulation 2016/679 “GDPR” - copying, dissemination or use of this e-mail or the information herein by anyone other than the intended recipient is prohibited. If you have received this email by mistake, please notify us immediately by telephone or e-mail.




--
Regards,
Daniele Romagnoli
==
GeoServer Professional Services from the experts! Visit http://goo.gl/it488V for more information.
==

Ing. Daniele Romagnoli
Senior Software Engineer

GeoSolutions S.A.S.
Via di Montramito 3/A
55054  Massarosa (LU)
Italy
phone: +39 0584 962313
fax:      +39 0584 1660272


-------------------------------------------------------

Con riferimento alla normativa sul trattamento dei dati personali (Reg. UE 2016/679 - Regolamento generale sulla protezione dei dati “GDPR”), si precisa che ogni circostanza inerente alla presente email (il suo contenuto, gli eventuali allegati, etc.) è un dato la cui conoscenza è riservata al/i solo/i destinatario/i indicati dallo scrivente. Se il messaggio Le è giunto per errore, è tenuta/o a cancellarlo, ogni altra operazione è illecita. Le sarei comunque grato se potesse darmene notizia.

This email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential or otherwise protected from disclosure. We remind that - as provided by European Regulation 2016/679 “GDPR” - copying, dissemination or use of this e-mail or the information herein by anyone other than the intended recipient is prohibited. If you have received this email by mistake, please notify us immediately by telephone or e-mail.

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If you want to request a feature or an improvement, also see this: https://github.com/geoserver/geoserver/wiki/Successfully-requesting-and-integrating-new-features-and-improvements-in-GeoServer


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Re: Netcdf import error - Netcdf supported formats?

Daniele Romagnoli-3


On Fri, Jul 6, 2018 at 4:32 PM, Daniele Romagnoli <[hidden email]> wrote:
Dear Lennert,
I did a very quick check on your sample files in order to provide you some quick feedback:
It looks like that the variable names containing dots are raising issues when creating the schema in the index.

So your files contain variables having names as:
log.x5
log.x5_L2
...
log.cal_hel
...

During initialization, a DB is created to index the records, by creating tables having same name of the variable name.
It looks like the variables with a "dot" ( . ) in the name are raising problems. 
The code is parsing it as a namespace prefix + local name when creating the feature type and "bad things happen".

As a very quick workaround you may want to rename those vars by removing the "dot" (ncml can do that quickly).

As an instance: 
  <ncml:variable orgName="log.cal_hel_L1" name="cal_hel_L1" shape="time depth lat lon" type="float">


That should allow to let you proceed with the store configuration.
Not sure if CF Convention allows variables with similar types of chars in the name, I should double check that.

More feedbacks on the variable names topic:
Variable, dimension and attribute names should begin with a letter and be composed of letters, digits, and underscores. 

Hope this helps.
Regards,
Daniele
 

Regards,
Daniele


On Fri, Jul 6, 2018 at 3:59 PM, Lennert Schepers <[hidden email]> wrote:

Hi Daniele

Sure, you can download two files here:

https://drive.google.com/drive/folders/1IKz-KVSmGLfCEsh30J4xg0lEB3kLkpM-?usp=sharing

 

Thanks a lot for your help!

Lennert

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Daniele Romagnoli
Sent: Friday, July 6, 2018 3:35 PM
To: Lennert Schepers <[hidden email]>
Cc: [hidden email]
Subject: Re: [Geoserver-users] Netcdf import error - Netcdf supported formats?

 

Dear Lennert,

do you have any chance to share one of these samples? (eventually, even through a private email).

If that's not an option, even a small sample dataset with "fake" values reporting the same problem should be fine for a quick check.

 

Best Regards,

Daniele

 

 

 

On Thu, Jul 5, 2018 at 5:55 PM, Lennert Schepers <[hidden email]> wrote:

Dear Geoserver Users list

 

I’m looking for a way to upload our Netcdf files with the Netcdf-plugin to GeoServer (Version 2.11.5).

The plugin works well with with CF and COARDS sample data from https://www.unidata.ucar.edu/software/netcdf/examples/files.html

 

However, when I try to upload our own Netcdf files, I receive an error when saving the store.

