koronascript 0.2.1__tar.gz → 3.0.0__tar.gz

koronascript-3.0.0/KoronaScript/Configuration.py

@@ -0,0 +1,3 @@
+# Auto-generated, do not edit directly
+# see genmodule.py
+modules_spec = {'AngleDeletion': {'Active': True, 'Comment': ''}, 'BroadbandNotchFilter': {'Active': True, 'Comment': ''}, 'BroadbandSplitter': {'Active': True, 'Comment': '', 'AutoSplit': False, 'SplitCount': 3, 'SplitBandwidth': '', 'StopBandDistance': 1.0, 'MinBandwidth': 10.0, 'Downsampling': 'FACTOR', 'DownsamplingFactor': 1, 'DownsamplingSampleSize': 0.01, 'ComputeAngles': True, 'ComputationalMethod': 'BANDPASS_FILTERING', 'FftWindowSize': 2.0}, 'BubblSpikeFilter': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': False, 'StartDepth': 10.0, 'EndDepth': 2500.0, 'TotalDelta': 15.0, 'VerticalDelta': 15.0, 'Debug': False, 'VerticalUnit': 'DURATION', 'VerticalMedianSearchHeight': 50, 'WindowMedianSearchHeight': 35, 'VerticalMedianSearchDuration': 2.0, 'WindowMedianSearchDuration': 4.4, 'VerticalMedianSearchDistance': 1.9, 'WindowMedianSearchDistance': 6.6}, 'Categorization': {'Active': True, 'Comment': '', 'CategoryCount': 3, 'ActiveFeatures': [], 'ActiveCategories': [], 'Categorizer': 'Gauss', 'Discriminant': 'Aposteriori', 'ContextualCorrection': 'ICM', 'ContextualIterations': 3, 'UseMinLogSv': True, 'MinLogSv': -100.0}, 'CdsViewer': {'Active': True, 'Comment': ''}, 'ChannelDataRemoval': {'Active': True, 'Comment': '', 'Channels': '', 'ChannelsFromEnd': '', 'Frequencies': '', 'DataType': '', 'TransmitMode': '', 'PingId': '', 'KeepSpecified': False}, 'ChannelRemoval': {'Active': True, 'Comment': '', 'Channels': '', 'ChannelsFromEnd': '', 'Frequencies': '', 'DataType': '', 'TransmitMode': '', 'PingId': '', 'KeepSpecified': False}, 'Combination': {'Active': True, 'Comment': '', 'FirstOperandKhz': 0, 'SecondOperandKhz': 0, 'FirstOperandChannel': 1, 'SecondOperandChannel': 2, 'LogarithmicOperands': False, 'Operation': 'mean'}, 'Comment': {'Active': True, 'Comment': '', 'GroupStart': False, 'GroupCollapsed': False, 'LineBreak': False, 'VerticalSpace': 8, 'Label': ''}, 'ComplexToReal': {'Active': True, 'Comment': '', 'ComputeAngles': True, 'KeepBroadband': False}, 'DataReduction': {'Active': True, 'Comment': '', 'BlindZone': False, 'MinRange': '', 'MinDepth': '', 'TransducerRange': True, 'MaxRange': '', 'MaxDepth': '', 'MaxBelowBottom': ''}, 'DepthDependentResampling': {'Active': True, 'Comment': '', 'MinFrequency': 150.0, 'SampleDistanceAtRange100': 0.0}, 'Depth': {'Active': True, 'Comment': '', 'Algorithm': 'EK500', 'MinDepthLimit': 10.0, 'MinDepthValueFraction': 0.001, 'SignalStrengthThreshold': -31.0, 'MinimumDepthThresholdFactor': 0.99, 'MaxRangeFactor': 1.5, 'AlwaysDetectBottom': True, 'MinBottomDepth': 0.0, 'MaxBottomDepth': 9999.0, 'PreferredKHz': '', 'MinKHz': 0.0, 'MaxKHz': 9999.0, 'DoNotUseKHz': ''}, 'Dilate': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0, 'VertResolution': 1}, 'Downsampling': {'Active': True, 'Comment': '', 'Downsampling': 'FACTOR', 'DownsamplingFactor': 1, 'DownsamplingSampleSize': 0.01}, 'ES60Correction': {'Active': True, 'Comment': '', 'ReliabilityDetectionWindow': 5, 'PerformScan': False, 'ContinueAcrossFiles': False}, 'EchoLineCompression': {'Active': True, 'Comment': '', 'Threshold': -82.0}, 'EdgeDetection': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0, 'ScaleFactor': 1.0, 'VertResolution': 1}, 'EmptyPingRemoval': {'Active': True, 'Comment': ''}, 'ErodeLowValues': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0, 'Threshold': -70.0, 'ReplacementValue': -120.0, 'VerticalExtent': 1.0}, 'Erode': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0, 'VertResolution': 1}, 'Expression': {'Active': True, 'Comment': '', 'Expression': ['C1']}, 'FillMissingData': {'Active': True, 'Comment': ''}, 'Filter3X3': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0, 'FilterType': 'User defined', '00': 1.0, '01': 1.0, '02': 1.0, '10': 1.0, '11': 1.0, '12': 1.0, '20': 1.0, '21': 1.0, '22': 1.0}, 'FiskViewDisplay': {'Active': True, 'Comment': ''}, 'GroupEnd': {'Active': True, 'Comment': ''}, 'HorizontalOffsetCorrection': {'Active': True, 'Comment': ''}, 'Isolation': {'Active': True, 'Comment': '', 'Category': ''}, 'Median': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0}, 'NetcdfWriter': {'Active': True, 'Comment': '', 'DirName': 'netcdf', 'MainFrequency': '38', 'WriterType': 'GRIDDED', 'GriddedOutputType': 'SV_AND_ANGLES', 'ChannelGroupOutputType': 'PULSE_COMPRESSION', 'DeltaRange': '', 'MaxRange': '', 'FftWindowSize': 2.0, 'DeltaFrequency': 1.0, 'WriteAngels': True}, 'NoiseAcceptance': {'Active': True, 'Comment': '', 'NoiseFraction': {'min': 0.25, 'max': 4.0}, 'UseFileNoiseFile': True, 'UseDayNoiseFile': True, 'UseSurveyNoiseFile': True, 'UseSurveyLowNoiseFile': True}, 'NoiseMedianQuantification': {'Active': True, 'Comment': '', 'PingHistory': 10, 'NoiseSamplesPerBeam': 100, 'DetectionDistance': 50.0, 'InnermostDistance': False}, 'NoiseQuantification': {'Active': True, 'Comment': '', 'Smooth': 'running averager', 'SmoothInterval': 5, 'Mask': 'dynamic', 'MinimumQuality': 60.0, 'ThresholdMasking': False, 'Threshold': -80.0, 'Histogram': 'geometric', 'UseTimeStepBuffer': True, 'TimeStepBufferMaxSize': 50, 'HistogramInitializationCellCount': 500, 'HistogramMaximumCellCount': 2000, 'HistogramInitializationSampleCount': 1000, 'HistogramMinimumSampleCount': 25000, 'HistogramSmooth': True, 'HistogramSmoothFactor': 100.0, 'SdevMasking': False, 'Sdev': 10.0, 'SNMasking': False, 'SNRatio': 10.0, 'UseFallbackNoiseQuantile': False, 'FallbackNoiseQuantile': 5.0, 'FallbackNoiseChannels': 'true', 'WritePlotParameters': False}, 'NoiseRemover': {'Active': True, 'Comment': '', 'RemoveNoiseFromStart': True, 'MaxBufferSize': 10, 'SampleSizeCorrection': ''}, 'NoiseVisualization': {'Active': True, 'Comment': '', 'TimeSeriesLength': 200, 'HistogramSpan': 3.0, 'MedianSampleCount': 500}, 'PingCollapsing': {'Active': True, 'Comment': ''}, 'PingThinning': {'Active': True, 'Comment': '', 'PingsToSkipInitially': 0, 'PingsToSkip': 0}, 'PlanktonInversion': {'Active': True, 'Comment': '', 'VerticalUnit': 'SAMPLES', 'PingsPerBin': 7, 'DepthSamplesPerBin': 30, 'DepthDurationPerBin': 