コード例 #1
0
ファイル: SeadasFileReader.java プロジェクト: bcdev/seadas
  public void addBandMetadata(Product product) throws ProductIOException {
    Group group = ncFile.findGroup("Geophysical_Data");
    if (productReader.getProductType() == SeadasProductReader.ProductType.Level2_Aquarius) {
      group = ncFile.findGroup("Aquarius_Data");
    }
    if (productReader.getProductType() == SeadasProductReader.ProductType.Level1B_HICO) {
      group = ncFile.findGroup("products");
    }
    if (group != null) {
      final MetadataElement bandAttributes = new MetadataElement("Band_Attributes");
      List<Variable> variables = group.getVariables();
      for (Variable variable : variables) {
        final String name = variable.getShortName();
        final MetadataElement sdsElement = new MetadataElement(name + ".attributes");
        final int dataType = getProductDataType(variable);
        final MetadataAttribute prodtypeattr = new MetadataAttribute("data_type", dataType);

        sdsElement.addAttribute(prodtypeattr);
        bandAttributes.addElement(sdsElement);

        final List<Attribute> list = variable.getAttributes();
        for (Attribute varAttribute : list) {
          addAttributeToElement(sdsElement, varAttribute);
        }
      }
      final MetadataElement metadataRoot = product.getMetadataRoot();
      metadataRoot.addElement(bandAttributes);
    }
  }
コード例 #2
0
  /* (non-Javadoc)
   * @see loci.formats.NetCDFService#getAttributeValue(java.lang.String)
   */
  public String getAttributeValue(String path) {
    String groupName = getDirectory(path);
    String attributeName = getName(path);
    Group group = getGroup(groupName);

    Attribute attribute = group.findAttribute(attributeName);
    if (attribute == null) return null;
    return arrayToString(attribute.getValues());
  }
コード例 #3
0
ファイル: HdfEos.java プロジェクト: julienchastang/thredds
  // 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());
  }
コード例 #4
0
ファイル: NcMLUtilTest.java プロジェクト: USGS-CIDA/ncETL
 /**
  * Test of globalAttributesToMeta method, of class NcMLUtilTest.
  *
  * @throws Exception
  */
 @Test
 public void testGlobalAttributesToMeta() throws Exception {
   Group metaGroup = NcMLUtil.globalAttributesToMeta(testFile, wrapper);
   Attribute attr = metaGroup.findAttribute("history");
   // TODO review the generated test code and remove the default call to fail.
   assertThat(attr, is(notNullValue()));
   assertThat(metaGroup.getAttributes().size(), is(equalTo(7)));
   assertThat(metaGroup.getShortName().contains("QPE.20110214.009.105"), is(true));
 }
コード例 #5
0
  /**
   * Set the currently selected Variable.
   *
   * @param v select this Variable, must be already in the tree.
   */
  public void setSelected(VariableIF v) {
    if (v == null) return;

    // construct chain of variables
    List<VariableIF> vchain = new ArrayList<>();
    vchain.add(v);

    VariableIF vp = v;
    while (vp.isMemberOfStructure()) {
      vp = vp.getParentStructure();
      vchain.add(0, vp); // reverse
    }

    // construct chain of groups
    List<Group> gchain = new ArrayList<>();
    Group gp = vp.getParentGroup();

    gchain.add(gp);
    while (gp.getParentGroup() != null) {
      gp = gp.getParentGroup();
      gchain.add(0, gp); // reverse
    }

    List<Object> pathList = new ArrayList<>();

    // start at root, work down through the nested groups, if any
    GroupNode gnode = (GroupNode) model.getRoot();
    pathList.add(gnode);
    Group parentGroup = gchain.get(0); // always the root group

    for (int i = 1; i < gchain.size(); i++) {
      parentGroup = gchain.get(i);
      gnode = gnode.findNestedGroup(parentGroup);
      assert gnode != null;
      pathList.add(gnode);
    }

    vp = vchain.get(0);
    VariableNode vnode = gnode.findNestedVariable(vp);
    if (vnode == null) return; // not found
    pathList.add(vnode);

