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Merge pull request #199 from upsonp/blank_header_lines_196
added fix for issue #196 and unit test
2 parents 37cd1b5 + 6d9231b commit 5f75b62

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‎ctd/read.py

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@@ -166,6 +166,10 @@ def _parse_seabird(lines, ftype):
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break
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else: # btl.
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# There is no *END* like in a .cnv file, skip two after header info.
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# Skip empty lines.
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if not line:
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continue
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if not (line.startswith("*") | line.startswith("#")):
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# Fix commonly occurring problem when Sbeox.* exists in the file
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# the name is concatenated to previous parameter

‎tests/data/btl/blank_line_header.btl

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* Sea-Bird SBE25 Data File:
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* FileName = C:\Users\Science\Documents\CAR2022102\ctd data\22102007.hex
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* Software Version 1.59
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* Temperature SN = Sbe03_1817
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* Conductivity SN = Sbe04-0735
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* System UpLoad Time = Mar 31 2022 08:30:05
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** Latitude: 41 12.513 N
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** Longitude: 067 09.722 W
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** Ship: CFA3098 CCGS Capt Jacques Cartier
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** Cruise: CAR2022102
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** Station_Label:755
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** Set_number:007
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** Stratum_number:5Z41
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** Station: 007
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** Sounding: 61
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** ID_Start:474815
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** Event_Comments: 2022 Georges Bank SurveyKP
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* ds
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* SBE 25 CTD V 4.0a SN 184 03/31/22 11:27:10.920
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* external pressure sensor, range = 1500 psia, tcval = 16
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* xtal = 9437427 clk = 32767.537 vmain = 12.5 iop = 4 vlith = 3.9
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* ncasts = 1 samples = 5815 free = 49165 lwait = 0 msec
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*
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* CTD configuration:
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* number of scans averaged = 1, data stored at 8 scans per second
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* real time data transmitted at 8 scans per second
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* minimum conductivity frequency for pump turn on = 1500
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* battery type = ALKALINE
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*
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* 7 external voltages sampled
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* stored voltage # 0 = external voltage 0
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* stored voltage # 1 = external voltage 1
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* stored voltage # 2 = external voltage 2
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* stored voltage # 3 = external voltage 3
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* stored voltage # 4 = external voltage 4
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* stored voltage # 5 = external voltage 5
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* stored voltage # 6 = external voltage 6
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*
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* S>
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* dh
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* cast 0 03/31 10:46:00 smpls 0 to 5814 nv = 7 avg = 1 stp = switch of
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* S>
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# interval = seconds: 0.125
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# start_time = Mar 31 2022 10:46:00 [Instrument's time stamp, header]
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# <Sensors count="10" >
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# <sensor Channel="1" >
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# <!-- Frequency 0, Temperature -->
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# <TemperatureSensor SensorID="55" >
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# <SerialNumber>Sbe03_1817</SerialNumber>
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# <CalibrationDate>24-Nov-2004</CalibrationDate>
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# <!-- t0pcor = -2.0600e-007 specified on DatCnv command line -->
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# <UseG_J>1</UseG_J>
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# <A>3.68120516e-003</A>
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# <B>6.00510844e-004</B>
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# <C>1.36911401e-005</C>
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# <D>1.80939934e-006</D>
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# <F0_Old>5918.752</F0_Old>
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# <G>4.85872870e-003</G>
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# <H>6.78186362e-004</H>
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# <I>2.69032925e-005</I>
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# <J>2.15066050e-006</J>
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# <F0>1000.000</F0>
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# <Slope>1.00000000</Slope>
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# <Offset>0.0000</Offset>
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# </TemperatureSensor>
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# </sensor>
