Java Code Examples for ucar.nc2.Variable#setSPobject()

private void writeVars(List<Variable> vars, boolean largeFile, Formatter fout) throws IOException {
  int n = vars.size();
  if (n == 0) {
    raf.writeInt(0);
    raf.writeInt(0);
  } else {
    raf.writeInt(MAGIC_VAR);
    raf.writeInt(n);
  }

  for (Variable var : vars) {
    writeString(var.getShortName());

    // dimensions
    long vsize = var.getDataType().getSize(); // works for all netcdf-3 data types
    List<Dimension> dims = var.getDimensions();
    raf.writeInt(dims.size());
    for (Dimension dim : dims) {
      int dimIndex = findDimensionIndex(ncfile, dim);
      raf.writeInt(dimIndex);

      if (!dim.isUnlimited())
        vsize *= dim.getLength();
    }
    long unpaddedVsize = vsize;
    vsize += padding(vsize);

    // variable attributes
    long varAttsPos = raf.getFilePointer();
    writeAtts(var.attributes(), fout);

    // data type, variable size, beginning file position
    DataType dtype = var.getDataType();
    int type = getType(dtype);
    raf.writeInt(type);

    int vsizeWrite = (vsize < MAX_UNSIGNED_INT) ? (int) vsize : -1;
    raf.writeInt(vsizeWrite);
    long pos = raf.getFilePointer();
    if (largeFile)
      raf.writeLong(0); // come back to this later
    else
      raf.writeInt(0); // come back to this later

    // From nc3 file format specification
    // (https://www.unidata.ucar.edu/software/netcdf/docs/netcdf.html#NetCDF-Classic-Format):
    // Note on padding: In the special case of only a single record variable of character,
    // byte, or short type, no padding is used between data values.
    // 2/15/2011: we will continue to write the (incorrect) padded vsize into the header, but we will use the unpadded
    // size to read/write
    if (uvars.size() == 1 && uvars.get(0) == var) {
      if ((dtype == DataType.CHAR) || (dtype == DataType.BYTE) || (dtype == DataType.SHORT)) {
        vsize = unpaddedVsize;
      }
    }
    var.setSPobject(new N3headerNew.Vinfo(var.getShortName(), vsize, pos, var.isUnlimited(), varAttsPos));
  }
}
 

private Structure makeChunkVariable(NetcdfFile ncfile, TagVH vh) {
  Vinfo vinfo = new Vinfo(vh.refno);
  vinfo.tags.add(vh);
  vh.vinfo = vinfo;
  vh.used = true;

  TagData data = (TagData) tagMap.get(tagid(vh.refno, TagEnum.VS.getCode()));
  if (data == null) {
    log.error("Cant find tag " + vh.refno + "/" + TagEnum.VS.getCode() + " for TagVH=" + vh.detail());
    return null;
  }
  vinfo.tags.add(data);
  data.used = true;
  data.vinfo = vinfo;

  if (vh.nfields < 1)
    throw new IllegalStateException();

  try {
    Structure.Builder sb = Structure.builder().setName(vh.name);
    vinfo.setVariable(sb);
    Structure s = new Structure(ncfile, null, null, vh.name); // LOOK cheating
    s.setSPobject(vinfo);

    if (vh.nvert > 1)
      s.setDimensionsAnonymous(new int[] {vh.nvert});
    else
      s.setIsScalar();

    for (int fld = 0; fld < vh.nfields; fld++) {
      Variable m = new Variable(ncfile, null, s, vh.fld_name[fld]);
      short type = vh.fld_type[fld];
      short nelems = vh.fld_order[fld];
      H4type.setDataType(type, m);
      if (nelems > 1)
        m.setDimensionsAnonymous(new int[] {nelems});
      else
        m.setIsScalar();

      m.setSPobject(new Minfo(vh.fld_offset[fld]));
      s.addMemberVariable(m);
    }

    vinfo.setData(data, vh.ivsize);
    return s;

  } catch (InvalidRangeException e) {
    throw new IllegalStateException(e.getMessage());
  }
}
 

private void transferGroup(Group srcGroup, Group targetGroup, NetcdfDataset target) throws IOException {
  // group attributes
  DatasetConstructor.transferGroupAttributes(srcGroup, targetGroup);

  // dimensions
  for (Dimension d : srcGroup.getDimensions()) {
    if (null == targetGroup.findDimensionLocal(d.getShortName())) {
      Dimension newd =
          new Dimension(d.getShortName(), d.getLength(), d.isShared(), d.isUnlimited(), d.isVariableLength());
      targetGroup.addDimension(newd);
    }
  }

  // transfer variables - eliminate any references to component files
  for (Variable v : srcGroup.getVariables()) {
    Variable targetV = targetGroup.findVariableLocal(v.getShortName());

    if (null == targetV) { // add it
      if (v instanceof Structure) {
        targetV = new StructureDS(target, targetGroup, null, v.getShortName(), v.getDimensionsString(),
            v.getUnitsString(), v.getDescription());
        // LOOK - not adding the members here - what to do ??

      } else {
        targetV = new VariableDS(target, targetGroup, null, v.getShortName(), v.getDataType(),
            v.getDimensionsString(), v.getUnitsString(), v.getDescription());
      }

      DatasetConstructor.transferVariableAttributes(v, targetV);
      VariableDS vds = (VariableDS) v;
      targetV.setSPobject(vds); // temporary, for non-agg variables when proto is made
      if (vds.hasCachedDataRecurse()) {
        if (vds.getSize() > 1000 * 1000) {
          boolean wtf = vds.hasCachedDataRecurse();
        }
        targetV.setCachedData(vds.read()); //
      }
      targetGroup.addVariable(targetV);
    }
  }

  // nested groups - check if target already has it
  for (Group srcNested : srcGroup.getGroups()) {
    Group nested = targetGroup.findGroupLocal(srcNested.getShortName());
    if (null == nested) {
      nested = new Group(target, targetGroup, srcNested.getShortName());
      targetGroup.addGroup(nested);
      for (EnumTypedef et : srcNested.getEnumTypedefs()) {
        targetGroup.addEnumeration(et);
      }
    }
    transferGroup(srcNested, nested, target);
  }
}