Examples with StaticLocationDataset org.n52.sos.netcdf.data.dataset.StaticLocationDataset used on opensource projects

Example 1 with StaticLocationDataset

use of org.n52.sos.netcdf.data.dataset.StaticLocationDataset in project SOS by 52North.

the class AbstractNetcdfEncoder method getLatitudeArray.

protected Array getLatitudeArray(AbstractSensorDataset sensorDataset) throws EncodingException {
    if (sensorDataset instanceof StaticLocationDataset) {
        StaticLocationDataset locationDataset = (StaticLocationDataset) sensorDataset;
        if (locationDataset.getLat() != null) {
            Array array = getArray();
            initArrayWithFillValue(array, getNetcdfHelper().getFillValue());
            Index index = array.getIndex();
            index.set(0);
            array.setDouble(index, locationDataset.getLat());
        }
    } else {
        // TODO support varying lat
        throw new EncodingException("Varying lat are not yet supported.");
    }
    return null;
}

Example 2 with StaticLocationDataset

use of org.n52.sos.netcdf.data.dataset.StaticLocationDataset in project SOS by 52North.

the class AbstractNetcdfEncoder method getLongitudeArray.

protected Array getLongitudeArray(AbstractSensorDataset sensorDataset) throws EncodingException {
    if (sensorDataset instanceof StaticLocationDataset) {
        StaticLocationDataset locationDataset = (StaticLocationDataset) sensorDataset;
        if (locationDataset.getLat() != null) {
            Array array = getArray();
            initArrayWithFillValue(array, getNetcdfHelper().getFillValue());
            Index index = array.getIndex();
            index.set(0);
            array.setDouble(index, locationDataset.getLat());
        }
    } else {
        // TODO support varying lat
        throw new EncodingException("Varying longs are not yet supported.");
    }
    return null;
}

Example 3 with StaticLocationDataset

use of org.n52.sos.netcdf.data.dataset.StaticLocationDataset in project SOS by 52North.

the class AbstractNetcdfEncoder method addGeospatialAttributes.

protected void addGeospatialAttributes(NetcdfFileWriter writer, AbstractSensorDataset sensorDataset) throws EncodingException {
    // AbstractSensorDataset during construction
    if (sensorDataset instanceof StaticLocationDataset) {
        StaticLocationDataset LocationDataset = (StaticLocationDataset) sensorDataset;
        writer.addGroupAttribute(null, new Attribute(ACDDConstants.GEOSPATIAL_LAT_MIN, LocationDataset.getLat()));
        writer.addGroupAttribute(null, new Attribute(ACDDConstants.GEOSPATIAL_LAT_MAX, LocationDataset.getLat()));
        writer.addGroupAttribute(null, new Attribute(ACDDConstants.GEOSPATIAL_LAT_UNITS, CFConstants.UNITS_DEGREES_NORTH));
        writer.addGroupAttribute(null, new Attribute(ACDDConstants.GEOSPATIAL_LON_MIN, LocationDataset.getLng()));
        writer.addGroupAttribute(null, new Attribute(ACDDConstants.GEOSPATIAL_LON_MAX, LocationDataset.getLng()));
        writer.addGroupAttribute(null, new Attribute(ACDDConstants.GEOSPATIAL_LON_UNITS, CFConstants.UNITS_DEGREES_EAST));
    } else {
        throw new EncodingException("Trajectory encoding is not supported (bbox)");
    }
}

Example 4 with StaticLocationDataset

use of org.n52.sos.netcdf.data.dataset.StaticLocationDataset in project SOS by 52North.

the class AbstractNetcdfEncoder method encodeSensorDataToNetcdf.

