public Map<Band, Variable> addBands(
Product product, Variable idxVariable, List<Variable> l3ProdVars) {
final Structure binListStruc = (Structure) idxVariable;
final Map<Band, Variable> bandToVariableMap = new HashMap<Band, Variable>();
// bandToVariableMap.put(addBand(product, "bin_num", ProductData.TYPE_UINT32),
// binListStruc.select("bin_num").findVariable("bin_num"));
bandToVariableMap.put(
addBand(product, "weights", ProductData.TYPE_FLOAT32),
binListStruc.select("weights").findVariable("weights"));
bandToVariableMap.put(
addBand(product, "nobs", ProductData.TYPE_UINT16),
binListStruc.select("nobs").findVariable("nobs"));
bandToVariableMap.put(
addBand(product, "nscenes", ProductData.TYPE_UINT16),
binListStruc.select("nscenes").findVariable("nscenes"));
// ncFile.getRootGroup().findGroup("Level-3 Binned Data").findVariable("BinList");
if (ncFile.getRootGroup().findGroup("Level-3_Binned_Data").findVariable("qual_l3") != null) {
bandToVariableMap.put(
addBand(product, "qual_l3", ProductData.TYPE_UINT8),
ncFile.getRootGroup().findGroup("Level-3_Binned_Data").findVariable("qual_l3"));
}
String groupnames = "";
for (Variable l3Var : l3ProdVars) {
String varName = l3Var.getShortName();
final int dataType = ProductData.TYPE_FLOAT32;
if (!varName.contains("Bin")
&& (!varName.startsWith("qual"))
&& (!varName.equalsIgnoreCase("SEAGrid"))
&& (!varName.equalsIgnoreCase("Input_Files"))) {
final Structure binStruc = (Structure) l3Var;
if (groupnames.length() == 0) {
groupnames = varName;
} else {
groupnames = groupnames + ":" + varName;
}
List<String> vnames = binStruc.getVariableNames();
for (String bandvar : vnames) {
bandToVariableMap.put(
addBand(product, bandvar, dataType), binStruc.select(bandvar).findVariable(bandvar));
}
// Add virtual band for product mean
StringBuilder prodname = new StringBuilder(varName);
prodname.append("_mean");
String calcmean = ComputeBinMeans(varName);
Band varmean =
new VirtualBand(
prodname.toString(),
ProductData.TYPE_FLOAT32,
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
calcmean);
varmean.setNoDataValue(Double.NaN);
varmean.setNoDataValueUsed(true);
product.addBand(varmean);
// Add virtual band for product stdev
int underscore = prodname.indexOf("_mean");
prodname.delete(underscore, underscore + 5);
prodname.append("_stdev");
String calcstdev = ComputeBinVariances(varName);
Band varstdev =
new VirtualBand(
prodname.toString(),
ProductData.TYPE_FLOAT32,
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
calcstdev);
varstdev.setNoDataValue(Double.NaN);
varstdev.setNoDataValueUsed(true);
product.addBand(varstdev);
}
}
product.setAutoGrouping(groupnames);
return bandToVariableMap;
}
private float getAvePixel(Tile inputTile, int iTarX, int iTarY) {
double value = 0;
double noDataValue = 0;
int n = 0;
final int minX = Math.max(0, iTarX - aveBlock);
final int minY = Math.max(0, iTarY - aveBlock);
final int maxX = Math.min(synergyProduct.getSceneRasterWidth() - 1, iTarX + aveBlock);
final int maxY = Math.min(synergyProduct.getSceneRasterHeight() - 1, iTarY + aveBlock);
for (int iy = minY; iy <= maxY; iy++) {
for (int ix = minX; ix <= maxX; ix++) {
final double val = inputTile.getSampleDouble(ix, iy);
noDataValue = inputTile.getRasterDataNode().getNoDataValue();
final boolean valid = (Double.compare(val, noDataValue) != 0);
if (valid) {
n++;
value += val;
}
}
}
if (!(n < minNAve)) {
value /= n;
} else {
value = noDataValue;
}
return (float) value;
}
/** This method creates the target product */
private void createTargetProduct() {
final String productType = synergyProduct.getProductType();
final String productName = synergyProduct.getName();
final int sceneWidth = synergyProduct.getSceneRasterWidth();
final int sceneHeight = synergyProduct.getSceneRasterHeight();
final int downscaledRasterWidth = (int) (Math.ceil((float) (sceneWidth / scalingFactor) - 0.5));
final int downscaledRasterHeight =
(int) (Math.ceil((float) (sceneHeight / scalingFactor) - 0.5));
targetProduct =
new Product(productName, productType, downscaledRasterWidth, downscaledRasterHeight);
// targetProduct.setPreferredTileSize(128, 128);
ProductUtils.copyGeoCoding(synergyProduct, targetProduct);
ProductUtils.copyMetadata(synergyProduct, targetProduct);
AerosolHelpers.copyDownscaledTiePointGrids(synergyProduct, targetProduct, scalingFactor);
AerosolHelpers.copyDownscaledFlagBands(synergyProduct, targetProduct, scalingFactor);
// AerosolHelpers.addAerosolFlagBand(targetProduct, downscaledRasterWidth,
// downscaledRasterHeight);
final BandMathsOp bandArithmeticOp =
BandMathsOp.createBooleanExpressionBand(INVALID_EXPRESSION, synergyProduct);
invalidBand = bandArithmeticOp.getTargetProduct().getBandAt(0);
setTargetBands();
}
/**
* Checks if all source products share the same raster size, otherwise throws an exception. Called
* by {@link #initialize()}.
*
* @throws OperatorException If the source product's raster sizes are not equal.
