Example #1
0
  @Test
  public void testNoValid2DVariable() throws Exception {
    final File file = TestData.file(this, "noVars.nc");
    NetcdfDataset dataset = NetcdfDataset.acquireDataset(file.getAbsolutePath(), null);
    List<Variable> variables = dataset.getVariables();
    boolean speedVariableIsPresent = false;
    String speedVariableName = "";

    for (Variable variable : variables) {
      if (variable.getShortName().equals("spd")) {
        speedVariableIsPresent = true;
        speedVariableName = variable.getFullName();
        break;
      }
    }

    assertTrue(speedVariableIsPresent);

    final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
    assertTrue(unidataImageReaderSpi.canDecodeInput(file));
    NetCDFImageReader reader = null;
    try {

      // sample dataset containing a water_speed variable having
      // only time, depth dimensions. No lon/lat dims are present
      // resulting into variable not usable.
      reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
      reader.setInput(file);
      final List<Name> names = reader.getCoveragesNames();

      boolean isSpeedCoverageAvailable = false;
      for (Name name : names) {
        if (name.toString().equals(speedVariableName)) {
          isSpeedCoverageAvailable = true;
          break;
        }
      }
      // Checking that only "mask" variable is found
      assertFalse(isSpeedCoverageAvailable);
    } finally {
      if (dataset != null) {
        dataset.close();
      }

      if (reader != null) {
        try {
          reader.dispose();
        } catch (Throwable t) {
          // Does nothing
        }
      }
    }
  }
Example #2
0
 public void testReadRegularNetCDF() throws IOException {
   NetCDFImageReaderSpi readerSpi = new NetCDFImageReaderSpi();
   File file = null;
   String name = "2DLatLonCoverageHDF5.nc";
   try {
     file = TestData.file(this, name);
   } catch (IOException e) {
     warnNoFile(name);
     return;
   }
   assertTrue(readerSpi.canDecodeInput(file));
 }
Example #3
0
  @Test
  public void testImageReaderPolyphemusSimple() throws Exception {
    final File file = TestData.file(this, "O3-NO2.nc");
    final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
    assertTrue(unidataImageReaderSpi.canDecodeInput(file));
    NetCDFImageReader reader = null;
    try {

      // checking low level
      reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
      reader.setInput(file);
      int numImages = reader.getNumImages(true);
      LOGGER.info("Found " + numImages + " images.");
      for (int i = 0; i < numImages; i++) {
        Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
        assertNotNull(sliceIndex);
        spitOutSliceInformation(i, sliceIndex);
      }

      // checking slice catalog
      final CoverageSlicesCatalog cs = reader.getCatalog();
      assertNotNull(cs);

      // get typenames
      final String[] typeNames = cs.getTypeNames();
      for (String typeName : typeNames) {
        final List<CoverageSlice> granules = cs.getGranules(new Query(typeName, Filter.INCLUDE));
        assertNotNull(granules);
        assertFalse(granules.isEmpty());
        for (CoverageSlice slice : granules) {
          final SimpleFeature sf = slice.getOriginator();
          if (TestData.isInteractiveTest()) {
            LOGGER.info(DataUtilities.encodeFeature(sf));
          }

          // checks
          for (Property p : sf.getProperties()) {
            assertNotNull("Property " + p.getName() + " had a null value!", p.getValue());
          }
        }
      }
    } finally {
      if (reader != null) {
        try {
          reader.dispose();
        } catch (Throwable t) {
          // Does nothing
        }
      }
    }
  }
Example #4
0
  @Test
  public void testImageReaderIASI() throws Exception {
    File file = null;
    try {
      file = TestData.file(this, "IASI_C_EUMP_20121120062959_31590_eps_o_l2.nc");
    } catch (IOException e) {
      LOGGER.warning("Unable to find file IASI_C_EUMP_20121120062959_31590_eps_o_l2.nc");
      return;
    }
    if (!file.exists()) {
      LOGGER.warning("Unable to find file IASI_C_EUMP_20121120062959_31590_eps_o_l2.nc");
      return;
    }
    final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
    assertTrue(unidataImageReaderSpi.canDecodeInput(file));
    NetCDFImageReader reader = null;
    try {
      reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
      reader.setInput(file);
      int numImages = reader.getNumImages(true);
      for (int i = 0; i < numImages; i++) {
        Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
        assertNotNull(sliceIndex);
        spitOutSliceInformation(i, sliceIndex);
      }

