Examples with Variable org.flyte.api.v1.Variable used on opensource projects

Example 96 with Variable

use of org.flyte.api.v1.Variable in project imageio-ext by geosolutions-it.

the class NetCDFUtilities method isVariableAccepted.

/**
 * NetCDF files may contains a wide set of variables. Some of them are
 * unuseful for our purposes. The method returns {@code true} if the
 * specified variable is accepted.
 */
public static boolean isVariableAccepted(final Variable var, final CheckType checkType) {
    if (var instanceof CoordinateAxis1D) {
        return false;
    } else if (checkType == CheckType.NOSCALARS) {
        List<Dimension> dimensions = var.getDimensions();
        if (dimensions.size() < 2) {
            return false;
        }
        DataType dataType = var.getDataType();
        if (dataType == DataType.CHAR) {
            return false;
        }
        return isVariableAccepted(var.getName(), CheckType.NONE);
    } else if (checkType == CheckType.ONLYGEOGRIDS) {
        List<Dimension> dimensions = var.getDimensions();
        if (dimensions.size() < 2) {
            return false;
        }
        for (Dimension dimension : dimensions) {
            String dimName = dimension.getName();
            // check the dimension to be defined
            Group group = dimension.getGroup();
            Variable dimVariable = group.findVariable(dimName);
            if (dimVariable == null) {
                return false;
            }
            if (dimVariable instanceof CoordinateAxis1D) {
                CoordinateAxis1D axis = (CoordinateAxis1D) dimVariable;
                AxisType axisType = axis.getAxisType();
                if (axisType == null) {
                    return false;
                }
            }
        }
        DataType dataType = var.getDataType();
        if (dataType == DataType.CHAR) {
            return false;
        }
        return isVariableAccepted(var.getName(), CheckType.NONE);
    } else
        return isVariableAccepted(var.getName(), checkType);
}

Example 97 with Variable

use of org.flyte.api.v1.Variable in project imageio-ext by geosolutions-it.

