Java Code Examples for ucar.nc2.NetcdfFile#getVariables()

public void showCompress(Formatter f) throws IOException {
  NetcdfFile ncfile = iosp.getNetcdfFile();

  Size totalSize = new Size(0, 0);
  for (Variable v : ncfile.getVariables()) {
    H5header.Vinfo vinfo = (H5header.Vinfo) v.getSPobject();
    showCompress(v, vinfo, totalSize, f);
  }
  f.format("%n");
  f.format(" total bytes   = %d%n", totalSize.nominal);
  f.format(" total storage = %d%n", totalSize.storage);
  f.format(" compression = %f%n", totalSize.getRatio());
  f.format(" nchunks     = %d%n", totalSize.count);

  File raf = new File(ncfile.getLocation());
  f.format(" file size    = %d%n", raf.length());
  float overhead = totalSize.storage == 0 ? 0 : ((float) raf.length() / totalSize.storage);
  f.format(" overhead     = %f%n", overhead);
}
 

public void setHdf5File(RandomAccessFile raf) throws IOException {
  closeOpenFiles();

  this.location = raf.getLocation();
  List<VarBean> beanList = new ArrayList<>();

  iosp = new H5iosp();
  NetcdfFile ncfile = new NetcdfFileSubclass(iosp, location);
  try {
    iosp.open(raf, ncfile, null);
  } catch (Throwable t) {
    StringWriter sw = new StringWriter(20000);
    t.printStackTrace(new PrintWriter(sw));
    infoTA.setText(sw.toString());
  }

  for (Variable v : ncfile.getVariables()) {
    beanList.add(new VarBean(v));
  }

  objectTable.setBeans(beanList);
}
 

public static int readAllData(NetcdfFile ncfile) throws IOException {
  logger.debug("------Reading ncfile {}", ncfile.getLocation());
  try {
    for (Variable v : ncfile.getVariables()) {
      if (v.getSize() > max_size) {
        Section s = makeSubset(v);
        logger.debug("  Try to read variable {} size={} section={}", v.getNameAndDimensions(), v.getSize(), s);
        v.read(s);
      } else {
        logger.debug("  Try to read variable {} size={}", v.getNameAndDimensions(), v.getSize());
        v.read();
      }
    }

    return 1;
  } catch (InvalidRangeException e) {
    throw new RuntimeException(e);
  }
}
 

/**
 * read data from netcdf file and write data to table store.
 * @param meta
 * @param ncFileName
 * @throws Exception
 */
public void importFromNcFile(GridDataSetMeta meta, String ncFileName) throws Exception {
    GridDataWriter writer = tableStoreGrid.getDataWriter(meta);
    NetcdfFile ncFile = NetcdfFile.open(ncFileName);
    List<Variable> variables = ncFile.getVariables();
    for (Variable variable : variables) {
        if (meta.getVariables().contains(variable.getShortName())) {
            for (int t = 0; t < meta.gettSize(); t++) {
                for (int z = 0; z < meta.getzSize(); z++) {
                    Array array = variable.read(new int[]{t, z, 0, 0}, new int[]{1, 1, meta.getxSize(), meta.getySize()});
                    Grid2D grid2D = new Grid2D(array.getDataAsByteBuffer(), variable.getDataType(),
                            new int[] {0, 0}, new int[] {meta.getxSize(), meta.getySize()});
                    writer.writeGrid2D(variable.getShortName(), t, z, grid2D);
                }
            }
        }
    }
}
 

static public int readAllData(NetcdfFile ncfile) throws IOException {
  logger.debug("------Reading ncfile {}", ncfile.getLocation());
  try {
    for (Variable v : ncfile.getVariables()) {
      if (v.getSize() > max_size) {
        Section s = makeSubset(v);
        logger.debug("  Try to read variable {} size={} section={}", v.getNameAndDimensions(), v.getSize(), s);
        v.read(s);
      } else {
        logger.debug("  Try to read variable {} size={}", v.getNameAndDimensions(), v.getSize());
        v.read();
      }
    }

    return 1;
  } catch (InvalidRangeException e) {
    throw new RuntimeException(e);
  }
}
 

private List<VariableBean> makeVariableBeans(NetcdfFile ds) {
  List<VariableBean> vlist = new ArrayList<>();
  for (Variable v : ds.getVariables()) {
    vlist.add(new VariableBean(v));
  }
  return vlist;
}
 

private List<VariableBean> getVariableBeans(NetcdfFile ds) {
  List<VariableBean> vlist = new ArrayList<>();
  for (Variable v : ds.getVariables()) {
    vlist.add(new VariableBean(v));
  }
  return vlist;
}
 

private long readAllData(NetcdfFile ncfile) throws IOException {
  System.out.println("------Open " + ncfile.getLocation());

  long total = 0;
  for (Variable v : ncfile.getVariables()) {
    long nbytes = v.getSize() * v.getElementSize();
    System.out.println("  Try to read variable " + v.getFullName() + " " + nbytes);
    v.read();
    total += v.getSize() * v.getElementSize();
  }
  ncfile.close();
  return total;
}
 