4.0, 'DepthDistancePerBin': 6.0, 'Use global noise threshold': True, 'Noise threshold': -90.0, 'Use min depth': False, 'Min depth': 20.0, 'Use max depth': False, 'Max depth': 110.0, 'CategoriesUsedForInversion': [], 'UseAllFrequencies': True, 'ActiveFrequencies': [], 'MinResidualErrorThreshold': 0.01, 'MaxResidualErrorThreshold': 0.2, 'LevenbergMarquardtFactor': 0.0005, 'MaxIter': 4, 'HardShelled': True, 'HardShelledR': 0.5, 'GaseousSphere': True, 'GasSphereG': 0.0012, 'GasSphereH': 0.22, 'FluidSpheriod': True, 'FluidSpheriodG': 1.043, 'FluidSpheriodH': 1.052, 'FluidSpheriodBeta': 5.0, 'FluidBent': True, 'FluidBentR': 0.058, 'FluidBentS': 0.1, 'FluidBentBeta': 11.0, 'FluidBent2': False, 'FluidBentR2': 0.058, 'FluidBentS2': 0.1, 'FluidBentBeta 2': 11.0, 'SDWBA': False, 'SDWBA coeff': 'N(0, 30)', 'SDWBA2': False, 'SDWBA 2 coeff': 'N(0, 30)', 'SDWBA3': False, 'SDWBA 3 coeff': 'N(0, 30)', 'SDWBA4': False, 'SDWBA 4 coeff': 'N(0, 30)', 'SDWBA5': False, 'SDWBA 5 coeff': 'N(0, 30)', 'SDWBAS': False, 'SDWBA smooth coeff': 'N(4, 2)', 'PlotResolution': 0.01, 'PlotMaxRange': 5.0}, 'Plugin': {'Active': True, 'Comment': '', 'Example': '', 'Implementation': ''}, 'PulseCompressionFilter': {'Active': True, 'Comment': ''}, 'RemoveBottom': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0, 'UseNeighbours': False, 'Above': 0, 'Below': 100, 'RemoveAboveBottom': False, 'RemoveBottom': True, 'RemoveBelowBottom': False, 'PixelValue': -120.0}, 'Rescale': {'Active': True, 'Comment': '', 'RescaleChannels': 'all', 'DesiredMinimum': -85.0, 'DesiredMaximum': -30.0, 'MinMaxFraction': 0.05, 'InitializationDatagramCount': 10, 'InitializationMaxPingCount': 100}, 'SchoolCategorization': {'Active': True, 'Comment': '', 'UseCellCategorization': True, 'Horizontal cell size': 16, 'Vertical cell size': 50, 'Upper sample offset': 5, 'Lower sample offset': 5, 'HorizontalOffset': 0, 'SecondaryCategoryFraction': 0.1, 'Fill factor for cells': 0.5, 'MinFractionCategorizedCells': 0.5, 'MinCells': 3, 'SchoolCategorizationDistribution': 'CELL', 'EnableUncategorizedCategory': False, 'EnableUnknownCategory': False}, 'SchoolDetection': {'Active': True, 'Comment': '', 'ProcessLast': True, 'Channel': 1, 'MinDepth': '', 'MaxDepth': '', 'Threshold': -62.0, 'Density': {'min': -120.0, 'max': -20.0}, 'MaxSv': {'min': '-Infinity', 'max': 'Infinity'}, 'Length': {'min': 25.0, 'max': 1000000.0}, 'Thickness': {'min': 10.0, 'max': 1000000.0}, 'Area': {'min': 75.0, 'max': 1000000.0}, 'Compactness': {'min': '-Infinity', 'max': 'Infinity'}, 'FillHoles': True}, 'Smoother': {'Active': True, 'Comment': '', 'OnlyLastChannel': False, 'MaskPelagic': False, 'MaskBottom': True, 'MaskSecondBottom': True, 'MaskNoise': False, 'MaskRegion': 'none', 'MaskTrack': 'none', 'MinPing': 0, 'MaxPing': 10, 'HorizontalKernelType': 'gaussian', 'VerticalKernelType': 'gaussian', 'HorizontalWidth': 8.0, 'VerticalWidth': 0.5, 'LogarithmicValues': False}, 'SpikeFilter': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': False, 'StartDepth': 10.0, 'EndDepth': 2500.0, 'TotalDelta': 15.0, 'VerticalDelta': 15.0, 'Debug': False, 'VerticalUnit': 'DURATION', 'VerticalMedianSearchHeight': 7, 'WindowMedianSearchHeight': 35, 'VerticalMedianSearchDuration': 0.9, 'WindowMedianSearchDuration': 4.4, 'VerticalMedianSearchDistance': 1.3, 'WindowMedianSearchDistance': 6.6}, 'SpotNoise': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': False, 'StartDepth': 10.0, 'EndDepth': 2500.0, 'Delta': 20.0, 'Debug': False}, 'TemporaryComputationsBegin': {'Active': True, 'Comment': ''}, 'TemporaryComputationsEnd': {'Active': True, 'Comment': ''}, 'ThresholdAllChannels': {'Active': True, 'Comment': '', 'Criterion': 'BELOW', 'Threshold': -70.0, 'Replacement': -120.0, 'MinFrequency': '', 'MaxFrequency': ''}, 'Threshold': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0, 'Threshold': -70.0, 'CutBelow': False, 'CutAbove': False, 'BelowVal': -120.0, 'AboveVal': 0.0}, 'TimeInterval': {'Active': True, 'Comment': '', 'StartDateString': '', 'EndDateString': '', 'StartRelativePingNumber': '', 'EndRelativePingNumber': ''}, 'Towfish': {'Active': True, 'Comment': '', 'TowfishBlindZone': 0.0, 'TowfishEchosounderTimeAddition': 0.0, 'DistBehindFunction': 'PYTAGORAS'}, 'TrackFilter': {'Active': True, 'Comment': '', 'MaxBufferSize': 50, 'KeepValid': True}, 'Tracking': {'Active': True, 'Comment': '', 'TrackerType': 'Aggregation', 'kHz': 38, 'PlatformMotionType': 'Floating', 'MinTS': -66.0, 'PulseLengthDeterminationLevel': 6.0, 'MinEchoLength': 0.01, 'MaxEchoLength': 1.8, 'MaxGainCompensation': 6.0, 'DoPhaseDeviationCheck': True, 'MaxPhaseDevSteps': 8.0, 'MaxTS': 0.0, 'MaxDepth': '', 'MaxAlongshipAngle': 10.0, 'MaxAthwartshipAngle': 10.0, 'InitiationGateFunction': [{'id': 'Alpha', 'description': '', 'unit': 'degree', 'defaultValue': 2.8}, {'id': 'Beta', 'description': '', 'unit': 'degree', 'defaultValue': 2.8}, {'id': 'Range', 'description': '', 'unit': 'm', 'defaultValue': 0.1}, {'id': 'TS', 'description': 'dB', 'unit': 'dB', 'defaultValue': 20.0}], 'InitiationMinLength': 1, 'GateFunction': [{'id': 'Alpha', 'description': '', 'unit': 'degree', 'defaultValue': 2.8}, {'id': 'Beta', 'description': '', 'unit': 'degree', 'defaultValue': 2.8}, {'id': 'Range', 'description': '', 'unit': 'm', 'defaultValue': 0.1}, {'id': 'TS', 'description': 'dB', 'unit': 'dB', 'defaultValue': 20.0}], 'AlphaBetaEstimator': [{'id': 'Alpha', 'description': '', 'allowedValuesDescription': '[0, 1]', 'defaultValue': 0.5}, {'id': 'Beta', 'description': '', 'allowedValuesDescription': '[0, 1]', 'defaultValue': 0.5}], 'MaxMissingPings': 4, 'MaxMissingSamples': 2, 'MaxMissingPingsFraction': 0.5, 'MinTrackLength': 8, 'MinSampleToLengthFraction': 2.0}, 'TsDetection': {'Active': True, 'Comment': '', 'DetectorType': 'SED', 'MinTS': -66.0, 'PulseLengthDeterminationLevel': 6.0, 'MinEchoLength': 0.01, 'MaxEchoLength': 1.8, 'MaxGainCompensation': 6.0, 'DoPhaseDeviationCheck': True, 'MaxPhaseDevSteps': 8.0, 'MaxDepth': ''}, 'VerticalOffsetCorrection': {'Active': True, 'Comment': ''}, 'Writer': {'Active': True, 'Comment': '', 'FileName': '', 'UseRelativeDirectory': False, 'RelativeDirectory': '', 'DirectoryName': ''}}

