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;
}
@Override
void setInvalidPixelExpression(Band band) {
if (band.isFlagBand()) {
band.setNoDataValueUsed(false);
} else {
band.setNoDataValueUsed(true);
band.setNoDataValue(-2);
}
}
@Override
public Band addBand(String name, String expression, double noDataValue) {
Band band = addBand(name, expression);
band.setNoDataValue(noDataValue);
band.setNoDataValueUsed(true);
return band;
}
@Override
public Band addBand(String name, int dataType, double noDataValue) {
Band band = addBand(name, dataType);
band.setNoDataValue(noDataValue);
band.setNoDataValueUsed(true);
return band;
}
private void setTargetBands() {
Band aot550Band =
targetProduct.addBand(SynergyConstants.OUTPUT_AOT_BAND_NAME, ProductData.TYPE_FLOAT32);
aot550Band.setNoDataValue(SynergyConstants.OUTPUT_AOT_BAND_NODATAVALUE);
aot550Band.setNoDataValueUsed(SynergyConstants.OUTPUT_AOT_BAND_NODATAVALUE_USED);
aot550Band.setUnit("dl");
Band aot550ErrBand =
targetProduct.addBand(SynergyConstants.OUTPUT_AOTERR_BAND_NAME, ProductData.TYPE_FLOAT32);
aot550ErrBand.setNoDataValue(SynergyConstants.OUTPUT_AOT_BAND_NODATAVALUE);
aot550ErrBand.setNoDataValueUsed(SynergyConstants.OUTPUT_AOT_BAND_NODATAVALUE_USED);
aot550ErrBand.setUnit("dl");
if (!computeLand) {
// write more bands specific for ocean retrieval
Band angBand =
targetProduct.addBand(SynergyConstants.OUTPUT_ANG_BAND_NAME, ProductData.TYPE_FLOAT32);
angBand.setNoDataValue(SynergyConstants.OUTPUT_ANG_BAND_NODATAVALUE);
angBand.setNoDataValueUsed(SynergyConstants.OUTPUT_ANG_BAND_NODATAVALUE_USED);
Band angErrBand =
targetProduct.addBand(SynergyConstants.OUTPUT_ANGERR_BAND_NAME, ProductData.TYPE_FLOAT32);
angErrBand.setNoDataValue(SynergyConstants.OUTPUT_ANG_BAND_NODATAVALUE);
angErrBand.setNoDataValueUsed(SynergyConstants.OUTPUT_ANG_BAND_NODATAVALUE_USED);
}
}
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;
}
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;
}
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));
}
}
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;
}
protected void addBandsToProduct(Product product) {
Debug.assertNotNull(getSourceProduct());
Debug.assertNotNull(product);
for (int i = 0; i < getSourceProduct().getNumBands(); i++) {
Band sourceBand = getSourceProduct().getBandAt(i);
String bandName = sourceBand.getName();
if (isNodeAccepted(bandName)) {
Band destBand;
boolean treatVirtualBandsAsRealBands = false;
if (getSubsetDef() != null && getSubsetDef().getTreatVirtualBandsAsRealBands()) {
treatVirtualBandsAsRealBands = true;
}
// @todo 1 se/se - extract copy of a band or virtual band to create deep clone of band and
// virtual band
if (!treatVirtualBandsAsRealBands && sourceBand instanceof VirtualBand) {
VirtualBand virtualSource = (VirtualBand) sourceBand;
destBand =
new VirtualBand(
bandName,
sourceBand.getDataType(),
getSceneRasterWidth(),
getSceneRasterHeight(),
virtualSource.getExpression());
} else {
destBand =
new Band(
bandName,
sourceBand.getDataType(),
getSceneRasterWidth(),
getSceneRasterHeight());
}
if (sourceBand.getUnit() != null) {
destBand.setUnit(sourceBand.getUnit());
}
if (sourceBand.getDescription() != null) {
destBand.setDescription(sourceBand.getDescription());
}
destBand.setScalingFactor(sourceBand.getScalingFactor());
destBand.setScalingOffset(sourceBand.getScalingOffset());
destBand.setLog10Scaled(sourceBand.isLog10Scaled());
destBand.setSpectralBandIndex(sourceBand.getSpectralBandIndex());
destBand.setSpectralWavelength(sourceBand.getSpectralWavelength());
destBand.setSpectralBandwidth(sourceBand.getSpectralBandwidth());
destBand.setSolarFlux(sourceBand.getSolarFlux());
if (sourceBand.isNoDataValueSet()) {
destBand.setNoDataValue(sourceBand.getNoDataValue());