Could not list layers for this store, an error occurred retrieving them: Failed to create reader from file:coverages/testLennertS/log.x5.20132013.0103.10001.10001.anl.nc and hints null

 

Ncdump:

netcdf log.x5.20132013.0103.10001.10001.anl {

dimensions:

        lon = 950 ;

        lat = 400 ;

        depth = 1 ;

        time = 1 ;

        nv = 2 ;

variables:

        float lon(lon) ;

                lon:units = "degrees_east" ;

        float lat(lat) ;

                lat:units = "degrees_north" ;

        float depth(depth) ;

                depth:units = "meters" ;

                depth:positive = "down" ;

        float time(time) ;

                time:units = "Days since 2013-01-01" ;

                time:climatology = "climatology_bounds" ;

        float climatology_bounds(time, nv) ;

        float CORRLEN(time, depth) ;

                CORRLEN:long_name = "Correlation Length" ;

                CORRLEN:units = "degrees_north" ;

        float SNR(time, depth) ;

                SNR:long_name = "Signal to Noise" ;

        float VARBACK(time, depth) ;

                VARBACK:long_name = "Background Field Variance" ;

                VARBACK:units = "logab^2" ;

        float log.x5(time, depth, lat, lon) ;

                log.x5:long_name = "log.x5" ;

                log.x5:units = "logab" ;

                log.x5:valid_min = -0.7f ;

                log.x5:valid_max = 5.8f ;

                log.x5:_FillValue = -99.f ;

                log.x5:cell_methods = "timebins" ;

                log.x5:missing_value = -99.f ;

        float log.x5_err(time, depth, lat, lon) ;

                log.x5_err:long_name = "Error standard deviation of log.x5" ;

                log.x5_err:units = "logab" ;

                log.x5_err:valid_min = 0.f ;

                log.x5_err:valid_max = 0.69f ;

                log.x5_err:_FillValue = -99.f ;

                log.x5_err:missing_value = -99.f ;

        float log.x5_L1(time, depth, lat, lon) ;

                log.x5_L1:long_name = "log.x5 masked using relative error threshold 0.3" ;

                log.x5_L1:units = "logab" ;

                log.x5_L1:valid_min = -0.4f ;

                log.x5_L1:valid_max = 5.8f ;

                log.x5_L1:_FillValue = -99.f ;

                log.x5_L1:missing_value = -99.f ;

        float log.x5_L2(time, depth, lat, lon) ;

                log.x5_L2:long_name = "log.x5 masked using relative error threshold 0.5" ;

                log.x5_L2:units = "logab" ;

                log.x5_L2:valid_min = -0.4f ;

                log.x5_L2:valid_max = 5.8f ;

                log.x5_L2:_FillValue = -99.f ;

                log.x5_L2:missing_value = -99.f ;

        float log.x5_relerr(time, depth, lat, lon) ;

                log.x5_relerr:long_name = "Relative error of log.x5" ;

                log.x5_relerr:valid_min = 0.f ;

                log.x5_relerr:valid_max = 1.f ;

                log.x5_relerr:_FillValue = -99.f ;

                log.x5_relerr:missing_value = -99.f ;

        float databins(time, depth, lat, lon) ;

                databins:long_name = "Logarithm10 of number of data in bins" ;

                databins:valid_min = 0.f ;

                databins:valid_max = 0.7f ;

                databins:_FillValue = -99.f ;

                databins:missing_value = -99.f ;

        float outlbins(time, depth, lat, lon) ;

                outlbins:long_name = "Logarithm10 of number of outliers data in bins" ;

                outlbins:valid_min = 0.f ;

                outlbins:valid_max = -99.f ;

                outlbins:_FillValue = -99.f ;

                outlbins:missing_value = -99.f ;

        float CLfield(time, depth, lat, lon) ;

                CLfield:long_name = "Correlation length field" ;

                CLfield:valid_min = 0.f ;

                CLfield:valid_max = 1.5f ;

                CLfield:_FillValue = -99.f ;

