refactoring, add PixelGeoCoding to subset reader, updated tests

Author: TomBlock

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

@@ -10,7 +10,7 @@ public class SlstrPixelLocator extends SNAP_PixelLocator {
 
     private final Transform transform;
 
-    SlstrPixelLocator(GeoCoding geoCoding, Transform transform) {
+    public SlstrPixelLocator(GeoCoding geoCoding, Transform transform) {
         super(geoCoding);
 
         this.transform = transform;

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

@@ -32,6 +32,7 @@
 
 import static com.bc.fiduceo.reader.slstr.VariableType.NADIR_1km;
 import static com.bc.fiduceo.reader.slstr.VariableType.NADIR_500m;
+import static com.bc.fiduceo.reader.slstr.utility.ManifestUtil.getObliqueGridOffset;
 import static ucar.ma2.DataType.INT;
 
 public class SlstrReader extends SNAP_Reader {
@@ -118,7 +119,7 @@ public void open(File file) throws IOException {
         }
         openCached(manifestFile, "Sen3");
 
-        final int obliqueGridOffset = getObliqueGridOffset();
+        final int obliqueGridOffset = getObliqueGridOffset(product.getMetadataRoot());
         transformFactory = new TransformFactory(product.getSceneRasterWidth(),
                 product.getSceneRasterHeight(),
                 obliqueGridOffset);
@@ -354,37 +355,6 @@ private void setOrbitNodeInfo(AcquisitionInfo acquisitionInfo) {
         }
     }
 
-    private int getObliqueGridOffset() {
-        final MetadataElement metadataRoot = product.getMetadataRoot();
-        final MetadataElement manifestElement = metadataRoot.getElement("Manifest");
-        final MetadataElement metadataElement = manifestElement.getElement("metadataSection");
-        final MetadataElement productInformationElement = metadataElement.getElement("slstrProductInformation");
-
-        int nadirTrackOffset = -1;
-        int obliqueTrackOffset = -1;
-        final MetadataElement[] elements = productInformationElement.getElements();
-        for (final MetadataElement element : elements) {
-            if (element.getName().equalsIgnoreCase("nadirImageSize")) {
-                final MetadataAttribute grid = element.getAttribute("grid");
-                if (grid.getData().getElemString().equalsIgnoreCase("1 km")) {
-                    nadirTrackOffset = ManifestUtil.extractTrackOffset(element);
-                }
-            }
-            if (element.getName().equalsIgnoreCase("obliqueImageSize")) {
-                final MetadataAttribute grid = element.getAttribute("grid");
-                if (grid.getData().getElemString().equalsIgnoreCase("1 km")) {
-                    obliqueTrackOffset = ManifestUtil.extractTrackOffset(element);
-                }
-            }
-        }
-
-        if (nadirTrackOffset < 0 | obliqueTrackOffset < 0) {
-            throw new RuntimeException("Unable to extract raster offsets from metadata.");
-        }
-
-        return nadirTrackOffset - obliqueTrackOffset;
-    }
-
     private void ensureTimingVector() {
         if (subs_times == null) {
             final MetadataElement metadataRoot = product.getMetadataRoot();

core/src/main/java/com/bc/fiduceo/reader/slstr/utility/ManifestUtil.java

@@ -5,7 +5,37 @@
 
 public class ManifestUtil {
 
-    public static int extractTrackOffset(MetadataElement element) {
+    public static int getObliqueGridOffset(MetadataElement metadataRoot) {
+        final MetadataElement manifestElement = metadataRoot.getElement("Manifest");
+        final MetadataElement metadataElement = manifestElement.getElement("metadataSection");
+        final MetadataElement productInformationElement = metadataElement.getElement("slstrProductInformation");
+
+        int nadirTrackOffset = -1;
+        int obliqueTrackOffset = -1;
+        final MetadataElement[] elements = productInformationElement.getElements();
+        for (final MetadataElement element : elements) {
+            if (element.getName().equalsIgnoreCase("nadirImageSize")) {
+                final MetadataAttribute grid = element.getAttribute("grid");
+                if (grid.getData().getElemString().equalsIgnoreCase("1 km")) {
+                    nadirTrackOffset = ManifestUtil.extractTrackOffset(element);
+                }
+            }
+            if (element.getName().equalsIgnoreCase("obliqueImageSize")) {
+                final MetadataAttribute grid = element.getAttribute("grid");
+                if (grid.getData().getElemString().equalsIgnoreCase("1 km")) {
+                    obliqueTrackOffset = ManifestUtil.extractTrackOffset(element);
+                }
+            }
+        }
+
+        if (nadirTrackOffset < 0 | obliqueTrackOffset < 0) {
+            throw new RuntimeException("Unable to extract raster offsets from metadata.");
+        }
+
+        return nadirTrackOffset - obliqueTrackOffset;
+    }
+
+    static int extractTrackOffset(MetadataElement element) {
         final MetadataAttribute trackOffset = element.getAttribute("trackOffset");
         final String trackOffsetString = trackOffset.getData().getElemString();
         return Integer.parseInt(trackOffsetString);

