Java Code Examples for ucar.nc2.ft.FeatureDatasetPoint#getPointFeatureCollectionList()

/**
 * Constructs a FlattenedDatasetPointCollection.
 *
 * @param fdPoint a point dataset.
 * @throws IllegalArgumentException if any of the feature collections in the dataset are not of type
 *         {@code PointFeatureCollection} or {@code NestedPointFeatureCollection}.
 */
public FlattenedDatasetPointCollection(FeatureDatasetPoint fdPoint) throws IllegalArgumentException {
  super(fdPoint.getLocation(), CalendarDateUnit.unixDateUnit, null); // Default dateUnit and altUnits.
  this.fdPoint = fdPoint;

  List<DsgFeatureCollection> featCols = fdPoint.getPointFeatureCollectionList();

  if (!featCols.isEmpty()) {
    DsgFeatureCollection firstFeatCol = featCols.get(0);

    // Replace this.dateUnit, this.altUnits, and this.extras with "typical" values from firstFeatCol.
    // We can't be certain that those values are representative of ALL collections in the dataset, but it's
    // a decent bet because in practice, firstFeatCol is so often the ONLY collection.
    copyFieldsFrom(firstFeatCol);
  }
}
 

private PointFeatureIterator getNextIterator() throws IOException {
  if (!iter.hasNext())
    return null;
  TimedCollection.Dataset td = iter.next();
  Formatter errlog = new Formatter();
  currentDataset = (FeatureDatasetPoint) FeatureDatasetFactoryManager.open(FeatureType.STATION, td.getLocation(),
      null, errlog);
  if (currentDataset == null)
    throw new IllegalStateException("Cant open FeatureDatasetPoint " + td.getLocation());

  List<DsgFeatureCollection> fcList = currentDataset.getPointFeatureCollectionList();
  StationTimeSeriesFeatureCollection stnCollection = (StationTimeSeriesFeatureCollection) fcList.get(0);
  StationFeature s = stnCollection.findStationFeature(getName());
  if (s == null) {
    log.debug("CompositeStationFeatureIterator dataset: {} missing station {}", td.getLocation(), getName());
    // close (or just release if cache is enabled) current dataset and check for station in
    // next dataset in collection
    currentDataset.close();
    return getNextIterator();
  }

  StationTimeSeriesFeature stnFeature = stnCollection.getStationTimeSeriesFeature(s);
  if (CompositeDatasetFactory.debug)
    System.out.printf("CompositeStationFeatureIterator open dataset: %s for %s%n", td.getLocation(), s.getName());
  return stnFeature.getPointFeatureIterator();
}
 

private PointFeatureIterator getNextIterator() throws IOException {
  if (!iter.hasNext())
    return null;
  TimedCollection.Dataset td = iter.next();

  Formatter errlog = new Formatter();
  currentDataset =
      (FeatureDatasetPoint) FeatureDatasetFactoryManager.open(FeatureType.POINT, td.getLocation(), null, errlog);
  if (currentDataset == null)
    throw new IllegalStateException("Cant open FeatureDatasetPoint " + td.getLocation());
  if (CompositeDatasetFactory.debug)
    System.out.printf("CompositePointFeatureIterator open dataset %s%n", td.getLocation());

  List<DsgFeatureCollection> fcList = currentDataset.getPointFeatureCollectionList();
  PointFeatureCollection pc = (PointFeatureCollection) fcList.get(0);
  return pc.getPointFeatureIterator();
}
 

/**
 * Write a FeatureDatasetPoint to a netcd3/4 file.
 *
 * @param fdpoint the FeatureDatasetPoint; do first FeatureCollection contained within.
 * @param fileOut write to the is file
 * @param config configuration
 * @return count of number of pointFeatures written.
 */
public static int writeFeatureCollection(FeatureDatasetPoint fdpoint, String fileOut, CFPointWriterConfig config)
    throws IOException {
  for (DsgFeatureCollection fc : fdpoint.getPointFeatureCollectionList()) {
    if (fc instanceof PointFeatureCollection) {
      return writePointFeatureCollection(fdpoint, (PointFeatureCollection) fc, fileOut, config);