*/
protected void checkRasterSize() throws OperatorException {
Product[] sourceProducts = getSourceProducts();
int w = 0;
int h = 0;
for (int i = 0; i < sourceProducts.length; i++) {
Product sourceProduct = sourceProducts[i];
if (i == 0) {
w = sourceProduct.getSceneRasterWidth();
h = sourceProduct.getSceneRasterHeight();
} else {
if (sourceProduct.getSceneRasterWidth() != w || sourceProduct.getSceneRasterHeight() != h) {
throw new OperatorException("Source products must all have the same raster size.");
}
}
}
}
private void createTargetProduct() {
// construct target product
targetProduct =
new Product(
PRODUCT_NAME,
sourceProduct.getProductType(),
sourceProduct.getSceneRasterWidth(),
sourceProduct.getSceneRasterHeight());
OperatorUtils.copyProductNodes(sourceProduct, targetProduct);
for (final Band band : targetProduct.getBands()) {
targetProduct.removeBand(band);
}
for (String key : targetMap.keySet()) {
String bandName = targetMap.get(key).targetBandName_I;
targetProduct.addBand(bandName, ProductData.TYPE_FLOAT32);
targetProduct.getBand(bandName).setUnit(Unit.METERS);
}
// targetProduct.setPreferredTileSize(1,1);
}
static void addBitmaskDefinitions(final Product product, final String flagsBandName) {
for (final Flags flag : Flags.values()) {
final String name =
new StringBuilder(flagsBandName.split("flags")[0]).append(flag.name()).toString();
final ProductNodeGroup<Mask> maskGroup = product.getMaskGroup();
if (maskGroup.contains(name)) {
continue;
}
final String expression =
new StringBuilder(flagsBandName).append(".").append(flag.name()).toString();
final int width = product.getSceneRasterWidth();
final int height = product.getSceneRasterHeight();
Mask mask =
Mask.BandMathsType.create(
name,
flag.getDescription(),
width,
height,
expression,
flag.getColor(),
flag.getTransparency());
maskGroup.add(mask);
}
}
private void setSceneRasterStartAndStopTime(Product product) {
final Product sourceProduct = getSourceProduct();
final ProductData.UTC startTime = sourceProduct.getStartTime();
final ProductData.UTC stopTime = sourceProduct.getEndTime();
final ProductSubsetDef subsetDef = getSubsetDef();
if (startTime != null
&& stopTime != null
&& subsetDef != null
&& subsetDef.getRegion() != null) {
final double height = sourceProduct.getSceneRasterHeight();
final Rectangle region = subsetDef.getRegion();
final double regionY = region.getY();
final double regionHeight = region.getHeight();
final double dStart = startTime.getMJD();
final double dStop = stopTime.getMJD();
final double vPerLine = (dStop - dStart) / (height - 1);
final double newStart = vPerLine * regionY + dStart;
final double newStop = vPerLine * (regionHeight - 1) + newStart;
product.setStartTime(new ProductData.UTC(newStart));
product.setEndTime(new ProductData.UTC(newStop));
} else {
product.setStartTime(startTime);
product.setEndTime(stopTime);
}
}
/** Calls the given handler for all frames of the product the operator executor product. */
public Object execute(Handler handler) throws Exception {
int parallelism = Runtime.getRuntime().availableProcessors();
System.out.println("parallelism = " + parallelism);
JAI.getDefaultInstance().getTileScheduler().setParallelism(parallelism);
Dimension frameSize = getFrameSize();
int numXFrames = 1 + (product.getSceneRasterWidth() - 1) / frameSize.width;
int numYFrames = 1 + (product.getSceneRasterHeight() - 1) / frameSize.height;
Rectangle sceneRegion =
new Rectangle(product.getSceneRasterWidth(), product.getSceneRasterHeight());
for (int frameY = 0; frameY < numYFrames; frameY++) {
for (int frameX = 0; frameX < numXFrames; frameX++) {
Rectangle frameRegion =
new Rectangle(
frameX * frameSize.width,
frameY * frameSize.height,
frameSize.width,
frameSize.height)
.intersection(sceneRegion);
int numBands = product.getNumBands();
Band[] bandArray = new Band[numBands];
ProductData[] dataArray = new ProductData[numBands];
for (int b = 0; b < numBands; b++) {
Band band = product.getBandAt(b);
PlanarImage planarImage = band.getSourceImage();
Point[] indices = planarImage.getTileIndices(null);
System.out.println("indices = " + indices.length);
TileRequest tileRequest = planarImage.queueTiles(indices);
Raster raster = planarImage.getData();
System.out.println("raster = " + raster);
ProductData data = band.createCompatibleRasterData(frameRegion.width, frameRegion.height);
band.readRasterData(
frameRegion.x, frameRegion.y, frameRegion.width, frameRegion.height, data);
bandArray[b] = band;
dataArray[b] = data;
}
MyFrame frame = new MyFrame(frameRegion, bandArray, dataArray);
handler.frameComputed(frame);
}
}
return new Object();
}
/**
* Creates the target product instance. Called by {@link #initialize()}.
*
* <p>The default implementation creates a target product instance given the raster size of the
* (first) source product.
*
* @return A new target product instance.
* @throws OperatorException If the target product cannot be created.
*/
protected Product createTargetProduct() throws OperatorException {
Product sourceProduct = getSourceProduct();
return new Product(
getId(),
getClass().getName(),
sourceProduct.getSceneRasterWidth(),
sourceProduct.getSceneRasterHeight());
}
/**
* Initializes this operator and sets the one and only target product.
*
* <p>The target product can be either defined by a field of type {@link
* org.esa.beam.framework.datamodel.Product} annotated with the {@link
* org.esa.beam.framework.gpf.annotations.TargetProduct TargetProduct} annotation or by calling
* {@link #setTargetProduct} method.
*
* <p>The framework calls this method after it has created this operator. Any client code that
* must be performed before computation of tile data should be placed here.
*
* @throws org.esa.beam.framework.gpf.OperatorException If an error occurs during operator
* initialisation.
* @see #getTargetProduct()
*/
@Override
public void initialize() throws OperatorException {
productName = sourceProduct.getName() + "_vgtComp";
targetProduct =
new Product(
productName,
"VGT_COMP",
sourceProduct.getSceneRasterWidth(),
sourceProduct.getSceneRasterHeight());
// Some target products may require more aid from ProductUtils methods...
ProductUtils.copyGeoCoding(sourceProduct, targetProduct);
sourceBandS1_B0 = sourceProduct.getBand(sourceBandNameS1_B0);
sourceBandS1_B2 = sourceProduct.getBand(sourceBandNameS1_B2);
sourceBandS1_B3 = sourceProduct.getBand(sourceBandNameS1_B3);
sourceBandS1_MIR = sourceProduct.getBand(sourceBandNameS1_MIR);
sourceBandS1_SM = sourceProduct.getBand(sourceBandNameS1_SM);
sourceBandP_B0 = sourceProduct.getBand(sourceBandNameP_B0);
sourceBandP_B2 = sourceProduct.getBand(sourceBandNameP_B2);
sourceBandP_B3 = sourceProduct.getBand(sourceBandNameP_B3);
sourceBandP_MIR = sourceProduct.getBand(sourceBandNameP_MIR);
sourceBandP_SM = sourceProduct.getBand(sourceBandNameP_SM);
sourceBandP_Idepix = sourceProduct.getBand(sourceBandNameP_Idepix);
targetDifferenceBandB0 =
targetProduct.addBand(targetDifferenceBandNameB0, ProductData.TYPE_FLOAT32);
targetDifferenceBandB2 =
targetProduct.addBand(targetDifferenceBandNameB2, ProductData.TYPE_FLOAT32);
targetDifferenceBandB3 =
targetProduct.addBand(targetDifferenceBandNameB3, ProductData.TYPE_FLOAT32);
targetDifferenceBandMIR =
targetProduct.addBand(targetDifferenceBandNameMIR, ProductData.TYPE_FLOAT32);
targetProduct.setPreferredTileSize(
new Dimension(targetProduct.getSceneRasterWidth(), targetProduct.getSceneRasterHeight()));
