Java Code Examples for ucar.nc2.dataset.NetcdfDataset#Enhance

/**
 * Add a dataset scan
 *
 * @param crawlableDatasetElement defines a CrawlableDataset, or null
 * @param dirName scan this directory
 * @param suffix filter on this suffix (may be null)
 * @param regexpPatternString include if full name matches this regular expression (may be null)
 * @param dateFormatMark create dates from the filename (may be null)
 * @param enhanceMode how should files be enhanced
 * @param subdirs equals "false" if should not descend into subdirectories
 * @param olderThan files must be older than this time (now - lastModified >= olderThan); must be a time unit, may ne
 *        bull
 */
public void addDatasetScan(Element crawlableDatasetElement, String dirName, String suffix, String regexpPatternString,
    String dateFormatMark, Set<NetcdfDataset.Enhance> enhanceMode, String subdirs, String olderThan) {

  datasetManager.addDirectoryScan(dirName, suffix, regexpPatternString, subdirs, olderThan, enhanceMode);

  this.dateFormatMark = dateFormatMark;
  if (dateFormatMark != null) {
    isDate = true;
    if (type == Type.joinExisting)
      type = Type.joinExistingOne; // tricky
    DateExtractor dateExtractor = new DateExtractorFromName(dateFormatMark, true);
    datasetManager.setDateExtractor(dateExtractor);
  }
}
 

protected AggDataset(MFile mfile, @Nullable Object spiObject, @Nullable Element ncmlElem) {
  this.mfile = mfile;
  this.cacheLocation = mfile.getPath();
  Set<NetcdfDataset.Enhance> wantEnhance = (Set<NetcdfDataset.Enhance>) mfile.getAuxInfo();
  this.enhance = (wantEnhance == null) ? NetcdfDataset.getEnhanceNone() : wantEnhance;
  this.id = null;
  this.reader = null;
  this.spiObject = spiObject;
  this.ncmlElem = ncmlElem;
}
 

/**
 * Add a dataset scan
 *
 * @param crawlableDatasetElement defines a CrawlableDataset, or null
 * @param dirName scan this directory
 * @param suffix filter on this suffix (may be null)
 * @param regexpPatternString include if full name matches this regular expression (may be null)
 * @param dateFormatMark create dates from the filename (may be null)
 * @param enhanceMode how should files be enhanced
 * @param subdirs equals "false" if should not descend into subdirectories
 * @param olderThan files must be older than this time (now - lastModified >= olderThan); must be a time unit, may ne
 *        bull
 */
public void addDatasetScan(Element crawlableDatasetElement, String dirName, String suffix, String regexpPatternString,
    String dateFormatMark, Set<NetcdfDataset.Enhance> enhanceMode, String subdirs, String olderThan) {

  datasetManager.addDirectoryScan(dirName, suffix, regexpPatternString, subdirs, olderThan, enhanceMode);

  this.dateFormatMark = dateFormatMark;
  if (dateFormatMark != null) {
    isDate = true;
    if (type == Type.joinExisting)
      type = Type.joinExistingOne; // tricky
    DateExtractor dateExtractor = new DateExtractorFromName(dateFormatMark, true);
    datasetManager.setDateExtractor(dateExtractor);
  }
}
 

/**
 * Returns all grid geometries (related to coordinate systems) found in the netCDF file.
 * This method returns a direct reference to an internal array - do not modify.
 *
 * @return all grid geometries, or an empty array if none.
 * @throws IOException if an I/O operation was necessary but failed.
 */
@Override
@SuppressWarnings({"ReturnOfCollectionOrArrayField", "null"})
public Grid[] getGrids() throws IOException {
    if (geometries == null) {
        List<CoordinateSystem> systems = null;
        if (file instanceof NetcdfDataset) {
            final NetcdfDataset ds = (NetcdfDataset) file;
            final EnumSet<NetcdfDataset.Enhance> mode = EnumSet.copyOf(ds.getEnhanceMode());
            if (mode.add(NetcdfDataset.Enhance.CoordSystems)) {
                /*
                 * Should not happen with NetcdfDataset opened by the constructor expecting a filename,
                 * because that constructor already enhanced the dataset. It may happen however if the
                 * NetcdfDataset was given explicitly by the user. We try to increase the chances to
                 * get information we need, but it is not guaranteed to work; it may be too late if we
                 * already started to use the NetcdfDataset before this point.
                 */
                ds.enhance(mode);
            }
            systems = ds.getCoordinateSystems();
            /*
             * If the UCAR library does not see any coordinate system in the file, verify if there is
             * a custom convention recognizing the axes. CSBuilderFallback uses the mechanism defined
             * by Apache SIS for determining variable role.
             */
            if (systems.isEmpty() && convention() != Convention.DEFAULT) {
                final CSBuilderFallback builder = new CSBuilderFallback(this);
                builder.buildCoordinateSystems(ds);
                systems = ds.getCoordinateSystems();
            }
        }
        geometries = new Grid[(systems != null) ? systems.size() : 0];
        for (int i=0; i<geometries.length; i++) {
            geometries[i] = new GridWrapper(systems.get(i));
        }
    }
    return geometries;
}
 