                CLfield:missing_value = -99.f ;

        float log.x5_deepest(time, lat, lon) ;

                log.x5_deepest:long_name = "Deepest values of log.x5" ;

                log.x5_deepest:units = "logab" ;

                log.x5_deepest:valid_min = -0.7f ;

                log.x5_deepest:valid_max = 5.8f ;

                log.x5_deepest:_FillValue = -99.f ;

                log.x5_deepest:missing_value = -99.f ;

        float log.x5_deepest_L1(time, lat, lon) ;

                log.x5_deepest_L1:long_name = "Deepest values of log.x5 masked using relative error threshold 0.3" ;

                log.x5_deepest_L1:units = "logab" ;

                log.x5_deepest_L1:valid_min = -0.4f ;

                log.x5_deepest_L1:valid_max = 5.8f ;

                log.x5_deepest_L1:_FillValue = -99.f ;

                log.x5_deepest_L1:missing_value = -99.f ;

        float log.x5_deepest_L2(time, lat, lon) ;

                log.x5_deepest_L2:long_name = "Deepest values of log.x5 masked using relative error threshold 0.5" ;

                log.x5_deepest_L2:units = "logab" ;

                log.x5_deepest_L2:valid_min = -0.4f ;

                log.x5_deepest_L2:valid_max = 5.8f ;

                log.x5_deepest_L2:_FillValue = -99.f ;

                log.x5_deepest_L2:missing_value = -99.f ;

 

// global attributes:

                :Conventions = "CF-1.0" ;

                :project = "SeaDataNetII" ;

                :institution = "SAHFOS" ;

                :production = "Flanders Marine Institute" ;

                :data_access = "GHER OPENDAB:;

                :WEB_visualisation = "" ;

                :Author_e-mail = "***" ;

                :date = "2015-11-25 04:21:30.00" ;

                :title = "Diva analysis" ;

                :file_name = "../output/3Danalysis/log.x5.20132013.0103.10001.10001.anl.nc" ;

                :source = "SAHFOS" ;

                :comment = "No comment" ;

}

 

Part of the log error:

2018-07-04 17:16:08,825 DEBUG [geoserver.config] - Persisting coverage store log.x5.20132013.0103.10001.10001.anl.nc

2018-07-04 17:16:08,827 DEBUG [geoserver.config] - Persisted com.sun.proxy.$Proxy17 to workspaces/testLennertS/log.x5.20132013.0103.10001.10001.anl.nc/coveragestore.xml

2018-07-04 17:16:08,828 DEBUG [geoserver.config] - Persisted com.sun.proxy.$Proxy22 to global.xml

2018-07-04 17:16:08,834 TRACE [geotools.factory] - ENTRY  (GridCoverageFactory)

2018-07-04 17:16:08,834 TRACE [geotools.factory] - RETURN (GridCoverageFactory): found implementation GridCoverageFactory.

2018-07-04 17:16:08,834 DEBUG [io.netcdf] - Provided URL is a file

2018-07-04 17:16:08,834 DEBUG [imageio.netcdf] - Found a valid FileImageInputStream

2018-07-04 17:16:08,840 DEBUG [imageio.netcdf] - File successfully opened

2018-07-04 17:16:08,851 DEBUG [geotools.jdbc] - CREATE CONNECTION

2018-07-04 17:16:08,948 DEBUG [geotools.jdbc] - CLOSE CONNECTION

2018-07-04 17:16:08,948 DEBUG [geotools.jdbc] - CREATE CONNECTION

2018-07-04 17:16:08,950 DEBUG [geotools.jdbc] - CLOSE CONNECTION

2018-07-04 17:16:08,951 DEBUG [io.catalog] - BBOXFilterExtractor::extractBasicProperties(): Problems when opening the index, no typenames for the schema are defined

2018-07-04 17:16:08,952 WARN [netcdf.NetCDFFormat] - Unable to connect

 

I looked up the documentation for netcdf files and this maillist archive, and tried different things, for example to explicitly add the ‘nv’ dimension as a variable (now ‘nv’ is only a dimension), but without success.

 

Does anyone know what (part) of my netcdf files are currently not supported?

Or where can I find more information?

 

Thanks a lot

Lennert Schepers

 


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--

Regards,

Daniele Romagnoli

==

GeoServer Professional Services from the experts! Visit http://goo.gl/it488V for more information.

==

 

Ing. Daniele Romagnoli

Senior Software Engineer

 

GeoSolutions S.A.S.

