Tb snap11

CHANGES.md

@@ -1,4 +1,5 @@
 ### Updates from version 1.5.8 to 1.6.0
+* Migrated to SNAP 11, several refactorings and library updates
 * The VariableCache now uses an LRU cache with a listener to automatically free the oldest cached, no longer
   needed variables and file handles when the maximum cache size is reached.* fix wrong corner point order of 
   era5 interpolation in SatelliteFields

core/pom.xml

@@ -39,13 +39,13 @@
         </dependency>
 
         <dependency>
-            <groupId>org.esa.s3tbx</groupId>
-            <artifactId>s3tbx-avhrr-reader</artifactId>
+            <groupId>eu.esa.opt</groupId>
+            <artifactId>opttbx-avhrr-reader</artifactId>
         </dependency>
 
         <dependency>
-            <groupId>org.esa.s3tbx</groupId>
-            <artifactId>s3tbx-sentinel3-reader</artifactId>
+            <groupId>eu.esa.opt</groupId>
+            <artifactId>opttbx-sentinel3-reader</artifactId>
         </dependency>
 
         <dependency>
@@ -89,14 +89,10 @@
             <artifactId>netcdfAll</artifactId>
         </dependency>
 
-        <!--<dependency>-->
-            <!--<groupId>edu.ucar</groupId>-->
-            <!--<artifactId>netcdf4</artifactId>-->
-        <!--</dependency>-->
-        <!--<dependency>-->
-        <!--<groupId>edu.ucar</groupId>-->
-        <!--<artifactId>cdm</artifactId>-->
-        <!--</dependency>-->
+        <dependency>
+            <groupId>org.jdom</groupId>
+            <artifactId>jdom2</artifactId>
+        </dependency>
 
         <dependency>
             <groupId>junit</groupId>
@@ -110,7 +106,7 @@
         </dependency>
         <dependency>
             <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest-all</artifactId>
+            <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>

core/src/main/java/com/bc/fiduceo/archive/ArchiveConfig.java

@@ -42,11 +42,11 @@
 
 
 import com.bc.fiduceo.util.JDomUtils;
-import org.jdom.Attribute;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
+import org.jdom2.Attribute;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.JDOMException;
+import org.jdom2.input.SAXBuilder;
 
 import java.io.ByteArrayInputStream;
 import java.io.IOException;

core/src/main/java/com/bc/fiduceo/core/SystemConfig.java

@@ -22,10 +22,10 @@
 
 import com.bc.fiduceo.archive.ArchiveConfig;
 import com.bc.fiduceo.util.JDomUtils;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.JDOMException;
+import org.jdom2.input.SAXBuilder;
 
 import java.io.File;
 import java.io.FileInputStream;

core/src/main/java/com/bc/fiduceo/core/UseCaseConfig.java

@@ -21,12 +21,12 @@
 package com.bc.fiduceo.core;
 
 import org.esa.snap.core.util.StringUtils;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.JDOMException;
+import org.jdom2.input.SAXBuilder;
+import org.jdom2.output.Format;
+import org.jdom2.output.XMLOutputter;
 
 import java.io.IOException;
 import java.io.InputStream;

core/src/main/java/com/bc/fiduceo/db/DbMaintenanceTool.java

@@ -8,7 +8,7 @@
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import java.io.IOException;
 import java.io.OutputStream;

core/src/main/java/com/bc/fiduceo/reader/avhrr_frac/AVHRR_FRAC_Reader.java

@@ -9,7 +9,7 @@
 import com.bc.fiduceo.reader.snap.SNAP_Reader;
 import com.bc.fiduceo.reader.time.TimeLocator;
 import com.bc.fiduceo.util.NetCDFUtils;
-import org.esa.s3tbx.dataio.avhrr.AvhrrConstants;
+import eu.esa.opt.dataio.avhrr.AvhrrConstants;
 import org.esa.snap.core.datamodel.ProductData;
 import org.esa.snap.core.datamodel.RasterDataNode;
 import org.esa.snap.core.datamodel.VirtualBand;

core/src/main/java/com/bc/fiduceo/reader/slstr/SlstrReaderConfig.java

@@ -3,10 +3,10 @@
 import com.bc.fiduceo.core.SystemConfig;
 import com.bc.fiduceo.log.FiduceoLogger;
 import com.bc.fiduceo.util.JDomUtils;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.JDOMException;
+import org.jdom2.input.SAXBuilder;
 
 import java.io.File;
 import java.io.FileInputStream;

core/src/main/java/com/bc/fiduceo/reader/slstr_subset/SlstrRegriddedSubsetReader.java

