// @todo Make sure units are meters public Array getElevation(Range range) throws IOException, InvalidRangeException { List section = new ArrayList(1); section.add(range); Array a = elevVar.read(section); if (elevVarUnitsConversionFactor == 1.0) return (a); for (IndexIterator it = a.getIndexIterator(); it.hasNext(); ) { if (elevVar.getDataType() == DataType.DOUBLE) { double val = it.getDoubleNext(); it.setDoubleCurrent(val * elevVarUnitsConversionFactor); } else if (elevVar.getDataType() == DataType.FLOAT) { float val = it.getFloatNext(); it.setFloatCurrent((float) (val * elevVarUnitsConversionFactor)); } else if (elevVar.getDataType() == DataType.INT) { int val = it.getIntNext(); it.setIntCurrent((int) (val * elevVarUnitsConversionFactor)); } else if (elevVar.getDataType() == DataType.LONG) { long val = it.getLongNext(); it.setLongCurrent((long) (val * elevVarUnitsConversionFactor)); } else { throw new IllegalStateException( "Elevation variable type <" + elevVar.getDataType().toString() + "> not double, float, int, or long."); } } return (a); }
private void createProfiles(int nprofiles) throws IOException { this.nprofiles = nprofiles; // add the dimensions Dimension profileDim = ncfile.addDimension(profileDimName, nprofiles); profileDims.add(profileDim); Variable v = ncfile.addVariable(numObsName, DataType.INT, profileDimName); ncfile.addVariableAttribute( v, new Attribute("long_name", "number of children in linked list for this profile")); v = ncfile.addVariable(numProfilesTotalName, DataType.INT, ""); ncfile.addVariableAttribute(v, new Attribute("long_name", "number of valid profiles")); v = ncfile.addVariable(firstObsName, DataType.INT, profileDimName); ncfile.addVariableAttribute( v, new Attribute("long_name", "record number of first obs in linked list for this profile")); // time variable Variable timeVar = ncfile.addStringVariable(timeName, profileDims, 20); ncfile.addVariableAttribute( timeVar, new Attribute("long_name", "ISO-8601 Date - time of observation")); v = ncfile.addVariable(parentStationIndex, DataType.INT, profileDimName); ncfile.addVariableAttribute(v, new Attribute("long_name", "index of parent station")); v = ncfile.addVariable(nextProfileName, DataType.INT, profileDimName); ncfile.addVariableAttribute( v, new Attribute("long_name", "index of next profile in linked list for this station")); }
/** * Create a new GridVertCoord for a layer * * @param record layer record * @param levelName name of this level * @param lookup lookup table * @param level1 level 1 * @param level2 level 2 */ GridVertCoord( GridRecord record, String levelName, GridTableLookup lookup, double[] level1, double[] level2) { this.typicalRecord = record; this.levelName = levelName; this.lookup = lookup; // dontUseVertical = !lookup.isVerticalCoordinate(record); positive = lookup.isPositiveUp(record) ? "up" : "down"; units = lookup.getLevelUnit(record); usesBounds = lookup.isLayer(this.typicalRecord); levels = new ArrayList<LevelCoord>(level1.length); for (int i = 0; i < level1.length; i++) { levels.add(new LevelCoord(level1[i], (level2 == null) ? 0.0 : level2[i])); } Collections.sort(levels); if (positive.equals("down")) { Collections.reverse(levels); } dontUseVertical = (levels.size() == 1); }
public Array getData(Range range, String parameterName) throws IOException, InvalidRangeException { Variable variable = ncfile.getRootGroup().findVariable(parameterName); int varRank = variable.getRank(); int[] varShape = variable.getShape(); List section = new ArrayList(varRank); section.add(range); for (int i = 1; i < varRank; i++) { section.add(new Range(0, varShape[i] - 1)); } Array array = variable.read(section); if (array.getShape()[0] == 1) { return (array.reduce(0)); } else { return (array); } // return( array.getShape()[0] == 1 ? array.reduce( 0 ) : array); }
