Java Code Examples for ucar.nc2.dataset.NetcdfDataset#openDataset()

private void compareBuilderDS() {
  if (ds == null)
    return;
  String fileLocation = ds.getLocation();
  try (NetcdfDataset org = NetcdfDataset.openDataset(fileLocation)) {
    try (NetcdfDataset withBuilder = NetcdfDatasets.openDataset(fileLocation)) {
      Formatter f = new Formatter();
      CompareNetcdf2 compare = new CompareNetcdf2(f, false, false, true);
      compare.compare(org, withBuilder, new CoordsObjFilter());
      infoTA.setText(f.toString());
      infoTA.gotoTop();
      infoWindow.setTitle("Compare Old (file1) with Builder (file 2)");
      infoWindow.show();
    }
  } catch (Throwable ioe) {
    StringWriter sw = new StringWriter(10000);
    ioe.printStackTrace(new PrintWriter(sw));
    infoTA.setText(sw.toString());
    infoTA.gotoTop();
    infoWindow.show();
  }
}
 

@Test
public void testCoordinateSystemDomain() throws Exception {
  System.err.printf("%nOpen %s grid='%s'%n", filename, gridName);
  Grib.setDebugFlags(new DebugFlagsImpl("Grib/indexOnly"));

  try (NetcdfDataset ncd = NetcdfDataset.openDataset(filename)) {
    Assert.assertNotNull(filename, ncd);
    VariableDS vds = (VariableDS) ncd.findVariable(gridName);
    Assert.assertNotNull(gridName, vds);
    for (CoordinateSystem cs : vds.getCoordinateSystems()) {
      System.err.printf("  CoordinateSystem= '%s'%n", cs);
      testDomain("CoordinateSystem ", vds.getDimensions(), cs.getCoordinateAxes());
    }

  } finally {
    Grib.setDebugFlags(new DebugFlagsImpl(""));
  }
}
 

public void run(Object o) throws IOException {
  try {
    boolean useBuilders = ToolsUI.getToolsUI().getUseBuilders();
    if (useCoords) {
      ncfile = useBuilders ? NetcdfDatasets.openDataset(filename, true, null)
          : NetcdfDataset.openDataset(filename, true, null);
    } else {
      DatasetUrl durl = DatasetUrl.findDatasetUrl(filename);
      ncfile = useBuilders ? NetcdfDatasets.openFile(durl, -1, null, null) : NetcdfDataset.openFile(filename, null);
    }

    StringWriter sw = new StringWriter(50000);
    Ncdump.ncdump(ncfile, command, sw, task);
    result = sw.toString();
  } finally {
    try {
      if (ncfile != null) {
        ncfile.close();
      }
      ncfile = null;
    } catch (IOException ioe) {
      System.out.printf("Error closing %n");
    }
  }
}
 

@Test(expected = IOException.class)
public void testNcmlDatasetNoProtocolInNcmlAbsPath() throws IOException, InvalidRangeException {
  // if using an absolute path in the NcML file location attr of the element netcdf, then
  // you must prepend file:
  // this should fail with an IOException
  String filename = "file:./" + TestNcMLRead.topDir + "exclude/aggExisting6.xml";

  NetcdfFile ncfile = NetcdfDataset.openDataset(filename, true, null);
  logger.debug(" TestNcmlAggExisting.open {}", filename);

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVar(ncfile);
  testReadData(ncfile);
  testReadSlice(ncfile);
  ncfile.close();
}
 

@Test
public void testPolygon() throws IOException {

  String failMessage, found, expected;
  boolean testCond;

  String tstFile = TestDir.cdmLocalTestDataDir + "dataset/SimpleGeos/outflow_3seg_5timesteps_vlen.nc";

  // open the test file
  NetcdfDataset ncd = NetcdfDataset.openDataset(tstFile);

  // make sure this dataset used the cfConvention
  expected = cfConvention;
  found = ncd.getConventionUsed();
  testCond = found.equals(expected);
  failMessage =
      format("This dataset used the %s convention, but should have used the %s convention.", found, expected);
  Assert.assertTrue(failMessage, testCond);

  // check that attributes were filled in correctly
  List<Variable> vars = ncd.getVariables();
  for (Variable v : vars) {
    if (v.findAttribute(CF.GEOMETRY) != null) {
      Assert.assertNotNull(v.findAttribute(CF.NODE_COORDINATES));
      Assert.assertNotNull(v.findAttribute(_Coordinate.Axes));
    }
  }
  ncd.close();
}
 

@Test
public void testLine() throws IOException {

  String failMessage, found, expected;
  boolean testCond;

  String tstFile = TestDir.cdmLocalTestDataDir + "dataset/SimpleGeos/hru_soil_moist_vlen_3hru_5timestep.nc";

  // open the test file
  NetcdfDataset ncd = NetcdfDataset.openDataset(tstFile);