{koronascript-0.2.1 → koronascript-3.0.0}/KoronaScript/Modules.py

@@ -1,6 +1,6 @@
 # Auto-generated, do not edit directly
 # see genmodule.py
-
+from .Configuration import modules_spec
 from .KoronaModule import KoronaModule
 
 class AngleDeletion(KoronaModule):
@@ -24,7 +24,7 @@ class BubblSpikeFilter(KoronaModule):
         super().__init__('BubblSpikeFilter', **parameters)
 
 class Categorization(KoronaModule):
-    """Module for categorization"""
+    """Categorizes each pixel using the configured training data"""
     def __init__(self, **parameters):
         super().__init__('Categorization', **parameters)
 
@@ -44,7 +44,7 @@ class ChannelRemoval(KoronaModule):
         super().__init__('ChannelRemoval', **parameters)
 
 class Combination(KoronaModule):
-    """Module for generating combination echograms"""
+    """Generates combination echograms"""
     def __init__(self, **parameters):
         super().__init__('Combination', **parameters)
 
@@ -69,7 +69,7 @@ class DepthDependentResampling(KoronaModule):
         super().__init__('DepthDependentResampling', **parameters)
 
 class Depth(KoronaModule):
-    """Bottom depth detection module"""
+    """Detects the bottom depth"""
     def __init__(self, **parameters):
         super().__init__('Depth', **parameters)
 
@@ -88,6 +88,11 @@ class ES60Correction(KoronaModule):
     def __init__(self, **parameters):
         super().__init__('ES60Correction', **parameters)
 
+class EchoLineCompression(KoronaModule):
+    """Keeps only data above a given threshold"""
+    def __init__(self, **parameters):
+        super().__init__('EchoLineCompression', **parameters)
+
 class EdgeDetection(KoronaModule):
     """Detects edges by using Sobel horizontal and vertical filter"""
     def __init__(self, **parameters):
@@ -109,22 +114,22 @@ class Erode(KoronaModule):
         super().__init__('Erode', **parameters)
 
 class Expression(KoronaModule):
-    """Module for generating combination echograms by an expression"""
+    """Generates combination echograms by a specified expression"""
     def __init__(self, **parameters):
         super().__init__('Expression', **parameters)
 
 class FillMissingData(KoronaModule):
-    """Creates missing pingdata"""
+    """Adds missing channel data"""
     def __init__(self, **parameters):
         super().__init__('FillMissingData', **parameters)
 
 class Filter3X3(KoronaModule):
-    """Class implementing a 3�3 filter"""
+    """Applies a 3×3 filter"""
     def __init__(self, **parameters):
         super().__init__('Filter3X3', **parameters)
 
 class FiskViewDisplay(KoronaModule):
-    """Display module"""
+    """Displays an echogram for each channel"""
     def __init__(self, **parameters):
         super().__init__('FiskViewDisplay', **parameters)
 
@@ -148,13 +153,18 @@ class Median(KoronaModule):
     def __init__(self, **parameters):
         super().__init__('Median', **parameters)
 
+class NetcdfWriter(KoronaModule):
+    """Writes to a .nc file"""
+    def __init__(self, **parameters):
+        super().__init__('NetcdfWriter', **parameters)
+
 class NoiseAcceptance(KoronaModule):
-    """Median noise acceptance"""
+    """Compares detected noise with values recorded in files"""
     def __init__(self, **parameters):
         super().__init__('NoiseAcceptance', **parameters)
 
 class NoiseMedianQuantification(KoronaModule):
-    """Median noise quantification"""
+    """Produces noise quantification datagrams using the median of selected sample values"""
     def __init__(self, **parameters):
         super().__init__('NoiseMedianQuantification', **parameters)
 
@@ -189,7 +199,7 @@ class PlanktonInversion(KoronaModule):
         super().__init__('PlanktonInversion', **parameters)
 
 class Plugin(KoronaModule):
-    """Plugin (beta)"""
+    """For writing Java code that implements an API interface for KORONA module computations"""
     def __init__(self, **parameters):
         super().__init__('Plugin', **parameters)
 
@@ -199,7 +209,7 @@ class PulseCompressionFilter(KoronaModule):
         super().__init__('PulseCompressionFilter', **parameters)
 
 class RemoveBottom(KoronaModule):
-    """Removes bottom data"""
+    """Assigns a specified value to samples close to the detected bottom"""
     def __init__(self, **parameters):
         super().__init__('RemoveBottom', **parameters)
 
@@ -249,12 +259,12 @@ class ThresholdAllChannels(KoronaModule):
         super().__init__('ThresholdAllChannels', **parameters)
 
 class Threshold(KoronaModule):
-    """Masks out values in specific range on individual channels"""
+    """Masks out values in a specified range on individual channels"""
     def __init__(self, **parameters):
         super().__init__('Threshold', **parameters)
 
 class TimeInterval(KoronaModule):
-    """Module for processing only the pings in a specified time interval"""
+    """Processes only the pings in a specified time interval"""
     def __init__(self, **parameters):
         super().__init__('TimeInterval', **parameters)
 
@@ -288,7 +298,3 @@ class Writer(KoronaModule):
     def __init__(self, **parameters):
         super().__init__('Writer', **parameters)
 
