fixed bug with non-square extractions

Author: TomBlock

core/src/main/java/com/bc/fiduceo/reader/snap/SNAP_Reader.java

@@ -227,9 +227,9 @@ protected void readSubsetData(RasterDataNode dataNode, Array targetArray, int wi
 
         final Index index = targetArray.getIndex();
         int readIndex = 0;
-        for (int y = 0; y < width; y++) {
+        for (int y = 0; y < height; y++) {
             final int currentY = yOffset + y;
-            for (int x = 0; x < height; x++) {
+            for (int x = 0; x < width; x++) {
                 final int currentX = xOffset + x;
                 index.set(y, x);
                 if (currentX >= 0 && currentX < sceneRasterWidth && currentY >= 0 && currentY < sceneRasterHeight) {

matchup-tool/src/test/java/com/bc/fiduceo/matchup/MatchupToolIntegrationTest_border_overlap_bug.java

@@ -0,0 +1,75 @@
+package com.bc.fiduceo.matchup;
+
+import com.bc.fiduceo.TestUtil;
+import com.bc.fiduceo.core.Dimension;
+import com.bc.fiduceo.core.SatelliteObservation;
+import com.bc.fiduceo.core.Sensor;
+import com.bc.fiduceo.core.UseCaseConfig;
+import com.bc.fiduceo.db.DbAndIOTestRunner;
+import org.apache.commons.cli.ParseException;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+
+import java.io.File;
+import java.io.IOException;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
+
+@RunWith(DbAndIOTestRunner.class)
+public class MatchupToolIntegrationTest_border_overlap_bug extends AbstractUsecaseIntegrationTest {
+
+    @Test
+    public void testMatchupWithBorderOverlap() throws IOException, SQLException, ParseException {
+        insert_AATSR();
+        insert_ARGO_SST();
+
+        final UseCaseConfig useCaseConfig = createUseCaseConfigBuilder()
+                .withTimeDeltaSeconds(63072000, null) // 2 years - just for testing
+                .withMaxPixelDistanceKm(1.f, null)
+                .createConfig();
+        final File useCaseConfigFile = storeUseCaseConfig(useCaseConfig, "usecase-test_SST.xml");
+
+        final String[] args = new String[]{"-c", configDir.getAbsolutePath(), "-u", useCaseConfigFile.getName(), "-start", "2012-046", "-end", "2013-256"};
+        MatchupToolMain.main(args);
+
+        System.out.println("args = " + args);
+
+    }
+
+    private MatchupToolTestUseCaseConfigBuilder createUseCaseConfigBuilder() {
+        final List<Sensor> sensorList = new ArrayList<>();
+        final Sensor primary = new Sensor("argo-sst");
+        primary.setPrimary(true);
+        sensorList.add(primary);
+        sensorList.add(new Sensor("aatsr-en"));
+
+        final List<Dimension> dimensions = new ArrayList<>();
+        dimensions.add(new Dimension("argo-sst", 1, 1));
+        dimensions.add(new Dimension("aatsr-en", 27, 5));
+
+        return (MatchupToolTestUseCaseConfigBuilder) new MatchupToolTestUseCaseConfigBuilder("mmd03_test")
+                .withSensors(sensorList)
+                .withOutputPath(new File(TestUtil.getTestDir().getPath(), "usecase-test_sst").getPath())
+                .withDimensions(dimensions);
+    }
+
+    private void insert_AATSR() throws IOException, SQLException {
+        final String sensorKey = "aatsr-en";
+        final String version = "v3";
+        final String relativeArchivePath = TestUtil.assembleFileSystemPath(new String[]{sensorKey, version, "2012", "02", "15", "ATS_TOA_1PUUPA20120215_010547_000065273111_00361_52099_6045.N1"}, true);
+        final String absolutePath = TestUtil.getTestDataDirectory().getAbsolutePath() + relativeArchivePath;
+
+        final SatelliteObservation satelliteObservation = readSatelliteObservation(sensorKey, absolutePath, version);
+        storage.insert(satelliteObservation);
+    }
+
+    private void insert_ARGO_SST() throws IOException, SQLException {
+        final String processingVersion = "v04.0";
+        final String sensorKey = "argo-sst";
+        final String relativeArchivePath = TestUtil.assembleFileSystemPath(new String[]{"insitu", "argo-sst", processingVersion, "insitu_5_WMOID_5904372_20130819_20161225.nc"}, true);
+        final String absolutePath = TestUtil.getTestDataDirectory().getAbsolutePath() + relativeArchivePath;
+        final SatelliteObservation argoInsitu = readSatelliteObservation(sensorKey, absolutePath, processingVersion);
+        storage.insert(argoInsitu);
+    }
+}