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

Example 16 with Array

use of org.openmuc.openiec61850.Array in project imageio-ext by geosolutions-it.

the class SWANConverter method run.

private void run(String fileNameIn, String fileNameOut) {
    try {
        final File fileIn = new File(fileNameIn);
        final NetcdfFile ncFileIn = NetcdfFile.open(fileNameIn);
        final File fileOut = new File(fileNameOut);
        // keep original name
        final File outputFile = File.createTempFile(fileIn.getName(), ".tmp");
        final NetcdfFileWriteable ncFileOut = NetcdfFileWriteable.createNew(outputFile.getAbsolutePath());
        boolean hasZeta = false;
        // input dimensions
        final Dimension timeDim0 = ncFileIn.findDimension("time");
        final int nTimes = timeDim0.getLength();
        final Dimension latDim0 = ncFileIn.findDimension(NetCDFUtilities.LATITUDE);
        final int nLat = latDim0.getLength();
        final Dimension lonDim0 = ncFileIn.findDimension(NetCDFUtilities.LONGITUDE);
        final int nLon = lonDim0.getLength();
        // input VARIABLES
        final Variable timeOriginalVar = ncFileIn.findVariable("time");
        final Array timeOriginalData = timeOriginalVar.read();
        final Index timeOriginalIndex = timeOriginalData.getIndex();
        final DataType timeDataType = timeOriginalVar.getDataType();
        final Variable lonOriginalVar = ncFileIn.findVariable(NetCDFUtilities.LONGITUDE);
        final DataType lonDataType = lonOriginalVar.getDataType();
        final Variable latOriginalVar = ncFileIn.findVariable(NetCDFUtilities.LATITUDE);
        final DataType latDataType = latOriginalVar.getDataType();
        final Array latOriginalData = latOriginalVar.read();
        final Array lonOriginalData = lonOriginalVar.read();
        // //
        // 
        // Depth related vars
        // 
        // //
        Array levelOriginalData = null;
        int nZeta = 0;
        Array zeta1Data = null;
        Dimension zDim = null;
        DataType zetaDataType = null;
        // Depth
        final Variable levelOriginalVar = ncFileIn.findVariable("z");
        if (levelOriginalVar != null) {
            nZeta = levelOriginalVar.getDimension(0).getLength();
            levelOriginalData = levelOriginalVar.read();
            zetaDataType = levelOriginalVar.getDataType();
            hasZeta = true;
        }
        Dimension timeDim = ncFileOut.addDimension("time", nTimes);
        Dimension latDim = ncFileOut.addDimension(NetCDFUtilities.LAT, nLat);
        Dimension lonDim = ncFileOut.addDimension(NetCDFUtilities.LON, nLon);
        if (hasZeta)
            zDim = ncFileOut.addDimension(NetCDFUtilities.HEIGHT, nZeta);
        NetCDFConverterUtilities.copyGlobalAttributes(ncFileOut, ncFileIn.getGlobalAttributes());
        // Dimensions
        Variable timeVar = ncFileOut.addVariable("time", timeDataType, new Dimension[] { timeDim });
        NetCDFConverterUtilities.setVariableAttributes(timeOriginalVar, ncFileOut, new String[] { "long_name" });
        ncFileOut.addVariableAttribute("time", "long_name", "time");
        ncFileOut.addVariable(NetCDFUtilities.LAT, latDataType, new Dimension[] { latDim });
        NetCDFConverterUtilities.setVariableAttributes(latOriginalVar, ncFileOut, NetCDFUtilities.LAT);
        ncFileOut.addVariable(NetCDFUtilities.LON, lonDataType, new Dimension[] { lonDim });
        NetCDFConverterUtilities.setVariableAttributes(lonOriginalVar, ncFileOut, NetCDFUtilities.LON);
        if (hasZeta) {
            ncFileOut.addVariable(NetCDFUtilities.HEIGHT, zetaDataType, new Dimension[] { zDim });
            NetCDFConverterUtilities.setVariableAttributes(levelOriginalVar, ncFileOut, NetCDFUtilities.HEIGHT, new String[] { "long_name" });
            ncFileOut.addVariableAttribute(NetCDFUtilities.HEIGHT, "positive", "up");
            ncFileOut.addVariableAttribute(NetCDFUtilities.HEIGHT, "long_name", NetCDFUtilities.HEIGHT);
        }
        // lat Variable
        Array lat1Data = NetCDFConverterUtilities.getArray(nLat, latDataType);
        NetCDFConverterUtilities.setData1D(latOriginalData, lat1Data, latDataType, nLat, true);
        // lon Variable