Italy

phone: +39 0584 962313

fax:      +39 0584 1660272

 

 

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Con riferimento alla normativa sul trattamento dei dati personali (Reg. UE 2016/679 - Regolamento generale sulla protezione dei dati “GDPR”), si precisa che ogni circostanza inerente alla presente email (il suo contenuto, gli eventuali allegati, etc.) è un dato la cui conoscenza è riservata al/i solo/i destinatario/i indicati dallo scrivente. Se il messaggio Le è giunto per errore, è tenuta/o a cancellarlo, ogni altra operazione è illecita. Le sarei comunque grato se potesse darmene notizia.

 

This email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential or otherwise protected from disclosure. We remind that - as provided by European Regulation 2016/679 “GDPR” - copying, dissemination or use of this e-mail or the information herein by anyone other than the intended recipient is prohibited. If you have received this email by mistake, please notify us immediately by telephone or e-mail.




--
Regards,
Daniele Romagnoli
==
GeoServer Professional Services from the experts! Visit http://goo.gl/it488V for more information.
==

Ing. Daniele Romagnoli
Senior Software Engineer

GeoSolutions S.A.S.
Via di Montramito 3/A
55054  Massarosa (LU)
Italy
phone: +39 0584 962313
fax:      +39 0584 1660272


-------------------------------------------------------

Con riferimento alla normativa sul trattamento dei dati personali (Reg. UE 2016/679 - Regolamento generale sulla protezione dei dati “GDPR”), si precisa che ogni circostanza inerente alla presente email (il suo contenuto, gli eventuali allegati, etc.) è un dato la cui conoscenza è riservata al/i solo/i destinatario/i indicati dallo scrivente. Se il messaggio Le è giunto per errore, è tenuta/o a cancellarlo, ogni altra operazione è illecita. Le sarei comunque grato se potesse darmene notizia.

This email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential or otherwise protected from disclosure. We remind that - as provided by European Regulation 2016/679 “GDPR” - copying, dissemination or use of this e-mail or the information herein by anyone other than the intended recipient is prohibited. If you have received this email by mistake, please notify us immediately by telephone or e-mail.



--
Regards,
Daniele Romagnoli
==
GeoServer Professional Services from the experts! Visit http://goo.gl/it488V for more information.
==

Ing. Daniele Romagnoli
Senior Software Engineer

GeoSolutions S.A.S.
Via di Montramito 3/A
55054  Massarosa (LU)
Italy
phone: +39 0584 962313
fax:      +39 0584 1660272


-------------------------------------------------------

Con riferimento alla normativa sul trattamento dei dati personali (Reg. UE 2016/679 - Regolamento generale sulla protezione dei dati “GDPR”), si precisa che ogni circostanza inerente alla presente email (il suo contenuto, gli eventuali allegati, etc.) è un dato la cui conoscenza è riservata al/i solo/i destinatario/i indicati dallo scrivente. Se il messaggio Le è giunto per errore, è tenuta/o a cancellarlo, ogni altra operazione è illecita. Le sarei comunque grato se potesse darmene notizia.

This email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential or otherwise protected from disclosure. We remind that - as provided by European Regulation 2016/679 “GDPR” - copying, dissemination or use of this e-mail or the information herein by anyone other than the intended recipient is prohibited. If you have received this email by mistake, please notify us immediately by telephone or e-mail.

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Please make sure you read the following two resources before posting to this list:
- Earning your support instead of buying it, but Ian Turton: http://www.ianturton.com/talks/foss4g.html#/
- The GeoServer user list posting guidelines: http://geoserver.org/comm/userlist-guidelines.html

If you want to request a feature or an improvement, also see this: https://github.com/geoserver/geoserver/wiki/Successfully-requesting-and-integrating-new-features-and-improvements-in-GeoServer


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Re: Netcdf import error - Netcdf supported formats?

lennert.schepers

Dear Daniele

Your solution works, thanks a lot for your help.

Lennert

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Daniele Romagnoli
Sent: Friday, July 6, 2018 5:06 PM
To: Lennert Schepers <[hidden email]>
Cc: [hidden email]
Subject: Re: [Geoserver-users] Netcdf import error - Netcdf supported formats?