}
public static Rectangle computePixelRegion(
Product product, Geometry geoRegion, int numBorderPixels) {
final Geometry productGeometry = computeProductGeometry(product);
final Geometry regionIntersection = geoRegion.intersection(productGeometry);
if (regionIntersection.isEmpty()) {
return new Rectangle();
}
final PixelRegionFinder pixelRegionFinder = new PixelRegionFinder(product.getGeoCoding());
regionIntersection.apply(pixelRegionFinder);
final Rectangle pixelRegion = pixelRegionFinder.getPixelRegion();
pixelRegion.grow(numBorderPixels, numBorderPixels);
return pixelRegion.intersection(
new Rectangle(product.getSceneRasterWidth(), product.getSceneRasterHeight()));
}
protected void addGeoCoding(Product product) throws IOException {
GeoPos ulPos = getUpperLeftPosition();
final Rectangle rect =
new Rectangle(product.getSceneRasterWidth(), product.getSceneRasterHeight());
AffineTransform transform = new AffineTransform();
transform.translate(ulPos.getLon(), ulPos.getLat());
transform.scale(PIXEL_SIZE_DEG, -PIXEL_SIZE_DEG);
transform.translate(-PIXEL_CENTER, -PIXEL_CENTER);
try {
product.setGeoCoding(new CrsGeoCoding(DefaultGeographicCRS.WGS84, rect, transform));
} catch (Exception e) {
throw new IOException("Cannot create GeoCoding: ", e);
}
}
private Band addBand(Product product, String varName, int productType) {
Band band =
new Band(
varName, productType, product.getSceneRasterWidth(), product.getSceneRasterHeight());
band.setScalingOffset(0.0);
band.setScalingFactor(1.0);
band.setLog10Scaled(false);
if (productType == ProductData.TYPE_FLOAT32) {
band.setNoDataValue(Double.NaN);
} else {
band.setNoDataValue(-999);
}
band.setNoDataValueUsed(true);
product.addBand(band);
return band;
}
private void addMask(
MetadataAttribute metadataSample, String expression, Color color, Product product) {
final ProductNodeGroup<Mask> maskGroup = product.getMaskGroup();
final int width = product.getSceneRasterWidth();
final int height = product.getSceneRasterHeight();
Mask mask =
Mask.BandMathsType.create(
metadataSample.getName().toLowerCase(),
metadataSample.getDescription(),
width,
height,
expression,
color,
0.5);
maskGroup.add(mask);
}
protected Band addNewBand(Product product, Variable variable) {
final int sceneRasterWidth = product.getSceneRasterWidth();
final int sceneRasterHeight = product.getSceneRasterHeight();
Band band = null;
int variableRank = variable.getRank();
if (variableRank == 2) {
final int[] dimensions = variable.getShape();
final int height = dimensions[0] - leadLineSkip - tailLineSkip;
final int width = dimensions[1];
if (height == sceneRasterHeight && width == sceneRasterWidth) {
final String name = variable.getShortName();
final int dataType = getProductDataType(variable);
band = new Band(name, dataType, width, height);
final String validExpression = bandInfoMap.get(name);
if (validExpression != null && !validExpression.equals("")) {
band.setValidPixelExpression(validExpression);
}
product.addBand(band);
try {
band.setNoDataValue(
(double) variable.findAttribute("bad_value_scaled").getNumericValue().floatValue());
band.setNoDataValueUsed(true);
} catch (Exception ignored) {
}
final List<Attribute> list = variable.getAttributes();
for (Attribute hdfAttribute : list) {
final String attribName = hdfAttribute.getShortName();
if ("units".equals(attribName)) {
band.setUnit(hdfAttribute.getStringValue());
} else if ("long_name".equals(attribName)) {
band.setDescription(hdfAttribute.getStringValue());
} else if ("slope".equals(attribName)) {
band.setScalingFactor(hdfAttribute.getNumericValue(0).doubleValue());
} else if ("intercept".equals(attribName)) {
band.setScalingOffset(hdfAttribute.getNumericValue(0).doubleValue());
}
}
}
}
return band;
}
private Product createClostProduct(RenderedOp blueAerosolPanCirrusImage) {
Product product =
new Product(
sourceProduct.getName() + "_clost",
sourceProduct.getProductType() + " (clost)",
sourceProduct.getSceneRasterWidth(),
sourceProduct.getSceneRasterHeight());
product.setGeoCoding(sourceProduct.getGeoCoding());
product.setDescription("Product holding Clost Image");
Band band = product.addBand(CLOST_BAND_NAME, ProductData.TYPE_FLOAT32);
band.setSourceImage(blueAerosolPanCirrusImage);
band.setUnit("dl");
band.setDescription("CLOST Image: aerosol * blue * pan * cirrus ");
return product;
}
protected void addBands(Product product, GCTileFile gcTileFile) {
final List<BandDescriptor> bandDescriptorList = gcTileFile.getBandDescriptorList();
for (BandDescriptor descriptor : bandDescriptorList) {
final Band band =
new Band(
descriptor.getName(),
descriptor.getDataType(),
product.getSceneRasterWidth(),
product.getSceneRasterHeight());
band.setScalingFactor(descriptor.getScaleFactor());
band.setScalingOffset(descriptor.getOffsetValue());
band.setDescription(descriptor.getDescription());
band.setUnit(descriptor.getUnit());
band.setNoDataValueUsed(descriptor.isFillValueUsed());
band.setNoDataValue(descriptor.getFillValue());
product.addBand(band);
band.setSourceImage(getMultiLevelImage(band));
}
}
// Creates the output product for the given request.
private void createOutputProduct(ProgressMonitor pm) throws IOException, ProcessorException {
// take only the first output product. There might be more but we will ignore
// these in SMAC.
ProductRef prod = getRequest().getOutputProductAt(0);
checkParamNotNull(prod, "output product");
String productType = _inputProduct.getProductType() + "_SMAC";
String productName = getOutputProductNameSafe();
int sceneWidth = _inputProduct.getSceneRasterWidth();
int sceneHeight = _inputProduct.getSceneRasterHeight();
_outputProduct = new Product(productName, productType, sceneWidth, sceneHeight);
ProductWriter writer = ProcessorUtils.createProductWriter(prod);
_outputProduct.setProductWriter(writer);
// loop over bands and create them
// -------------------------------
if (ObjectUtils.equalObjects(_sensorType, SensorCoefficientManager.MERIS_NAME)) {
addBandsToOutput("Atmosphere corrected MERIS band ", true);
} else {
addBandsToOutput("Atmosphere corrected band ");
}
ProductUtils.copyTiePointGrids(_inputProduct, _outputProduct);
copyRequestMetaData(_outputProduct);
copyFlagBands(_inputProduct, _outputProduct);
// for MERIS FSG / FRG products
copyBand(
EnvisatConstants.MERIS_AMORGOS_L1B_CORR_LATITUDE_BAND_NAME, _inputProduct, _outputProduct);
copyBand(
EnvisatConstants.MERIS_AMORGOS_L1B_CORR_LONGITUDE_BAND_NAME, _inputProduct, _outputProduct);
copyBand(EnvisatConstants.MERIS_AMORGOS_L1B_ALTIUDE_BAND_NAME, _inputProduct, _outputProduct);
copyGeoCoding(_inputProduct, _outputProduct);
// and initialize the disk represenation
writer.writeProductNodes(_outputProduct, new File(prod.getFilePath()));
copyBandData(getBandNamesToCopy(), _inputProduct, _outputProduct, pm);
}
@Override
public void initialize() throws OperatorException {
if (computeErrorBands) {
deactivateComputeTileMethod();
}
if (endmemberFile != null) {
loadEndmemberFile();
}
if (sourceBandNames == null || sourceBandNames.length == 0) {
Band[] bands = sourceProduct.getBands();
ArrayList<String> bandNameList = new ArrayList<String>();
for (Band band : bands) {
if (band.getSpectralWavelength() > 0) {
bandNameList.add(band.getName());
}
}
sourceBandNames = bandNameList.toArray(new String[bandNameList.size()]);
}
validateParameters();
sourceBands = new Band[sourceBandNames.length];
for (int i = 0; i < sourceBandNames.length; i++) {