      // cloud_phase
      CoverageSourceDescriptor cd = reader.getCoverageDescriptor(new NameImpl("cloud_phase"));
      final List<AdditionalDomain> additionalDomains = cd.getAdditionalDomains();
      assertTrue(!additionalDomains.isEmpty());
      final AdditionalDomain ad = additionalDomains.get(0);
      assertTrue(ad.getType().equals(DomainType.NUMBER));
      assertEquals("cloud_phase", ad.getName());

    } finally {
      if (reader != null) {
        try {
          reader.dispose();
        } catch (Throwable t) {
          // Does nothing
        }
      }
    }
  }
Example #5
0
 @Test
 public void testReadNC4() throws IOException {
   NetCDFImageReaderSpi readerSpi = new NetCDFImageReaderSpi();
   boolean isNC4available = NetCDFUtilities.isNC4CAvailable();
   if (!isNC4available) {
     LOGGER.warning(
         "NetCDF4 reading test will be skipped due to "
             + "missing NetCDF C library.\nIf you want test to be executed, make sure you have "
             + "added the NetCDF C libraries location to the PATH environment variable");
     return;
   }
   String name = "temperatureisobaricNC4.nc";
   File file = null;
   try {
     file = TestData.file(this, name);
   } catch (IOException e) {
     warnNoFile(name);
     return;
   }
   assertTrue(readerSpi.canDecodeInput(file));
 }
Example #6
0
  @Test
  public void testImageReaderPolyphemunsComplex() throws Exception {
    File file = null;
    try {
      file = TestData.file(this, "polyphemus_20130301.nc");
    } catch (IOException e) {
      LOGGER.warning("Unable to find file polyphemus_20130301.nc");
      return;
    }
    if (!file.exists()) {
      LOGGER.warning("Unable to find file polyphemus_20130301.nc");
      return;
    }
    final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
    assertTrue(unidataImageReaderSpi.canDecodeInput(file));
    NetCDFImageReader reader = null;
    try {
      reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
      reader.setInput(file);
      int numImages = reader.getNumImages(true);
      assertEquals(1008, numImages);
      for (int i = 0; i < numImages; i++) {
        Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
        assertNotNull(sliceIndex);
        spitOutSliceInformation(i, sliceIndex);
      }

      // check coverage names
      final List<Name> names = reader.getCoveragesNames();
      assertNotNull(names);
      assertTrue(!names.isEmpty());
      assertTrue(3 == names.size());
      assertTrue(names.contains(new NameImpl("NO2")));
      assertTrue(names.contains(new NameImpl("O3")));
      assertTrue(names.contains(new NameImpl("V")));

      // checking slice catalog
      final CoverageSlicesCatalog cs = reader.getCatalog();
      assertNotNull(cs);

      // get typenames
      final String[] typeNames = cs.getTypeNames();
      for (String typeName : typeNames) {
        final List<CoverageSlice> granules = cs.getGranules(new Query(typeName, Filter.INCLUDE));
        assertNotNull(granules);
        assertFalse(granules.isEmpty());
        for (CoverageSlice slice : granules) {
          final SimpleFeature sf = slice.getOriginator();
          if (TestData.isInteractiveTest()) {
            LOGGER.info(DataUtilities.encodeFeature(sf));
          }