    // now work down through the structure members, if any
    for (int i = 1; i < vchain.size(); i++) {
      vp = vchain.get(i);
      vnode = vnode.findNestedVariable(vp);
      if (vnode == null) return; // not found
      pathList.add(vnode);
    }

    // convert to TreePath, and select it
    Object[] paths = pathList.toArray();
    TreePath treePath = new TreePath(paths);
    tree.setSelectionPath(treePath);
    tree.scrollPathToVisible(treePath);
  }
コード例 #6
0
ファイル: HdfEos.java プロジェクト: julienchastang/thredds
  // look for a group with the given name. recurse into subgroups if needed. breadth first
  private Group findGroupNested(Group parent, String name) {

    for (Group g : parent.getGroups()) {
      if (g.getShortName().equals(name)) return g;
    }
    for (Group g : parent.getGroups()) {
      Group result = findGroupNested(g, name);
      if (result != null) return result;
    }
    return null;
  }
コード例 #7
0
ファイル: AvhrrConvention.java プロジェクト: nbald/thredds
  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;
  }
コード例 #8
0
  @Test
  public void testForStructMetadata() throws IOException {
    System.out.printf("TestH4eosReadAll %s%n", filename);
    try (NetcdfFile ncfile = NetcdfFile.open(filename)) {
      Group root = ncfile.getRootGroup();
      Group g = root.findGroup("HDFEOS INFORMATION");
      if (g == null) g = ncfile.getRootGroup();

      Variable dset = g.findVariable("StructMetadata.0");
      assert (dset != null);
    }
  }
コード例 #9
0
  /**
   * Retrieves a group based on its fully qualified path.
   *
   * @param path Fully qualified path to the group.
   * @return Group or <code>root</code> if the group cannot be found.
   */
  private Group getGroup(String path) {
    if (path.indexOf("/") == -1) {
      return root;
    }

    StringTokenizer tokens = new StringTokenizer(path, "/");
    Group parent = root;
    while (tokens.hasMoreTokens()) {
      parent = parent.findGroup(tokens.nextToken());
    }
    return parent == null ? root : parent;
  }
コード例 #10
0
  /* (non-Javadoc)
   * @see loci.formats.NetCDFService#getVariableAttributes(java.lang.String)
   */
  public Hashtable<String, Object> getVariableAttributes(String name) {
    String groupName = getDirectory(name);
    String variableName = getName(name);
    Group group = getGroup(groupName);

    Variable variable = group.findVariable(variableName);
    List<Attribute> attributes = variable.getAttributes();
    Hashtable<String, Object> toReturn = new Hashtable<String, Object>();
    for (Attribute attribute : attributes) {
      toReturn.put(attribute.getName(), arrayToString(attribute.getValues()));
    }
    return toReturn;
  }
コード例 #11
0
ファイル: HdfEos.java プロジェクト: julienchastang/thredds
  private void fixAttributes(Group g) {
    for (Variable v : g.getVariables()) {
      for (Attribute a : v.getAttributes()) {
        if (a.getShortName().equalsIgnoreCase("UNIT") || a.getShortName().equalsIgnoreCase("UNITS"))
          a.setShortName(CDM.UNITS);
        if (a.getShortName().equalsIgnoreCase("SCALE_FACTOR")) a.setShortName(CDM.SCALE_FACTOR);
        if (a.getShortName().equalsIgnoreCase("OFFSET")) a.setShortName(CDM.ADD_OFFSET);
      }
    }

    for (Group ng : g.getGroups()) {
      fixAttributes(ng);
    }
  }
コード例 #12
0
ファイル: SeadasFileReader.java プロジェクト: bcdev/seadas
  private void handleMetadataGroup(Group group, MetadataElement metadataElement)
      throws ProductIOException {
    List<Variable> variables = group.getVariables();
    for (Variable variable : variables) {
      final String name = variable.getShortName();
      final int dataType = getProductDataType(variable);
      Array array;
      try {
        array = variable.read();
      } catch (IOException e) {
        throw new ProductIOException(e.getMessage());
      }
      final ProductData data = ProductData.createInstance(dataType, array.getStorage());
      final MetadataAttribute attribute = new MetadataAttribute("data", data, true);