String sourceBandName = sourceBandNames[i];
Band sourceBand = sourceProduct.getBand(sourceBandName);
if (sourceBand == null) {
throw new OperatorException("Source band not found: " + sourceBandName);
}
if (sourceBand.getSpectralWavelength() <= 0) {
throw new OperatorException("Source band without spectral wavelength: " + sourceBandName);
}
sourceBands[i] = sourceBand;
}
int numSourceBands = sourceBands.length;
int numEndmembers = endmembers.length;
if (numSourceBands < numEndmembers) {
throw new OperatorException("Number of source bands must be >= number of endmembers.");
}
double[][] lsuMatrixElements = new double[numSourceBands][numEndmembers];
for (int j = 0; j < numEndmembers; j++) {
Endmember endmember = endmembers[j];
double[] wavelengths = endmember.getWavelengths();
double[] radiations = endmember.getRadiations();
for (int i = 0; i < numSourceBands; i++) {
Band sourceBand = sourceBands[i];
float wavelength = sourceBand.getSpectralWavelength();
float bandwidth = sourceBand.getSpectralBandwidth();
int k =
findEndmemberSpectralIndex(wavelengths, wavelength, Math.max(bandwidth, minBandwidth));
if (k == -1) {
throw new OperatorException(
String.format(
"Band %s: No matching endmember wavelength found (%f nm)",
sourceBand.getName(), wavelength));
}
lsuMatrixElements[i][j] = radiations[k];
}
}
if (UC_LSU.equals(unmixingModelName)) {
spectralUnmixing = new UnconstrainedLSU(lsuMatrixElements);
} else if (C_LSU.equals(unmixingModelName)) {
spectralUnmixing = new ConstrainedLSU(lsuMatrixElements);
} else if (FC_LSU.equals(unmixingModelName)) {
spectralUnmixing = new FullyConstrainedLSU(lsuMatrixElements);
} else if (unmixingModelName == null) {
spectralUnmixing = new UnconstrainedLSU(lsuMatrixElements);
}
int width = sourceProduct.getSceneRasterWidth();
int height = sourceProduct.getSceneRasterHeight();
targetProduct =
new Product(sourceProduct.getName() + "_unmixed", "SpectralUnmixing", width, height);
abundanceBands = new Band[numEndmembers];
for (int i = 0; i < numEndmembers; i++) {
abundanceBands[i] =
targetProduct.addBand(
endmembers[i].getName() + abundanceBandNameSuffix, ProductData.TYPE_FLOAT32);
}
if (computeErrorBands) {
errorBands = new Band[numSourceBands];
for (int i = 0; i < errorBands.length; i++) {
final String erroBandName = sourceBands[i].getName() + errorBandNameSuffix;
errorBands[i] = targetProduct.addBand(erroBandName, ProductData.TYPE_FLOAT32);
ProductUtils.copySpectralBandProperties(sourceBands[i], errorBands[i]);
}
summaryErrorBand = targetProduct.addBand("summary_error", ProductData.TYPE_FLOAT32);
summaryErrorBand.setDescription("Root mean square error");
}
ProductUtils.copyMetadata(sourceProduct, targetProduct);
ProductUtils.copyTiePointGrids(sourceProduct, targetProduct);
ProductUtils.copyGeoCoding(sourceProduct, targetProduct);
}
@Override
protected void addFlagsAndMasks(Product product) {
Band QFBand = product.getBand("l3m_qual");
if (QFBand != null) {
FlagCoding flagCoding = new FlagCoding("SST_Quality");
flagCoding.addFlag("Best", 0x00, "Highest quality retrieval");
flagCoding.addFlag("Good", 0x01, "Good quality retrieval");
flagCoding.addFlag("Questionable", 0x02, "Questionable quality retrieval");
flagCoding.addFlag("Bad", 0x03, "Bad quality retrieval");
product.getFlagCodingGroup().add(flagCoding);
QFBand.setSampleCoding(flagCoding);
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Best",
"Highest quality retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l3m_qual == 0",
SeadasFileReader.Cornflower,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Good",
"Good quality retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l3m_qual == 1",
SeadasFileReader.LightPurple,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Questionable",
"Questionable quality retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l3m_qual == 2",
SeadasFileReader.BurntUmber,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Bad",
"Bad quality retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l3m_qual == 3",
SeadasFileReader.FailRed,
0.6));
}
QFBand = product.getBand("qual_sst");
if (QFBand != null) {
FlagCoding flagCoding = new FlagCoding("SST_Quality");
flagCoding.addFlag("Best", 0x00, "Highest quality retrieval");
flagCoding.addFlag("Good", 0x01, "Good quality retrieval");
flagCoding.addFlag("Questionable", 0x02, "Questionable quality retrieval");
flagCoding.addFlag("Bad", 0x03, "Bad quality retrieval");
product.getFlagCodingGroup().add(flagCoding);
QFBand.setSampleCoding(flagCoding);
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Best",
"Highest quality retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst == 0",
SeadasFileReader.Cornflower,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Good",
"Good quality retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst == 1",
SeadasFileReader.LightPurple,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Questionable",
"Questionable quality retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst == 2",
SeadasFileReader.BurntUmber,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Bad",
"Bad quality retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst == 3",
SeadasFileReader.FailRed,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"No Data",
"No data retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst == -1",
SeadasFileReader.MediumGray,
0.6));
}
QFBand = product.getBand("qual_sst4");
if (QFBand != null) {
FlagCoding flagCoding = new FlagCoding("SST_Quality");
flagCoding.addFlag("Best", 0x00, "Highest quality retrieval");
flagCoding.addFlag("Good", 0x01, "Good quality retrieval");
flagCoding.addFlag("Questionable", 0x02, "Questionable quality retrieval");
flagCoding.addFlag("Bad", 0x03, "Bad quality retrieval");
product.getFlagCodingGroup().add(flagCoding);
QFBand.setSampleCoding(flagCoding);
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Best",
"Highest quality retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst4 == 0",
SeadasFileReader.Cornflower,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Good",
"Good quality retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst4 == 1",
SeadasFileReader.LightPurple,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Questionable",
"Questionable quality retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst4 == 2",
SeadasFileReader.BurntUmber,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Bad",
"Bad quality retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst4 == 3",
SeadasFileReader.FailRed,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"No Data",
"No data retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst4 == -1",
SeadasFileReader.MediumGray,
0.6));
}
}
public void addGeocoding(Product product) throws IOException {
double pixelX = 0.5;
double pixelY = 0.5;
double easting;
double northing;
double pixelSizeX;
double pixelSizeY;
boolean pixelRegistered = true;
if (productReader.getProductType() == SeadasProductReader.ProductType.ANCNRT) {
pixelRegistered = false;
}
if (productReader.getProductType() == SeadasProductReader.ProductType.OISST) {
Variable lon = ncFile.findVariable("lon");
Variable lat = ncFile.findVariable("lat");
Array lonData = lon.read();
// TODO: handle the 180 degree shift with the NOAA products - need to modify
// SeaDasFileReader:readBandData
// Below is a snippet from elsewhere in BEAM that deals with this issue...
