Java Code Examples for ucar.nc2.Variable#Builder

/** Copy metadata from orgVar. */
public T copyFrom(Sequence orgVar) {
  super.copyFrom(orgVar);
  for (Variable v : orgVar.getVariables()) {
    Variable.Builder newVar;
    if (v instanceof Sequence) {
      newVar = SequenceDS.builder().copyFrom((Sequence) v);
    } else if (v instanceof Structure) {
      newVar = StructureDS.builder().copyFrom((Structure) v);
    } else {
      newVar = VariableDS.builder().copyFrom(v);
    }
    addMemberVariable(newVar);
  }
  setOriginalVariable(orgVar);
  setOriginalName(orgVar.getShortName());
  return self();
}
 

private void addDpiStructure(Structure.Builder parent, BufrConfig.FieldConverter parentFld,
    BufrConfig.FieldConverter dpiField) {
  DataDescriptor dpiKey = dpiField.dds;
  String uname = findUniqueName(parent, dpiField.getName(), "struct");
  dpiKey.name = uname; // name may need to be changed for uniqueness

  Structure.Builder struct = Structure.builder().setName(uname);
  parent.addMemberVariable(struct);
  int n = parentFld.dds.replication;
  struct.setDimensionsAnonymous(new int[] {n}); // anon vector

  Variable.Builder v = Variable.builder().setName("name");
  v.setDataType(DataType.STRING); // scalar
  struct.addMemberVariable(v);

  v = Variable.builder().setName("data");
  v.setDataType(DataType.FLOAT); // scalar
  struct.addMemberVariable(v);

  struct.setSPobject(dpiField); // ??
}
 

private String findUniqueName(Structure.Builder<?> struct, String want, String def) {
  if (want == null) {
    return def + tempNo++;
  }

  String vwant = NetcdfFiles.makeValidCdmObjectName(want);
  Optional<Variable.Builder<?>> oldV = struct.findMemberVariable(vwant);
  if (!oldV.isPresent()) {
    return vwant;
  }

  int seq = 2;
  while (true) {
    String wantSeq = vwant + "-" + seq;
    oldV = struct.findMemberVariable(wantSeq);
    if (!oldV.isPresent()) {
      return wantSeq;
    }
    seq++;
  }
}
 

private void enhanceGroup(Group.Builder group) {

    for (Variable.Builder vb : group.vbuilders) {
      if (vb instanceof StructureDS.Builder<?>) {
        enhanceStructure((StructureDS.Builder<?>) vb);
      } else if (vb instanceof VariableDS.Builder) {
        enhanceVariable((VariableDS.Builder) vb);
      } else {
        throw new IllegalStateException("Not a VariableDS " + vb.shortName);
      }
    }

    for (Group.Builder gb : group.gbuilders) {
      enhanceGroup(gb);
    }
  }
 

/**
 * look for aliases.
 *
 * @param axisType look for this axis type
 * @return name of axis of that type
 */
@Nullable
private String findCoordinateName(AxisType axisType) {
  for (Variable.Builder vb : rootGroup.vbuilders) {
    if (vb instanceof VariableDS.Builder) {
      VariableDS.Builder vds = (VariableDS.Builder) vb;
      if (axisType == getAxisType(vds)) {
        return vds.getFullName();
      }
    }
  }
  return null;
}
 

private void addCoordTransforms(CoverageCollection subsetDataset, Group.Builder group) {
  for (CoverageTransform ct : subsetDataset.getCoordTransforms()) {
    // scalar coordinate transform variable - container for transform info
    Variable.Builder ctv = Variable.builder().setName(ct.getName()).setDataType(DataType.INT);
    group.addVariable(ctv);
    ctv.addAttributes(ct.attributes());
  }
}
 

private boolean makeCoordinateAxis(Variable.Builder ncvar, Dimension dim) {
  if (ncvar.getRank() != 1)
    return false;
  String vdimName = ncvar.getFirstDimensionName();
  if (!vdimName.equals(dim.getShortName()))
    return false;

  if (!dim.getShortName().equals(ncvar.shortName)) {
    ncvar.addAttribute(new Attribute(_Coordinate.AliasForDimension, dim.getShortName()));
  }
  return true;
}
 

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;
}
 

private void setDatasetAcquireProxy(AggProxyReader proxy, Group.Builder g) throws IOException {

