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

Example 36 with Array

use of org.openmuc.openiec61850.Array in project geotoolkit by Geomatys.

the class NetCDFExtractor method parseDataBlockTS.

private static ExtractionResult parseDataBlockTS(final NCFieldAnalyze analyze, final String procedureID, final List<String> acceptedSensorID, Set<org.opengis.observation.Phenomenon> phenomenons) throws NetCDFParsingException {
    final ExtractionResult results = new ExtractionResult();
    if (analyze.mainField == null) {
        LOGGER.warning("No main field found");
        return results;
    }
    LOGGER.info("parsing netCDF TS");
    try {
        final List<String> separators = parseSeparatorValues(analyze);
        final boolean single = separators.isEmpty();
        Array latArray = null;
        Array lonArray = null;
        if (analyze.hasSpatial()) {
            latArray = analyze.getArrayFromField(analyze.latField);
            lonArray = analyze.getArrayFromField(analyze.lonField);
        }
        final Variable timeVar = analyze.vars.get(analyze.mainField.name);
        final String timeUnits = analyze.mainField.uom;
        final Array timeArray = analyze.file.readArrays(Arrays.asList(timeVar)).get(0);
        final boolean constantT = analyze.mainField.dimension == 1;
        final boolean timeFirst = analyze.mainField.mainVariableFirst;
        final Map<String, Array> phenArrays = analyze.getPhenomenonArrayMap();
        results.fields.addAll(phenArrays.keySet());
        final AbstractDataRecord datarecord = OMUtils.getDataRecordTimeSeries("2.0.0", analyze.phenfields);
        final Phenomenon phenomenon = OMUtils.getPhenomenon("2.0.0", analyze.phenfields, phenomenons);
        results.phenomenons.add(phenomenon);
        if (single) {
            if (acceptedSensorID == null || acceptedSensorID.contains(procedureID)) {
                final Process proc = (Process) OMUtils.buildProcess(procedureID);
                final ProcedureTree compo = new ProcedureTree(proc.getHref(), proc.getName(), proc.getDescription(), "Component", "timeseries");
                results.procedures.add(compo);
                final MeasureStringBuilder sb = new MeasureStringBuilder();
                final int count = timeVar.getDimension(0).getLength();
                final GeoSpatialBound gb = new GeoSpatialBound();
                final String identifier = UUID.randomUUID().toString();
                // read geometry (assume point)
                SamplingFeature sp = null;
                if (analyze.hasSpatial()) {
                    final double latitude = getDoubleValue(latArray, analyze.latField.fillValue);
                    final double longitude = Longitude.normalize(getDoubleValue(lonArray, analyze.lonField.fillValue));
                    if (!Double.isNaN(latitude) && !Double.isNaN(longitude)) {
                        sp = OMUtils.buildSamplingPoint(identifier, latitude, longitude);
                        results.addFeatureOfInterest(sp);
                        gb.addXYCoordinate(longitude, latitude);
                        gb.addGeometry((AbstractGeometry) sp.getGeometry());
                    }
                }
                // iterating over time
                for (int i = 0; i < count; i++) {
                    final long millis = getTimeValue(timeUnits, timeArray, i);
                    if (millis == 0 || millis == LIMIT) {
                        continue;
                    }
                    gb.addDate(millis);
                    sb.appendDate(millis);
                    for (NCField field : analyze.phenfields) {
                        final Array phenArray = phenArrays.get(field.name);
                        final Double value = getDoubleValue(phenArray, i, field.fillValue);
                        sb.appendValue(value);
                    }
                    sb.closeBlock();
                }
                results.observations.add(// id
                OMUtils.buildObservation(// id
                identifier, // foi