/** * Constructor. * * @param dataset belongs to this dataset * @param dsvar wraps this Variable * @param gcs has this grid coordinate system */ public GeoGrid(GridDataset dataset, VariableDS dsvar, GridCoordSys gcs) { this.dataset = dataset; this.vs = dsvar; this.gcs = gcs; CoordinateAxis xaxis = gcs.getXHorizAxis(); if (xaxis instanceof CoordinateAxis1D) { xDimOrgIndex = findDimension(gcs.getXHorizAxis().getDimension(0)); yDimOrgIndex = findDimension(gcs.getYHorizAxis().getDimension(0)); } else { // 2D case yDimOrgIndex = findDimension(gcs.getXHorizAxis().getDimension(0)); xDimOrgIndex = findDimension(gcs.getXHorizAxis().getDimension(1)); } if (gcs.getVerticalAxis() != null) zDimOrgIndex = findDimension(gcs.getVerticalAxis().getDimension(0)); if (gcs.getTimeAxis() != null) { if (gcs.getTimeAxis1D() != null) tDimOrgIndex = findDimension(gcs.getTimeAxis1D().getDimension(0)); else tDimOrgIndex = findDimension(gcs.getTimeAxis().getDimension(1)); } if (gcs.getEnsembleAxis() != null) eDimOrgIndex = findDimension(gcs.getEnsembleAxis().getDimension(0)); if (gcs.getRunTimeAxis() != null) rtDimOrgIndex = findDimension(gcs.getRunTimeAxis().getDimension(0)); // construct canonical dimension list int count = 0; this.mydims = new ArrayList<Dimension>(); if ((rtDimOrgIndex >= 0) && (rtDimOrgIndex != tDimOrgIndex)) { mydims.add(dsvar.getDimension(rtDimOrgIndex)); rtDimNewIndex = count++; } if (eDimOrgIndex >= 0) { mydims.add(dsvar.getDimension(eDimOrgIndex)); eDimNewIndex = count++; } if (tDimOrgIndex >= 0) { mydims.add(dsvar.getDimension(tDimOrgIndex)); tDimNewIndex = count++; } if (zDimOrgIndex >= 0) { mydims.add(dsvar.getDimension(zDimOrgIndex)); zDimNewIndex = count++; } if (yDimOrgIndex >= 0) { mydims.add(dsvar.getDimension(yDimOrgIndex)); yDimNewIndex = count++; } if (xDimOrgIndex >= 0) { mydims.add(dsvar.getDimension(xDimOrgIndex)); xDimNewIndex = count; } }
/** * Match levels * * @param records records to match * @return true if they have the same levels */ boolean matchLevels(List<GridRecord> records) { // first create a new list List<LevelCoord> levelList = new ArrayList<LevelCoord>(records.size()); for (GridRecord record : records) { LevelCoord lc = new LevelCoord(record.getLevel1(), record.getLevel2()); if (!levelList.contains(lc)) { levelList.add(lc); } } Collections.sort(levelList); if (positive.equals("down")) { Collections.reverse(levelList); } // gotta equal existing list return levelList.equals(levels); }
private void writeHeader(ProfileFeature profile, PointFeature obs) throws IOException { Formatter coordNames = new Formatter().format("%s %s %s", profileTimeName, latName, lonName); List<VariableSimpleIF> coords = new ArrayList<>(); if (useAlt) { coords.add( VariableSimpleImpl.makeScalar( altitudeCoordinateName, "obs altitude", altUnits, DataType.DOUBLE) .add(new Attribute(CF.STANDARD_NAME, "altitude")) .add( new Attribute( CF.POSITIVE, CF1Convention.getZisPositive(altitudeCoordinateName, altUnits)))); coordNames.format(" %s", altitudeCoordinateName); } super.writeHeader( coords, profile.getFeatureData(), obs.getFeatureData(), coordNames.toString()); }
protected void makeFeatureVariables(StructureData featureData, boolean isExtended) throws IOException { // LOOK why not unlimited here ? Dimension profileDim = writer.addDimension(null, profileDimName, nfeatures); // Dimension profileDim = isExtendedModel ? writer.addUnlimitedDimension(profileDimName) : // writer.addDimension(null, profileDimName, nprofiles); // add the profile Variables using the profile dimension List<VariableSimpleIF> profileVars = new ArrayList<>(); profileVars.add( VariableSimpleImpl.makeScalar(latName, "profile latitude", CDM.LAT_UNITS, DataType.DOUBLE)); profileVars.add( VariableSimpleImpl.makeScalar( lonName, "profile longitude", CDM.LON_UNITS, DataType.DOUBLE)); profileVars.add( VariableSimpleImpl.makeString(profileIdName, "profile identifier", null, id_strlen) .add(new