// SPECIAL CASE: check if we have a global geographic lat/lon with lon from 0..360 instead of
// -180..180
// if (isShifted180(lonData)) {
// // if this is true, subtract 180 from all longitudes and
// // add a global attribute which will be analyzed when setting up the
// image(s)
// final List<Variable> variables = ncFile.getVariables();
// for (Variable next : variables) {
// next.getAttributes().add(new Attribute("LONGITUDE_SHIFTED_180", 1));
// }
// for (int i = 0; i < lonData.getSize(); i++) {
// final Index ii = lonData.getIndex().set(i);
// final double theLon = lonData.getDouble(ii) - 180.0;
// lonData.setDouble(ii, theLon);
// }
// }
final Array latData = lat.read();
final int lonSize = lon.getShape(0);
final Index i0 = lonData.getIndex().set(0);
final Index i1 = lonData.getIndex().set(lonSize - 1);
pixelSizeX =
(lonData.getDouble(i1) - lonData.getDouble(i0)) / (product.getSceneRasterWidth() - 1);
easting = lonData.getDouble(i0);
final int latSize = lat.getShape(0);
final Index j0 = latData.getIndex().set(0);
final Index j1 = latData.getIndex().set(latSize - 1);
pixelSizeY =
(latData.getDouble(j1) - latData.getDouble(j0)) / (product.getSceneRasterHeight() - 1);
// this should be the 'normal' case
if (pixelSizeY < 0) {
pixelSizeY = -pixelSizeY;
northing = latData.getDouble(latData.getIndex().set(0));
} else {
northing = latData.getDouble(latData.getIndex().set(latSize - 1));
}
northing -= pixelSizeX / 2.0;
easting += pixelSizeY / 2.0;
try {
product.setGeoCoding(
new CrsGeoCoding(
DefaultGeographicCRS.WGS84,
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
easting,
northing,
pixelSizeX,
pixelSizeY,
pixelX,
pixelY));
} catch (FactoryException e) {
throw new IllegalStateException(e);
} catch (TransformException e) {
throw new IllegalStateException(e);
}
} else {
String east = "Easternmost_Longitude";
String west = "Westernmost_Longitude";
String north = "Northernmost_Latitude";
String south = "Southernmost_Latitude";
Attribute latmax = ncFile.findGlobalAttributeIgnoreCase("geospatial_lat_max");
if (latmax != null) {
east = "geospatial_lon_max";
west = "geospatial_lon_min";
north = "geospatial_lat_max";
south = "geospatial_lat_min";
} else {
latmax = ncFile.findGlobalAttributeIgnoreCase("upper_lat");
if (latmax != null) {
east = "right_lon";
west = "left_lon";
north = "upper_lat";
south = "lower_lat";
}
}
final MetadataElement globalAttributes =
product.getMetadataRoot().getElement("Global_Attributes");
easting = (float) globalAttributes.getAttribute(east).getData().getElemDouble();
float westing = (float) globalAttributes.getAttribute(west).getData().getElemDouble();
pixelSizeX = Math.abs(easting - westing) / product.getSceneRasterWidth();
northing = (float) globalAttributes.getAttribute(north).getData().getElemDouble();
float southing = (float) globalAttributes.getAttribute(south).getData().getElemDouble();
if (northing < southing) {
mustFlipY = true;
northing = (float) globalAttributes.getAttribute(south).getData().getElemDouble();
southing = (float) globalAttributes.getAttribute(north).getData().getElemDouble();
}
pixelSizeY = Math.abs(northing - southing) / product.getSceneRasterHeight();
if (pixelRegistered) {
northing -= pixelSizeY / 2.0;
westing += pixelSizeX / 2.0;
} else {
pixelX = 0.0;
pixelY = 0.0;
}
try {
product.setGeoCoding(
new CrsGeoCoding(
DefaultGeographicCRS.WGS84,
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
westing,
northing,
pixelSizeX,
pixelSizeY,
pixelX,
pixelY));
} catch (FactoryException e) {
throw new IllegalStateException(e);
} catch (TransformException e) {
throw new IllegalStateException(e);
}
}
}
protected Map<Band, Variable> addSmiBands(Product product, List<Variable> variables) {
final int sceneRasterWidth = product.getSceneRasterWidth();
final int sceneRasterHeight = product.getSceneRasterHeight();
Map<Band, Variable> bandToVariableMap = new HashMap<Band, Variable>();
for (Variable variable : variables) {
int variableRank = variable.getRank();
if (variableRank == 2) {
final int[] dimensions = variable.getShape();
final int height = dimensions[0];
final int width = dimensions[1];
if (height == sceneRasterHeight && width == sceneRasterWidth) {
String name = variable.getShortName();
if (name.equals("l3m_data")) {
try {
name = getStringAttribute("Parameter") + " " + getStringAttribute("Measure");
} catch (Exception e) {
e.printStackTrace();
}
}
final int dataType = getProductDataType(variable);
final Band band = new Band(name, dataType, width, height);
// band = new Band(name, dataType, width, height);
product.addBand(band);
try {
Attribute fillvalue = variable.findAttribute("_FillValue");
if (fillvalue == null) {
fillvalue = variable.findAttribute("Fill");
}
if (fillvalue != null) {
band.setNoDataValue((double) fillvalue.getNumericValue().floatValue());
band.setNoDataValueUsed(true);
}
} catch (Exception ignored) {
}
bandToVariableMap.put(band, variable);
// Set units, if defined
try {
band.setUnit(getStringAttribute("Units"));
} catch (Exception ignored) {
}
final List<Attribute> list = variable.getAttributes();
double[] validMinMax = {0.0, 0.0};
for (Attribute hdfAttribute : list) {
final String attribName = hdfAttribute.getShortName();
if ("units".equals(attribName)) {
band.setUnit(hdfAttribute.getStringValue());
} else if ("long_name".equalsIgnoreCase(attribName)) {
band.setDescription(hdfAttribute.getStringValue());
} else if ("slope".equalsIgnoreCase(attribName)) {
band.setScalingFactor(hdfAttribute.getNumericValue(0).doubleValue());
} else if ("intercept".equalsIgnoreCase(attribName)) {
band.setScalingOffset(hdfAttribute.getNumericValue(0).doubleValue());
} else if ("scale_factor".equals(attribName)) {
band.setScalingFactor(hdfAttribute.getNumericValue(0).doubleValue());
} else if ("add_offset".equals(attribName)) {
band.setScalingOffset(hdfAttribute.getNumericValue(0).doubleValue());
} else if (attribName.startsWith("valid_")) {
if ("valid_min".equals(attribName)) {
validMinMax[0] = hdfAttribute.getNumericValue(0).doubleValue();
} else if ("valid_max".equals(attribName)) {
validMinMax[1] = hdfAttribute.getNumericValue(0).doubleValue();
} else if ("valid_range".equals(attribName)) {
validMinMax[0] = hdfAttribute.getNumericValue(0).doubleValue();
validMinMax[1] = hdfAttribute.getNumericValue(1).doubleValue();
}
}
}
if (validMinMax[0] != validMinMax[1]) {
double[] minmax = {0.0, 0.0};
minmax[0] = validMinMax[0];
minmax[1] = validMinMax[1];
if (band.getScalingFactor() != 1.0) {
minmax[0] *= band.getScalingFactor();
minmax[1] *= band.getScalingFactor();
}
if (band.getScalingOffset() != 0.0) {
minmax[0] += band.getScalingOffset();
minmax[1] += band.getScalingOffset();
}
String validExp = format("%s >= %.2f && %s <= %.2f", name, minmax[0], name, minmax[1]);
band.setValidPixelExpression(
validExp); // .format(name, validMinMax[0], name, validMinMax[1]));
}
}
} else if (variableRank == 4) {
final int[] dimensions = variable.getShape();
final int height = dimensions[2];
final int width = dimensions[3];
if (height == sceneRasterHeight && width == sceneRasterWidth) {
String name = variable.getShortName();
final int dataType = getProductDataType(variable);
final Band band = new Band(name, dataType, width, height);
// band = new Band(name, dataType, width, height);
Variable sliced = null;
try {
sliced = variable.slice(0, 0).slice(0, 0);
} catch (InvalidRangeException e) {
e.printStackTrace(); // Todo change body of catch statement.
}
bandToVariableMap.put(band, sliced);
product.addBand(band);
try {
Attribute fillvalue = variable.findAttribute("_FillValue");
if (fillvalue != null) {
band.setNoDataValue((double) fillvalue.getNumericValue().floatValue());
band.setNoDataValueUsed(true);
}
} catch (Exception ignored) {
}
// Set units, if defined
try {
band.setUnit(getStringAttribute("units"));
} catch (Exception ignored) {
}
final List<Attribute> list = variable.getAttributes();
for (Attribute hdfAttribute : list) {
final String attribName = hdfAttribute.getShortName();
if ("scale_factor".equals(attribName)) {
band.setScalingFactor(hdfAttribute.getNumericValue(0).doubleValue());
} else if ("add_offset".equals(attribName)) {
band.setScalingOffset(hdfAttribute.getNumericValue(0).doubleValue());
}
}
}
}
}
return bandToVariableMap;
}
/**
* Writes the systems byte order to the out stream. In java only high byte first.
