Examples with Array org.openmuc.openiec61850.Array used on opensource projects

Example 41 with Array

use of org.openmuc.openiec61850.Array in project rosetta by Unidata.

the class TestTagUniversalFileFormatOneLocOneOb method testMatchup.

@Test
public void testMatchup() throws IOException {
    // for this date and ob:
    // "2005-04-16 00:00:00",6,21.50,"temperature","Celsius"
    // there is a lat/lon matchup
    CalendarDate findTimeCd = CalendarDate.parseISOformat("gregorian", "2005-04-16 00:00:00");
    long findTime = findTimeCd.toDate().getTime() / 1000;
    Variable time = ncd.findVariable("time");
    Array timeVals = time.read();
    int foundIndex = 0;
    boolean found = false;
    for (int i = 0; i < timeVals.getSize(); i++) {
        long checkTime = timeVals.getLong(i);
        if (checkTime == findTime) {
            found = true;
            foundIndex = i;
        }
    }
    assertTrue(found);
    // check that temperature value is as expected
    Variable temp = ncd.findVariable("temperature");
    Array tempVals = temp.read();
    assertEquals(21.50, tempVals.getFloat(foundIndex), 0.001);
}

Example 42 with Array

use of org.openmuc.openiec61850.Array in project rosetta by Unidata.

the class NetcdfFileManager method calculateCoordVarAttrs.

/**
 * Get the auto-computed attributes for a given coordinate VariableInfo object
 *
 * @param variableInfo The coordinate variable for which attributes should be computed
 * @return A list of computed attributes
 */
List<Attribute> calculateCoordVarAttrs(VariableInfo variableInfo) {
    List<Attribute> calculatedCoordVarAttrs = new ArrayList<>();
    // CoordinateVariable axis
    String type = VariableInfoUtils.getCoordVarType(variableInfo);
    if (type.equalsIgnoreCase(VariableInfoUtils.longitude)) {
        calculatedCoordVarAttrs.add(new Attribute("axis", "X"));
    } else if (type.equalsIgnoreCase(VariableInfoUtils.latitude)) {
        calculatedCoordVarAttrs.add(new Attribute("axis", "Y"));
    } else if (type.equalsIgnoreCase(VariableInfoUtils.vertical)) {
        calculatedCoordVarAttrs.add(new Attribute("axis", "Z"));
        RosettaAttribute positive = VariableInfoUtils.findAttributeByName(VariableInfoUtils.positiveAttrName, variableInfo);
        if (positive != null) {
            calculatedCoordVarAttrs.add(new Attribute(positive.getName(), positive.getValue()));
        }
    }
    // CoordinateVariable coverage_content_type
    // no good way to guess this - will need to come from the template
    int colId = variableInfo.getColumnId();
    calculatedCoordVarAttrs.add(new Attribute(colIdAttrName, variableInfo.getColumnId()));
    // only for coordinate variables defined in columnar data block (i.e. non-attribute based)
    if (colId > 0) {
        // CoordinateVariable valid_min, valid_max*
        Array data = arrayData.get(variableInfo.getColumnId());
        Optional<Double> missingValue = VariableInfoUtils.findMissingValue(variableInfo);
        calculatedCoordVarAttrs.addAll(getMaxMinAttrs(data, missingValue));
    }
    return calculatedCoordVarAttrs;
}

Example 43 with Array

use of org.openmuc.openiec61850.Array in project rosetta by Unidata.

the class TagUniversalFileFormat method convert.

