Continue cmd line scripts for multitasking/multilevel. Reorganize sam…

…ple data.

.gitignore

@@ -15,20 +15,50 @@
 Data/Zhang_rho_db.mat
 Data/Anc/
 Data/L*/
-Data/Sample_Data/L*/
 Data/Reports/
-Data/Sample_Data/Reports/
 Data/Photos/
-Plots/
-Logs/
-# The /* is required if you later want to unignored subsets
-Config/* 
+# The /* is required if you later want to unignore subsets (i.e., to keep the directory itself)
+Data/Sample_Data/DALEC/*
+!Data/Sample_Data/DALEC/RAW
+!Data/Sample_Data/DALEC/RAW/*
+!Data/Sample_Data/DALEC/Instrument_Characterization*/
+!Data/Sample_Data/DALEC/Instrument_Characterization*/*
+!Data/Sample_Data/DALEC/*Ancillary.sb
+Data/Sample_Data/Manual_TriOS/*
+!Data/Sample_Data/Manual_TriOS/RAW
+!Data/Sample_Data/Manual_TriOS/RAW/*
+!Data/Sample_Data/Manual_TriOS/Instrument_Characterization*/
+!Data/Sample_Data/Manual_TriOS/Instrument_Characterization*/*
+!Data/Sample_Data/Manual_TriOS/*Ancillary.sb
+Data/Sample_Data/pySAS/*
+!Data/Sample_Data/pySAS/RAW
+!Data/Sample_Data/pySAS/RAW/*
+!Data/Sample_Data/pySAS/Instrument_Characterization*/
+!Data/Sample_Data/pySAS/Instrument_Characterization*/*
+!Data/Sample_Data/pySAS/Photos/
+!Data/Sample_Data/pySAS/*Ancillary.sb
+Data/Sample_Data/SolarTracker/*
+!Data/Sample_Data/SolarTracker/RAW
+!Data/Sample_Data/SolarTracker/RAW/*
+!Data/Sample_Data/SolarTracker/Instrument_Characterization*/
+!Data/Sample_Data/SolarTracker/Instrument_Characterization*/*
+!Data/Sample_Data/SolarTracker/*Ancillary.sb
+Data/Sample_Data/SoRad/*
+!Data/Sample_Data/SoRad/RAW
+!Data/Sample_Data/SoRad/RAW/*
+!Data/Sample_Data/SoRad/Instrument_Characterization*/
+!Data/Sample_Data/SoRad/Instrument_Characterization*/*
+!Data/Sample_Data/SoRad/*Ancillary.sb
 
+Config/* 
 # To update sample configurations, uncomment:
 # !Config/sample_*_Calibration/
 # !Config/sample_*.cfg
 # !Config/sample_*.hdr
 # !Config/sample_*.csv
+Plots/
+Logs/
+
 ## To allow local changes to a file on remote, but not have those tracked:
 # git update-index --skip-worktree Config/sample_SEABIRD_pySAS.cfg
 #   Had to be run for each file due to conflicts with unrelated config files

