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

@Test
public void testUnsignedWrap() throws IOException {
  String ncml = "<?xml version='1.0' encoding='UTF-8'?>\n"
      + "<netcdf xmlns='http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2' location='"
      + TestDir.cdmLocalTestDataDir + "testWrite.nc'>\n" + "  <variable name='bvar' shape='lat' type='byte'>\n"
      + "    <attribute name='_Unsigned' value='true' />\n"
      + "    <attribute name='scale_factor' type='float' value='2.0' />\n" + "   </variable>\n" + "</netcdf>";

  try (NetcdfFile ncfile = NcMLReader.readNcML(new StringReader(ncml), null);
      NetcdfFile ncd = NetcdfDataset.wrap(ncfile, NetcdfDataset.getEnhanceAll())) {

    Variable v = ncd.findVariable("bvar");
    Assert.assertNotNull(v);
    Assert.assertEquals(DataType.FLOAT, v.getDataType());

    boolean hasSigned = false;
    Array data = v.read();
    while (data.hasNext()) {
      float b = data.nextFloat();
      if (b < 0)
        hasSigned = true;
    }
    Assert.assertTrue(!hasSigned);
  }
}
 

@Test
public void testVarWithUnsignedAttribute() throws IOException {
  String ncml = "<?xml version='1.0' encoding='UTF-8'?>\n"
      + "<netcdf xmlns='http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2' location='"
      + TestDir.cdmLocalTestDataDir + "testWrite.nc'>\n" + "  <variable name='bvar' shape='lat' type='byte'>\n"
      + "    <attribute name='_Unsigned' value='true' />\n" + "   </variable>\n" + "</netcdf>";

  try (NetcdfFile ncfile = NcMLReader.readNcML(new StringReader(ncml), null);
      NetcdfFile ncd = NetcdfDataset.wrap(ncfile, NetcdfDataset.getEnhanceAll())) {

    Variable v = ncd.findVariable("bvar");
    Assert.assertNotNull(v);
    Assert.assertEquals(DataType.USHORT, v.getDataType());

    boolean hasSigned = false;
    Array data = v.read();
    while (data.hasNext()) {
      float b = data.nextFloat();
      if (b < 0)
        hasSigned = true;
    }
    Assert.assertTrue(!hasSigned);
  }
}
 

@Test
public void testVarWithUnsignedType() throws IOException {
  String ncml = "<?xml version='1.0' encoding='UTF-8'?>\n"
      + "<netcdf xmlns='http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2' location='"
      + TestDir.cdmLocalTestDataDir + "testWrite.nc'>\n" + "  <variable name='bvar' shape='lat' type='ubyte'/>"
      + "</netcdf>";

  try (NetcdfFile ncfile = NcMLReader.readNcML(new StringReader(ncml), null);
      NetcdfFile ncd = NetcdfDataset.wrap(ncfile, NetcdfDataset.getEnhanceAll())) {

    Variable v = ncd.findVariable("bvar");
    Assert.assertNotNull(v);
    Assert.assertEquals(DataType.USHORT, v.getDataType());

    boolean hasSigned = false;
    Array data = v.read();
    while (data.hasNext()) {
      float b = data.nextFloat();
      if (b < 0)
        hasSigned = true;
    }
    Assert.assertTrue(!hasSigned);
  }
}
 

@Test
public void testAttWithUnsignedType() throws IOException {
  String ncml = "<?xml version='1.0' encoding='UTF-8'?>\n"
      + "<netcdf xmlns='http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2' location='"
      + TestDir.cdmLocalTestDataDir + "testWrite.nc'>\n" + "  <attribute name='gatt' type='ubyte'>1 0 -1</attribute>"
      + "</netcdf>";

  try (NetcdfFile ncfile = NcMLReader.readNcML(new StringReader(ncml), null);
      NetcdfFile ncd = NetcdfDataset.wrap(ncfile, NetcdfDataset.getEnhanceAll())) {

