public Float10TrajectoryObsDataset(NetcdfDataset ncd) throws IOException { super(ncd); // Get the names of the two coordinate variables and dimensions // and grab the variables and dimensions themselves. trajDimName = trajDimNameDefault; trajVarName = trajVarNameDefault; timeDimName = timeDimNameDefault; timeVarName = timeVarNameDefault; latVarName = latVarNameDefault; lonVarName = lonVarNameDefault; elevVarName = elevVarNameDefault; Variable latVar = ncd.getRootGroup().findVariable(latVarName); latVar.addAttribute(new Attribute("units", "degrees_north")); Variable lonVar = ncd.getRootGroup().findVariable(lonVarName); lonVar.addAttribute(new Attribute("units", "degrees_east")); this.setTrajectoryInfo( netcdfDataset.getRootGroup().findDimension(trajDimName), netcdfDataset.getRootGroup().findVariable(trajVarName), netcdfDataset.getRootGroup().findDimension(timeDimName), netcdfDataset.getRootGroup().findVariable(timeVarName), netcdfDataset.getRootGroup().findVariable(latVarName), netcdfDataset.getRootGroup().findVariable(lonVarName), netcdfDataset.getRootGroup().findVariable(elevVarName)); }
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); }
// @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); }
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); }
// @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)); }
/** * Setup needed for all SingleTrajectoryObsDatatypes. Can only be called once. * * <p>Units of time varible must be udunits time units. Units of latitude variable must be * convertible to "degrees_north" by udunits. Units of longitude variable must be convertible to * "degrees_east" by udunits. Units of altitude variable must be convertible to "meters" by * udunits. * * @throws IllegalArgumentException if units of time, latitude, longitude, or altitude variables * are not as required. * @throws IllegalStateException if this method has already been called. */ public void setTrajectoryInfo(Config trajConfig) throws IOException { if (timeDim != null) throw new IllegalStateException("The setTrajectoryInfo() method can only be called once."); this.trajectoryId = trajConfig.getTrajectoryId(); this.timeDim = trajConfig.getTimeDim(); this.timeVar = trajConfig.getTimeVar(); this.latVar = trajConfig.getLatVar(); this.lonVar = trajConfig.getLonVar(); this.elevVar = trajConfig.getElevVar(); trajectoryNumPoint = this.timeDim.getLength(); timeVarUnitsString = this.timeVar.findAttribute("units").getStringValue(); // Check that time, lat, lon, elev units are acceptable. if (DateUnit.getStandardDate(timeVarUnitsString) == null) { throw new IllegalArgumentException( "Units of time variable <" + timeVarUnitsString + "> not a date unit."); } String latVarUnitsString = this.latVar.findAttribute("units").getStringValue(); if (!SimpleUnit.isCompatible(latVarUnitsString, "degrees_north")) { throw new IllegalArgumentException( "Units of lat var <" + latVarUnitsString + "> not compatible with \"degrees_north\"."); } String lonVarUnitsString = this.lonVar.findAttribute("units").getStringValue(); if (!SimpleUnit.isCompatible(lonVarUnitsString, "degrees_east")) { throw new IllegalArgumentException( "Units of lon var <" + lonVarUnitsString + "> not compatible with \"degrees_east\"."); } String elevVarUnitsString = this.elevVar.findAttribute("units").getStringValue(); if (!SimpleUnit.isCompatible(elevVarUnitsString, "meters")) { throw new IllegalArgumentException( "Units of elev var <" + elevVarUnitsString + "> not compatible with \"meters\"."); } try { elevVarUnitsConversionFactor = getMetersConversionFactor(elevVarUnitsString); } catch (Exception e) { throw new IllegalArgumentException( "Exception on getMetersConversionFactor() for the units of elev var <" + elevVarUnitsString + ">."); } if (this.ncfile.hasUnlimitedDimension() && this.ncfile.getUnlimitedDimension().equals(timeDim)) { Object result = this.ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE); if ((result != null) && (Boolean) result) this.recordVar = (Structure) this.ncfile.getRootGroup().findVariable("record"); else this.recordVar = new StructurePseudo(this.ncfile, null, "record", timeDim); } else { this.recordVar = new StructurePseudo(this.ncfile, null, "record", timeDim); } // @todo HACK, HACK, HACK - remove once addRecordStructure() deals with ncd attribute changes. Variable elevVarInRecVar = this.recordVar.findVariable(this.elevVar.getFullNameEscaped()); if (!elevVarUnitsString.equals(elevVarInRecVar.findAttribute("units").getStringValue())) { elevVarInRecVar.addAttribute(new Attribute("units", elevVarUnitsString)); } trajectoryVarsMap = new HashMap(); // for ( Iterator it = this.recordVar.getVariables().iterator(); it.hasNext(); ) for (Iterator it = this.ncfile.getRootGroup().getVariables().iterator(); it.hasNext(); ) { Variable curVar = (Variable) it.next(); if (curVar.getRank() > 0 && !curVar.equals(this.timeVar) && !curVar.equals(this.latVar) && !curVar.equals(this.lonVar) && !curVar.equals(this.elevVar) && (this.recordVar == null ? true : !curVar.equals(this.recordVar))) { MyTypedDataVariable typedVar = new MyTypedDataVariable(new VariableDS(null, curVar, true)); dataVariables.add(typedVar); trajectoryVarsMap.put(typedVar.getShortName(), typedVar); } } trajectory = new SingleTrajectory( this.trajectoryId, trajectoryNumPoint, this.timeVar, timeVarUnitsString, this.latVar, this.lonVar, this.elevVar, dataVariables, trajectoryVarsMap); startDate = trajectory.getTime(0); endDate = trajectory.getTime(trajectoryNumPoint - 1); ((SingleTrajectory) trajectory).setStartDate(startDate); ((SingleTrajectory) trajectory).setEndDate(endDate); }
public static boolean isValidFile(NetcdfDataset ds) { // Check that has a time dimension and a trajectory dimension. List list = ds.getRootGroup().getDimensions(); if (list.size() != 2) return (false); Dimension d; for (int i = 0; i < 2; i++) { d = (Dimension) list.get(i); if (!d.getShortName().equals(timeDimNameDefault) && !d.getShortName().equals(trajDimNameDefault)) return (false); } // Check that has a trajectory coordinate variable. Variable var = ds.getRootGroup().findVariable(trajVarNameDefault); if (var == null) return (false); list = var.getDimensions(); if (list.size() != 1) return (false); d = (Dimension) list.get(0); if (!d.getShortName().equals(trajDimNameDefault)) return (false); // Check that has a time coordinate variable with units that are udunits time var = ds.getRootGroup().findVariable(timeVarNameDefault); if (var == null) return (false); list = var.getDimensions(); if (list.size() != 1) return (false); d = (Dimension) list.get(0); if (!d.getShortName().equals(timeDimNameDefault)) return (false); String units = var.findAttribute("units").getStringValue(); Date date = DateUnit.getStandardDate("0 " + units); if (date == null) return (false); // Check for variable latitude(time) with units of "deg". var = ds.getRootGroup().findVariable(latVarNameDefault); if (var == null) return (false); list = var.getDimensions(); if (list.size() != 2) return (false); for (int i = 0; i < 2; i++) { d = (Dimension) list.get(i); if (!d.getShortName().equals(timeDimNameDefault) && !d.getShortName().equals(trajDimNameDefault)) return (false); } // units = var.findAttribute( "units").getStringValue(); // if ( ! SimpleUnit.isCompatible( units, "degrees_north")) return( false); // Check for variable longitude(time) with units of "deg". var = ds.getRootGroup().findVariable(lonVarNameDefault); if (var == null) return (false); list = var.getDimensions(); if (list.size() != 2) return (false); for (int i = 0; i < 2; i++) { d = (Dimension) list.get(i); if (!d.getShortName().equals(timeDimNameDefault) && !d.getShortName().equals(trajDimNameDefault)) return (false); } // units = var.findAttribute( "units").getStringValue(); // if ( ! SimpleUnit.isCompatible( units, "degrees_east")) return( false); // Check for variable altitude(time) with units of "m". var = ds.getRootGroup().findVariable(elevVarNameDefault); if (var == null) return (false); list = var.getDimensions(); if (list.size() != 2) return (false); for (int i = 0; i < 2; i++) { d = (Dimension) list.get(i); if (!d.getShortName().equals(timeDimNameDefault) && !d.getShortName().equals(trajDimNameDefault)) return (false); } units = var.findAttribute("units").getStringValue(); if (!SimpleUnit.isCompatible(units, "m")) return (false); return (true); }