    // all normal (non agg) variables must use a proxy to lock the file
    for (Variable.Builder v : g.vbuilders) {

      if (v.proxyReader != v && v.proxyReader != null) {
        if (debugProxy)
          System.out.println(" debugProxy: hasProxyReader " + v.shortName);
        continue; // dont mess with agg variables
      }
      /*
       * LOOK no caching
       * if (v.isCaching()) { // cache the small ones
       * v.setCachedData(v.read()); // cache the variableDS directly
       * 
       * } else { // put proxy on the rest
       */
      v.setProxyReader(proxy);
      if (debugProxy)
        System.out.println(" debugProxy: set proxy on " + v.shortName);
    }

    // recurse
    for (Group.Builder nested : g.gbuilders) {
      setDatasetAcquireProxy(proxy, nested);
    }
  }
 

/** Add a Variable to the root group. */
public Variable.Builder addVariable(String shortName, DataType dataType, String dimString) {
  if (!isNewFile && !useJna) {
    throw new UnsupportedOperationException("Cant add variable to existing netcdf-3 files");
  }
  Variable.Builder vb = Variable.builder().setName(shortName).setDataType(dataType).setParentGroupBuilder(rootGroup)
      .setDimensionsByName(dimString);
  rootGroup.addVariable(vb);
  return vb;
}
 

private Optional<CoordinateAxis.Builder> findAxisByVerticalSearch(Variable.Builder vb, String shortName) {
  Optional<Variable.Builder<?>> axis = vb.getParentGroupBuilder().findVariableOrInParent(shortName);
  if (axis.isPresent()) {
    if (axis.get() instanceof CoordinateAxis.Builder) {
      return Optional.of((CoordinateAxis.Builder) axis.get());
    }
  }
  return Optional.empty();
}
 

private void addVariables(Group.Builder group) {
  for (Variable.Builder vb : group.vbuilders) {
    if (vb instanceof VariableDS.Builder) {
      varList.add(new VarProcess(group, (VariableDS.Builder) vb));
    } else if (vb instanceof StructureDS.Builder) {
      addStructure(group, (StructureDS.Builder) vb);
    }
  }

  for (Group.Builder nested : group.gbuilders) {
    addVariables(nested);
  }
}
 

/** Add a Variable to the root group. */
public Variable.Builder addVariable(String shortName, DataType dataType, List<Dimension> dims) {
  if (!isNewFile && !useJna) {
    throw new UnsupportedOperationException("Cant add variable to existing netcdf-3 files");
  }
  Variable.Builder vb = Variable.builder().setName(shortName).setDataType(dataType).setParentGroupBuilder(rootGroup)
      .setDimensions(dims);
  rootGroup.addVariable(vb);
  return vb;
}
 

@Override
protected void augmentDataset(CancelTask cancelTask) throws IOException {
  NcMLReaderNew.wrapNcMLresource(datasetBuilder, CoordSystemFactory.resourcesDir + "Zebra.ncml", cancelTask);

  // special time handling
  // the time coord var is created in the NcML
  // set its values = base_time + time_offset(time)
  Dimension timeDim = rootGroup.findDimension("time").orElse(null);
  VariableDS.Builder base_time = (VariableDS.Builder) rootGroup.findVariableLocal("base_time").orElse(null);
  VariableDS.Builder time_offset = (VariableDS.Builder) rootGroup.findVariableLocal("time_offset").orElse(null);
  Variable.Builder time = rootGroup.findVariableLocal("time").orElse(null);
  if ((timeDim == null) || (base_time == null) || (time_offset == null) || (time == null))
    return;

  String units =
      base_time.getAttributeContainer().findAttributeString(CDM.UNITS, "seconds since 1970-01-01 00:00 UTC");
  time.addAttribute(new Attribute(CDM.UNITS, units));

  Array data;
  try {
    double baseValue = base_time.orgVar.readScalarDouble();

    data = time_offset.orgVar.read();
    IndexIterator iter = data.getIndexIterator();
    while (iter.hasNext())
      iter.setDoubleCurrent(iter.getDoubleNext() + baseValue);

  } catch (IOException ioe) {
    parseInfo.format("ZebraConvention failed to create time Coord Axis for file %s err= %s%n",
        datasetBuilder.location, ioe);
    return;
  }

  time.setCachedData(data, true);
}
 

private void addMembersToStructure(Group.Builder parent, Structure.Builder<?> s, MessageDatatype mdt)
    throws IOException {
  for (StructureMember m : mdt.members) {
    Variable.Builder v = makeVariableMember(parent, m.name, m.offset, m.mdt);
    if (v != null) {
      s.addMemberVariable(v);
      if (debug1) {
        log.debug("  made Member Variable " + v.shortName + "\n" + v);
      }
    }
  }
}
 

void setVariable(Variable.Builder v) {
  this.v = v;
  v.setSPobject(this);
}
 

/**
 * Read the NcML variable element, and nested elements.
 *
 * @param groupBuilder put dimension into this group
 * @param refGroup parent Group in referenced dataset, may be null
 * @param varElem ncml variable element
 */
private void readVariable(Group.Builder groupBuilder, @Nullable Group refGroup, Element varElem) {
  String name = varElem.getAttributeValue("name");
  if (name == null) {
    errlog.format("NcML Variable name is required (%s)%n", varElem);
    return;
  }
  String nameInFile = Optional.ofNullable(varElem.getAttributeValue("orgName")).orElse(name);

