Java Code Examples for ucar.nc2.NetcdfFiles#open()

private void compareBuilder() {
  if (ds == null)
    return;
  String fileLocation = ds.getLocation();
  try (NetcdfFile org = NetcdfFile.open(fileLocation)) {
    try (NetcdfFile withBuilder = NetcdfFiles.open(fileLocation)) {
      Formatter f = new Formatter();
      CompareNetcdf2 compare = new CompareNetcdf2(f, false, false, true);
      boolean ok = 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();
  }
}
 

private boolean doCompare(String location, boolean showCompare, boolean showEach, boolean compareData)
    throws IOException {
  try (NetcdfFile ncfile = NetcdfFiles.open(location); NetcdfFile jni = openJni(location)) {
    jni.setLocation(location + " (jni)");
    // System.out.printf("Compare %s to %s%n", ncfile.getIosp().getClass().getName(),
    // jni.getIosp().getClass().getName());

    Formatter f = new Formatter();
    CompareNetcdf2 tc = new CompareNetcdf2(f, showCompare, showEach, compareData);
    boolean ok = tc.compare(ncfile, jni, new CompareNetcdf2.Netcdf4ObjectFilter());
    System.out.printf(" %s compare %s ok = %s%n", ok ? "" : "***", location, ok);
    if (!ok || (showCompare && showCompareResults))
      System.out.printf("%s%n=====================================%n", f);
    return ok;
  }
}
 

@Test
public void code1_spherical_specified_bad() throws IOException {
  String filename = dir + "sfc_d01_20080430_1200_f00000.grb2";
  try (NetcdfFile ncfile = NetcdfFiles.open(filename, null)) {
    Variable v = ncfile.findVariable("LambertConformal_Projection");
    Attribute axis = v.findAttribute("earth_radius");
    Assert.assertEquals(6371200., axis.getNumericValue().doubleValue(), 0.1);
  }
}
 

@Test
public void testDrs2() throws IOException {
  final String testfile = "../grib/src/test/data/ds.snow.grib2";
  try (NetcdfFile nc = NetcdfFiles.open(testfile)) {
    Variable var = nc.findVariable("Total_snowfall_surface_6_Hour_Accumulation");
    float[] data = (float[]) var.read().get1DJavaArray(DataType.FLOAT);

    Assert.assertTrue(Float.isNaN(data[0]));
    Assert.assertTrue(Float.isNaN(data[1234]));
  }
}
 

private void compareWithBuilder(String filename) throws IOException {
  logger.info("TestBuilders on {}%n", filename);
  try (NetcdfFile org = NetcdfFile.open(filename)) {
    try (NetcdfFile withBuilder = NetcdfFiles.open(filename)) {
      Formatter f = new Formatter();
      CompareNetcdf2 compare = new CompareNetcdf2(f, false, false, true);
      if (!compare.compare(org, withBuilder, new DimensionsFilter())) {
        System.out.printf("Compare %s%n%s%n", filename, f);
        fail();
      }
    }
  }
}
 

private void showNew(String filename) throws IOException {

    try (NetcdfFile withBuilder = NetcdfFiles.open(filename)) {
      // Variable v = withBuilder.findVariable("catchments_x");
      // Array data = v.read();
      System.out.printf("withBuilder = %s%n", withBuilder);
    }
  }
 

@Test
@Category(NeedsUcarNetwork.class)
public void testActiveScaleS3() throws IOException {
  // do not need credentials to run this one, just access to the internal ucar network.
  String host = "stratus.ucar.edu";
  String bucket = "rda-data";
  String key = "ds262.0/CERFACS/uo_Omon_NEMO3-2_FRCCORE2_f_r1i1p1_199801-200712.nc";
  String s3Uri = "cdms3://" + host + "/" + bucket + "?" + key;
  try (NetcdfFile ncfile = NetcdfFiles.open(s3Uri)) {
    Attribute conv = ncfile.findGlobalAttributeIgnoreCase("Conventions");
    assertThat(conv).isNotNull();
    assertThat(conv.getStringValue()).ignoringCase().isEqualTo("CF-1.4");
  }
}
 

