Merge branch 'maint-5.x' into maint-5.x_sigmet

cdm/core/src/main/java/ucar/nc2/ft2/coverage/CoverageDatasetFactory.java

@@ -126,8 +126,21 @@ public static Optional<FeatureDatasetCoverage> openGrib(String endpoint) {
 
   }
 
+  /**
+   * @deprecated Use openNcmlString(String, String)
+   */
+  @Deprecated
   public static Optional<FeatureDatasetCoverage> openNcmlString(String ncml) throws IOException {
-    NetcdfDataset ncd = NetcdfDatasets.openNcmlDataset(new StringReader(ncml), null, null);
+    return openNcmlString(ncml, null);
+  }
+
+  /**
+   * @param ncml the NcML as a String
+   * @param location the URL location string of the NcML document,
+   *        or may be just a unique name for caching purposes (if null, aggregation cache will not be used).
+   */
+  public static Optional<FeatureDatasetCoverage> openNcmlString(String ncml, String location) throws IOException {
+    NetcdfDataset ncd = NetcdfDatasets.openNcmlDataset(new StringReader(ncml), location, null);
 
     DtCoverageDataset gds = new DtCoverageDataset(ncd);
     if (!gds.getGrids().isEmpty()) {

cdm/core/src/main/java/ucar/nc2/util/Misc.java

@@ -96,19 +96,19 @@ public static boolean nearlyEquals(float a, float b) {
     return nearlyEquals(a, b, defaultMaxRelativeDiffFloat);
   }
 
-  /** AbsoluteDifference is less than maxAbsDiff. */
-  public static boolean nearlyEquals(float a, float b, float maxAbsDiff) {
-    return DoubleMath.fuzzyEquals(a, b, maxAbsDiff);
+  /** RelativeDifference is less than maxRelDiff. */
+  public static boolean nearlyEquals(float a, float b, float maxRelDiff) {
+    return relativeDifference(a, b) < maxRelDiff;
   }
 
   /** AbsoluteDifference is less than {@link #defaultMaxRelativeDiffDouble}. */
   public static boolean nearlyEquals(double a, double b) {
     return nearlyEquals(a, b, defaultMaxRelativeDiffDouble);
   }
 
-  /** AbsoluteDifference is less than maxAbsDiff. */
-  public static boolean nearlyEquals(double a, double b, double maxAbsDiff) {
-    return DoubleMath.fuzzyEquals(a, b, maxAbsDiff);
+  /** RelativeDifference is less than maxRelDiff. */
+  public static boolean nearlyEquals(double a, double b, double maxRelDiff) {
+    return relativeDifference(a, b) < maxRelDiff;
   }
 
   /** AbsoluteDifference is less than maxAbsDiff. */

cdm/core/src/test/java/ucar/nc2/filter/TestEnhancements.java

@@ -17,6 +17,7 @@
 import static com.google.common.truth.Truth.assertThat;
 
 import java.io.IOException;
+import java.util.Arrays;
 
 public class TestEnhancements {
 
@@ -75,6 +76,13 @@ public static void setUp() throws IOException, InvalidRangeException {
         .addAttribute(new Attribute(CDM.FILL_VALUE, SIGNED_SCALED_FILL_VALUE))
         .addAttribute(new Attribute(CDM.MISSING_VALUE, SIGNED_SCALED_MISSING_VALUE));
 
+    // short data with small scale and offsets
+    Array smallVals = Array.factory(DataType.FLOAT, new int[] {dataLen}, missingData);
+
+    builder.addVariable("smallVals", DataType.FLOAT, "dim").addAttribute(new Attribute(CDM.SCALE_FACTOR, 1e-12))
+        .addAttribute(new Attribute(CDM.ADD_OFFSET, 1e-12)).addAttribute(new Attribute(CDM.FILL_VALUE, 110));
+
+
     // write data
     NetcdfFormatWriter writer = builder.build();
     writer.write(writer.findVariable("signedVar"), new int[1], signedData);
@@ -85,6 +93,7 @@ public static void setUp() throws IOException, InvalidRangeException {
     writer.write(writer.findVariable("validMinMax"), new int[1], missingDataArray);
     writer.write(writer.findVariable("validRange"), new int[1], missingDataArray);
     writer.write(writer.findVariable("enhanceAll"), new int[1], enhanceAllArray);
+    writer.write(writer.findVariable("smallVals"), new int[1], smallVals);
     writer.close();
     ncd = NetcdfDatasets.openDataset(filePath);
   }
@@ -152,4 +161,12 @@ public void testCombinedEnhancements() throws IOException {
     Array data = v.read();
     assertThat((double[]) data.copyTo1DJavaArray()).isEqualTo(expected);
   }
+
+  @Test
+  public void testConvertMissingWithSmallScaleAndOffset() throws IOException {
+    Variable v = ncd.findVariable("smallVals");
+    Array data = v.read();
+    assertThat(Double.isNaN(data.getDouble(2))).isTrue();
+    assertThat(Double.isNaN(data.getDouble(1))).isFalse();
+  }
 }

cdm/s3/src/test/java/ucar/nc2/internal/ncml/s3/S3AggScanFeatureType.java

@@ -96,7 +96,7 @@ public void testAggNewOpenAsCoverage() throws IOException, InvalidRangeException
       ncml = ncmlStream.collect(Collectors.joining());
     }
     assertThat(ncml).isNotNull();
-    Optional<FeatureDatasetCoverage> fdc = CoverageDatasetFactory.openNcmlString(ncml);
+    Optional<FeatureDatasetCoverage> fdc = CoverageDatasetFactory.openNcmlString(ncml, null);
     assertThat(fdc.isPresent()).isTrue();
     List<CoverageCollection> cc = fdc.get().getCoverageCollections();
     checkCoverages(cc);