Attribute(CF.CF_ROLE, CF.PROFILE_ID))); // profileId:cf_role = "profile_id"; profileVars.add( VariableSimpleImpl.makeScalar( numberOfObsName, "number of obs for this profile", null, DataType.INT) .add( new Attribute( CF.SAMPLE_DIMENSION, recordDimName))); // rowSize:sample_dimension = "obs" profileVars.add( VariableSimpleImpl.makeScalar( profileTimeName, "nominal time of profile", timeUnit.getUnitsString(), DataType.DOUBLE)); for (StructureMembers.Member m : featureData.getMembers()) { VariableSimpleIF dv = getDataVar(m.getName()); if (dv != null) profileVars.add(dv); } if (isExtended) { profileStruct = (Structure) writer.addVariable(null, profileStructName, DataType.STRUCTURE, profileDimName); addCoordinatesExtended(profileStruct, profileVars); } else { addCoordinatesClassic(profileDim, profileVars, featureVarMap); } }
/** * 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); } }
public static void main(String args[]) throws Exception { long start = System.currentTimeMillis(); Map<String, ucar.unidata.geoloc.Station> staHash = new HashMap<String, ucar.unidata.geoloc.Station>(); String location = "R:/testdata/sounding/netcdf/Upperair_20070401_0000.nc"; NetcdfDataset ncfile = NetcdfDataset.openDataset(location); ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE); // look through record varibles, for those that have "manLevel" dimension // make a StructureData object for those StructureMembers sm = new StructureMembers("manLevel"); Dimension manDim = ncfile.findDimension("manLevel"); Structure record = (Structure) ncfile.findVariable("record"); List<Variable> allList = record.getVariables(); List<VariableSimpleIF> varList = new ArrayList<VariableSimpleIF>(); for (Variable v : allList) { if ((v.getRank() == 1) && v.getDimension(0).equals(manDim)) { // public VariableDS(NetcdfDataset ds, Group group, Structure parentStructure, String // shortName, DataType dataType, // String dims, String units, String desc) { varList.add( new VariableDS( ncfile, null, null, v.getShortName(), v.getDataType(), "", v.getUnitsString(), v.getDescription())); // (String name, String desc, String units, DataType dtype, int []shape) sm.addMember( v.getShortName(), v.getDescription(), v.getUnitsString(), v.getDataType(), new int[0]); // scalar } } ArrayStructureMA manAS = new ArrayStructureMA(sm, new int[] {manDim.getLength()}); // need the date units Variable time = ncfile.findVariable("synTime"); String timeUnits = ncfile.findAttValueIgnoreCase(time, "units", null); timeUnits = StringUtil.remove(timeUnits, '('); // crappy fsl'ism timeUnits = StringUtil.remove(timeUnits, ')'); DateUnit timeUnit = new DateUnit(timeUnits); // extract stations int nrecs = 0; StructureDataIterator iter = record.getStructureIterator(); while (iter.hasNext()) { StructureData sdata = iter.next(); String name = sdata.getScalarString("staName"); ucar.unidata.geoloc.Station s = staHash.get(name); if (s == null) { float lat = sdata.convertScalarFloat("staLat"); float lon = sdata.convertScalarFloat("staLon"); float elev = sdata.convertScalarFloat("staElev"); s = new StationImpl(name, "", lat, lon, elev); staHash.put(name, s); } nrecs++; } List<ucar.unidata.geoloc.Station> stnList = Arrays.asList(staHash.values().toArray(new ucar.unidata.geoloc.Station[staHash.size()])); Collections.sort(stnList); // create the writer WriterProfileObsDataset writer = new WriterProfileObsDataset(location + ".out", "rewrite " + location); writer.writeHeader(stnList, varList, nrecs, "prMan"); // extract records iter = record.getStructureIterator(); while (iter.hasNext()) { StructureData sdata = iter.next(); String name = sdata.getScalarString("staName"); double timeValue = sdata.convertScalarDouble("synTime"); Date date = timeUnit.makeDate(timeValue); // transfer to the ArrayStructure List<String> names = sm.getMemberNames(); for (String mname : names) { manAS.setMemberArray(mname, sdata.getArray(mname)); } // each level is weritten as a seperate structure int numMand = sdata.getScalarInt("numMand"); if (numMand >= manDim.getLength()) continue; for (int i = 0; i < numMand; i++) { StructureData useData = manAS.getStructureData(i); writer.writeRecord(name, date, useData); } } writer.finish(); long took = System.currentTimeMillis() - start; System.out.println("That took = " + took); }
