Java tutorial
/** * Copyright: 2009 Regents of the University of Hawaii and the * School of Ocean and Earth Science and Technology * Purpose: A class that represents a converted sample of data produced by * a Seabird Seacat 19plus CTD profiler as described in * the SBE 19plus SEACAT Profiler User's Manual * (Manual Version #010, 01/02/03 ). The converter is intended to * convert raw frequencies and voltages as described in OUTPUTFORMAT * 2 in the manual. It uses formulas stated in the SBE19plus * calibration sheets for converting temperature counts to degrees * celsius, conductivity frequencies to Siemens/m, and pressure counts * to decibars. * * Authors: Christopher Jones * * $HeadURL$ * $LastChangedDate$ * $LastChangedBy$ * $LastChangedRevision$ * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */ package edu.hawaii.soest.kilonalu.ctd; import edu.hawaii.soest.kilonalu.ctd.CTDParser; import java.text.ParseException; import java.util.ArrayList; import java.util.List; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.commons.math.linear.Array2DRowRealMatrix; import org.apache.commons.math.linear.ArrayRealVector; import org.apache.commons.math.linear.RealMatrix; /** * A class that represents converted CTD data values. The class takes a * CTDParser class as input, which stores decimal data values for raw * frequencies and voltages, and metadata fields used to convert those voltages * to usable engineering units. */ public class CTDConverter { /** * The Logger instance used to log system messages */ static Log logger = LogFactory.getLog(CTDConverter.class); /** * The instance of the CTDParser object that holds the original data and * metadata values. */ private CTDParser ctdParser; /** * The original matrix of raw frequency and voltage values (counts, Hz, V ...) */ private RealMatrix dataValuesMatrix; /** * The converted matrix of values in engineering units (degrees, S/m, decibars ...) */ private RealMatrix convertedDataValuesMatrix; /** * Constructor: Builds all of the components of the CTD data object from * the CTDParser object being passed in. The data string must contain the results * of the 'DS' command and the 'DCAL' command in order to inform the parser * which data fields should be expected, and which CTD output format to expect. * The data observations should follow the output of the 'DS' and 'DCAL' commands. * * @param dataString The CTDParser object that contains the data and metadata * from the instrument */ public CTDConverter(CTDParser ctdParser) { // set the data values matrix this.dataValuesMatrix = ctdParser.getConvertedMatrix(); // create an equally-sized array for the converted values this.convertedDataValuesMatrix = new Array2DRowRealMatrix(this.dataValuesMatrix.getRowDimension(), this.dataValuesMatrix.getColumnDimension()); // set the CTD parser object field this.ctdParser = ctdParser; } /* * A method used to apply all of the conversion formulas to the data matrix * The converted matrix is populated with the new values. */ public void convert() { // For the following conversions, each variable's data vector position // is determined by the position of the variable name as they are listed // in the ctdParser.dataVariableNames list. // convert the temperature vector if (this.ctdParser.getDataVariableNames().indexOf(ctdParser.RAW_TEMPERATURE_FIELD_NAME) >= 0) { int temperatureVariableIndex = this.ctdParser.getDataVariableNames() .indexOf(this.ctdParser.RAW_TEMPERATURE_FIELD_NAME); convertTemperature(temperatureVariableIndex); } // convert the pressure vector (relies on pressure-temp compensation) if ((this.ctdParser.getDataVariableNames().indexOf(this.ctdParser.RAW_PRESSURE_FIELD_NAME) >= 