/**
 * Print top-level details about a NetCDF file.  Used for debugging.
 * @param netcdfFile The NetCDF file whose details to print.
 */
public static void printNetcdfFileDetails(NetcdfFile netcdfFile) {
  System.out.format("Details: %s\n", netcdfFile.getDetailInfo());
  System.out.format("File type description: %s\n", netcdfFile.getFileTypeDescription());
  System.out.format("Title: %s\n", netcdfFile.getTitle());
  System.out.println("Variables:");
  for (Variable v : netcdfFile.getVariables()) {
    System.out.format("  %s\n", v.getNameAndDimensions());
  }
  System.out.println("Global attributes:");
  for (Attribute a : netcdfFile.getGlobalAttributes()) {
    System.out.format("  %s: %s (%s)\n", a.getFullName(), a.getStringValue(), a.getDataType().toString());
  }
}
 

@Test
public void testFilterVariables() throws Exception {
    final URL resource = getClass().getResource("test.nc");
    final NetcdfFile netcdfFile = NetcdfFileOpener.open(resource.toString());
    final List<Variable> variables = netcdfFile.getVariables();
    final List<String> variableNames = new ArrayList<String>();
    for (Variable variable : variables) {
        variableNames.add(variable.getFullName());
    }
    String constraintExpression = null;
    List<String> filteredVariables = DAPDownloader.filterVariables(variableNames, constraintExpression);
    assertEquals(2, filteredVariables.size());
    assertEquals("sst", filteredVariables.get(0));
    assertEquals("wind", filteredVariables.get(1));

    constraintExpression = "sst[0:1:10][0:1:10]";
    filteredVariables = DAPDownloader.filterVariables(variableNames, constraintExpression);
    assertEquals(1, filteredVariables.size());
    assertEquals("sst", filteredVariables.get(0));

    constraintExpression = "bogusVariable[0:1:10][0:1:10]";
    filteredVariables = DAPDownloader.filterVariables(variableNames, constraintExpression);
    assertEquals(2, filteredVariables.size());
    assertEquals("sst", filteredVariables.get(0));
    assertEquals("wind", filteredVariables.get(1));

    constraintExpression = "sst[0:1:10][0:1:10],wind[0:1:10][0:1:10]";
    filteredVariables = DAPDownloader.filterVariables(variableNames, constraintExpression);
    assertEquals(2, filteredVariables.size());
    assertEquals("sst", filteredVariables.get(0));
    assertEquals("wind", filteredVariables.get(1));

    constraintExpression = "sst[0:1:10][0:1:10],wind[0:1:10][0:1:10],sst";
    filteredVariables = DAPDownloader.filterVariables(variableNames, constraintExpression);
    assertEquals(2, filteredVariables.size());
    assertEquals("sst", filteredVariables.get(0));
    assertEquals("wind", filteredVariables.get(1));
}
 

private List<String> getVariableNames(NetcdfFile nc) {
  List<String> result = new ArrayList<>();
  for (Variable v : nc.getVariables())
    result.add(v.getFullName());
  return result;
}
 

/**
 * Read data from netcdf file.
 *
 * @throws IOException
 */
//TODO remove, always read data lazily. AK
private void readNetcdfFile() throws IOException  {
	this.exchangeItems.clear();
	NetcdfFile netcdfFile = this.netcdfFileWriter.getNetcdfFile();

	Results.putMessage(this.getClass().getSimpleName() + ": reading data from file " + this.file.getAbsolutePath());

	//in most netcdfFiles the time and spatial coordinate variables are shared between multiple data variables.
	//Therefore cache timeInfo objects so that time coordinate variables
	//are never read more than once.
	Map<Variable, IArrayTimeInfo> timeInfoCache = new HashMap<Variable, IArrayTimeInfo>();
	for (Variable variable : netcdfFile.getVariables()) {
		//do not create exchangeItems for coordinate variables.
		//the coordinate values will be stored in the metadata objects contained in the exchangeItems.
		if (variable.isCoordinateVariable()) {
			continue;
		}

		if (!variable.getDataType().isNumeric()) {
			continue;
		}

		//create exchangeItem.
		IExchangeItem exchangeItem;
		//Note: never use standard name or long name as exchangeItemId, since these are not always unique within a netcdf file.
		String exchangeItemId = variable.getShortName();
		if (variable.getDimensions().isEmpty()) {//if scalar.
			exchangeItem = new DoubleExchangeItem(exchangeItemId, Role.InOut, variable.readScalarDouble());

		} else {//if array.
			ArrayExchangeItem arrayBasedExchangeItem = new ArrayExchangeItem(exchangeItemId, IPrevExchangeItem.Role.InOut);
			arrayBasedExchangeItem.setQuantityInfo(new QuantityInfo(exchangeItemId, variable.getUnitsString()));
			IArrayTimeInfo newTimeInfo = NetcdfUtils.createTimeInfo(variable, netcdfFile, timeInfoCache);
			//skip variables that do not depend on time.
			if (newTimeInfo == null && !allowTimeIndependentItems) continue;

			arrayBasedExchangeItem.setTimeInfo(newTimeInfo);
			//TODO cache variables with spatial coordinates. AK
			arrayBasedExchangeItem.setGeometryInfo(NetcdfUtils.createGeometryInfo(variable, netcdfFile));
			IArray array = (IArray) NetcdfUtils.readData(variable);
			arrayBasedExchangeItem.setArray(array);
			exchangeItem = arrayBasedExchangeItem;
		}

		this.exchangeItems.add(exchangeItem);
	}
}