the class INGVConverter 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
        String timeName = "time_counter";
        Dimension timeOriginalDim = ncFileIn.findDimension(timeName);
        if (timeOriginalDim == null) {
            timeOriginalDim = ncFileIn.findDimension("time");
            timeName = "time";
        }
        final Dimension yDim = ncFileIn.findDimension("y");
        final Dimension xDim = ncFileIn.findDimension("x");
        // input VARIABLES
        final Variable timeOriginalVar = ncFileIn.findVariable(timeName);
        final Array timeOriginalData = timeOriginalVar.read();
        final DataType timeDataType = timeOriginalVar.getDataType();
        final Variable navLat = ncFileIn.findVariable(NAV_LAT);
        final DataType navLatDataType = navLat.getDataType();
        final Variable navLon = ncFileIn.findVariable(NAV_LON);
        final DataType navLonDataType = navLon.getDataType();
        final int nLat = yDim.getLength();
        final int nLon = xDim.getLength();
        final int nTimes = timeOriginalDim.getLength();
        final Array latOriginalData = navLat.read("0:" + (nLat - 1) + ":1, 0:0:1").reduce();
        final Array lonOriginalData = navLon.read("0:0:1, 0:" + (nLon - 1) + ":1").reduce();
        // //
        // 
        // Depth related vars
        // 
        // //
        Array depthOriginalData = null;
        DataType depthDataType = null;
        int nDepths = 0;
        Array depthDestData = null;
        Dimension depthDim = null;
        String depthName = "depth";
        Variable depthOriginalVar = null;
        int dName = 0;
        while (depthOriginalVar == null) {
            if (dName == depthNames.length)
                break;
            String name = depthNames[dName++];
            // Depth
            depthOriginalVar = ncFileIn.findVariable(name);
        }
        if (depthOriginalVar != null) {
            depthName = depthNames[dName - 1];
            nDepths = depthOriginalVar.getDimension(0).getLength();
            depthOriginalData = depthOriginalVar.read();
            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);
        // writing file
        NetCDFConverterUtilities.copyGlobalAttributes(ncFileOut, ncFileIn.getGlobalAttributes());
        // //
        // 
        // Time requires a special Management
        // 
        // //
        // time Variable
        Variable timeVar = ncFileOut.addVariable(NetCDFUtilities.TIME, timeDataType, new Dimension[] { timeDim });
        NetCDFConverterUtilities.setVariableAttributes(timeOriginalVar, ncFileOut, NetCDFUtilities.TIME);
        // Dimensions
        ncFileOut.addVariable(NetCDFUtilities.LAT, navLatDataType, new Dimension[] { latDim });
        NetCDFConverterUtilities.setVariableAttributes(navLat, ncFileOut, NetCDFUtilities.LAT);
        ncFileOut.addVariable(NetCDFUtilities.LON, navLonDataType, new Dimension[] { lonDim });
        NetCDFConverterUtilities.setVariableAttributes(navLon, ncFileOut, NetCDFUtilities.LON);
        Array lat1Data = NetCDFConverterUtilities.getArray(nLat, navLatDataType);
        NetCDFConverterUtilities.setData1D(latOriginalData, lat1Data, navLatDataType, nLat, true);
        // lon Variable
        Array lon1Data = NetCDFConverterUtilities.getArray(nLon, navLonDataType);
        NetCDFConverterUtilities.setData1D(lonOriginalData, lon1Data, navLonDataType, nLon, false);
        if (hasDepth) {
            depthDataType = depthOriginalVar.getDataType();
            ncFileOut.addVariable(NetCDFUtilities.DEPTH, depthDataType, new Dimension[] { depthDim });
            NetCDFConverterUtilities.setVariableAttributes(depthOriginalVar, ncFileOut, NetCDFUtilities.DEPTH);
        }
        if (hasDepth) {
            // depth level Variable
            depthDestData = NetCDFConverterUtilities.getArray(nDepths, depthDataType);
            NetCDFConverterUtilities.setData1D(depthOriginalData, depthDestData, depthDataType, nDepths, false);
        }
        // {} Variables
        final ArrayList<String> variables = new ArrayList<String>(5);
        final HashMap<String, String> updatingValidRange = new HashMap<String, String>(5);
        final HashMap<String, String> updatingFilLValue = 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);
                boolean hasLocalDepth = NetCDFConverterUtilities.hasThisDimension(var, depthName);
                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 });
                // //
                // 
                // Check for updating valid range