          // checks
          for (Property p : sf.getProperties()) {
            assertNotNull("Property " + p.getName() + " had a null value!", p.getValue());
          }
        }
      }
    } finally {
      if (reader != null) {
        try {
          reader.dispose();
        } catch (Throwable t) {
          // Does nothing
        }
      }
    }
  }
Example #7
0
  @Test
  public void testImageReaderPolyphemunsComplex2() throws Exception {
    File file = null;
    try {
      file = TestData.file(this, "polyphemus_20130301.nc");
    } catch (IOException e) {
      LOGGER.warning("Unable to find file polyphemus_20130301.nc");
      return;
    }
    if (!file.exists()) {
      LOGGER.warning("Unable to find file polyphemus_20130301.nc");
      return;
    }
    FileUtils.copyFile(file, new File(TestData.file(this, null), "polyphemus.nc"));
    file = TestData.file(this, "polyphemus.nc");
    final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
    assertTrue(unidataImageReaderSpi.canDecodeInput(file));
    NetCDFImageReader reader = null;
    try {
      reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
      reader.setInput(file);
      int numImages = reader.getNumImages(true);
      assertEquals(1008, numImages);
      for (int i = 0; i < numImages; i++) {
        Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
        assertNotNull(sliceIndex);
        spitOutSliceInformation(i, sliceIndex);
      }

      // check dimensions
      CoverageSourceDescriptor cd = reader.getCoverageDescriptor(new NameImpl("NO2"));
      final List<AdditionalDomain> additionalDomains = cd.getAdditionalDomains();
      assertNull(additionalDomains);

      final List<DimensionDescriptor> dimensions = cd.getDimensionDescriptors();
      assertNotNull(dimensions);
      assertTrue(!dimensions.isEmpty());
      assertEquals("wrong dimensions", 2, dimensions.size());
      DimensionDescriptor dim = dimensions.get(0);
      assertTrue(dim.getName().equals("TIME"));
      assertTrue(dim.getStartAttribute().equals("time"));
      dim = dimensions.get(1);
      assertTrue(dim.getName().equals("ELEVATION"));
      assertTrue(dim.getStartAttribute().equals("z"));

      // check coverage names
      final List<Name> names = reader.getCoveragesNames();
      assertNotNull(names);
      assertTrue(!names.isEmpty());
      assertTrue(3 == names.size());
      assertTrue(names.contains(new NameImpl("NO2")));
      assertTrue(names.contains(new NameImpl("O3")));
      assertTrue(names.contains(new NameImpl("V")));

      // checking slice catalog
      final CoverageSlicesCatalog cs = reader.getCatalog();
      assertNotNull(cs);

      // get typenames
      final String[] typeNames = cs.getTypeNames();
      for (String typeName : typeNames) {
        final List<CoverageSlice> granules = cs.getGranules(new Query(typeName, Filter.INCLUDE));
        assertNotNull(granules);
        assertFalse(granules.isEmpty());
        for (CoverageSlice slice : granules) {
          final SimpleFeature sf = slice.getOriginator();
          if (TestData.isInteractiveTest()) {
            LOGGER.info(DataUtilities.encodeFeature(sf));
          }

          // checks
          for (Property p : sf.getProperties()) {
            assertNotNull("Property " + p.getName() + " had a null value!", p.getValue());
          }
        }
      }
    } finally {

      // close reader
      if (reader != null) {
        try {
          reader.dispose();
        } catch (Throwable t) {
          // Does nothing
        }
      }

      // specific clean up
      FileUtils.deleteDirectory(TestData.file(this, ".polyphemus"));
    }
  }
Example #8
0
  @Test
  public void testImageReaderAscat() throws Exception {
    File file = null;
    try {
      file = TestData.file(this, "ascatl1.nc");
    } catch (IOException e) {
      LOGGER.warning("Unable to find file ascatl1.nc");
      return;
    }
    if (!file.exists()) {
      LOGGER.warning("Unable to find file ascatl1.nc");
      return;
    }
    final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
    assertTrue(unidataImageReaderSpi.canDecodeInput(file));
    NetCDFImageReader reader = null;
    try {
      reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
      reader.setInput(file);
      int numImages = reader.getNumImages(true);
      for (int i = 0; i < numImages; i++) {
        Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
        assertNotNull(sliceIndex);
        spitOutSliceInformation(i, sliceIndex);
      }