    Attribute att = ncd.findGlobalAttribute("gatt");
    Assert.assertNotNull(att);
    Assert.assertEquals(DataType.UBYTE, att.getDataType());

    Assert.assertEquals(3, att.getLength());
    Array gattValues = att.getValues();

    boolean hasSigned = false;
    while (gattValues.hasNext()) {
      short b = gattValues.nextShort();
      if (b < 0)
        hasSigned = true;
    }
    Assert.assertTrue(!hasSigned);
  }
}
 

@Test
public void testAttWithUnsignedAtt() throws IOException {
  String ncml = "<?xml version='1.0' encoding='UTF-8'?>\n"
      + "<netcdf xmlns='http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2' location='"
      + TestDir.cdmLocalTestDataDir + "testWrite.nc'>\n"
      + "  <attribute name='gatt' type='byte' isUnsigned='true'>1 0 -1</attribute>" + "</netcdf>";

  try (NetcdfFile ncfile = NcMLReader.readNcML(new StringReader(ncml), null);
      NetcdfFile ncd = NetcdfDataset.wrap(ncfile, NetcdfDataset.getEnhanceAll())) {

    Attribute att = ncd.findGlobalAttribute("gatt");
    Assert.assertNotNull(att);
    Assert.assertEquals(DataType.UBYTE, att.getDataType());

    Assert.assertEquals(3, att.getLength());
    Array gattValues = att.getValues();

    boolean hasSigned = false;
    while (gattValues.hasNext()) {
      short b = gattValues.nextShort();
      if (b < 0)
        hasSigned = true;
    }
    Assert.assertTrue(!hasSigned);
  }
}
 

@Test
public void testAttWithUnsignedType2() throws IOException {
  String ncml = "<?xml version='1.0' encoding='UTF-8'?>\n"
      + "<netcdf xmlns='http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2' location='"
      + TestDir.cdmLocalTestDataDir + "testWrite.nc'>\n" + "  <attribute name='gatt' type='ubyte' value='1 0 -1' />"
      + "</netcdf>";

  try (NetcdfFile ncfile = NcMLReader.readNcML(new StringReader(ncml), null);
      NetcdfFile ncd = NetcdfDataset.wrap(ncfile, NetcdfDataset.getEnhanceAll())) {

    Attribute att = ncd.findGlobalAttribute("gatt");
    Assert.assertNotNull(att);
    Assert.assertEquals(DataType.UBYTE, att.getDataType());

    Assert.assertEquals(3, att.getLength());
    Array gattValues = att.getValues();

    boolean hasSigned = false;
    while (gattValues.hasNext()) {
      short b = gattValues.nextShort();
      if (b < 0)
        hasSigned = true;
    }
    Assert.assertTrue(!hasSigned);
  }
}
 

@Override
protected void dispatchWmsRequest(String request, RequestParams params, HttpServletRequest httpServletRequest,
    HttpServletResponse httpServletResponse, WmsCatalogue catalogue) throws Exception {
  /*
   * The super implementation of this gets called with a servlet-wide
   * catalogue, which "should" have been injected with the
   * WmsServlet.setCatalogue() method. Since we want one catalogue per
   * dataset, we never call setCatalogue(), but instead we generate a
   * WmsCatalogue (or more likely in a final version, retrieve a cached
   * one) on each request, and pass that to the super implementation.
   */

  /*
   * Map the request to a file path
   */
  // Look - is setting this to null the right thing to do??
  String removePrefix = null;
  TdsRequestedDataset tdsDataset = new TdsRequestedDataset(httpServletRequest, removePrefix);
  if (catalogueCache.containsKey(tdsDataset.getPath())) {
    catalogue = catalogueCache.get(tdsDataset.getPath());
  } else {
    NetcdfFile ncf = tdsDataset.getNetcdfFile(httpServletRequest, httpServletResponse, tdsDataset.getPath());
    NetcdfDataset ncd;
    if (tdsDataset.useNetcdfJavaBuilders()) {
      ncd = NetcdfDatasets.enhance(ncf, NetcdfDataset.getDefaultEnhanceMode(), null);
    } else {
      ncd = NetcdfDataset.wrap(ncf, NetcdfDataset.getDefaultEnhanceMode());
    }