                // 
                // //
                boolean hasMinMax = false;
                Attribute validMax = var.findAttribute(NetCDFUtilities.DatasetAttribs.VALID_MAX);
                Attribute validMin = var.findAttribute(NetCDFUtilities.DatasetAttribs.VALID_MIN);
                Attribute fillValue = var.findAttribute(NetCDFUtilities.DatasetAttribs.FILL_VALUE);
                boolean hasMissingValue = false;
                boolean hasFillValue = true;
                if (fillValue == null) {
                    hasFillValue = false;
                    fillValue = var.findAttribute(NetCDFUtilities.DatasetAttribs.MISSING_VALUE);
                    if (fillValue != null)
                        hasMissingValue = true;
                }
                Attribute validRange = var.findAttribute(NetCDFUtilities.DatasetAttribs.VALID_RANGE);
                boolean hasValidRange = false;
                boolean rewriteAttribute = false;
                if (validMin != null && validMax != null && fillValue != null) {
                    rewriteAttribute = !NetCDFConverterUtilities.isFillValueOutsideValidRange(validMax, validMin, fillValue, var.getDataType());
                    hasMinMax = true;
                } else if (validRange != null && fillValue != null) {
                    rewriteAttribute = !NetCDFConverterUtilities.isFillValueOutsideValidRange(validRange, fillValue, var.getDataType());
                    hasValidRange = true;
                } else {
                    rewriteAttribute = true;
                }
                if (rewriteAttribute) {
                    updatingValidRange.put(varName, "");
                    DataType varDatatype = var.getDataType();
                    Array range = NetCDFConverterUtilities.getRangeArray(varDatatype);
                    ncFileOut.addVariableAttribute(varName, NetCDFUtilities.DatasetAttribs.VALID_RANGE, range);
                    if (hasMissingValue && !hasFillValue) {
                        updatingFilLValue.put(varName, "");
                        Number fillVal = NetCDFConverterUtilities.getNumber(varDatatype);
                        ncFileOut.addVariableAttribute(varName, NetCDFUtilities.DatasetAttribs.FILL_VALUE, fillVal);
                    }
                }
                String[] exceptions = null;
                if (hasMinMax) {
                    if (hasMissingValue)
                        exceptions = new String[] { NetCDFUtilities.DatasetAttribs.VALID_MAX, NetCDFUtilities.DatasetAttribs.VALID_MIN, NetCDFUtilities.DatasetAttribs.MISSING_VALUE };
                    else
                        exceptions = new String[] { NetCDFUtilities.DatasetAttribs.VALID_MAX, NetCDFUtilities.DatasetAttribs.VALID_MIN };
                } else if (hasValidRange) {
                    if (hasMissingValue)
                        exceptions = new String[] { NetCDFUtilities.DatasetAttribs.VALID_RANGE, NetCDFUtilities.DatasetAttribs.MISSING_VALUE };
                    else
                        exceptions = new String[] { NetCDFUtilities.DatasetAttribs.VALID_RANGE };
                } else if (hasMissingValue)
                    exceptions = new String[] { NetCDFUtilities.DatasetAttribs.MISSING_VALUE };
                NetCDFConverterUtilities.setVariableAttributes(var, ncFileOut, exceptions);
                numVars++;
            }
        }
        // writing bin data ...
        ncFileOut.create();
        Array timeData = NetCDFConverterUtilities.getArray(nTimes, timeDataType);
        NetCDFConverterUtilities.setData1D(timeOriginalData, timeData, timeDataType, nTimes, false);
        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, depthDestData);
        }
        for (int i = 0; i < numVars; i++) {
            String varName = (String) variables.get(i);
            Variable var = ncFileIn.findVariable(varName);
            final boolean hasLocalDepth = NetCDFConverterUtilities.hasThisDimension(var, depthName);
            Array originalVarArray = var.read();
            DataType varDataType = var.getDataType();
            Array destArray = null;
            int[] dimensions = null;
            final boolean setDepth = hasDepth && hasLocalDepth;
            if (setDepth) {
                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);
            boolean updateFillValue = updatingFilLValue.containsKey(varName);
            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, updateFillValue, 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);
    }
}