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# <sensor Channel="2" >
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# <!-- Frequency 1, Conductivity -->
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# <ConductivitySensor SensorID="3" >
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# <SerialNumber>Sbe04-0735</SerialNumber>
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# <CalibrationDate>07-Jan-2009</CalibrationDate>
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# <UseG_J>1</UseG_J>
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# <!-- Cell const and series R are applicable only for wide range sensors. -->
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# <SeriesR>0.0000</SeriesR>
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# <CellConst>2000.0000</CellConst>
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# <ConductivityType>0</ConductivityType>
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# <Coefficients equation="0" >
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# <A>0.00000000e+000</A>
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# <B>0.00000000e+000</B>
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# <C>-9.57000000e-008</C>
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# <D>0.00000000e+000</D>
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# <M>0.0</M>
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# <CPcor>0.00000000e+000</CPcor>
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# </Coefficients>
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# <Coefficients equation="1" >
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# <G>-3.99405308e+000</G>
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# <H>4.26940024e-001</H>
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# <I>2.75670483e-004</I>
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# <J>7.86847868e-006</J>
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# <CPcor>-9.57000000e-008</CPcor>
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# <CTcor>3.2500e-006</CTcor>
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# <!-- WBOTC not applicable unless ConductivityType = 1. -->
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# <WBOTC>0.00000000e+000</WBOTC>
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# </Coefficients>
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# <Slope>1.00000000</Slope>
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# <Offset>0.00000</Offset>
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# </ConductivitySensor>
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# </sensor>
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# <sensor Channel="3" >
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# <!-- Pressure voltage, Pressure, Strain Gauge -->
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# <PressureSensor SensorID="49" >
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# <SerialNumber>Sbe29-0274</SerialNumber>
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# <CalibrationDate>12-Jan-2009</CalibrationDate>
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# <A0>7.888379e+002</A0>
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# <A1>-2.082626e-001</A1>
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# <A2>3.829048e-007</A2>
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# <Offset>0.00000</Offset>
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# </PressureSensor>
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# </sensor>
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# <sensor Channel="4" >
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# <!-- A/D voltage 0, Oxygen, SBE 43 -->
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# <OxygenSensor SensorID="38" >
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# <SerialNumber>Sbe43-1157</SerialNumber>
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# <CalibrationDate>23-May-2017</CalibrationDate>
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# <Use2007Equation>1</Use2007Equation>
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# <CalibrationCoefficients equation="0" >
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# <!-- Coefficients for Owens-Millard equation. -->
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# <Boc>0.0000</Boc>
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# <Soc>0.0000e+000</Soc>
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# <offset>0.0000</offset>
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# <Pcor>0.00e+000</Pcor>
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# <Tcor>0.0000</Tcor>
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# <Tau>0.0</Tau>
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# </CalibrationCoefficients>
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# <CalibrationCoefficients equation="1" >
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# <!-- Coefficients for Sea-Bird equation - SBE calibration in 2007 and later. -->
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# <Soc>4.8000e-001</Soc>
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# <offset>-0.5166</offset>
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# <A>-3.8247e-003</A>
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# <B> 1.8386e-004</B>
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# <C>-2.9783e-006</C>
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# <D0> 2.5826e+000</D0>
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# <D1> 1.92634e-004</D1>
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# <D2>-4.64803e-002</D2>
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# <E> 3.6000e-002</E>
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# <Tau20> 1.6900</Tau20>
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# <H1>-3.3000e-002</H1>
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# <H2> 5.0000e+003</H2>
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# <H3> 1.4500e+003</H3>
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# </CalibrationCoefficients>
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# </OxygenSensor>
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# </sensor>
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# <sensor Channel="5" >
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# <!-- A/D voltage 1, Free -->
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# </sensor>
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# <sensor Channel="6" >
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# <!-- A/D voltage 2, Free -->
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# </sensor>
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# <sensor Channel="7" >