    } else if (fc instanceof StationTimeSeriesFeatureCollection) {
      return writeStationFeatureCollection(fdpoint, (StationTimeSeriesFeatureCollection) fc, fileOut, config);

    } else if (fc instanceof ProfileFeatureCollection) {
      return writeProfileFeatureCollection(fdpoint, (ProfileFeatureCollection) fc, fileOut, config);

    } else if (fc instanceof TrajectoryFeatureCollection) {
      return writeTrajectoryFeatureCollection(fdpoint, (TrajectoryFeatureCollection) fc, fileOut, config);

    } else if (fc instanceof StationProfileFeatureCollection) {
      return writeStationProfileFeatureCollection(fdpoint, (StationProfileFeatureCollection) fc, fileOut, config);

    } else if (fc instanceof TrajectoryProfileFeatureCollection) {
      return writeTrajectoryProfileFeatureCollection(fdpoint, (TrajectoryProfileFeatureCollection) fc, fileOut,
          config);
    }
  }
  return 0;
}
 

public static StationTimeSeriesFeatureCollection getStationFeatures(FeatureDatasetPoint fdPoint) {
  String datasetFileName = new File(fdPoint.getNetcdfFile().getLocation()).getName();

  if (fdPoint.getFeatureType() != FeatureType.STATION) {
    throw new IllegalArgumentException(String.format("In %s, expected feature type to be STATION, not %s.",
        datasetFileName, fdPoint.getFeatureType()));
  }

  List<DsgFeatureCollection> featCollList = fdPoint.getPointFeatureCollectionList();

  if (featCollList.size() != 1) {
    throw new IllegalArgumentException(
        String.format("Expected %s to contain 1 FeatureCollection, not %s.", datasetFileName, featCollList.size()));
  } else if (!(featCollList.get(0) instanceof StationTimeSeriesFeatureCollection)) {
    String expectedClassName = StationTimeSeriesFeatureCollection.class.getName();
    String actualClassName = featCollList.get(0).getClass().getName();

    throw new IllegalArgumentException(String.format("Expected %s's FeatureCollection to be a %s, not a %s.",
        datasetFileName, expectedClassName, actualClassName));
  }

  return (StationTimeSeriesFeatureCollection) featCollList.get(0);
}
 

private PointFeatureIterator getNextIterator() throws IOException {
  if (!iter.hasNext())
    return null;
  TimedCollection.Dataset td = iter.next();
  Formatter errlog = new Formatter();

  // open the next dataset
  currentDataset =
      (FeatureDatasetPoint) FeatureDatasetFactoryManager.open(FeatureType.STATION, td.getLocation(), null, errlog);
  if (currentDataset == null) {
    logger.error("FeatureDatasetFactoryManager failed to open: " + td.getLocation() + " \nerrlog = " + errlog);
    return getNextIterator();
  }

  if (CompositeDatasetFactory.debug)
    System.out.printf("CompositeStationCollectionFlattened.Iterator open new dataset: %s%n", td.getLocation());

  // it will have a StationTimeSeriesFeatureCollection
  List<DsgFeatureCollection> fcList = currentDataset.getPointFeatureCollectionList();
  StationTimeSeriesFeatureCollection stnCollection = (StationTimeSeriesFeatureCollection) fcList.get(0);