*
* @param out the stream to write to
* @param rasterDataNode
*/
private static void writeMapProjectionInfo(PrintWriter out, RasterDataNode rasterDataNode) {
Product product = rasterDataNode.getProduct();
if (product == null) {
return;
}
String mapProjectionName = "Arbitrary";
String mapUnits = "Meters";
double referencePixelX = 0, referencePixelY = 0;
double easting = 0, northing = 0;
double pixelSizeX = 0, pixelSizeY = 0;
String datumName = "";
int utmZone = -1;
String utmHemisphere = "";
MapProjection mapProjection = null;
if (product.getGeoCoding() instanceof CrsGeoCoding) {
final CrsGeoCoding crsGeoCoding = (CrsGeoCoding) product.getGeoCoding();
final CoordinateReferenceSystem crs = crsGeoCoding.getMapCRS();
final ImageGeometry imgGeom =
ImageGeometry.createTargetGeometry(
product, crs, null, null, null, null, null, null, null, null, null);
final String crsName = crs.getName().toString().toUpperCase();
if (crsName.equals("WGS84(DD)")) {
mapProjectionName = "Geographic Lat/Lon";
mapUnits = "Degrees";
} else if (crsName.contains("UTM")) {
mapProjectionName = "UTM";
String zoneStr = crsName.substring(crsName.indexOf("ZONE") + 5, crsName.length()).trim();
int i = 0;
String zoneNumStr = "";
while (Character.isDigit(zoneStr.charAt(i))) {
zoneNumStr += zoneStr.charAt(i++);
}
utmZone = Integer.parseInt(zoneNumStr);
GeoPos centrePos =
crsGeoCoding.getGeoPos(
new PixelPos(product.getSceneRasterWidth() / 2, product.getSceneRasterHeight() / 2),
null);
utmHemisphere = centrePos.getLat() > 0 ? "North" : "South";
}
referencePixelX = imgGeom.getReferencePixelX();
referencePixelY = imgGeom.getReferencePixelY();
easting = imgGeom.getEasting();
northing = imgGeom.getNorthing();
pixelSizeX = imgGeom.getPixelSizeX();
pixelSizeY = imgGeom.getPixelSizeY();
datumName = crsGeoCoding.getDatum().getName();
} else if (product.getGeoCoding() instanceof MapGeoCoding) {
final MapGeoCoding mapGeoCoding = (MapGeoCoding) product.getGeoCoding();
final MapInfo info = mapGeoCoding.getMapInfo();
if (info == null) {
return;
}
mapProjection = info.getMapProjection();
if (mapProjection instanceof UTMProjection) {
mapProjectionName = "UTM";
final UTMProjection utmProjection = (UTMProjection) mapProjection;
utmZone = utmProjection.getZone();
utmHemisphere = utmProjection.isNorth() ? "North" : "South";
} else if (mapProjection.isPreDefined()) {
mapProjectionName = mapProjection.getName();
}
if ("meter".equals(mapProjection.getMapUnit())) {
mapUnits = "Meters";
} else if ("degree".equals(mapProjection.getMapUnit())) {
mapUnits = "Degrees";
} else {
mapUnits = mapProjection.getMapUnit();
}
datumName = mapGeoCoding.getDatum().getName();
} else {
return;
}
out.print(_enviMapInfo);
out.print(" = {");
out.print(mapProjectionName);
out.print(",");
out.print(referencePixelX + 1.0f);
out.print(",");
out.print(referencePixelY + 1.0f);
out.print(",");
out.print(easting);
out.print(",");
out.print(northing);
out.print(",");
out.print(pixelSizeX);
out.print(",");
out.print(pixelSizeY);
out.print(",");
if (utmZone != -1) {
out.print(utmZone);
out.print(",");
out.print(utmHemisphere);
out.print(",");
}
out.print(datumName);
out.print(",");
out.print("units=" + mapUnits);
out.print("}");
out.println();
if (mapProjection != null && !mapProjection.isPreDefined()) {
final MapTransform mapTransform = mapProjection.getMapTransform();
final double[] parameterValues = mapTransform.getParameterValues();
final String transformName = mapTransform.getDescriptor().getName();
out.print(_enviProjectionInfo);
out.print(" = {");
if (transformName.equals(TransverseMercatorDescriptor.NAME)) {
out.print(3);
out.print(",");
out.print(parameterValues[0]); // semi_major (meters)
out.print(",");
out.print(parameterValues[1]); // semi_minor (meters)
out.print(",");
out.print(parameterValues[2]); // latitude_of_origin (degree)
out.print(",");
out.print(parameterValues[3]); // central_meridian (degree)
out.print(",");
out.print(parameterValues[5]); // false_easting (meters)
out.print(",");
out.print(parameterValues[6]); // false_northing (meters)
out.print(",");
out.print(parameterValues[4]); // scaling_factor (no unit)
out.print(",");
} else if (transformName.equals(LambertConformalConicDescriptor.NAME)) {
out.print(4);
out.print(",");
out.print(parameterValues[0]); // semi_major (meters)
out.print(",");
out.print(parameterValues[1]); // semi_minor (meters)
out.print(",");
out.print(parameterValues[2]); // latitude_of_origin (degree)
out.print(",");
out.print(parameterValues[3]); // central_meridian (degree)
out.print(",");
out.print(0.0); // false_easting (meters)
out.print(",");
out.print(0.0); // false_northing (meters)
out.print(",");
out.print(parameterValues[4]); // latitude_of_intersection_1 (meters)
out.print(",");
out.print(parameterValues[5]); // latitude_of_intersection_2 (meters)
out.print(",");
}
out.print(mapProjectionName);
out.print(",");
out.print("units=" + mapUnits);
out.print("}");
out.println();
}
}
private static void updateMetadata(
final Product sourceProduct, final Product targetProduct, ProductSubsetDef subsetDef)
throws IOException {
try {
final MetadataElement root = targetProduct.getMetadataRoot();
if (root == null) return;
final MetadataElement absRoot = root.getElement("Abstracted_Metadata");
if (absRoot == null) return;
boolean nearRangeOnLeft = isNearRangeOnLeft(targetProduct);
final MetadataAttribute firstLineTime = absRoot.getAttribute("first_line_time");
if (firstLineTime != null) {
final ProductData.UTC startTime = targetProduct.getStartTime();
if (startTime != null) firstLineTime.getData().setElems(startTime.getArray());
}
final MetadataAttribute lastLineTime = absRoot.getAttribute("last_line_time");
if (lastLineTime != null) {
final ProductData.UTC endTime = targetProduct.getEndTime();
if (endTime != null) lastLineTime.getData().setElems(endTime.getArray());
}
final MetadataAttribute totalSize = absRoot.getAttribute("total_size");
if (totalSize != null) totalSize.getData().setElemUInt(targetProduct.getRawStorageSize());
if (nearRangeOnLeft) {
setLatLongMetadata(targetProduct, absRoot, "first_near_lat", "first_near_long", 0.5f, 0.5f);
setLatLongMetadata(
targetProduct,
absRoot,
"first_far_lat",
"first_far_long",
targetProduct.getSceneRasterWidth() - 1 + 0.5f,
0.5f);
setLatLongMetadata(
targetProduct,
absRoot,
"last_near_lat",
"last_near_long",
0.5f,
targetProduct.getSceneRasterHeight() - 1 + 0.5f);
setLatLongMetadata(
targetProduct,
absRoot,
"last_far_lat",
"last_far_long",
targetProduct.getSceneRasterWidth() - 1 + 0.5f,
targetProduct.getSceneRasterHeight() - 1 + 0.5f);
} else {
setLatLongMetadata(
targetProduct,
absRoot,
"first_near_lat",
"first_near_long",
targetProduct.getSceneRasterWidth() - 1 + 0.5f,
0.5f);
setLatLongMetadata(targetProduct, absRoot, "first_far_lat", "first_far_long", 0.5f, 0.5f);
setLatLongMetadata(
targetProduct,
absRoot,
"last_near_lat",
"last_near_long",
targetProduct.getSceneRasterWidth() - 1 + 0.5f,
targetProduct.getSceneRasterHeight() - 1 + 0.5f);
setLatLongMetadata(
targetProduct,
absRoot,
"last_far_lat",
"last_far_long",
0.5f,
targetProduct.getSceneRasterHeight() - 1 + 0.5f);
}
final MetadataAttribute height = absRoot.getAttribute("num_output_lines");
if (height != null) height.getData().setElemUInt(targetProduct.getSceneRasterHeight());
final MetadataAttribute width = absRoot.getAttribute("num_samples_per_line");
if (width != null) width.getData().setElemUInt(targetProduct.getSceneRasterWidth());
