Java Code Examples for ucar.ma2.Section#getRange()

/**
 * Read the data for the variable
 *
 * @param v2 Variable to read
 * @param section section infomation
 * @return Array of data
 * @throws IOException problem reading from file
 * @throws InvalidRangeException invalid Range
 */
public Array readData(Variable v2, Section section) throws IOException, InvalidRangeException {

  Array dataArray = Array.factory(DataType.FLOAT, section.getShape());
  GradsVariable gradsVar = findVar(v2);
  if (gradsVar == null)
    throw new IOException();

  // Canonical ordering is ens, time, level, lat, lon
  int rangeIdx = 0;
  Range ensRange = (gradsDDF.getEnsembleDimension() != null) ? section.getRange(rangeIdx++) : new Range(0, 0);
  Range timeRange = (section.getRank() > 2) ? section.getRange(rangeIdx++) : new Range(0, 0);
  Range levRange = (gradsVar.getNumLevels() > 0) ? section.getRange(rangeIdx++) : new Range(0, 0);
  Range yRange = section.getRange(rangeIdx++);
  Range xRange = section.getRange(rangeIdx);

  IndexIterator ii = dataArray.getIndexIterator();

  for (int ensIdx : ensRange)
    for (int timeIdx : timeRange)
      for (int levelIdx : levRange)
        readXY(v2, ensIdx, timeIdx, levelIdx, yRange, xRange, ii);

  return dataArray;
}
 

@Override
public void writeData(Variable v2, Section section, Array values) throws java.io.IOException, InvalidRangeException {
  N3headerNew.Vinfo vinfo = (N3headerNew.Vinfo) v2.getSPobject();
  DataType dataType = v2.getDataType();

  if (v2.isUnlimited()) {
    Range firstRange = section.getRange(0);
    setNumrecs(firstRange.last() + 1);
  }

  if (v2 instanceof Structure) {
    if (!(values instanceof ArrayStructure))
      throw new IllegalArgumentException("writeData for Structure: data must be ArrayStructure");

    if (v2.getRank() == 0)
      throw new IllegalArgumentException("writeData for Structure: must have rank > 0");

    Dimension d = v2.getDimension(0);
    if (!d.isUnlimited())
      throw new IllegalArgumentException("writeData for Structure: must have unlimited dimension");

    writeRecordData((Structure) v2, section, (ArrayStructure) values);

  } else {
    Layout layout = (!v2.isUnlimited()) ? new LayoutRegular(vinfo.begin, v2.getElementSize(), v2.getShape(), section)
        : new LayoutRegularSegmented(vinfo.begin, v2.getElementSize(), header.recsize, v2.getShape(), section);
    writeData(values, layout, dataType);
  }
}
 

private void writeRecordData(ucar.nc2.Structure s, Section section, ArrayStructure structureArray)
    throws java.io.IOException, ucar.ma2.InvalidRangeException {
  int countSrcRecnum = 0;
  Range recordRange = section.getRange(0);
  for (int recnum : recordRange) {
    StructureData sdata = structureArray.getStructureData(countSrcRecnum);
    writeRecordData(s, recnum, sdata);
    countSrcRecnum++;
  }
}
 

private long readRecordData(ucar.nc2.Structure s, Section section, WritableByteChannel out)
    throws java.io.IOException {
  long count = 0;

  /*
   * RegularIndexer index = new RegularIndexer( s.getShape(), recsize, recStart, section, recsize);
   * while (index.hasNext()) {
   * Indexer.Chunk chunk = index.next();
   * count += raf.readBytes( out, chunk.getFilePos(), chunk.getNelems() * s.getElementSize());
   * }
   */

  // LOOK this is the OTW layout based on netcdf-3
  // not sure this works but should give an idea of timing
  Range recordRange = section.getRange(0);
  /*
   * int stride = recordRange.stride();
   * if (stride == 1) {
   * int first = recordRange.first();
   * int n = recordRange.length();
   * if (false) System.out.println(" read record " + first+" "+ n * header.recsize+" bytes ");
   * return raf.readToByteChannel(out, header.recStart + first * header.recsize, n * header.recsize);
   *
   * } else {
   */

  for (int recnum : recordRange) {
    if (debugRecord)
      System.out.println(" read record " + recnum);
    raf.seek(header.recStart + recnum * header.recsize); // where the record starts
    count += raf.readToByteChannel(out, header.recStart + recnum * header.recsize, header.recsize);
  }
  // }

  return count;
}
 

/**
 * Read data from record structure. For N3, this is the only possible structure, and there can be no nesting.
 * Read all variables for each record, put in ByteBuffer.
 *
 * @param s the record structure
 * @param section the record range to read
 * @return an ArrayStructure, with all the data read in.
 * @throws IOException on error
 */
private ucar.ma2.Array readRecordData(ucar.nc2.Structure s, Section section) throws java.io.IOException {
  // has to be 1D
  Range recordRange = section.getRange(0);

  // create the ArrayStructure
  StructureMembers members = s.makeStructureMembers();
  for (StructureMembers.Member m : members.getMembers()) {
    Variable v2 = s.findVariable(m.getName());
    Vinfo vinfo = (Vinfo) v2.getSPobject();
    m.setDataParam((int) (vinfo.begin - header.recStart));
  }

  // protect against too large of reads
  if (header.recsize > Integer.MAX_VALUE)
    throw new IllegalArgumentException("Cant read records when recsize > " + Integer.MAX_VALUE);
  long nrecs = section.computeSize();
  if (nrecs * header.recsize > Integer.MAX_VALUE)
    throw new IllegalArgumentException(
        "Too large read: nrecs * recsize= " + (nrecs * header.recsize) + "bytes exceeds " + Integer.MAX_VALUE);

  members.setStructureSize((int) header.recsize);
  ArrayStructureBB structureArray = new ArrayStructureBB(members, new int[] {recordRange.length()});

  // loop over records
  byte[] result = structureArray.getByteBuffer().array();
  int count = 0;
  for (int recnum : recordRange) {
    if (debugRecord)
      System.out.println(" read record " + recnum);
    raf.seek(header.recStart + recnum * header.recsize); // where the record starts

    if (recnum != header.numrecs - 1) {
      raf.readFully(result, (int) (count * header.recsize), (int) header.recsize);
    } else {
      // "wart" allows file to be one byte short. since its always padding, we allow
      raf.read(result, (int) (count * header.recsize), (int) header.recsize);
    }
    count++;
  }

  return structureArray;
}