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Add vectorize enhancement
Addresses Unidata#527. Issue with values as seen through OPeNDAP fixed by Unidata/netcdf-java#1482
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‎tds/src/integrationTests/java/thredds/exp/enhancement/vectorize/TestVectorize.java‎

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/*
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* Copyright (c) 2025 University Corporation for Atmospheric Research/Unidata
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* See LICENSE for license information.
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*/
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package thredds.exp.enhancement.vectorize;
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import static com.google.common.truth.Truth.assertThat;
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import java.io.IOException;
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import org.junit.BeforeClass;
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import org.junit.Test;
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import thredds.client.catalog.Access;
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import thredds.client.catalog.Catalog;
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import thredds.client.catalog.Dataset;
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import thredds.client.catalog.ServiceType;
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import thredds.client.catalog.tools.DataFactory;
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import thredds.server.catalog.TdsLocalCatalog;
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import ucar.ma2.Array;
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import ucar.ma2.MAMath;
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import ucar.ma2.MAMath.MinMax;
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import ucar.nc2.dataset.NetcdfDataset;
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public class TestVectorize {
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private static Dataset dsNcmlFile;
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private static Dataset dsNcmlCat;
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private static DataFactory fac = new DataFactory();
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@BeforeClass
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public static void setup() {
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Catalog cat = TdsLocalCatalog.open("/catalog/catalog.xml");
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dsNcmlFile = cat.findDatasetByID("vectorizeNcmlFile");
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dsNcmlCat = cat.findDatasetByID("vectorizeNcmlCat");
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assert dsNcmlFile != null;
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assert dsNcmlCat != null;
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}
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@Test
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public void testTestVectorizeFileOpendap() throws IOException {
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Access access = dsNcmlFile.getAccess(ServiceType.OPENDAP);
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assertThat(access).isNotNull();
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testAccessMethod(access);
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}
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@Test
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public void testTestVectorizeCatOpendap() throws IOException {
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Access access = dsNcmlCat.getAccess(ServiceType.OPENDAP);
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assertThat(access).isNotNull();
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testAccessMethod(access);
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}
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@Test
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public void testTestVectorizeFileCdmremote() throws IOException {
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Access access = dsNcmlFile.getAccess(ServiceType.CdmRemote);
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assertThat(access).isNotNull();
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testAccessMethod(access);
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}
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@Test
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public void testTestVectorizeCatCdmremote() throws IOException {
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Access access = dsNcmlCat.getAccess(ServiceType.CdmRemote);
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assertThat(access).isNotNull();
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testAccessMethod(access);
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}
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private void testAccessMethod(Access access) throws IOException {
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NetcdfDataset ds = fac.openDataset(access, false, null, null);
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assertThat(ds).isNotNull();
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checkSpeed(ds);
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checkDir(ds);
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}
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private void checkSpeed(NetcdfDataset ds) throws IOException {
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Array speed = ds.findVariable("cspd").read();
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MinMax minMaxSpeed = MAMath.getMinMax(speed);
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assertThat(minMaxSpeed.min).isWithin(0.01).of(0.05);
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assertThat(minMaxSpeed.max).isWithin(0.01).of(0.27);
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}
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private void checkDir(NetcdfDataset ds) throws IOException {
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Array dir = ds.findVariable("cdir").read();
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MinMax minMaxDir = MAMath.getMinMax(dir);
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assertThat(minMaxDir.min).isWithin(0.1).of(121.1);
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assertThat(minMaxDir.max).isWithin(0.1).of(223.9);
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}
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}

