Examples of ucar.nc2.Structure

ucar.nc2.Structure
A Structure is a type of Variable that contains other Variables, like a struct in C. A Structure can be scalar or multidimensional.
A call to structure.read() will read all of the data in a Structure, including nested structures, and returns an Array of StructureData, with all of the data in memory. If there is a nested sequence, the sequence data may be read into memory all at once, ot it may be read in increments as the iteration proceeds.
Generally, the programmer can assume that the data in one Structure are stored together, so that it is efficient to read an entire Structure, and then access the Variable data through the Arrays in the StructureData. @author caron

        if (!(ncvar instanceof VariableDS)) continue; // cant be a structure


        String dimName = findAlias(ds, ncvar);
        if (dimName.length() == 0) // none
          continue;
        Dimension dim = ds.findDimension(dimName);
        if (null != dim) {
          vp.isCoordinateAxis = true;
          parseInfo.format(" Coordinate Axis added (alias) = %s for dimension %s\n", vp.v.getFullName(), dimName);
        }
      }

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   * @param ncfile test this NetcdfFile
   * @return true if we think this is a ATDRadarConvention file.
   */
  public static boolean isMine(NetcdfFile ncfile) {
    // not really sure until we can examine more files
    Dimension s = ncfile.findDimension("cedric_general_scaling_factor");
    Variable v = ncfile.findVariable("cedric_run_date");
    if(v != null && s != null)
        return true;
    else
        return false;

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    }


    Variable v = ds.findVariable("time_offset");
    v.addAttribute(new Attribute( "units", "seconds since "+dfo.toDateTimeString(start)));


    Group root = ds.getRootGroup();
    root.addAttribute(new Attribute( "Convention", "Suomi-Station-CDM"));    
    ds.finish();
  }

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 }


  public void problemV() throws IOException {
    H5header.setDebugFlags(new ucar.nc2.util.DebugFlagsImpl("H5header/header"));
    String filename = testDir + "ssec-h5/MYD04_L2.A2006188.1830.005.2006194121515.hdf";
    NetcdfFile ncfile = NetcdfFile.open(filename);
    Variable v = ncfile.findVariable("/U-MARF/EPS/IASI_xxx_1C/DATA/SPECT_LAT_ARRAY");
    Array data = v.read();
    System.out.println("\n**** testReadNetcdf4 done\n\n" + ncfile);
    NCdump.printArray(data, "primary_cloud", System.out, null);
    ncfile.close();
  }

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  }


  static public void readAllData( String filename) {
    System.out.println("\n------Reading filename "+filename);
    try {
      NetcdfFile ncfile = TestH5.open(filename);
      //System.out.println("\n"+ncfile);


      for (Variable v : ncfile.getVariables()) {
        if (v.getSize() > max_size) {
          Section s = makeSubset(v);
          System.out.println("  Try to read variable " + v.getNameAndDimensions() + " size= " + v.getSize() + " section= " + s);
          v.read(s);
        } else {
          System.out.println("  Try to read variable " + v.getNameAndDimensions() + " size= " + v.getSize());
          v.read();
        }
      }
      ncfile.close();
    } catch (Exception e) {
      e.printStackTrace();
      //assert false;
    }
  }

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  // section reading for member data
  static public ucar.ma2.Array readSection(ParsedSectionSpec cer) throws IOException, InvalidRangeException {
    Variable inner = null;
    List<Range> totalRanges = new ArrayList<Range>();
    ParsedSectionSpec current = cer;
    while (current != null) {
      totalRanges.addAll( current.section.getRanges());
      inner = current.v;
      current = current.child;
    }

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    Section total = new Section( totalRanges);
    Array result = Array.factory(inner.getDataType(), total.getShape());


    // must be a Structure
    Structure outer = (Structure) cer.v;
    Structure outerSubset = outer.select( cer.child.v.getShortName()); // allows IOSPs to optimize for  this case
    ArrayStructure outerData = (ArrayStructure) outerSubset.read(cer.section);
    extractSection( cer.child, outerData, result.getIndexIterator());


    result.setUnsigned(cer.v.isUnsigned());
    return result;
  }

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  protected Array readData(ucar.nc2.Variable v, Section section) throws IOException, InvalidRangeException {
    if (unlocked)
      throw new IllegalStateException("File is unlocked - cannot use");


    if (v.getDataType() == DataType.SEQUENCE) {
      Structure s = (Structure) v;
      StructureDataIterator siter = getStructureIterator(s, -1);
      return new ArraySequence(s.makeStructureMembers(), siter, -1);
    }


    StringBuilder sbuff = new StringBuilder(remoteURI);
    sbuff.append("?var=");
    Formatter f = new Formatter();

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    if (debug) System.out.println("  readData data len= " + dsize);
    byte[] datab = new byte[dsize];
    NcStream.readFully(is, datab);


    if (dataType == DataType.STRUCTURE) {
      Structure s = (Structure) ncfile.findVariable(dproto.getVarName());
      StructureMembers members = s.makeStructureMembers();


      if (dproto.getVersion() == 0) {
        ArrayStructureBB.setOffsets(members); // not setting heap objects for version 0
        ArrayStructureBB data = new ArrayStructureBB(members, section.getShape(), ByteBuffer.wrap(datab), 0);
        return new DataResult(dproto.getVarName(), section, data);

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    byte[] dp = new byte[psize];
    NcStream.readFully(is, dp);
    NcStreamProto.Data dproto = NcStreamProto.Data.parseFrom(dp);
    // if (debug) System.out.println(" readData proto = " + dproto);


    Structure s = (Structure) ncfile.findVariable(dproto.getVarName());
    StructureMembers members = s.makeStructureMembers();
    ArrayStructureBB.setOffsets(members);


    return new StreamDataIterator(is, members);
  }

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