added ASCAT section

TomBlock · TomBlock · commit ea7bc9619abe · 2022-11-11T14:19:21.000+01:00
diff --git a/core/src/main/java/com/bc/fiduceo/reader/insitu/sic_cci/ASCATSectionParser.java b/core/src/main/java/com/bc/fiduceo/reader/insitu/sic_cci/ASCATSectionParser.java
@@ -0,0 +1,84 @@
+package com.bc.fiduceo.reader.insitu.sic_cci;
+
+import com.bc.fiduceo.util.NetCDFUtils;
+import com.bc.fiduceo.util.VariableProxy;
+import ucar.ma2.DataType;
+import ucar.nc2.Attribute;
+import ucar.nc2.Variable;
+
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.List;
+
+import static com.bc.fiduceo.util.NetCDFUtils.*;
+
+public class ASCATSectionParser extends AbstractSectionParser {
+
+    @Override
+    List<Variable> getVariables() {
+        final List<Variable> variables = new ArrayList<>();
+
+        createCommonVariables(variables, "ASCAT_");
+
+        ArrayList<Attribute> attributes = new ArrayList<>();
+        variables.add(new VariableProxy("ASCAT_upstreamfile", DataType.CHAR, attributes));
+
+        attributes = new ArrayList<>();
+        attributes.add(new Attribute(CF_FILL_VALUE_NAME, NetCDFUtils.getDefaultFillValue(float.class)));
+        attributes.add(new Attribute(CF_LONG_NAME, "ASCAT backscatter (dB)"));
+        attributes.add(new Attribute(CF_UNITS_NAME, "db"));
+        variables.add(new VariableProxy("ASCAT_sigma_40", DataType.FLOAT, attributes));
+
+        attributes = new ArrayList<>();
+        attributes.add(new Attribute(CF_FILL_VALUE_NAME, NetCDFUtils.getDefaultFillValue(float.class)));
+        attributes.add(new Attribute(CF_LONG_NAME, "ASCAT backscatter (dB) - masked"));
+        attributes.add(new Attribute(CF_UNITS_NAME, "db"));
+        variables.add(new VariableProxy("ASCAT_sigma_40_mask", DataType.FLOAT, attributes));
+
+        attributes = new ArrayList<>();
+        attributes.add(new Attribute(CF_FILL_VALUE_NAME, NetCDFUtils.getDefaultFillValue(short.class)));
+        attributes.add(new Attribute(CF_LONG_NAME, "Number of ASCAT samples"));
+        variables.add(new VariableProxy("ASCAT_nb_samples", DataType.SHORT, attributes));
+
+        attributes = new ArrayList<>();
+        attributes.add(new Attribute(CF_FILL_VALUE_NAME, NetCDFUtils.getDefaultFillValue(short.class)));
+        attributes.add(new Attribute(CF_LONG_NAME, "ASCAT flag"));
+        variables.add(new VariableProxy("ASCAT_warning", DataType.SHORT, attributes));
+
+        attributes = new ArrayList<>();
+        attributes.add(new Attribute(CF_FILL_VALUE_NAME, NetCDFUtils.getDefaultFillValue(float.class)));
+        attributes.add(new Attribute(CF_LONG_NAME, "Standard deviation of ASCAT data"));
+        attributes.add(new Attribute(CF_UNITS_NAME, "db"));
+        variables.add(new VariableProxy("ASCAT_std", DataType.FLOAT, attributes));
+
+        return variables;
+    }
+
+    @Override
+    int getNumVariables() {
+        return 10;
+    }
+
+    @Override
+    String getNamePrefix() {
+        return "ASCAT";
+    }
+
+    @Override
+    Section parse(String[] tokens, int offset) throws ParseException {
+        final Section section = new Section();
+
+        section.add("ASCAT_latitude", parseFloat(tokens[offset]));
+        section.add("ASCAT_longitude", parseFloat(tokens[offset + 1]));
+        section.add("ASCAT_time", parseUtcTime(tokens[offset + 2]));
+        section.add("ASCAT_reference-id", parseString(tokens[offset + 3]));
+        section.add("ASCAT_upstreamfile", parseString(tokens[offset + 4]));
+        section.add("ASCAT_sigma_40", parseFloat(tokens[offset + 5]));
+        section.add("ASCAT_sigma_40_mask", parseFloat(tokens[offset + 6]));
+        section.add("ASCAT_nb_samples", parseShort(tokens[offset + 7]));
+        section.add("ASCAT_warning", parseShort(tokens[offset + 8]));
+        section.add("ASCAT_std", parseFloat(tokens[offset + 9]));
+
+        return section;
+    }
+}
diff --git a/core/src/main/java/com/bc/fiduceo/reader/insitu/sic_cci/AbstractSectionParser.java b/core/src/main/java/com/bc/fiduceo/reader/insitu/sic_cci/AbstractSectionParser.java
@@ -66,8 +66,14 @@ static Array parseFloat(String token) {
     }
 
