Exemple #1
0
  public boolean compareVariables(
      Variable org, Variable copy, boolean compareData, boolean justOne) {
    boolean ok = true;

    if (showCompare)
      f.format("compare Variable %s to %s %n", org.getFullName(), copy.getFullName());
    if (!org.getFullName().equals(copy.getFullName())) {
      f.format(" ** names are different %s != %s %n", org.getFullName(), copy.getFullName());
      ok = false;
    }

    // dimensions
    ok &= checkAll(org.getDimensions(), copy.getDimensions(), null);

    // attributes
    ok &= checkAll(org.getAttributes(), copy.getAttributes(), null);

    // coord sys
    if ((org instanceof VariableEnhanced) && (copy instanceof VariableEnhanced)) {
      VariableEnhanced orge = (VariableEnhanced) org;
      VariableEnhanced copye = (VariableEnhanced) copy;
      ok &= checkAll(orge.getCoordinateSystems(), copye.getCoordinateSystems(), null);
    }

    // data !!
    if (compareData) {
      try {
        compareVariableData(org, copy, showCompare, justOne);

      } catch (IOException e) {
        ByteArrayOutputStream bos = new ByteArrayOutputStream(10000);
        e.printStackTrace(new PrintStream(bos));
        f.format("%s", bos.toString());
      }
    }

    // nested variables
    if (org instanceof Structure) {
      if (!(copy instanceof Structure)) {
        f.format("  ** %s not Structure%n", org);
        ok = false;

      } else {
        Structure orgS = (Structure) org;
        Structure ncmlS = (Structure) copy;

        List vars = new ArrayList();
        ok &= checkAll(orgS.getVariables(), ncmlS.getVariables(), vars);
        for (int i = 0; i < vars.size(); i += 2) {
          Variable orgV = (Variable) vars.get(i);
          Variable ncmlV = (Variable) vars.get(i + 1);
          ok &= compareVariables(orgV, ncmlV, false, true);
        }
      }
    }

    return ok;
  }
Exemple #2
0
  private void doVariable(Variable v, opendap.dap.AttributeTable parentTable) {

    List dims = v.getDimensions();
    for (int i = 0; i < dims.size(); i++) {
      Dimension dim = (Dimension) dims.get(i);
      if (dim.isShared()) usedDims.put(dim.getName(), dim);
    }

    // if (v.getAttributes().size() == 0) return; // LOOK DAP 2 say must have empty

    String name = NcDDS.escapeName(v.getShortName());
    opendap.dap.AttributeTable table;

    if (parentTable == null) {
      table = new opendap.dap.AttributeTable(name);
      try {
        addAttributeTable(name, table);
      } catch (AttributeExistsException e) {
        log.error("Cant add " + name, e);
      }
    } else {
      table = parentTable.appendContainer(name);
    }

    addAttributes(table, v, v.getAttributes().iterator());

    if (v instanceof Structure) {
      Structure s = (Structure) v;
      List nested = s.getVariables();
      for (int i = 0; i < nested.size(); i++) {
        Variable nv = (Variable) nested.get(i);
        doVariable(nv, table);
      }
    }
  }
 public List<VariableBean> getStructureVariables(Structure s) {
   List<VariableBean> vlist = new ArrayList<VariableBean>();
   for (Variable v : s.getVariables()) {
     vlist.add(new VariableBean(v));
   }
   return vlist;
 }
    void makeChildren() {
      children = new ArrayList<>();

      if (var instanceof Structure) {
        Structure s = (Structure) var;
        List vars = s.getVariables();
        for (int i = 0; i < vars.size(); i++)
          children.add(new VariableNode(this, (VariableIF) vars.get(i)));
      }

      if (debugTree) System.out.println("children=" + var.getShortName() + " ");
    }
  public static void main(String args[]) throws Exception {
    long start = System.currentTimeMillis();
    Map<String, ucar.unidata.geoloc.Station> staHash =
        new HashMap<String, ucar.unidata.geoloc.Station>();

