Java Code Examples for ucar.unidata.io.RandomAccessFile#close()

/**
 * Open the service provider for reading.
 *
 * @param raf file to read from
 * @param ncfile netCDF file we are writing to (memory)
 * @param cancelTask task for cancelling
 * @throws IOException problem reading file
 */
public void open(RandomAccessFile raf, NetcdfFile ncfile, CancelTask cancelTask) throws IOException {
  super.open(raf, ncfile, cancelTask);

  if (areaReader == null)
    areaReader = new AreaReader();

  try {
    areaReader.init(raf.getLocation(), ncfile);

  } catch (Throwable e) {
    close(); // try not to leak files
    throw new IOException(e);

  } finally {
    raf.close(); // avoid leaks
  }

}
 

/**
 * Open a RandomAccessFile as a NetcdfFile, if possible.
 *
 * @param raf The open raf, is not cloised by this method.
 * @param location human readable locatoin of this dataset.
 * @param cancelTask used to monitor user cancellation; may be null.
 * @param iospMessage send this message to iosp; may be null.
 * @return NetcdfFile or throw an Exception.
 * @throws IOException if cannot open as a CDM NetCDF.
 * @deprecated use NetcdfFiles.open
 */
@Deprecated
public static NetcdfFile open(RandomAccessFile raf, String location, CancelTask cancelTask, Object iospMessage)
    throws IOException {

  IOServiceProvider spi = getIosp(raf);
  if (spi == null) {
    raf.close();
    throw new IOException("Cant read " + location + ": not a valid CDM file.");
  }

  // send iospMessage before the iosp is opened
  if (iospMessage != null)
    spi.sendIospMessage(iospMessage);

  if (log.isDebugEnabled())
    log.debug("Using IOSP {}", spi.getClass().getName());

  NetcdfFile result = new NetcdfFile(spi, raf, location, cancelTask);

  // send iospMessage after iosp is opened
  if (iospMessage != null)
    spi.sendIospMessage(iospMessage);

  return result;
}
 

/**
 *
 */
public void setNcStreamFile(String filename) throws IOException {
  closeOpenFiles();

  List<MessBean> messages = new ArrayList<>();
  ncd = new NetcdfFileSubclass();
  iosp = new NcStreamIosp();
  try {
    raf = new RandomAccessFile(filename, "r");
    List<NcStreamIosp.NcsMess> ncm = new ArrayList<>();
    iosp.openDebug(raf, ncd, ncm);
    for (NcStreamIosp.NcsMess m : ncm) {
      messages.add(new MessBean(m));
    }
  } finally {
    if (raf != null) {
      raf.close();
    }
  }

  messTable.setBeans(messages);
  // System.out.printf("mess = %d%n", messages.size());
}
 

private void doDuplicatePds(Formatter f, MFile mfile) throws IOException {
  Set<Long> pdsMap = new HashSet<>();
  int dups = 0;
  int count = 0;

  RandomAccessFile raf = new RandomAccessFile(mfile.getPath(), "r");
  Grib2RecordScanner scan = new Grib2RecordScanner(raf);
  while (scan.hasNext()) {
    ucar.nc2.grib.grib2.Grib2Record gr = scan.next();
    Grib2SectionProductDefinition pds = gr.getPDSsection();
    long crc = pds.calcCRC();
    if (pdsMap.contains(crc))
      dups++;
    else
      pdsMap.add(crc);
    count++;
  }
  raf.close();

  f.format("PDS duplicates = %d / %d for %s%n%n", dups, count, mfile.getPath());
  countPDS += count;
  countPDSdup += dups;
}
 

public static GribCollectionImmutable openGribCollectionFromRaf(RandomAccessFile raf, FeatureCollectionConfig config,
    CollectionUpdateType updateType, org.slf4j.Logger logger) throws IOException {

  GribCollectionImmutable result;