0) && (this.ctdParser.getDataVariableNames() .indexOf(this.ctdParser.RAW_PRESSURE_TEMP_COMP_FIELD_NAME) >= 0)) { int pressureVariableIndex = this.ctdParser.getDataVariableNames() .indexOf(this.ctdParser.RAW_PRESSURE_FIELD_NAME); int pressureTempCompVariableIndex = this.ctdParser.getDataVariableNames() .indexOf(this.ctdParser.RAW_PRESSURE_TEMP_COMP_FIELD_NAME); convertPressure(pressureVariableIndex, pressureTempCompVariableIndex); } // convert the conductivity vector (relies on converted temp and pressure) if ((this.ctdParser.getDataVariableNames().indexOf(this.ctdParser.RAW_CONDUCTIVITY_FIELD_NAME) >= 0) && (this.ctdParser.getDataVariableNames().indexOf(this.ctdParser.RAW_TEMPERATURE_FIELD_NAME) >= 0) && (this.ctdParser.getDataVariableNames().indexOf(this.ctdParser.RAW_PRESSURE_FIELD_NAME) >= 0)) { int conductivityVariableIndex = this.ctdParser.getDataVariableNames() .indexOf(this.ctdParser.RAW_CONDUCTIVITY_FIELD_NAME); int temperatureVariableIndex = this.ctdParser.getDataVariableNames() .indexOf(this.ctdParser.RAW_TEMPERATURE_FIELD_NAME); int pressureVariableIndex = this.ctdParser.getDataVariableNames() .indexOf(this.ctdParser.RAW_PRESSURE_FIELD_NAME); convertConductivity(conductivityVariableIndex, temperatureVariableIndex, pressureVariableIndex); } System.out.println("Converted Data Matrix is: " + convertedDataValuesMatrix.toString()); // TODO: convert voltage channels based on the metadata from the data // type being collected on each channel } /* * A method used to apply the temperature conversion formula to the data * matrix. The converted matrix is populated with the new values in the given * vector position. */ private void convertTemperature(int temperatureVectorIndex) { // define the constants from the temperature conversion formulas double MV_CONSTANT_ONE = 524288d; double MV_CONSTANT_TWO = 1.6e+007; double R_CONSTANT_ONE = 2.900e+009; double R_CONSTANT_TWO = 1.024e+008; double R_CONSTANT_THREE = 2.048e+004; double R_CONSTANT_FOUR = 2.0e+005; double T_CONSTANT_ONE = 273.15d; //get the calibration coefficients from the CTDParser instance double temperatureCoefficientTA0 = this.ctdParser.getTemperatureCoefficientTA0(); double temperatureCoefficientTA1 = this.ctdParser.getTemperatureCoefficientTA1(); double temperatureCoefficientTA2 = this.ctdParser.getTemperatureCoefficientTA2(); double temperatureCoefficientTA3 = this.ctdParser.getTemperatureCoefficientTA3(); ArrayRealVector temperatureVector = (ArrayRealVector) this.dataValuesMatrix .getColumnVector(temperatureVectorIndex); ArrayRealVector convertedTemperatureVector = new ArrayRealVector(temperatureVector.getDimension()); // iterate through the temperature values and apply the conversion for (int count = 0; count < temperatureVector.getDimension(); count++) { // calculate the temperature in degrees C from the calibration sheet formula // note: the mv, r, and tDegreesC variables come from the calibration sheet double countValue = temperatureVector.getEntry(count); double mv = (countValue - MV_CONSTANT_ONE) / MV_CONSTANT_TWO; double r = (mv * R_CONSTANT_ONE + R_CONSTANT_TWO) / (R_CONSTANT_THREE - mv * R_CONSTANT_FOUR); double tDegreesC = 1 / (temperatureCoefficientTA0 + temperatureCoefficientTA1 * (Math.log(r)) + temperatureCoefficientTA2 * (Math.pow(Math.log(r), 2)) + temperatureCoefficientTA3 * (Math.pow(Math.log(r), 3))) - T_CONSTANT_ONE; convertedTemperatureVector.setEntry(count, tDegreesC); } // set the new vector in the converted values matrix this.convertedDataValuesMatrix.setColumnVector(temperatureVectorIndex, convertedTemperatureVector); } /* * A method used to apply the conductivity conversion formula to the