  // make sure this dataset used the cfConvention
  expected = cfConvention;
  found = ncd.getConventionUsed();
  testCond = found.equals(expected);
  failMessage =
      format("This dataset used the %s convention, but should have used the %s convention.", found, expected);
  Assert.assertTrue(failMessage, testCond);

  // check that attributes were filled in correctly
  List<Variable> vars = ncd.getVariables();
  for (Variable v : vars) {
    if (v.findAttribute(CF.GEOMETRY) != null) {
      Assert.assertNotNull(v.findAttribute(CF.NODE_COORDINATES));
      Assert.assertNotNull(v.findAttribute(_Coordinate.Axes));
    }
  }
  ncd.close();
}
 

@BeforeClass
public static void setUp() throws IOException {
  if (ncfile != null)
    return;
  String filename = "file:./" + TestNcMLRead.topDir + "aggUnionSimple.xml";
  ncfile = NetcdfDataset.openDataset(filename, false, null);
}
 

private void compareDS(String ncmlLocation) throws IOException {
  System.out.printf("Compare NetcdfDataset.openDataset %s%n", ncmlLocation);
  try (NetcdfDataset org = NetcdfDataset.openDataset(ncmlLocation)) {
    try (NetcdfDataset withBuilder = NetcdfDatasets.openDataset(ncmlLocation)) {
      Formatter f = new Formatter();
      CompareNetcdf2 compare = new CompareNetcdf2(f, false, false, true);
      boolean ok = compare.compare(org, withBuilder, new CoordsObjFilter());
      System.out.printf("%s %s%n", ok ? "OK" : "NOT OK", f);
      assertThat(ok).isTrue();
    }
  }
}
 

@Test
public void testTryWithWrap() throws IOException {
  String location = TestDir.cdmLocalFromTestDataDir + "testWrite.nc";
  NetcdfDataset ncd = NetcdfDataset.openDataset(location);
  Formatter errlog = new Formatter();
  try (FeatureDataset fdataset = FeatureDatasetFactoryManager.wrap(null, ncd, null, errlog)) {
    assert (fdataset == null);
  }
  ncd.close();
}
 

@Test
public void testNcmlDatasetWcoords() throws IOException, InvalidRangeException {
  String filename = "file:./" + TestNcMLRead.topDir + "aggExistingWcoords.xml";

  NetcdfFile ncfile = NetcdfDataset.openDataset(filename, true, null);
  logger.debug(" testNcmlDatasetWcoords.open {}", filename);

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVar(ncfile);
  testReadData(ncfile);
  testReadSlice(ncfile);
  ncfile.close();
  logger.debug(" testNcmlDatasetWcoords.closed ");
}
 

@Test
public void testNcmlDatasetNoProtocolInNcmlRelPath() throws IOException, InvalidRangeException {
  String filename = "file:./" + TestNcMLRead.topDir + "aggExisting7.xml";

  NetcdfFile ncfile = NetcdfDataset.openDataset(filename, true, null);
  logger.debug(" TestNcmlAggExisting.open {}", filename);

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVar(ncfile);
  testReadData(ncfile);
  testReadSlice(ncfile);
  ncfile.close();
}
 

public static NetcdfDataset openH5dataset(String filename) {
  try {
    System.out.println("**** Open " + testDir + filename);
    NetcdfDataset ncfile = NetcdfDataset.openDataset(testDir + filename);
    if (TestH5.dumpFile)
      System.out.println("open H5 " + ncfile);
    return ncfile;

  } catch (java.io.IOException e) {
    System.out.println(" fail = " + e);
    e.printStackTrace();
    assert (false);
    return null;
  }
}
 

private static boolean compareNetCDFOld(File expectedResultFile, File actualResultFile) throws IOException {
  try (NetcdfFile expectedNcFile = NetcdfDataset.openDataset(expectedResultFile.getAbsolutePath());
      NetcdfFile actualNcFile = NetcdfDataset.openDataset(actualResultFile.getAbsolutePath())) {
    Formatter formatter = new Formatter();
    boolean contentsAreEqual = new CompareNetcdf2(formatter, false, false, true).compare(expectedNcFile, actualNcFile,
        new NcssNetcdfObjFilter());

    if (!contentsAreEqual) {
      System.err.println(formatter.toString());
    }

    return contentsAreEqual;
  }
}
 

@Test
public void testNcmlDataset() throws IOException, InvalidRangeException {
  String filename = "file:./" + TestNcMLRead.topDir + "aggExisting.xml";

  NetcdfFile ncfile = NetcdfDataset.openDataset(filename, true, null);
  logger.debug(" TestNcmlAggExisting.open {}", filename);

  testDimensions(ncfile);
  testCoordVar(ncfile);
  testAggCoordVar(ncfile);
  testReadData(ncfile);
  testReadSlice(ncfile);
  ncfile.close();
}
 

private void testEnhanceEquals(String ncmlLocation) throws IOException {
  System.out.println("testEnhanceEquals");
  try (NetcdfDataset ncml = NcMLReader.readNcML(ncmlLocation, null);
      NetcdfDataset ncmlEnhanced = new NetcdfDataset(ncml, true)) {