‎tds/src/main/java/thredds/exp/enhancement/vectorize/VectorDirection.java‎

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/*
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* Copyright (c) 2025 University Corporation for Atmospheric Research/Unidata
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* See LICENSE for license information.
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*/
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package thredds.exp.enhancement.vectorize;
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import java.util.Set;
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import java.util.concurrent.locks.ReentrantLock;
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import ucar.ma2.DataType;
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import ucar.nc2.Variable;
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import ucar.nc2.dataset.NetcdfDataset.Enhance;
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import ucar.nc2.dataset.VariableDS;
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import ucar.nc2.filter.Enhancement;
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import ucar.nc2.filter.EnhancementProvider;
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public class VectorDirection extends Vectorize {
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private static org.slf4j.Logger logger = org.slf4j.LoggerFactory.getLogger(VectorDirection.class);
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public static final String ATTRIBUTE_NAME = "vectorize_dir";
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public VectorDirection(Variable var) {
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super(var);
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}
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ReentrantLock lock = new ReentrantLock();
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@Override
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public double convert(double num) {
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lock.lock();
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try {
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double u_val = uVar.read(indexToCoords((int) num), this.n_dimensional_array).getDouble(0);
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double v_val = vVar.read(indexToCoords((int) num), this.n_dimensional_array).getDouble(0);
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// atan2(0, 0) is undefined, so just return 0
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if (Math.sqrt(u_val * u_val + v_val * v_val) == 0.0f) {
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return 0.0f;
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}
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// return values in the [0, 360) range
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return ((Math.toDegrees(Math.atan2(u_val, v_val)) + 360.0f + this.convention_offset) % 360.0f);
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} catch (Exception ex) {
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logger.error("error converting u and v to direction", ex);
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return Double.NaN;
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} finally {
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lock.unlock();
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}
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}
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@Override
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protected String getAttributeName() {
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return ATTRIBUTE_NAME;
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}
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public static class Provider implements EnhancementProvider {
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@Override
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public String getAttributeName() {
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return ATTRIBUTE_NAME;
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}
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@Override
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public boolean appliesTo(Set<Enhance> enhance, DataType dt) {
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return dt.isNumeric();
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}
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@Override
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public Enhancement create(VariableDS var) {
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return new VectorDirection(var);
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}
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}
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}

‎tds/src/main/java/thredds/exp/enhancement/vectorize/VectorMagnitude.java‎

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/*
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* Copyright (c) 2025 University Corporation for Atmospheric Research/Unidata
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* See LICENSE for license information.
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*/
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package thredds.exp.enhancement.vectorize;
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import java.util.Set;
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import java.util.concurrent.locks.ReentrantLock;
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import ucar.ma2.DataType;
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import ucar.nc2.Variable;
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import ucar.nc2.dataset.NetcdfDataset.Enhance;
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import ucar.nc2.dataset.VariableDS;
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import ucar.nc2.filter.Enhancement;
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import ucar.nc2.filter.EnhancementProvider;
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public class VectorMagnitude extends Vectorize {
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private static org.slf4j.Logger logger = org.slf4j.LoggerFactory.getLogger(VectorMagnitude.class);
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public static final String ATTRIBUTE_NAME = "vectorize_mag";
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public VectorMagnitude(Variable var) {
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super(var);
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}
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ReentrantLock lock = new ReentrantLock();
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@Override
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public double convert(double num) {
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lock.lock();
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try {
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double u_val = uVar.read(indexToCoords((int) num), this.n_dimensional_array).getDouble(0);
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double v_val = vVar.read(indexToCoords((int) num), this.n_dimensional_array).getDouble(0);
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return Math.sqrt(u_val * u_val + v_val * v_val);
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} catch (Exception ex) {
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logger.error("error converting u and v to magnitude", ex);
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return Double.NaN;
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} finally {
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lock.unlock();
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}
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}
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@Override
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protected String getAttributeName() {
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return ATTRIBUTE_NAME;
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}
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public static class Provider implements EnhancementProvider {
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@Override
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public String getAttributeName() {
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return ATTRIBUTE_NAME;
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}
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@Override
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public boolean appliesTo(Set<Enhance> enhance, DataType dt) {
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return dt.isNumeric();
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}
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@Override
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public Enhancement create(VariableDS var) {
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return new VectorMagnitude(var);
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}
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}
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}