@Test
@Category(NeedsUcarNetwork.class)
public void testActiveScaleWithCredsS3() throws IOException {
  String host = "stratus.ucar.edu";
  String bucket = "unidata-netcdf-zarr-testing";
  String key = "netcdf-java/test/GFS_Global_0p25deg_20200326_1200_apparent_temperature.nc4";
  String s3Uri = "cdms3://" + NCAR_PROFILE_NAME + "@" + host + "/" + bucket + "?" + key;
  try (NetcdfFile ncfile = NetcdfFiles.open(s3Uri)) {
    Attribute conv = ncfile.findGlobalAttributeIgnoreCase("Conventions");
    assertThat(conv).isNotNull();
    assertThat(conv.getStringValue()).ignoringCase().isEqualTo("CF-1.6");
  }
}
 

@Test
@Category(NeedsUcarNetwork.class)
public void ncarPartialReadFile() throws IOException, InvalidRangeException {
  try (NetcdfFile ncfile = NetcdfFiles.open(NCAR_G16_S3_URI)) {
    testPartialReadGoes16S3(ncfile);
  }
}
 

@Test
public void testEcmwfExtendedComplexData2() throws IOException {
  final String testfile = "../grib/src/test/data/complex_packing2.grib1";
  try (NetcdfFile nc = NetcdfFiles.open(testfile)) {

    Variable var = nc.findVariable("Snowfall_surface");
    Array data = var.read();

    float first = data.getFloat(0);

    Assert.assertEquals(.326607, first, 1e-6);
  }
}
 

private void openNetcdf(String filename) throws IOException {
  System.out.printf("%n***openNetcdf bufr %s%n", filename);
  try (NetcdfFile ncfile = NetcdfFiles.open(filename)) {
    if (show)
      System.out.printf("%s%n", ncfile);
  }
}
 

@Test
public void awsSharedCredsPrecedence() throws IOException {
  // Test that the region set in the custom shared credentials file takes precedence
  System.setProperty(AWS_REGION_PROP_NAME, Region.AP_SOUTH_1.id());
  System.setProperty(AWS_SHARED_CREDENTIALS_FILE_PROP, credentialsFileBadDefault);
  String cdmS3Uri = String.format("cdms3://%s@aws/noaa-goes16?", GOOD_PROFILE_NAME) + COMMON_G16_KEY;
  try (NetcdfFile ncfile = NetcdfFiles.open(cdmS3Uri)) {
    assertThat(ncfile).isNotNull();
  } finally {
    System.clearProperty(AWS_SHARED_CREDENTIALS_FILE_PROP);
    System.clearProperty(AWS_REGION_PROP_NAME);
  }
}
 

@Test
public void code5_assume_WGS84() throws IOException {
  String filename = dir + "Albers_viirs_s.grb2";
  try (NetcdfFile ncfile = NetcdfFiles.open(filename, null)) {
    Variable v = ncfile.findVariable("AlbersEqualArea_Projection");
    Attribute axis = v.findAttribute("semi_major_axis");
    Assert.assertEquals(6378137., axis.getNumericValue().doubleValue(), 0.1);
  }
}
 

@Override
public void readDataInfo(String fileName) {
    this.setFileName(fileName);
    try {
        //ncfile = NetcdfFile.open(fileName);
        //ncfile = NetcdfDatasets.openDataset(fileName);
        ncfile = NetcdfFiles.open(fileName);
        readDataInfo(false);
    } catch (IOException e) {
        e.printStackTrace();
    }
}
 

public static void subsetVariables(String filename, String varName, Section s)
    throws InvalidRangeException, IOException {
  System.out.println("testVariableSubset=" + filename + "," + varName);

  try (NetcdfFile ncfile = NetcdfFiles.open(filename)) {
    Variable v = ncfile.findVariable(varName);
    assert (null != v);
    subsetVariable(v, s, v.read());
  }
}
 

