Examples with DataType ucar.ma2.DataType used on opensource projects

Example 1 with DataType

use of ucar.ma2.DataType in project imageio-ext by geosolutions-it.

the class NCOMConverter 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 hasDepth = false;
        // input dimensions
        final Dimension timeDim0 = ncFileIn.findDimension("time");
        final int nTimes = timeDim0.getLength();
        final Dimension latDim0 = ncFileIn.findDimension("lat");
        final int nLat = latDim0.getLength();
        final Dimension lonDim0 = ncFileIn.findDimension("lon");
        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("lon");
        final DataType lonDataType = lonOriginalVar.getDataType();
        final Variable latOriginalVar = ncFileIn.findVariable("lat");
        final DataType latDataType = latOriginalVar.getDataType();
        final Array latOriginalData = latOriginalVar.read();
        final Array lonOriginalData = lonOriginalVar.read();
        // //
        // 
        // Depth related vars
        // 
        // //
        Array depthOriginalData = null;
        int nDepths = 0;
        Array depth1Data = null;
        Dimension depthDim = null;
        DataType depthDataType = null;
        // Depth
        final Variable depthOriginalVar = ncFileIn.findVariable("depth");
        if (depthOriginalVar != null) {
            nDepths = depthOriginalVar.getDimension(0).getLength();
            depthOriginalData = depthOriginalVar.read();
            depthDataType = depthOriginalVar.getDataType();
            hasDepth = true;
        }
        Dimension timeDim = ncFileOut.addDimension("time", nTimes);
        Dimension latDim = ncFileOut.addDimension(NetCDFUtilities.LAT, nLat);
        Dimension lonDim = ncFileOut.addDimension(NetCDFUtilities.LON, nLon);
        if (hasDepth)
            depthDim = ncFileOut.addDimension(NetCDFUtilities.DEPTH, nDepths);
        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);
        ncFileOut.addVariable(NetCDFUtilities.LON, lonDataType, new Dimension[] { lonDim });
        NetCDFConverterUtilities.setVariableAttributes(lonOriginalVar, ncFileOut);
        if (hasDepth) {
            ncFileOut.addVariable(NetCDFUtilities.DEPTH, depthDataType, new Dimension[] { depthDim });
            NetCDFConverterUtilities.setVariableAttributes(depthOriginalVar, ncFileOut);
        }
        // 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 (hasDepth) {
            // depth level Variable
            depth1Data = NetCDFConverterUtilities.getArray(nDepths, depthDataType);
            NetCDFConverterUtilities.setData1D(depthOriginalData, depth1Data, depthDataType, nDepths, false);
        }
        // {} Variables
        final ArrayList<String> variables = new ArrayList<String>(5);
        final HashMap<String, String> updatingValidRange = new HashMap<String, String>(5);
        int numVars = 0;
        for (int i = 0; i < NUMVARS; i++) {
            String varName = (String) VARIABLES.get(i);
            Variable var = ncFileIn.findVariable(varName);
            if (var != null) {
                variables.add(varName);
                List<Dimension> dims = var.getDimensions();
                boolean hasLocalDepth = false;
                for (Dimension dim : dims) {
                    if (dim.getName().equalsIgnoreCase("depth")) {
                        hasLocalDepth = true;
                        break;
                    }
                }
                if (hasDepth && hasLocalDepth)
                    ncFileOut.addVariable(varName, var.getDataType(), new Dimension[] { timeDim, depthDim, latDim, lonDim });
                else
                    ncFileOut.addVariable(varName, var.getDataType(), new Dimension[] { timeDim, latDim, lonDim });
                Attribute validRange = var.findAttribute(NetCDFUtilities.DatasetAttribs.VALID_MAX);
                if (validRange != null)
                    validRange = var.findAttribute(NetCDFUtilities.DatasetAttribs.VALID_MIN);
                if (validRange == null)
                    validRange = var.findAttribute(NetCDFUtilities.DatasetAttribs.VALID_RANGE);
                if (validRange == null) {
                    updatingValidRange.put(varName, "");
                    ArrayShort range = new ArrayShort(new int[] { 2 });
                    Index index = range.getIndex();
                    range.setShort(index.set(0), Short.MIN_VALUE);
                    range.setShort(index.set(1), Short.MAX_VALUE);
                    ncFileOut.addVariableAttribute(varName, NetCDFUtilities.DatasetAttribs.VALID_RANGE, range);
                }
                NetCDFConverterUtilities.setVariableAttributes(var, ncFileOut);
                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 (hasDepth) {
            Variable depthVar = ncFileOut.findVariable("depth");
            depthDim.addCoordinateVariable(depthVar);
            ncFileOut.write(NetCDFUtilities.DEPTH, depth1Data);
        }
        for (int i = 0; i < numVars; i++) {
            String varName = (String) variables.get(i);
            Variable var = ncFileIn.findVariable(varName);
            boolean hasLocalDepth = NetCDFConverterUtilities.hasThisDimension(var, "depth");
            Array originalVarArray = var.read();
            DataType varDataType = var.getDataType();
            Array destArray = null;
            int[] dimensions = null;
            if (hasDepth && hasLocalDepth) {
                dimensions = new int[] { timeDim.getLength(), depthDim.getLength(), latDim.getLength(), lonDim.getLength() };
            } else {
                dimensions = new int[] { timeDim.getLength(), latDim.getLength(), lonDim.getLength() };
            }
            destArray = NetCDFConverterUtilities.getArray(dimensions, varDataType);
            boolean findNewRange = updatingValidRange.containsKey(varName);
            final boolean setDepth = hasDepth && hasLocalDepth;
            final int[] loopLengths;
            if (setDepth)
                loopLengths = new int[] { nTimes, nDepths, nLat, nLon };
            else
                loopLengths = new int[] { nTimes, nLat, nLon };
            NetCDFConverterUtilities.writeData(ncFileOut, varName, var, originalVarArray, destArray, findNewRange, 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 2 with DataType