    String netcdfFilePath = ncf.getLocation();

    /*
     * Generate a new catalogue for the given dataset
     * 
     * In the full system, we should keep a cache of these
     * ThreddsWmsCatalogues, but in this example we just create each new one
     * on the fly.
     * 
     * If a feature cache is required on the WMS (a Good Idea), I recommend
     * a single cache in this servlet which gets passed to each WmsCatalogue
     * upon construction (i.e. HERE). That's a TDS implementation detail
     * though, hence not in this example.
     */
    if (netcdfFilePath == null) {
      throw new EdalLayerNotFoundException("The requested dataset is not available on this server");
    }
    catalogue = new ThreddsWmsCatalogue(ncd, tdsDataset.getPath());
    catalogueCache.put(tdsDataset.getPath(), catalogue);
  }

  /*
   * Now that we've got a WmsCatalogue, we can pass this request to the
   * super implementation which will handle things from here.
   */
  super.dispatchWmsRequest(request, params, httpServletRequest, httpServletResponse, catalogue);
}
 

/**
 * Open a file as a GridDataset, using getNetcdfFile(), so that it gets wrapped in NcML if needed.
 */
// return null means request has been handled, and calling routine should exit without further processing
public GridDataset openGridDataset(HttpServletRequest req, HttpServletResponse res, String reqPath)
    throws IOException {
  // first look for a feature collection
  DataRootManager.DataRootMatch match = dataRootManager.findDataRootMatch(reqPath);
  if ((match != null) && (match.dataRoot.getFeatureCollection() != null)) {
    // see if its under resource control
    if (!resourceAuthorized(req, res, match.dataRoot.getRestrict()))
      return null;

    FeatureCollectionRef featCollection = match.dataRoot.getFeatureCollection();
    if (log.isDebugEnabled())
      log.debug("  -- DatasetHandler found FeatureCollection= " + featCollection);

    InvDatasetFeatureCollection fc = featureCollectionCache.get(featCollection);
    GridDataset gds = fc.getGridDataset(match.remaining);
    if (gds == null)
      throw new FileNotFoundException(reqPath);
    return gds;
  }

  // fetch it as a NetcdfFile; this deals with possible NcML
  NetcdfFile ncfile = openNetcdfFile(req, res, reqPath);
  if (ncfile == null)
    return null;

  NetcdfDataset ncd = null;
  try {
    // Convert to NetcdfDataset
    if (useNetcdfJavaBuilders || isLocationObjectStore(ncfile.getLocation())) {
      ncd = NetcdfDatasets.enhance(ncfile, NetcdfDataset.getDefaultEnhanceMode(), null);
    } else {
      ncd = NetcdfDataset.wrap(ncfile, NetcdfDataset.getDefaultEnhanceMode());
    }
    return new ucar.nc2.dt.grid.GridDataset(ncd);


  } catch (Throwable t) {
    if (ncd == null)
      ncfile.close();
    else
      ncd.close();

    if (t instanceof IOException)
      throw (IOException) t;

    String msg = ncd == null ? "Problem wrapping NetcdfFile in NetcdfDataset"
        : "Problem creating GridDataset from NetcdfDataset";
    log.error("openGridDataset(): " + msg, t);
    throw new IOException(msg + t.getMessage());
  }
}
 

public FeatureDatasetPoint openPointDataset(HttpServletRequest req, HttpServletResponse res, String reqPath)
    throws IOException {
  // first look for a feature collection
  DataRootManager.DataRootMatch match = dataRootManager.findDataRootMatch(reqPath);
  if ((match != null) && (match.dataRoot.getFeatureCollection() != null)) {
    // see if its under resource control
    if (!resourceAuthorized(req, res, match.dataRoot.getRestrict()))
      return null;

    FeatureCollectionRef featCollection = match.dataRoot.getFeatureCollection();
    if (log.isDebugEnabled())
      log.debug("  -- DatasetHandler found FeatureCollection= " + featCollection);