     static Array parseShort(String token) {
-        final short wd = Short.parseShort(token);
-        return Array.factory(DataType.SHORT, SCALAR, new short[]{wd});
+        final short shortVal;
+
+        if (token.equals("noval")) {
+            shortVal = NetCDFUtils.getDefaultFillValue(short.class).shortValue();
+        } else {
+            shortVal = Short.parseShort(token);
+        }
+        return Array.factory(DataType.SHORT, SCALAR, new short[]{shortVal});
     }
 
     static Array parseByte(String token) {
diff --git a/core/src/main/java/com/bc/fiduceo/reader/insitu/sic_cci/SicCciInsituReader.java b/core/src/main/java/com/bc/fiduceo/reader/insitu/sic_cci/SicCciInsituReader.java
@@ -54,6 +54,9 @@ public void open(File file) throws IOException {
         if (fileName.contains("AMSR2")) {
             parsers.add(new AMSR2SectionParser());
         }
+        if (fileName.contains("ASCAT")) {
+            parsers.add(new ASCATSectionParser());
+        }
 
         sectionCache = new SectionCache(linelist, parsers.toArray(new AbstractSectionParser[0]));
     }
diff --git a/core/src/test/java/com/bc/fiduceo/reader/insitu/sic_cci/ASCATSectionParserTest.java b/core/src/test/java/com/bc/fiduceo/reader/insitu/sic_cci/ASCATSectionParserTest.java
@@ -0,0 +1,91 @@
+package com.bc.fiduceo.reader.insitu.sic_cci;
+
+import org.junit.Before;
+import org.junit.Test;
+import ucar.ma2.Array;
+import ucar.ma2.DataType;
+import ucar.nc2.Variable;
+
+import java.text.ParseException;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+
+public class ASCATSectionParserTest {
+
+    private ASCATSectionParser parser;
+
+    @Before
+    public void setUp() {
+        parser = new ASCATSectionParser();
+    }
+
+    @Test
+    public void testGetVariables() {
+        final List<Variable> variables = parser.getVariables();
+
+        assertEquals(10, variables.size());
+        assertEquals(variables.size(), parser.getNumVariables());
+
+        Variable variable = variables.get(0);
+        assertEquals("ASCAT_longitude", variable.getShortName());
+        assertEquals(DataType.FLOAT, variable.getDataType());
+
+        variable = variables.get(4);
+        assertEquals("ASCAT_upstreamfile", variable.getShortName());
+        assertEquals(DataType.CHAR, variable.getDataType());
+
+        variable = variables.get(5);
+        assertEquals("ASCAT_sigma_40", variable.getShortName());
+        assertEquals(DataType.FLOAT, variable.getDataType());
+
+        variable = variables.get(6);
+        assertEquals("ASCAT_sigma_40_mask", variable.getShortName());
+        assertEquals(DataType.FLOAT, variable.getDataType());
+
+        variable = variables.get(7);
+        assertEquals("ASCAT_nb_samples", variable.getShortName());
+        assertEquals(DataType.SHORT, variable.getDataType());
+
+        variable = variables.get(8);
+        assertEquals("ASCAT_warning", variable.getShortName());
+        assertEquals(DataType.SHORT, variable.getDataType());
+
+        variable = variables.get(9);
+        assertEquals("ASCAT_std", variable.getShortName());
+        assertEquals(DataType.FLOAT, variable.getDataType());
+    }
+
+    @Test
+    public void testGetNamePrefix() {
+        assertEquals("ASCAT", parser.getNamePrefix());
+    }
+
+    @Test
+    public void testParse() throws ParseException {
+        // first two tokens don't belong to ASCAT - just as offset for testing tb 2022-11-11
+        final String[] tokens = {"GW1AM2_201701210013_184D_L1SGRTBR_2220220.h5", "4852",
+                "-70.990", "-044.510", "2017-01-20T12:00:00Z", "ASCAT_CERSAT_IFREMER", "ASCAT_A_B_20170120.nc", "-16.44920",
+                "-16.44920", "21", "0", "0.10924"};
+
+        final Section section = parser.parse(tokens, 2);
+
+        assertEquals(-70.99f, section.get("ASCAT_latitude").getFloat(0), 1e-8);
+        assertEquals(-44.51f, section.get("ASCAT_longitude").getFloat(0), 1e-8);
+        assertEquals(1484913600, section.get("ASCAT_time").getInt(0));
+
+        final Array refId = section.get("ASCAT_reference-id");
+        char[] valueAsArray = (char[]) refId.get1DJavaArray(DataType.CHAR);
+        assertEquals("ASCAT_CERSAT_IFREMER", new String(valueAsArray));
+
+        final Array filename = section.get("ASCAT_upstreamfile");
+        valueAsArray = (char[]) filename.get1DJavaArray(DataType.CHAR);
+        assertEquals("ASCAT_A_B_20170120.nc", new String(valueAsArray));
+
+        assertEquals(-16.4492f, section.get("ASCAT_sigma_40").getFloat(0), 1e-8);
+        assertEquals(-16.4492f, section.get("ASCAT_sigma_40_mask").getFloat(0), 1e-8);
+        assertEquals(21, section.get("ASCAT_nb_samples").getShort(0));
+        assertEquals(0, section.get("ASCAT_warning").getShort(0));
+        assertEquals(0.10924f, section.get("ASCAT_std").getFloat(0), 1e-8);
+    }
+}
diff --git a/core/src/test/java/com/bc/fiduceo/reader/insitu/sic_cci/SciCciInsituReader_IO_Test.java b/core/src/test/java/com/bc/fiduceo/reader/insitu/sic_cci/SciCciInsituReader_IO_Test.java
@@ -256,6 +256,11 @@ public void testReadRaw_1x1_DMISIC0() throws InvalidRangeException, IOException
             array = reader.readRaw(5, 28, new Interval(1, 1), "AMSR2_6.9GHzH");
             assertEquals(DataType.FLOAT, array.getDataType());
             assertEquals(88.62f, array.getFloat(0), 1e-8);
+
+            // ASCAT
+            array = reader.readRaw(5, 29, new Interval(1, 1), "ASCAT_sigma_40");
+            assertEquals(DataType.FLOAT, array.getDataType());
+            assertEquals(-15.76655f, array.getFloat(0), 1e-8);
         } finally {
             reader.close();
         }
@@ -281,6 +286,10 @@ public void testReadRaw_1x1_DTUSIC1() throws InvalidRangeException, IOException
             array = reader.readRaw(7, 6, new Interval(1, 1), "AMSR2_6.9GHzV");
             assertEquals(257.9100036621094f, array.getFloat(0), 1e-8);
 