public String convert(String ncfileFinal, Template template) throws InvalidRangeException, IOException {
    Path ncPath = PathUtils.replaceExtension(Paths.get(ncfileFinal), "temp");
    String ncfile = ncPath.toString();
    // metadata extracted from the eTuff file
    if (template != null) {
        Template metadataFromFileTemplate = new Template();
        // make a template object containing just the global metadata from the eTuff file
        metadataFromFileTemplate.setGlobalMetadata(rosettaGlobalAttributes);
        // update the file metadata with template metadata
        metadataFromFileTemplate.update(template);
        // pull out the updated globalmetata list from the updated template
        rosettaGlobalAttributes = metadataFromFileTemplate.getGlobalMetadata();
    }
    rootGroup = null;
    if (useNetcdf4) {
        ncfw = NetcdfFileWriter.createNew(NetcdfFileWriter.Version.netcdf4, ncfile);
        rootGroup = ncfw.addGroup(null, null);
    } else {
        ncfw = NetcdfFileWriter.createNew(NetcdfFileWriter.Version.netcdf3, ncfile);
    }
    // create time dimension
    int numTimeRecords = matchupOneLocOneOb ? data.get(latDimName).size() : getMaxNumRecords();
    Dimension timeDimension = ncfw.addDimension(rootGroup, timeDimName, numTimeRecords);
    // add global attributes
    if (useNetcdf4) {
        // netCDF-4 installed - write global attributes in rootGroup
        makeMetadataGroups();
    } else {
        for (RosettaGlobalAttribute rga : rosettaGlobalAttributes) {
            Attribute ga = RosettaGlobalAttributeUtils.getAttributeFromGlobalAttr(rga);
            ncfw.addGroupAttribute(rootGroup, ga);
        }
    }
    // add the needed CF traj attributes
    ncfw.addGroupAttribute(rootGroup, new Attribute("Conventions", "CF-1.6"));
    ncfw.addGroupAttribute(rootGroup, new Attribute("featureType", "trajectory"));
    String trajectoryId = getTrajId();
    ncfw.addDimension(null, "str_len", trajectoryId.length());
    Variable trajId = ncfw.addVariable(rootGroup, trajectoryIdName, DataType.CHAR, "str_len");
    trajId.addAttribute(new Attribute("cf_role", "trajectory_id"));
    // create time coordinate variable (special since it's not part of the data object
    Variable theNewVar = ncfw.addVariable(rootGroup, timeDimName, DataType.INT, timeDimName);
    theNewVar.addAttribute(new Attribute("standard_name", timeDimName));
    theNewVar.addAttribute(new Attribute("long_name", timeDimName));
    theNewVar.addAttribute(new Attribute("axis", "T"));
    String timeUnit = "seconds since 1970-01-01T00:00:00 UTC";
    theNewVar.addAttribute(new Attribute("units", timeUnit));
    if (!matchupOneLocOneOb) {
        // create freshness time coordinate variable
        // because we are matching one location with more than one ob, it's important to know
        // how "fresh" the location data are compared to the individual data point
        theNewVar = ncfw.addVariable(rootGroup, freshnessVarName, DataType.FLOAT, timeDimName);
        theNewVar.addAttribute(new Attribute("long_name", freshnessVarName));
        theNewVar.addAttribute(new Attribute("units", "seconds"));
        theNewVar.addAttribute(new Attribute("description", "time since last latitude and longitude observation were obtained."));
    }
    // create variables:
    List<String> sortedKeys = new ArrayList<>(data.keySet());
    Collections.sort(sortedKeys);
    List<String> trajVarNames = new ArrayList<>();
    for (Object name : sortedKeys) {
        String strName = name.toString();
        // todo: grab obs to find max/min, add to attributes
        if (trajCoordVarNames.contains(name.toString())) {
            List<String> strData = data.get(strName).values().stream().map(Ob::getValue).collect(Collectors.toList());
            makeCoordinateVariables(name, strData);
        } else {
            int numVarRecords = data.get(strName).size();
            // only add variables which have time series available (i.e. not histogram)
            // add a small fudge factor in identifying possible time series variables
            // from which we want matchup with lat/lon values.
            // one loc many obs check
            int expectedTimeseriesLength = matchupOneLocOneOb ? getMaxNumRecords() : timeDimension.getLength();
            boolean isVar = Math.abs(numVarRecords - expectedTimeseriesLength) <= 10;
            if (isVar) {
                if (!name.equals("datetime")) {
                    List<String> strData = data.get(strName).values().stream().map(Ob::getValue).collect(Collectors.toList());
                    // compute max/min
                    List<Attribute> maxMinAttrs = getMaxMinAttrs(Array.makeArray(DataType.FLOAT, strData));
                    theNewVar = ncfw.addVariable(rootGroup, name.toString(), DataType.FLOAT, timeDimName);
                    trajVarNames.add(name.toString());
                    String unit = data.get(strName).firstEntry().getValue().getUnit();
                    if (!unit.isEmpty()) {
                        theNewVar.addAttribute(new Attribute("units", unit));
                    }
                    theNewVar.addAttribute(new Attribute("coordinates", trajCoordVarNames));
                    theNewVar.addAll(maxMinAttrs);
                }
            } else {
                logger.warn("Skipping non time series variable " + name.toString());
            }
        }
    }
    trajVarNames.add(latDimName);
    trajVarNames.add(lonDimName);
    trajVarNames.add(depthDimName);
    // create the file - writes medata and basic structure
    ncfw.create();
    // write the data, yo!
    // since this is a trajectory file, only write out data when we have lat, lon, and depth obs
    // for a given date
    // get latitude variable
    TreeMap<Long, Ob> dateTimeVar = data.get(maxTimeVar);
    TreeMap<Long, Ob> latVar = data.get("latitude");
    // because we use a TreeMap, the iterator of the Set returned by keySet() are sorted
    // in ascending order.
    Set<Long> times = matchupOneLocOneOb ? latVar.keySet() : dateTimeVar.keySet();
    List<String> varValues;
    List<String> freshnessValues = new ArrayList<>();
    // the netCDF file
    for (Object name : trajVarNames) {
        String strName = name.toString();
        varValues = new ArrayList<>();
        // find a matching ob for the given trajectory time
        if (matchupOneLocOneOb) {
            // we are matching one location to a single ob
            for (Long time : times) {
                TreeMap<Long, Ob> varTM = data.get(strName);
                // ob time closest to before the trajectory time
                Long before = varTM.floorKey(time);
                // ob time closest to after the trajectory time
                Long after = varTM.ceilingKey(time);
                Ob value = null;
                // find which is actually closest
                if ((before != null) && (after != null)) {
                    if ((time - before) < (after - time)) {
                        value = varTM.get(before);
                    } else {
                        value = varTM.get(after);
                    }
                } else if (before != null) {
                    value = varTM.get(before);
                } else if (after != null) {
                    value = varTM.get(after);
                } else {
                    logger.error("no time match found!");
                }
                varValues.add(value.getValue());
            }
        } else {
            // we are matching one location to many obs
            for (Long time : times) {
                TreeMap<Long, Ob> varTM = data.get(strName);
                // ob time closest to before the datetime time
                Long before = varTM.floorKey(time);
                Ob value = null;
                // find which is actually closest
                if (before != null) {
                    value = varTM.get(before);
                } else {
                    logger.error("no time match found!");
                }
                varValues.add(value.getValue());
                if (name.equals(latDimName)) {
                    freshnessValues.add(String.valueOf(time - before));
                }
            }
        }
        Array thisData = ArrayFloat.makeArray(DataType.FLOAT, varValues);
        Variable thisVar = ncfw.findVariable(name.toString());
        ncfw.write(thisVar, thisData);
    }
    // write out the values for the time variable
    varValues = new ArrayList<>();
    for (Long time : times) {
        varValues.add(time.toString());
    }
    Array thisData = ArrayInt.makeArray(DataType.INT, varValues);
    Variable thisVar = ncfw.findVariable(timeDimName);
    ncfw.write(thisVar, thisData);
    thisData = ArrayChar.makeFromString(trajectoryId, trajectoryId.length());
    thisVar = ncfw.findVariable(trajId.getFullName());
    ncfw.write(thisVar, thisData);
    if (!matchupOneLocOneOb) {
        // write out "freshness" of the location data
        thisData = Array.makeArray(DataType.FLOAT, freshnessValues);
        thisVar = ncfw.findVariable(freshnessVarName);
        ncfw.write(thisVar, thisData);
    }
    // close up
    ncfw.close();
    // we don't know all of the data values for all variables at the time we are writing
    // metadata, so we must re-write the file with the max/min metadata here.
    NetcdfFile ncf = NetcdfFile.open(ncfile);
    Variable theVar = ncf.findVariable(timeDimName);
    List<Attribute> theAttrs = getMaxMinAttrs(theVar.read());
    theVar.addAll(theAttrs);
    if (!matchupOneLocOneOb) {
        theVar = ncf.findVariable(freshnessVarName);
        theAttrs = getMaxMinAttrs(theVar.read());
        theVar.addAll(theAttrs);
    }
    if (useNetcdf4) {
        FileWriter2 fw2 = new FileWriter2(ncf, ncfileFinal, NetcdfFileWriter.Version.netcdf4, null);
        NetcdfFile ncfw2 = fw2.write();
        ncfw2.close();
    } else {
        FileWriter2 fw2 = new FileWriter2(ncf, ncfileFinal, NetcdfFileWriter.Version.netcdf3, null);
        NetcdfFile ncfw2 = fw2.write();
        ncfw2.close();
    }
    ncf.close();
    Files.delete(ncPath);
    return ncfileFinal;
}