  // check if its a plain ole GRIB1/2 data file
  boolean isGrib1 = false;
  boolean isGrib2 = Grib2RecordScanner.isValidFile(raf);
  if (!isGrib2)
    isGrib1 = Grib1RecordScanner.isValidFile(raf);

  if (isGrib1 || isGrib2) {
    result = openGribCollectionFromDataFile(isGrib1, raf, config, updateType, null, logger);
    // close the data file, the ncx raf file is managed by gribCollection
    raf.close();

  } else { // check its an ncx file
    result = openGribCollectionFromIndexFile(raf, config, logger);
  }

  return result;
}
 

private void doDrsSummaryScan(Formatter f, MFile mf, boolean extra, Counters counters) throws IOException {
  RandomAccessFile raf = new RandomAccessFile(mf.getPath(), "r");
  Grib2RecordScanner scan = new Grib2RecordScanner(raf);
  while (scan.hasNext()) {
    ucar.nc2.grib.grib2.Grib2Record gr = scan.next();
    doDrsSummary(gr, raf, extra, counters);
  }
  raf.close();
}
 

private void _open(RandomAccessFile raf, NetcdfFile ncfile, boolean readOnly) throws IOException {
  if (!isClibraryPresent()) {
    throw new UnsupportedOperationException("Couldn't load NetCDF C library (see log for details).");
  }

  if (raf != null)
    raf.close(); // not used

  // open
  // netcdf-c can't handle "file:" prefix. Must remove it.
  String location = NetcdfFile.canonicalizeUriString(ncfile.getLocation());
  log.debug("open {}", location);

  IntByReference ncidp = new IntByReference();
  int ret = nc4.nc_open(location, readOnly ? NC_NOWRITE : NC_WRITE, ncidp);
  if (ret != 0)
    throw new IOException(ret + ": " + nc4.nc_strerror(ret));

  isClosed = false;
  ncid = ncidp.getValue();

  // format
  IntByReference formatp = new IntByReference();
  ret = nc4.nc_inq_format(ncid, formatp);
  if (ret != 0)
    throw new IOException(ret + ": " + nc4.nc_strerror(ret));
  format = formatp.getValue();
  log.debug("open {} id={} format={}", ncfile.getLocation(), ncid, format);

  // read root group
  makeGroup(new Group4(ncid, ncfile.getRootGroup(), null));

  // check if its an HDF5-EOS file
  Group eosInfo = ncfile.getRootGroup().findGroupLocal(HdfEos.HDF5_GROUP);
  if (eosInfo != null && useHdfEos) {
    isEos = HdfEos.amendFromODL(ncfile, eosInfo);
  }

  ncfile.finish();
}
 

public void open(RandomAccessFile raf, NetcdfFile ncfile, CancelTask cancelTask) throws IOException {
  int n;

  try {
    n = readAllData(raf);
  } catch (ParseException e) {
    e.printStackTrace();
    throw new IOException("bad data");
  }
  raf.close();

  Dimension recordDim = new Dimension("record", n, true);
  ncfile.addDimension(null, recordDim);

  Variable date = new Variable(ncfile, null, null, "date");
  date.setDimensions("record");
  date.setDataType(DataType.INT);
  String timeUnit = "seconds since 1970-01-01 00:00:00";
  date.addAttribute(new Attribute("long_name", "date of strike"));
  date.addAttribute(new Attribute("units", timeUnit));
  date.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));
  date.setCachedData(dateArray, false);
  ncfile.addVariable(null, date);

  Variable lat = new Variable(ncfile, null, null, "lat");
  lat.setDimensions("record");
  lat.setDataType(DataType.DOUBLE);
  lat.addAttribute(new Attribute("long_name", "latitude"));
  lat.addAttribute(new Attribute("units", "degrees_north"));
  lat.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
  lat.setCachedData(latArray, false);
  ncfile.addVariable(null, lat);