  PointFeatureCollection pc;
  if (wantStationsubset) {
    pc = stnCollection.flatten(stationsSubset, dateRange, varList);
  } else if (bbSubset == null) {
    pc = stnCollection.flatten(null, dateRange, null);
  } else {
    List<StationFeature> stations = stnCollection.getStationFeatures(bbSubset);
    List<String> names = new ArrayList<>();
    for (StationFeature s : stations)
      names.add(s.getName());

    pc = stnCollection.flatten(names, dateRange, null);
  }

  return pc.getPointFeatureIterator();
}
 

/**
 * Write a ucar.nc2.ft.PointFeatureCollection in CF point format.
 *
 * @param pfDataset find the first PointFeatureCollection, and write all data from it
 * @param fileOut write to this netcdf-3 file
 * @return number of records written
 * @throws IOException on read/write error, or if no PointFeatureCollection in pfDataset
 */
public static int writePointFeatureCollection(FeatureDatasetPoint pfDataset, String fileOut) throws IOException {
  // extract the PointFeatureCollection
  PointFeatureCollection pointFeatureCollection = null;
  List<DsgFeatureCollection> featureCollectionList = pfDataset.getPointFeatureCollectionList();
  for (DsgFeatureCollection featureCollection : featureCollectionList) {
    if (featureCollection instanceof PointFeatureCollection)
      pointFeatureCollection = (PointFeatureCollection) featureCollection;
  }
  if (null == pointFeatureCollection)
    throw new IOException("There is no PointFeatureCollection in  " + pfDataset.getLocation());

  long start = System.currentTimeMillis();

  FileOutputStream fos = new FileOutputStream(fileOut);
  DataOutputStream out = new DataOutputStream(new BufferedOutputStream(fos, 10000));
  WriterCFPointDataset writer = null;

  /*
   * LOOK BAD
   * List<VariableSimpleIF> dataVars = new ArrayList<VariableSimpleIF>();
   * ucar.nc2.NetcdfFile ncfile = pfDataset.getNetcdfFile();
   * if ((ncfile == null) || !(ncfile instanceof NetcdfDataset)) {
   * dataVars.addAll(pfDataset.getDataVariables());
   * } else {
   * NetcdfDataset ncd = (NetcdfDataset) ncfile;
   * for (VariableSimpleIF vs : pfDataset.getDataVariables()) {
   * if (ncd.findCoordinateAxis(vs.getName()) == null)
   * dataVars.add(vs);
   * }
   * }
   */

  int count = 0;
  for (PointFeature pointFeature : pointFeatureCollection) {
    StructureData data = pointFeature.getDataAll();
    if (count == 0) {
      EarthLocation loc = pointFeature.getLocation(); // LOOK we dont know this until we see the obs
      String altUnits = Double.isNaN(loc.getAltitude()) ? null : "meters"; // LOOK units may be wrong
      writer = new WriterCFPointDataset(out, pfDataset.getGlobalAttributes(), altUnits);
      writer.writeHeader(pfDataset.getDataVariables(), -1);
    }
    writer.writeRecord(pointFeature, data);
    count++;
  }

  writer.finish();
  out.flush();
  out.close();

  long took = System.currentTimeMillis() - start;
  System.out.printf("Write %d records from %s to %s took %d msecs %n", count, pfDataset.getLocation(), fileOut, took);
  return count;
}
 

/**
 * Write a ucar.nc2.ft.PointFeatureCollection in CF point format.
 *
 * @param pfDataset find the first PointFeatureCollection, and write all data from it
 * @param fileOut write to this netcdf-3 file
 * @return number of records written
 * @throws IOException on read/write error, or if no PointFeatureCollection in pfDataset
 */
public static int writePointFeatureCollection(FeatureDatasetPoint pfDataset, String fileOut) throws IOException {
  // extract the PointFeatureCollection
  PointFeatureCollection pointFeatureCollection = null;
  List<DsgFeatureCollection> featureCollectionList = pfDataset.getPointFeatureCollectionList();
  for (DsgFeatureCollection featureCollection : featureCollectionList) {
    if (featureCollection instanceof PointFeatureCollection)
      pointFeatureCollection = (PointFeatureCollection) featureCollection;
  }
  if (null == pointFeatureCollection)
    throw new IOException("There is no PointFeatureCollection in  " + pfDataset.getLocation());

  long start = System.currentTimeMillis();

  FileOutputStream fos = new FileOutputStream(fileOut);
  DataOutputStream out = new DataOutputStream(new BufferedOutputStream(fos, 10000));
  WriterCFPointDataset writer = null;