-class NetcdfWriter(KoronaModule):
-    """Writes to a .nc file"""
-    def __init__(self, **parameters):
-        super().__init__('NetcdfWriter', **parameters)

{koronascript-0.2.1 → koronascript-3.0.0}/KoronaScript/__init__.py

@@ -10,12 +10,33 @@ import subprocess
 import tempfile
 import os
 import sys
+from zipfile import ZipFile
+import importlib.resources as resources
+import requests
 
 from .KoronaModule import global_spec
 
-lsss = os.getenv('LSSS')
-if lsss is None:
-    print('KoronaScript: Warning: $LSSS is not set.')
+CURRENT_LSSS = 'lsss-3.0.0-20250204-0841'
+
+if os.getenv('LSSS') is not None:
+    lsss = os.getenv('LSSS')
+    print(f'KoronaScript: Using external LSSS from variable $LSSS={lsss}.')
+else:
+    myos = sys.platform
+    lsss = str(resources.files('KoronaScript').joinpath('lsss-3.0.0'))
+    if not os.path.exists(lsss):
+        basedir = os.path.dirname(lsss)
+        print(f'{lsss} does not exist, downloading it.')
+        resp = requests.get(f'https://www.marec.no/downloads/{CURRENT_LSSS}/{CURRENT_LSSS}-{myos}.zip')
+        resp.raise_for_status()
+        with open(f'{basedir}/{CURRENT_LSSS}.zip', 'wb') as f:
+            f.write(resp.content)
+        with ZipFile(f'{basedir}/{CURRENT_LSSS}.zip', 'r') as z:
+            z.extractall(basedir)
+        with ZipFile(f'{os.path.dirname(lsss)}/{CURRENT_LSSS}/lsss-3.0.0-{myos}.zip') as z:
+            z.extractall(basedir)
+        os.chmod(f'{lsss}/jre/bin/java', 0o755)
+
 
 class KoronaScript():
     '''Construct, store, and run a set of Korona modules'''
@@ -80,7 +101,10 @@ class KoronaScript():
         cmd = [java] + javaopts + ['no.imr.korona.main.KoronaCliMain', 'batch', '--cfs', cfsname, '--source', src, '--destination', dst]
         if debug: print('Running:\n  ', cmd)
         res = subprocess.run(cmd, capture_output=True, text=True)
-        if debug: print(res.stdout)
+        if debug:
+            print(res.stdout)
+            print()
+            print(res.stderr)
         if res.returncode != 0:
             err_str = f'Korona subprocess returned an error code: {res.returncode}\n' + '----------------------------------------\n' + res.stderr
             raise Exception(err_str)

koronascript-3.0.0/MANIFEST.in

@@ -0,0 +1 @@
+recursive-include KoronaScript/lsss-3.0.0 *

koronascript-3.0.0/PKG-INFO

@@ -0,0 +1,52 @@
+Metadata-Version: 2.4
+Name: koronascript
+Version: 3.0.0
+Summary: Wrapper around Korona modules for processing echosounder data
+Home-page: https://github.com/CRIMAC-WP4-Machine-learning/CRIMAC-KoronaScript
+Author: Ketil Malde
+Author-email: ketil@malde.org
+Description-Content-Type: text/markdown
+Requires-Dist: matplotlib
+Requires-Dist: netCDF4
+Requires-Dist: xarray
+Requires-Dist: pytest
+Requires-Dist: requests
+
+# Running Korona through Python
+
+## Prerequisites
+
+KoronaScript depends on LSSS and Korona version 3.0.0.  The `LSSS`
+environment variable can be set to point to an existing installation,
+otherwise, the LSSS distribution will be automatically downloaded from
+the Marec web pages and installed as part of this package.
+
+# Usage
+
+Import the modules:
+
+	import KoronaScript as ks
+	import KoronaScript.Modules as ksm
+
+Create a script object:
+
+	ks = ks.KoronaScript(Categorization='categorization.xml',
+                     HorizontalTransducerOffsets='HorizontalTransducerOffsets.xml')
+
+Add some modules:
+
+	ks.add(ksm.EmptyPingRemoval())
+	ks.add(ksm.Comment(LineBreak='false', Label='CW_0256ms'))
+	ks.add(ksm.ChannelRemoval(Channels=[1,5,9,13,17],KeepSpecified='true'))
+	ks.add(ksm.Writer(RelativeDirectory='CW_0256ms'))
+
+Write out the resulting configuration:
+
+	ks.write()
+	
+Run the script:
+
+	ks.run(src="input_dir", dst="output_dir")
+
+The list of modules and their parameters can be found in the
+[configuration/korona-info.json](configuration/korona-info.json) file. 

koronascript-3.0.0/README.md

@@ -0,0 +1,38 @@
+# Running Korona through Python
+
+## Prerequisites
+
+KoronaScript depends on LSSS and Korona version 3.0.0.  The `LSSS`
+environment variable can be set to point to an existing installation,
+otherwise, the LSSS distribution will be automatically downloaded from
+the Marec web pages and installed as part of this package.
+
+# Usage
+
+Import the modules:
+
+	import KoronaScript as ks
+	import KoronaScript.Modules as ksm
+
+Create a script object:
+
+	ks = ks.KoronaScript(Categorization='categorization.xml',
+                     HorizontalTransducerOffsets='HorizontalTransducerOffsets.xml')
+
+Add some modules:
+
+	ks.add(ksm.EmptyPingRemoval())
+	ks.add(ksm.Comment(LineBreak='false', Label='CW_0256ms'))
+	ks.add(ksm.ChannelRemoval(Channels=[1,5,9,13,17],KeepSpecified='true'))
+	ks.add(ksm.Writer(RelativeDirectory='CW_0256ms'))
+
+Write out the resulting configuration:
+
+	ks.write()
+	
+Run the script:
+
+	ks.run(src="input_dir", dst="output_dir")
+
+The list of modules and their parameters can be found in the
+[configuration/korona-info.json](configuration/korona-info.json) file. 

koronascript-3.0.0/koronascript.egg-info/PKG-INFO

@@ -0,0 +1,52 @@
+Metadata-Version: 2.4
+Name: koronascript
+Version: 3.0.0
+Summary: Wrapper around Korona modules for processing echosounder data
+Home-page: https://github.com/CRIMAC-WP4-Machine-learning/CRIMAC-KoronaScript
+Author: Ketil Malde
+Author-email: ketil@malde.org
+Description-Content-Type: text/markdown
+Requires-Dist: matplotlib
+Requires-Dist: netCDF4
+Requires-Dist: xarray
+Requires-Dist: pytest
+Requires-Dist: requests
+
+# Running Korona through Python
+
+## Prerequisites
+
+KoronaScript depends on LSSS and Korona version 3.0.0.  The `LSSS`
+environment variable can be set to point to an existing installation,
+otherwise, the LSSS distribution will be automatically downloaded from
+the Marec web pages and installed as part of this package.
+
+# Usage
+
+Import the modules:
+
+	import KoronaScript as ks
+	import KoronaScript.Modules as ksm
+
+Create a script object:
+
+	ks = ks.KoronaScript(Categorization='categorization.xml',
+                     HorizontalTransducerOffsets='HorizontalTransducerOffsets.xml')
+
+Add some modules:
+
+	ks.add(ksm.EmptyPingRemoval())
+	ks.add(ksm.Comment(LineBreak='false', Label='CW_0256ms'))
+	ks.add(ksm.ChannelRemoval(Channels=[1,5,9,13,17],KeepSpecified='true'))
+	ks.add(ksm.Writer(RelativeDirectory='CW_0256ms'))
+
+Write out the resulting configuration:
+
+	ks.write()
+	
+Run the script:
+
+	ks.run(src="input_dir", dst="output_dir")
+
+The list of modules and their parameters can be found in the
+[configuration/korona-info.json](configuration/korona-info.json) file. 