  Variable lon = new Variable(ncfile, null, null, "lon");
  lon.setDimensions("record");
  lon.setDataType(DataType.DOUBLE);
  lon.addAttribute(new Attribute("long_name", "longitude"));
  lon.addAttribute(new Attribute("units", "degrees_east"));
  lon.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
  lon.setCachedData(lonArray, false);
  ncfile.addVariable(null, lon);

  Variable amp = new Variable(ncfile, null, null, "strikeAmplitude");
  amp.setDimensions("record");
  amp.setDataType(DataType.DOUBLE);
  amp.addAttribute(new Attribute("long_name", "amplitude of strike"));
  amp.addAttribute(new Attribute("units", "kAmps"));
  amp.addAttribute(new Attribute("missing_value", new Double(999)));
  amp.setCachedData(ampArray, false);
  ncfile.addVariable(null, amp);

  Variable nstrokes = new Variable(ncfile, null, null, "strokeCount");
  nstrokes.setDimensions("record");
  nstrokes.setDataType(DataType.INT);
  nstrokes.addAttribute(new Attribute("long_name", "number of strokes per flash"));
  nstrokes.addAttribute(new Attribute("units", ""));
  nstrokes.setCachedData(nstrokesArray, false);
  ncfile.addVariable(null, nstrokes);

  ncfile.addAttribute(null, new Attribute("title", "USPN Lightning Data"));
  ncfile.addAttribute(null, new Attribute("history", "Read directly by Netcdf Java IOSP"));

  ncfile.addAttribute(null, new Attribute("Conventions", "Unidata Observation Dataset v1.0"));
  ncfile.addAttribute(null, new Attribute("cdm_data_type", "Point"));
  ncfile.addAttribute(null, new Attribute("observationDimension", "record"));

  MAMath.MinMax mm = MAMath.getMinMax(dateArray);
  ncfile.addAttribute(null, new Attribute("time_coverage_start", ((int) mm.min) + " " + timeUnit));
  ncfile.addAttribute(null, new Attribute("time_coverage_end", ((int) mm.max) + " " + timeUnit));

  mm = MAMath.getMinMax(latArray);
  ncfile.addAttribute(null, new Attribute("geospatial_lat_min", new Double(mm.min)));
  ncfile.addAttribute(null, new Attribute("geospatial_lat_max", new Double(mm.max)));

  mm = MAMath.getMinMax(lonArray);
  ncfile.addAttribute(null, new Attribute("geospatial_lon_min", new Double(mm.min)));
  ncfile.addAttribute(null, new Attribute("geospatial_lon_max", new Double(mm.max)));

  ncfile.finish();
}
 

public void open(RandomAccessFile raf, NetcdfFile ncfile, CancelTask cancelTask) throws IOException {
  int n;

  try {
    n = readAllData(raf);
  } catch (ParseException e) {
    e.printStackTrace();
    throw new IOException("bad data");
  }
  raf.close();

  Dimension recordDim = new Dimension("record", n, true);
  ncfile.addDimension(null, recordDim);

  Variable date = new Variable(ncfile, null, null, "date");
  date.setDimensions("record");
  date.setDataType(DataType.INT);
  String timeUnit = "seconds since 1970-01-01 00:00:00";
  date.addAttribute(new Attribute("long_name", "date of strike"));
  date.addAttribute(new Attribute("units", timeUnit));
  date.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));
  date.setCachedData(dateArray, false);
  ncfile.addVariable(null, date);

  Variable lat = new Variable(ncfile, null, null, "lat");
  lat.setDimensions("record");
  lat.setDataType(DataType.DOUBLE);
  lat.addAttribute(new Attribute("long_name", "latitude"));
  lat.addAttribute(new Attribute("units", "degrees_north"));
  lat.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
  lat.setCachedData(latArray, false);
  ncfile.addVariable(null, lat);