Config/sample_TRIOS_NOTRACKER.cfg

@@ -1 +1 @@
-{"CalibrationFiles": {"SAM_8329.ini": {"enabled": true, "frameType": "ES"}, "SAM_8166.ini": {"enabled": true, "frameType": "LI"}, "SAM_8595.ini": {"enabled": true, "frameType": "LT"}}, "SensorType": "TriOS", "fL1aUTCOffset": 0.0, "bL1aCleanSZA": 1, "fL1aCleanSZAMax": 70.0, "bL1aqcSolarTracker": 0, "bL1aqcCleanPitchRoll": 0, "fL1aqcPitchRollPitch": 5.0, "fL1aqcPitchRollRoll": 5.0, "fL1aqcRotatorHomeAngle": 0.0, "bL1aqcRotatorDelay": 0, "fL1aqcRotatorDelay": 2.0, "bL1aqcRotatorAngle": 0, "fL1aqcRotatorAngleMin": -40.0, "fL1aqcRotatorAngleMax": 40.0, "bL1aqcCleanSunAngle": 1, "fL1aqcSunAngleMin": 90.0, "fL1aqcSunAngleMax": 135.0, "bL1aqcDeglitch": 0, "fL1aqcESWindowDark": 11, "fL1aqcESWindowLight": 5, "fL1aqcESSigmaDark": 3.2, "fL1aqcESSigmaLight": 2.3, "fL1aqcLIWindowDark": 11, "fL1aqcLIWindowLight": 5, "fL1aqcLISigmaDark": 3.3, "fL1aqcLISigmaLight": 3.0, "fL1aqcLTWindowDark": 11, "fL1aqcLTWindowLight": 13, "fL1aqcLTSigmaDark": 3.2, "fL1aqcLTSigmaLight": 2.7, "bL1aqcThreshold": 0, "fL1aqcESMinDark": null, "fL1aqcESMinLight": null, "fL1aqcESMaxDark": null, "fL1aqcESMaxLight": null, "fL1aqcESMinMaxBandDark": null, "fL1aqcESMinMaxBandLight": null, "fL1aqcLIMinDark": null, "fL1aqcLIMinLight": null, "fL1aqcLIMaxDark": null, "fL1aqcLIMaxLight": null, "fL1aqcLIMinMaxBandDark": null, "fL1aqcLIMinMaxBandLight": null, "fL1aqcLTMinDark": null, "fL1aqcLTMinLight": null, "fL1aqcLTMaxDark": null, "fL1aqcLTMaxLight": null, "fL1aqcLTMinMaxBandDark": null, "fL1aqcLTMinMaxBandLight": null, "fL1aqcAnomalyStep": 20, "bL1bGetAnc": 2, "bL1bObpgCreds": 0, "fL1bDefaultWindSpeed": 5.0, "fL1bDefaultAOD": 0.2, "fL1bDefaultSalt": 38.0, "fL1bDefaultSST": 28.0, "bL1bCal": 3, "FullCalDir": "Config/sample_TRIOS_NOTRACKER_Calibration", "RadCalDir": "Config/sample_TRIOS_NOTRACKER_Calibration", "FidRadDB": false, "fL1bInterpInterval": 3.3, "bL1bPlotTimeInterp": 0, "fL1bPlotInterval": 20.0, "bL1bqcLtUVNIR": 1, "fL1bqcMaxWind": 10.0, "fL1bqcSZAMin": 20.0, "fL1bqcSZAMax": 60.0, "bL1bqcEnableSpecQualityCheck": 1, "bL1bqcEnableSpecQualityCheckPlot": 0, "fL1bqcSpecFilterEs": 5.0, "fL1bqcSpecFilterLi": 8.0, "fL1bqcSpecFilterLt": 3.0, "bL1bqcEnableQualityFlags": 1, "fL1bqcCloudFlag": 1.0, "fL1bqcSignificantEsFlag": 2.0, "fL1bqcDawnDuskFlag": 1.0, "fL1bqcRainfallHumidityFlag": 1.095, "bL2Stations": 0, "fL2TimeInterval": 300, "bL2EnablePercentLt": 1, "fL2PercentLt": 10.0, "fL2RhoSky": 0.0256, "bL23CRho": 0, "bL2ZhangRho": 0, "bL2DefaultRho": 1, "bL2PerformNIRCorrection": 1, "bL2SimpleNIRCorrection": 0, "bL2SimSpecNIRCorrection": 1, "bL2NegativeSpec": 1, "bL2BRDF": 1, "bL2BRDF_fQ": 0, "bL2BRDF_IOP": 1, "bL2WeightMODISA": 1, "bL2WeightSentinel3A": 0, "bL2WeightVIIRSN": 0, "bL2WeightMODIST": 0, "bL2WeightSentinel3B": 0, "bL2WeightVIIRSJ": 0, "bL2PlotRrs": 1, "bL2PlotnLw": 1, "bL2PlotEs": 1, "bL2PlotLi": 1, "bL2PlotLt": 1, "seaBASSHeaderFileName": "sample_TRIOS_NOTRACKER.hdr", "bL2SaveSeaBASS": 1, "bL2WriteReport": 1, "bL1dDeglitch": 0, "bL2EnableQualityFlags": 1, "bL2Prodoc3m": 1, "bL2Prodkd490": 0, "bL2Prodpic": 0, "bL2Prodpoc": 0, "bL2Prodipar": 0, "bL2Prodavw": 0, "bL2Prodqwip": 0, "bL2ProdweiQA": 0, "bL2Prodgocad": 0, "bL2Prodag": 0, "bL2ProdSg": 0, "bL2ProdDOC": 0, "bL2Prodgiop": 0, "bL2ProdaGiop": 0, "bL2ProdadgGiop": 0, "bL2ProdadgSGiop": 0, "bL2ProdaphGiop": 0, "bL2ProdaphSGiop": 0, "bL2ProdbbGiop": 0, "bL2ProdbbpGiop": 0, "bL2ProdbbpSGiop": 0, "bL2Prodqaa": 1, "bL2ProdaQaa": 0, "bL2ProdadgQaa": 1, "bL2ProdaphQaa": 0, "bL2ProdbQaa": 0, "bL2ProdbbQaa": 0, "bL2ProdbbpQaa": 1, "bL2ProdcQaa": 0}
