Java Code Examples for ucar.ma2.Section#Builder

@Nonnull
public static Section decodeSection(NcStreamProto.Section proto) {
  Section.Builder section = Section.builder();

  for (ucar.nc2.stream.NcStreamProto.Range pr : proto.getRangeList()) {
    try {
      long stride = pr.getStride();
      if (stride == 0)
        stride = 1; // default in protobuf2 was 1, but protobuf3 is 0, luckily 0 is illegal
      if (pr.getSize() == 0)
        section.appendRange(Range.EMPTY); // used for scalars LOOK really used ??
      else {
        // this.last = first + (this.length-1) * stride;
        section.appendRange((int) pr.getStart(), (int) (pr.getStart() + (pr.getSize() - 1) * stride), (int) stride);
      }

    } catch (InvalidRangeException e) {
      throw new RuntimeException("Bad Section in ncstream", e);
    }
  }
  return section.build();
}
 

/**
 * Use this when this is a one dimensional array of Structures, or you are doing the index calculation yourself for
 * a multidimension array. This will read only the ith structure, and return the data as a StructureData object.
 * 
 * @param index index into 1D array
 * @return ith StructureData
 * @throws java.io.IOException on read error
 * @throws ucar.ma2.InvalidRangeException if index out of range
 */
public StructureData readStructure(int index) throws IOException, ucar.ma2.InvalidRangeException {
  Section.Builder sb = Section.builder();

  if (getRank() == 1) {
    sb.appendRange(index, index);

  } else if (getRank() > 1) {
    Index ii = Index.factory(shape); // convert to nD index
    ii.setCurrentCounter(index);
    int[] origin = ii.getCurrentCounter();
    for (int anOrigin : origin)
      sb.appendRange(anOrigin, anOrigin);
  }

  Array dataArray = read(sb.build());
  ArrayStructure data = (ArrayStructure) dataArray;
  return data.getStructureData(0);
}
 

private void readNextGeneralRank() throws IOException {

      try {
        Section.Builder sb = Section.builder().appendRanges(shape);
        sb.setRange(0, new Range(outerCount, outerCount));

        as = (ArrayStructure) read(sb.build());

        if (NetcdfFile.debugStructureIterator)
          System.out.println("readNext inner=" + outerCount + " total=" + outerCount);

        outerCount++;

      } catch (InvalidRangeException e) {
        log.error("Structure.Iterator.readNext() ", e);
        throw new IllegalStateException("Structure.Iterator.readNext() ", e);
      } // cant happen

      readStart += as.getSize();
      readCount = 0;
    }
 

private void fillRecordVariables(int recStart, int recEnd) throws IOException, InvalidRangeException {
  // do each record completely, should be a bit more efficient

  for (int i = recStart; i < recEnd; i++) { // do one record at a time
    Range r = new Range(i, i);

    // run through each variable
    for (Variable v : ncfile.getVariables()) {
      if (!v.isUnlimited() || (v instanceof Structure))
        continue;
      Section.Builder recordSection = Section.builder().appendRanges(v.getRanges());
      recordSection.setRange(0, r);
      writeData(v, recordSection.build(), makeConstantArray(v));
    }
  }
}
 

private Array read(TimeInventory.Instance timeInstance, String fullNameEsc, List<Range> innerSection,
    HashMap<String, NetcdfDataset> openFilesRead) throws IOException, InvalidRangeException {
  NetcdfFile ncfile = open(timeInstance.getDatasetLocation(), openFilesRead);
  if (ncfile == null)
    return null; // file might be deleted ??

  Variable v = ncfile.findVariable(fullNameEsc);
  if (v == null)
    return null; // v could be missing, return missing data i think

  // assume time is first dimension LOOK: out of-order; ensemble; section different ??
  Range timeRange = new Range(timeInstance.getDatasetIndex(), timeInstance.getDatasetIndex());
  Section.Builder sb = Section.builder().appendRanges(innerSection);
  sb.insertRange(0, timeRange);
  return v.read(sb.build());
}
 

private StructureData nextStructureData() {
  StructureDataW sdata = new StructureDataW(members);

  for (Variable var : vars) {
    Section.Builder sb = Section.builder();
    try {
      sb.appendRange(outerIndex, outerIndex);
      sb.appendRange(count, count);
      for (int i = 2; i < var.getRank(); i++)
        sb.appendRangeAll();
      Array data = var.read(sb.build());
      sdata.setMemberData(var.getShortName(), data);

    } catch (InvalidRangeException | IOException e) {
      throw new RuntimeException(e);
    }

  }

  return sdata;
}
 

private static Variable.Builder decodeVar(NcStreamProto.Variable var) {
  DataType varType = convertDataType(var.getDataType());
  Variable.Builder ncvar = Variable.builder().setName(var.getName()).setDataType(varType);

  if (varType.isEnum()) {
    ncvar.setEnumTypeName(var.getEnumType());
  }

  // The Dimensions are stored redunantly in the Variable.
  // If shared, they must also exist in a parent Group. However, we dont yet have the Groups wired together,
  // so that has to wait until build().
  List<Dimension> dims = new ArrayList<>(6);
  Section.Builder section = Section.builder();
  for (ucar.nc2.stream.NcStreamProto.Dimension dim : var.getShapeList()) {
    dims.add(decodeDim(dim));
    section.appendRange((int) dim.getLength());
  }
  ncvar.addDimensions(dims);

  for (ucar.nc2.stream.NcStreamProto.Attribute att : var.getAttsList())
    ncvar.addAttribute(decodeAtt(att));

  if (!var.getData().isEmpty()) {
    // LOOK may mess with ability to change var size later.
    ByteBuffer bb = ByteBuffer.wrap(var.getData().toByteArray());
    Array data = Array.factory(varType, section.build().getShape(), bb);
    ncvar.setCachedData(data, true);
  }

  return ncvar;
}
 

@Override
public StructureDataIterator getStructureDataIterator(Cursor cursor) throws IOException {
  int recnum = cursor.getParentRecnum();
  try {
    Section.Builder sb = Section.builder().appendRange(recnum, recnum);
    int count = 1;
    while (count++ < struct.getRank()) // handles multidim case
      sb.appendRangeAll();
    ArrayStructure data = (ArrayStructure) struct.read(sb.build()); // read all the data for a fixed outer index
    return data.getStructureDataIterator();
  } catch (InvalidRangeException e) {
    throw new IllegalStateException(e);
  }
}
 

@Override
public Array reallyRead(Variable client, Section section, CancelTask cancelTask)
    throws IOException, InvalidRangeException {
  Section.Builder orgSection = Section.builder().appendRanges(section.getRanges());
  for (int dim : dims) {
    orgSection.insertRange(dim, Range.ONE); // lowest first
  }

  Array data = orgClient._read(orgSection.build());
  for (int i = dims.size() - 1; i >= 0; i--)
    data = data.reduce(dims.get(i)); // highest first

  return data;
}