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Merge pull request #13 from bcdev/TAO_TB
Tao tb
2 parents a306ce4 + 00601c4 commit 0f856b5

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‎core/src/main/java/com/bc/fiduceo/reader/insitu/ndbc/NdbcSMReader.java‎

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@@ -116,6 +116,7 @@ public TimeLocator getTimeLocator() throws IOException {
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@Override
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public Array readRaw(int centerX, int centerY, Interval interval, String variableName) throws IOException, InvalidRangeException {
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final SmRecord record = records.get(centerY);
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// @todo 2 tb/tb handle positions out of range 2023-05-02
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switch (variableName) {
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case STATION_ID:

‎core/src/main/java/com/bc/fiduceo/reader/insitu/tao/TaoReader.java‎

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package com.bc.fiduceo.reader.insitu.tao;
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import com.bc.fiduceo.core.Dimension;
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import com.bc.fiduceo.core.Interval;
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import com.bc.fiduceo.core.NodeType;
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import com.bc.fiduceo.geometry.Polygon;
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import com.bc.fiduceo.location.PixelLocator;
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import com.bc.fiduceo.reader.AcquisitionInfo;
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import com.bc.fiduceo.reader.Reader;
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import com.bc.fiduceo.reader.netcdf.StringVariable;
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import com.bc.fiduceo.reader.time.TimeLocator;
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import com.bc.fiduceo.reader.time.TimeLocator_MillisSince1970;
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import com.bc.fiduceo.util.NetCDFUtils;
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import com.bc.fiduceo.util.VariableProxy;
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import org.esa.snap.core.util.StringUtils;
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import ucar.ma2.Array;
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import ucar.ma2.ArrayInt;
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import ucar.ma2.DataType;
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import ucar.ma2.InvalidRangeException;
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import ucar.nc2.Attribute;
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import ucar.nc2.Variable;
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import java.io.BufferedReader;
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import java.io.File;
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import java.io.FileReader;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Date;
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import java.util.List;
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import static com.bc.fiduceo.util.NetCDFUtils.*;
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class TaoReader implements Reader {
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private final static String REG_EX = "(?:TAO|TRITON)_\\w+_\\w+(-\\w+)??\\d{4}-\\d{2}.txt";
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private static final String TIME = "time";
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private static final String LONGITUDE = "longitude";
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private static final String LATITUDE = "latitude";
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private static final String SSS = "SSS";
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private static final float SSS_FILL = -9.999f;
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private static final String SST = "SST";
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private static final float SST_FILL = -9.999f;
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private static final String AIRT = "AIRT";
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private static final double AIRT_FILL = -9.99;
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private static final String RH = "RH";
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private static final double RH_FILL = -9.99;
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private static final String WSPD = "WSPD";
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private static final double WSPD_FILL = -99.9;
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private static final String WDIR = "WDIR";
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private static final double WDIR_FILL = -99.9;
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private static final String BARO = "BARO";
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private static final double BARO_FILL = -9.9;
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private static final String RAIN = "RAIN";
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private static final double RAIN_FILL = -9.99;
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private static final String Q = "Q";
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private static final String M = "M";
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private ArrayList<TaoRecord> records;
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private TimeLocator timeLocator;
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static TaoRecord parseLine(String line) {
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line = line.replaceAll(" +", " "); // ensure that we only have single blanks as separator tb 2023-04-28
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final String[] tokens = StringUtils.split(line, new char[]{' '}, true);
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final TaoRecord record = new TaoRecord();
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record.time = Integer.parseInt(tokens[0]);
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record.longitude = Float.parseFloat(tokens[1]);
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record.latitude = Float.parseFloat(tokens[2]);
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record.SSS = Float.parseFloat(tokens[3]);
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record.SST = Float.parseFloat(tokens[4]);
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record.AIRT = Float.parseFloat(tokens[5]);
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record.RH = Float.parseFloat(tokens[6]);
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record.WSPD = Float.parseFloat(tokens[7]);
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record.WDIR = Float.parseFloat(tokens[8]);
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record.BARO = Float.parseFloat(tokens[9]);
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record.RAIN = Float.parseFloat(tokens[10]);
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record.Q = Integer.parseInt(tokens[11]);
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record.M = tokens[12];
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return record;
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}
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@Override
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public void open(File file) throws IOException {
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try (final FileReader fileReader = new FileReader(file)) {
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records = new ArrayList<>();
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final BufferedReader bufferedReader = new BufferedReader(fileReader);
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String line;
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while ((line = bufferedReader.readLine()) != null) {
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if (line.startsWith("#")) {
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// skip comment lines tb 2023-04-28
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continue;
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}
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final TaoRecord record = parseLine(line);
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records.add(record);
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}
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}
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}
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@Override
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public void close() throws IOException {
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if (records != null) {
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records.clear();
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records = null;
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}
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timeLocator = null;
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}
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@Override
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public AcquisitionInfo read() throws IOException {