‎tds/src/main/java/thredds/exp/enhancement/vectorize/Vectorize.java‎

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/*
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* Copyright (c) 2025 University Corporation for Atmospheric Research/Unidata
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* See LICENSE for license information.
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*/
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package thredds.exp.enhancement.vectorize;
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import ucar.nc2.Attribute;
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import ucar.nc2.Variable;
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import ucar.nc2.filter.Enhancement;
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public abstract class Vectorize implements Enhancement {
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private static org.slf4j.Logger logger = org.slf4j.LoggerFactory.getLogger(Vectorize.class);
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protected Variable uVar;
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protected Variable vVar;
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private String convention;
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protected float convention_offset;
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private int nDims;
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protected int[] shape;
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protected int[] n_dimensional_array;
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public Vectorize(Variable var) {
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try {
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Attribute att = var.findAttribute(getAttributeName());
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String[] vars = att.getStringValue().split("/");
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this.uVar = var.getParentGroup().findVariableLocal(vars[0]);
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this.vVar = var.getParentGroup().findVariableLocal(vars[1]);
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this.convention = vars[2];
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if ("to".equals(this.convention)) {
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this.convention_offset = 0.0f;
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} else if ("from".equals(this.convention)) {
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this.convention_offset = 180.0f;
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} else {
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throw new IllegalArgumentException("The convention must be either 'to' or 'from'.");
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}
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this.shape = var.getShape();
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this.nDims = this.shape.length;
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if (!validateDims()) {
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return;
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}
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this.n_dimensional_array = new int[this.nDims];
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for (int d = 0; d < this.nDims; d++) {
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this.n_dimensional_array[d] = 1;
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}
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} catch (NullPointerException ex) {
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logger.error("Could not parse attribute {}", getAttributeName());
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}
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}
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protected int[] indexToCoords(int index) {
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int[] coords = new int[this.nDims];
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int innerDims = 1;
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for (int i = this.nDims - 1; i >= 0; i--) {
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coords[i] = (index / innerDims) % this.shape[i];
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innerDims *= this.shape[i];
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}
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return coords;
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}
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private boolean validateDims() {
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return checkDims(this.uVar) && checkDims(this.vVar);
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}
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private boolean checkDims(Variable var) {
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if (this.nDims != var.getShape().length) {
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return false;
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}
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for (int i = 0; i < this.nDims; i++) {
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if (this.shape[i] != var.getShape()[i]) {
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return false;
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}
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}
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return true;
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}
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abstract protected String getAttributeName();
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}

‎tds/src/main/resources/META-INF/services/ucar.nc2.filter.EnhancementProvider‎

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thredds.exp.enhancement.vectorize.VectorMagnitude$Provider
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thredds.exp.enhancement.vectorize.VectorDirection$Provider

‎tds/src/test/content/thredds/catalog.xml‎

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</variable>
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</ncml:netcdf>
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</dataset>
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<dataset name="Vectorize NcML File" ID="vectorizeNcmlFile" urlPath="localContent/vectorize/test_dataset.ncml" dataType="Grid"/>
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<dataset name="Vectorize NcML Catalog" ID="vectorizeNcmlCat" urlPath="vectorizeNcmlCat.nc">
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<serviceName>all</serviceName>
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<ncml:netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2"
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enhance="all"
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location="content/testdata/vectorize/vectorize_test.nc">
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<variable name="cspd" shape="time depth latitude longitude" type="float">
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<attribute name="vectorize_mag" value="uo/vo/to" />
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<attribute name="long_name" value="current speed" />
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<attribute name="units" value="m/s" />
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<values start="0" increment="1" />
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</variable>
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<variable name="cdir" shape="time depth latitude longitude" type="float">
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<attribute name="vectorize_dir" value="uo/vo/to" />
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<attribute name="long_name" value="current direction" />
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<attribute name="units" value="degrees" />
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<values start="0" increment="1" />
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</variable>
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</ncml:netcdf>
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</dataset>
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</dataset>
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<dataset name="Test Dap4 Dataset" ID="testDap4Dataset" serviceName="dap4"

‎tds/src/test/content/thredds/public/testdata/vectorize/test_dataset.ncml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2"
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enhance="all"
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location="vectorize_test.nc">
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<variable name="cspd" shape="time depth latitude longitude" type="float">
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<attribute name="vectorize_mag" value="uo/vo/to" />
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<attribute name="long_name" value="current speed" />
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<attribute name="units" value="m/s" />
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<values start="0" increment="1" />
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</variable>
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<variable name="cdir" shape="time depth latitude longitude" type="float">
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<attribute name="vectorize_dir" value="uo/vo/to" />
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<attribute name="long_name" value="current direction" />
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<attribute name="units" value="degrees" />
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<values start="0" increment="1" />
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</variable>
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</netcdf>

‎tds/src/test/content/thredds/public/testdata/vectorize/vectorize_test.nc‎

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