Promote 6S factory. MET_FLAG attribute. Linting.

Config/sample_SEABIRD_pySAS.cfg

@@ -113,7 +113,7 @@
     "fL1bqcSpecFilterEs": 5.0,
     "fL1bqcSpecFilterLi": 8.0,
     "fL1bqcSpecFilterLt": 3.0,
-    "bL1bqcEnableQualityFlags": 0,
+    "bL1bqcEnableQualityFlags": 1,
     "fL1bqcCloudFlag": 1.0,
     "fL1bqcSignificantEsFlag": 2.0,
     "fL1bqcDawnDuskFlag": 1.0,
@@ -148,9 +148,8 @@
     "seaBASSHeaderFileName": "sample_SEABIRD_pySAS.hdr",
     "bL2SaveSeaBASS": 1,
     "bL2WriteReport": 1,
-    "bL1b_InterpPlotTimeInterp": 1,
     "bL1dDeglitch": 1,
-    "bL2EnableQualityFlags": 0,
+    "bL2EnableQualityFlags": 1,
     "bL2Prodoc3m": 1,
     "bL2Prodkd490": 0,
     "bL2Prodpic": 0,

Config/sample_SEABIRD_pySAS.hdr

@@ -30,7 +30,7 @@
     "south_latitude": "",
     "east_longitude": "",
     "west_longitude": "",
-    "comments": "! HyperInSPACE vers = 1.2.4\n! HyperInSPACE Config = sample_SEABIRD_pySAS.cfg\n! Rotator Home Angle = 0.0\n! Rotator Delay = 2.0\n! Pitch/Roll Filter = On\n! Max Pitch/Roll = 5.0\n! Rotator Min/Max Filter = On\n! Rotator Min = -126.0\n! Rotator Max = 42.0\n! Rel Azimuth Filter = On\n! Rel Azimuth Min = 90.0\n! Rel Azimuth Max = 135.0\n! Deglitch Filter = On\n! ES Dark Window = 11\n! ES Light Window = 5\n! ES Dark Sigma = 3.2\n! ES Light Sigma = 2.3\n! LI Dark Window = 11\n! LI Light Window = 5\n! LI Dark Sigma = 3.3\n! LI Light Sigma = 3.0\n! LT Dark Window = 11\n! LT Light Window = 13\n! LT Dark Sigma = 3.2\n! LT Light Sigma = 2.7\n! FRM Pathway = FRM_Class-based\n! Wavelength Interp Int = 3.3\n! Max Wind = 10.0\n! Min SZA = 20.0\n! Max SZA = 60.0\n! Spectral Filter = On\n! Filter Sigma Es = 5.0\n! Filter Sigma Li = 8.0\n! Filter Sigma Lt = 3.0\n! Meteorological Filter = Off\n! Cloud Flag = 1.0\n! Es Flag = 2.0\n! Dawn/Dusk Flag = 1.0\n! Rain/Humidity Flag = 1.095\n! Ensemble Interval = 300\n! Percent Lt Filter = On\n! Percent Light = 10.0\n! Remove Negatives = On",
+    "comments": "! HyperInSPACE vers = 1.2.4\n! HyperInSPACE Config = sample_SEABIRD_pySAS.cfg\n! Rotator Home Angle = 0.0\n! Rotator Delay = 2.0\n! Pitch/Roll Filter = On\n! Max Pitch/Roll = 5.0\n! Rotator Min/Max Filter = On\n! Rotator Min = -126.0\n! Rotator Max = 42.0\n! Rel Azimuth Filter = On\n! Rel Azimuth Min = 90.0\n! Rel Azimuth Max = 135.0\n! Deglitch Filter = On\n! ES Dark Window = 11\n! ES Light Window = 5\n! ES Dark Sigma = 3.2\n! ES Light Sigma = 2.3\n! LI Dark Window = 11\n! LI Light Window = 5\n! LI Dark Sigma = 3.3\n! LI Light Sigma = 3.0\n! LT Dark Window = 11\n! LT Light Window = 13\n! LT Dark Sigma = 3.2\n! LT Light Sigma = 2.7\n! FRM Pathway = FRM_Class-based\n! Wavelength Interp Int = 3.3\n! Max Wind = 10.0\n! Min SZA = 20.0\n! Max SZA = 60.0\n! Spectral Filter = On\n! Filter Sigma Es = 5.0\n! Filter Sigma Li = 8.0\n! Filter Sigma Lt = 3.0\n! Meteorological Filter = On\n! Cloud Flag = 1.0\n! Es Flag = 2.0\n! Dawn/Dusk Flag = 1.0\n! Rain/Humidity Flag = 1.095\n! Ensemble Interval = 300\n! Percent Lt Filter = On\n! Percent Light = 10.0\n! Remove Negatives = On",
     "other_comments": "!\n! COMMENTS\n!\n! FRM4SOC-2 Field InterComparison Experiment (FICE)\n! July 11 - 21, 2022\n! Acqua Alta Oceanographic Tower (AAOT), CNR-ISMAR\n!\n! Ancillary data from: % https://www.comune.venezia.it/content/3-piattaforma-ISMAR-CNR\n! and field notes. relAz refers to target relative azimuth in pySAS.\n!\n! Home",
     "missing": -9999,
     "delimiter": "comma",