+{"CalibrationFiles": {"SAM_8329.ini": {"enabled": true, "frameType": "ES"}, "SAM_8166.ini": {"enabled": true, "frameType": "LI"}, "SAM_8595.ini": {"enabled": true, "frameType": "LT"}}, "SensorType": "TriOS", "fL1aUTCOffset": 0.0, "bL1aCleanSZA": 1, "fL1aCleanSZAMax": 70.0, "bL1aqcSolarTracker": 0, "bL1aqcCleanPitchRoll": 0, "fL1aqcPitchRollPitch": 5.0, "fL1aqcPitchRollRoll": 5.0, "fL1aqcRotatorHomeAngle": 0.0, "bL1aqcRotatorDelay": 0, "fL1aqcRotatorDelay": 2.0, "bL1aqcRotatorAngle": 0, "fL1aqcRotatorAngleMin": -40.0, "fL1aqcRotatorAngleMax": 40.0, "bL1aqcCleanSunAngle": 1, "fL1aqcSunAngleMin": 90.0, "fL1aqcSunAngleMax": 135.0, "bL1aqcDeglitch": 0, "fL1aqcESWindowDark": 11, "fL1aqcESWindowLight": 5, "fL1aqcESSigmaDark": 3.2, "fL1aqcESSigmaLight": 2.3, "fL1aqcLIWindowDark": 11, "fL1aqcLIWindowLight": 5, "fL1aqcLISigmaDark": 3.3, "fL1aqcLISigmaLight": 3.0, "fL1aqcLTWindowDark": 11, "fL1aqcLTWindowLight": 13, "fL1aqcLTSigmaDark": 3.2, "fL1aqcLTSigmaLight": 2.7, "bL1aqcThreshold": 0, "fL1aqcESMinDark": null, "fL1aqcESMinLight": null, "fL1aqcESMaxDark": null, "fL1aqcESMaxLight": null, "fL1aqcESMinMaxBandDark": null, "fL1aqcESMinMaxBandLight": null, "fL1aqcLIMinDark": null, "fL1aqcLIMinLight": null, "fL1aqcLIMaxDark": null, "fL1aqcLIMaxLight": null, "fL1aqcLIMinMaxBandDark": null, "fL1aqcLIMinMaxBandLight": null, "fL1aqcLTMinDark": null, "fL1aqcLTMinLight": null, "fL1aqcLTMaxDark": null, "fL1aqcLTMaxLight": null, "fL1aqcLTMinMaxBandDark": null, "fL1aqcLTMinMaxBandLight": null, "fL1aqcAnomalyStep": 20, "bL1bGetAnc": 2, "bL1bObpgCreds": 0, "fL1bDefaultWindSpeed": 5.0, "fL1bDefaultAOD": 0.2, "fL1bDefaultSalt": 38.0, "fL1bDefaultSST": 28.0, "bL1bCal": 3, "FullCalDir": "Config/sample_TRIOS_NOTRACKER_Calibration", "RadCalDir": "Config/sample_TRIOS_NOTRACKER_Calibration", "FidRadDB": false, "fL1bInterpInterval": 3.3, "bL1bPlotTimeInterp": 0, "fL1bPlotInterval": 20.0, "bL1bqcLtUVNIR": 1, "fL1bqcMaxWind": 10.0, "fL1bqcSZAMin": 20.0, "fL1bqcSZAMax": 60.0, "bL1bqcEnableSpecQualityCheck": 1, "bL1bqcEnableSpecQualityCheckPlot": 0, "fL1bqcSpecFilterEs": 5.0, "fL1bqcSpecFilterLi": 8.0, "fL1bqcSpecFilterLt": 3.0, "bL1bqcEnableQualityFlags": 1, "fL1bqcCloudFlag": 1.0, "fL1bqcSignificantEsFlag": 2.0, "fL1bqcDawnDuskFlag": 1.0, "fL1bqcRainfallHumidityFlag": 1.095, "bL2Stations": 0, "fL2TimeInterval": 300, "bL2EnablePercentLt": 1, "fL2PercentLt": 10.0, "fL2RhoSky": 0.0256, "bL23CRho": 0, "bL2ZhangRho": 0, "bL2DefaultRho": 1, "bL2PerformNIRCorrection": 1, "bL2SimpleNIRCorrection": 0, "bL2SimSpecNIRCorrection": 1, "bL2NegativeSpec": 1, "bL2BRDF": 1, "bL2BRDF_fQ": 0, "bL2BRDF_IOP": 1, "bL2WeightMODISA": 1, "bL2WeightSentinel3A": 0, "bL2WeightVIIRSN": 0, "bL2WeightMODIST": 0, "bL2WeightSentinel3B": 0, "bL2WeightVIIRSJ": 0, "bL2PlotRrs": 1, "bL2PlotnLw": 1, "bL2PlotEs": 1, "bL2PlotLi": 1, "bL2PlotLt": 1, "seaBASSHeaderFileName": "sample_TRIOS_NOTRACKER_Full.hdr", "bL2SaveSeaBASS": 1, "bL2WriteReport": 1, "bL1dDeglitch": 0, "bL2EnableQualityFlags": 1, "bL2Prodoc3m": 1, "bL2Prodkd490": 0, "bL2Prodpic": 0, "bL2Prodpoc": 0, "bL2Prodipar": 0, "bL2Prodavw": 1, "bL2Prodqwip": 1, "bL2ProdweiQA": 1, "bL2Prodgocad": 1, "bL2Prodag": 1, "bL2ProdSg": 1, "bL2ProdDOC": 1, "bL2Prodgiop": 0, "bL2ProdaGiop": 0, "bL2ProdadgGiop": 0, "bL2ProdadgSGiop": 0, "bL2ProdaphGiop": 0, "bL2ProdaphSGiop": 0, "bL2ProdbbGiop": 0, "bL2ProdbbpGiop": 0, "bL2ProdbbpSGiop": 0, "bL2Prodqaa": 1, "bL2ProdaQaa": 0, "bL2ProdadgQaa": 1, "bL2ProdaphQaa": 1, "bL2ProdbQaa": 0, "bL2ProdbbQaa": 0, "bL2ProdbbpQaa": 1, "bL2ProdcQaa": 0}

