Exemple #1
0
  public static boolean isMine(NetcdfFile ncfile) {
    if (!ncfile.getFileTypeId().equals("HDF5")) return false;

    Group loc = ncfile.findGroup("VHRR/Geo-Location");
    if (null == loc) return false;
    if (null == loc.findVariable("Latitude")) return false;
    if (null == loc.findVariable("Longitude")) return false;

    if (null == ncfile.findGroup("VHRR/Image Data")) return false;
    return true;
  }
Exemple #2
0
  private static String getStructMetadata(Group eosGroup) throws IOException {
    StringBuilder sbuff = null;
    String structMetadata = null;

    int n = 0;
    while (true) {
      Variable structMetadataVar = eosGroup.findVariable("StructMetadata." + n);
      if (structMetadataVar == null) break;
      if ((structMetadata != null) && (sbuff == null)) { // more than 1 StructMetadata
        sbuff = new StringBuilder(64000);
        sbuff.append(structMetadata);
      }

      // read and parse the ODL
      Array A = structMetadataVar.read();
      if (A instanceof ArrayChar.D1) {
        ArrayChar ca = (ArrayChar) A;
        structMetadata = ca.getString(); // common case only StructMetadata.0, avoid extra copy
      } else if (A instanceof ArrayObject.D0) {
        ArrayObject ao = (ArrayObject) A;
        structMetadata = (String) ao.getObject(0);
      } else {
        log.error("Unsupported array type {} for StructMetadata", A.getElementType());
      }

      if (sbuff != null) sbuff.append(structMetadata);
      n++;
    }
    return (sbuff != null) ? sbuff.toString() : structMetadata;
  }
Exemple #3
0
  private boolean compareGroups(Group org, Group copy) {
    if (showCompare) f.format("compare Group %s to %s %n", org.getName(), copy.getName());
    boolean ok = true;

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

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

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

    // variables
    // cant use object equality, just match on short name
    for (Variable orgV : org.getVariables()) {
      Variable copyVar = copy.findVariable(orgV.getShortName());
      if (copyVar == null) {
        f.format(" ** cant find variable %s in 2nd file%n", orgV.getFullName());
        ok = false;
      } else {
        ok &= compareVariables(orgV, copyVar, compareData, true);
      }
    }

    for (Variable copyV : copy.getVariables()) {
      Variable orgV = org.findVariable(copyV.getShortName());
      if (orgV == null) {
        f.format(" ** cant find variable %s in 1st file%n", copyV.getFullName());
        ok = false;
      }
    }

    // nested groups
    List groups = new ArrayList();
    ok &= checkAll(org.getGroups(), copy.getGroups(), groups);
    for (int i = 0; i < groups.size(); i += 2) {
      Group orgGroup = (Group) groups.get(i);
      Group ncmlGroup = (Group) groups.get(i + 1);
      ok &= compareGroups(orgGroup, ncmlGroup);
    }

    return ok;
  }
Exemple #4
0
  private FeatureType amendGrid(
      Element gridElem, NetcdfFile ncfile, Group parent, String location) {
    List<Dimension> unknownDims = new ArrayList<>();

    // always has x and y dimension
    String xdimSizeS = gridElem.getChild("XDim").getText().trim();
    String ydimSizeS = gridElem.getChild("YDim").getText().trim();
    int xdimSize = Integer.parseInt(xdimSizeS);
    int ydimSize = Integer.parseInt(ydimSizeS);
    parent.addDimensionIfNotExists(new Dimension("XDim", xdimSize));
    parent.addDimensionIfNotExists(new Dimension("YDim", ydimSize));

    /* see HdfEosModisConvention
    UpperLeftPointMtrs=(-20015109.354000,1111950.519667)
    		LowerRightMtrs=(-18903158.834333,-0.000000)
    		Projection=GCTP_SNSOID
    		ProjParams=(6371007.181000,0,0,0,0,0,0,0,0,0,0,0,0)
    		SphereCode=-1
     */
    Element proj = gridElem.getChild("Projection");
    if (proj != null) {
      Variable crs = new Variable(ncfile, parent, null, HDFEOS_CRS);
      crs.setDataType(DataType.SHORT);
      crs.setDimensions(""); // scalar
      crs.setCachedData(Array.makeArray(DataType.SHORT, 1, 0, 0)); // fake data
      parent.addVariable(crs);

      addAttributeIfExists(gridElem, HDFEOS_CRS_Projection, crs, false);
      addAttributeIfExists(gridElem, HDFEOS_CRS_UpperLeft, crs, true);
      addAttributeIfExists(gridElem, HDFEOS_CRS_LowerRight, crs, true);
      addAttributeIfExists(gridElem, HDFEOS_CRS_ProjParams, crs, true);
      addAttributeIfExists(gridElem, HDFEOS_CRS_SphereCode, crs, false);
    }

    // global Dimensions
    Element d = gridElem.getChild("Dimension");
    List<Element> dims = d.getChildren();
    for (Element elem : dims) {
      String name = elem.getChild("DimensionName").getText().trim();
      name = NetcdfFile.makeValidCdmObjectName(name);
      if (name.equalsIgnoreCase("scalar")) continue;

      String sizeS = elem.getChild("Size").getText().trim();
      int length = Integer.parseInt(sizeS);
      Dimension old = parent.findDimension(name);
      if ((old == null) || (old.getLength() != length)) {
        if (length > 0) {
          Dimension dim = new Dimension(name, length);
          if (parent.addDimensionIfNotExists(dim) && showWork)
            System.out.printf(" Add dimension %s %n", dim);
        } else {
          log.warn("Dimension {} has size {} {} ", sizeS, name, location);
          Dimension udim = new Dimension(name, 1);
          udim.setGroup(parent);
          unknownDims.add(udim);
          if (showWork) System.out.printf(" Add dimension %s %n", udim);
        }
      }
    }

    // Geolocation Variables
    Group geoFieldsG = parent.findGroup(GEOLOC_FIELDS);
    if (geoFieldsG == null) geoFieldsG = parent.findGroup(GEOLOC_FIELDS2);

    if (geoFieldsG != null) {
      Element floc = gridElem.getChild("GeoField");
      List<Element> varsLoc = floc.getChildren();
      for (Element elem : varsLoc) {
        String varname = elem.getChild("GeoFieldName").getText().trim();
        Variable v = geoFieldsG.findVariable(varname);
        // if (v == null)
        //  v = geoFieldsG.findVariable( H4header.createValidObjectName(varname));
        assert v != null : varname;

        Element dimList = elem.getChild("DimList");
        List<Element> values = dimList.getChildren("value");
        setSharedDimensions(v, values, unknownDims, location);
      }
    }

    // Data Variables
    Group dataG = parent.findGroup(DATA_FIELDS);
    if (dataG == null)
      dataG =
          parent.findGroup(
              DATA_FIELDS2); // eg C:\data\formats\hdf4\eos\mopitt\MOP03M-200501-L3V81.0.1.hdf

    if (dataG != null) {
      Element f = gridElem.getChild("DataField");
      List<Element> vars = f.getChildren();
      for (Element elem : vars) {
        String varname = elem.getChild("DataFieldName").getText().trim();
        varname = NetcdfFile.makeValidCdmObjectName(varname);
        Variable v = dataG.findVariable(varname);
        // if (v == null)
        //  v = dataG.findVariable( H4header.createValidObjectName(varname));
        assert v != null : varname;

        Element dimList = elem.getChild("DimList");
        List<Element> values = dimList.getChildren("value");
        setSharedDimensions(v, values, unknownDims, location);
      }

      // get projection
      String projS = null;
      Element projElem = gridElem.getChild("Projection");
      if (projElem != null) projS = projElem.getText().trim();
      boolean isLatLon = "GCTP_GEO".equals(projS);

      // look for XDim, YDim coordinate variables
      if (isLatLon) {
        for (Variable v : dataG.getVariables()) {
          if (v.isCoordinateVariable()) {
            if (v.getShortName().equals("YDim")) {
              v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
              v.addAttribute(new Attribute(CDM.UNITS, CDM.LAT_UNITS));
            }
            if (v.getShortName().equals("XDim"))
              v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
          }
        }
      }
    }
    return FeatureType.GRID;
  }
Exemple #5
0
  private FeatureType amendSwath(NetcdfFile ncfile, Element swathElem, Group parent) {
    FeatureType featureType = FeatureType.SWATH;
    List<Dimension> unknownDims = new ArrayList<>();

    // Dimensions
    Element d = swathElem.getChild("Dimension");
    List<Element> dims = d.getChildren();
    for (Element elem : dims) {
      String name = elem.getChild("DimensionName").getText().trim();
      name = NetcdfFile.makeValidCdmObjectName(name);

      if (name.equalsIgnoreCase("scalar")) continue;
      String sizeS = elem.getChild("Size").getText().trim();
      int length = Integer.parseInt(sizeS);
      if (length > 0) {
        Dimension dim = parent.findDimensionLocal(name);
        if (dim != null) { // already added - may be dimension scale ?
          if (dim.getLength() != length) { // ok as long as it matches
            log.error("Conflicting Dimensions = {} {}", dim, ncfile.getLocation());
            throw new IllegalStateException("Conflicting Dimensions = " + name);
          }
        } else {
          dim = new Dimension(name, length);
          if (parent.addDimensionIfNotExists(dim) && showWork)
            System.out.printf(" Add dimension %s %n", dim);
        }
      } else {
        log.warn("Dimension " + name + " has size " + sizeS, ncfile.getLocation());
        Dimension udim = new Dimension(name, 1);
        udim.setGroup(parent);
        unknownDims.add(udim);
        if (showWork) System.out.printf(" Add dimension %s %n", udim);
      }
    }

    // Dimension Maps
    Element dmap = swathElem.getChild("DimensionMap");
    List<Element> dimMaps = dmap.getChildren();
    for (Element elem : dimMaps) {
      String geoDimName = elem.getChild("GeoDimension").getText().trim();
      geoDimName = NetcdfFile.makeValidCdmObjectName(geoDimName);
      String dataDimName = elem.getChild("DataDimension").getText().trim();
      dataDimName = NetcdfFile.makeValidCdmObjectName(dataDimName);

      String offsetS = elem.getChild("Offset").getText().trim();
      String incrS = elem.getChild("Increment").getText().trim();
      int offset = Integer.parseInt(offsetS);
      int incr = Integer.parseInt(incrS);

      // make new variable for this dimension map
      Variable v = new Variable(ncfile, parent, null, dataDimName);
      v.setDimensions(geoDimName);
      v.setDataType(DataType.INT);
      int npts = (int) v.getSize();
      Array data = Array.makeArray(v.getDataType(), npts, offset, incr);
      v.setCachedData(data, true);
      v.addAttribute(new Attribute("_DimensionMap", ""));
      parent.addVariable(v);
      if (showWork) System.out.printf(" Add dimensionMap %s %n", v);
    }

    // Geolocation Variables
    Group geoFieldsG = parent.findGroup(GEOLOC_FIELDS);
    if (geoFieldsG == null) geoFieldsG = parent.findGroup(GEOLOC_FIELDS2);
    if (geoFieldsG != null) {
      Variable latAxis = null, lonAxis = null;
      Element floc = swathElem.getChild("GeoField");
      List<Element> varsLoc = floc.getChildren();
      for (Element elem : varsLoc) {
        String varname = elem.getChild("GeoFieldName").getText().trim();
        Variable v = geoFieldsG.findVariable(varname);
        // if (v == null)
        //  v = geoFieldsG.findVariable( H4header.createValidObjectName(varname));
        assert v != null : varname;
        AxisType axis = addAxisType(ncfile, v);
        if (axis == AxisType.Lat) latAxis = v;
        if (axis == AxisType.Lon) lonAxis = v;

        Element dimList = elem.getChild("DimList");
        List<Element> values = dimList.getChildren("value");
        setSharedDimensions(v, values, unknownDims, ncfile.getLocation());
        if (showWork) System.out.printf(" set coordinate %s %n", v);
      }
      if ((latAxis != null) && (lonAxis != null)) {
        List<Dimension> xyDomain = CoordinateSystem.makeDomain(new Variable[] {latAxis, lonAxis});
        if (xyDomain.size() < 2) featureType = FeatureType.PROFILE; // ??
      }
    }

    // Data Variables
    Group dataG = parent.findGroup(DATA_FIELDS);
    if (dataG == null) dataG = parent.findGroup(DATA_FIELDS2);
    if (dataG != null) {
      Element f = swathElem.getChild("DataField");
      List<Element> vars = f.getChildren();
      for (Element elem : vars) {
        Element dataFieldNameElem = elem.getChild("DataFieldName");
        if (dataFieldNameElem == null) continue;
        String varname = NetcdfFile.makeValidCdmObjectName(dataFieldNameElem.getText().trim());
        Variable v = dataG.findVariable(varname);
        // if (v == null)
        //  v = dataG.findVariable( H4header.createValidObjectName(varname));
        if (v == null) {
          log.error("Cant find variable {} {}", varname, ncfile.getLocation());
          continue;
        }

        Element dimList = elem.getChild("DimList");
        List<Element> values = dimList.getChildren("value");
        setSharedDimensions(v, values, unknownDims, ncfile.getLocation());
      }
    }

    return featureType;
  }
  /**
   * Add this coord as a variable in the netCDF file
   *
   * @param ncfile netCDF file to add to
   * @param g group in file
   */
  void addToNetcdfFile(NetcdfFile ncfile, Group g) {
    if (dontUseVertical) {
      typicalRecord = null;
      return;
    }

    if (g == null) {
      g = ncfile.getRootGroup();
    }

    // coordinate axis
    Variable v = new Variable(ncfile, g, null, getVariableName());
    v.setDataType(DataType.DOUBLE);

    String desc = lookup.getLevelDescription(typicalRecord);
    if (lookup instanceof Grib2GridTableLookup && usesBounds) {
      desc = "Layer between " + desc;
    }

    v.addAttribute(new Attribute("long_name", desc));
    v.addAttribute(new Attribute("units", lookup.getLevelUnit(typicalRecord)));

    // positive attribute needed for CF-1 Height and Pressure
    if (positive != null) {
      v.addAttribute(new Attribute("positive", positive));
    }

    if (units != null) {
      AxisType axisType;
      if (SimpleUnit.isCompatible("millibar", units)) {
        axisType = AxisType.Pressure;
      } else if (SimpleUnit.isCompatible("m", units)) {
        axisType = AxisType.Height;
      } else {
        axisType = AxisType.GeoZ;
      }

      if (lookup instanceof Grib2GridTableLookup || lookup instanceof Grib1GridTableLookup) {
        v.addAttribute(
            new Attribute("GRIB_level_type", Integer.toString(typicalRecord.getLevelType1())));
      } else {
        v.addAttribute(
            new Attribute("level_type", Integer.toString(typicalRecord.getLevelType1())));
      }
      v.addAttribute(new Attribute(_Coordinate.AxisType, axisType.toString()));
    }

    if (coordValues == null) {
      coordValues = new double[levels.size()];
      for (int i = 0; i < levels.size(); i++) {
        LevelCoord lc = (LevelCoord) levels.get(i);
        coordValues[i] = lc.mid;
      }
    }
    Array dataArray = Array.factory(DataType.DOUBLE, new int[] {coordValues.length}, coordValues);

    v.setDimensions(getVariableName());
    v.setCachedData(dataArray, true);

    ncfile.addVariable(g, v);

    if (usesBounds) {
      String boundsDimName = "bounds_dim";
      if (g.findDimension(boundsDimName) == null) {
        ncfile.addDimension(g, new Dimension(boundsDimName, 2, true));
      }

      String bname = getVariableName() + "_bounds";
      v.addAttribute(new Attribute("bounds", bname));
      v.addAttribute(new Attribute(_Coordinate.ZisLayer, "true"));

      Variable b = new Variable(ncfile, g, null, bname);
      b.setDataType(DataType.DOUBLE);
      b.setDimensions(getVariableName() + " " + boundsDimName);
      b.addAttribute(new Attribute("long_name", "bounds for " + v.getName()));
      b.addAttribute(new Attribute("units", lookup.getLevelUnit(typicalRecord)));

      Array boundsArray = Array.factory(DataType.DOUBLE, new int[] {coordValues.length, 2});
      ucar.ma2.Index ima = boundsArray.getIndex();
      for (int i = 0; i < coordValues.length; i++) {
        LevelCoord lc = (LevelCoord) levels.get(i);
        boundsArray.setDouble(ima.set(i, 0), lc.value1);
        boundsArray.setDouble(ima.set(i, 1), lc.value2);
      }
      b.setCachedData(boundsArray, true);

      ncfile.addVariable(g, b);
    }

    if (factors != null) {
      // check if already created
      if (g == null) {
        g = ncfile.getRootGroup();
      }
      if (g.findVariable("hybrida") != null) return;
      v.addAttribute(new Attribute("standard_name", "atmosphere_hybrid_sigma_pressure_coordinate"));
      v.addAttribute(new Attribute("formula_terms", "ap: hybrida b: hybridb ps: Pressure"));
      // create  hybrid factor variables
      // add hybrida variable
      Variable ha = new Variable(ncfile, g, null, "hybrida");
      ha.setDataType(DataType.DOUBLE);
      ha.addAttribute(new Attribute("long_name", "level_a_factor"));
      ha.addAttribute(new Attribute("units", ""));
      ha.setDimensions(getVariableName());
      // add data
      int middle = factors.length / 2;
      double[] adata;
      double[] bdata;
      if (levels.size() < middle) { // only partial data wanted
        adata = new double[levels.size()];
        bdata = new double[levels.size()];
      } else {
        adata = new double[middle];
        bdata = new double[middle];
      }
      for (int i = 0; i < middle && i < levels.size(); i++) adata[i] = factors[i];
      Array haArray = Array.factory(DataType.DOUBLE, new int[] {adata.length}, adata);
      ha.setCachedData(haArray, true);
      ncfile.addVariable(g, ha);

      // add hybridb variable
      Variable hb = new Variable(ncfile, g, null, "hybridb");
      hb.setDataType(DataType.DOUBLE);
      hb.addAttribute(new Attribute("long_name", "level_b_factor"));
      hb.addAttribute(new Attribute("units", ""));
      hb.setDimensions(getVariableName());
      // add data
      for (int i = 0; i < middle && i < levels.size(); i++) bdata[i] = factors[i + middle];
      Array hbArray = Array.factory(DataType.DOUBLE, new int[] {bdata.length}, bdata);
      hb.setCachedData(hbArray, true);
      ncfile.addVariable(g, hb);

      /*  // TODO: delete next time modifying code
      double[] adata = new double[ middle ];
      for( int i = 0; i < middle; i++ )
        adata[ i ] = factors[ i ];
      Array haArray = Array.factory(DataType.DOUBLE, new int[]{adata.length}, adata);
      ha.setCachedData(haArray, true);
      ncfile.addVariable(g, ha);

      // add hybridb variable
      Variable hb = new Variable(ncfile, g, null, "hybridb");
      hb.setDataType(DataType.DOUBLE);
      hb.addAttribute(new Attribute("long_name",  "level_b_factor" ));
      //hb.addAttribute(new Attribute("standard_name", "atmosphere_hybrid_sigma_pressure_coordinate" ));
      hb.addAttribute(new Attribute("units", ""));
      hb.setDimensions(getVariableName());
      // add data
      double[] bdata = new double[ middle ];
      for( int i = 0; i < middle; i++ )
        bdata[ i ] = factors[ i + middle ];
      Array hbArray = Array.factory(DataType.DOUBLE, new int[]{bdata.length}, bdata);
      hb.setCachedData(hbArray, true);
      ncfile.addVariable(g, hb);
      */
    }
  }
Exemple #7
0
  public void augmentDataset(NetcdfDataset ds, CancelTask cancelTask) throws IOException {
    ds.addAttribute(null, new Attribute("FeatureType", FeatureType.IMAGE.toString())); // LOOK

    Group vhrr = ds.findGroup("VHRR");
    Group loc = vhrr.findGroup("Geo-Location");
    Variable lat = loc.findVariable("Latitude");
    lat.addAttribute(new Attribute(CDM.UNITS, "degrees_north"));
    lat.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
    Variable lon = loc.findVariable("Longitude");
    lon.addAttribute(new Attribute(CDM.UNITS, "degrees_east"));
    lon.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));

    int[] shape = lat.getShape();
    assert shape.length == 2;
    Dimension scan = new Dimension("scan", shape[0]);
    Dimension xscan = new Dimension("xscan", shape[1]);
    vhrr.addDimension(scan);
    vhrr.addDimension(xscan);

    lat.setDimensions("scan xscan");
    lon.setDimensions("scan xscan");

    Group data = vhrr.findGroup("Image Data");
    for (Variable v : data.getVariables()) {
      int[] vs = v.getShape();
      if ((vs.length == 2) && (vs[0] == shape[0]) && (vs[1] == shape[1])) {
        v.setDimensions("scan xscan");
        v.addAttribute(new Attribute(_Coordinate.Axes, "lat lon time"));
      }
    }

    /* Group PRODUCT_METADATA {

    Group PRODUCT_DETAILS {
      PRODUCT_DETAILS:UNIQUE_ID = "3AVHR_22NOV2007_0902";
      PRODUCT_DETAILS:PRODUCT_TYPE = "STANDARD(FULL DISK) ";
      PRODUCT_DETAILS:PROCESSING_SOFTWARE = "InPGS_XXXXXXXXXXXXXX";
      PRODUCT_DETAILS:SPACECRAFT_ID = "INSAT-3A  ";
      PRODUCT_DETAILS:SENSOR_ID = "VHR";
      PRODUCT_DETAILS:ACQUISITION_TYPE = "FULL FRAME     ";
      PRODUCT_DETAILS:ACQUISITION_DATE = "22NOV2007";
      PRODUCT_DETAILS:ACQUISITION_TIME_IN_GMT = "0902";
      PRODUCT_DETAILS:PRODUCT_NAME = "      FULL DISK";
      PRODUCT_DETAILS:PROCESSING_LEVEL = "L1B";
      PRODUCT_DETAILS:BAND_COMBINATION = "Visible(VIS),Thermal Infrared(TIR),Water Vapour(WV)";
      PRODUCT_DETAILS:PRODUCT_CODE = "ST00001HD";
    } */

    Group info = ds.findGroup("PRODUCT_METADATA/PRODUCT_DETAILS");
    String dateS = info.findAttribute("ACQUISITION_DATE").getStringValue();
    String timeS = info.findAttribute("ACQUISITION_TIME_IN_GMT").getStringValue();

    SimpleDateFormat format = new SimpleDateFormat("ddMMMyyyyHHmm");
    format.setTimeZone(java.util.TimeZone.getTimeZone("GMT"));
    try {
      Date d = format.parse(dateS + timeS);
      VariableDS time =
          new VariableDS(
              ds,
              vhrr,
              null,
              "time",
              DataType.LONG,
              "",
              "seconds since 1970-01-01 00:00",
              "time generated from PRODUCT_METADATA/PRODUCT_DETAILS");

      time.addAttribute(
          new Attribute(
              _Coordinate.AxisType,
              AxisType.Time.toString())); // // LOOK : cant handle scalar coordinates yet ??
      time.addAttribute(new Attribute("IsoDate", new DateFormatter().toDateTimeStringISO(d)));
      CoordinateAxis1D timeAxis = new CoordinateAxis1D(ds, time);
      ds.addVariable(vhrr, timeAxis);
      ArrayLong.D0 timeData = new ArrayLong.D0();
      timeData.set(d.getTime() / 1000);
      time.setCachedData(timeData, true);

    } catch (ParseException e) {
      e.printStackTrace();
      throw new IOException(e.getMessage());
    }

    ds.finish();
  }