    String location = "R:/testdata/sounding/netcdf/Upperair_20070401_0000.nc";
    NetcdfDataset ncfile = NetcdfDataset.openDataset(location);
    ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);

    // look through record varibles, for those that have "manLevel" dimension
    // make a StructureData object for those
    StructureMembers sm = new StructureMembers("manLevel");
    Dimension manDim = ncfile.findDimension("manLevel");
    Structure record = (Structure) ncfile.findVariable("record");
    List<Variable> allList = record.getVariables();
    List<VariableSimpleIF> varList = new ArrayList<VariableSimpleIF>();
    for (Variable v : allList) {
      if ((v.getRank() == 1) && v.getDimension(0).equals(manDim)) {
        // public VariableDS(NetcdfDataset ds, Group group, Structure parentStructure, String
        // shortName, DataType dataType,
        // String dims, String units, String desc) {
        varList.add(
            new VariableDS(
                ncfile,
                null,
                null,
                v.getShortName(),
                v.getDataType(),
                "",
                v.getUnitsString(),
                v.getDescription()));
        // (String name, String desc, String units, DataType dtype, int []shape)
        sm.addMember(
            v.getShortName(),
            v.getDescription(),
            v.getUnitsString(),
            v.getDataType(),
            new int[0]); // scalar
      }
    }

    ArrayStructureMA manAS = new ArrayStructureMA(sm, new int[] {manDim.getLength()});

    // need the date units
    Variable time = ncfile.findVariable("synTime");
    String timeUnits = ncfile.findAttValueIgnoreCase(time, "units", null);
    timeUnits = StringUtil.remove(timeUnits, '('); // crappy fsl'ism
    timeUnits = StringUtil.remove(timeUnits, ')');
    DateUnit timeUnit = new DateUnit(timeUnits);

    // extract stations
    int nrecs = 0;
    StructureDataIterator iter = record.getStructureIterator();
    while (iter.hasNext()) {
      StructureData sdata = iter.next();
      String name = sdata.getScalarString("staName");
      ucar.unidata.geoloc.Station s = staHash.get(name);
      if (s == null) {
        float lat = sdata.convertScalarFloat("staLat");
        float lon = sdata.convertScalarFloat("staLon");
        float elev = sdata.convertScalarFloat("staElev");
        s = new StationImpl(name, "", lat, lon, elev);
        staHash.put(name, s);
      }
      nrecs++;
    }
    List<ucar.unidata.geoloc.Station> stnList =
        Arrays.asList(staHash.values().toArray(new ucar.unidata.geoloc.Station[staHash.size()]));
    Collections.sort(stnList);

    // create the writer
    WriterProfileObsDataset writer =
        new WriterProfileObsDataset(location + ".out", "rewrite " + location);
    writer.writeHeader(stnList, varList, nrecs, "prMan");

    // extract records
    iter = record.getStructureIterator();
    while (iter.hasNext()) {
      StructureData sdata = iter.next();
      String name = sdata.getScalarString("staName");
      double timeValue = sdata.convertScalarDouble("synTime");
      Date date = timeUnit.makeDate(timeValue);

      // transfer to the ArrayStructure
      List<String> names = sm.getMemberNames();
      for (String mname : names) {
        manAS.setMemberArray(mname, sdata.getArray(mname));
      }

      // each level is weritten as a seperate structure
      int numMand = sdata.getScalarInt("numMand");
      if (numMand >= manDim.getLength()) continue;

      for (int i = 0; i < numMand; i++) {
        StructureData useData = manAS.getStructureData(i);
        writer.writeRecord(name, date, useData);
      }
    }

    writer.finish();