{koronascript-0.2.1 → koronascript-3.0.0}/koronascript.egg-info/SOURCES.txt

@@ -1,3 +1,4 @@
+MANIFEST.in
 README.md
 setup.cfg
 setup.py
@@ -9,5 +10,6 @@ koronascript.egg-info/PKG-INFO
 koronascript.egg-info/SOURCES.txt
 koronascript.egg-info/dependency_links.txt
 koronascript.egg-info/not-zip-safe
+koronascript.egg-info/requires.txt
 koronascript.egg-info/top_level.txt
 tests/test_examples.py

koronascript-3.0.0/koronascript.egg-info/requires.txt

@@ -0,0 +1,5 @@
+matplotlib
+netCDF4
+xarray
+pytest
+requests

koronascript-3.0.0/setup.cfg

@@ -0,0 +1,28 @@
+[metadata]
+name = koronascript
+version = 3.0.0
+author = Ketil Malde
+author_email = ketil@malde.org
+description = Wrapper around Korona modules for processing echosounder data
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/CRIMAC-WP4-Machine-learning/CRIMAC-KoronaScript
+
+[options]
+packages = find:
+include_package_data = True
+zip_safe = False
+install_requires = 
+	matplotlib
+	netCDF4
+	xarray
+	pytest
+	requests
+
+[flake8]
+ignore = E302,E501,E203,E701
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

koronascript-3.0.0/setup.py

@@ -0,0 +1,3 @@
+from setuptools import setup
+
+setup()

koronascript-3.0.0/tests/test_examples.py

@@ -0,0 +1,26 @@
+import sys
+import os
+
+sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
+
+from examples import channelRemoval as CR
+from examples import pulseCompression as PC
+from examples import tracking as T
+from examples import tsDetection as TS
+
+TESTDATA = 'testdata'
+
+def test_channelRemoval():
+    """This fails to fail if no data is present"""
+    CR.ksi.run(TESTDATA, 'test_out/cr_out')
+
+def test_pulseCompression():
+    PC.ksi.run(TESTDATA, 'test_out/pc_out')
+
+def test_tracking():
+    """This fails to fail if no data is present"""
+    T.ksi.run(TESTDATA, 'test_out/t_out')
+
+def test_tsDetection():
+    """This fails to fail if no data is present"""
+    TS.ksi.run(TESTDATA, 'test_out/ts_out')

