Integration of echometrics

[jr3cermak]

• Add default dtypes to ascii2nc and bin2ascii argument processor.
• Pass the data block when processing extras data.
• If pseudogram is present, reassign echometric values with the extras dimension.
• Interweave echometrics data into pseudogram with extras dimension.
• Return data block from extras if modified.
• Decoding the pseudogram now uses a python library "dbdreader" for reading the raw binary instead of a prior code. This could eliminate the need for any of the slocum binaries that are only usable on x86 systems.
• dbdreader: https://github.com/smerckel/dbdreader
• Updated decodePsudogram.py and teledyne.py files using "dbdreader".
• Update covertDbd.sh with API/args updates to decodePseudogram.py

[jr3cermak]

The netCDF file that is created has echometrics variables with the extras dimension:

        double sci_echodroid_aggindex(extras) ;
                sci_echodroid_aggindex:_FillValue = -9999.9 ;
                sci_echodroid_aggindex:units = "m-1" ;
                sci_echodroid_aggindex:long_name = "Aggregation Index" ;
                sci_echodroid_aggindex:colorBarMinimum = 0. ;
                sci_echodroid_aggindex:colorBarMaximum = 1. ;
                sci_echodroid_aggindex:ioos_category = "Other" ;
                sci_echodroid_aggindex:platform = "platform" ;
                sci_echodroid_aggindex:observation_type = "measured" ;
                sci_echodroid_aggindex:coordinates = "time depth lon lat" ;

The data is inserted into the first matching pseudogram_time when multiple times exist.

sci_echodroid_aggindex = _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, 0.0379715003073215, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    0.0335540995001793, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, 0.0404663011431694, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, 0.0362090989947319, _, _, _, _, _, 
....

Next steps?

[kwilcox]

Thanks @jr3cermak! Is there anyway we can get a test written that produces the ecometrics and pseudogram data on the extras dimension so I see how the file looks? The three tests I have written for ecometrics don't end up producing any netCDF files with the extras dimension. You can send me the subset of *.*bd files and the *.cac files and I can whip up the test.

We may want to always create extras dimension for the ecometric variables, even if there is no pseudogram data available. If the ecometric variables witch between using the time dimension and the extras dimension in different profiles it will be difficult to aggregate them together over the entire deployment.