protected Dataset(MFile mfile) {
  this.mfile = mfile;
  this.cacheLocation = mfile.getPath();
  this.enhance = (Set<NetcdfDataset.Enhance>) mfile.getAuxInfo();
}
 

@Override
protected Dataset makeDataset(String cacheName, String location, String id, String ncoordS, String coordValueS,
    String sectionSpec, EnumSet<NetcdfDataset.Enhance> enhance, ucar.nc2.util.cache.FileFactory reader) {
  return new DatasetOuterDimension(cacheName, location, id, ncoordS, coordValueS, enhance, reader);
}
 

@Override
protected Dataset makeDataset(String cacheName, String location, String id, String ncoordS, String coordValueS,
    String sectionSpec, EnumSet<NetcdfDataset.Enhance> enhance, ucar.nc2.util.cache.FileFactory reader) {
  return new DatasetTiled(cacheName, location, id, sectionSpec, enhance, reader);
}
 

/**
 * parse a netcdf JDOM Element, and add contents to the targetDS NetcdfDataset.
 * <p/>
 * This is a bit tricky, because it handles several cases When targetDS == refds, we are just modifying targetDS. When
 * targetDS != refds,
 * we keep them seperate, and copy from refds to newds.
 * <p/>
 * The user may be defining new elements or modifying old ones. The only way to tell is by seeing if the elements
 * already exist.
 *
 * @param ncmlLocation NcML URL location, or may be just a unique name for caching purposes.
 * @param builder add the info to this one
 * @param netcdfElem JDOM netcdf element
 * @param cancelTask allow user to cancel the task; may be null
 * @throws IOException on read error
 */
private void readNetcdf(String ncmlLocation, NetcdfDataset.Builder builder, Element netcdfElem,
    @Nullable CancelTask cancelTask) throws IOException {
  this.location = ncmlLocation; // log messages need this

  // detect incorrect namespace
  Namespace use = netcdfElem.getNamespace();
  if (!use.equals(ncNSHttp) && !use.equals(ncNSHttps)) {
    String message = String.format("Namespace specified in NcML must be either '%s' or '%s', but was '%s'.",
        ncNSHttp.getURI(), ncNSHttps.getURI(), use.getURI());
    throw new IllegalArgumentException(message);
  }

  if (ncmlLocation != null) {
    builder.setLocation(ncmlLocation);
  }
  builder.setId(netcdfElem.getAttributeValue("id"));
  builder.setTitle(netcdfElem.getAttributeValue("title"));

  Element aggElem = netcdfElem.getChild("aggregation", ncNS);
  if (aggElem != null) {
    Aggregation agg = readAgg(aggElem, ncmlLocation, builder, cancelTask);
    builder.setAggregation(agg);
    agg.build(cancelTask);

    // LOOK seems like we should add the agg metadata here, so that it can be modified.
  }

  // read the root group and recurse
  readGroup(builder, null, null, netcdfElem);
  String errors = errlog.toString();
  if (!errors.isEmpty()) {
    throw new IllegalArgumentException("NcML had fatal errors:" + errors);
  }

  // enhance means do scale/offset and/or add CoordSystems
  Set<NetcdfDataset.Enhance> mode = parseEnhanceMode(netcdfElem.getAttributeValue("enhance"));
  if (mode != null) {
    // cant just set enhance mode
    if (DatasetEnhancer.enhanceNeeded(mode, null)) {
      DatasetEnhancer enhancer = new DatasetEnhancer(builder, mode, cancelTask);
      enhancer.enhance();
      builder.setEnhanceMode(mode);
    }
  }