koronascript-0.2.1/KoronaScript/Configuration.py

@@ -1,3 +0,0 @@
-# Auto-generated, do not edit directly
-# see genmodule.py
-modules_spec = {'AngleDeletion': {'Active': True, 'Comment': ''}, 'BroadbandNotchFilter': {'Active': True, 'Comment': ''}, 'BroadbandSplitter': {'Active': True, 'Comment': '', 'AutoSplit': False, 'SplitCount': 3, 'StopBandDistance': 1.0, 'MinBandwidth': 10.0, 'Downsampling': 'FACTOR', 'DownsamplingFactor': 1, 'DownsamplingSampleSize': 0.01, 'ComputeAngles': True, 'ComputationalMethod': 'BANDPASS_FILTERING', 'FftWindowSize': 2.0}, 'BubblSpikeFilter': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': False, 'StartDepth': 10.0, 'EndDepth': 2500.0, 'TotalDelta': 15.0, 'VerticalDelta': 15.0, 'Debug': False, 'VerticalUnit': 'DURATION', 'VerticalMedianSearchHeight': 50, 'WindowMedianSearchHeight': 35, 'VerticalMedianSearchDuration': 2.0, 'WindowMedianSearchDuration': 4.4, 'VerticalMedianSearchDistance': 1.9, 'WindowMedianSearchDistance': 6.6}, 'Categorization': {'Active': True, 'Comment': '', 'CategoryCount': 3, 'ActiveFeatures': [], 'ActiveCategories': [], 'Categorizer': 'Gauss', 'Discriminant': 'Aposteriori', 'ContextualCorrection': 'ICM', 'ContextualIterations': 3, 'UseMinLogSv': True, 'MinLogSv': -100.0}, 'CdsViewer': {'Active': True, 'Comment': ''}, 'ChannelDataRemoval': {'Active': True, 'Comment': '', 'Channels': '', 'ChannelsFromEnd': '', 'Frequencies': '', 'KeepSpecified': False}, 'ChannelRemoval': {'Active': True, 'Comment': '', 'Channels': '', 'ChannelsFromEnd': '', 'Frequencies': '', 'KeepSpecified': False}, 'Combination': {'Active': True, 'Comment': '', 'FirstOperandKhz': 0, 'SecondOperandKhz': 0, 'FirstOperandChannel': 1, 'SecondOperandChannel': 2, 'LogarithmicOperands': False, 'Operation': 'mean'}, 'Comment': {'Active': True, 'Comment': '', 'GroupStart': False, 'GroupCollapsed': False, 'LineBreak': False, 'VerticalSpace': 8, 'Label': ''}, 'ComplexToReal': {'Active': True, 'Comment': '', 'ComputeAngles': True, 'KeepBroadband': False}, 'DataReduction': {'Active': True, 'Comment': '', 'BlindZone': False, 'MinRange': '', 'MinDepth': '', 'TransducerRange': True, 'MaxRange': '', 'MaxDepth': ''}, 'DepthDependentResampling': {'Active': True, 'Comment': '', 'MinFrequency': 150.0, 'SampleDistanceAtRange100': 0.0}, 'Depth': {'Active': True, 'Comment': '', 'Algorithm': 'EK500', 'MinDepthLimit': 10.0, 'MinDepthValueFraction': 0.001, 'SignalStrengthThreshold': -31.0, 'MinimumDepthThresholdFactor': 0.99, 'MaxRangeFactor': 1.5, 'AlwaysDetectBottom': True, 'MinBottomDepth': 0.0, 'MaxBottomDepth': 9999.0, 'MinKHz': 0.0, 'MaxKHz': 9999.0, 'DoNotUseKHz': ''}, 'Dilate': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0, 'VertResolution': 1}, 'Downsampling': {'Active': True, 'Comment': '', 'Downsampling': 'FACTOR', 'DownsamplingFactor': 1, 'DownsamplingSampleSize': 0.01}, 'ES60Correction': {'Active': True, 'Comment': '', 'ReliabilityDetectionWindow': 5, 'PerformScan': False, 'ContinueAcrossFiles': False}, 'EdgeDetection': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0, 'ScaleFactor': 1.0, 'VertResolution': 1}, 'EmptyPingRemoval': {'Active': True, 'Comment': ''}, 'ErodeLowValues': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0, 'Threshold': -70.0, 'ReplacementValue': -120.0, 'VerticalExtent': 1.0}, 'Erode': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0, 'VertResolution': 1}, 'Expression': {'Active': True, 'Comment': '', 'Expression': ['C1']}, 'FillMissingData': {'Active': True, 'Comment': ''}, 'Filter3X3': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0, 'FilterType': 'User defined', '00': 1.0, '01': 1.0, '02': 1.0, '10': 1.0, '11': 1.0, '12': 1.0, '20': 1.0, '21': 1.0, '22': 1.0}, 'FiskViewDisplay': {'Active': True, 'Comment': ''}, 'GroupEnd': {'Active': True, 'Comment': ''}, 'HorizontalOffsetCorrection': {'Active': True, 'Comment': ''}, 'Isolation': {'Active': True, 'Comment': '', 'Category': ''}, 'Median': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0}, 'NoiseAcceptance': {'Active': True, 'Comment': '', 'NoiseFraction': {'min': 0.25, 'max': 4.0}, 'UseFileNoiseFile': True, 'UseDayNoiseFile': True, 'UseSurveyNoiseFile': True, 'UseSurveyLowNoiseFile': True}, 'NoiseMedianQuantification': {'Active': True, 'Comment': '', 'PingHistory': 10, 'NoiseSamplesPerBeam': 100, 'DetectionDistance': 50.0, 'InnermostDistance': False}, 'NoiseQuantification': {'Active': True, 'Comment': '', 'Smooth': 'running averager', 'SmoothInterval': 5, 'Mask': 'dynamic', 'MinimumQuality': 60.0, 'ThresholdMasking': False, 'Threshold': -80.0, 'Histogram': 'geometric', 'UseTimeStepBuffer': True, 'TimeStepBufferMaxSize': 50, 'HistogramInitializationCellCount': 500, 'HistogramMaximumCellCount': 2000, 'HistogramInitializationSampleCount': 1000, 'HistogramMinimumSampleCount': 25000, 'HistogramSmooth': True, 'HistogramSmoothFactor': 100.0, 'SdevMasking': False, 'Sdev': 10.0, 'SNMasking': False, 'SNRatio': 10.0, 'UseFallbackNoiseQuantile': False, 'FallbackNoiseQuantile': 5.0, 'FallbackNoiseChannels': 'true', 'WritePlotParameters': False}, 'NoiseRemover': {'Active': True, 'Comment': '', 'RemoveNoiseFromStart': True, 'MaxBufferSize': 10}, 'NoiseVisualization': {'Active': True, 'Comment': '', 'UpdatePeriod': 20, 'TimeSeriesLength': 200, 'HistogramSpan': 3.0, 'MedianSampleCount': 500}, 'PingCollapsing': {'Active': True, 'Comment': ''}, 'PingThinning': {'Active': True, 'Comment': '', 'PingsToSkipInitially': 0, 'PingsToSkip': 0}, 'PlanktonInversion': {'Active': True, 'Comment': '', 'VerticalUnit': 'SAMPLES', 'PingsPerBin': 7, 'DepthSamplesPerBin': 30, 'DepthDurationPerBin': 4.0, 'DepthDistancePerBin': 6.0, 'Use global noise threshold': True, 'Noise threshold': -90.0, 'Use min depth': False, 'Min depth': 20.0, 'Use max depth': False, 'Max depth': 110.0, 'CategoriesUsedForInversion': [], 'UseAllFrequencies': True, 'ActiveFrequencies': [], 'MinResidualErrorThreshold': 0.01, 'MaxResidualErrorThreshold': 0.2, 'LevenbergMarquardtFactor': 0.0005, 'MaxIter': 4, 'HardShelled': True, 'HardShelledR': 0.5, 'GaseousSphere': True, 'GasSphereG': 0.0012, 'GasSphereH': 0.22, 'FluidSpheriod': True, 'FluidSpheriodG': 1.043, 'FluidSpheriodH': 1.052, 'FluidSpheriodBeta': 5.0, 'FluidBent': True, 'FluidBentR': 0.058, 'FluidBentS': 0.1, 'FluidBentBeta': 11.0, 'FluidBent2': False, 'FluidBentR2': 0.058, 'FluidBentS2': 0.1, 'FluidBentBeta 2': 11.0, 'SDWBA': False, 'SDWBA coeff': 'N(0, 30)', 'SDWBA2': False, 'SDWBA 2 coeff': 'N(0, 30)', 'SDWBA3': False, 'SDWBA 3 coeff': 'N(0, 30)', 'SDWBA4': False, 'SDWBA 4 coeff': 'N(0, 30)', 'SDWBA5': False, 'SDWBA 5 coeff': 'N(0, 30)', 'SDWBAS': False, 'SDWBA smooth coeff': 'N(4, 2)', 'PlotResolution': 0.01, 'PlotMaxRange': 5.0}, 'Plugin': {'Active': True, 'Comment': '', 'Example': '', 'Implementation': ''}, 'PulseCompressionFilter': {'Active': True, 'Comment': ''}, 'RemoveBottom': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0, 'UseNeighbours': False, 'Above': 0, 'Below': 100, 'RemoveAboveBottom': False, 'RemoveBottom': True, 'RemoveBelowBottom': False, 'PixelValue': -120.0}, 'Rescale': {'Active': True, 'Comment': '', 'RescaleChannels': 'all', 'DesiredMinimum': -85.0, 'DesiredMaximum': -30.0, 'MinMaxFraction': 0.05, 'InitializationDatagramCount': 10, 'InitializationMaxPingCount': 100}, 'SchoolCategorization': {'Active': True, 'Comment': '', 'UseCellCategorization': True, 'Horizontal cell size': 16, 'Vertical cell size': 50, 'Upper sample offset': 5, 'Lower sample offset': 5, 'HorizontalOffset': 0, 'SecondaryCategoryFraction': 0.1, 'Fill factor for cells': 0.5, 'MinFractionCategorizedCells': 0.5, 'MinCells': 3, 'SchoolCategorizationDistribution': 'CELL', 'EnableUncategorizedCategory': False, 'EnableUnknownCategory': False}, 'SchoolDetection': {'Active': True, 'Comment': '', 'ProcessLast': True, 'Channel': 1, 'MinDepth': '', 'MaxDepth': '', 'Threshold': -62.0, 'Density': {'min': -120.0, 'max': -20.0}, 'MaxSv': {'min': '-Infinity', 'max': 'Infinity'}, 'Length': {'min': 25.0, 'max': 1000000.0}, 'Thickness': {'min': 10.0, 'max': 1000000.0}, 'Area': {'min': 75.0, 'max': 1000000.0}, 'Compactness': {'min': '-Infinity', 'max': 'Infinity'}, 'FillHoles': True}, 'Smoother': {'Active': True, 'Comment': '', 'OnlyLastChannel': False, 'MaskPelagic': False, 'MaskBottom': True, 'MaskSecondBottom': True, 'MaskNoise': False, 'MaskRegion': 'none', 'MaskTrack': 'none', 'MinPing': 0, 'MaxPing': 10, 'HorizontalKernelType': 'gaussian', 'VerticalKernelType': 'gaussian', 'HorizontalWidth': 8.0, 'VerticalWidth': 0.5, 'LogarithmicValues': False}, 'SpikeFilter': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': False, 'StartDepth': 10.0, 'EndDepth': 2500.0, 'TotalDelta': 15.0, 'VerticalDelta': 15.0, 'Debug': False, 'VerticalUnit': 'DURATION', 'VerticalMedianSearchHeight': 7, 'WindowMedianSearchHeight': 35, 'VerticalMedianSearchDuration': 0.9, 'WindowMedianSearchDuration': 4.4, 'VerticalMedianSearchDistance': 1.3, 'WindowMedianSearchDistance': 6.6}, 'SpotNoise': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': False, 'StartDepth': 10.0, 'EndDepth': 2500.0, 'Delta': 20.0, 'Debug': False}, 'TemporaryComputationsBegin': {'Active': True, 'Comment': ''}, 'TemporaryComputationsEnd': {'Active': True, 'Comment': ''}, 'ThresholdAllChannels': {'Active': True, 'Comment': '', 'Criterion': 'BELOW', 'Threshold': -70.0, 'Replacement': -120.0, 'MinFrequency': '', 'MaxFrequency': ''}, 'Threshold': {'Active': True, 'Comment': '', 'LogarithmicValues': True, 'ShowDetails': False, 'OnlyLast': False, 'ChannelsToProcess': -1, 'AutomaticDepthRange': True, 'StartDepth': 10.0, 'EndDepth': 1000.0, 'Threshold': -70.0, 'CutBelow': False, 'CutAbove': False, 'BelowVal': -120.0, 'AboveVal': 0.0}, 'TimeInterval': {'Active': True, 'Comment': '', 'StartDateString': '', 'EndDateString': '', 'StartRelativePingNumber': '', 'EndRelativePingNumber': ''}, 'Towfish': {'Active': True, 'Comment': '', 'TowfishBlindZone': 0.0, 'TowfishEchosounderTimeAddition': 0.0, 'DistBehindFunction': 'PYTAGORAS'}, 'TrackFilter': {'Active': True, 'Comment': '', 'MaxBufferSize': 50, 'KeepValid': True}, 'Tracking': {'Active': True, 'Comment': '', 'TrackerType': 'Aggregation', 'kHz': 38, 'PlatformMotionType': 'Floating', 'MinTS': -66.0, 'PulseLengthDeterminationLevel': 6.0, 'MinEchoLength': 0.01, 'MaxEchoLength': 1.8, 'MaxGainCompensation': 6.0, 'DoPhaseDeviationCheck': True, 'MaxPhaseDevSteps': 8.0, 'MaxTS': 0.0, 'MaxDepth': '', 'MaxAlongshipAngle': 10.0, 'MaxAthwartshipAngle': 10.0, 'InitiationGateFunction': [{'id': 'Alpha', 'description': '', 'unit': 'degree', 'defaultValue': 2.8}, {'id': 'Beta', 'description': '', 'unit': 'degree', 'defaultValue': 2.8}, {'id': 'Range', 'description': '', 'unit': 'm', 'defaultValue': 0.1}, {'id': 'TS', 'description': 'dB', 'unit': 'dB', 'defaultValue': 20.0}], 'InitiationMinLength': 1, 'GateFunction': [{'id': 'Alpha', 'description': '', 'unit': 'degree', 'defaultValue': 2.8}, {'id': 'Beta', 'description': '', 'unit': 'degree', 'defaultValue': 2.8}, {'id': 'Range', 'description': '', 'unit': 'm', 'defaultValue': 0.1}, {'id': 'TS', 'description': 'dB', 'unit': 'dB', 'defaultValue': 20.0}], 'AlphaBetaEstimator': [{'id': 'Alpha', 'description': '', 'allowedValuesDescription': '[0, 1]', 'defaultValue': 0.5}, {'id': 'Beta', 'description': '', 'allowedValuesDescription': '[0, 1]', 'defaultValue': 0.5}], 'MaxMissingPings': 4, 'MaxMissingSamples': 2, 'MaxMissingPingsFraction': 0.5, 'MinTrackLength': 8, 'MinSampleToLengthFraction': 2.0}, 'TsDetection': {'Active': True, 'Comment': '', 'DetectorType': 'SED', 'MinTS': -66.0, 'PulseLengthDeterminationLevel': 6.0, 'MinEchoLength': 0.01, 'MaxEchoLength': 1.8, 'MaxGainCompensation': 6.0, 'DoPhaseDeviationCheck': True, 'MaxPhaseDevSteps': 8.0, 'MaxDepth': ''}, 'VerticalOffsetCorrection': {'Active': True, 'Comment': ''}, 'Writer': {'Active': True, 'Comment': '', 'FileName': '', 'UseRelativeDirectory': False, 'RelativeDirectory': '', 'DirectoryName': ''}, 'NetcdfWriter': {'Active': True, 'Comment': '', 'DirName': 'netcdf', 'MainFrequency': 38, 'WriterType': 'GRIDDED', 'DeltaRange': '', 'MaxRange': '', 'GriddedOutputType': 'SV_AND_ANGLES', 'WriteAngels': True, 'FftWindowSize': 2.0, 'DeltaFrequency': 1.0, 'ChannelGroupOutputType': 'PULSE_COMPRESSION'}}