Example 44 with Array

use of org.openmuc.openiec61850.Array in project Protocol-Adapter-IEC61850 by OSGP.

the class NodeContainer method writeFloatArray.

public void writeFloatArray(final SubDataAttribute child, final Float[] values) throws NodeWriteException {
    final Array array = (Array) this.parent.getChild(child.getDescription());
    if (array.size() != values.length) {
        throw new NodeWriteException(String.format("Invalid array size %d. Size on device is %d", values.length, array.size()));
    }
    for (int i = 0; i < values.length; i++) {
        final BdaFloat32 bdaFloat = (BdaFloat32) array.getChild(i);
        bdaFloat.setFloat(values[i]);
        this.writeNode(bdaFloat);
    }
// Unfortunately writing an array using "this.writeNode(array);"
// doesn't seem to work...
// Therefore the items are written in individual calls...
}

Example 45 with Array

use of org.openmuc.openiec61850.Array in project Protocol-Adapter-IEC61850 by OSGP.

the class NodeContainer method writeDateArray.

public void writeDateArray(final SubDataAttribute child, final Date[] values) throws NodeWriteException {
    final Array array = (Array) this.parent.getChild(child.getDescription());
    if (array.size() != values.length) {
        throw new NodeWriteException(String.format("Invalid array size %d. Size on device is %d", values.length, array.size()));
    }
    for (int i = 0; i < values.length; i++) {
        final BdaTimestamp bdaTimestamp = (BdaTimestamp) array.getChild(i);
        bdaTimestamp.setDate(values[i]);
        this.writeNode(bdaTimestamp);
    }
// Unfortunately writing an array using "this.writeNode(array);"
// doesn't seem to work...
// Therefore the items are written in individual calls...
}