    long took = System.currentTimeMillis() - start;
    System.out.println("That took = " + took);
  }
    // create from a dataset
    public ObsBean(Structure obs, StructureData sdata) {
      // first choice
      for (Variable v : obs.getVariables()) {
        Attribute att = v.findAttribute("BUFR:TableB_descriptor");
        if (att == null) continue;
        String val = att.getStringValue();
        if (val.equals("0-5-1") && Double.isNaN(lat)) {
          lat = sdata.convertScalarDouble(v.getShortName());
        } else if (val.equals("0-6-1") && Double.isNaN(lon)) {
          lon = sdata.convertScalarDouble(v.getShortName());
        } else if (val.equals("0-7-30") && Double.isNaN(alt)) {

          alt = sdata.convertScalarDouble(v.getShortName());
        } else if (val.equals("0-4-1") && (year < 0)) {
          year = sdata.convertScalarInt(v.getShortName());
        } else if (val.equals("0-4-2") && (month < 0)) {
          month = sdata.convertScalarInt(v.getShortName());
        } else if (val.equals("0-4-3") && (day < 0)) {
          day = sdata.convertScalarInt(v.getShortName());
        } else if (val.equals("0-4-4") && (hour < 0)) {
          hour = sdata.convertScalarInt(v.getShortName());
        } else if (val.equals("0-4-5") && (minute < 0)) {
          minute = sdata.convertScalarInt(v.getShortName());
        } else if (val.equals("0-4-6") && (sec < 0)) {
          sec = sdata.convertScalarInt(v.getShortName());

        } else if (val.equals("0-1-1") && (wmo_block < 0)) {
          wmo_block = sdata.convertScalarInt(v.getShortName());
        } else if (val.equals("0-1-2") && (wmo_id < 0)) {
          wmo_id = sdata.convertScalarInt(v.getShortName());

        } else if ((stn == null)
            && (val.equals("0-1-7")
                || val.equals("0-1-194")
                || val.equals("0-1-11")
                || val.equals("0-1-18"))) {
          if (v.getDataType().isString()) stn = sdata.getScalarString(v.getShortName());
          else stn = Integer.toString(sdata.convertScalarInt(v.getShortName()));
        }
      }

      // second choice
      for (Variable v : obs.getVariables()) {
        Attribute att = v.findAttribute("BUFR:TableB_descriptor");
        if (att == null) continue;
        String val = att.getStringValue();
        if (val.equals("0-5-2") && Double.isNaN(lat)) {
          lat = sdata.convertScalarDouble(v.getShortName());
        } else if (val.equals("0-6-2") && Double.isNaN(lon)) {
          lon = sdata.convertScalarDouble(v.getShortName());
        } else if (val.equals("0-7-1") && Double.isNaN(alt)) {
          alt = sdata.convertScalarDouble(v.getShortName());
        } else if ((val.equals("0-4-7")) && (sec < 0)) {
          sec = sdata.convertScalarInt(v.getShortName());
        }
      }

      // third choice
      for (Variable v : obs.getVariables()) {
        Attribute att = v.findAttribute("BUFR:TableB_descriptor");
        if (att == null) continue;
        String val = att.getStringValue();
        if (val.equals("0-7-10") && Double.isNaN(alt)) {
          alt = sdata.convertScalarDouble(v.getShortName());
        } else if (val.equals("0-7-2") && Double.isNaN(alt)) {
          alt = sdata.convertScalarDouble(v.getShortName());
        }
      }
    }
Exemple #7
0
  Write2ncRect(NetcdfFile bufr, String fileOutName, boolean fill)
      throws IOException, InvalidRangeException {

    NetcdfFileWriteable ncfile = NetcdfFileWriteable.createNew(fileOutName, fill);
    if (debug) {
      System.out.println("FileWriter write " + bufr.getLocation() + " to " + fileOutName);
    }

    // global attributes
    List<Attribute> glist = bufr.getGlobalAttributes();
    for (Attribute att : glist) {
      String useName = N3iosp.makeValidNetcdfObjectName(att.getName());
      Attribute useAtt;
      if (att.isArray()) useAtt = ncfile.addGlobalAttribute(useName, att.getValues());
      else if (att.isString()) useAtt = ncfile.addGlobalAttribute(useName, att.getStringValue());
      else useAtt = ncfile.addGlobalAttribute(useName, att.getNumericValue());
      if (debug) System.out.println("add gatt= " + useAtt);
    }