koronascript-0.2.1/PKG-INFO

@@ -1,81 +0,0 @@
-Metadata-Version: 2.1
-Name: koronascript
-Version: 0.2.1
-Summary: Wrapper around Korona modules for processing echosounder data
-Home-page: https://github.com/CRIMAC-WP4-Machine-learning/CRIMAC-KoronaScript
-Author: Ketil Malde
-Author-email: ketil@malde.org
-Description-Content-Type: text/markdown
-
-# Running Korona through Python
-
-## Prerequisites
-
-### Install LSSS/Korona.
-
-This version of the KoronaScript is tested against lsss-2.16.0-alpha
-version. LSSS and korona is usually placed at
-`~/lsss/lsss-2.16.0-alpha` or a similar directory.
-
-Download the appropriate version from here:
-
-https://marec.no/tmp/lsss-2.16.0-alpha-20230922-1417-linux.zip
-
-https://marec.no/tmp/lsss-2.18.0-alpha-20240918-0847-linux.zip
-
-https://marec.no/tmp/lsss-2.16.0-alpha-20230922-1417-windows.zip
-
-https://marec.no/tmp/lsss-2.18.0-alpha-20240918-0847-windows.zip
-
-If you run linux you need to install the netcdf separately:
-
-`apt-get install libnetcdf` or `sudo apt install libnetcdf-dev`
-
-
-### Add license 
-
-You need an LSSS licence. The licence have to be added according to the LSSS manual. the licence files are typically placed at the `~/marec/license` directory.
-
-### Set system variables
-
-The `LSSS` environment variable should point to the root directory of your
-LSSS installation.  It can be set at run time either by setting the LSSS environment
-variable in the shell
-~~~
-export LSSS=~/lsss-2.16.0-alpha
-~~~
-before running your script, or by adding it manually from inside Python:
-~~~
-lsss = '~/lsss-2.16.0-alpha'
-os.environ["LSSS"] = lsss
-~~~
-
-# Usage
-
-Import the modules:
-
-	import KoronaScript as ks
-	import KoronaScript.Modules as ksm
-
-Create a script object:
-
-	ks = ks.KoronaScript(Categorization='categorization.xml',
-                     HorizontalTransducerOffsets='HorizontalTransducerOffsets.xml')
-
-Add some modules:
-
-	ks.add(ksm.EmptyPingRemoval())
-	ks.add(ksm.Comment(LineBreak='false', Label='CW_0256ms'))
-	ks.add(ksm.ChannelRemoval(Channels=[1,5,9,13,17],KeepSpecified='true'))
-	ks.add(ksm.Writer(RelativeDirectory='CW_0256ms'))
-
-Write out the resulting configuration:
-
-	ks.write()
-	
-Run the script:
-
-	ks.run(src="input_dir", dst="output_dir")
-
-The list of modules and their parameters can be found in the
-[configuration/korona-info.json](configuration/korona-info.json) file. 