                sp, // phenomenon
                phenomenon, // procedure
                proc, // result
                count, // result
                datarecord, // result
                sb, // time
                gb.getTimeObject("2.0.0")));
                results.spatialBound.merge(gb);
                compo.spatialBound.merge(gb);
            }
        } else {
            final Process proc = (Process) OMUtils.buildProcess(procedureID);
            final ProcedureTree system = new ProcedureTree(proc.getHref(), proc.getName(), proc.getDescription(), "System", "timeseries");
            results.procedures.add(system);
            for (int j = 0; j < separators.size(); j++) {
                final String identifier = separators.get(j);
                final MeasureStringBuilder sb = new MeasureStringBuilder();
                final int count = getGoodTimeDimension(timeVar, analyze.dimensionSeparator).getLength();
                final GeoSpatialBound gb = new GeoSpatialBound();
                final String currentProcID = procedureID + '-' + identifier;
                final Process currentProc = (Process) OMUtils.buildProcess(currentProcID);
                final ProcedureTree compo = new ProcedureTree(currentProc.getHref(), currentProc.getName(), currentProc.getDescription(), "Component", "timeseries");
                if (acceptedSensorID == null || acceptedSensorID.contains(currentProcID)) {
                    // read geometry (assume point)
                    SamplingFeature sp = null;
                    if (analyze.hasSpatial()) {
                        final double latitude = getDoubleValue(latArray, j, analyze.latField.fillValue);
                        final double longitude = Longitude.normalize(getDoubleValue(lonArray, j, analyze.lonField.fillValue));
                        if (!Double.isNaN(latitude) && !Double.isNaN(longitude)) {
                            sp = OMUtils.buildSamplingPoint(identifier, latitude, longitude);
                            results.addFeatureOfInterest(sp);
                            gb.addXYCoordinate(longitude, latitude);
                            gb.addGeometry((AbstractGeometry) sp.getGeometry());
                        }
                    }
                    for (int i = 0; i < count; i++) {
                        final long millis = getTimeValue(timeUnits, timeFirst, constantT, timeArray, i, j);
                        if (millis == 0 || millis == LIMIT) {
                            continue;
                        }
                        gb.addDate(millis);
                        sb.appendDate(millis);
                        for (NCField field : analyze.phenfields) {
                            final Array phenArray = phenArrays.get(field.name);
                            final boolean mainFirst = field.mainVariableFirst;
                            final Double value = getDoubleValue(mainFirst, phenArray, i, j, field.fillValue);
                            sb.appendValue(value);
                        }
                        // remove the last token separator
                        sb.closeBlock();
                    }
                    compo.spatialBound.merge(gb);
                    system.children.add(compo);
                    final String obsid = UUID.randomUUID().toString();
                    results.observations.add(// id
                    OMUtils.buildObservation(// id
                    obsid, // foi
                    sp, // phenomenon
                    phenomenon, // procedure
                    currentProc, // result
                    count, // result
                    datarecord, // result
                    sb, // time
                    gb.getTimeObject("2.0.0")));
                    results.spatialBound.merge(gb);
                }
            }
        }
    } catch (IOException | IllegalArgumentException ex) {
        throw new NetCDFParsingException("error while parsing netcdf timeserie", ex);
    }
    LOGGER.info("datablock parsed");
    return results;
}