      final MetadataElement sdsElement = new MetadataElement(name);
      sdsElement.addAttribute(attribute);
      metadataElement.addElement(sdsElement);

      final List<Attribute> list = variable.getAttributes();
      for (Attribute hdfAttribute : list) {
        final String attribName = hdfAttribute.getShortName();
        if ("units".equals(attribName)) {
          attribute.setUnit(hdfAttribute.getStringValue());
        } else if ("long_name".equals(attribName)) {
          attribute.setDescription(hdfAttribute.getStringValue());
        } else {
          addAttributeToElement(sdsElement, hdfAttribute);
        }
      }
    }
  }
コード例 #13
0
ファイル: HdfEos.java プロジェクト: julienchastang/thredds
 // 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;
 }
コード例 #14
0
ファイル: HdfEos.java プロジェクト: julienchastang/thredds
  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;
  }
コード例 #15
0
  /* (non-Javadoc)
   * @see loci.formats.NetCDFService#getArray(java.lang.String, int[], int[])
   */
  public Object getArray(String path, int[] origin, int[] shape) throws ServiceException {
    String groupName = getDirectory(path);
    String variableName = getName(path);
    Group group = getGroup(groupName);

    Variable variable = group.findVariable(variableName);
    try {
      if (origin != null && shape != null) {
        return variable.read(origin, shape).reduce().copyToNDJavaArray();
      }
      return variable.read().copyToNDJavaArray();
    } catch (InvalidRangeException e) {
      throw new ServiceException(e);
    } catch (IOException e) {
      throw new ServiceException(e);
    }
  }
コード例 #16
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    void makeChildren() {
      children = new ArrayList<>();

      List dims = group.getDimensions();
      for (int i = 0; i < dims.size(); i++)
        children.add(new DimensionNode(this, (Dimension) dims.get(i)));

      List vars = group.getVariables();
      for (int i = 0; i < vars.size(); i++)
        children.add(new VariableNode(this, (VariableIF) vars.get(i)));

      List groups = group.getGroups();
      for (int i = 0; i < groups.size(); i++)
        children.add(new GroupNode(this, (Group) groups.get(i)));

      if (debugTree) System.out.println("children=" + group.getFullName() + " ");
    }
コード例 #17
0
 /**
  * Recursively parses attribute and variable paths, filling <code>attributeList</code> and <code>
  * variableList</code>.
  *
  * @param groups List of groups to recursively parse.
  */
 private void parseAttributesAndVariables(List<Group> groups) {
   for (Group group : groups) {
     String groupName = group.getName();
     List<Attribute> attributes = group.getAttributes();
     for (Attribute attribute : attributes) {
       String attributeName = attribute.getName();
       if (!groupName.endsWith("/")) attributeName = "/" + attributeName;
       attributeList.add(groupName + attributeName);
     }
     List<Variable> variables = group.getVariables();
     for (Variable variable : variables) {
       String variableName = variable.getName();
       if (!groupName.endsWith("/")) variableName = "/" + variableName;
       variableList.add(variableName);
     }
     groups = group.getGroups();
     parseAttributesAndVariables(groups);
   }
 }
コード例 #18
0
ファイル: HdfEos.java プロジェクト: julienchastang/thredds
 public static boolean getEosInfo(NetcdfFile ncfile, Group eosGroup, Formatter f)
     throws IOException {
   String smeta = getStructMetadata(eosGroup);
   if (smeta == null) {
     f.format("No StructMetadata variables in group %s %n", eosGroup.getFullName());
     return false;
   }
   f.format("raw = %n%s%n", smeta);
   ODLparser parser = new ODLparser();
   parser.parseFromString(smeta); // now we have the ODL in JDOM elements
   StringWriter sw = new StringWriter(5000);
   parser.showDoc(new PrintWriter(sw));
   f.format("parsed = %n%s%n", sw.toString());
   return true;
 }
コード例 #19
0
    private void count(Group g) {
      ndims += g.getDimensions().size();
      nvars += g.getVariables().size();
      ngatts += g.getAttributes().size();
      ngroups += g.getGroups().size();