  Variable lon = new Variable(ncfile, null, null, "lon");
  lon.setDimensions("record");
  lon.setDataType(DataType.DOUBLE);
  lon.addAttribute(new Attribute("long_name", "longitude"));
  lon.addAttribute(new Attribute("units", "degrees_east"));
  lon.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
  lon.setCachedData(lonArray, false);
  ncfile.addVariable(null, lon);

  Variable amp = new Variable(ncfile, null, null, "strikeAmplitude");
  amp.setDimensions("record");
  amp.setDataType(DataType.DOUBLE);
  amp.addAttribute(new Attribute("long_name", "amplitude of strike"));
  amp.addAttribute(new Attribute("units", "kAmps"));
  amp.addAttribute(new Attribute("missing_value", new Double(999)));
  amp.setCachedData(ampArray, false);
  ncfile.addVariable(null, amp);

  Variable nstrokes = new Variable(ncfile, null, null, "strokeCount");
  nstrokes.setDimensions("record");
  nstrokes.setDataType(DataType.INT);
  nstrokes.addAttribute(new Attribute("long_name", "number of strokes per flash"));
  nstrokes.addAttribute(new Attribute("units", ""));
  nstrokes.setCachedData(nstrokesArray, false);
  ncfile.addVariable(null, nstrokes);

  ncfile.addAttribute(null, new Attribute("title", "USPN Lightning Data"));
  ncfile.addAttribute(null, new Attribute("history", "Read directly by Netcdf Java IOSP"));

  ncfile.addAttribute(null, new Attribute("Conventions", "Unidata Observation Dataset v1.0"));
  ncfile.addAttribute(null, new Attribute("cdm_data_type", "Point"));
  ncfile.addAttribute(null, new Attribute("observationDimension", "record"));

  MAMath.MinMax mm = MAMath.getMinMax(dateArray);
  ncfile.addAttribute(null, new Attribute("time_coverage_start", ((int) mm.min) + " " + timeUnit));
  ncfile.addAttribute(null, new Attribute("time_coverage_end", ((int) mm.max) + " " + timeUnit));

  mm = MAMath.getMinMax(latArray);
  ncfile.addAttribute(null, new Attribute("geospatial_lat_min", new Double(mm.min)));
  ncfile.addAttribute(null, new Attribute("geospatial_lat_max", new Double(mm.max)));

  mm = MAMath.getMinMax(lonArray);
  ncfile.addAttribute(null, new Attribute("geospatial_lon_min", new Double(mm.min)));
  ncfile.addAttribute(null, new Attribute("geospatial_lon_max", new Double(mm.max)));

  ncfile.finish();
}
 

/**
 * Read all of the data records that have been added.
 * The full (x,y) record is read, the reciever will subset the (x, y) as needed.
 * 
 * @param dataReceiver send data here.
 */
private void read(DataReceiverIF dataReceiver) throws IOException {
  Collections.sort(records);

  int currFile = -1;
  RandomAccessFile rafData = null;
  try {
    for (DataRecord dr : records) {
      if (Grib.debugIndexOnly || Grib.debugGbxIndexOnly) {
        GribIosp.debugIndexOnlyCount++;
        currentDataRecord = dr.record;
        currentDataRafFilename = gribCollection.getDataRafFilename(dr.record.fileno);
        if (Grib.debugIndexOnlyShow)
          dr.show(gribCollection);
        dataReceiver.setDataToZero();
        continue;
      }

      if (dr.record.fileno != currFile) {
        if (rafData != null)
          rafData.close();
        rafData = gribCollection.getDataRaf(dr.record.fileno);
        currFile = dr.record.fileno;
      }

      if (dr.record.pos == GribCollectionMutable.MISSING_RECORD)
        continue;

      if (GribDataReader.validator != null && dr.validation != null && rafData != null) {
        GribDataReader.validator.validate(gribCollection.cust, rafData, dr.record.pos + dr.record.drsOffset,
            dr.validation);