      // check coverage names
      final List<Name> names = reader.getCoveragesNames();
      assertNotNull(names);
      assertTrue(!names.isEmpty());
      assertTrue(2 == names.size());
      assertEquals("cell_index", names.get(0).toString());
      assertEquals("f_land", names.get(1).toString());

      // checking slice catalog
      final CoverageSlicesCatalog cs = reader.getCatalog();
      assertNotNull(cs);

      // get typenames
      final String[] typeNames = cs.getTypeNames();
      for (String typeName : typeNames) {
        final List<CoverageSlice> granules = cs.getGranules(new Query(typeName, Filter.INCLUDE));
        assertNotNull(granules);
        assertFalse(granules.isEmpty());
        for (CoverageSlice slice : granules) {
          final SimpleFeature sf = slice.getOriginator();
          if (TestData.isInteractiveTest()) {
            LOGGER.info(DataUtilities.encodeFeature(sf));
          }

          // checks
          for (Property p : sf.getProperties()) {
            final String pName = p.getName().toString();
            if (!pName.equalsIgnoreCase("time") && !pName.equalsIgnoreCase("elevation")) {
              assertNotNull("Property " + p.getName() + " had a null value!", p.getValue());
            } else {
              assertNull("Property " + p.getName() + " did not have a null value!", p.getValue());
            }
          }
        }
      }

    } finally {
      if (reader != null) {
        try {
          reader.dispose();
        } catch (Throwable t) {
          // Does nothing
        }
      }
    }
  }
Example #9
0
  @Test
  public void testImageReaderGOME2AncillaryFiles() throws Exception {
    final File file = TestData.file(this, "20130101.METOPA.GOME2.NO2.DUMMY.nc");
    final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
    assertTrue(unidataImageReaderSpi.canDecodeInput(file));
    NetCDFImageReader reader = null;
    try {

      // checking low level
      reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
      reader.setInput(file);
      int numImages = reader.getNumImages(true);
      assertEquals(1, numImages);
      LOGGER.info("Found " + numImages + " images.");
      for (int i = 0; i < numImages; i++) {
        Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
        assertNotNull(sliceIndex);
        spitOutSliceInformation(i, sliceIndex);
      }

      // check coverage names
      final List<Name> names = reader.getCoveragesNames();
      assertNotNull(names);
      assertTrue(!names.isEmpty());
      assertTrue(1 == names.size());
      assertEquals("NO2", names.get(0).toString());

      // checking slice catalog
      final CoverageSlicesCatalog cs = reader.getCatalog();
      assertNotNull(cs);

      MessageDigest md = MessageDigest.getInstance("SHA-1");
      md.update(file.getCanonicalPath().getBytes());
      String hashCode = AncillaryFileManager.convertToHex(md.digest());

      // Check if the auxiliary files directory is present
      File parentDir = file.getParentFile();

      String auxiliaryDirPath =
          parentDir
              + File.separator
              + "."
              + FilenameUtils.getBaseName(file.getName())
              + "_"
              + hashCode;

      File auxiliaryDir = new File(auxiliaryDirPath);

      assertTrue(auxiliaryDir.exists());
      assertTrue(auxiliaryDir.isDirectory());

      // Check if the Auxiliary File Directory contains the origin.txt file
      FilenameFilter nameFileFilter = FileFilterUtils.nameFileFilter("origin.txt");
      File[] files = auxiliaryDir.listFiles(nameFileFilter);
      assertTrue(files != null);
      assertTrue(files[0].exists());
    } finally {
      if (reader != null) {
        try {
          reader.dispose();
        } catch (Throwable t) {
          // Does nothing
        }
      }
    }
  }