  // LOOK BAD
  List<VariableSimpleIF> dataVars = new ArrayList<VariableSimpleIF>();
  ucar.nc2.NetcdfFile ncfile = pfDataset.getNetcdfFile();
  if ((ncfile == null) || !(ncfile instanceof NetcdfDataset)) {
    dataVars.addAll(pfDataset.getDataVariables());
  } else {
    NetcdfDataset ncd = (NetcdfDataset) ncfile;
    for (VariableSimpleIF vs : pfDataset.getDataVariables()) {
      if (ncd.findCoordinateAxis(vs.getShortName()) == null)
        dataVars.add(vs);
    }
  }

  int count = 0;
  for (PointFeature pointFeature : pointFeatureCollection) {
    StructureData data = pointFeature.getDataAll();
    if (count == 0) {
      EarthLocation loc = pointFeature.getLocation(); // LOOK we dont know this until we see the obs
      String altUnits = Double.isNaN(loc.getAltitude()) ? null : "meters"; // LOOK units may be wrong
      writer = new WriterCFPointDataset(out, pfDataset.getGlobalAttributes(), altUnits);
      writer.writeHeader(dataVars, -1);
    }
    writer.writeRecord(pointFeature, data);
    count++;
  }

  writer.finish();
  out.flush();
  out.close();

  long took = System.currentTimeMillis() - start;
  System.out.printf("Write %d records from %s to %s took %d msecs %n", count, pfDataset.getLocation(), fileOut, took);
  return count;
}
 

public static int checkPointFeatureDataset(FeatureDataset fdataset, boolean show) throws IOException {
  long start = System.currentTimeMillis();
  int count = 0;

  CalendarDate d1 = fdataset.getCalendarDateStart();
  CalendarDate d2 = fdataset.getCalendarDateEnd();
  if ((d1 != null) && (d2 != null))
    Assert.assertTrue("calendar date min <= max", d1.isBefore(d2) || d1.equals(d2));

  List<VariableSimpleIF> dataVars = fdataset.getDataVariables();
  Assert.assertNotNull("fdataset.getDataVariables()", dataVars);
  for (VariableSimpleIF v : dataVars) {
    Assert.assertNotNull(v.getShortName(), fdataset.getDataVariable(v.getShortName()));
  }

  // FeatureDatasetPoint
  Assert.assertTrue("fdataset instanceof FeatureDatasetPoint", fdataset instanceof FeatureDatasetPoint);
  FeatureDatasetPoint fdpoint = (FeatureDatasetPoint) fdataset;

  for (DsgFeatureCollection fc : fdpoint.getPointFeatureCollectionList()) {
    checkDsgFeatureCollection(fc);

    if (fc instanceof PointFeatureCollection) {
      PointFeatureCollection pfc = (PointFeatureCollection) fc;
      count = checkPointFeatureCollection(pfc, show);
      Assert.assertEquals("PointFeatureCollection getData count = size", count, pfc.size());

    } else if (fc instanceof StationTimeSeriesFeatureCollection) {
      count = checkStationFeatureCollection((StationTimeSeriesFeatureCollection) fc);
      // testNestedPointFeatureCollection((StationTimeSeriesFeatureCollection) fc, show);

    } else if (fc instanceof StationProfileFeatureCollection) {
      count = checkStationProfileFeatureCollection((StationProfileFeatureCollection) fc, show);
      if (showStructureData)
        showStructureData((StationProfileFeatureCollection) fc);

    } else if (fc instanceof TrajectoryProfileFeatureCollection) {
      count = checkSectionFeatureCollection((TrajectoryProfileFeatureCollection) fc, show);

    } else if (fc instanceof ProfileFeatureCollection) {
      count = checkProfileFeatureCollection((ProfileFeatureCollection) fc, show);

    } else {
      count = checkOther(fc, show);
    }
    checkInfo(fc);
  }

  long took = System.currentTimeMillis() - start;
  System.out.printf(" nobs=%d took= %d msec%n", count, took);
  return count;
}