protected void encodeSensorDataToNetcdf(File netcdfFile, AbstractSensorDataset sensorDataset, Version version) throws EncodingException, IOException {
    String sensor = sensorDataset.getSensorIdentifier();
    sensorDataset.getSensor().setSensorDescription(getProcedureDescription(sensor, sensorDataset.getProcedureDescription()));
    NetcdfFileWriter writer = getNetcdfFileWriter(netcdfFile, version);
    // set fill on, doesn't seem to have any effect though
    writer.setFill(true);
    Map<Variable, Array> variableArrayMap = Maps.newHashMap();
    int numTimes = sensorDataset.getTimes().size();
    // FIXME shouldn't assume that all subsensors are heights (or rename
    // subsensors if they are)
    int numHeightDepth = sensorDataset.getSubSensors().size() > 0 ? sensorDataset.getSubSensors().size() : 1;
    // global attributes
    addGlobaleAttributes(writer, sensorDataset);
    // add appropriate dims for feature type
    List<Dimension> timeDims = Lists.newArrayList();
    List<Dimension> latLngDims = Lists.newArrayList();
    List<Dimension> latDims = Lists.newArrayList();
    List<Dimension> lngDims = Lists.newArrayList();
    List<Dimension> zDims = Lists.newArrayList();
    List<Dimension> obsPropDims = Lists.newArrayList();
    // REQUIRED for NetCDF-3
    // add Dimensions
    // dTime = writer.addDimension(null, CFStandardNames.TIME.getName(),
    // numTimes);
    Dimension dTime = writer.addUnlimitedDimension(getVariableDimensionCaseName(CFStandardNames.TIME.getName()));
    dTime.setLength(numTimes);
    timeDims.add(dTime);
    if (!(sensorDataset instanceof StaticLocationDataset)) {
        zDims.add(dTime);
    }
    obsPropDims.add(dTime);
    // set up lat/lng dimensions
    // FIXME do not set time dimension for static location dataset
    // if ((sensorDataset instanceof StaticLocationDataset)) {
    // latLngDims.add(dTime);
    // }
    // set up z dimensions
    String dimensionName;
    if (useHeight()) {
        dimensionName = getVariableDimensionCaseName(CFStandardNames.HEIGHT.getName());
    } else {
        dimensionName = getVariableDimensionCaseName(CFStandardNames.DEPTH.getName());
    }
    // profile/timeSeriesProfile
    Dimension dZ = writer.addDimension(null, dimensionName, numHeightDepth);
    if (!(sensorDataset instanceof StaticLocationDataset)) {
        // trajectory
        zDims.add(dTime);
    }
    zDims.add(dZ);
    obsPropDims.add(dZ);
    variableArrayMap.putAll(getNetcdfProfileSpecificVariablesArrays(writer, sensorDataset));
    // time var
    Variable vTime = addVariableTime(writer, timeDims);
    if (numTimes > 1 && writer.getVersion().isNetdf4format()) {
        vTime.addAttribute(new Attribute(CDM.CHUNK_SIZES, getNetcdfHelper().getChunkSizeTime()));
    }
    ArrayDouble timeArray = new ArrayDouble(getDimShapes(timeDims));
    initArrayWithFillValue(timeArray, getNetcdfHelper().getFillValue());
    Array latArray = getLatitudeArray(sensorDataset);
    Array lonArray = getLongitudeArray(sensorDataset);
    // add lat/long dimensions
    long latSize = 1;
    if (latArray != null) {
        latSize = latArray.getSize();
    }
    Dimension dLat = writer.addDimension(null, getVariableDimensionCaseName(CFStandardNames.LATITUDE.getName()), (int) latSize);
    latDims.add(dLat);
    long lonSize = 1;
    if (lonArray != null) {
        lonSize = lonArray.getSize();
    }
    Dimension dLon = writer.addDimension(null, getVariableDimensionCaseName(CFStandardNames.LONGITUDE.getName()), (int) lonSize);
    lngDims.add(dLon);
    // lat/lon var
    Variable vLat;
    Variable vLon;
    if (latLngDims.size() > 0) {
        vLat = addVariableLatitude(writer, latLngDims);
        vLon = addVariableLongitude(writer, latLngDims);
    } else {
        vLat = addVariableLatitude(writer, latDims);
        vLon = addVariableLongitude(writer, lngDims);
    }
    // height/depth var
    Variable vHeightDepth;
    if (useHeight()) {
        vHeightDepth = addVariableHeight(writer, zDims);
    } else {
        vHeightDepth = addVariableDepth(writer, zDims);
    }
    String coordinateString = Joiner.on(' ').join(Lists.newArrayList(vTime.getFullName(), vLat.getFullName(), vLon.getFullName(), vHeightDepth.getFullName()));