Example 37 with Array

use of org.openmuc.openiec61850.Array in project seadas-toolbox by seadas.

the class BathymetryOp method computeTile.

@Override
public void computeTile(Band targetBand, Tile targetTile, ProgressMonitor pm) throws OperatorException {
    final String targetBandName = targetBand.getName();
    final Rectangle rectangle = targetTile.getRectangle();
    // not sure if this is really needed but just in case
    if (!targetBandName.equals(BATHYMETRY_BAND_NAME) && !targetBandName.equals(TOPOGRAPHY_BAND_NAME) && !targetBandName.equals(ELEVATION_BAND_NAME)) {
        for (int y = rectangle.y; y < rectangle.y + rectangle.height; y++) {
            for (int x = rectangle.x; x < rectangle.x + rectangle.width; x++) {
                int dataValue = 0;
                targetTile.setSample(x, y, dataValue);
            }
        }
        return;
    }
    try {
        final GeoCoding geoCoding = sourceProduct.getSceneGeoCoding();
        final PixelPos pixelPos = new PixelPos();
        final GeoPos geoPos = new GeoPos();
        // loop through tile, adding each pixel geolocation to it's appropriate earthBox via motherEarthBox
        // at this point the earthBoxes will adjust their mins and maxes based on the given lats and lons.
        MotherEarthBox motherEarthBox = new MotherEarthBox();
        for (int y = rectangle.y; y < rectangle.y + rectangle.height; y++) {
            for (int x = rectangle.x; x < rectangle.x + rectangle.width; x++) {
                pixelPos.setLocation(x, y);
                geoCoding.getGeoPos(pixelPos, geoPos);
                motherEarthBox.add(geoPos);
            }
        }
        for (EarthBox earthBox : motherEarthBox.getFilledEarthBoxes()) {
            // add dimensions to the earthBox
            int minLatIndex = bathymetryReader.getLatIndex(earthBox.getMinLat());
            int maxLatIndex = bathymetryReader.getLatIndex(earthBox.getMaxLat());
            int minLonIndex = bathymetryReader.getLonIndex(earthBox.getMinLon());
            int maxLonIndex = bathymetryReader.getLonIndex(earthBox.getMaxLon());
            if (minLatIndex > 0) {
                minLatIndex--;
            }
            if (maxLatIndex < bathymetryReader.dimensionLat - 1) {
                maxLatIndex++;
            }
            if (minLonIndex > 0) {
                minLonIndex--;
            }
            if (maxLonIndex < bathymetryReader.dimensionLon - 1) {
                maxLonIndex++;
            }
            // determine length of each dimension for the chunk array to be pulled out of the netcdf source
            int latDimensionLength = maxLatIndex - minLatIndex + 1;
            int lonDimensionLength = maxLonIndex - minLonIndex + 1;
            // get the bathymetry height array from the netcdf source
            int[] origin = new int[] { minLatIndex, minLonIndex };
            int[] shape = new int[] { latDimensionLength, lonDimensionLength };
            // retrieve the bathymetry height array from netcdf
            Array heightArray = bathymetryReader.getHeightArray(origin, shape);
            Array waterSurfaceheightArray = bathymetryReader.getWaterSurfaceHeightArray(origin, shape);
            // convert heightArray from ucar.ma2.Array format to regular java array
            short[][] heights = (short[][]) heightArray.copyToNDJavaArray();
            short[][] waterSurfaceHeights = (short[][]) waterSurfaceheightArray.copyToNDJavaArray();
            // add the value array to the earthBox
            float minLat = bathymetryReader.getLat(minLatIndex);
            float maxLat = bathymetryReader.getLat(maxLatIndex);
            float minLon = bathymetryReader.getLon(minLonIndex);
            float maxLon = bathymetryReader.getLon(maxLonIndex);
            short missingValue = bathymetryReader.getMissingValue();
            earthBox.setValues(minLat, maxLat, minLon, maxLon, heights, waterSurfaceHeights, missingValue);
            earthBox.setGetValueAverage(true);
        }
        // loop through all the tile pixels, geolocate them, and get their bathymetry height from motherEarthBox.
        for (int y = rectangle.y; y < rectangle.y + rectangle.height; y++) {
            for (int x = rectangle.x; x < rectangle.x + rectangle.width; x++) {
                pixelPos.setLocation(x, y);
                geoCoding.getGeoPos(pixelPos, geoPos);
                int value;
                int waterSurfaceHeight;
                int height;
                if (geoPos.isValid()) {
                    height = motherEarthBox.getValue(geoPos);
                    waterSurfaceHeight = motherEarthBox.getWaterSurfaceValue(geoPos);
                    if (targetBandName.equals(ELEVATION_BAND_NAME)) {
                        value = height;
                    } else if (targetBandName.equals(TOPOGRAPHY_BAND_NAME)) {
                        int valueSurface = height - waterSurfaceHeight;
                        if (valueSurface > 0) {
                            value = motherEarthBox.getValue(geoPos);
                        } else {
                            value = bathymetryReader.getMissingValue();
                        }
                    } else if (targetBandName.equals(BATHYMETRY_BAND_NAME)) {
                        int valueSurface = height - waterSurfaceHeight;
                        if (valueSurface <= 0) {
                            value = valueSurface;
                        } else {
                            value = bathymetryReader.getMissingValue();
                        }
                        // convert  to positive if not NaN
                        if (value > -32000) {
                            value = -value;
                        }
                    } else {
                        value = bathymetryReader.getMissingValue();
                    }
                } else {
                    value = bathymetryReader.getMissingValue();
                }
                targetTile.setSample(x, y, value);
            }
        }
    } catch (Exception e) {
        throw new OperatorException("Error computing tile '" + targetTile.getRectangle().toString() + "'.", e);
    }
}

Example 38 with Array

use of org.openmuc.openiec61850.Array in project SOS by 52North.

the class AbstractNetcdfEncoder method initHeightDephtArray.

private Array initHeightDephtArray(List<Dimension> zDims) {
    Array array = getArray(zDims);
    initArrayWithFillValue(array, getNetcdfHelper().getFillValue());
    return array;
}

Example 39 with Array

use of org.openmuc.openiec61850.Array 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 40 with Array

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

the class TestTagUniversalFileFormatOneLocManyOb 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);
}