+            // ASCAT
+            array = reader.readRaw(5, 7, new Interval(1, 1), "ASCAT_sigma_40_mask");
+            assertEquals(-15.17677f, array.getFloat(0), 1e-8);
+
         } finally {
             reader.close();
         }
@@ -311,6 +320,12 @@ public void testReadRaw_3x3_ANTXXXI() throws InvalidRangeException, IOException
             NCTestUtils.assertValueAt(9.969209968386869E36f, 0, 1, array);
             NCTestUtils.assertValueAt(129.34f, 1, 1, array);
             NCTestUtils.assertValueAt(9.969209968386869E36f, 2, 1, array);
+
+            // ASCAT
+            array = reader.readRaw(7, 8, new Interval(3, 3), "ASCAT_nb_samples");
+            NCTestUtils.assertValueAt(-32767, 0, 1, array);
+            NCTestUtils.assertValueAt(-32767, 1, 1, array);
+            NCTestUtils.assertValueAt(-32767, 2, 1, array);
         } finally {
             reader.close();
         }
@@ -339,6 +354,11 @@ public void testReadScaled_1x1_DMISIC0() throws InvalidRangeException, IOExcepti
             array = reader.readScaled(5, 29, new Interval(1, 1), "AMSR2_7.3GHzV");
             assertEquals(DataType.FLOAT, array.getDataType());
             assertEquals(162.24f, array.getFloat(0), 1e-8);
+
+            // ASCAT
+            array = reader.readScaled(5, 30, new Interval(1, 1), "ASCAT_warning");
+            assertEquals(DataType.SHORT, array.getDataType());
+            assertEquals(0, array.getShort(0), 1e-8);
         } finally {
             reader.close();
         }

Original file line number	Diff line number	Diff line change
`@@ -54,6 +54,9 @@ public void open(File file) throws IOException {`
`54`	`54`	`if (fileName.contains("AMSR2")) {`
`55`	`55`	`parsers.add(new AMSR2SectionParser());`
`56`	`56`	`}`
	`57`	`+ if (fileName.contains("ASCAT")) {`
	`58`	`+ parsers.add(new ASCATSectionParser());`
	`59`	`+ }`
`57`	`60`
`58`	`61`	`sectionCache = new SectionCache(linelist, parsers.toArray(new AbstractSectionParser[0]));`
`59`	`62`	`}`