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

@@ -8,30 +8,44 @@
 import com.bc.fiduceo.geometry.LineString;
 import com.bc.fiduceo.geometry.Polygon;
 import com.bc.fiduceo.location.PixelLocator;
-import com.bc.fiduceo.location.PixelLocatorFactory;
 import com.bc.fiduceo.reader.*;
+import com.bc.fiduceo.reader.slstr.utility.TransformFactory;
+import com.bc.fiduceo.reader.snap.SNAP_PixelLocator;
 import com.bc.fiduceo.reader.time.TimeLocator;
 import com.bc.fiduceo.reader.time.TimeLocator_MicrosSince2000;
 import com.bc.fiduceo.store.FileSystemStore;
 import com.bc.fiduceo.store.Store;
 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 org.esa.snap.core.dataio.geocoding.*;
+import org.esa.snap.core.dataio.geocoding.forward.PixelForward;
+import org.esa.snap.core.dataio.geocoding.inverse.PixelQuadTreeInverse;
+import org.esa.snap.core.datamodel.MetadataElement;
 import org.esa.snap.core.datamodel.ProductData;
 import org.esa.snap.core.util.StringUtils;
+import org.w3c.dom.Document;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
 import ucar.ma2.DataType;
 import ucar.ma2.*;
 import ucar.nc2.NetcdfFile;
 import ucar.nc2.Variable;
 
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
 import java.io.File;
 import java.io.IOException;
+import java.io.StringReader;
 import java.text.ParseException;
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.zip.ZipFile;
 
+import static com.bc.fiduceo.reader.slstr.utility.ManifestUtil.getObliqueGridOffset;
 import static com.bc.fiduceo.util.NetCDFUtils.scaleIfNecessary;
 import static ucar.ma2.DataType.INT;
 import static ucar.nc2.NetcdfFiles.openInMemory;
@@ -40,15 +54,16 @@ public class SlstrRegriddedSubsetReader implements Reader {
 
     private final ReaderContext _readerContext;
     private final boolean _nadirView;
-    private final String LONGITUDE_VAR_NAME = "longitude_tx";
-    private final String LATITUDE_VAR_NAME = "latitude_tx";
+    private final String LONGITUDE_VAR_NAME = "longitude_in";
+    private final String LATITUDE_VAR_NAME = "latitude_in";
     private TreeMap<String, NetcdfFile> _ncFiles;
     private ArrayList<Variable> _variables;
     private HashMap<String, Variable> _variablesLUT;
     private String _manifest;
     private PixelLocator pixelLocator;
     private TimeLocator_MicrosSince2000 _timeLocator;
     private long[] _timeStamps2000;
+    private TransformFactory transformFactory;
 
     public SlstrRegriddedSubsetReader(ReaderContext readerContext, boolean nadirView) {
         _readerContext = readerContext;
@@ -71,6 +86,21 @@ public void open(File file) throws IOException {
             _manifest = new String(store.getBytes(keyManifest.first()));
             openNcFiles(store);
             initVariables();
+
+            final InputSource is = new InputSource(new StringReader(_manifest));
+            final Document document = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(is);
+            final Manifest manifest = XfduManifest.createManifest(document);
+
+            final MetadataElement metadataRoot = new MetadataElement("root");
+            metadataRoot.addElement(manifest.getMetadata());
+            final int obliqueGridOffset = getObliqueGridOffset(metadataRoot);
+            final Dimension productSize = getProductSize();
+
+            transformFactory = new TransformFactory(productSize.getNx() * 2,
+                    productSize.getNy() * 2,
+                    obliqueGridOffset);
+        } catch (ParserConfigurationException | SAXException e) {
+            throw new IOException(e.getMessage());
         } finally {
             store.close();
         }
@@ -79,6 +109,7 @@ public void open(File file) throws IOException {
     @Override
     public void close() throws IOException {
         _ncFiles.clear();
+        transformFactory = null;
     }
 