data * matrix. The converted matrix is populated with the new values in the given * vector position. */ private void convertConductivity(int conductivityVectorIndex, int temperatureVectorIndex, int pressureVectorIndex) { // define the constants from the conductivity conversion formulas double F_CONSTANT_ONE = 1000d; //get the calibration coefficients from the CTDParser instance double conductivityCoefficientG = this.ctdParser.getConductivityCoefficientG(); double conductivityCoefficientH = this.ctdParser.getConductivityCoefficientH(); double conductivityCoefficientI = this.ctdParser.getConductivityCoefficientI(); double conductivityCoefficientJ = this.ctdParser.getConductivityCoefficientJ(); double conductivityCoefficientCF0 = this.ctdParser.getConductivityCoefficientCF0(); double conductivityCoefficientCPCOR = this.ctdParser.getConductivityCoefficientCPCOR(); double conductivityCoefficientCTCOR = this.ctdParser.getConductivityCoefficientCTCOR(); double conductivityCoefficientCSLOPE = this.ctdParser.getConductivityCoefficientCSLOPE(); ArrayRealVector conductivityVector = (ArrayRealVector) this.dataValuesMatrix .getColumnVector(conductivityVectorIndex); ArrayRealVector convertedConductivityVector = new ArrayRealVector(conductivityVector.getDimension()); ArrayRealVector convertedTemperatureVector = (ArrayRealVector) this.convertedDataValuesMatrix .getColumnVector(temperatureVectorIndex); ArrayRealVector convertedPressureVector = (ArrayRealVector) this.convertedDataValuesMatrix .getColumnVector(pressureVectorIndex); // iterate through the conductivity values and apply the conversion for (int count = 0; count < conductivityVector.getDimension(); count++) { // calculate the conductivity in Siemens/m from the calibration sheet formula double frequencyValue = conductivityVector.getEntry(count); double tDegreesC = convertedTemperatureVector.getEntry(count); double pressureDB = convertedPressureVector.getEntry(count); double f = frequencyValue / F_CONSTANT_ONE; double cSiemensPerM = (conductivityCoefficientG + (conductivityCoefficientH * Math.pow(f, 2)) + (conductivityCoefficientI * Math.pow(f, 3)) + (conductivityCoefficientJ * Math.pow(f, 4))) / (1 + (conductivityCoefficientCTCOR * tDegreesC) + (conductivityCoefficientCPCOR * pressureDB)); convertedConductivityVector.setEntry(count, cSiemensPerM); } // set the new vector in the converted values matrix this.convertedDataValuesMatrix.setColumnVector(conductivityVectorIndex, convertedConductivityVector); } /* * A method used to apply the temperature conversion formula to the data * matrix. The converted matrix is populated with the new values in the given * vector position. */ private void convertPressure(int pressureVectorIndex, int pressureTempCompIndex) { double P_CONTSTANT_ONE = 14.7d; // atmospheric pressure influence double P_CONTSTANT_TWO = 0.689476d; // psia to decibars factor //get the calibration coefficients from the CTDParser instance double pressureCoefficientPA0 = this.ctdParser.getPressureCoefficientPA0(); double pressureCoefficientPA1 = this.ctdParser.getPressureCoefficientPA1(); double pressureCoefficientPA2 = this.ctdParser.getPressureCoefficientPA2(); double pressureCoefficientPTCA0 = this.ctdParser.getPressureCoefficientPTCA0(); double pressureCoefficientPTCA1 = this.ctdParser.getPressureCoefficientPTCA1(); double pressureCoefficientPTCA2 = this.ctdParser.getPressureCoefficientPTCA2(); double pressureCoefficientPTCB0 = this.ctdParser.getPressureCoefficientPTCB0(); double pressureCoefficientPTCB1 = this.ctdParser.getPressureCoefficientPTCB1(); double pressureCoefficientPTCB2 = this.ctdParser.getPressureCoefficientPTCB2(); double