use of ucar.ma2.DataType in project imageio-ext by geosolutions-it.

the class NetCDFConverterUtilities method setData1D.

public static void setData1D(Array originalData, Array destinationData, final DataType navLatDataType, final int maxIndex, final boolean flipData) {
    Index originalDataIndex = originalData.getIndex();
    Index destinationDataIndex = flipData ? destinationData.getIndex() : originalDataIndex;
    if (navLatDataType == DataType.FLOAT) {
        for (int pos = 0; pos < maxIndex; pos++) {
            float f = originalData.getFloat(originalDataIndex.set(pos));
            // Flipping latitudes
            if (flipData) {
                destinationDataIndex.set(maxIndex - pos - 1);
            }
            destinationData.setFloat(destinationDataIndex, f);
        }
    } else if (navLatDataType == DataType.DOUBLE) {
        for (int pos = 0; pos < maxIndex; pos++) {
            double d = originalData.getDouble(originalDataIndex.set(pos));
            // Flipping latitudes
            if (flipData) {
                destinationDataIndex.set(maxIndex - pos - 1);
            }
            destinationData.setDouble(destinationDataIndex, d);
        }
    } else if (navLatDataType == DataType.BYTE) {
        for (int pos = 0; pos < maxIndex; pos++) {
            byte b = originalData.getByte(originalDataIndex.set(pos));
            // Flipping latitudes
            if (flipData) {
                destinationDataIndex.set(maxIndex - pos - 1);
            }
            destinationData.setByte(destinationDataIndex, b);
        }
    } else if (navLatDataType == DataType.SHORT) {
        for (int pos = 0; pos < maxIndex; pos++) {
            short s = originalData.getShort(originalDataIndex.set(pos));
            // Flipping latitudes
            if (flipData) {
                destinationDataIndex.set(maxIndex - pos - 1);
            }
            destinationData.setShort(destinationDataIndex, s);
        }
    } else if (navLatDataType == DataType.INT) {
        for (int pos = 0; pos < maxIndex; pos++) {
            int i = originalData.getInt(originalDataIndex.set(pos));
            // Flipping latitudes
            if (flipData) {
                destinationDataIndex.set(maxIndex - pos - 1);
            }
            destinationData.setInt(destinationDataIndex, i);
        }
    }
}

Example 3 with DataType

use of ucar.ma2.DataType in project imageio-ext by geosolutions-it.

the class NetCDFConverterUtilities method isFillValueOutsideValidRange.