Example 98 with Variable

use of org.flyte.api.v1.Variable in project imageio-ext by geosolutions-it.

the class MercatorOceanConverter 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());
        // input dimensions
        final Dimension latOriginalDim = ncFileIn.findDimension(NetCDFUtilities.LATITUDE);
        final Dimension lonOriginalDim = ncFileIn.findDimension(NetCDFUtilities.LONGITUDE);
        // input VARIABLES
        // Variable time_0 = ncFileIn.findVariable("time");
        // Array time_0_Data = time_0.read();
        // Index time_0_Index = time_0_Data.getIndex();
        final Variable lonOriginalVar = ncFileIn.findVariable(NetCDFUtilities.LONGITUDE);
        final int nLon = lonOriginalDim.getLength();
        final Variable latOriginalVar = ncFileIn.findVariable(NetCDFUtilities.LATITUDE);
        final int nLat = latOriginalDim.getLength();
        final Array latOriginalData = latOriginalVar.read();
        final Index latOriginalIndex = latOriginalData.getIndex();
        final Array lonOriginalData = lonOriginalVar.read();
        final Index lonOriginalIndex = lonOriginalData.getIndex();
        final Variable depthOriginalVar = ncFileIn.findVariable(// Depth
        NetCDFUtilities.DEPTH);
        final int nLevels = depthOriginalVar.getDimension(0).getLength();
        final Array depthOriginalData = depthOriginalVar.read();
        // Dimension timeDim = ncFileOut.addDimension("time",
        // timeDim0.getLength());
        Dimension latDim = ncFileOut.addDimension(NetCDFUtilities.LAT, nLat);
        Dimension lonDim = ncFileOut.addDimension(NetCDFUtilities.LON, nLon);
        Dimension depthDim = ncFileOut.addDimension(NetCDFUtilities.DEPTH, nLevels);
        Dimension timeDim = ncFileOut.addDimension(NetCDFUtilities.TIME, 1);
        // writing file
        computeMatrixExtremes(latOriginalData, lonOriginalData, nLon, nLat, latOriginalIndex, lonOriginalIndex);
        NetCDFConverterUtilities.copyGlobalAttributes(ncFileOut, ncFileIn.getGlobalAttributes());
        // //
        // 
        // Time requires a special Management
        // 
        // //
        // time Variable
        Variable timeVar = ncFileOut.addVariable(NetCDFUtilities.TIME, DataType.FLOAT, new Dimension[] { timeDim });
        Attribute referenceTime = ncFileIn.findGlobalAttribute(TIME_ORIGIN);
        Attribute forecastDate = ncFileIn.findGlobalAttribute(FORECAST_DAY);
        int numDay = 0;
        if (referenceTime != null && forecastDate != null) {
            numDay = setTime(ncFileOut, referenceTime, forecastDate);
        }
        // final float referenceTime = setTimeVariableAttributes(timeVar,
        // ncFileOut);
        // lat Variable
        ArrayFloat latDestData = new ArrayFloat(new int[] { latOriginalDim.getLength() });
        Index latDestIndex = latDestData.getIndex();
        ncFileOut.addVariable(NetCDFUtilities.LAT, DataType.FLOAT, new Dimension[] { latDim });
        // NOTE: A Strange BUG (I guess)
        // when you copy attributes from old vars to new vars, it overwrite
        // coordvars!!!
        ncFileOut.addVariableAttribute(NetCDFUtilities.LAT, "long_name", NetCDFUtilities.LATITUDE);
        ncFileOut.addVariableAttribute(NetCDFUtilities.LAT, UNITS, latOriginalVar.getUnitsString());
        // new String[] { "long_name", UNITS, "step" , "axis"});
        for (int yPos = 0; yPos < latOriginalDim.getLength(); yPos++) {
            latDestData.setFloat(latDestIndex.set(yPos), new Float(this.ymax - (new Float(yPos).floatValue() * this.periodY)).floatValue());
        }
        // lon Variable
        ArrayFloat lonDestData = new ArrayFloat(new int[] { lonOriginalDim.getLength() });
        Index lonDestIndex = lonDestData.getIndex();
        ncFileOut.addVariable(NetCDFUtilities.LON, DataType.FLOAT, new Dimension[] { lonDim });
        ncFileOut.addVariableAttribute(NetCDFUtilities.LON, "long_name", NetCDFUtilities.LONGITUDE);
        ncFileOut.addVariableAttribute(NetCDFUtilities.LON, UNITS, lonOriginalVar.getUnitsString());
        // new String[] { "long_name", UNITS, "step", "axis"});
        for (int xPos = 0; xPos < lonOriginalDim.getLength(); xPos++) {
            lonDestData.setFloat(lonDestIndex.set(xPos), new Float(this.xmin + (new Float(xPos).floatValue() * this.periodX)).floatValue());
        }
        // depth level Variable
        ArrayFloat depthDestData = new ArrayFloat(new int[] { depthDim.getLength() });
        Index depthDestIndex = depthDestData.getIndex();
        ncFileOut.addVariable(NetCDFUtilities.DEPTH, DataType.FLOAT, new Dimension[] { depthDim });
        ncFileOut.addVariableAttribute(NetCDFUtilities.DEPTH, "long_name", NetCDFUtilities.DEPTH);
        ncFileOut.addVariableAttribute(NetCDFUtilities.DEPTH, UNITS, depthOriginalVar.getUnitsString());
        final Attribute positiveAttrib = depthOriginalVar.findAttribute("positive");
        String positiveValue = "down";
        if (positiveAttrib != null)
            positiveValue = positiveAttrib.getStringValue();
        ncFileOut.addVariableAttribute(NetCDFUtilities.DEPTH, "positive", positiveValue);
        for (int wPos = 0; wPos < depthDim.getLength(); wPos++) {
            depthDestData.setFloat(depthDestIndex.set(wPos), depthOriginalData.getFloat(depthDestIndex));
        }
        int numVars = 0;