    InvDatasetFeatureCollection fc = featureCollectionCache.get(featCollection);
    FeatureDatasetPoint fd = fc.getPointDataset(match.remaining);
    if (fd == null)
      throw new IllegalArgumentException("Not a Point Dataset " + fc.getName());
    return fd;
  }

  // fetch it as a NetcdfFile; this deals with possible NcML
  NetcdfFile ncfile = openNetcdfFile(req, res, reqPath);
  if (ncfile == null)
    return null;

  Formatter errlog = new Formatter();
  NetcdfDataset ncd = null;
  try {
    if (useNetcdfJavaBuilders || isLocationObjectStore(ncfile.getLocation())) {
      ncd = NetcdfDatasets.enhance(ncfile, NetcdfDataset.getDefaultEnhanceMode(), null);
    } else {
      ncd = NetcdfDataset.wrap(ncfile, NetcdfDataset.getDefaultEnhanceMode());
    }
    return (FeatureDatasetPoint) FeatureDatasetFactoryManager.wrap(FeatureType.ANY_POINT, ncd, null, errlog);

  } catch (Throwable t) {
    if (ncd == null)
      ncfile.close();
    else
      ncd.close();

    if (t instanceof IOException)
      throw (IOException) t;

    String msg = ncd == null ? "Problem wrapping NetcdfFile in NetcdfDataset; "
        : "Problem calling FeatureDatasetFactoryManager; ";
    msg += errlog.toString();
    log.error("openGridDataset(): " + msg, t);
    throw new IOException(msg + t.getMessage());
  }
}
 

public SimpleGeometryFeatureDataset openSimpleGeometryDataset(HttpServletRequest req, HttpServletResponse res,
    String reqPath) throws IOException {
  // first look for a feature collection
  DataRootManager.DataRootMatch match = dataRootManager.findDataRootMatch(reqPath);
  if ((match != null) && (match.dataRoot.getFeatureCollection() != null)) {
    // see if its under resource control
    if (!resourceAuthorized(req, res, match.dataRoot.getRestrict()))
      return null;

    FeatureCollectionRef featCollection = match.dataRoot.getFeatureCollection();
    if (log.isDebugEnabled())
      log.debug("  -- DatasetHandler found FeatureCollection= " + featCollection);

    InvDatasetFeatureCollection fc = featureCollectionCache.get(featCollection);
    SimpleGeometryFeatureDataset fd = fc.getSimpleGeometryDataset(match.remaining);
    if (fd == null)
      throw new IllegalArgumentException("Not a Simple Geometry Dataset " + fc.getName());
    return fd;
  }

  // fetch it as a NetcdfFile; this deals with possible NcML
  NetcdfFile ncfile = openNetcdfFile(req, res, reqPath);
  if (ncfile == null)
    return null;

  Formatter errlog = new Formatter();
  NetcdfDataset ncd = null;
  try {
    if (useNetcdfJavaBuilders || isLocationObjectStore(ncfile.getLocation())) {
      ncd = NetcdfDatasets.enhance(ncfile, NetcdfDataset.getDefaultEnhanceMode(), null);
    } else {
      ncd = NetcdfDataset.wrap(ncfile, NetcdfDataset.getDefaultEnhanceMode());
    }
    return (SimpleGeometryFeatureDataset) FeatureDatasetFactoryManager.wrap(FeatureType.SIMPLE_GEOMETRY, ncd, null,
        errlog);

  } catch (Throwable t) {
    if (ncd == null)
      ncfile.close();
    else
      ncd.close();

    if (t instanceof IOException)
      throw (IOException) t;

    String msg = ncd == null ? "Problem wrapping NetcdfFile in NetcdfDataset; "
        : "Problem calling FeatureDatasetFactoryManager; ";
    msg += errlog.toString();
    log.error("openSimpleGeometryDataset(): " + msg, t);
    throw new IOException(msg + t.getMessage());
  }
}