Pseudograms remix #16
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- Add some extra_kwargs to deployment.json - Duplicate entries in instrument.json for instrument_acoustics - filters.py: extra_kwargs passed to reader.extras() - filters.py: trigger adding empty profiles to extras to allow writing ecometrics variables with extra dimension to keep all the profiles/netCDF files consistent. - slocum/__init__.py: refactor using the extra_kwargs passed to SlocumReader.extras(). Handle situations where there may or may not be a pseudogram and or ecometrics data available. In all cases if enable_pseudograms is set to true, ensure ecometrics(echodroid) and pseudogram variables use the extras dimension. - TODO: deployment.json (extra_kwargs) needs to become available to SlocumMerger class via watch/binary.py to grab arguments for pseudogram processing.
- remove POSITIONAL_VARS; afterthought for providing geographic information for extras variables - misc spacing errors - properly spelled a local variable
- slocum/__init__.py change default echosounderRange to -60.0 for current deployment.
- Moved read_attrs() from gutils.nc into gutils.__init__ so SlocumMerge() can read deployment.json extra_kwargs. Requires API additions to SlocumMerge(). - gutils.filters: move pseudogram arguments into a group; remove stale debug print statement - gutils.nc: access read_attrs() from gutils.__init__ - slocum.__init__: Add read_attrs() from gutils.__init__; detect keywords now moved to pseudogram group; remove stale debugging code - if both pseudogram and ecometrics data is missing, we have to create a single element in the extras data frame for it to appear in the netCDF file. - in all cases, we need to drop ecometric variables from the data array when pseudograms are enabled. - SlocumMerger(): add optional arguments deployments_path and template to allow detection of pseudogram extra_kwargs. Loosely based on how it operated in gutils.nc. - The pseudogram code is no longer active when not enabled. Added an option to turn pseudogram plotting on and off. Default is off to focus on the data. - echosounderRange is now enabled and should be adjustable if the sensor is pointed "up" or "down". At present, these should not changed mid-deployment. - Add extra_kwargs to ecometrics2 deployment.json - Adjust pytest ecometrics3 deployment.json to reflect grouping of pseudogram arguments. - Add extra arguments to SlocumMerge() for EcoMetrics tests One to Four. - Add EcoMetricsFour test with data. - NOTE: EcoMetricsOne deliberately turns pseudograms off to test storage to netCDF. Ecometrics information is stored in the time dimension instead of the extras dimension. - Added netCDF compliance testing to EcoMetrics One to Four. They all seem to pass. - All pytests pass at last check
- Remove pocean.meta.MetaInterface import from gutils.nc - Fix bare 'except' warnings in slocum.__init__ - Add blank lines in gutils.__init__
- Fix up exceptions again in slocum.__init__
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This PR addresses most issues in #12 and leaves one item open.
Adding entries to deployment.json enable and disabling of ecometrics/pseudogram processing:
The other keywords will need to be passed to the binary to ascii processor. We need a kwargs hook installed there to grab those options and pass to the pseudogram decoder.
pytests for the ecometrics3 set produce variables in the right dimension for the three known profiles. I had to kludge the extras profiles and add a single time element for it to output the
sci_echodroid*andpseudogram_*variables. For now, profiles that do not have an overlapping pseudogram end up with a single time element will all missing data. When the profile is missing, the variable is not written.This PR is incomplete. The ecometrics and ecometrics2 pytests still have signs of
pseudogram_*variables. If they are not present, those variables should not be written out. I can finalize this portion hopefully Friday.