Merge pull request #7 from bcdev/SE_ReaderSlstrSubset_CCI+SST_COO-02

Se reader slstr subset cci+sst coo 02

Author: TomBlock

CHANGES.md

@@ -1,4 +1,5 @@
 ### Updates from version 1.5.5 to 1.5.6
+* added support for SLSTR regridded subseted data in safe format 
 * corrected TAI 1993 to UTC conversion for MODIS data
 * updated H2 database driver
 * added support for MODIS MxD035 cloud data

core/src/main/java/com/bc/fiduceo/reader/modis/MxD35BowTieVariable.java

@@ -1,30 +1,25 @@
 package com.bc.fiduceo.reader.modis;
 
+import com.bc.fiduceo.util.NetCDFUtils;
 import com.bc.fiduceo.util.VariableProxy;
 import org.esa.snap.core.datamodel.TiePointGrid;
 import ucar.ma2.Array;
 import ucar.ma2.DataType;
 import ucar.ma2.InvalidRangeException;
 import ucar.ma2.MAMath;
-import ucar.nc2.Attribute;
-import ucar.nc2.AttributeContainer;
 import ucar.nc2.Variable;
 
 import java.io.IOException;
-import java.util.ArrayList;
 
-import static com.bc.fiduceo.util.NetCDFUtils.CF_ADD_OFFSET_NAME;
-import static com.bc.fiduceo.util.NetCDFUtils.CF_FILL_VALUE_NAME;
 import static com.bc.fiduceo.util.NetCDFUtils.CF_SCALE_FACTOR_NAME;
-import static com.bc.fiduceo.util.NetCDFUtils.CF_VALID_RANGE_NAME;
 
 public class MxD35BowTieVariable extends VariableProxy {
 
     private final Variable _variable;
     private TiePointGrid[] grids;
 
     public MxD35BowTieVariable(Variable variable, int width, int height) throws IOException {
-        super(variable.getShortName(), DataType.FLOAT, getAttributes(variable));
+        super(variable.getShortName(), DataType.FLOAT, NetCDFUtils.getAttributes(variable));
         setShape(new int[]{height, width});
         this._variable = variable;
         init();
@@ -54,35 +49,6 @@ public Array read() throws IOException {
         return targetArray;
     }
 
-    private static ArrayList<Attribute> getAttributes(Variable variable) {
-        final AttributeContainer inAtts = variable.attributes();
-        final double scaling = inAtts.findAttributeDouble(CF_SCALE_FACTOR_NAME, 1.0);
-        final double offset = inAtts.findAttributeDouble(CF_ADD_OFFSET_NAME, 0.0);
-        final Attribute fillAtt = inAtts.findAttribute(CF_FILL_VALUE_NAME);
-        final Number newFill;
-        if (fillAtt != null && (scaling != 1.0 || offset != 0.0)) {
-            final Number value = fillAtt.getNumericValue();
-            newFill = value.doubleValue() * scaling + offset;
-        } else {
-            newFill = null;
-        }
-
-        final ArrayList<Attribute> attributes = new ArrayList<>();
-        inAtts.forEach(attribute -> {
-            final String name = attribute.getShortName();
-            if (CF_SCALE_FACTOR_NAME.equals(name)) {
-                attributes.add(new Attribute(CF_SCALE_FACTOR_NAME, 1.0F));
-            } else if (CF_ADD_OFFSET_NAME.equals(name)) {
-                attributes.add(new Attribute(CF_ADD_OFFSET_NAME, 0.0F));
-            } else if (newFill != null && CF_FILL_VALUE_NAME.equals(name)) {
-                attributes.add(new Attribute(CF_FILL_VALUE_NAME, newFill.floatValue()));
-            } else if (!(name.contains("_Swath_Sampling") || CF_VALID_RANGE_NAME.equals(name))) {
-                attributes.add(attribute);
-            }
-        });
-        return attributes;
-    }
-
     private void init() throws IOException {
         final int[] shape = getShape();
         final int[] tiePointShape = _variable.getShape();