      } else if (show && rafData != null) { // for validation
        show(dr.validation);
        show(rafData, dr.record.pos + dr.record.drsOffset);
      }

      float[] data = readData(rafData, dr);
      GdsHorizCoordSys hcs = vindex.group.getGdsHorizCoordSys();
      dataReceiver.addData(data, dr.resultIndex, hcs.nx);
    }

  } finally {
    if (rafData != null)
      rafData.close(); // make sure its closed even on exception
  }
}
 

private void readPartitioned(DataReceiverIF dataReceiver) throws IOException {
  Collections.sort(records);

  PartitionCollectionImmutable.DataRecord lastRecord = null;
  RandomAccessFile rafData = null;
  try {

    for (DataRecord dr : records) {
      PartitionCollectionImmutable.DataRecord drp = (PartitionCollectionImmutable.DataRecord) dr;
      if (Grib.debugIndexOnly || Grib.debugGbxIndexOnly) {
        GribIosp.debugIndexOnlyCount++;
        if (Grib.debugIndexOnlyShow)
          drp.show();
        dataReceiver.setDataToZero();
        continue;
      }

      if ((rafData == null) || !drp.usesSameFile(lastRecord)) {
        if (rafData != null)
          rafData.close();
        rafData = drp.usePartition.getRaf(drp.partno, dr.record.fileno);
      }
      lastRecord = drp;

      if (dr.record.pos == GribCollectionMutable.MISSING_RECORD)
        continue;

      if (GribDataReader.validator != null && dr.validation != null) {
        GribDataReader.validator.validate(gribCollection.cust, rafData, dr.record.pos + dr.record.drsOffset,
            dr.validation);
      } else if (show) { // for validation
        show(dr.validation);
        show(rafData, dr.record.pos + dr.record.drsOffset);
      }

      float[] data = readData(rafData, dr);
      GdsHorizCoordSys hcs = dr.hcs;
      dataReceiver.addData(data, dr.resultIndex, hcs.nx);
    }

  } finally {
    if (rafData != null)
      rafData.close(); // make sure its closed even on exception
  }
}
 

public void open(RandomAccessFile raf, NetcdfFile ncfile, CancelTask cancelTask) throws IOException {
  int n;

  try {
    n = readAllData(raf);
  } catch (ParseException e) {
    e.printStackTrace();
    throw new IOException("bad data");
  }
  raf.close();

  Dimension recordDim = new Dimension("record", n, true);
  ncfile.addDimension(null, recordDim);

  Variable date = new Variable(ncfile, null, null, "date");
  date.setDimensions("record");
  date.setDataType(DataType.INT);
  String timeUnit = "seconds since 1970-01-01 00:00:00";
  date.addAttribute(new Attribute("long_name", "date of strike"));
  date.addAttribute(new Attribute("units", timeUnit));
  date.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));
  date.setCachedData(dateArray, false);
  ncfile.addVariable(null, date);

  Variable lat = new Variable(ncfile, null, null, "lat");
  lat.setDimensions("record");
  lat.setDataType(DataType.DOUBLE);
  lat.addAttribute(new Attribute("long_name", "latitude"));
  lat.addAttribute(new Attribute("units", "degrees_north"));
  lat.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
  lat.setCachedData(latArray, false);
  ncfile.addVariable(null, lat);

  Variable lon = new Variable(ncfile, null, null, "lon");
  lon.setDimensions("record");
  lon.setDataType(DataType.DOUBLE);
  lon.addAttribute(new Attribute("long_name", "longitude"));
  lon.addAttribute(new Attribute("units", "degrees_east"));
  lon.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
  lon.setCachedData(lonArray, false);
  ncfile.addVariable(null, lon);

  Variable amp = new Variable(ncfile, null, null, "strikeAmplitude");
  amp.setDimensions("record");
  amp.setDataType(DataType.DOUBLE);
  amp.addAttribute(new Attribute("long_name", "amplitude of strike"));
  amp.addAttribute(new Attribute("units", "kAmps"));
  amp.addAttribute(new Attribute("missing_value", new Double(999)));
  amp.setCachedData(ampArray, false);
  ncfile.addVariable(null, amp);