    // global dimensions
    Dimension recordDim = null;
    Map<String, Dimension> dimHash = new HashMap<String, Dimension>();
    for (Dimension oldD : bufr.getDimensions()) {
      String useName = N3iosp.makeValidNetcdfObjectName(oldD.getName());
      boolean isRecord = useName.equals("record");
      Dimension newD = ncfile.addDimension(useName, oldD.getLength(), true, false, false);
      dimHash.put(newD.getName(), newD);
      if (isRecord) recordDim = newD;
      if (debug) System.out.println("add dim= " + newD);
    }

    // Variables
    Structure recordStruct = (Structure) bufr.findVariable(BufrIosp.obsRecord);
    for (Variable oldVar : recordStruct.getVariables()) {
      if (oldVar.getDataType() == DataType.STRUCTURE) continue;

      String varName = N3iosp.makeValidNetcdfObjectName(oldVar.getShortName());
      DataType newType = oldVar.getDataType();

      List<Dimension> newDims = new ArrayList<Dimension>();
      newDims.add(recordDim);
      for (Dimension dim : oldVar.getDimensions()) {
        newDims.add(ncfile.addDimension(oldVar.getShortName() + "_strlen", dim.getLength()));
      }

      Variable newVar = ncfile.addVariable(varName, newType, newDims);
      if (debug) System.out.println("add var= " + newVar);

      // attributes
      List<Attribute> attList = oldVar.getAttributes();
      for (Attribute att : attList) {
        String useName = N3iosp.makeValidNetcdfObjectName(att.getName());
        if (att.isArray()) ncfile.addVariableAttribute(varName, useName, att.getValues());
        else if (att.isString())
          ncfile.addVariableAttribute(varName, useName, att.getStringValue());
        else ncfile.addVariableAttribute(varName, useName, att.getNumericValue());
      }
    }

    // int max_seq = countSeq(recordStruct);
    // Dimension seqD = ncfile.addDimension("level", max_seq);

    for (Variable v : recordStruct.getVariables()) {
      if (v.getDataType() != DataType.STRUCTURE) continue;
      String structName = N3iosp.makeValidNetcdfObjectName(v.getShortName());
      int shape[] = v.getShape();

      Dimension structDim = ncfile.addDimension(structName, shape[0]);

      Structure struct = (Structure) v;
      for (Variable seqVar : struct.getVariables()) {
        String varName = N3iosp.makeValidNetcdfObjectName(seqVar.getShortName() + "-" + structName);
        DataType newType = seqVar.getDataType();

        List<Dimension> newDims = new ArrayList<Dimension>();
        newDims.add(recordDim);
        newDims.add(structDim);
        for (Dimension dim : seqVar.getDimensions()) {
          newDims.add(ncfile.addDimension(seqVar.getShortName() + "_strlen", dim.getLength()));
        }

        Variable newVar = ncfile.addVariable(varName, newType, newDims);
        if (debug) System.out.println("add var= " + newVar);

        // attributes
        List<Attribute> attList = seqVar.getAttributes();
        for (Attribute att : attList) {
          String useName = N3iosp.makeValidNetcdfObjectName(att.getName());
          if (att.isArray()) ncfile.addVariableAttribute(varName, useName, att.getValues());
          else if (att.isString())
            ncfile.addVariableAttribute(varName, useName, att.getStringValue());
          else ncfile.addVariableAttribute(varName, useName, att.getNumericValue());
        }
      }
    }

    // create the file
    ncfile.create();
    if (debug) System.out.println("File Out= " + ncfile.toString());

    // boolean ok = (Boolean) ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);

    double total = copyVarData(ncfile, recordStruct);
    ncfile.flush();
    System.out.println("FileWriter done total bytes = " + total);
    ncfile.close();
  }