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 static void setSubsetSRGRCoefficients(
final Product sourceProduct,
final Product targetProduct,
final ProductSubsetDef subsetDef,
final MetadataElement absRoot,
final boolean nearRangeOnLeft) {
final MetadataElement SRGRCoefficientsElem = absRoot.getElement("SRGR_Coefficients");
if (SRGRCoefficientsElem != null) {
final double rangeSpacing = absRoot.getAttributeDouble("RANGE_SPACING", 0);
final double colIndex = subsetDef.getRegion() == null ? 0 : subsetDef.getRegion().getX();
for (MetadataElement srgrList : SRGRCoefficientsElem.getElements()) {
final double grO = srgrList.getAttributeDouble("ground_range_origin", 0);
double ground_range_origin_subset;
if (nearRangeOnLeft) {
ground_range_origin_subset = grO + colIndex * rangeSpacing;
} else {
final double colIndexFromRight =
sourceProduct.getSceneRasterWidth() - colIndex - targetProduct.getSceneRasterWidth();
ground_range_origin_subset = grO + colIndexFromRight * rangeSpacing;
}
srgrList.setAttributeDouble("ground_range_origin", ground_range_origin_subset);
}
}
}
private static boolean isNearRangeOnLeft(final Product product) {
final TiePointGrid incidenceAngle = product.getTiePointGrid("incident_angle");
if (incidenceAngle != null) {
final double incidenceAngleToFirstPixel = incidenceAngle.getPixelDouble(0, 0);
final double incidenceAngleToLastPixel =
incidenceAngle.getPixelDouble(product.getSceneRasterWidth() - 1, 0);
return (incidenceAngleToFirstPixel < incidenceAngleToLastPixel);
} else {
return true;
}
}
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;
}
@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;
}
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 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);
}
}