pressureCoefficientPTEMPA0 = this.ctdParser.getPressureCoefficientPTEMPA0(); double pressureCoefficientPTEMPA1 = this.ctdParser.getPressureCoefficientPTEMPA1(); double pressureCoefficientPTEMPA2 = this.ctdParser.getPressureCoefficientPTEMPA2(); double pressureOffsetCoefficient = this.ctdParser.getPressureOffsetCoefficient(); // convert raw values ... ArrayRealVector pressureVector = (ArrayRealVector) this.dataValuesMatrix .getColumnVector(pressureVectorIndex); ArrayRealVector pressureTempCompVector = (ArrayRealVector) this.dataValuesMatrix .getColumnVector(pressureTempCompIndex); // to engineering values ArrayRealVector convertedPressureVector = new ArrayRealVector(pressureVector.getDimension()); // iterate through the pressure values and apply the conversion for (int count = 0; count < pressureVector.getDimension(); count++) { // calculate the pressure in decibars from the calibration sheet formula double pressureValue = pressureVector.getEntry(count); double ptCompValue = pressureTempCompVector.getEntry(count); double t = pressureCoefficientPTEMPA0 + (pressureCoefficientPTEMPA1 * ptCompValue) + (pressureCoefficientPTEMPA2 * Math.pow(ptCompValue, 2)); double x = pressureValue - pressureCoefficientPTCA0 - pressureCoefficientPTCA1 * t - pressureCoefficientPTCA2 * Math.pow(t, 2); double n = x * pressureCoefficientPTCB0 / (pressureCoefficientPTCB0 + pressureCoefficientPTCB1 * t + pressureCoefficientPTCB2 * Math.pow(t, 2)); double pressurePSIA = pressureCoefficientPA0 + pressureCoefficientPA1 * n + pressureCoefficientPA2 * Math.pow(n, 2); // pressure (decibels) = [pressure (psia) - 14.7] * 0.689476 from the CTD manual double pressureDB = (pressurePSIA - P_CONTSTANT_ONE) * P_CONTSTANT_TWO; convertedPressureVector.setEntry(count, pressureDB); } // set the new vector in the converted values matrix this.convertedDataValuesMatrix.setColumnVector(pressureVectorIndex, convertedPressureVector); } /** * A method that returns the converted data values matrix as a RealMatrix * * @return convertedDataValuesMatrix - the matrix of converted data values */ public RealMatrix getConvertedDataValuesMatrix() { return this.convertedDataValuesMatrix; } /** * The main method */ public static void main(String[] args) { String file = "* Sea-Bird SBE19plus Data File:\r\n" + "* FileName = sh__0002.hex\r\n" + "* Software Version \r\n" + "* Temperature SN = 5251\r\n" + "* Conductivity SN = 5251\r\n" + "* System UpLoad Time = Sep 23 2009 11:29:01\r\n" + "** Cruise: Sea Engineering C&C Project\r\n" + "** Station: Kilo Nalu, 20meter[D[D[D[D[D meter site \r\n" + "** Ship: Huki Pau, Sea Engineering\r\n" + "** Chief_Scientist: McManus\r\n" + "** Organization: UH\r\n" + "** Area_of_Operation: Offshore Kewalo Basin\r\n" + "** Package: SH2\r\n" + "** Mooring_Number: N/A\r\n" + "** Latitude: \r\n" + "** Longitude: \r\n" + "** Sounding: 20.6 m\r\n" + "** Profile_Number: 2\r\n" + "** Profile_Direction: up\r\n" + "** Notes: \r\n" + "* ds\r\n" + "* SeacatPlus V 1.6b SERIAL NO. 5251 23 Sep 2009 11:29:02\r\n" + "* vbatt = 12.0, vlith = 8.4, ioper = 61.8 ma, ipump = 134.7 ma, \r\n" + "* iext01 = 5.4 ma\r\n" + "* iext23 = 77.8 ma\r\n" + "* \r\n" + "* status = not logging\r\n" + "* number of scans to average = 1\r\n" + "* samples = 493446, free = 1, casts = 1\r\n" + "* mode = profile, minimum cond freq = 3000, pump delay = 20 sec\r\n" + "* autorun = no, ignore magnetic switch = yes\r\n" + "* battery type = alkaline, battery cutoff = 7.3 volts\r\n" + "* pressure sensor = strain gauge, range = 508.0\r\n" + "* SBE 38 = no, Gas Tension Device = no\r\n" + "* Ext Volt 0 = yes, Ext Volt 1 = no, Ext Volt 2 = yes, Ext Volt 3 = yes\r\n" + "* echo commands = yes\r\n" + "* output format = raw HEX\r\n" + "* S>\r\n" + "* dcal\r\n" + "* SeacatPlus V 1.6b SERIAL NO. 5251 23 Sep 2009 11:29:08\r\n" + "* temperature: 09-oct-07\r\n" + "* TA0 = 1.276108e-03\r\n" + "* TA1 = 2.615414e-04\r\n" + "* TA2 = -1.590756e-07\r\n" + "* TA3 = 1.496275e-07\r\n" + "* TOFFSET = 0.000000e+00\r\n" + "* conductivity: 09-oct-07\r\n" + "* G = -1.016034e+00\r\n" + "* H = 1.583915e-01\r\n" + "* I = -5.990283e-04\r\n" + "* J = 7.154628e-05\r\n" + "* CF0 = 2.541437e+03\r\n" + "* CPCOR = -9.570000e-08\r\n" + "* CTCOR = 3.250000e-06\r\n" + "* CSLOPE = 1.000000e+00\r\n" + "* pressure S/N = 2458922, range = 508 psia: 04-oct-07\r\n" + "* PA0 = 3.174352e-01\r\n" + "* PA1 = 1.542191e-03\r\n" + "* PA2 = 6.554083e-12\r\n" + "* PTCA0 = 5.251525e+05\r\n" + "* PTCA1 = 1.352052e+01\r\n" + "* PTCA2 = -1.455316e-01\r\n" + "* PTCB0 = 2.558650e+01\r\n" + "* PTCB1 = -1.500000e-03\r\n" + "* PTCB2 = 0.000000e+00\r\n" + "* PTEMPA0 = -5.795848e+01\r\n" + "* PTEMPA1 = 5.427466e+01\r\n" + "* PTEMPA2 = -5.522354e-01\r\n" + "* POFFSET = 0.000000e+00\r\n" + "* volt 0: offset = -4.678210e-02, slope = 1.248624e+00\r\n" + "* volt 1: offset = -4.696105e-02, slope = 1.248782e+00\r\n" + "* volt 2: offset = -4.683263e-02, slope = 1.249537e+00\r\n" + "* volt 3: offset = -4.670842e-02, slope = 1.249841e+00\r\n" + "* EXTFREQSF = 1.000012e+00\r\n" + "* S>\r\n" + "** First Sample Time: 23 Sep 2009 11:29:15\r\n" + "*END*\r\n" + "03B7DA1909A2086F85510B6E950574D157\r\n" + "03B7DB1909A3086FC9510C6E9A05B2E8FD\r\n" + "03B7DF1909A9087032510B6EB3059DFCB5\r\n" + "03B7E51909A9087090510B6F1B05C7E0FD\r\n" + "03B7E61909A30870AD510C6FEE05A5E723\r\n" + 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"039A681931B40831FB51117AE205F6E3F0\r\n" + "039A901932000831EF51137AC105EFE576\r\n" + "039ABF1931C50831E551117A9C05EBE227\r\n" + "039AE91931730831E951137A520608E5A5\r\n" + "039B191931C10831DF51137A2405EBE3C3\r\n" + "039B261932240831BD51137A1A05CCD963\r\n" + "039B091932BD08319151137A2205E2DFBA\r\n" + "039ACB1932FD08319051147A460602DEC6\r\n" + "039A8B19330F0831A851147A8D05FCE398\r\n" + "039A6019330E0831BB51137AD605E9DF3A\r\n" + "039A491933320831AD51157AEF05D1E03D\r\n" + "039A3A19332D08319451137AFC05D3E01E\r\n" + "039A311933090831A251137AF005CBDF6F\r\n" + "039A3619329F0831C051147AF805D8E1A9\r\n" + "039A561932590831CF51137AFF05CDE24F\r\n" + "039A851931FA0831BF51157B1C05CBDDDE\r\n" + "039AB81932240831AC51157B3805CCE03E\r\n" + "039AD41932180831AA51127B3805CBDF14\r\n" + "039ADF19321E0831C451137B2405B9E2B7\r\n" + "039AE51932040831E851137AFD05B2E2FF\r\n" + "039AEA1931D708320151167AFF05A8E322\r\n" + "039AFD1931A208320551157B14059CE5B3\r\n" + "039B171931DD08320051147B3405B6E6C0\r\n" + "039B2019325908320351167B6A05B2E5E4\r\n" + "039AFC19323208320851167B950597E804\r\n" + "039AE51932180831FE51157BB0059DE6E8\r\n" + "039AE61932240831E451147B940585E718\r\n" + "039AE61932B70831C651147B5D058EE88E\r\n" + "039AC11932F80831A551167B330596E8A9\r\n" + "039A8B1932D008317C51147B2B05A4E899\r\n" + "039A7819326A08314451137B4105A3E618\r\n" + "039A8919324D08313951167B610585DD1C\r\n" + "039AA519326A08316F51147B7005A0E285\r\n" + "039AB11932AB0831C351157B7D05A5DD05\r\n" + "039AA019329D0831F751147B93059BE50B\r\n" + "039A9619327008320551157B8B058FDE93\r\n" + "039A9F19325E0831FE51157B720590DA65\r\n" + "039AAC1932B70831F151157B450582DE2F\r\n" + "039A9F1932F20831E651137B1C0593DEDA\r\n" + "039A7C1933400831D851167AF7059FE1F3\r\n"; try { CTDParser ctdParser = new CTDParser(file); CTDConverter ctdConverter = new CTDConverter(ctdParser); ctdConverter.convert(); } catch (ParseException pe) { System.out.println("There was a parse exception:" + pe.getMessage()); System.exit(0); } } }