aodn/imos-toolbox

Incorrect `coordinates` attributes in ADCP files processed with 2.6.11

Closed this issue · 1 comments

mhidas commented

We've just received some ADCP data processed with the latest version of the toolbox, and one file failed the compliance checks (both CF and IMOS), hopefully due to a simple variable attribute issue:

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                                             IOOS Compliance Checker Report
                                                         cf:1.6
                                                http://cfconventions.org
------------------------------------------------------------------------------------------------------------------------
                                                   Corrective Actions 
IMOS_ANMN-NRS_AETVZ_20201028T231500Z_NRSNSI-ADCP_FV01_NRSNSI-ADCP-25-2020-10-Sentinel-or-Monitor-Workhorse-ADCP-63_END-20210309T231600Z_C-20210423T035526Z.nc has 4 potential issues


                                                         Errors
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Name                                                       Reasoning  
§5.0 Auxiliary Coordinates of PERG1 must have a subset of  auxiliary coordinate specified by the coordinates attribute,
PERG1's dimensions:                                        DIST_ALONG_BEAMS, is not a variable in this dataset
§5.0 Auxiliary Coordinates of PERG2 must have a subset of  auxiliary coordinate specified by the coordinates attribute,
PERG2's dimensions:                                        DIST_ALONG_BEAMS, is not a variable in this dataset
§5.0 Auxiliary Coordinates of PERG3 must have a subset of  auxiliary coordinate specified by the coordinates attribute,
PERG3's dimensions:                                        DIST_ALONG_BEAMS, is not a variable in this dataset
§5.0 Auxiliary Coordinates of PERG4 must have a subset of  auxiliary coordinate specified by the coordinates attribute,
PERG4's dimensions:                                        DIST_ALONG_BEAMS, is not a variable in this dataset


------------------------------------------------------------------------------------------------------------------------
                                             IOOS Compliance Checker Report
                                                        imos:1.4
                   http://content.aodn.org.au/Documents/IMOS/Conventions/IMOS_NetCDF_Conventions.pdf                    
------------------------------------------------------------------------------------------------------------------------
                                                   Corrective Actions                                                   
IMOS_ANMN-NRS_AETVZ_20201028T231500Z_NRSNSI-ADCP_FV01_NRSNSI-ADCP-25-2020-10-Sentinel-or-Monitor-Workhorse-ADCP-63_END-20210309T231600Z_C-20210423T035526Z.nc has 4 potential issues


                                                        Required                                                        
------------------------------------------------------------------------------------------------------------------------
Name    Reasoning
PERG1:  Coordinates attribute must contain a blank-separated list of
        valid variable names
PERG2:  Coordinates attribute must contain a blank-separated list of
        valid variable names
PERG3:  Coordinates attribute must contain a blank-separated list of
        valid variable names
PERG4:  Coordinates attribute must contain a blank-separated list of
        valid variable names

These variables have attribute PERG1:coordinates = "TIME LATITUDE LONGITUDE DIST_ALONG_BEAMS". However, there is no DIST_ALONG_BEAMS variable in this file. As the comment on other variables says

adcpBinMappingPP.m: data in beam coordinates originally referenced to DIST_ALONG_BEAMS has been vertically bin-mapped to HEIGHT_ABOVE_SENSOR using tilt information.

Does that also apply to the PERGx variables? In that case, they just need their coordinates attribute updated.
Or, if these variables have not been bin-mapped, then DIST_ALONG_BEAMS should still be included as a variable.

ocehugo commented

Thanks, @mhidas, confirmed & fix is here

These variables are not remapped, so the problem here is on the wrong removal of the DIST_ALONG_BEAMS dimensions. The current logic is removing the dimensions inadvertently and we are having PERG variables with coordinates that don't exist.

Also, since we don't run/have any compliance check at the toolbox level, this kind of stuff goes undetected.

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