     @Override
@@ -100,8 +131,12 @@ public AcquisitionInfo read() throws IOException {
     private void extractGeometries(AcquisitionInfo acquisitionInfo) throws IOException {
         final GeometryFactory geometryFactory = _readerContext.getGeometryFactory();
         final BoundingPolygonCreator boundingPolygonCreator = new BoundingPolygonCreator(new Interval(250, 250), geometryFactory);
-        final Array longitude = _variablesLUT.get(LONGITUDE_VAR_NAME).read();
-        final Array latitude = _variablesLUT.get(LATITUDE_VAR_NAME).read();
+
+        final Variable lonVariable = _variablesLUT.get(LONGITUDE_VAR_NAME);
+        final Array longitude = NetCDFUtils.readAndScaleIfNecessary(lonVariable);
+        final Variable latVariable = _variablesLUT.get(LATITUDE_VAR_NAME);
+        final Array latitude = NetCDFUtils.readAndScaleIfNecessary(latVariable);
+
         final Geometry boundingGeometry = boundingPolygonCreator.createBoundingGeometry(longitude, latitude);
         if (!boundingGeometry.isValid()) {
             throw new RuntimeException("Detected invalid bounding geometry");
@@ -147,10 +182,24 @@ public String getRegEx() {
     @Override
     public PixelLocator getPixelLocator() throws IOException {
         if (pixelLocator == null) {
-            final Array longitude = _variablesLUT.get(LONGITUDE_VAR_NAME).read();
-            final Array latitude = _variablesLUT.get(LATITUDE_VAR_NAME).read();
+            final Variable lonVariable = _variablesLUT.get(LONGITUDE_VAR_NAME);
+            final Array longitude = NetCDFUtils.readAndScaleIfNecessary(lonVariable);
+            final Variable latVariable = _variablesLUT.get(LATITUDE_VAR_NAME);
+            final Array latitude = NetCDFUtils.readAndScaleIfNecessary(latVariable);
             final int[] shape = latitude.getShape();
-            pixelLocator = PixelLocatorFactory.getSwathPixelLocator(longitude, latitude, shape[1], shape[0]);
+
+            final GeoRaster geoRaster = new GeoRaster((double[]) longitude.get1DJavaArray(DataType.DOUBLE),
+                    (double[]) latitude.get1DJavaArray(DataType.DOUBLE),
+                    LONGITUDE_VAR_NAME, LATITUDE_VAR_NAME,
+                    shape[1], shape[0], shape[1], shape[0],
+                    1.0, 0.5, 0.5, 1.0, 1.0);
+
+            final ForwardCoding forward = ComponentFactory.getForward(PixelForward.KEY);
+            final InverseCoding inverse = ComponentFactory.getInverse(PixelQuadTreeInverse.KEY);
+            final ComponentGeoCoding componentGeoCoding = new ComponentGeoCoding(geoRaster, forward, inverse, GeoChecks.ANTIMERIDIAN);
+            componentGeoCoding.initialize();
+
+            pixelLocator = new SNAP_PixelLocator(componentGeoCoding);
         }
         return pixelLocator;
     }