        Array lon1Data = NetCDFConverterUtilities.getArray(nLon, lonDataType);
        NetCDFConverterUtilities.setData1D(lonOriginalData, lon1Data, lonDataType, nLon, false);
        if (hasZeta) {
            // depth level Variable
            zeta1Data = NetCDFConverterUtilities.getArray(nZeta, zetaDataType);
            NetCDFConverterUtilities.setData1D(levelOriginalData, zeta1Data, zetaDataType, nZeta, false);
        }
        // {} Variables
        final ArrayList<String> variables = new ArrayList<String>(5);
        int numVars = 0;
        List<Variable> findVariables = ncFileIn.getVariables();
        for (Variable var : findVariables) {
            if (var != null) {
                String varName = var.getName();
                if (varName.equalsIgnoreCase(NetCDFUtilities.LATITUDE) || varName.equalsIgnoreCase(NetCDFUtilities.LONGITUDE) || varName.equalsIgnoreCase(NetCDFUtilities.TIME) || varName.equalsIgnoreCase(NetCDFUtilities.ZETA))
                    continue;
                variables.add(varName);
                List<Dimension> dims = var.getDimensions();
                boolean hasLocalZeta = false;
                for (Dimension dim : dims) {
                    if (dim.getName().equalsIgnoreCase(NetCDFUtilities.ZETA)) {
                        hasLocalZeta = true;
                        break;
                    }
                }
                if (hasZeta && hasLocalZeta)
                    ncFileOut.addVariable(varName, var.getDataType(), new Dimension[] { timeDim, zDim, latDim, lonDim });
                else
                    ncFileOut.addVariable(varName, var.getDataType(), new Dimension[] { timeDim, latDim, lonDim });
                NetCDFConverterUtilities.setVariableAttributes(var, ncFileOut, new String[] { "missing_value" });
                numVars++;
            }
        }
        // writing bin data ...
        ncFileOut.create();
        ArrayFloat timeData = new ArrayFloat(new int[] { timeDim.getLength() });
        Index timeIndex = timeData.getIndex();
        for (int t = 0; t < timeDim.getLength(); t++) {
            timeData.setFloat(timeIndex.set(t), timeOriginalData.getFloat(timeOriginalIndex.set(t)));
        }
        ncFileOut.write("time", timeData);
        timeVar = ncFileOut.findVariable("time");
        timeDim.addCoordinateVariable(timeVar);
        ncFileOut.write(NetCDFUtilities.LAT, lat1Data);
        ncFileOut.write(NetCDFUtilities.LON, lon1Data);
        if (hasZeta) {
            Variable heightVar = ncFileOut.findVariable(NetCDFUtilities.HEIGHT);
            zDim.addCoordinateVariable(heightVar);
            ncFileOut.write(NetCDFUtilities.HEIGHT, zeta1Data);
        }
        for (int i = 0; i < numVars; i++) {
            String varName = (String) variables.get(i);
            Variable var = ncFileIn.findVariable(varName);
            boolean hasLocalZeta = NetCDFConverterUtilities.hasThisDimension(var, NetCDFUtilities.ZETA);
            Array originalVarArray = var.read();
            DataType varDataType = var.getDataType();
            Array destArray = null;
            int[] dimensions = null;
            if (hasZeta && hasLocalZeta) {
                dimensions = new int[] { timeDim.getLength(), zDim.getLength(), latDim.getLength(), lonDim.getLength() };
            } else {
                dimensions = new int[] { timeDim.getLength(), latDim.getLength(), lonDim.getLength() };
            }
            destArray = NetCDFConverterUtilities.getArray(dimensions, varDataType);
            final boolean setZeta = hasZeta && hasLocalZeta;
            final int[] loopLengths;
            if (setZeta)
                loopLengths = new int[] { nTimes, nZeta, nLat, nLon };
            else
                loopLengths = new int[] { nTimes, nLat, nLon };
            NetCDFConverterUtilities.writeData(ncFileOut, varName, var, originalVarArray, destArray, false, false, loopLengths, true);
        }
        ncFileOut.close();
        outputFile.renameTo(fileOut);
    } catch (Exception e) {
        // something bad happened
        if (NetCDFConverterUtilities.LOGGER.isLoggable(Level.INFO))
            NetCDFConverterUtilities.LOGGER.log(Level.INFO, e.getLocalizedMessage(), e);
        JAI.getDefaultInstance().getTileCache().flush();
    }
}