        final ArrayList<String> variables = new ArrayList<String>(5);
        // {} Variables
        for (int i = 0; i < NUMVARS; i++) {
            String varName = (String) VARIABLES.get(i);
            Variable var = ncFileIn.findVariable(varName);
            if (var != null) {
                variables.add(varName);
                boolean hasLocalDepth = NetCDFConverterUtilities.hasThisDimension(var, "depth");
                if (hasLocalDepth)
                    ncFileOut.addVariable(varName, var.getDataType(), new Dimension[] { timeDim, depthDim, latDim, lonDim });
                else
                    ncFileOut.addVariable(varName, var.getDataType(), new Dimension[] { timeDim, latDim, lonDim });
                NetCDFConverterUtilities.setVariableAttributes(var, ncFileOut, new String[] { "positions" });
                numVars++;
            }
        }
        // writing bin data ...
        ncFileOut.create();
        ArrayFloat timeData = new ArrayFloat(new int[] { timeDim.getLength() });
        Index timeIndex = timeData.getIndex();
        timeData.setFloat(timeIndex.set(0), numDay);
        ncFileOut.write(NetCDFUtilities.TIME, timeData);
        timeDim.addCoordinateVariable(timeVar);
        Variable latitudeVar = ncFileOut.findVariable(NetCDFUtilities.LAT);
        latDim.addCoordinateVariable(latitudeVar);
        ncFileOut.write(NetCDFUtilities.LAT, latDestData);
        Variable longitudeVar = ncFileOut.findVariable(NetCDFUtilities.LON);
        lonDim.addCoordinateVariable(longitudeVar);
        ncFileOut.write(NetCDFUtilities.LON, lonDestData);
        Variable depthVar = ncFileOut.findVariable(NetCDFUtilities.DEPTH);
        depthDim.addCoordinateVariable(depthVar);
        ncFileOut.write(NetCDFUtilities.DEPTH, depthDestData);
        for (int i = 0; i < numVars; i++) {
            final String varName = (String) variables.get(i);
            final Variable var = ncFileIn.findVariable(varName);
            final boolean hasLocalDepth = NetCDFConverterUtilities.hasThisDimension(var, "depth");
            final Array originalData = var.read();
            Index varIndex = originalData.getIndex();
            final DataType varDataType = var.getDataType();
            final Attribute fv = var.findAttribute("_FillValue");
            float fillValue = Float.NaN;
            if (fv != null) {
                fillValue = (fv.getNumericValue()).floatValue();
            }
            Array destArray = null;
            int[] dimensions = null;
            if (hasLocalDepth) {
                dimensions = new int[] { timeDim.getLength(), depthDim.getLength(), nLat, nLon };
            } else {
                dimensions = new int[] { timeDim.getLength(), nLat, nLon };
            }
            destArray = NetCDFConverterUtilities.getArray(dimensions, varDataType);
            Index destIndex = destArray.getIndex();
            ArrayFloat tempData = new ArrayFloat(new int[] { latOriginalDim.getLength(), lonOriginalDim.getLength() });
            Index tempIndex = tempData.getIndex();
            if (hasLocalDepth) {
                for (int levelPos = 0; levelPos < depthDim.getLength(); levelPos++) {
                    for (int yPos = 0; yPos < latOriginalDim.getLength(); yPos++) {
                        for (int xPos = 0; xPos < lonOriginalDim.getLength(); xPos++) {
                            tempData.setFloat(tempIndex.set(yPos, xPos), originalData.getFloat(varIndex.set(levelPos, yPos, xPos)));
                        }
                    }
                    final WritableRaster outData = Resampler(latOriginalData, lonOriginalData, lonOriginalDim.getLength(), latOriginalDim.getLength(), 2, tempData, fillValue);
                    for (int j = 0; j < latOriginalDim.getLength(); j++) {
                        for (int k = 0; k < lonOriginalDim.getLength(); k++) {
                            float sample = outData.getSampleFloat(k, j, 0);
                            destArray.setFloat(destIndex.set(0, levelPos, j, k), sample);
                        }
                    }
                }
            } else {
                for (int yPos = 0; yPos < latOriginalDim.getLength(); yPos++) {
                    for (int xPos = 0; xPos < lonOriginalDim.getLength(); xPos++) {
                        tempData.setFloat(tempIndex.set(yPos, xPos), originalData.getFloat(varIndex.set(yPos, xPos)));
                    }
                }
                final WritableRaster outData = Resampler(latOriginalData, lonOriginalData, lonOriginalDim.getLength(), latOriginalDim.getLength(), 2, tempData, fillValue);
                for (int j = 0; j < latOriginalDim.getLength(); j++) {
                    for (int k = 0; k < lonOriginalDim.getLength(); k++) {
                        float sample = outData.getSampleFloat(k, j, 0);
                        destArray.setFloat(destIndex.set(0, j, k), sample);
                    }
                }
            }
            // }
            ncFileOut.write(varName, destArray);
        }
        ncFileOut.close();
        outputFile.renameTo(fileOut);
    } catch (Exception e) {
        // something bad happened
        if (LOGGER.isLoggable(Level.INFO))
            LOGGER.log(Level.INFO, e.getLocalizedMessage(), e);
        JAI.getDefaultInstance().getTileCache().flush();
    }
}