    String locref = ncml.getReferencedFile().getLocation();
    NetcdfDataset ncdrefEnhanced = NetcdfDataset.openDataset(locref, true, null);

    Assert
        .assertTrue(CompareNetcdf2.compareFiles(ncmlEnhanced, ncdrefEnhanced, new Formatter(), false, false, false));
  }
}
 

static void testNcd() throws IOException {
  String filename = "C:/data/test2.nc";
  NetcdfDataset ncfile = NetcdfDataset.openDataset(filename);
  measureSize("C:/data/test2.nc", ncfile, null, true);

  NetcdfDatasetInfo info = new NetcdfDatasetInfo(filename);
  measureSize("info", info, null, true);
  String pifo = info.getParseInfo();
  System.out.println("info= " + pifo);
  ncfile.close();
}
 

/**
 * Read text from textArea through NcMLReader
 * then write it back out via resulting dataset
 */
private void checkNcml(Formatter f) {
  if (ncmlLocation == null) {
    return;
  }
  boolean useBuilders = ToolsUI.getToolsUI().getUseBuilders();
  try (NetcdfDataset ncd =
      useBuilders ? NetcdfDatasets.openDataset(ncmlLocation) : NetcdfDataset.openDataset(ncmlLocation)) {
    ncd.check(f);
  } catch (IOException ioe) {
    JOptionPane.showMessageDialog(this, "ERROR: " + ioe.getMessage());
    ioe.printStackTrace();
  }
}
 

@Test
public void testCoordinateVariable() throws IOException {
  String tstFile = TestDir.cdmLocalTestDataDir + "dataset/SimpleGeos/outflow_3seg_5timesteps_vlen.nc";
  // open the test file
  try (NetcdfDataset ncd = NetcdfDataset.openDataset(tstFile)) {
    for (CoordinateAxis axis : ncd.getCoordinateAxes()) {
      System.out.printf("Try to read %s ", axis.getFullName());
      Array data = axis.read();
      System.out.printf(" OK (%d) %n", data.getSize());
    }
  }
}
 

/**
 * Read aggregation of unsigned variable for test
 */
@Before
public void prepAggDataset() {
  String filenameScan = "file:./" + TestNcMLRead.topDir + "fmrc/" + FILENAME_SCAN;
  String filenameExplicit = "file:./" + TestNcMLRead.topDir + "fmrc/" + FILENAME_EXPLICIT;
  String filenameA = "file:./" + TestNcMLRead.topDir + "fmrc/" + FILENAME_A;
  String filenameB = "file:./" + TestNcMLRead.topDir + "fmrc/" + FILENAME_B;
  String filenameC = "file:./" + TestNcMLRead.topDir + "fmrc/" + FILENAME_C;
  try {

    fmrcScan = Fmrc.open(filenameScan, null);
    Assert.assertNotNull(fmrcScan);
    GridDataset bestScan = fmrcScan.getDatasetBest();
    Variable bestScanVar = bestScan.findGridByName(AGG_VAR_NAME).getVariable();
    valuesBestScanVar = bestScanVar.read();

    fmrcExplicit = Fmrc.open(filenameExplicit, null);
    Assert.assertNotNull(fmrcExplicit);
    GridDataset bestExplicit = fmrcExplicit.getDatasetBest();
    Variable bestExplicitVar = bestExplicit.findGridByName(AGG_VAR_NAME).getVariable();
    valuesBestExplicitVar = bestExplicitVar.read();

    ncfileScan = NcMLReader.readNcML(filenameScan, null);
    varScan = ncfileScan.findVariable(AGG_VAR_NAME);
    valuesScan = varScan.read();

    ncfileExplicit = NcMLReader.readNcML(filenameExplicit, null);
    varExplicit = ncfileScan.findVariable(AGG_VAR_NAME);
    valuesExplicit = varExplicit.read();

    ncfileA = NetcdfDataset.openDataset(filenameA);
    varA = ncfileA.findVariable(AGG_VAR_NAME);
    valuesA = varA.read();

    ncfileB = NetcdfDataset.openDataset(filenameB);
    varB = ncfileB.findVariable(AGG_VAR_NAME);
    valuesB = varB.read();

    ncfileC = NetcdfDataset.openDataset(filenameC);
    varC = ncfileC.findVariable(AGG_VAR_NAME);
    valuesC = varC.read();

  } catch (IOException e) {
    e.printStackTrace();
  }
}
 

static void testNcml() throws IOException {
  String filename = "C:/dev/tds/thredds/cdm/src/test/data/ncml/aggUnionSimple.xml";
  NetcdfDataset ncfile = NetcdfDataset.openDataset(filename, false, null);
  measureSize("aggUnionSimple", ncfile, null, true);
  ncfile.close();
}