@Test
public void awsPartialReadFileSimple() throws IOException, InvalidRangeException {
  System.setProperty(AWS_REGION_PROP_NAME, AWS_G16_REGION);
  try (NetcdfFile ncfile = NetcdfFiles.open(AWS_G16_S3_URI_SIMPLE)) {
    testPartialReadGoes16S3(ncfile);
  } finally {
    System.clearProperty(AWS_REGION_PROP_NAME);
  }
}
 

@Test
public void osdcPartialReadFile() throws IOException, InvalidRangeException {
  try (NetcdfFile ncfile = NetcdfFiles.open(OSDC_G16_S3_URI)) {
    testPartialReadGoes16S3(ncfile);
  }
}
 

@Test
public void gcsPartialReadFile() throws IOException, InvalidRangeException {
  try (NetcdfFile ncfile = NetcdfFiles.open(GCS_G16_S3_URI)) {
    testPartialReadGoes16S3(ncfile);
  }
}
 

@Override
public int doAct(String filename) throws IOException {
  try (NetcdfFile ncfile = NetcdfFiles.open(filename)) {
    return readAllData(ncfile);
  }
}
 

@Test
public void writeTestFile() throws IOException, InvalidRangeException {
  // skip test requiring netcdf4 if not present.
  NetcdfFileWriter.Version version = NetcdfFormatWriter.convertToNetcdfFileWriterVersion(format);
  if (version.useJniIosp() && !Nc4Iosp.isClibraryPresent()) {
    return;
  }
  System.out.printf("Test Dataset %s type %s%n", endpoint, type);
  File tempFile = tempFolder.newFile();
  File tempFile2 = tempFolder.newFile();

  try (FeatureDatasetCoverage cc = CoverageDatasetFactory.open(endpoint)) {
    Assert.assertNotNull(endpoint, cc);
    CoverageCollection gcs = cc.findCoverageDataset(type);

    for (String covName : covList) {
      Assert.assertNotNull(covName, gcs.findCoverage(covName));
    }

    // write the file using CFGridCoverageWriter2
    System.out.printf(" CFGridCoverageWriter2 write to %s%n", tempFile2.getAbsolutePath());

    try (NetcdfFileWriter writer = NetcdfFileWriter
        .createNew(NetcdfFormatWriter.convertToNetcdfFileWriterVersion(format), tempFile2.getPath(), null)) {
      Optional<Long> estimatedSizeo = CFGridCoverageWriter2.write(gcs, covList, params, false, writer);
      if (!estimatedSizeo.isPresent()) {
        throw new InvalidRangeException("Request contains no data: " + estimatedSizeo.getErrorMessage());
      }
    }

    // write the file using CFGridCoverageWriter
    System.out.printf(" CFGridCoverageWriter write to %s%n", tempFile.getAbsolutePath());
    NetcdfFormatWriter.Builder writerb =
        NetcdfFormatWriter.builder().setNewFile(true).setFormat(format).setLocation(tempFile.getPath());
    NetcdfFormatWriter.Result result = CFGridCoverageWriter.write(gcs, covList, params, false, writerb, 0);
    if (!result.wasWritten()) {
      throw new InvalidRangeException("Error writing: " + result.getErrorMessage());
    }
  }

  // Compare that the files are identical
  try (NetcdfFile org = NetcdfFile.open(tempFile2.getPath())) {
    try (NetcdfFile copy = NetcdfFiles.open(tempFile.getPath())) {
      Formatter f = new Formatter();
      CompareNetcdf2 compare = new CompareNetcdf2(f, false, false, true);
      boolean ok = compare.compare(org, copy, new FileWritingObjFilter());
      System.out.printf("%s %s%n", ok ? "OK" : "NOT OK", f);
      assertThat(ok).isTrue();
    }
  }
}