final MetadataAttribute offsetX = absRoot.getAttribute("subset_offset_x");
if (offsetX != null && subsetDef.getRegion() != null)
offsetX.getData().setElemUInt(subsetDef.getRegion().x);
final MetadataAttribute offsetY = absRoot.getAttribute("subset_offset_y");
if (offsetY != null && subsetDef.getRegion() != null)
offsetY.getData().setElemUInt(subsetDef.getRegion().y);
final MetadataAttribute slantRange = absRoot.getAttribute("slant_range_to_first_pixel");
if (slantRange != null) {
final TiePointGrid srTPG = targetProduct.getTiePointGrid("slant_range_time");
if (srTPG != null) {
final double slantRangeTime;
if (nearRangeOnLeft) {
slantRangeTime = srTPG.getPixelDouble(0, 0) / 1000000000.0; // ns to s
} else {
slantRangeTime =
srTPG.getPixelDouble(targetProduct.getSceneRasterWidth() - 1, 0)
/ 1000000000.0; // ns to s
}
final double halfLightSpeed = 299792458.0 / 2.0;
final double slantRangeDist = slantRangeTime * halfLightSpeed;
slantRange.getData().setElemDouble(slantRangeDist);
}
}
setSubsetSRGRCoefficients(sourceProduct, targetProduct, subsetDef, absRoot, nearRangeOnLeft);
} catch (Exception e) {
throw new IOException(e);
}
}
protected void addFlagsAndMasks(Product product) {
Band QFBand = product.getBand("l2_flags");
if (QFBand != null) {
FlagCoding flagCoding = new FlagCoding("L2Flags");
flagCoding.addFlag("ATMFAIL", 0x01, "Atmospheric correction failure");
flagCoding.addFlag("LAND", 0x02, "Land");
flagCoding.addFlag("PRODWARN", 0x04, "One (or more) product algorithms generated a warning");
flagCoding.addFlag("HIGLINT", 0x08, "High glint determined");
flagCoding.addFlag("HILT", 0x10, "High (or saturating) TOA radiance");
flagCoding.addFlag("HISATZEN", 0x20, "Large satellite zenith angle");
flagCoding.addFlag("COASTZ", 0x40, "Shallow water (<30m)");
flagCoding.addFlag("SPARE8", 0x80, "Unused");
flagCoding.addFlag("STRAYLIGHT", 0x100, "Straylight determined");
flagCoding.addFlag("CLDICE", 0x200, "Cloud/Ice determined");
flagCoding.addFlag("COCCOLITH", 0x400, "Coccolithophores detected");
flagCoding.addFlag("TURBIDW", 0x800, "Turbid water determined");
flagCoding.addFlag("HISOLZEN", 0x1000, "High solar zenith angle");
flagCoding.addFlag("SPARE14", 0x2000, "Unused");
flagCoding.addFlag("LOWLW", 0x4000, "Low Lw @ 555nm (possible cloud shadow)");
flagCoding.addFlag("CHLFAIL", 0x8000, "Chlorophyll algorithm failure");
flagCoding.addFlag("NAVWARN", 0x10000, "Navigation suspect");
flagCoding.addFlag("ABSAER", 0x20000, "Absorbing Aerosols determined");
flagCoding.addFlag("SPARE19", 0x40000, "Unused");
flagCoding.addFlag("MAXAERITER", 0x80000, "Maximum iterations reached for NIR iteration");
flagCoding.addFlag("MODGLINT", 0x100000, "Moderate glint determined");
flagCoding.addFlag("CHLWARN", 0x200000, "Chlorophyll out-of-bounds (<0.01 or >100 mg m^-3)");
flagCoding.addFlag(
"ATMWARN", 0x400000, "Atmospheric correction warning; Epsilon out-of-bounds");
flagCoding.addFlag("SPARE24", 0x800000, "Unused");
flagCoding.addFlag("SEAICE", 0x1000000, "Sea ice determined");
flagCoding.addFlag("NAVFAIL", 0x2000000, "Navigation failure");
flagCoding.addFlag("FILTER", 0x4000000, "Insufficient data for smoothing filter");
flagCoding.addFlag("SSTWARN", 0x8000000, "Sea surface temperature suspect");
flagCoding.addFlag("SSTFAIL", 0x10000000, "Sea surface temperature algorithm failure");
flagCoding.addFlag("HIPOL", 0x20000000, "High degree of polariztion determined");
flagCoding.addFlag(
"PRODFAIL", 0x40000000, "One (or more) product algorithms produced a failure");
flagCoding.addFlag("SPARE32", 0x80000000, "Unused");
product.getFlagCodingGroup().add(flagCoding);
QFBand.setSampleCoding(flagCoding);
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"ATMFAIL",
"Atmospheric correction failure",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.ATMFAIL",
FailRed,
0.0));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"LAND",
"Land",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.LAND",
LandBrown,
0.0));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"PRODWARN",
"One (or more) product algorithms generated a warning",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.PRODWARN",
DeepBlue,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"HILT",
"High (or saturating) TOA radiance",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.HILT",
Color.GRAY,
0.2));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"HIGLINT",
"High glint determined",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.HIGLINT",
BrightPink,
0.2));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"HISATZEN",
"Large satellite zenith angle",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.HISATZEN",
LightCyan,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"COASTZ",
"Shallow water (<30m)",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.COASTZ",
BurntUmber,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"STRAYLIGHT",
"Straylight determined",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.STRAYLIGHT",
Color.YELLOW,
0.2));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"CLDICE",
"Cloud/Ice determined",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.CLDICE",
Color.WHITE,
0.0));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"COCCOLITH",
"Coccolithophores detected",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.COCCOLITH",
Color.CYAN,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"TURBIDW",
"Turbid water determined",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.TURBIDW",
LightBrown,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"HISOLZEN",
"High solar zenith angle",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.HISOLZEN",
Purple,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"LOWLW",
"Low Lw @ 555nm (possible cloud shadow)",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.LOWLW",
Cornflower,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"CHLFAIL",
"Chlorophyll algorithm failure",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.CHLFAIL",
FailRed,
0.0));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"NAVWARN",
"Navigation suspect",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.NAVWARN",
Color.MAGENTA,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"ABSAER",
"Absorbing Aerosols determined",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.ABSAER",
Color.ORANGE,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"MAXAERITER",
"Maximum iterations reached for NIR correction",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.MAXAERITER",
MediumGray,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"MODGLINT",
"Moderate glint determined",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.MODGLINT",
LightPurple,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"CHLWARN",
"Chlorophyll out-of-bounds (<0.01 or >100 mg m^-3)",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.CHLWARN",
Color.LIGHT_GRAY,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"ATMWARN",
"Atmospheric correction warning; Epsilon out-of-bounds",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.ATMWARN",
Color.MAGENTA,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"SEAICE",
"Sea ice determined",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.SEAICE",
Color.DARK_GRAY,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"NAVFAIL",
"Navigation failure",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.NAVFAIL",
FailRed,
0.0));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"FILTER",
