Merge branch 'dev'

.gitignore

@@ -75,6 +75,7 @@ run_*.py
 
 # copernicus url and keys
 .cdsapirc
+# gitignore only skips new files, not updates to existing files
 .ecmwf_api_config
 
 #ignore ".idea/" if working with pycharm:

Config/sample_SEABIRD_pySAS.cfg

@@ -50,9 +50,9 @@
     "fL1aqcPitchRollPitch": 5.0,
     "fL1aqcPitchRollRoll": 5.0,
     "fL1aqcRotatorHomeAngle": 0.0,
-    "bL1aqcRotatorDelay": 1,
+    "bL1aqcRotatorDelay": 0,
     "fL1aqcRotatorDelay": 2.0,
-    "bL1aqcRotatorAngle": 1,
+    "bL1aqcRotatorAngle": 0,
     "fL1aqcRotatorAngleMin": -126.0,
     "fL1aqcRotatorAngleMax": 42.0,
     "bL1aqcCleanSunAngle": 1,
@@ -92,7 +92,6 @@
     "fL1aqcLTMinMaxBandLight": null,
     "fL1aqcAnomalyStep": 20,
     "bL1bGetAnc": 1,
-    "bL1bObpgCreds": 0,
     "fL1bDefaultWindSpeed": 5.0,
     "fL1bDefaultAOD": 0.2,
     "fL1bDefaultSalt": 38.0,
@@ -148,7 +147,6 @@
     "seaBASSHeaderFileName": "sample_SEABIRD_pySAS.hdr",
     "bL2SaveSeaBASS": 1,
     "bL2WriteReport": 1,
-    "bL1b_InterpPlotTimeInterp": 1,
     "bL2EnableQualityFlags": 1,
     "bL2Prodoc3m": 1,
     "bL2Prodkd490": 0,

Config/sample_SEABIRD_pySAS.hdr

@@ -34,7 +34,7 @@
     "rho_correction": "M99",
     "NIR_residual_correction": "R06",
     "BRDF_correction": "L11",
-    "comments": "! HyperInSPACE vers = 1.2.7\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-Full-Characterization\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",
+    "comments": "! HyperInSPACE vers = 1.2.9\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 = Off\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-Full-Characterization\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"

Config/sample_TRIOS_NOTRACKER.cfg

@@ -120,7 +120,6 @@
     "seaBASSHeaderFileName": "sample_TRIOS_NOTRACKER.hdr",
     "bL2SaveSeaBASS": 1,
     "bL2WriteReport": 1,
-    "bL1b_InterpPlotTimeInterp": 1,
     "bL2EnableQualityFlags": 1,
     "bL2Prodoc3m": 0,
     "bL2Prodkd490": 0,

Config/sample_TRIOS_NOTRACKER.hdr

@@ -34,7 +34,7 @@
     "rho_correction": "M99",
     "NIR_residual_correction": "R06",
     "BRDF_correction": "L11",
-    "comments": "! HyperInSPACE vers = 1.2.7\n! HyperInSPACE Config = sample_TRIOS_NOTRACKER.cfg\n! Rotator Home Angle = 0.0\n! Rotator Delay = 2.0\n! Pitch/Roll Filter = Off\n! Max Pitch/Roll = 5.0\n! Rotator Min/Max Filter = Off\n! Rotator Min = -40.0\n! Rotator Max = 40.0\n! Rel Azimuth Filter = On\n! Rel Azimuth Min = 90.0\n! Rel Azimuth Max = 135.0\n! Deglitch Filter = Off\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-Full-Characterization\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",
+    "comments": "! HyperInSPACE vers = 1.2.9\n! HyperInSPACE Config = sample_TRIOS_NOTRACKER.cfg\n! Rotator Home Angle = 0.0\n! Rotator Delay = 2.0\n! Pitch/Roll Filter = Off\n! Max Pitch/Roll = 5.0\n! Rotator Min/Max Filter = Off\n! Rotator Min = -40.0\n! Rotator Max = 40.0\n! Rel Azimuth Filter = On\n! Rel Azimuth Min = 90.0\n! Rel Azimuth Max = 135.0\n! Deglitch Filter = Off\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-Full-Characterization\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! Sample dataset for TriOS triplet with no GPS or sun tracker.\n! FRM4SOC-2 Field InterComparison Experiment (FICE)\n! July 11 - 21, 2022\n! Acqua Alta Oceanographic Tower (AAOT), CNR-ISMAR\n! \n! RelAz refer to solar-sensor relative azimuth angle.\n! Manually operated TriOS triplet. Height: ~15 m, Tower color: Red/yellow.\n!",
     "missing": -9999,
     "delimiter": "comma"

Main.py

@@ -16,6 +16,7 @@
 import sys
 import time
 from PyQt5 import QtCore, QtGui, QtWidgets
+from PIL import Image, ImageTk
 