  Variable nstrokes = new Variable(ncfile, null, null, "strokeCount");
  nstrokes.setDimensions("record");
  nstrokes.setDataType(DataType.INT);
  nstrokes.addAttribute(new Attribute("long_name", "number of strokes per flash"));
  nstrokes.addAttribute(new Attribute("units", ""));
  nstrokes.setCachedData(nstrokesArray, false);
  ncfile.addVariable(null, nstrokes);

  ncfile.addAttribute(null, new Attribute("title", "USPN Lightning Data"));
  ncfile.addAttribute(null, new Attribute("history", "Read directly by Netcdf Java IOSP"));

  ncfile.addAttribute(null, new Attribute("Conventions", "Unidata Observation Dataset v1.0"));
  ncfile.addAttribute(null, new Attribute("cdm_data_type", "Point"));
  ncfile.addAttribute(null, new Attribute("observationDimension", "record"));

  MAMath.MinMax mm = MAMath.getMinMax(dateArray);
  ncfile.addAttribute(null, new Attribute("time_coverage_start", ((int) mm.min) + " " + timeUnit));
  ncfile.addAttribute(null, new Attribute("time_coverage_end", ((int) mm.max) + " " + timeUnit));

  mm = MAMath.getMinMax(latArray);
  ncfile.addAttribute(null, new Attribute("geospatial_lat_min", new Double(mm.min)));
  ncfile.addAttribute(null, new Attribute("geospatial_lat_max", new Double(mm.max)));

  mm = MAMath.getMinMax(lonArray);
  ncfile.addAttribute(null, new Attribute("geospatial_lon_min", new Double(mm.min)));
  ncfile.addAttribute(null, new Attribute("geospatial_lon_max", new Double(mm.max)));

  ncfile.finish();
}
 

/**
 * Open an existing file (read only), with option of cancelling, setting the RandomAccessFile buffer size for
 * efficiency,
 * with an optional special object for the iosp.
 *
 * @param location location of file. This may be a
 *        <ol>
 *        <li>local netcdf-3 filename (with a file: prefix or no prefix)
 *        <li>remote netcdf-3 filename (with an http: prefix)
 *        <li>local netcdf-4 filename (with a file: prefix or no prefix)
 *        <li>local hdf-5 filename (with a file: prefix or no prefix)
 *        <li>local iosp filename (with a file: prefix or no prefix)
 *        </ol>
 *        http://thredds.ucar.edu/thredds/fileServer/grib/NCEP/GFS/Alaska_191km/files/GFS_Alaska_191km_20130416_0600.grib1
 *        If file ends with ".Z", ".zip", ".gzip", ".gz", or ".bz2", it will uncompress/unzip and write to new file
 *        without the suffix,
 *        then use the uncompressed file. It will look for the uncompressed file before it does any of that. Generally
 *        it prefers to
 *        place the uncompressed file in the same directory as the original file. If it does not have write permission
 *        on that directory,
 *        it will use the directory defined by ucar.nc2.util.DiskCache class.
 * @param buffer_size RandomAccessFile buffer size, if <= 0, use default size
 * @param cancelTask allow task to be cancelled; may be null.
 * @param iospMessage special iosp tweaking (sent before open is called), may be null
 * @return NetcdfFile object, or null if cant find IOServiceProver
 * @throws IOException if error
 * @deprecated use NetcdfFiles.open
 */
@Deprecated
public static NetcdfFile open(String location, int buffer_size, CancelTask cancelTask, Object iospMessage)
    throws IOException {

  RandomAccessFile raf = getRaf(location, buffer_size);

  try {
    return open(raf, location, cancelTask, iospMessage);
  } catch (Throwable t) {
    raf.close();
    throw new IOException(t);
  }
}