    Map<OmObservableProperty, Variable> obsPropVarMap = Maps.newHashMap();
    Map<Variable, Array> varDataArrayMap = Maps.newHashMap();
    for (OmObservableProperty obsProp : sensorDataset.getPhenomena()) {
        // obs prop var
        Variable vObsProp = addVariableForObservedProperty(writer, obsProp, obsPropDims, coordinateString);
        obsPropVarMap.put(obsProp, vObsProp);
        // init obs prop data array
        Array obsPropArray = getArray(obsPropDims);
        initArrayWithFillValue(obsPropArray, getNetcdfHelper().getFillValue());
        varDataArrayMap.put(vObsProp, obsPropArray);
    }
    // populate heights array for profile
    Array heightDephtArray = null;
    if (zDims.size() == 1 && hasDimension(zDims, dZ) && !sensorDataset.getSubSensors().isEmpty()) {
        heightDephtArray = initHeightDephtArray(zDims);
        Double consistentBinHeight = populateHeightDepthArray(sensorDataset, heightDephtArray, vHeightDepth);
        String verticalResolution = null;
        if (consistentBinHeight == null) {
            verticalResolution = ACDDConstants.POINT;
        } else if (consistentBinHeight != getNetcdfHelper().getFillValue()) {
            verticalResolution = consistentBinHeight + " " + CFConstants.UNITS_METERS + " " + ACDDConstants.BINNED;
        }
        if (verticalResolution != null) {
            writer.addGroupAttribute(null, new Attribute(ACDDConstants.GEOSPATIAL_VERTICAL_RESOLUTION, verticalResolution));
        }
    }
    // iterate through sensorDataset, set values
    int timeCounter = 0;
    for (Time time : sensorDataset.getTimes()) {
        // set time value
        Index timeIndex = timeArray.getIndex();
        int timeIndexCounter = 0;
        // }
        if (hasDimension(timeDims, dTime)) {
            timeIndex.setDim(timeIndexCounter++, timeCounter++);
        }
        timeArray.set(timeIndex, getTimeValue(time));
        // data values
        Map<OmObservableProperty, Map<SubSensor, Value<?>>> obsPropMap = sensorDataset.getDataValues().get(time);
        for (Entry<OmObservableProperty, Map<SubSensor, Value<?>>> entry : obsPropMap.entrySet()) {
            OmObservableProperty obsProp = entry.getKey();
            Variable variable = obsPropVarMap.get(obsProp);
            Array array = varDataArrayMap.get(variable);
            for (Entry<SubSensor, Value<?>> subSensorEntry : obsPropMap.get(obsProp).entrySet()) {
                SubSensor subSensor = subSensorEntry.getKey();
                Value<?> value = subSensorEntry.getValue();
                Object valObj = value.getValue();
                if (!(valObj instanceof Number)) {
                    throw new EncodingException("Value class %s not supported", valObj.getClass().getCanonicalName());
                }
                Index index = array.getIndex();
                int obsPropDimCounter = 0;
                for (Dimension dim : obsPropDims) {
                    // } else if (dim.equals(dTime)){
                    if (dim.equals(dTime)) {
                        // time index dim
                        index.setDim(obsPropDimCounter++, timeCounter - 1);
                    } else if (dim.equals(dZ) && dim.getLength() > 1) {
                        // height/depth index dim
                        index.setDim(obsPropDimCounter++, sensorDataset.getSubSensors().indexOf(subSensor));
                    }
                }
                if (array instanceof ArrayFloat) {
                    ((ArrayFloat) array).set(index, ((Number) valObj).floatValue());
                } else {
                    ((ArrayDouble) array).set(index, ((Number) valObj).doubleValue());
                }
            }
        }
    }
    // create the empty netCDF with dims/vars/attributes defined
    variableArrayMap.put(vTime, timeArray);
    if (latArray != null) {
        variableArrayMap.put(vLat, latArray);
    }
    if (lonArray != null) {
        variableArrayMap.put(vLon, lonArray);
    }
    if (heightDephtArray != null) {
        variableArrayMap.put(vHeightDepth, heightDephtArray);
    }
    variableArrayMap.putAll(varDataArrayMap);
    // create the empty netCDF with dims/vars/attributes defined
    writeToFile(writer, variableArrayMap);
    writer.close();
}