@@ -20,8 +20,8 @@
 import com.bc.fiduceo.store.ZipStore;
 import com.bc.fiduceo.util.NetCDFUtils;
 import com.bc.fiduceo.util.TimeUtils;
-import org.esa.s3tbx.dataio.s3.Manifest;
-import org.esa.s3tbx.dataio.s3.XfduManifest;
+import eu.esa.opt.dataio.s3.Manifest;
+import eu.esa.opt.dataio.s3.XfduManifest;
 import org.esa.snap.core.dataio.geocoding.*;
 import org.esa.snap.core.dataio.geocoding.forward.PixelForward;
 import org.esa.snap.core.dataio.geocoding.inverse.PixelQuadTreeInverse;

core/src/main/java/com/bc/fiduceo/util/JDomUtils.java

@@ -16,9 +16,9 @@
  */
 package com.bc.fiduceo.util;
 
-import org.jdom.Attribute;
-import org.jdom.Document;
-import org.jdom.Element;
+import org.jdom2.Attribute;
+import org.jdom2.Document;
+import org.jdom2.Element;
 
 import java.util.List;
 

core/src/test/java/com/bc/fiduceo/TestUtil.java

@@ -29,10 +29,10 @@
 import org.hamcrest.Factory;
 import org.hamcrest.Matcher;
 import org.hamcrest.TypeSafeMatcher;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.JDOMException;
+import org.jdom2.input.SAXBuilder;
 
 import java.io.*;
 import java.nio.file.Files;

core/src/test/java/com/bc/fiduceo/core/UseCaseConfigBuilder.java

@@ -16,9 +16,9 @@
  */
 package com.bc.fiduceo.core;
 
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.output.XMLOutputter;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.output.XMLOutputter;
 
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;

core/src/test/java/com/bc/fiduceo/core/UseCaseConfigTest.java

@@ -20,7 +20,7 @@
 
 package com.bc.fiduceo.core;
 
-import org.jdom.JDOMException;
+import org.jdom2.JDOMException;
 import org.junit.Before;
 import org.junit.Test;
 

core/src/test/java/com/bc/fiduceo/geometry/GeometryTestUtils.java

@@ -0,0 +1,16 @@
+package com.bc.fiduceo.geometry;
+
+import static org.junit.Assert.assertEquals;
+
+public class GeometryTestUtils {
+
+    public static void assertSameGeometry(Geometry expected, Geometry geoBounds) {
+        Point[] expectedCoords = expected.getCoordinates();
+        Point[] actualCoords = geoBounds.getCoordinates();
+        assertEquals(expectedCoords.length, actualCoords.length);
+        for(int i = 0; i < expectedCoords.length; i++) {
+            assertEquals(expectedCoords[i].getLon(), actualCoords[i].getLon(), 1e-8);
+            assertEquals(expectedCoords[i].getLat(), actualCoords[i].getLat(), 1e-8);
+        }
+    }
+}

core/src/test/java/com/bc/fiduceo/geometry/s2/BcS2GeometryFactoryTest.java

@@ -120,7 +120,7 @@ public void testFormat_point() {
         final Point point = factory.createPoint(34.8, -72.44);
 
         final String wkt = factory.format(point);
-        assertEquals("POINT(34.8,-72.44)", wkt);
+        assertEquals("POINT(34.8 -72.44)", wkt);
     }
 
     @Test
@@ -267,7 +267,7 @@ public void testToStorageFormat_point() {
         final Geometry point = factory.parse("POINT(-22.5 67.23)");
 
         final byte[] storageFormat = factory.toStorageFormat(point);
-        assertEquals("POINT(-22.500000000000004,67.23)", new String(storageFormat));
+        assertEquals("POINT(-22.500000000000004 67.23)", new String(storageFormat));
     }
 
     @Test

core/src/test/java/com/bc/fiduceo/reader/RawDataReaderTest_context2D_double.java

@@ -5,9 +5,7 @@
 import com.bc.fiduceo.util.NetCDFUtils;
 import org.junit.Before;
 import org.junit.Test;
-import sun.nio.ch.Net;
 import ucar.ma2.Array;
-import ucar.ma2.DataType;
 
 import java.io.IOException;
 

core/src/test/java/com/bc/fiduceo/reader/amsr/amsre/AMSRE_Reader_IO_Test.java

@@ -459,7 +459,7 @@ public void testGetPixelLocator() throws IOException {
             Point2D[] pixelLocation = pixelLocator.getPixelLocation(-51.034195, 52.659184);
             assertEquals(1, pixelLocation.length);
             assertEquals(132.51219668358698, pixelLocation[0].getX(), 1e-8);
-            assertEquals(411.4166814102514, pixelLocation[0].getY(), 1e-8);
+            assertEquals(411.4166814102514, pixelLocation[0].getY(), 1e-6);
 
             pixelLocation = pixelLocator.getPixelLocation(-4, 1176);
             assertEquals(0, pixelLocation.length);

core/src/test/java/com/bc/fiduceo/reader/fiduceo_fcdr/HIRS_FCDR_Reader_IO_Test.java