 

 

 

On Fri, Jul 6, 2018 at 4:32 PM, Daniele Romagnoli <[hidden email]> wrote:

Dear Lennert,

I did a very quick check on your sample files in order to provide you some quick feedback:

It looks like that the variable names containing dots are raising issues when creating the schema in the index.

 

So your files contain variables having names as:

log.x5

log.x5_L2

...

log.cal_hel

...

 

During initialization, a DB is created to index the records, by creating tables having same name of the variable name.

It looks like the variables with a "dot" ( . ) in the name are raising problems. 

The code is parsing it as a namespace prefix + local name when creating the feature type and "bad things happen".

 

As a very quick workaround you may want to rename those vars by removing the "dot" (ncml can do that quickly).

 

As an instance: 

  <ncml:variable orgName="log.cal_hel_L1" name="cal_hel_L1" shape="time depth lat lon" type="float">

 

 

That should allow to let you proceed with the store configuration.

Not sure if CF Convention allows variables with similar types of chars in the name, I should double check that.

 

More feedbacks on the variable names topic:

Variable, dimension and attribute names should begin with a letter and be composed of letters, digits, and underscores. 

 

Hope this helps.

Regards,

Daniele

 

 

Regards,

Daniele

 

 

On Fri, Jul 6, 2018 at 3:59 PM, Lennert Schepers <[hidden email]> wrote:

Hi Daniele

Sure, you can download two files here:

https://drive.google.com/drive/folders/1IKz-KVSmGLfCEsh30J4xg0lEB3kLkpM-?usp=sharing

 

Thanks a lot for your help!

Lennert

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Daniele Romagnoli
Sent: Friday, July 6, 2018 3:35 PM
To: Lennert Schepers <[hidden email]>
Cc: [hidden email]
Subject: Re: [Geoserver-users] Netcdf import error - Netcdf supported formats?

 

Dear Lennert,

do you have any chance to share one of these samples? (eventually, even through a private email).

If that's not an option, even a small sample dataset with "fake" values reporting the same problem should be fine for a quick check.

 

Best Regards,

Daniele

 

 

 

On Thu, Jul 5, 2018 at 5:55 PM, Lennert Schepers <[hidden email]> wrote:

Dear Geoserver Users list

 

I’m looking for a way to upload our Netcdf files with the Netcdf-plugin to GeoServer (Version 2.11.5).

The plugin works well with with CF and COARDS sample data from https://www.unidata.ucar.edu/software/netcdf/examples/files.html

 

However, when I try to upload our own Netcdf files, I receive an error when saving the store.

Could not list layers for this store, an error occurred retrieving them: Failed to create reader from file:coverages/testLennertS/log.x5.20132013.0103.10001.10001.anl.nc and hints null

 

Ncdump:

netcdf log.x5.20132013.0103.10001.10001.anl {

dimensions:

        lon = 950 ;

        lat = 400 ;

        depth = 1 ;

        time = 1 ;

        nv = 2 ;

variables:

        float lon(lon) ;

                lon:units = "degrees_east" ;

        float lat(lat) ;

                lat:units = "degrees_north" ;

        float depth(depth) ;

                depth:units = "meters" ;

                depth:positive = "down" ;

        float time(time) ;

                time:units = "Days since 2013-01-01" ;

                time:climatology = "climatology_bounds" ;

        float climatology_bounds(time, nv) ;

        float CORRLEN(time, depth) ;

                CORRLEN:long_name = "Correlation Length" ;

                CORRLEN:units = "degrees_north" ;

        float SNR(time, depth) ;

                SNR:long_name = "Signal to Noise" ;

        float VARBACK(time, depth) ;

                VARBACK:long_name = "Background Field Variance" ;

