feat: Add SBE 911+ HEX reader support

.gitignore

@@ -1,5 +1,6 @@
 # Output folder and generated files
 output/
+.coverage
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -45,4 +46,4 @@ build/
 seasenselib.egg-info/
 
 # Large data files (hosted externally)
-examples/moor/raw/msm76_2018/adcp/DS0218_RDI_000_24289.mat
+examples/moor/raw/msm76_2018/adcp/DS0218_RDI_000_24289.mat

seasenselib/knowledge/pipeline/mapping/allowed_parameters.json

@@ -20,6 +20,7 @@
   "north_amplitude": "North Amplitude",
   "north_velocity": "Northward velocity (m/s)",
   "oxygen": "Oxygen",
+  "par": "Photosynthetically Active Radiation (umol m-2 s-1)",
   "pitch": "Pitch angle (degrees)",
   "potential_temperature": "Potential Temperature \u03b8 (degC)",
   "power_supply_input": "Power supply input voltage (V)",

seasenselib/knowledge/pipeline/mapping/mappings_default.json

@@ -5,6 +5,12 @@
     "CTDALTIMETER",
     "ctd_altimeter"
   ],
+  "par": [
+    "par",
+    "PAR",
+    "ctd_fluor_par",
+    "CTDPAR"
+  ],
   "battery_voltage": [
     "Vbatt",
     "BATTV",

seasenselib/knowledge/pipeline/metadata_enrichment/parameters_metadata.json

@@ -75,10 +75,25 @@
     "standard_name": "northward_sea_water_velocity",
     "units": "m/s"
   },
+  "fluorescence": {
+    "coverage_content_type": "physicalMeasurement",
+    "long_name": "Fluorescence",
+    "measurement_type": "Measured",
+    "standard_name": "mass_concentration_of_chlorophyll_in_sea_water",
+    "units": "mg m-3"
+  },
   "oxygen": {
     "coverage_content_type": "physicalMeasurement",
     "long_name": "Oxygen",
-    "standard_name": "volume_fraction_of_oxygen_in_sea_water"
+    "standard_name": "moles_of_oxygen_per_unit_mass_in_sea_water",
+    "units": "umol kg-1"
+  },
+  "par": {
+    "coverage_content_type": "physicalMeasurement",
+    "long_name": "Photosynthetically Active Radiation",
+    "measurement_type": "Measured",
+    "standard_name": "downwelling_photosynthetic_photon_flux_in_sea_water",
+    "units": "umol m-2 s-1"
   },
   "pitch": {
     "long_name": "Pitch angle",
@@ -125,7 +140,7 @@
     "long_name": "Salinity",
     "measurement_type": "Derived",
     "short_name": "SAL",
-    "standard_name": "sea_water_salinity"
+    "standard_name": "sea_water_practical_salinity"
   },
   "speed_of_sound": {
     "long_name": "Speed of sound in sea water",

seasenselib/parameters.py

@@ -39,6 +39,7 @@
 BATTERY_VOLTAGE = 'battery_voltage'
 ALTIMETER = 'altimeter'
 REDOX_POTENTIAL = 'redox_potential'
+PAR = 'par'
 
 # Meta data should use standardized values from https://cfconventions.org/
 metadata = {
@@ -69,9 +70,9 @@
     SALINITY: {
         'long_name': "Salinity",
         'coverage_content_type': 'physicalMeasurement',
-        'standard_name': 'sea_water_salinity',
+        'standard_name': 'sea_water_practical_salinity',
         'short_name': 'SAL',
-        'measurement_type': 'Derived', 
+        'measurement_type': 'Derived',
     },
     TURBIDITY: {
         'long_name': "Turbidity",
@@ -82,8 +83,23 @@
     }, 
     OXYGEN: {
         'long_name': "Oxygen",
+        'units': 'umol kg-1',
+        'coverage_content_type': 'physicalMeasurement',
+        'standard_name': 'moles_of_oxygen_per_unit_mass_in_sea_water',
+    },
+    FLUORESCENCE: {
+        'long_name': "Fluorescence",
+        'units': 'mg m-3',
         'coverage_content_type': 'physicalMeasurement',
-        'standard_name': 'volume_fraction_of_oxygen_in_sea_water'
+        'standard_name': 'mass_concentration_of_chlorophyll_in_sea_water',
+        'measurement_type': 'Measured',
+    },
+    PAR: {
+        'long_name': "Photosynthetically Active Radiation",
+        'units': 'umol m-2 s-1',
+        'coverage_content_type': 'physicalMeasurement',
+        'standard_name': 'downwelling_photosynthetic_photon_flux_in_sea_water',
+        'measurement_type': 'Measured',
     },
     DEPTH: {
         'long_name': 'Depth',
@@ -304,6 +320,9 @@
     ALTIMETER: [
         'altM', 'altimeter'
     ],
+    PAR: [
+        'par', 'PAR',
+    ],
     DENSITY: [ 
         'sigma-t00', 'sigma-t11',
         'sigma-theta00', 'sigma-theta11',