private void createStations(List<ucar.unidata.geoloc.Station> stnList) throws IOException { int nstns = stnList.size(); // see if there's altitude, wmoId for any stations for (int i = 0; i < nstns; i++) { ucar.unidata.geoloc.Station stn = stnList.get(i); // if (!Double.isNaN(stn.getAltitude())) // useAlt = true; if ((stn.getWmoId() != null) && (stn.getWmoId().trim().length() > 0)) useWmoId = true; } /* if (useAlt) ncfile.addGlobalAttribute("altitude_coordinate", altName); */ // find string lengths for (int i = 0; i < nstns; i++) { ucar.unidata.geoloc.Station station = stnList.get(i); name_strlen = Math.max(name_strlen, station.getName().length()); desc_strlen = Math.max(desc_strlen, station.getDescription().length()); if (useWmoId) wmo_strlen = Math.max(wmo_strlen, station.getName().length()); } LatLonRect llbb = getBoundingBox(stnList); ncfile.addGlobalAttribute( "geospatial_lat_min", Double.toString(llbb.getLowerLeftPoint().getLatitude())); ncfile.addGlobalAttribute( "geospatial_lat_max", Double.toString(llbb.getUpperRightPoint().getLatitude())); ncfile.addGlobalAttribute( "geospatial_lon_min", Double.toString(llbb.getLowerLeftPoint().getLongitude())); ncfile.addGlobalAttribute( "geospatial_lon_max", Double.toString(llbb.getUpperRightPoint().getLongitude())); // add the dimensions Dimension recordDim = ncfile.addUnlimitedDimension(recordDimName); recordDims.add(recordDim); Dimension stationDim = ncfile.addDimension(stationDimName, nstns); stationDims.add(stationDim); // add the station Variables using the station dimension Variable v = ncfile.addVariable(latName, DataType.DOUBLE, stationDimName); ncfile.addVariableAttribute(v, new Attribute("units", "degrees_north")); ncfile.addVariableAttribute(v, new Attribute("long_name", "station latitude")); v = ncfile.addVariable(lonName, DataType.DOUBLE, stationDimName); ncfile.addVariableAttribute(v, new Attribute("units", "degrees_east")); ncfile.addVariableAttribute(v, new Attribute("long_name", "station longitude")); if (useAlt) { v = ncfile.addVariable(altName, DataType.DOUBLE, stationDimName); ncfile.addVariableAttribute(v, new Attribute("units", "meters")); ncfile.addVariableAttribute(v, new Attribute("long_name", "station altitude")); } v = ncfile.addStringVariable(idName, stationDims, name_strlen); ncfile.addVariableAttribute(v, new Attribute("long_name", "station identifier")); v = ncfile.addStringVariable(descName, stationDims, desc_strlen); ncfile.addVariableAttribute(v, new Attribute("long_name", "station description")); if (useWmoId) { v = ncfile.addStringVariable(wmoName, stationDims, wmo_strlen); ncfile.addVariableAttribute(v, new Attribute("long_name", "station WMO id")); } v = ncfile.addVariable(numProfilesName, DataType.INT, stationDimName); ncfile.addVariableAttribute( v, new Attribute("long_name", "number of profiles in linked list for this station")); v = ncfile.addVariable(firstProfileName, DataType.INT, stationDimName); ncfile.addVariableAttribute( v, new Attribute("long_name", "index of first profile in linked list for this station")); }
// @todo Make sure units are degrees_east public Array getLongitude(Range range) throws IOException, InvalidRangeException { List section = new ArrayList(1); section.add(range); return (lonVar.read(section)); }
public List getTrajectories() // throws IOException; { List l = new ArrayList(); l.add(trajectory); return (l); }
public List getTrajectoryIds() { List l = new ArrayList(); l.add(trajectoryId); return (l); }