Example 99 with Variable

use of org.flyte.api.v1.Variable in project imageio-ext by geosolutions-it.

the class HDF4TeraScanImageReader method initializeProfile.

/**
 * Retrieve Terascan specific information.
 *
 * @throws IOException
 */
protected void initializeProfile() throws IOException {
    boolean checkProducts = true;
    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();
    reader.setNumGlobalAttributes(attributes.size());
    productList = HDF4TeraScanProperties.refineProductList(variables);
    final int numImages = productList != null ? productList.length : 0;
    setNumImages(numImages);
    reader.setNumImages(numImages);
    final Map<Range, TerascanDatasetWrapper> indexMap = new HashMap<Range, TerascanDatasetWrapper>(numImages);
    // Scanning all the datasets
    try {
        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 (!checkProducts || name.equals(productList[j])) {
                    // Updating the subDatasetsMap map
                    indexMap.put(new Range(j, j + 1), new TerascanDatasetWrapper(var));
                    break;
                }
            }
        }
    } catch (InvalidRangeException e) {
        throw new IllegalArgumentException("Error occurred during NetCDF file parsing", e);
    }
    reader.setIndexMap(indexMap);
}

Example 100 with Variable

use of org.flyte.api.v1.Variable in project imageio-ext by geosolutions-it.

the class NetCDFImageReader method initialize.

/**
 * Initialize main properties for this reader.
 *
 * @throws exception
 *                 {@link InvalidRangeException}
 */
protected synchronized void initialize() {
    int numImages = 0;
    final Map<Range, NetCDFVariableWrapper> indexMap = new HashMap<Range, NetCDFVariableWrapper>();
    final NetcdfDataset dataset = reader.getDataset();
    try {
        if (dataset != null) {
            checkType = NetCDFUtilities.getCheckType(dataset);
            final List<Variable> variables = dataset.getVariables();
            if (variables != null) {
                for (final Variable variable : variables) {
                    if (variable != null && variable instanceof VariableDS) {
                        if (!NetCDFUtilities.isVariableAccepted(variable, checkType))
                            continue;
                        int[] shape = variable.getShape();
                        switch(shape.length) {
                            case 2:
                                indexMap.put(new Range(numImages, numImages + 1), new NetCDFVariableWrapper(variable));
                                numImages++;
                                break;
                            case 3:
                                indexMap.put(new Range(numImages, numImages + shape[0]), new NetCDFVariableWrapper(variable));
                                numImages += shape[0];
                                break;
                            case 4:
                                indexMap.put(new Range(numImages, numImages + shape[0] * shape[1]), new NetCDFVariableWrapper(variable));
                                numImages += shape[0] * shape[1];
                                break;
                        }
                    }
                }
            }
        } else
            throw new IllegalArgumentException("Not a valid dataset has been found");
    } catch (InvalidRangeException e) {
        throw new IllegalArgumentException("Error occurred during NetCDF file parsing", e);
    }
    reader.setIndexMap(indexMap);
    setNumImages(numImages);
    reader.setNumImages(numImages);
    int numAttribs = 0;
    final List<Attribute> globalAttributes = dataset.getGlobalAttributes();
    if (globalAttributes != null && !globalAttributes.isEmpty())
        numAttribs = globalAttributes.size();
    reader.setNumGlobalAttributes(numAttribs);
}