core/src/main/java/com/bc/fiduceo/reader/modis/MxD35_Reader.java

@@ -30,6 +30,7 @@
 import com.bc.fiduceo.geometry.Polygon;
 import com.bc.fiduceo.hdf.HdfEOSUtil;
 import com.bc.fiduceo.location.PixelLocator;
+import com.bc.fiduceo.location.PixelLocatorFactory;
 import com.bc.fiduceo.reader.AcquisitionInfo;
 import com.bc.fiduceo.reader.BoundingPolygonCreator;
 import com.bc.fiduceo.reader.Geometries;
@@ -77,6 +78,7 @@ public class MxD35_Reader extends NetCDFReader {
     private static final int SMALLEST_DIM_IDX = 0;
     private static final int SMALLEST_DIM_SIZE = 1;
     private static final HashMap<String, FlagDefinition> FLAG_DEFINITIONS = new HashMap<>();
+    private BoundingPolygonCreator boundingPolygonCreator;
 
     {
         final FlagDefinition cloudMaskFlagDef = new FlagDefinition();
@@ -356,7 +358,13 @@ public PixelLocator getPixelLocator() throws IOException {
 
     @Override
     public PixelLocator getSubScenePixelLocator(Polygon sceneGeometry) throws IOException {
-        return getPixelLocator();
+        final Dimension productSize = getProductSize();
+        final int height = productSize.getNy();
+        final int width = productSize.getNx();
+        final int subsetHeight = boundingPolygonCreator.getSubsetHeight(height, 250);
+        final PixelLocator pixelLocator = getPixelLocator();
+
+        return PixelLocatorFactory.getSubScenePixelLocator(sceneGeometry, width, height, subsetHeight, pixelLocator);
     }
 
     @Override
@@ -606,7 +614,7 @@ private int[] findSlicingConditions(Variable variable) {
     }
 
     private void extractGeometries(AcquisitionInfo acquisitionInfo) throws IOException {
-        final BoundingPolygonCreator boundingPolygonCreator = new BoundingPolygonCreator(new Interval(250, 250), geometryFactory);
+        boundingPolygonCreator = new BoundingPolygonCreator(new Interval(250, 250), geometryFactory);
         final Array longitude = arrayCache.get(GEOLOCATION_GROUP, LONGITUDE_VAR_NAME);
         final Array latitude = arrayCache.get(GEOLOCATION_GROUP, LATITUDE_VAR_NAME);
         final Geometry boundingGeometry = boundingPolygonCreator.createBoundingGeometry(longitude, latitude);

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

@@ -8,9 +8,9 @@
 import com.bc.fiduceo.reader.AcquisitionInfo;
 import com.bc.fiduceo.reader.ReaderContext;
 import com.bc.fiduceo.reader.ReaderUtils;
-import com.bc.fiduceo.reader.time.TimeLocator;
 import com.bc.fiduceo.reader.snap.SNAP_Reader;
 import com.bc.fiduceo.reader.snap.VariableProxy;
+import com.bc.fiduceo.reader.time.TimeLocator;
 import com.bc.fiduceo.reader.time.TimeLocator_MicrosSince2000;
 import com.bc.fiduceo.util.NetCDFUtils;
 import com.bc.fiduceo.util.TimeUtils;
@@ -20,7 +20,6 @@
 import ucar.ma2.Array;
 import ucar.ma2.ArrayInt;
 import ucar.ma2.DataType;
-import ucar.ma2.Index;
 import ucar.nc2.Variable;
 
 import java.io.File;
@@ -213,7 +212,6 @@ public Array readRaw(int centerX, int centerY, Interval interval, String variabl
 
         final VariableType variableType = variableNames.getVariableType(variableName);
         final Transform transform = transformFactory.get(variableType);
-        final Dimension rasterSize = transform.getRasterSize();
 
         final RasterDataNode dataNode = getRasterDataNode(variableName);
 
@@ -225,7 +223,6 @@ public Array readRaw(int centerX, int centerY, Interval interval, String variabl
         final int height = mappedInterval.getY();
         final int[] shape = getShape(mappedInterval);
         final Array readArray = Array.factory(targetDataType, shape);
-        final Array targetArray = NetCDFUtils.create(targetDataType, shape, noDataValue);
 
         final int mappedX = (int) (transform.mapCoordinate_X(centerX) + 0.5);
         final int mappedY = (int) (transform.mapCoordinate_Y(centerY) + 0.5);