}
destBand.setNoDataValueUsed(sourceBand.isNoDataValueUsed());
destBand.setValidPixelExpression(sourceBand.getValidPixelExpression());
FlagCoding sourceFlagCoding = sourceBand.getFlagCoding();
IndexCoding sourceIndexCoding = sourceBand.getIndexCoding();
if (sourceFlagCoding != null) {
String flagCodingName = sourceFlagCoding.getName();
FlagCoding destFlagCoding = product.getFlagCodingGroup().get(flagCodingName);
Debug.assertNotNull(
destFlagCoding); // should not happen because flag codings should be already in
// product
destBand.setSampleCoding(destFlagCoding);
} else if (sourceIndexCoding != null) {
String indexCodingName = sourceIndexCoding.getName();
IndexCoding destIndexCoding = product.getIndexCodingGroup().get(indexCodingName);
Debug.assertNotNull(
destIndexCoding); // should not happen because index codings should be already in
// product
destBand.setSampleCoding(destIndexCoding);
} else {
destBand.setSampleCoding(null);
}
if (isFullScene(getSubsetDef()) && sourceBand.isStxSet()) {
copyStx(sourceBand, destBand);
}
product.addBand(destBand);
bandMap.put(destBand, sourceBand);
}
}
for (final Map.Entry<Band, RasterDataNode> entry : bandMap.entrySet()) {
copyImageInfo(entry.getValue(), entry.getKey());
}
}
@Override
public void initialize() throws OperatorException {
if (category == DataCategory.NDVI_MAXCOMPOSIT_NEW) {
Arrays.sort(sourceProducts, new ProductNameComparator());
sortedDataSourceProducts = sourceProducts;
} else {
final String sourceDataProductFilter = "_data";
final String sourceFlagProductFilter = "_flag";
sortedDataSourceProducts =
DiversityAuxdataUtils.sortProductsByMonth(sourceProducts, sourceDataProductFilter, 2, 7);
sortedFlagSourceProducts =
DiversityAuxdataUtils.sortProductsByMonth(sourceProducts, sourceFlagProductFilter, 2, 7);
}
final Product yearlyNdviProduct = createYearlyProduct();
if (writeFlags) {
final FlagCoding ndviFlagCoding = DiversityAuxdataUtils.createNdviFlagCoding();
yearlyNdviProduct.getFlagCodingGroup().add(ndviFlagCoding);
TARGET_BAND_PREFIX += "flag_";
DiversityAuxdataUtils.addPatternToAutoGrouping(yearlyNdviProduct, "ndvi_max_flag");
} else {
DiversityAuxdataUtils.addPatternToAutoGrouping(yearlyNdviProduct, "ndvi_max");
}
halfmonthlyDataProductsMap = new HashMap<String, List<Product>>();
halfmonthlyFlagProductsMap = new HashMap<String, List<Product>>();
for (int i = 0; i < Constants.MONTHS.length; i++) {
final String month = Constants.MONTHS[i];
List<Product> thisMonthDataProducts = new ArrayList<Product>();
List<Product> thisMonthFlagProducts = new ArrayList<Product>();
for (Product product : sortedDataSourceProducts) {
if (category == DataCategory.NDVI_MAXCOMPOSIT_NEW) {
if (product.getName().contains(String.format("_%02d_", i + 1))) {
thisMonthDataProducts.add(product);
}
} else {
if (product.getName().contains(month)) {
thisMonthDataProducts.add(product);
}
}
}
if (category == DataCategory.NDVI_MAXCOMPOSIT) {
for (Product product : sortedFlagSourceProducts) {
if (product.getName().contains(month)) {
thisMonthFlagProducts.add(product);
}
}
}
if (thisMonthDataProducts.size() == 2
&& (thisMonthFlagProducts.size() == 2 || category == DataCategory.NDVI_MAXCOMPOSIT_NEW)) {
// the normal case
halfmonthlyDataProductsMap.put(month, thisMonthDataProducts);
halfmonthlyFlagProductsMap.put(month, thisMonthFlagProducts);
Band targetBand =
new Band(TARGET_BAND_PREFIX + month, ProductData.TYPE_FLOAT32, width, height);
targetBand.setNoDataValue(Constants.NDVI_INVALID_VALUE);
targetBand.setNoDataValueUsed(true);
yearlyNdviProduct.addBand(targetBand);
} else {
System.err.println(
"Warning: NDVI products for '" + month + "' missing or incomplete - skipping.");
}
}
setTargetProduct(yearlyNdviProduct);
}