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# <!-- A/D voltage 3, Free -->
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# </sensor>
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# <sensor Channel="8" >
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# <!-- A/D voltage 4, Fluorometer, Chelsea Minitracka -->
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# <FluoroChelseaMinitrackaSensor SensorID="6" >
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# <SerialNumber>Mini-175028</SerialNumber>
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# <CalibrationDate>28 Jan 1998</CalibrationDate>
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# <Vacetone>0.067</Vacetone>
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# <Vacetone100>5.419</Vacetone100>
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# <Offset>0.000</Offset>
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# </FluoroChelseaMinitrackaSensor>
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# </sensor>
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# <sensor Channel="9" >
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# <!-- A/D voltage 5, Free -->
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# </sensor>
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# <sensor Channel="10" >
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# <!-- A/D voltage 6, PAR/Irradiance, Biospherical/Licor -->
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# <PAR_BiosphericalLicorChelseaSensor SensorID="42" >
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# <SerialNumber>SPQA-4859</SerialNumber>
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# <CalibrationDate>04-Sept-2014</CalibrationDate>
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# <M>-0.77060200</M>
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# <B>-3.52671700</B>
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# <CalibrationConstant>4.28000000</CalibrationConstant>
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# <Multiplier>1.00000000</Multiplier>
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# <Offset>0.00000000</Offset>
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# </PAR_BiosphericalLicorChelseaSensor>
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# </sensor>
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# </Sensors>
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# datcnv_date = Apr 19 2022 11:52:32, 7.26.6.28
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# datcnv_in = C:\Users\PROUDFOOTMA\Documents\.MISSIONS\2022\CAR2022102_WinterGF\Data\CTD\Reprocessed_Pinky\CTDDATA\22102007.hex C:\Users\PROUDFOOTMA\Documents\.MISSIONS\2022\CAR2022102_WinterGF\Data\CTD\Reprocessed_Pinky\Pinky1_Sbe25-0184standalone_Apr2022.xmlcon
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# datcnv_ox_hysteresis_correction = yes
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# datcnv_bottle_scan_range_source = BL file
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# datcnv_scans_per_bottle = 37
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# bottlesum_date = Apr 19 2022 11:52:36, 7.26.6.28
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# bottlesum_in = C:\Users\PROUDFOOTMA\Documents\.MISSIONS\2022\CAR2022102_WinterGF\Data\CTD\Reprocessed_Pinky\CTDDATA\22102007.ros C:\Users\PROUDFOOTMA\Documents\.MISSIONS\2022\CAR2022102_WinterGF\Data\CTD\Reprocessed_Pinky\Pinky1_Sbe25-0184standalone_Apr2022.xmlcon C:\Users\PROUDFOOTMA\Documents\.MISSIONS\2022\CAR2022102_WinterGF\Data\CTD\Reprocessed_Pinky\CTDDATA\22102007.BL
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# bottlesum_ox_tau_correction = yes
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Bottle Bottle Date Sbeox0ML/L Sal00 Potemp090C Sigma-é00 Scan TimeS PrSM T090C C0S/m Sbeox0V FlCM Par
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Position S/N Time
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4 474818 Mar 31 2022 6.0542 33.2232 6.7908 26.0473 792 98.875 5.556 6.7912 3.348640 2.3385 5.3210 2.2323e+00 (avg)
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10:47:36 11 1.353 0.329 0.0067 0.000340 0.0249 0.3117 1.9796e-01 (sdev)
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3 474817 Mar 31 2022 6.7306 33.2207 6.7863 26.0459 3250 406.125 26.130 6.7886 3.349098 2.5941 5.8026 4.8180e-02 (avg)
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10:52:43 11 1.353 0.503 0.0009 0.000096 0.0016 0.2241 6.2121e-03 (sdev)
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2 474816 Mar 31 2022 6.7188 33.2219 6.7951 26.0457 3691 461.250 51.103 6.7996 3.351271 2.5846 6.2792 3.1472e-03 (avg)
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10:53:38 11 1.353 0.476 0.0026 0.000221 0.0019 0.3323 1.0053e-04 (sdev)
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1 474815 Mar 31 2022 6.7283 33.2220 6.7985 26.0453 3969 496.000 59.278 6.8037 3.352000 2.5782 6.0967 2.0116e-03 (avg)
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10:54:13 11 1.353 0.365 0.0004 0.000037 0.0022 0.2897 0.0000e+00 (sdev)

‎tests/test_read.py

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@@ -112,6 +112,22 @@ def test_header_parse():
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np.testing.assert_almost_equal(xbt._metadata["lat"], -19.7174805)
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def test_header_parse_blank_line():
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# check that a BTL file can still be loaded if the header section contains blank lines
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# if the blank line in the header causes the reader to exit before reading the file
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# the line looking for the Date in the ctd.from_btl() will throw a ValueError.
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btl = ctd.from_btl(
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data_path.joinpath(
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"btl",
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"blank_line_header.btl",
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),
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)
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# if a value error wasn't thrown, ensure the names array for the _metadata was set
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assert btl._metadata["names"].index("Date")
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def test_pressure_field_labels():
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"""
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Support different pressure field labels encountered in Sea-Bird cnv files.

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