  DataType dtype = null;
  String typeS = varElem.getAttributeValue("type");
  if (typeS != null) {
    dtype = DataType.getType(typeS);
  }

  // see if it already exists
  Variable refv = (refGroup == null) ? null : refGroup.findVariableLocal(nameInFile);
  Optional<Variable.Builder<?>> addedFromAgg = groupBuilder.findVariableLocal(nameInFile);
  if (refv == null && !addedFromAgg.isPresent()) { // new
    if (dtype == null) {
      errlog.format("NcML Variable dtype is required for new variable (%s)%n", name);
      return;
    }
    if (dtype == DataType.STRUCTURE || dtype == DataType.SEQUENCE) {
      groupBuilder.addVariable(readStructureNew(groupBuilder, varElem));
    } else {
      groupBuilder.addVariable(readVariableNew(groupBuilder, dtype, varElem));
    }
    return;
  }

  // refv exists
  if (refv != null) {
    if (dtype == null) {
      dtype = refv.getDataType();
    }
    if (dtype == DataType.STRUCTURE || dtype == DataType.SEQUENCE) {
      readStructureExisting(groupBuilder, null, dtype, (Structure) refv, varElem)
          .ifPresent(groupBuilder::addVariable);
    } else {
      readVariableExisting(groupBuilder, null, dtype, refv, varElem).ifPresent(groupBuilder::addVariable);
    }
    return;
  }

  // refv does not exist, but addedFromAgg may be present
  DataType finalDtype = dtype;
  addedFromAgg.ifPresent(agg -> {
    if (agg instanceof VariableDS.Builder<?>) {
      VariableDS.Builder<?> aggDs = (VariableDS.Builder<?>) agg;
      aggDs.setOriginalName(nameInFile);
    }
    DataType reallyFinalDtype = finalDtype != null ? finalDtype : agg.dataType;
    augmentVariableNew(agg, reallyFinalDtype, varElem);
  });
}
 

private Variable.Builder copyVariable(Group.Builder parent, Variable oldVar) throws IOException {
  Variable.Builder vb;
  DataType newType = oldVar.getDataType();
  String dimNames = Dimensions.makeDimensionsString(oldVar.getDimensions());

  if (newType == DataType.STRUCTURE) {
    Structure oldStruct = (Structure) oldVar;
    Structure.Builder sb = Structure.builder().setName(oldVar.getShortName());
    for (Variable nested : oldStruct.getVariables()) {
      sb.addMemberVariable(copyVariable(parent, nested));
    }
    vb = sb;
  } else {
    vb = Variable.builder().setName(oldVar.getShortName()).setDataType(newType);
    if (!extended && newType == DataType.STRING) {
      // find maximum length
      Array data = oldVar.read();
      IndexIterator ii = data.getIndexIterator();
      int max_len = 0;
      while (ii.hasNext()) {
        String s = (String) ii.getObjectNext();
        max_len = Math.max(max_len, s.length());
      }

      // add last dimension
      String strlenDimName = oldVar.getShortName() + "_strlen";
      parent.addDimension(Dimension.builder(strlenDimName, max_len).setIsShared(false).build());

      newType = DataType.CHAR;
      vb.setDataType(DataType.CHAR);
      dimNames += " " + strlenDimName;
    }
  }
  vb.setParentGroupBuilder(parent).setDimensionsByName(dimNames);

  if (newType.isEnum()) {
    EnumTypedef en = oldVar.getEnumTypedef();
    vb.setEnumTypeName(en.getShortName());
  }

  // attributes
  for (Attribute att : oldVar.attributes()) {
    vb.addAttribute(convertAttribute(att));
    if (debug) {
      System.out.println("add varAtt= " + att);
    }
  }

  return vb;
}
 

private void addVariableToGroup(Group.Builder g, Variable.Builder v, Tag tag) {
  g.findVariableLocal(v.shortName).ifPresent(varExisting -> v.setName(v.shortName + tag.refno)); // disambiguate
  g.addVariable(v);
  tag.vinfo.group = g;
}
 

String readStructMetadata(Variable.Builder<?> structMetadataVar) throws IOException;