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

@@ -107,7 +107,7 @@ public class TestData {
     public static final String SLSTR_S3A_GEOMETRY = "POLYGON((169.3240509033203 83.7747802734375,169.69239807128906 82.9089126586914,169.9518280029297 82.0425796508789,170.1349639892578 81.17589569091797,170.2621612548828 80.30894470214844,170.34710693359375 79.44176483154297,170.39923095703128 78.57439422607422,170.4256134033203 77.70684814453125,170.43130493164062 76.83914184570312,170.4200897216797 75.9712905883789,170.3948211669922 75.1032943725586,170.3578643798828 74.23516845703125,170.31150817871094 73.37557983398438,-150.1357879638672 68.54389953613281,-148.5464630126953 69.24473571777344,-146.85427856445312 69.93047332763672,-145.05076599121094 70.59950256347656,-143.12680053710938 71.24998474121094,-141.07395935058594 71.88002014160156,-138.88314819335938 72.48741149902344,-136.5452117919922 73.06970977783203,-134.0511932373047 73.62413787841797,-131.3943328857422 74.14793395996094,-128.56874084472656 74.63796997070312,-125.5705108642578 75.09088134765625,-122.4310836791992 75.49915313720703,169.3240509033203 83.7747802734375))";
     public static final String SLSTR_S3A_AXIS_GEOMETRY = "LINESTRING(-141.54843139648438 81.09320831298828,-145.39883422851562 80.44935607910156,-148.76324462890625 79.76988983154297,-151.71571350097656 79.06163024902344,-154.31826782226562 78.32980346679688,-156.62396240234375 77.57853698730469,-158.6761016845703 76.81105041503906,-160.51385498046878 76.03009033203125,-162.16822814941406 75.23777770996094,-163.66510009765625 74.43582153320312,-165.0253143310547 73.6255874633789,-166.26788330078125 72.80826568603516,-167.39700317382812 71.9930648803711)";
 
-    public static final String SLSTR_S3A_SUBSET_GEOMETRY_NADIR = "POLYGON((-3.6059465890532283 -25.83171070667771,-4.345504921512899 -23.67864966189537,-5.052072612521223 -21.520252164726024,-5.728582321482214 -19.357061619885766,-6.37765716254036 -17.189568690832207,-6.876289272507739 -15.461472451383527,-9.12879558299108 -16.049479602572756,-11.394288612408165 -16.61363566749959,-13.672762795816437 -17.152907111528886,-15.964104321709264 -17.666325891819774,-18.268145294360917 -18.152904337946932,-20.57531176627247 -18.60994342420135,-20.10950018672568 -20.816586841507654,-19.64196757071521 -23.022254278473003,-19.17169653558319 -25.22683658674446,-18.6975794442004 -27.430220475843065,-18.316647922477475 -29.183193062900383,-15.802946517978485 -28.735338550717177,-13.311672466783627 -28.241151165591027,-10.844300390148879 -27.70193352839235,-8.402016394859132 -27.11917511036397,-5.985816523722878 -26.494335474052875,-3.6059465890532283 -25.83171070667771))";
+    public static final String SLSTR_S3A_SUBSET_GEOMETRY_NADIR = "POLYGON((-3.605947 -25.831709,-4.345505 -23.678649999999998,-5.052073 -21.520253000000004,-5.7285819999999985 -19.357061,-6.377657 -17.189569,-6.876289 -15.461471999999999,-9.131362 -16.047251000000003,-11.394941 -16.607987999999995,-13.671509 -17.155166,-15.968603 -17.663905,-18.269608 -18.157285999999996,-20.575312 -18.609944000000002,-20.109500000000004 -20.816586999999995,-19.641969 -23.022255,-19.171696999999998 -25.226836000000002,-18.697578999999998 -27.430221,-18.316648999999998 -29.183193000000003,-15.807929999999999 -28.733388,-13.315321999999998 -28.243854999999993,-10.84056 -27.702752999999998,-8.400936999999999 -27.118316000000004,-5.984294 -26.500103000000006,-3.605947 -25.831709))";
     public static final String SLSTR_S3A_SUBSET_GEOMETRY_OBLIQUE = "POLYGON((-8.878673644279557 -27.236764407917907,-9.53544928644125 -25.04967680985631,-10.168283586553411 -22.85918001143884,-10.77966001357282 -20.665598368117607,-11.371805324633522 -18.469237570892084,-11.830750577579213 -16.719139725495783,-14.111707091253587 -17.25351940512691,-16.405503939106993 -17.761861031693723,-18.711951540661282 -18.243180789270152,-20.092489043445035 -18.516825426872682,-19.619832834325003 -20.72437811748543,-19.144536603427568 -22.930904108536893,-18.665514146303046 -25.136288353275976,-18.18158387263854 -27.340416146148723,-17.792023457963918 -29.09393425591276,-15.282864211399815 -28.6363146380642,-12.796449865715998 -28.132648799227454,-10.334198582889915 -27.584267693764158,-8.878673644279557 -27.236764407917907))";
 