                VARBACK:units = "logab^2" ;

        float log.x5(time, depth, lat, lon) ;

                log.x5:long_name = "log.x5" ;

                log.x5:units = "logab" ;

                log.x5:valid_min = -0.7f ;

                log.x5:valid_max = 5.8f ;

                log.x5:_FillValue = -99.f ;

                log.x5:cell_methods = "timebins" ;

                log.x5:missing_value = -99.f ;

        float log.x5_err(time, depth, lat, lon) ;

                log.x5_err:long_name = "Error standard deviation of log.x5" ;

                log.x5_err:units = "logab" ;

                log.x5_err:valid_min = 0.f ;

                log.x5_err:valid_max = 0.69f ;

                log.x5_err:_FillValue = -99.f ;

                log.x5_err:missing_value = -99.f ;

        float log.x5_L1(time, depth, lat, lon) ;

                log.x5_L1:long_name = "log.x5 masked using relative error threshold 0.3" ;

                log.x5_L1:units = "logab" ;

                log.x5_L1:valid_min = -0.4f ;

                log.x5_L1:valid_max = 5.8f ;

                log.x5_L1:_FillValue = -99.f ;

                log.x5_L1:missing_value = -99.f ;

        float log.x5_L2(time, depth, lat, lon) ;

                log.x5_L2:long_name = "log.x5 masked using relative error threshold 0.5" ;

                log.x5_L2:units = "logab" ;

                log.x5_L2:valid_min = -0.4f ;

                log.x5_L2:valid_max = 5.8f ;

                log.x5_L2:_FillValue = -99.f ;

                log.x5_L2:missing_value = -99.f ;

        float log.x5_relerr(time, depth, lat, lon) ;

                log.x5_relerr:long_name = "Relative error of log.x5" ;

                log.x5_relerr:valid_min = 0.f ;

                log.x5_relerr:valid_max = 1.f ;

                log.x5_relerr:_FillValue = -99.f ;

                log.x5_relerr:missing_value = -99.f ;

        float databins(time, depth, lat, lon) ;

                databins:long_name = "Logarithm10 of number of data in bins" ;

                databins:valid_min = 0.f ;

                databins:valid_max = 0.7f ;

                databins:_FillValue = -99.f ;

                databins:missing_value = -99.f ;

        float outlbins(time, depth, lat, lon) ;

                outlbins:long_name = "Logarithm10 of number of outliers data in bins" ;

                outlbins:valid_min = 0.f ;

                outlbins:valid_max = -99.f ;

                outlbins:_FillValue = -99.f ;

                outlbins:missing_value = -99.f ;

        float CLfield(time, depth, lat, lon) ;

                CLfield:long_name = "Correlation length field" ;

                CLfield:valid_min = 0.f ;

                CLfield:valid_max = 1.5f ;

                CLfield:_FillValue = -99.f ;

                CLfield:missing_value = -99.f ;

        float log.x5_deepest(time, lat, lon) ;

                log.x5_deepest:long_name = "Deepest values of log.x5" ;

                log.x5_deepest:units = "logab" ;

                log.x5_deepest:valid_min = -0.7f ;

                log.x5_deepest:valid_max = 5.8f ;

                log.x5_deepest:_FillValue = -99.f ;

                log.x5_deepest:missing_value = -99.f ;

        float log.x5_deepest_L1(time, lat, lon) ;

                log.x5_deepest_L1:long_name = "Deepest values of log.x5 masked using relative error threshold 0.3" ;

                log.x5_deepest_L1:units = "logab" ;

                log.x5_deepest_L1:valid_min = -0.4f ;

                log.x5_deepest_L1:valid_max = 5.8f ;

                log.x5_deepest_L1:_FillValue = -99.f ;

                log.x5_deepest_L1:missing_value = -99.f ;

        float log.x5_deepest_L2(time, lat, lon) ;

                log.x5_deepest_L2:long_name = "Deepest values of log.x5 masked using relative error threshold 0.5" ;

                log.x5_deepest_L2:units = "logab" ;

                log.x5_deepest_L2:valid_min = -0.4f ;

                log.x5_deepest_L2:valid_max = 5.8f ;

                log.x5_deepest_L2:_FillValue = -99.f ;

                log.x5_deepest_L2:missing_value = -99.f ;

 

// global attributes:

                :Conventions = "CF-1.0" ;

                :project = "SeaDataNetII" ;

                :institution = "SAHFOS" ;

                :production = "Flanders Marine Institute" ;

                :data_access = "GHER OPENDAB:;

                :WEB_visualisation = "" ;

                :Author_e-mail = "***" ;

                :date = "2015-11-25 04:21:30.00" ;

                :title = "Diva analysis" ;

                :file_name = "../output/3Danalysis/log.x5.20132013.0103.10001.10001.anl.nc" ;