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final AcquisitionInfo acquisitionInfo = new AcquisitionInfo();
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int minTime = Integer.MAX_VALUE;
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int maxTime = Integer.MIN_VALUE;
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for (final TaoRecord record : records) {
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if (record.time < minTime) {
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minTime = record.time;
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}
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if (record.time > maxTime) {
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maxTime = record.time;
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}
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}
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acquisitionInfo.setSensingStart(new Date(minTime * 1000L));
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acquisitionInfo.setSensingStop(new Date(maxTime * 1000L));
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acquisitionInfo.setNodeType(NodeType.UNDEFINED);
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return acquisitionInfo;
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}
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@Override
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public String getRegEx() {
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return REG_EX;
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}
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@Override
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public PixelLocator getPixelLocator() throws IOException {
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throw new RuntimeException("not implemented");
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}
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@Override
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public PixelLocator getSubScenePixelLocator(Polygon sceneGeometry) throws IOException {
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throw new RuntimeException("not implemented");
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}
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@Override
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public TimeLocator getTimeLocator() throws IOException {
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if (timeLocator == null) {
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createTimeLocator();
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}
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return timeLocator;
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}
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@Override
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public int[] extractYearMonthDayFromFilename(String fileName) {
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final int endIdx = fileName.indexOf(".txt");
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final String yearString = fileName.substring(endIdx - 7, endIdx - 3);
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final String monthString = fileName.substring(endIdx - 2, endIdx);
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final int[] ymd = new int[3];
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ymd[0] = Integer.parseInt(yearString);
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ymd[1] = Integer.parseInt(monthString);
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ymd[2] = 1;
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return ymd;
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}
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@Override
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public Array readRaw(int centerX, int centerY, Interval interval, String variableName) throws IOException, InvalidRangeException {
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final TaoRecord record = records.get(centerY);
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switch (variableName) {
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case TIME:
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return createResultArray(record.time, NetCDFUtils.getDefaultFillValue(DataType.INT, false), DataType.INT, interval);
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case LONGITUDE:
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return createResultArray(record.longitude, NetCDFUtils.getDefaultFillValue(DataType.FLOAT, false), DataType.FLOAT, interval);
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case LATITUDE:
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return createResultArray(record.latitude, NetCDFUtils.getDefaultFillValue(DataType.FLOAT, false), DataType.FLOAT, interval);
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case SSS:
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return createResultArray(record.SSS, SSS_FILL, DataType.FLOAT, interval);
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case SST:
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return createResultArray(record.SST, SST_FILL, DataType.FLOAT, interval);
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case AIRT:
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return createResultArray(record.AIRT, AIRT_FILL, DataType.FLOAT, interval);
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case RH:
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return createResultArray(record.RH, RH_FILL, DataType.FLOAT, interval);
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case WSPD:
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return createResultArray(record.WSPD, WSPD_FILL, DataType.FLOAT, interval);
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case WDIR:
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return createResultArray(record.WDIR, WDIR_FILL, DataType.FLOAT, interval);
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case BARO:
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return createResultArray(record.BARO, BARO_FILL, DataType.FLOAT, interval);
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case RAIN:
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return createResultArray(record.RAIN, RAIN_FILL, DataType.FLOAT, interval);
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case Q:
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return createResultArray(record.Q, NetCDFUtils.getDefaultFillValue(DataType.INT, false), DataType.INT, interval);
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case M:
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final Array resultArray = Array.factory(DataType.STRING, new int[]{1, 1});
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resultArray.setObject(0, record.M);
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return resultArray;
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}
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return null;
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}
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@Override
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public Array readScaled(int centerX, int centerY, Interval interval, String variableName) throws IOException, InvalidRangeException {
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return readRaw(centerX, centerY, interval, variableName); // no scaled data in this product type tb 2023-05-02
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}
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@Override
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public ArrayInt.D2 readAcquisitionTime(int x, int y, Interval interval) throws IOException, InvalidRangeException {
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final Array timeArray = readRaw(x, y, interval, TIME);
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return (ArrayInt.D2) timeArray;
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}
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@Override
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public List<Variable> getVariables() throws InvalidRangeException, IOException {
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final ArrayList<Variable> variables = new ArrayList<>();
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List<Attribute> attributes = new ArrayList<>();
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attributes.add(new Attribute(CF_UNITS_NAME, "degree_east"));
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attributes.add(new Attribute(CF_STANDARD_NAME, "longitude"));
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variables.add(new VariableProxy(LONGITUDE, DataType.FLOAT, attributes));
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attributes = new ArrayList<>();
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attributes.add(new Attribute(CF_UNITS_NAME, "degree_north"));
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attributes.add(new Attribute(CF_STANDARD_NAME, "latitude"));
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variables.add(new VariableProxy(LATITUDE, DataType.FLOAT, attributes));
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attributes = new ArrayList<>();
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attributes.add(new Attribute(CF_UNITS_NAME, "seconds since 1970-01-01"));
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attributes.add(new Attribute(CF_STANDARD_NAME, "time"));
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variables.add(new VariableProxy(TIME, DataType.INT, attributes));