Example 17 with Array

use of org.openmuc.openiec61850.Array in project open-smart-grid-platform by OSGP.

the class NodeContainer method getDateArray.

public Date[] getDateArray(final SubDataAttribute child) {
    final Array array = (Array) this.parent.getChild(child.getDescription());
    final int size = array.size();
    final Date[] result = new Date[size];
    for (int i = 0; i < size; i++) {
        result[i] = ((BdaTimestamp) array.getChild(i)).getDate();
    }
    return result;
}

Example 18 with Array

use of org.openmuc.openiec61850.Array in project risky by amsa-code.

the class DistanceTravelledCalculator method saveCalculationResultAsNetcdf.

public static void saveCalculationResultAsNetcdf(Options options, CalculationResult calculationResult, String filename) {
    List<CellValue> list = calculationResult.getCells().toList().toBlocking().single();
    int maxLonIndex = list.stream().map(cell -> options.getGrid().cellAt(cell.getCentreLat(), cell.getCentreLon())).filter(// 
    x -> x.isPresent()).map(x -> x.get().getLonIndex()).max(// 
    Comparator.<Long>naturalOrder()).get().intValue();
    int maxLatIndex = list.stream().map(cell -> options.getGrid().cellAt(cell.getCentreLat(), cell.getCentreLon())).filter(x -> x.isPresent()).map(x -> x.get().getLatIndex()).max(Comparator.<Long>naturalOrder()).get().intValue();
    File file = new File(filename);
    // Create the file.
    NetcdfFileWriter f = null;
    try {
        // Create new netcdf-3 file with the given filename
        f = NetcdfFileWriter.createNew(NetcdfFileWriter.Version.netcdf3, file.getPath());
        // In addition to the latitude and longitude dimensions, we will
        // also create latitude and longitude netCDF variables which will
        // hold the actual latitudes and longitudes. Since they hold data
        // about the coordinate system, the netCDF term for these is:
        // "coordinate variables."
        Dimension dimLat = f.addDimension(null, "latitude", maxLatIndex + 1);
        Dimension dimLon = f.addDimension(null, "longitude", maxLonIndex + 1);
        List<Dimension> dims = new ArrayList<Dimension>();
        dims.add(dimLat);
        dims.add(dimLon);
        // coordinate variables
        Variable vLat = f.addVariable(null, "latitude", DataType.DOUBLE, "latitude");
        Variable vLon = f.addVariable(null, "longitude", DataType.DOUBLE, "longitude");
        // value variables
        Variable vDensity = f.addVariable(null, "traffic_density", DataType.DOUBLE, dims);
        // Define units attributes for coordinate vars. This attaches a
        // text attribute to each of the coordinate variables, containing
        // the units.
        vLon.addAttribute(new Attribute("units", "degrees_east"));
        vLat.addAttribute(new Attribute("units", "degrees_north"));
        // Define units attributes for variables.
        vDensity.addAttribute(new Attribute("units", "nm-1"));
        vDensity.addAttribute(new Attribute("long_name", ""));
        // Write the coordinate variable data. This will put the latitudes
        // and longitudes of our data grid into the netCDF file.
        f.create();
        {
            Array dataLat = Array.factory(DataType.DOUBLE, new int[] { dimLat.getLength() });
            Array dataLon = Array.factory(DataType.DOUBLE, new int[] { dimLon.getLength() });
            // set latitudes
            for (int i = 0; i <= maxLatIndex; i++) {
                dataLat.setDouble(i, options.getGrid().centreLat(i));
            }
            // set longitudes
            for (int i = 0; i <= maxLonIndex; i++) {
                dataLon.setDouble(i, options.getGrid().centreLon(i));
            }
            f.write(vLat, dataLat);
            f.write(vLon, dataLon);
        }
        // write the value variable data
        {
            int[] iDim = new int[] { dimLat.getLength(), dimLon.getLength() };
            Array dataDensity = ArrayDouble.D2.factory(DataType.DOUBLE, iDim);
            Index2D idx = new Index2D(iDim);
            for (CellValue point : list) {
                Optional<Cell> cell = options.getGrid().cellAt(point.getCentreLat(), point.getCentreLon());
                if (cell.isPresent()) {
                    idx.set((int) cell.get().getLatIndex(), (int) cell.get().getLonIndex());
                    dataDensity.setDouble(idx, point.getValue());
                }
            }
            f.write(vDensity, dataDensity);
        }
    } catch (IOException | InvalidRangeException e) {
        throw new RuntimeException(e);
    } finally {
        if (f != null) {
            try {
                f.close();
            } catch (IOException ioe) {
                throw new RuntimeException(ioe);
            }
        }
    }
}