Source/ProcessL1b_FactoryCal.py

@@ -264,6 +264,8 @@ def processL1b_SeaBird(node, calibrationMap):
         node.attributes["SATPYR_UNITS"] = pyrUnits
 
         # Calculate 6S model
+        print('Running Py6S')
+
         sensortype = "ES"
         # Irradiance direct and diffuse ratio
         res_py6s = ProcessL1b_FRMCal.get_direct_irradiance_ratio(node, sensortype)

Source/ProcessL1bqc.py

@@ -1,7 +1,6 @@
-
+''' Process L1B to L1BQC '''
 import numpy as np
 import scipy as sp
-import datetime as datetime
 
 from Source.MainConfig import MainConfig
 from Source.Utilities import Utilities
@@ -120,8 +119,8 @@ def ltQuality(sasGroup):
 
         badTimes = np.unique(badTimes)
         # Duplicate each element to a list of two elements in a list
-        ''' BUG: This is not optimal as it creates one badTimes record for each bad
-            timestamp, rather than span of timestamps from badtimes[i][0] to badtimes[i][1]'''
+        # BUG: This is not optimal as it creates one badTimes record for each bad
+        #    timestamp, rather than span of timestamps from badtimes[i][0] to badtimes[i][1]
         badTimes = np.rot90(np.matlib.repmat(badTimes,2,1), 3)
         msg = f'{len(np.unique(badTimes))/len(ltDatetime)*100:.1f}% of spectra flagged'
         print(msg)
@@ -191,7 +190,6 @@ def metQualityCheck(refGroup, sasGroup, py6sGroup, ancGroup):
             if li750[indx]/es750[indx] >= cloudFLAG:
                 badTimes.append(dateTime)
                 flags2[indx] = True
-
 
             # Flag for significant es
             # Wernand 2002
@@ -208,7 +206,7 @@ def metQualityCheck(refGroup, sasGroup, py6sGroup, ancGroup):
 
             # Flag spectra affected by rainfall and high humidity
             # Wernand 2002 (940/370), Garaba et al. 2012 also uses Es(940/370), presumably 720 was developed by Wang...???
-            ''' Follow up on the source of this flag'''
+            # NOTE: Follow up on the source of this flag
             if es720[indx]/es370[indx] < humidityFlag:
                 badTimes.append(dateTime)
                 flags5[indx] = True
@@ -218,7 +216,7 @@ def metQualityCheck(refGroup, sasGroup, py6sGroup, ancGroup):
         msg = f'{len(np.unique(badTimes))/len(esTime)*100:.1f}% of spectra flagged (not filtered)'
         print(msg)
         Utilities.writeLogFile(msg)
-        
+
         # Restore timestamps to columns (since it's not going to filterData, where it otherwise happens)
         esData.datasetToColumns()
         liData.datasetToColumns()
@@ -719,6 +717,7 @@ def processL1bqc(node):
         gp.attributes["HUMIDITY_UNITS"] = "percent"
         gp.attributes["LATITUDE_UNITS"] = "dec. deg. N"
         gp.attributes["LONGITUDE_UNITS"] = "dec. deg. E"
+        gp.attributes["MET_FLAGS"] = "1: 6S Cloud, 2: Ruddick Cloud, 3: Es, 4: Dark,s 5: Rain"
         gp.attributes["PITCH_UNITS"] = "degrees"
         gp.attributes["POINTING_UNITS"] = "degrees"
         gp.attributes["REL_AZ_UNITS"] = "degrees"

Source/ProcessL2.py

@@ -2035,7 +2035,6 @@ def stationsEnsemblesReflectance(node, root, station=None):
                 rootCopy.getGroup('PY6S_MODEL').copy(root.getGroup('PY6S_MODEL'))
                 break
 
-
         if ConfigFile.settings['SensorType'].lower() == 'seabird':
             rootCopy.addGroup("ES_DARK_L1AQC")
             rootCopy.addGroup("ES_LIGHT_L1AQC")
@@ -2112,17 +2111,17 @@ def stationsEnsemblesReflectance(node, root, station=None):
             for index, stn in enumerate(stations):
                 # print(f'index: {index}, station: {station}, datetime: {dateTime[index]}')
                 # if np.isnan(station) and start == False:
-                if (stn != station) and (start == False):
+                if (stn != station) and (start is False):
                     start = dateTime[index]
                 # if not np.isnan(station) and not (start == False) and (stop == False):
-                if not (stn!=station) and not (start == False) and (stop == False):
+                if not (stn!=station) and (start is not False) and (stop is False):
                     stop = dateTime[index-1]
                     badTimes.append([start, stop])
                     start = False
                     stop = False
                 # End of file, no active station
                 # if np.isnan(station) and not (start == False) and (index == len(stations)-1):
-                if (stn != station) and not (start == False) and (index == len(stations)-1):
+                if (stn != station) and not (start is False) and (index == len(stations)-1):
                     stop = dateTime[index]
                     badTimes.append([start, stop])