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attributes = new ArrayList<>();
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attributes.add(new Attribute(CF_UNITS_NAME, "psu"));
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attributes.add(new Attribute(CF_STANDARD_NAME, "sea_surface_salinity"));
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attributes.add(new Attribute(CF_FILL_VALUE_NAME, SSS_FILL));
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variables.add(new VariableProxy(SSS, DataType.FLOAT, attributes));
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attributes = new ArrayList<>();
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attributes.add(new Attribute(CF_UNITS_NAME, "degree_Celsius"));
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attributes.add(new Attribute(CF_STANDARD_NAME, "sea_surface_temperature"));
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attributes.add(new Attribute(CF_FILL_VALUE_NAME, SST_FILL));
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variables.add(new VariableProxy(SST, DataType.FLOAT, attributes));
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attributes = new ArrayList<>();
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attributes.add(new Attribute(CF_UNITS_NAME, "degree_Celsius"));
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attributes.add(new Attribute(CF_STANDARD_NAME, "air_temperature"));
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attributes.add(new Attribute(CF_FILL_VALUE_NAME, AIRT_FILL));
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variables.add(new VariableProxy(AIRT, DataType.FLOAT, attributes));
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attributes = new ArrayList<>();
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attributes.add(new Attribute(CF_UNITS_NAME, "percent"));
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attributes.add(new Attribute(CF_STANDARD_NAME, "relative_humidity"));
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attributes.add(new Attribute(CF_FILL_VALUE_NAME, RH_FILL));
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variables.add(new VariableProxy(RH, DataType.FLOAT, attributes));
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attributes = new ArrayList<>();
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attributes.add(new Attribute(CF_UNITS_NAME, "m/s"));
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attributes.add(new Attribute(CF_STANDARD_NAME, "wind_speed"));
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attributes.add(new Attribute(CF_FILL_VALUE_NAME, WSPD_FILL));
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variables.add(new VariableProxy(WSPD, DataType.FLOAT, attributes));
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attributes = new ArrayList<>();
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attributes.add(new Attribute(CF_UNITS_NAME, "degree"));
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attributes.add(new Attribute(CF_STANDARD_NAME, "wind_to_direction"));
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attributes.add(new Attribute(CF_LONG_NAME, "Wind To Direction degree true in Oceanographic Convention"));
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attributes.add(new Attribute(CF_FILL_VALUE_NAME, WDIR_FILL));
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variables.add(new VariableProxy(WDIR, DataType.FLOAT, attributes));
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attributes = new ArrayList<>();
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attributes.add(new Attribute(CF_UNITS_NAME, "hPa"));
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attributes.add(new Attribute(CF_STANDARD_NAME, "air_pressure_at_mean_sea_level"));
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attributes.add(new Attribute(CF_FILL_VALUE_NAME, BARO_FILL));
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variables.add(new VariableProxy(BARO, DataType.FLOAT, attributes));
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attributes = new ArrayList<>();
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attributes.add(new Attribute(CF_UNITS_NAME, "mm/hour"));
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attributes.add(new Attribute(CF_STANDARD_NAME, "rainfall_rate"));
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attributes.add(new Attribute(CF_FILL_VALUE_NAME, RAIN_FILL));
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variables.add(new VariableProxy(RAIN, DataType.FLOAT, attributes));
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attributes = new ArrayList<>();
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attributes.add(new Attribute(CF_LONG_NAME, "Data Quality Codes"));
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variables.add(new VariableProxy(Q, DataType.INT, attributes));
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/*
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@todo 1 tb/tb move this to documentation 2023-04-28
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Data Quality Codes(Q):
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0 = unknown
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1 = good data
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2 = probably good data
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3 = questionable data
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4 = bad data
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5 = adjusted data
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9 = missing data
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*/
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attributes = new ArrayList<>();
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attributes.add(new Attribute(CF_LONG_NAME, "Data Mode Codes"));
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variables.add(new StringVariable(new VariableProxy(M, DataType.STRING, attributes), 8));
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/*
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@todo 1 tb/tb move this to documentation 2023-04-28
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Data Mode Codes(M):
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R = real-time data
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P = provisional data
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D = delayed mode data
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M = mixed real-time and delayed mode data
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*/
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return variables;
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}
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@Override
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public Dimension getProductSize() throws IOException {
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return new Dimension("product_size", 1, records.size());
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}
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@Override
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public String getLongitudeVariableName() {
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return "longitude";
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}
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@Override
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public String getLatitudeVariableName() {
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return "latitude";
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}
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private void createTimeLocator() {
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long[] timeArray = new long[records.size()];
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int i = 0;
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for (final TaoRecord record : records) {
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timeArray[i] = record.time * 1000L;
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i++;
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}
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timeLocator = new TimeLocator_MillisSince1970(timeArray);
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}
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// @todo 2 tb/tb create generic in-itu record and move this method to it tb 2023-05-02
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private Array createResultArray(Number value, Number fillValue, DataType dataType, Interval interval) {
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final int windowHeight = interval.getY();
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final int windowWidth = interval.getX();
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final Array windowArray = NetCDFUtils.create(dataType,
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new int[]{windowHeight, windowWidth},
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fillValue);
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final int windowCenterX = windowWidth / 2;
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final int windowCenterY = windowHeight / 2;
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windowArray.setObject(windowWidth * windowCenterY + windowCenterX, value);
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return windowArray;
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}
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}

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