      for (Variable v : g.getVariables()) {
        natts += v.getAttributes().size();
        if (v instanceof Structure) {
          nstructFields += ((Structure) v).getVariables().size();
        }
      }
      for (Group ng : g.getGroups()) count(ng);
    }
コード例 #20
0
  @Override
  public Product createProduct() throws ProductIOException {

    int[] dims;
    int sceneHeight = 0;
    int sceneWidth = 0;
    Group geodata = ncFile.findGroup("geophysical_data");
    if (productReader.getProductType() == SeadasProductReader.ProductType.OISST) {
      dims = ncFile.getVariables().get(4).getShape();
      sceneHeight = dims[2];
      sceneWidth = dims[3];
      mustFlipY = true;
    } else if (productReader.getProductType() == SeadasProductReader.ProductType.ANCCLIM) {
      List<Variable> vars = ncFile.getVariables();
      for (Variable v : vars) {
        if (v.getRank() == 2) {
          dims = v.getShape();
          sceneHeight = dims[0];
          sceneWidth = dims[1];
        }
      }
    } else {
      if (geodata != null) {
        dims = geodata.getVariables().get(0).getShape();
        sceneHeight = dims[0];
        sceneWidth = dims[1];
      } else {
        ucar.nc2.Dimension latdim = ncFile.findDimension("lat");
        ucar.nc2.Dimension londim = ncFile.findDimension("lon");
        if (latdim != null) {
          sceneHeight = latdim.getLength();
          sceneWidth = londim.getLength();
        } else {
          dims = ncFile.getVariables().get(0).getShape();
          sceneHeight = dims[0];
          sceneWidth = dims[1];
        }
      }
    }

    String productName = productReader.getInputFile().getName();
    try {
      productName = getStringAttribute("Product_Name");
    } catch (Exception ignored) {

    }

    SeadasProductReader.ProductType productType = productReader.getProductType();

    Product product = new Product(productName, productType.toString(), sceneWidth, sceneHeight);
    product.setDescription(productName);

    product.setFileLocation(productReader.getInputFile());
    product.setProductReader(productReader);

    addGlobalMetadata(product);
    addSmiMetadata(product);
    //        variableMap = addBands(product, ncFile.getVariables());
    variableMap = addSmiBands(product, ncFile.getVariables());
    try {
      addGeocoding(product);
    } catch (Exception ignored) {
    }
    addFlagsAndMasks(product);
    if (productReader.getProductType() == SeadasProductReader.ProductType.Bathy) {
      mustFlipY = true;
      Dimension tileSize = new Dimension(640, 320);
      product.setPreferredTileSize(tileSize);
    }
    return product;
  }
コード例 #21
0
  /**
   * 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);
      */
    }
  }
コード例 #22
0
 GroupNode(GroupNode parent, Group group) {
   this.parent = parent;
   this.group = group;
   if (debugTree) System.out.println("new=" + group.getFullName() + " ");
   // firePropertyChangeEvent(new PropertyChangeEvent(this, "TreeNode", null, group));
 }
コード例 #23
0
ファイル: CompareNetcdf2.java プロジェクト: jnbek/thredds
  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;
  }
コード例 #24
0
ファイル: HdfEos.java プロジェクト: julienchastang/thredds
  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;
  }
コード例 #25
0
ファイル: HdfEos.java プロジェクト: julienchastang/thredds
  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;
  }
コード例 #26
0
ファイル: HdfEos.java プロジェクト: julienchastang/thredds
  /**
   * 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"));
    }
  }
コード例 #27
0
 public int getIndex(TreeNode child) {
   if (debugTree) System.out.println("getIndex=" + group.getFullName() + " " + child);
   return children.indexOf(child);
 }
コード例 #28
0
 public int getDimension(String name) {
   String groupName = getDirectory(name);
   String variableName = getName(name);
   Group group = getGroup(groupName);
   return group.findDimension(variableName).getLength();
 }
コード例 #29
0
 public String getToolTipText() {
   return group.getNameAndAttributes();
 }
コード例 #30
0
 public String toString() {
   if (parent == null) // root group
   return currentDataset.getLocation();
   else return group.getShortName();
 }