koronascript-0.2.1/README.md

@@ -1,72 +0,0 @@
-# Running Korona through Python
-
-## Prerequisites
-
-### Install LSSS/Korona.
-
-This version of the KoronaScript is tested against lsss-2.16.0-alpha
-version. LSSS and korona is usually placed at
-`~/lsss/lsss-2.16.0-alpha` or a similar directory.
-
-Download the appropriate version from here:
-
-https://marec.no/tmp/lsss-2.16.0-alpha-20230922-1417-linux.zip
-
-https://marec.no/tmp/lsss-2.18.0-alpha-20240918-0847-linux.zip
-
-https://marec.no/tmp/lsss-2.16.0-alpha-20230922-1417-windows.zip
-
-https://marec.no/tmp/lsss-2.18.0-alpha-20240918-0847-windows.zip
-
-If you run linux you need to install the netcdf separately:
-
-`apt-get install libnetcdf` or `sudo apt install libnetcdf-dev`
-
-
-### Add license 
-
-You need an LSSS licence. The licence have to be added according to the LSSS manual. the licence files are typically placed at the `~/marec/license` directory.
-
-### Set system variables
-
-The `LSSS` environment variable should point to the root directory of your
-LSSS installation.  It can be set at run time either by setting the LSSS environment
-variable in the shell
-~~~
-export LSSS=~/lsss-2.16.0-alpha
-~~~
-before running your script, or by adding it manually from inside Python:
-~~~
-lsss = '~/lsss-2.16.0-alpha'
-os.environ["LSSS"] = lsss
-~~~
-
-# Usage
-
-Import the modules:
-
-	import KoronaScript as ks
-	import KoronaScript.Modules as ksm
-
-Create a script object:
-
-	ks = ks.KoronaScript(Categorization='categorization.xml',
-                     HorizontalTransducerOffsets='HorizontalTransducerOffsets.xml')
-
-Add some modules:
-
-	ks.add(ksm.EmptyPingRemoval())
-	ks.add(ksm.Comment(LineBreak='false', Label='CW_0256ms'))
-	ks.add(ksm.ChannelRemoval(Channels=[1,5,9,13,17],KeepSpecified='true'))
-	ks.add(ksm.Writer(RelativeDirectory='CW_0256ms'))
-
-Write out the resulting configuration:
-
-	ks.write()
-	
-Run the script:
-
-	ks.run(src="input_dir", dst="output_dir")
-
-The list of modules and their parameters can be found in the
-[configuration/korona-info.json](configuration/korona-info.json) file. 

koronascript-0.2.1/koronascript.egg-info/PKG-INFO

@@ -1,81 +0,0 @@
-Metadata-Version: 2.1
-Name: koronascript
-Version: 0.2.1
-Summary: Wrapper around Korona modules for processing echosounder data
-Home-page: https://github.com/CRIMAC-WP4-Machine-learning/CRIMAC-KoronaScript
-Author: Ketil Malde
-Author-email: ketil@malde.org
-Description-Content-Type: text/markdown
-
-# Running Korona through Python
-
-## Prerequisites
-
-### Install LSSS/Korona.
-
-This version of the KoronaScript is tested against lsss-2.16.0-alpha
-version. LSSS and korona is usually placed at
-`~/lsss/lsss-2.16.0-alpha` or a similar directory.
-
-Download the appropriate version from here:
-
-https://marec.no/tmp/lsss-2.16.0-alpha-20230922-1417-linux.zip
-
-https://marec.no/tmp/lsss-2.18.0-alpha-20240918-0847-linux.zip
-
-https://marec.no/tmp/lsss-2.16.0-alpha-20230922-1417-windows.zip
-
-https://marec.no/tmp/lsss-2.18.0-alpha-20240918-0847-windows.zip
-
-If you run linux you need to install the netcdf separately:
-
-`apt-get install libnetcdf` or `sudo apt install libnetcdf-dev`
-
-
-### Add license 
-
-You need an LSSS licence. The licence have to be added according to the LSSS manual. the licence files are typically placed at the `~/marec/license` directory.
-
-### Set system variables
-
-The `LSSS` environment variable should point to the root directory of your
-LSSS installation.  It can be set at run time either by setting the LSSS environment
-variable in the shell
-~~~
-export LSSS=~/lsss-2.16.0-alpha
-~~~
-before running your script, or by adding it manually from inside Python:
-~~~
-lsss = '~/lsss-2.16.0-alpha'
-os.environ["LSSS"] = lsss
-~~~
-
-# Usage
-
-Import the modules:
-
-	import KoronaScript as ks
-	import KoronaScript.Modules as ksm
-
-Create a script object:
-
-	ks = ks.KoronaScript(Categorization='categorization.xml',
-                     HorizontalTransducerOffsets='HorizontalTransducerOffsets.xml')
-
-Add some modules:
-
-	ks.add(ksm.EmptyPingRemoval())
-	ks.add(ksm.Comment(LineBreak='false', Label='CW_0256ms'))
-	ks.add(ksm.ChannelRemoval(Channels=[1,5,9,13,17],KeepSpecified='true'))
-	ks.add(ksm.Writer(RelativeDirectory='CW_0256ms'))
-
-Write out the resulting configuration:
-
-	ks.write()
-	
-Run the script:
-
-	ks.run(src="input_dir", dst="output_dir")
-
-The list of modules and their parameters can be found in the
-[configuration/korona-info.json](configuration/korona-info.json) file. 

koronascript-0.2.1/setup.cfg

@@ -1,7 +0,0 @@
-[flake8]
-ignore = E302,E501,E203,E701
-
-[egg_info]
-tag_build = 
-tag_date = 0
-

koronascript-0.2.1/setup.py

@@ -1,14 +0,0 @@
-from setuptools import setup
-
-setup(name='koronascript',
-      version='0.2.1',
-      description='Wrapper around Korona modules for processing echosounder data',
-      long_description=open('README.md').read(),
-      long_description_content_type='text/markdown',
-      url='https://github.com/CRIMAC-WP4-Machine-learning/CRIMAC-KoronaScript',
-      author='Ketil Malde',
-      author_email='ketil@malde.org',
-      packages=['KoronaScript'],
-      package_data={'': ['configuration/korona-info.json']},
-      include_package_data=True,
-      zip_safe=False)

koronascript-0.2.1/tests/test_examples.py

@@ -1,15 +0,0 @@
-import os
-import examples.channelRemoval as CR
-
-TESTDATA = 'test_data/EK60'
-
-def test_get_data():
-    if not os.path.exists(TESTDATA):
-        # Get test data from pyEchoLab examples:
-        os.system('mkdir -p test_data && cd test_data && wget --recursive --no-parent -nH --cut-dirs=6 ftp://ftp.ngdc.noaa.gov/pub/outgoing/mgg/wcd/pyEcholab_data/examples/EK60')
-
-def test_channelRemoval():
-    """This fails to fail if no data is present"""
-    CR.ks.run('test_data/EK60', 'test_out/cr_out')
-
-