 # import requests
 # from tqdm import tqdm
@@ -25,12 +26,12 @@
 from Source.Controller import Controller
 from Source.ConfigFile import ConfigFile
 from Source.ConfigWindow import ConfigWindow
-from Source.GetAnc import GetAnc
+import Source.GetAnc_credentials as credentials
 from Source.SeaBASSHeader import SeaBASSHeader
 from Source.SeaBASSHeaderWindow import SeaBASSHeaderWindow
 from Source.Utilities import Utilities
 
-VERSION = "1.2.8"
+VERSION = "1.2.9"
 
 
 class Window(QtWidgets.QWidget):
@@ -44,6 +45,13 @@ def __init__(self, parent=None):
         super().__init__(parent)
         # self.setStyleSheet("background-color: #e3e6e1;")
 
+        icon_path = os.path.join(os.path.dirname(__file__), 'Data', 'Img', 'logo.ico')
+        # load_icon = Image.open(icon_path)
+        # render = ImageTk.PhotoImage(load_icon)  # Loads the given icon
+        # app.iconphoto(False, render)
+
+        self.setWindowIcon(QtGui.QIcon(icon_path))
+
         # Create - if inexistent - directories Plots, Config and Logs
         hypercpDirs = ["Plots", "Config", "Logs"]
         for directory in hypercpDirs:
@@ -60,7 +68,6 @@ def __init__(self, parent=None):
 
     def initUI(self):
         """Initialize the user interface"""
-
         # Main window configuration restore
         MainConfig.loadConfig(
             MainConfig.fileName, VERSION
@@ -421,21 +428,6 @@ def processSingle(self, lvl):
         ConfigFile.loadConfig(configFileName)
         seaBASSHeaderFileName = ConfigFile.settings["seaBASSHeaderFileName"]
         SeaBASSHeader.loadSeaBASSHeader(seaBASSHeaderFileName)
-        InstrumentType = ConfigFile.settings["SensorType"]
-
-        # To check instrument type
-        if InstrumentType.lower() == "trios":
-            flag_Trios = 1
-        elif InstrumentType.lower() == "seabird":
-            flag_Trios = 0
-        else:
-            print("Error in configuration file: Sensor type not specified")
-            sys.exit()
-
-        # Select data files
-        # if not self.inputDirectory[0]:
-        #     print("Bad input parent directory.")
-        #     return
 
         if lvl == "L1A":
             inLevel = "raw"
@@ -471,14 +463,17 @@ def processSingle(self, lvl):
         print("Process Calibration Files")
         calFiles = ConfigFile.settings["CalibrationFiles"]
 
-        if flag_Trios == 0:
+        # if flag_Trios == 0:
+        calibrationMap = None
+        if ConfigFile.settings["SensorType"].lower() == "seabird":
             calibrationMap = Controller.processCalibrationConfig(
                 configFileName, calFiles
             )
-        else:
+        # else:
+        elif ConfigFile.settings["SensorType"].lower() == "trios":
             calibrationMap = Controller.processCalibrationConfigTrios(calFiles)
-            # calibrationMap = 0
-        if not calibrationMap.keys():
+
+        if not calibrationMap:
             print(
                 "No calibration files found. "
                 "Check Config directory for your instrument files."
@@ -490,9 +485,11 @@ def processSingle(self, lvl):
             print("Bad output directory.")
             return
 
+        # Controller.processFilesSingleLevel(
+        #     self.outputDirectory, fileNames, calibrationMap, lvl, flag_Trios
+        # )
         Controller.processFilesSingleLevel(
-            self.outputDirectory, fileNames, calibrationMap, lvl, flag_Trios
-        )
+            self.outputDirectory, fileNames, calibrationMap, lvl)
         t1Single = time.time()
         print(f"Time elapsed: {str(round((t1Single-t0Single)/60))} minutes")
 
@@ -544,8 +541,7 @@ def processMulti(self):
             return
 
         openFileNames = QtWidgets.QFileDialog.getOpenFileNames(
-            self, "Open File", self.inputDirectory
-        )
+            self, "Open File", self.inputDirectory)
 
         print("Files:", openFileNames)
 
@@ -557,14 +553,11 @@ def processMulti(self):
         if not self.outputDirectory:
             return
 
-        InstrumentType = ConfigFile.settings["SensorType"]
         calFiles = ConfigFile.settings["CalibrationFiles"]
         # To check instrument type
-        if InstrumentType.lower() == "trios":
-            flag_Trios = 1
+        if ConfigFile.settings["SensorType"].lower() == "trios":
             calibrationMap = Controller.processCalibrationConfigTrios(calFiles)
-        elif InstrumentType.lower() == "seabird":
-            flag_Trios = 0
+        elif ConfigFile.settings["SensorType"].lower() == "seabird":
             print("Process Calibration Files")
             filename = ConfigFile.filename
             calibrationMap = Controller.processCalibrationConfig(filename, calFiles)
@@ -573,8 +566,7 @@ def processMulti(self):
             sys.exit()
 
         Controller.processFilesMultiLevel(
-            self.outputDirectory, fileNames, calibrationMap, flag_Trios
-        )
+            self.outputDirectory, fileNames, calibrationMap)
         t1Multi = time.time()
         print(f"Time elapsed: {str(round((t1Multi-t0Multi)/60))} Minutes")
 
