Add Lowell Tilt Current Meter (TCM) support (#184)

This PR also fixes some Git LFS file issues.

* addtcm 1st commit

* add tcm 1st working test

* add spd, dir and update tests, docs

* fixes to cdir, lfs files

* restore *.txt *.yaml to git

* upadte lfs and attr

doc/config.rst

@@ -164,10 +164,10 @@ WXT-specific options include:
 EofE ECHOLOGGER
 ---------------
 - All the _min, _max, _bad_ens, etc. options available to the EXO.
-- instrument_type: types "ea" and "aa" are supported.
-- orientation: orientation of transducers types 'DOWN' or 'UP' are supported.
-- average_salinity: average salinity value (PSU) for the water mass for the deployment site and time period.
-- average_salinity_note: source of average salinity value.
+- ``instrument_type``: types "ea" and "aa" are supported.
+- ``orientation``: orientation of transducers types 'DOWN' or 'UP' are supported.
+- ``average_salinity``: average salinity value (PSU) for the water mass for the deployment site and time period.
+- ``average_salinity_note``: source of average salinity value.
 
 Sequoia Scientific LISST
 ------------------------
@@ -190,4 +190,12 @@ Onset Hobo
 - ``instrument_type``: can be ``hwl`` (water level), ``hwlb`` (water level as barometer), ``hdo`` (dissolved oxygen) or ``hcnd`` (conductivity) use these based on parameter measured by hobo logger
 - ``skipfooter``: number of lines to skip in the CSV file at the end of the file
 - ``ncols``: number of columns of data to read, starting at first
-- ``names``: option for user specified column names (only recommended when code will read names using automated/default method)
+- ``names``: option for user specified column names (only recommended when code will not read names using automated/default method)
+
+Lowell TCM Hobo
+----------
+
+- All the _min, _max, _bad_ens, etc. options available to the EXO.
+- ``skipfooter``: number of lines to skip in the CSV file at the end of the file
+- ``ncols``: number of columns of data to read, starting at first
+- ``names``: option for user specified column names (only recommended when code will not read names using automated/default method)

doc/tcm.rst

@@ -0,0 +1,29 @@
+Lowell Tilt Current Meter (TCM)
+*******************************
+
+Data will generally be processed using a series of run scripts. The first script for each instrument type
+depends on two :doc:`configuration files </config>`.
+
+Instrument data to raw .cdf
+===========================
+
+Convert from exported CSV file to a raw netCDF file with .cdf extension using ``runtcmcsv2cdf.py``.
+
+runtcmcsv2cdf.py
+-----------------
+
+.. argparse::
+   :ref: stglib.core.cmd.tcmcsv2cdf_parser
+   :prog: runtcmcsv2cdf.py
+
+Raw .cdf to CF-compliant .nc
+============================
+
+Convert the raw .cdf data into CF-compliant netCDF file with .nc extension using ``runtcmcdf2nc.py``.
+
+runtcmcdf2nc.py
+----------------
+
+.. argparse::
+   :ref: stglib.core.cmd.tcmcdf2nc_parser
+   :prog: runtcmcdf2nc.py

setup.py

@@ -75,6 +75,8 @@
             "runsigcdf2nc.py=stglib.core.runcmd:runsigcdf2nc",
             "runlisstcsv2cdf.py=stglib.core.runcmd:runlisstcsv2cdf",
             "runlisstcdf2nc.py=stglib.core.runcmd:runlisstcdf2nc",
+            "runtcmcsv2cdf.py=stglib.core.runcmd:runtcmcsv2cdf",
+            "runtcmcdf2nc.py=stglib.core.runcmd:runtcmcdf2nc",
         ],
     },
     include_package_data=True,

stglib/__init__.py

@@ -13,6 +13,7 @@
     rdi,
     rsk,
     sig,
+    tcm,
     troll,
     vec,
     wxt,

stglib/core/cmd.py

@@ -359,3 +359,20 @@ def sigdlfncdf2nc_parser():
     atmarg(parser)
 
     return parser
+
+
+def tcmcsv2cdf_parser():
+    description = "Convert Lowell Tilt Current Meter .txt file to raw .cdf format. Run this script from the directory containing TCM file."
+    parser = argparse.ArgumentParser(description=description)
+    gattsarg(parser)
+    yamlarg(parser)
+
+    return parser
+
+
+def tcmcdf2nc_parser():
+    description = "Convert raw TCM .cdf format to processed .nc files"
+    parser = argparse.ArgumentParser(description=description)
+    cdfarg(parser)
+
+    return parser

stglib/core/runcmd.py

@@ -291,3 +291,17 @@ def runwxtcsv2cdf():
     metadata = get_metadata(args)
 
     stglib.wxt.csv_to_cdf(metadata)
+
+
+def runtcmcdf2nc():
+    args = stglib.cmd.tcmcdf2nc_parser().parse_args()
+
+    run_cdf_to_nc(stglib.tcm.cdf_to_nc, args)
+
+
+def runtcmcsv2cdf():
+    args = stglib.cmd.tcmcsv2cdf_parser().parse_args()
+
+    metadata = get_metadata(args)
+
+    stglib.tcm.csv_to_cdf(metadata)

stglib/hobo.py

@@ -328,7 +328,12 @@ def ds_add_attrs(ds):
 
     if "BPR_915" in ds:
         ds["BPR_915"].attrs.update(
-            {"units": "mbar", "long_name": "Barometric pressure", "epic_code": 915}
+            {
+                "units": "mbar",
+                "long_name": "Barometric pressure",
+                "epic_code": 915,
+                "standard_name": "air_pressure",
+            }
         )
 
     if "T_21" in ds: