Пример #1
0
  /** Create a DAS for this netcdf file */
  NcDAS(NetcdfFile ncfile) {

    // Variable attributes
    Iterator iter = ncfile.getVariables().iterator();
    while (iter.hasNext()) {
      Variable v = (Variable) iter.next();
      doVariable(v, null);
    }

    // Global attributes
    opendap.dap.AttributeTable gtable = new opendap.dap.AttributeTable("NC_GLOBAL");
    int count = addAttributes(gtable, null, ncfile.getGlobalAttributes().iterator());
    if (count > 0)
      try {
        addAttributeTable("NC_GLOBAL", gtable);
      } catch (AttributeExistsException e) {
        log.error("Cant add NC_GLOBAL", e);
      }

    // unlimited  dimension
    iter = ncfile.getDimensions().iterator();
    while (iter.hasNext()) {
      Dimension d = (Dimension) iter.next();
      if (d.isUnlimited()) {
        opendap.dap.AttributeTable table = new opendap.dap.AttributeTable("DODS_EXTRA");
        try {
          table.appendAttribute("Unlimited_Dimension", opendap.dap.Attribute.STRING, d.getName());
          addAttributeTable("DODS_EXTRA", table);
        } catch (Exception e) {
          log.error("Error adding Unlimited_Dimension =" + e);
        }
        break;
      }
    }

    // unused dimensions
    opendap.dap.AttributeTable dimTable = null;
    iter = ncfile.getDimensions().iterator();
    while (iter.hasNext()) {
      Dimension d = (Dimension) iter.next();
      if (null == usedDims.get(d.getName())) {
        if (dimTable == null) dimTable = new opendap.dap.AttributeTable("EXTRA_DIMENSION");
        try {
          dimTable.appendAttribute(
              d.getName(), opendap.dap.Attribute.INT32, Integer.toString(d.getLength()));
        } catch (Exception e) {
          log.error("Error adding Unlimited_Dimension =" + e);
        }
      }
    }
    if (dimTable != null)
      try {
        addAttributeTable("EXTRA_DIMENSION", dimTable);
      } catch (AttributeExistsException e) {
        log.error("Cant add EXTRA_DIMENSION", e);
      }
  }
Пример #2
0
  // convert to shared dimensions
  private void setSharedDimensions(
      Variable v, List<Element> values, List<Dimension> unknownDims, String location) {
    if (values.size() == 0) return;

    // remove the "scalar" dumbension
    Iterator<Element> iter = values.iterator();
    while (iter.hasNext()) {
      Element value = iter.next();
      String dimName = value.getText().trim();
      if (dimName.equalsIgnoreCase("scalar")) iter.remove();
    }

    // gotta have same number of dimensions
    List<Dimension> oldDims = v.getDimensions();
    if (oldDims.size() != values.size()) {
      log.error("Different number of dimensions for {} {}", v, location);
      return;
    }

    List<Dimension> newDims = new ArrayList<>();
    Group group = v.getParentGroup();

    for (int i = 0; i < values.size(); i++) {
      Element value = values.get(i);
      String dimName = value.getText().trim();
      dimName = NetcdfFile.makeValidCdmObjectName(dimName);

      Dimension dim = group.findDimension(dimName);
      Dimension oldDim = oldDims.get(i);
      if (dim == null) dim = checkUnknownDims(dimName, unknownDims, oldDim, location);

      if (dim == null) {
        log.error(
            "Unknown Dimension= {} for variable = {} {} ", dimName, v.getFullName(), location);
        return;
      }
      if (dim.getLength() != oldDim.getLength()) {
        log.error(
            "Shared dimension ("
                + dim.getShortName()
                + ") has different length than data dimension ("
                + oldDim.getShortName()
                + ") shared="
                + dim.getLength()
                + " org="
                + oldDim.getLength()
                + " for "
                + v
                + " "
                + location);
        return;
      }
      newDims.add(dim);
    }
    v.setDimensions(newDims);
    if (showWork) System.out.printf(" set shared dimensions for %s %n", v.getNameAndDimensions());
  }
Пример #3
0
  private int addAttributes(opendap.dap.AttributeTable table, Variable v, Iterator iter) {
    int count = 0;

    // add attribute table for this variable
    while (iter.hasNext()) {
      Attribute att = (Attribute) iter.next();
      int dods_type = DODSNetcdfFile.convertToDODSType(att.getDataType(), false);

      try {
        String attName = NcDDS.escapeName(att.getName());
        if (att.isString()) {
          /* FIX String value = escapeAttributeStringValues(att.getStringValue());
          table.appendAttribute(attName, dods_type, "\""+value+"\"");
          */
          table.appendAttribute(attName, dods_type, att.getStringValue());
        } else {
          // cant send signed bytes
          if (att.getDataType() == DataType.BYTE) {
            boolean signed = false;
            for (int i = 0; i < att.getLength(); i++) {
              if (att.getNumericValue(i).byteValue() < 0) signed = true;
            }
            if (signed) // promote to signed short
            dods_type = opendap.dap.Attribute.INT16;
          }

          for (int i = 0; i < att.getLength(); i++)
            table.appendAttribute(attName, dods_type, att.getNumericValue(i).toString());
        }
        count++;

      } catch (Exception e) {
        log.error(
            "Error appending attribute " + att.getName() + " = " + att.getStringValue() + "\n" + e);
      }
    } // loop over variable attributes

    // kludgy thing to map char arrays to DODS Strings
    if ((v != null) && (v.getDataType().getPrimitiveClassType() == char.class)) {
      int rank = v.getRank();
      int strlen = (rank == 0) ? 0 : v.getShape(rank - 1);
      Dimension dim = (rank == 0) ? null : v.getDimension(rank - 1);
      try {
        opendap.dap.AttributeTable dodsTable = table.appendContainer("DODS");
        dodsTable.appendAttribute("strlen", opendap.dap.Attribute.INT32, Integer.toString(strlen));
        if ((dim != null) && dim.isShared())
          dodsTable.appendAttribute("dimName", opendap.dap.Attribute.STRING, dim.getName());
        count++;
      } catch (Exception e) {
        log.error("Error appending attribute strlen\n" + e);
      }
    }

    return count;
  }
Пример #4
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;
  }
Пример #5
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);
      }
    }
  }
Пример #6
0
 // look if the wanted dimension is in the  unknownDims list.
 private Dimension checkUnknownDims(
     String wantDim, List<Dimension> unknownDims, Dimension oldDim, String location) {
   for (Dimension dim : unknownDims) {
     if (dim.getShortName().equals(wantDim)) {
       int len = oldDim.getLength();
       if (len == 0) dim.setUnlimited(true); // allow zero length dimension !!
       dim.setLength(len); // use existing (anon) dimension
       Group parent = dim.getGroup();
       parent.addDimensionIfNotExists(dim); // add to the parent
       unknownDims.remove(dim); // remove from list LOOK is this ok?
       log.warn("unknownDim {} length set to {}{}", wantDim, oldDim.getLength(), location);
       return dim;
     }
   }
   return null;
 }
  private double getTime(StructureMembers.Member timeVar, StructureData sdata) {
    if (timeVar == null) return 0.0;

    if ((timeVar.getDataType() == DataType.CHAR) || (timeVar.getDataType() == DataType.STRING)) {
      String time = sdata.getScalarString(timeVar);
      CalendarDate date = CalendarDateFormatter.isoStringToCalendarDate(null, time);
      if (date == null) {
        log.error("Cant parse date - not ISO formatted, = " + time);
        return 0.0;
      }
      return date.getMillis() / 1000.0;

    } else {
      return sdata.convertScalarDouble(timeVar);
    }
  }
  /**
   * Add levels
   *
   * @param records GridRecords, one for each level
   */
  void addLevels(List<GridRecord> records) {
    for (int i = 0; i < records.size(); i++) {
      GridRecord record = records.get(i);

      if (coordIndex(record) < 0) {
        levels.add(new LevelCoord(record.getLevel1(), record.getLevel2()));
        if (dontUseVertical && (levels.size() > 1)) {
          if (GridServiceProvider.debugVert) {
            logger.warn(
                "GribCoordSys: unused level coordinate has > 1 levels = "
                    + levelName
                    + " "
                    + record.getLevelType1()
                    + " "
                    + levels.size());
          }
        }
      }
    }
    Collections.sort(levels);
    if (positive.equals("down")) {
      Collections.reverse(levels);
    }
  }
Пример #9
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;
  }
Пример #10
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;
  }
Пример #11
0
  /**
   * Amend the given NetcdfFile with metadata from HDF-EOS structMetadata
   *
   * @param ncfile Amend this file
   * @param structMetadata structMetadata as String
   * @throws IOException on read error
   */
  private void amendFromODL(NetcdfFile ncfile, String structMetadata) throws IOException {
    Group rootg = ncfile.getRootGroup();

    ODLparser parser = new ODLparser();
    Element root = parser.parseFromString(structMetadata); // now we have the ODL in JDOM elements
    FeatureType featureType = null;

    // SWATH
    Element swathStructure = root.getChild("SwathStructure");
    if (swathStructure != null) {
      List<Element> swaths = swathStructure.getChildren();
      for (Element elemSwath : swaths) {
        Element swathNameElem = elemSwath.getChild("SwathName");
        if (swathNameElem == null) {
          log.warn("No SwathName element in {} {} ", elemSwath.getName(), ncfile.getLocation());
          continue;
        }
        String swathName = NetcdfFile.makeValidCdmObjectName(swathNameElem.getText().trim());
        Group swathGroup = findGroupNested(rootg, swathName);
        // if (swathGroup == null)
        //  swathGroup = findGroupNested(rootg, H4header.createValidObjectName(swathName));

        if (swathGroup != null) {
          featureType = amendSwath(ncfile, elemSwath, swathGroup);
        } else {
          log.warn("Cant find swath group {} {}", swathName, ncfile.getLocation());
        }
      }
    }

    // GRID
    Element gridStructure = root.getChild("GridStructure");
    if (gridStructure != null) {
      List<Element> grids = gridStructure.getChildren();
      for (Element elemGrid : grids) {
        Element gridNameElem = elemGrid.getChild("GridName");
        if (gridNameElem == null) {
          log.warn("No GridName element in {} {} ", elemGrid.getName(), ncfile.getLocation());
          continue;
        }
        String gridName = NetcdfFile.makeValidCdmObjectName(gridNameElem.getText().trim());
        Group gridGroup = findGroupNested(rootg, gridName);
        // if (gridGroup == null)
        //  gridGroup = findGroupNested(rootg, H4header.createValidObjectName(gridName));
        if (gridGroup != null) {
          featureType = amendGrid(elemGrid, ncfile, gridGroup, ncfile.getLocation());
        } else {
          log.warn("Cant find Grid group {} {}", gridName, ncfile.getLocation());
        }
      }
    }

    // POINT - NOT DONE YET
    Element pointStructure = root.getChild("PointStructure");
    if (pointStructure != null) {
      List<Element> pts = pointStructure.getChildren();
      for (Element elem : pts) {
        Element nameElem = elem.getChild("PointName");
        if (nameElem == null) {
          log.warn("No PointName element in {} {}", elem.getName(), ncfile.getLocation());
          continue;
        }
        String name = nameElem.getText().trim();
        Group ptGroup = findGroupNested(rootg, name);
        // if (ptGroup == null)
        //  ptGroup = findGroupNested(rootg, H4header.createValidObjectName(name));
        if (ptGroup != null) {
          featureType = FeatureType.POINT;
        } else {
          log.warn("Cant find Point group {} {}", name, ncfile.getLocation());
        }
      }
    }

    if (featureType != null) {
      if (showWork) System.out.println("***EOS featureType= " + featureType.toString());
      rootg.addAttribute(new Attribute(CF.FEATURE_TYPE, featureType.toString()));
      // rootg.addAttribute(new Attribute(CDM.CONVENTIONS, "HDFEOS"));
    }
  }
Пример #12
0
  /**
   * This reads an arbitrary data slice, returning the data in canonical order (rt-e-t-z-y-x). If
   * any dimension does not exist, ignore it.
   *
   * @param rt if < 0, get all of runtime dim; if valid index, fix slice to that value.
   * @param e if < 0, get all of ensemble dim; if valid index, fix slice to that value.
   * @param t if < 0, get all of time dim; if valid index, fix slice to that value.
   * @param z if < 0, get all of z dim; if valid index, fix slice to that value.
   * @param y if < 0, get all of y dim; if valid index, fix slice to that value.
   * @param x if < 0, get all of x dim; if valid index, fix slice to that value.
   * @return data[rt,e,t,z,y,x], eliminating missing or fixed dimension.
   */
  public Array readDataSlice(int rt, int e, int t, int z, int y, int x) throws java.io.IOException {

    int rank = vs.getRank();
    int[] start = new int[rank];
    int[] shape = new int[rank];
    for (int i = 0; i < rank; i++) {
      start[i] = 0;
      shape[i] = 1;
    }
    Dimension xdim = getXDimension();
    Dimension ydim = getYDimension();
    Dimension zdim = getZDimension();
    Dimension tdim = getTimeDimension();
    Dimension edim = getEnsembleDimension();
    Dimension rtdim = getRunTimeDimension();

    // construct the shape of the data volume to be read
    if (rtdim != null) {
      if ((rt >= 0) && (rt < rtdim.getLength())) start[rtDimOrgIndex] = rt; // fix rt
      else {
        shape[rtDimOrgIndex] = rtdim.getLength(); // all of rt
      }
    }

    if (edim != null) {
      if ((e >= 0) && (e < edim.getLength())) start[eDimOrgIndex] = e; // fix e
      else {
        shape[eDimOrgIndex] = edim.getLength(); // all of e
      }
    }

    if (tdim != null) {
      if ((t >= 0) && (t < tdim.getLength())) start[tDimOrgIndex] = t; // fix t
      else {
        shape[tDimOrgIndex] = tdim.getLength(); // all of t
      }
    }

    if (zdim != null) {
      if ((z >= 0) && (z < zdim.getLength())) start[zDimOrgIndex] = z; // fix z
      else {
        shape[zDimOrgIndex] = zdim.getLength(); // all of z
      }
    }

    if (ydim != null) {
      if ((y >= 0) && (y < ydim.getLength())) start[yDimOrgIndex] = y; // fix y
      else {
        shape[yDimOrgIndex] = ydim.getLength(); // all of y
      }
    }

    if (xdim != null) {
      if ((x >= 0) && (x < xdim.getLength())) // all of x
      start[xDimOrgIndex] = x; // fix x
      else {
        shape[xDimOrgIndex] = xdim.getLength(); // all of x
      }
    }

    if (debugArrayShape) {
      System.out.println("read shape from org variable = ");
      for (int i = 0; i < rank; i++)
        System.out.println(
            "   start = "
                + start[i]
                + " shape = "
                + shape[i]
                + " name = "
                + vs.getDimension(i).getName());
    }

    // read it
    Array dataVolume;
    try {
      dataVolume = vs.read(start, shape);
    } catch (Exception ex) {
      log.error(
          "GeoGrid.getdataSlice() on dataset " + getFullName() + " " + dataset.getLocation(), ex);
      throw new java.io.IOException(ex.getMessage());
    }

    // LOOK: the real problem is the lack of named dimensions in the Array object
    // figure out correct permutation for canonical ordering for permute
    List<Dimension> oldDims = new ArrayList<Dimension>(vs.getDimensions());
    int[] permuteIndex = new int[dataVolume.getRank()];
    int count = 0;
    if (oldDims.contains(rtdim)) permuteIndex[count++] = oldDims.indexOf(rtdim);
    if (oldDims.contains(edim)) permuteIndex[count++] = oldDims.indexOf(edim);
    if (oldDims.contains(tdim)) permuteIndex[count++] = oldDims.indexOf(tdim);
    if (oldDims.contains(zdim)) permuteIndex[count++] = oldDims.indexOf(zdim);
    if (oldDims.contains(ydim)) permuteIndex[count++] = oldDims.indexOf(ydim);
    if (oldDims.contains(xdim)) permuteIndex[count] = oldDims.indexOf(xdim);

    if (debugArrayShape) {
      System.out.println("oldDims = ");
      for (Dimension oldDim : oldDims) System.out.println("   oldDim = " + oldDim.getName());
      System.out.println("permute dims = ");
      for (int aPermuteIndex : permuteIndex)
        System.out.println("   oldDim index = " + aPermuteIndex);
    }

    // check to see if we need to permute
    boolean needPermute = false;
    for (int i = 0; i < permuteIndex.length; i++) {
      if (i != permuteIndex[i]) needPermute = true;
    }

    // permute to the order rt,e,t,z,y,x
    if (needPermute) dataVolume = dataVolume.permute(permuteIndex);

    // eliminate fixed dimensions, but not all dimensions of length 1.
    count = 0;
    if (rtdim != null) {
      if (rt >= 0) dataVolume = dataVolume.reduce(count);
      else count++;
    }
    if (edim != null) {
      if (e >= 0) dataVolume = dataVolume.reduce(count);
      else count++;
    }
    if (tdim != null) {
      if (t >= 0) dataVolume = dataVolume.reduce(count);
      else count++;
    }
    if (zdim != null) {
      if (z >= 0) dataVolume = dataVolume.reduce(count);
      else count++;
    }
    if (ydim != null) {
      if (y >= 0) dataVolume = dataVolume.reduce(count);
      else count++;
    }
    if (xdim != null) {
      if (x >= 0) dataVolume = dataVolume.reduce(count);
    }

    return dataVolume;
  }
Пример #13
0
  private void makeCoordinateDataWithMissing(
      int datatype,
      Variable time,
      Variable elev,
      Variable azi,
      Variable nradialsVar,
      Variable ngatesVar,
      List groups) {

    Array timeData = Array.factory(time.getDataType().getPrimitiveClassType(), time.getShape());
    Index timeIndex = timeData.getIndex();

    Array elevData = Array.factory(elev.getDataType().getPrimitiveClassType(), elev.getShape());
    Index elevIndex = elevData.getIndex();

    Array aziData = Array.factory(azi.getDataType().getPrimitiveClassType(), azi.getShape());
    Index aziIndex = aziData.getIndex();

    Array nradialsData =
        Array.factory(nradialsVar.getDataType().getPrimitiveClassType(), nradialsVar.getShape());
    IndexIterator nradialsIter = nradialsData.getIndexIterator();

    Array ngatesData =
        Array.factory(ngatesVar.getDataType().getPrimitiveClassType(), ngatesVar.getShape());
    IndexIterator ngatesIter = ngatesData.getIndexIterator();

    // first fill with missing data
    IndexIterator ii = timeData.getIndexIterator();
    while (ii.hasNext()) ii.setIntNext(MISSING_INT);

    ii = elevData.getIndexIterator();
    while (ii.hasNext()) ii.setFloatNext(MISSING_FLOAT);

    ii = aziData.getIndexIterator();
    while (ii.hasNext()) ii.setFloatNext(MISSING_FLOAT);

    // now set the  coordinate variables from the Cinrad2Record radial
    int last_msecs = Integer.MIN_VALUE;
    int nscans = groups.size();
    try {
      for (int scan = 0; scan < nscans; scan++) {
        List scanGroup = (List) groups.get(scan);
        int nradials = scanGroup.size();

        Cinrad2Record first = null;
        for (int j = 0; j < nradials; j++) {
          Cinrad2Record r = (Cinrad2Record) scanGroup.get(j);
          if (first == null) first = r;

          int radial = r.radial_num - 1;
          timeData.setInt(timeIndex.set(scan, radial), r.data_msecs);
          elevData.setFloat(elevIndex.set(scan, radial), r.getElevation());
          aziData.setFloat(aziIndex.set(scan, radial), r.getAzimuth());

          if (r.data_msecs < last_msecs)
            logger.warn("makeCoordinateData time out of order " + r.data_msecs);
          last_msecs = r.data_msecs;
        }

        nradialsIter.setIntNext(nradials);
        ngatesIter.setIntNext(first.getGateCount(datatype));
      }
    } catch (java.lang.ArrayIndexOutOfBoundsException ae) {
      logger.debug("Cinrad2IOSP.uncompress ", ae);
    }
    time.setCachedData(timeData, false);
    elev.setCachedData(elevData, false);
    azi.setCachedData(aziData, false);
    nradialsVar.setCachedData(nradialsData, false);
    ngatesVar.setCachedData(ngatesData, false);
  }
Пример #14
0
  private void makeCoordinateData(
      int datatype,
      Variable time,
      Variable elev,
      Variable azi,
      Variable nradialsVar,
      Variable ngatesVar,
      List groups) {

    Array timeData = Array.factory(time.getDataType().getPrimitiveClassType(), time.getShape());
    IndexIterator timeDataIter = timeData.getIndexIterator();

    Array elevData = Array.factory(elev.getDataType().getPrimitiveClassType(), elev.getShape());
    IndexIterator elevDataIter = elevData.getIndexIterator();

    Array aziData = Array.factory(azi.getDataType().getPrimitiveClassType(), azi.getShape());
    IndexIterator aziDataIter = aziData.getIndexIterator();

    Array nradialsData =
        Array.factory(nradialsVar.getDataType().getPrimitiveClassType(), nradialsVar.getShape());
    IndexIterator nradialsIter = nradialsData.getIndexIterator();

    Array ngatesData =
        Array.factory(ngatesVar.getDataType().getPrimitiveClassType(), ngatesVar.getShape());
    IndexIterator ngatesIter = ngatesData.getIndexIterator();

    int last_msecs = Integer.MIN_VALUE;
    int nscans = groups.size();
    int maxRadials = volScan.getMaxRadials();
    for (int i = 0; i < nscans; i++) {
      List scanGroup = (List) groups.get(i);
      int nradials = scanGroup.size();

      Cinrad2Record first = null;
      for (int j = 0; j < nradials; j++) {
        Cinrad2Record r = (Cinrad2Record) scanGroup.get(j);
        if (first == null) first = r;

        timeDataIter.setIntNext(r.data_msecs);
        elevDataIter.setFloatNext(r.getElevation());
        aziDataIter.setFloatNext(r.getAzimuth());

        if (r.data_msecs < last_msecs)
          logger.warn("makeCoordinateData time out of order " + r.data_msecs);
        last_msecs = r.data_msecs;
      }

      for (int j = nradials; j < maxRadials; j++) {
        timeDataIter.setIntNext(MISSING_INT);
        elevDataIter.setFloatNext(MISSING_FLOAT);
        aziDataIter.setFloatNext(MISSING_FLOAT);
      }

      nradialsIter.setIntNext(nradials);
      ngatesIter.setIntNext(first.getGateCount(datatype));
    }

    time.setCachedData(timeData, false);
    elev.setCachedData(elevData, false);
    azi.setCachedData(aziData, false);
    nradialsVar.setCachedData(nradialsData, false);
    ngatesVar.setCachedData(ngatesData, false);
  }