@@ -652,19 +644,16 @@ def __init__(
 
         ConfigFile.loadConfig(self.configFilename)
 
-        InstrumentType = ConfigFile.settings["SensorType"]
         calFiles = ConfigFile.settings["CalibrationFiles"]
 
-        if InstrumentType.lower() == "trios":
-            flag_Trios = 1
+        if ConfigFile.settings["SensorType"].lower() == "trios":
             calibrationMap = Controller.processCalibrationConfigTrios(calFiles)
-        elif InstrumentType.lower() == "seabird":
-            flag_Trios = 0
+        elif ConfigFile.settings["SensorType"].lower() == "seabird":
             print("Process Calibration Files")
             filename = ConfigFile.filename
             calibrationMap = Controller.processCalibrationConfig(filename, calFiles)
         else:
-            print("Error in configuration file: Sensor type not specified")
+            print(f'CalibrationConfig is not yet ready for {ConfigFile.settings["SensorType"]}')
             sys.exit()
 
         # Update the SeaBASS .hdr file in case changes were made to the configuration without using the GUI
@@ -673,19 +662,16 @@ def __init__(
         SeaBASSHeader.saveSeaBASSHeader(ConfigFile.settings['seaBASSHeaderFileName'])
 
         if processMultiLevel:
-            if InstrumentType.lower() == "trios" and to_level == "L1A":
+            if ConfigFile.settings["SensorType"].lower() == "trios" and to_level == "L1A":
                 Controller.processFilesMultiLevel(
-                    self.outputDirectory, iFile, calibrationMap, flag_Trios
-                )
+                    self.outputDirectory, iFile, calibrationMap)
             else:
                 Controller.processFilesMultiLevel(
-                    self.outputDirectory, [iFile], calibrationMap, flag_Trios
-                )
+                    self.outputDirectory, [iFile], calibrationMap)
         else:
             # processSingleLevel is only prepared for a singleton file at a time
             Controller.processSingleLevel(
-                self.outputDirectory, iFile, calibrationMap, to_level, flag_Trios
-            )
+                self.outputDirectory, iFile, calibrationMap, to_level)
 
 
 if __name__ == "__main__":
@@ -751,22 +737,6 @@ def __init__(
         default=None,
         type=str,
     )
-    required.add_argument(
-        "-u",
-        action="store",
-        dest="username",
-        help="Username of the account on https://oceancolor.gsfc.nasa.gov/",
-        default=None,
-        type=str,
-    )
-    required.add_argument(
-        "-p",
-        action="store",
-        dest="password",
-        help="Password of the account on https://oceancolor.gsfc.nasa.gov/",
-        default=None,
-        type=str,
-    )
 
     args = parser.parse_args()
 
@@ -798,8 +768,6 @@ def __init__(
     outputDirectory = args.outputDirectory
     level = args.level
     ancFile = args.ancFile
-    username = args.username
-    password = args.password
     multiLevel = args.multiLevel
 
 
@@ -817,12 +785,15 @@ def __init__(
     # If the cmd argument is given, run the Command class without the GUI
     if cmd:
         os.environ["HYPERINSPACE_CMD"] = "TRUE" # Must be a string
-        if not (args.username is None or args.password is None):
-            # Only for L2 processing set credentials
-            GetAnc.userCreds(username, password)
+
+        # Pop up credential windows if credentials not stored...
+        credentials.credentialsWindow('NASA_Earth_Data')
+        credentials.credentialsWindow('ECMWF_ADS')
+
         Command(configFilePath, inputFile, multiLevel, outputDirectory, level, ancFile)
     else:
         os.environ["HYPERINSPACE_CMD"] = "FALSE" # Must be a string
+
         app = QtWidgets.QApplication(sys.argv)
         win = Window()
         sys.exit(app.exec_())

README.md

@@ -13,7 +13,7 @@ retrieval. Data outputs are formatted to text files for submission to the [SeaBA
 Currently, HyperCP supports <a href='https://www.seabird.com/'>Sea-Bird Scientific</a> HyperSAS packages with and
 without SolarTracker or pySAS robotic platforms as well as [TriOS](https://www.trios.de/en/radiometers.html) used in manual configuration. If you are interested in integrating support for your platform, contact us at the email addresses below or in the Discussions tab of the GitHub repository.
 
-## Version 1.2.8
+## Version 1.2.9
 
 ```
 The MIT license
@@ -93,6 +93,11 @@ If environment problems are encountered after updating HyperCP (e.g, dependencie
 ```
 conda env update --file environment.yml --prune
 ```
+**NOTE:** If you started with working with v1.2.8 or less and are now in v1.2.9 or higher, you may need to remove the old hypercp environment and reinstall the environment as described above.
+```
+prompt$ conda deactivate
+prompt$ conda remove -n hypercp --all
+```
 
 To report a bug, please submit it [here](https://github.com/nasa/HyperCP/issues), the HyperCP Team will take
 care of it :). All other support inquiries should be directed to the Discussions board [here](https://github.com/nasa/HyperCP/discussions)