"Insufficient data for smoothing filter",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.FILTER",
Color.LIGHT_GRAY,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"SSTWARN",
"Sea surface temperature suspect",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.SSTWARN",
Color.MAGENTA,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"SSTFAIL",
"Sea surface temperature algorithm failure",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.SSTFAIL",
FailRed,
0.1));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"HIPOL",
"High degree of polariztion determined",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.HIPOL",
Color.PINK,
0.5));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"PRODFAIL",
"One (or more) product algorithms produced a failure",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"l2_flags.PRODFAIL",
FailRed,
0.1));
}
Band QFBandSST = product.getBand("qual_sst");
if (QFBandSST != null) {
// FlagCoding flagCoding = new FlagCoding("SSTFlags");
// product.getFlagCodingGroup().add(flagCoding);
//
// QFBandSST.setSampleCoding(flagCoding);
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Best",
"Highest quality SST retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst == 0",
SeadasFileReader.Cornflower,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Good",
"Good quality SST retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst == 1",
SeadasFileReader.LightPurple,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Questionable",
"Questionable quality SST retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst == 2",
SeadasFileReader.BurntUmber,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Bad",
"Bad quality SST retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst == 3",
SeadasFileReader.FailRed,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"No SST Retrieval",
"No SST retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst == 4",
SeadasFileReader.FailRed,
0.6));
}
Band QFBandSST4 = product.getBand("qual_sst4");
if (QFBandSST4 != null) {
// FlagCoding flagCoding = new FlagCoding("SST4Flags");
// product.getFlagCodingGroup().add(flagCoding);
// QFBandSST4.setSampleCoding(flagCoding);
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Best",
"Highest quality SST4 retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst4 == 0",
SeadasFileReader.Cornflower,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Good",
"Good quality SST4 retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst4 == 1",
SeadasFileReader.LightPurple,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Questionable",
"Questionable quality SST4 retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst4 == 2",
SeadasFileReader.BurntUmber,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"Bad",
"Bad quality SST4 retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst4 == 3",
SeadasFileReader.FailRed,
0.6));
product
.getMaskGroup()
.add(
Mask.BandMathsType.create(
"No SST Retrieval",
"No SST retrieval",
product.getSceneRasterWidth(),
product.getSceneRasterHeight(),
"qual_sst4 == 4",
SeadasFileReader.FailRed,
0.6));
}
}
private void getSourceImageDimension() {
sourceImageWidth = sourceProduct.getSceneRasterWidth();
sourceImageHeight = sourceProduct.getSceneRasterHeight();
}
public void initialize() throws OperatorException {
// System.out.println("starting...");
if (new File(SynergyConstants.SYNERGY_AUXDATA_HOME_DEFAULT).exists()) {
auxdataPath =
SynergyConstants.SYNERGY_AUXDATA_HOME_DEFAULT
+ File.separator
+ "aerosolLUTs"
+ File.separator
+ "ocean";
} else {
// try this one (in case of calvalus processing)
auxdataPath = SynergyConstants.SYNERGY_AUXDATA_CALVALUS_DEFAULT;
}
noDataVal = (float) SynergyConstants.OUTPUT_AOT_BAND_NODATAVALUE;
// get the glint product...
Map<String, Product> glintInput = new HashMap<String, Product>(3);
glintInput.put("l1bSynergy", synergyProduct);
Map<String, Object> glintAveParams = new HashMap<String, Object>(2);
glintAveParams.put("aveBlock", aveBlock);
glintProduct =
GPF.createProduct(
OperatorSpi.getOperatorAlias(GlintAveOp.class), glintAveParams, glintInput);
scalingFactor = aveBlock;
aveBlock /= 2;
minNAve = (int) (scalingFactor * scalingFactor - 1);
noDataVal = (float) SynergyConstants.OUTPUT_AOT_BAND_NODATAVALUE;
createTargetProduct();
// targetProduct = glintProduct; // test
// correction of azimuth discontinuity:
// set up tiles for MERIS and AATSR which cover the whole scene...
final int sceneWidth = synergyProduct.getSceneRasterWidth();
final int sceneHeight = synergyProduct.getSceneRasterHeight();
final Rectangle rect = new Rectangle(0, 0, sceneWidth, sceneHeight);
vaMerisTileComplete = getSourceTile(synergyProduct.getTiePointGrid("view_azimuth"), rect);
vaAatsrNadirTileComplete =
getSourceTile(
synergyProduct.getBand(
"view_azimuth_nadir" + "_" + SynergyConstants.INPUT_BANDS_SUFFIX_AATSR + ""),
rect);
aot550Result = new float[sceneWidth][sceneHeight];
angResult = new float[sceneWidth][sceneHeight];
aot550ErrorResult = new float[sceneWidth][sceneHeight];
angErrorResult = new float[sceneWidth][sceneHeight];
glintResult = new float[sceneWidth][sceneHeight];
wsResult = new float[sceneWidth][sceneHeight];
// read aerosol class table
try {
aerosolClassTable = AerosolAuxData.getInstance().createAerosolClassTable();
} catch (IOException e) {
throw new OperatorException("Failed to read aerosol class table:\n" + e.getMessage(), e);
}
// read aerosol models
try {
aerosolModelTable = AerosolAuxData.getInstance().createAerosolModelTable(auxdataPath);
} catch (IOException e) {
throw new OperatorException("Failed to read aerosol class table:\n" + e.getMessage(), e);
}
// wvl=[ 865, 885,1610, 885,1610, 885]
wvl = new float[] {865.0f, 885.0f, 1610.0f, 885.0f, 1610.0f, 885.0f};
wvlWeight = new float[] {1.0f, 1.0f, 3.0f, 1.0f, 3.0f, 3.0f};
wvlIndex = new int[] {0, 3, 5};
// at this point, just use 1 MERIS and 1 AATSR channel...
// todo: clarify with RP which we should finally use
// find model indices belonging to aerosol classes...
final List<Integer> modelIndices = aerosolModelTable.getMaritimeAndDesertIndices();
nMod = modelIndices.size();
nWvl = wvlIndex.length;
try {
aerosolLookupTables =
AerosolAuxData.getInstance()
.createAerosolOceanLookupTables(
auxdataPath, modelIndices,
wvl, wvlIndex);
} catch (IOException e) {
throw new OperatorException("Failed to create aerosol lookup tables:\n" + e.getMessage(), e);
// String msg = SynergyConstants.AUXDATA_ERROR_MESSAGE;
// SynergyUtils.logErrorMessage(msg);
}
nTauLut = aerosolLookupTables[0][0].getDimensions()[4].getSequence().length;
interpol5DResultLow = new double[nMod][nWvl][nTauLut];
interpol5DResultHigh = new double[nMod][nWvl][nTau];
interpolAngResult = new float[nWvl][nTau][nAng];
costFunction = new float[nWvl][nTau][nAng];
vectorTauLut = new double[nTauLut];
for (int i = 0; i < nTauLut; i++) {
vectorTauLut[i] = i * 2.0 / (nTauLut - 1);
}
vectorTauLutHigh = new double[nTau];
for (int i = 0; i < nTau; i++) {
vectorTauLutHigh[i] = i * 2.0 / (nTau - 1);
}
final float[] angArray = aerosolModelTable.getAngArray(modelIndices, 0);
angstroemParameters = AerosolHelpers.getInstance().getAngstroemParameters(angArray, nAng);
// read corresponding small LUTs and make a big LUT...
// correct azimuths in these tiles for later usage...
GlintPreparation.correctViewAzimuthLinear(vaMerisTileComplete, rect);
GlintPreparation.correctViewAzimuthLinear(vaAatsrNadirTileComplete, rect);
}