     public static final String MYD012KM_AQ_GEOMETRY = "POLYGON((-120.74213409423832 68.62024688720705,-120.30563354492188 70.80646514892578,-119.72577667236328 72.99201202392578,-118.85693359375001 75.1676025390625,-117.59951782226565 77.33758544921875,-115.6713638305664 79.48979949951172,-112.61078643798828 81.6218948364258,-107.26968383789062 83.70146942138672,-96.62190246582033 85.66376495361328,-94.63011932373047 85.88507080078125,-176.4346160888672 85.02908325195312,167.89881896972656 82.63666534423828,161.38035583496094 80.52845001220703,156.9112091064453 78.12504577636719,152.57432556152344 74.17381286621094,150.42385864257812 71.04139709472656,157.0630340576172 70.52552032470703,163.29258728027344 69.77429962158203,169.0470428466797 68.82127380371094,174.27406311035156 67.68644714355469,178.98196411132812 66.39373779296875,-176.81396484375 64.96495056152344,-173.0399169921875 63.432212829589844,-169.67312622070312 61.80479812622071,-169.29559326171875 61.602462768554695,-158.47267150878906 65.08183288574219,-152.23338317871094 66.42942810058594,-146.80239868164062 67.30343627929688,-140.41331481933594 68.03364562988281,-129.48439025878906 68.64893341064453,-120.74213409423832 68.62024688720705))";

core/src/test/java/com/bc/fiduceo/reader/slstr/utility/ManifestUtilTest.java

@@ -3,12 +3,29 @@
 import org.esa.snap.core.datamodel.MetadataAttribute;
 import org.esa.snap.core.datamodel.MetadataElement;
 import org.esa.snap.core.datamodel.ProductData;
+import org.junit.Before;
 import org.junit.Test;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
 
 public class ManifestUtilTest {
 
+    private MetadataElement root;
+    private MetadataElement productInformation;
+
+    @Before
+    public void setUp() {
+        root = new MetadataElement("root");
+        final MetadataElement manifest = new MetadataElement("Manifest");
+        final MetadataElement metadataSection = new MetadataElement("metadataSection");
+        productInformation = new MetadataElement("slstrProductInformation");
+
+        metadataSection.addElement(productInformation);
+        manifest.addElement(metadataSection);
+        root.addElement(manifest);
+    }
+
     @Test
     public void testExtractTrackOffset() {
         final MetadataElement element = new MetadataElement("whatever");
@@ -17,4 +34,34 @@ public void testExtractTrackOffset() {
         final int offset = ManifestUtil.extractTrackOffset(element);
         assertEquals(235, offset);
     }
+
+    @Test
+    public void testGetObliqueGridOffset_missingElements() {
+        try {
+            ManifestUtil.getObliqueGridOffset(root);
+            fail("RuntimeException expected");
+        } catch (RuntimeException expected) {
+        }
+    }
+
+    @Test
+    public void testGetObliqueGridOffset() {
+        final MetadataElement nadirImageSize = new MetadataElement("nadirImageSize");
+        MetadataAttribute gridAttribute = new MetadataAttribute("grid", new ProductData.ASCII("1 km"), true);
+        nadirImageSize.addAttribute(gridAttribute);
+        MetadataAttribute nadirOffsetAttribute = new MetadataAttribute("trackOffset", new ProductData.ASCII("550"), true);
+        nadirImageSize.addAttribute(nadirOffsetAttribute);
+
+        final MetadataElement obliqueImageSize = new MetadataElement("obliqueImageSize");
+        gridAttribute = new MetadataAttribute("grid", new ProductData.ASCII("1 km"), true);
+        obliqueImageSize.addAttribute(gridAttribute);
+        nadirOffsetAttribute = new MetadataAttribute("trackOffset", new ProductData.ASCII("300"), true);
+        obliqueImageSize.addAttribute(nadirOffsetAttribute);
+
+        productInformation.addElement(nadirImageSize);
+        productInformation.addElement(obliqueImageSize);
+
+        final int offset = ManifestUtil.getObliqueGridOffset(root);
+        assertEquals(250, offset);
+    }
 }