@@ -515,7 +515,7 @@ public void testGetPixelLocator() throws IOException {
             assertNotNull(pixelLocation);
             assertEquals(1, pixelLocation.length);
 
-            assertEquals(38.317269513397704, pixelLocation[0].getX(), 1e-8);
+            assertEquals(38.317269513397704, pixelLocation[0].getX(), 1e-6);
             assertEquals(781.666865947429, pixelLocation[0].getY(), 1e-8);
         } finally {
             reader.close();
@@ -540,7 +540,7 @@ public void testGetPixelLocator_N09() throws IOException {
             assertNotNull(pixelLocation);
             assertEquals(1, pixelLocation.length);
 
-            assertEquals(38.50497313441438, pixelLocation[0].getX(), 1e-8);
+            assertEquals(38.50497313441438, pixelLocation[0].getX(), 1e-6);
             assertEquals(783.6241097278424, pixelLocation[0].getY(), 1e-8);
         } finally {
             reader.close();
@@ -567,7 +567,7 @@ public void testGetSubScenePixelLocator() throws IOException {
             assertNotNull(pixelLocation);
             assertEquals(1, pixelLocation.length);
 
-            assertEquals(33.59545482099081, pixelLocation[0].getX(), 1e-8);
+            assertEquals(33.59545482099081, pixelLocation[0].getX(), 1e-6);
             assertEquals(416.5860033509568, pixelLocation[0].getY(), 1e-8);
 
         } finally {

core/src/test/java/com/bc/fiduceo/reader/slstr_subset/SlstrRegriddedSubsetReaderTest.java

@@ -2,8 +2,8 @@
 
 import com.bc.fiduceo.reader.Reader;
 import com.bc.fiduceo.reader.ReaderContext;
-import org.esa.s3tbx.dataio.s3.Manifest;
-import org.esa.s3tbx.dataio.s3.XfduManifest;
+import eu.esa.opt.dataio.s3.Manifest;
+import eu.esa.opt.dataio.s3.XfduManifest;
 import org.junit.Test;
 import org.w3c.dom.Document;
 import org.xml.sax.InputSource;

core/src/test/java/com/bc/fiduceo/util/JDomUtilsTest.java

@@ -21,9 +21,9 @@
 package com.bc.fiduceo.util;
 
 import com.bc.fiduceo.core.UseCaseConfig;
-import org.jdom.Attribute;
-import org.jdom.Document;
-import org.jdom.Element;
+import org.jdom2.Attribute;
+import org.jdom2.Document;
+import org.jdom2.Element;
 import org.junit.Test;
 
 import java.util.List;

core/src/test/java/com/bc/fiduceo/util/TempFileUtils_IO_Test.java

@@ -27,7 +27,6 @@
 import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
-import sun.net.www.protocol.file.FileURLConnection;
 
 import java.io.File;
 import java.io.IOException;

google-s2/src/main/java/com/bc/geometry/s2/S2WKTWriter.java

@@ -87,7 +87,7 @@ private static String writePointWkt(S2LatLng geometry) {
         final StringBuilder builder = new StringBuilder();
         builder.append("POINT(");
         builder.append(geometry.lngDegrees());
-        builder.append(",");
+        builder.append(" ");
         builder.append(geometry.latDegrees());
         builder.append(")");
         return builder.toString();

google-s2/src/test/java/com/bc/geometry/s2/S2WKTWriterTest.java

@@ -62,7 +62,7 @@ public void testWritePoint() {
         final S2Point s2Point = createS2Point(-18.7, 45.9);
 
         final String wkt = S2WKTWriter.write(s2Point);
-        assertEquals("POINT(-18.7,45.9)", wkt);
+        assertEquals("POINT(-18.7 45.9)", wkt);
     }
 
     @Test
@@ -71,7 +71,7 @@ public void testWritePoint_S2LatLong() {
         final S2LatLng s2LatLng = new S2LatLng(s2Point);
 
         final String wkt = S2WKTWriter.write(s2LatLng);
-        assertEquals("POINT(-19.800000000000004,46.0)", wkt);
+        assertEquals("POINT(-19.800000000000004 45.99999999999999)", wkt);
     }
 
     @Test