  /*
   * LOOK optionally add record structure to netcdf-3
   * String addRecords = netcdfElem.getAttributeValue("addRecords");
   * if ("true".equalsIgnoreCase(addRecords))
   * targetDS.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);
   */
}
 

@Override
protected AggDataset makeDataset(String cacheName, String location, String id, String ncoordS, String coordValueS,
    String sectionSpec, EnumSet<NetcdfDataset.Enhance> enhance, ucar.nc2.util.cache.FileFactory reader) {
  return new AggDatasetOuter(this, cacheName, location, id, ncoordS, coordValueS, enhance, reader);
}
 

private void showModes(Set<NetcdfDataset.Enhance> modes) {
  for (NetcdfDataset.Enhance mode : modes) {
    System.out.printf("%s,", mode);
  }
  System.out.printf("%n");
}
 

/**
 * Dataset constructor.
 * With this constructor, the actual opening of the dataset is deferred, and done by the reader.
 * Used with explicit netcdf elements, and scanned files.
 *
 * @param cacheLocation a unique name to use for caching
 * @param location attribute "location" on the netcdf element
 * @param id attribute "id" on the netcdf element
 * @param enhance open dataset in enhance mode, may be null NOT USED
 * @param reader factory for reading this netcdf dataset; if null, use NetcdfDataset.open( location)
 */
protected Dataset(String cacheLocation, String location, String id, EnumSet<NetcdfDataset.Enhance> enhance,
    ucar.nc2.util.cache.FileFactory reader) {
  this.mfile = MFileOS.getExistingFile(location);
  this.cacheLocation = cacheLocation;
  this.id = id;
  // this.enhance = enhance; // LOOK why ??
  this.reader = reader;
}
 

/**
 * Dataset constructor.
 * With this constructor, the actual opening of the dataset is deferred, and done by the reader.
 * Used with explicit netcdf elements, and scanned files.
 *
 * @param cacheName a unique name to use for caching
 * @param location attribute "location" on the netcdf element
 * @param id attribute "id" on the netcdf element
 * @param sectionSpec attribute "sectionSpec" on the netcdf element
 * @param enhance open dataset in enhance mode
 * @param reader factory for reading this netcdf dataset; if null, use NetcdfDataset.open( location)
 */
protected DatasetTiled(String cacheName, String location, String id, String sectionSpec,
    EnumSet<NetcdfDataset.Enhance> enhance, ucar.nc2.util.cache.FileFactory reader) {
  super(cacheName, location, id, enhance, reader);
  this.sectionSpec = sectionSpec;

  try {
    section = new Section(sectionSpec);
  } catch (InvalidRangeException e) {
    throw new IllegalArgumentException(e);
  }
}
 

/**
 * Dataset factory, so subclasses can override
 *
 * @param cacheName a unique name to use for caching
 * @param location attribute "location" on the netcdf element
 * @param id attribute "id" on the netcdf element
 * @param ncoordS attribute "ncoords" on the netcdf element
 * @param coordValueS attribute "coordValue" on the netcdf element
 * @param sectionSpec attribute "sectionSpec" on the netcdf element
 * @param enhance open dataset in enhance mode NOT USED
 * @param reader factory for reading this netcdf dataset
 * @return a Aggregation.Dataset
 */
protected Dataset makeDataset(String cacheName, String location, String id, String ncoordS, String coordValueS,
    String sectionSpec, EnumSet<NetcdfDataset.Enhance> enhance, ucar.nc2.util.cache.FileFactory reader) {
  return new Dataset(cacheName, location, id, enhance, reader); // overridden in OuterDim, tiled
}
 

/**
 * Dataset factory, so subclasses can override
 *
 * @param cacheName a unique name to use for caching
 * @param location attribute "location" on the netcdf element
 * @param id attribute "id" on the netcdf element
 * @param ncoordS attribute "ncoords" on the netcdf element
 * @param coordValueS attribute "coordValue" on the netcdf element
 * @param sectionSpec attribute "sectionSpec" on the netcdf element
 * @param enhance open dataset in enhance mode NOT USED
 * @param reader factory for reading this netcdf dataset
 * @return a Dataset
 */
protected AggDataset makeDataset(String cacheName, String location, String id, String ncoordS, String coordValueS,
    String sectionSpec, EnumSet<NetcdfDataset.Enhance> enhance, ucar.nc2.util.cache.FileFactory reader) {
  return new AggDataset(cacheName, location, id, enhance, reader, spiObject, ncmlElem); // overridden in OuterDim,
                                                                                        // tiled
}