                :source = "SAHFOS" ;

                :comment = "No comment" ;

}

 

Part of the log error:

2018-07-04 17:16:08,825 DEBUG [geoserver.config] - Persisting coverage store log.x5.20132013.0103.10001.10001.anl.nc

2018-07-04 17:16:08,827 DEBUG [geoserver.config] - Persisted com.sun.proxy.$Proxy17 to workspaces/testLennertS/log.x5.20132013.0103.10001.10001.anl.nc/coveragestore.xml

2018-07-04 17:16:08,828 DEBUG [geoserver.config] - Persisted com.sun.proxy.$Proxy22 to global.xml

2018-07-04 17:16:08,834 TRACE [geotools.factory] - ENTRY  (GridCoverageFactory)

2018-07-04 17:16:08,834 TRACE [geotools.factory] - RETURN (GridCoverageFactory): found implementation GridCoverageFactory.

2018-07-04 17:16:08,834 DEBUG [io.netcdf] - Provided URL is a file

2018-07-04 17:16:08,834 DEBUG [imageio.netcdf] - Found a valid FileImageInputStream

2018-07-04 17:16:08,840 DEBUG [imageio.netcdf] - File successfully opened

2018-07-04 17:16:08,851 DEBUG [geotools.jdbc] - CREATE CONNECTION

2018-07-04 17:16:08,948 DEBUG [geotools.jdbc] - CLOSE CONNECTION

2018-07-04 17:16:08,948 DEBUG [geotools.jdbc] - CREATE CONNECTION

2018-07-04 17:16:08,950 DEBUG [geotools.jdbc] - CLOSE CONNECTION

2018-07-04 17:16:08,951 DEBUG [io.catalog] - BBOXFilterExtractor::extractBasicProperties(): Problems when opening the index, no typenames for the schema are defined

2018-07-04 17:16:08,952 WARN [netcdf.NetCDFFormat] - Unable to connect

 

I looked up the documentation for netcdf files and this maillist archive, and tried different things, for example to explicitly add the ‘nv’ dimension as a variable (now ‘nv’ is only a dimension), but without success.

 

Does anyone know what (part) of my netcdf files are currently not supported?

Or where can I find more information?

 

Thanks a lot

Lennert Schepers

 


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Re: Netcdf import error - Netcdf supported formats?

GeoServer - User mailing list
In reply to this post by lennert.schepers
Hi Lennert,

A quick question, is the nv dimension the depth ? So you actually have also
time dimension, the parameter (air_temperature for example) and you also
have the depth? I am asking because I also use netcdf files and some
parameters also have depth dimension and I thought it is not possible to
ingest this kind of netcdf in GeoServer.   Did you used a coveragestore or
an imagemosaic?

Kind regards,
Corina



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Re: Netcdf import error - Netcdf supported formats?

lennert.schepers
Hi Corina

Sorry, my reply apparently didn't reach its destination.
The nv is a dimension to specify climatological time intervals,  nv is 2 because this refers to the start and stop of a subinterval. More info on climatological time intervals here: http://cfconventions.org/cf-conventions/cf-conventions.html#climatological-statistics.
But yes, we also have the time dimension together with depth/elevation. I'm using a coveragestore with the Geoserver plugin.
Here's a tutorial on how to configure a netcdf as a store: https://geoserver.geo-solutions.it/edu/en/multidim/netcdf/netcdf_config.html 

If you want to combine different netcdf file in one mosaic, see here: https://geoserver.geo-solutions.it/edu/en/multidim/mosaic_config/netcdf_mosaic.html

I hope this helps

Lennert

-----Original Message-----
From: Corina Tudorache via Geoserver-users [mailto:[hidden email]]
Sent: Friday, July 13, 2018 3:42 PM
To: [hidden email]
Subject: Re: [Geoserver-users] Netcdf import error - Netcdf supported formats?

Hi Lennert,

A quick question, is the nv dimension the depth ? So you actually have also time dimension, the parameter (air_temperature for example) and you also have the depth? I am asking because I also use netcdf files and some parameters also have depth dimension and I thought it is not possible to
ingest this kind of netcdf in GeoServer.   Did you used a coveragestore or
an imagemosaic?

Kind regards,
Corina



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