public static boolean isFillValueOutsideValidRange(Attribute validRange, Attribute fillValue, DataType dataType) {
    Array range = validRange.getValues();
    Index index = range.getIndex();
    if (dataType == DataType.FLOAT) {
        final float min = range.getFloat(index.set(0));
        final float max = range.getFloat(index.set(1));
        final float fill = fillValue.getNumericValue().floatValue();
        if (fill == min || fill == max)
            return false;
        else
            return true;
    } else if (dataType == DataType.DOUBLE) {
        final double min = range.getDouble(index.set(0));
        final double max = range.getDouble(index.set(1));
        final double fill = fillValue.getNumericValue().doubleValue();
        if (fill == min || fill == max)
            return false;
        else
            return true;
    } else if (dataType == DataType.BYTE) {
        final byte min = range.getByte(index.set(0));
        final byte max = range.getByte(index.set(1));
        final byte fill = fillValue.getNumericValue().byteValue();
        if (fill == min || fill == max)
            return false;
        else
            return true;
    } else if (dataType == DataType.SHORT) {
        final short min = range.getShort(index.set(0));
        final short max = range.getShort(index.set(1));
        final short fill = fillValue.getNumericValue().shortValue();
        if (fill == min || fill == max)
            return false;
        else
            return true;
    } else if (dataType == DataType.INT) {
        final int min = range.getInt(index.set(0));
        final int max = range.getInt(index.set(1));
        final int fill = fillValue.getNumericValue().intValue();
        if (fill == min || fill == max)
            return false;
        else
            return true;
    }
    throw new IllegalArgumentException("Actually unsupported Datatype");
}

Example 4 with DataType

use of ucar.ma2.DataType in project imageio-ext by geosolutions-it.

the class HDF4APSImageReader method initializeProfile.

/**
 * Initialize main properties for this <code>HDF4APSImageReader</code>
 */
protected void initializeProfile() throws IOException {
    final NetcdfDataset dataset = reader.getDataset();
    if (dataset == null) {
        throw new IOException("Unable to initialize profile due to a null dataset");
    }
    final List<Variable> variables = dataset.getVariables();
    final List<Attribute> attributes = dataset.getGlobalAttributes();
    final int numVars = variables.size();
    reader.setNumGlobalAttributes(attributes.size());
    // //
    // 
    // Getting projection dataset name
    // 
    // //
    final String navAttrib = NetCDFUtilities.getGlobalAttributeAsString(dataset, HDF4APSProperties.PFA_NA_MAPPROJECTION);
    if (navAttrib != null && navAttrib.length() > 0) {
        projectionDatasetName = navAttrib;
    }
    final String prodAttrib = NetCDFUtilities.getGlobalAttributeAsString(dataset, HDF4APSProperties.PRODLIST);
    int numImages = 0;
    if (prodAttrib != null && prodAttrib.length() > 0) {
        String[] products = prodAttrib.split(",");
        productList = HDF4APSProperties.refineProductList(products);
        numImages = productList.length;
    } else {
        numImages = numVars;
    }
    setNumImages(numImages);
    reader.setNumImages(numImages);
    final Map<Range, APSDatasetWrapper> indexMap = new HashMap<Range, APSDatasetWrapper>(numImages);
    Variable varProjection;
    // //
    // 
    // Setting spatial domain
    // 
    // //
    // getting map dataset
    varProjection = dataset.findVariable(projectionDatasetName);
    if (varProjection != null && varProjection.getName().equalsIgnoreCase(projectionDatasetName)) {
        // TODO: All projection share the same dataset
        // structure?
        Array data = varProjection.read();
        final int datatype = NetCDFUtilities.getRawDataType(varProjection);
        if (projectionMap == null) {
            projectionMap = buildProjectionAttributesMap(data, datatype);
        // Force UoM of MapBoundary product as the last element in
        // the map
        }
    }
    try {
        // Scanning all the datasets
        for (Variable var : variables) {
            final String name = var.getName();
            for (int j = 0; j < numImages; j++) {
                // Checking if the actual dataset is a product.
                if (name.equals(productList[j])) {
                    // Updating the subDatasetsMap map
                    indexMap.put(new Range(j, j + 1), new APSDatasetWrapper(var));
                    break;
                }
            }
        }
    } catch (InvalidRangeException e) {
        throw new IllegalArgumentException("Error occurred during NetCDF file parsing", e);
    }
    reader.setIndexMap(indexMap);
}

Example 5 with DataType

use of ucar.ma2.DataType 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();
    }
}