Example 19 with Array

use of org.openmuc.openiec61850.Array in project risky by amsa-code.

the class NetcdfFixesWriterTest method testNetcdfConverter.

@Test
public void testNetcdfConverter() throws IOException, InvalidRangeException {
    TestingUtil.writeTwoBinaryFixes("target/987654321.track", BinaryFixesFormat.WITHOUT_MMSI);
    int count = NetcdfFixesWriter.convertToNetcdf(new File("target"), new File("target/nc"), Pattern.compile("987654321.track")).count().toBlocking().single();
    assertEquals(1, count);
    // test output
    File ncFile = new File("target/nc/987654321.nc");
    assertTrue(ncFile.exists());
    assertTrue(ncFile.length() > 0);
    NetcdfFile nc = NetcdfFile.open(ncFile.getCanonicalPath());
    List<Attribute> attributes = nc.findGroup(null).getAttributes();
    System.out.println(attributes);
    assertFalse(attributes.isEmpty());
    System.out.println(nc.getDimensions());
    {
        Array array = nc.readSection("latitude");
        assertEquals(-10f, array.getFloat(0), PRECISION);
        assertEquals(-10.1f, array.getFloat(1), PRECISION);
        assertEquals(2, array.getSize());
    }
    {
        Array array = nc.readSection("longitude");
        assertEquals(135f, array.getFloat(0), PRECISION);
        assertEquals(135.2f, array.getFloat(1), PRECISION);
        assertEquals(2, array.getSize());
    }
    {
        Array array = nc.readSection("source");
        assertEquals((short) 1, array.getShort(0));
        assertEquals((short) 2, array.getShort(1));
        assertEquals(2, array.getSize());
    }
    {
        Array array = nc.readSection("latency");
        assertEquals(12, array.getInt(0));
        assertEquals(13, array.getInt(1));
        assertEquals(2, array.getSize());
    }
    {
        Array array = nc.readSection("navigational_status");
        assertEquals(NavigationalStatus.ENGAGED_IN_FISHING.ordinal(), array.getByte(0));
        assertEquals(NavigationalStatus.AT_ANCHOR.ordinal(), array.getByte(1));
        assertEquals(2, array.getSize());
    }
    {
        Array array = nc.readSection("rate_of_turn");
        assertEquals(-128, array.getByte(0));
        assertEquals(-128, array.getByte(1));
        assertEquals(2, array.getSize());
    }
    {
        Array array = nc.readSection("speed_over_ground");
        assertEquals(75, array.getInt(0));
        assertEquals(45, array.getInt(1));
        assertEquals(2, array.getSize());
    }
    {
        Array array = nc.readSection("course_over_ground");
        assertEquals(450, array.getShort(0));
        assertEquals(200, array.getShort(1));
        assertEquals(2, array.getSize());
    }
    {
        Array array = nc.readSection("heading");
        assertEquals(46, array.getShort(0));
        assertEquals(30, array.getShort(1));
        assertEquals(2, array.getSize());
    }
    {
        Array array = nc.readSection("ais_class");
        assertEquals(1, array.getInt(0));
        assertEquals(1, array.getInt(1));
        assertEquals(2, array.getSize());
    }
}

Example 20 with Array

use of org.openmuc.openiec61850.Array in project risky by amsa-code.

the class NetCdfWriter method close.

@Override
public void close() {
    try {
        f.create();
        for (Var<?> var : map.keySet()) {
            List<?> list = map.get(var);
            int[] shape = new int[] { list.size() };
            Array data = Array.factory(DataType.getType(var.cls()), shape);
            for (int i = 0; i < list.size(); i++) {
                data.setObject(i, list.get(i));
            }
            f.write(var.variable(), data);
        }
        f.close();
    } catch (IOException e) {
        throw new RuntimeException(e);
    } catch (InvalidRangeException e) {
        throw new RuntimeException(e);
    }
}