Main.py

@@ -559,13 +559,13 @@ class Command():
     ''' Class for batching without using the GUI. Scripted calls preferred, but 
         direct call possible. '''
 
-    def __init__(self, configFilePath, from_level, inputFile, outputDirectory, to_level, 
+    def __init__(self, configFilePath, from_level, inputFile, dataDirectory, to_level, 
                  ancFile=None, processMultiLevel=False):
 
         self.configFilename = configFilePath
         self.inputFile = inputFile
-        self.inputDirectory = os.path.join(outputDirectory,from_level)
-        self.outputDirectory = outputDirectory
+        self.inputDirectory = os.path.join(dataDirectory,from_level)
+        self.outputDirectory = dataDirectory
         self.level = to_level
         self.ancFile = ancFile
 
@@ -609,7 +609,7 @@ def __init__(self, configFilePath, from_level, inputFile, outputDirectory, to_le
         MainConfig.settings['cfgPath'] = configFilePath
         MainConfig.settings['version'] = version
         MainConfig.settings["metFile"] = self.ancFile
-        MainConfig.settings["outDir"] = outputDirectory
+        MainConfig.settings["outDir"] = self.outputDirectory
 
         if type(inputFile) is list:
             # Process the entire directory of the first file in the list

Source/GetAnc.py

@@ -124,7 +124,7 @@ def getAnc(inputGroup):
                     alert = QtWidgets.QMessageBox()
                     alert.setText(f'Request error: {status}\n \
                                     Check that server credentials have \n \
-                                    been entered in Configuration Window L1BQC. \n  \
+                                    been entered in Configuration Window L1B. \n  \
                                     MERRA2 model data are not available until \n \
                                     the third week of the following month.')
                     alert.exec_()