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 ProductNodeSubsetPane createBandSubsetPane() {
Band[] bands = product.getBands();
if (bands.length == 0) {
return null;
}
return new ProductNodeSubsetPane(product.getBands(), true);
}
/**
* Provides an implementation of the <code>readProductNodes</code> interface method. Clients
* implementing this method can be sure that the input object and eventually the subset
* information has already been set.
*
* <p>
*
* <p>This method is called as a last step in the <code>readProductNodes(input, subsetInfo)</code>
* method.
*
* @throws java.io.IOException if an I/O error occurs
*/
@Override
protected Product readProductNodesImpl() throws IOException {
Product product;
try {
final File fileFromInput = ReaderUtils.getFileFromInput(getInput());
dataDir = createDirectory(fileFromInput);
dataDir.readProductDirectory();
product = dataDir.createProduct();
addCalibrationLUT(product, fileFromInput.getParentFile());
product.getGcpGroup();
product.setFileLocation(fileFromInput);
product.setProductReader(this);
product.setModified(false);
final MetadataElement absRoot = AbstractMetadata.getAbstractedMetadata(product);
isAscending = absRoot.getAttributeString(AbstractMetadata.PASS).equals("ASCENDING");
isAntennaPointingRight =
absRoot.getAttributeString(AbstractMetadata.antenna_pointing).equals("right");
} catch (Exception e) {
Debug.trace(e.toString());
final IOException ioException = new IOException(e.getMessage());
ioException.initCause(e);
throw ioException;
}
return product;
}
private void addSubsetInfoMetadata(Product product) {
if (getSubsetDef() != null) {
ProductSubsetDef subsetDef = getSubsetDef();
Product sourceProduct = getSourceProduct();
String nameSubsetinfo = "SubsetInfo";
MetadataElement subsetElem = new MetadataElement(nameSubsetinfo);
addAttribString("SourceProduct.name", sourceProduct.getName(), subsetElem);
subsetElem.setAttributeInt("SubSampling.x", subsetDef.getSubSamplingX());
subsetElem.setAttributeInt("SubSampling.y", subsetDef.getSubSamplingY());
if (subsetDef.getRegion() != null) {
Rectangle region = subsetDef.getRegion();
subsetElem.setAttributeInt("SubRegion.x", region.x);
subsetElem.setAttributeInt("SubRegion.y", region.y);
subsetElem.setAttributeInt("SubRegion.width", region.width);
subsetElem.setAttributeInt("SubRegion.height", region.height);
}
String[] nodeNames = subsetDef.getNodeNames();
if (nodeNames != null) {
for (int i = 0; i < nodeNames.length; i++) {
addAttribString("ProductNodeName." + (i + 1), nodeNames[i], subsetElem);
}
}
ProductUtils.addElementToHistory(product, subsetElem);
}
}
@Override
public Product createProduct() throws IOException {
sceneHeight =
ncFile.getRootGroup().findGroup("Level-3_Binned_Data").findVariable("BinIndex").getShape(0);
sceneWidth = sceneHeight * 2;
grid = new ISINGrid(sceneHeight);
String productName = getStringAttribute("Product_Name");
Product product =
new Product(productName, "NASA-OBPG-L3", sceneWidth, sceneHeight, productReader);
product.setFileLocation(productReader.getInputFile());
product.setProductReader(productReader);
addGlobalMetadata(product);
final Variable idxVariable =
ncFile.getRootGroup().findGroup("Level-3_Binned_Data").findVariable("BinList");
List<Variable> l3ProdVars = ncFile.getVariables();
variableMap = addBands(product, idxVariable, l3ProdVars);
// try {
// addBandsBinMap(product);
// } catch (InvalidRangeException e) {
// e.printStackTrace();
// }
if (product.getNumBands() == 0) {
throw new ProductIOException("No bands found.");
}
initGeoCoding(product);
return product;
}
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 ProductNodeSubsetPane createTiePointGridSubsetPane() {
TiePointGrid[] tiePointGrids = product.getTiePointGrids();
if (tiePointGrids.length == 0) {
return null;
}
return new ProductNodeSubsetPane(
product.getTiePointGrids(),
new String[] {BeamConstants.LAT_DS_NAME, BeamConstants.LON_DS_NAME},
true);
}
private MetadataElement getMetadataElementSave(Product product, String name) {
final MetadataElement metadataElement = product.getMetadataRoot().getElement(name);
final MetadataElement namedElem;
if (metadataElement == null) {
namedElem = new MetadataElement(name);
product.getMetadataRoot().addElement(namedElem);
} else {
namedElem = metadataElement;
}
return namedElem;
}
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 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);
}
}
private static RasterDataNode[] getReferencedNodes(final RasterDataNode node) {
final Product product = node.getProduct();
if (product != null) {
final List<String> expressions = new ArrayList<String>(10);
if (node.getValidPixelExpression() != null) {
expressions.add(node.getValidPixelExpression());
}
final ProductNodeGroup<Mask> overlayMaskGroup = node.getOverlayMaskGroup();
if (overlayMaskGroup.getNodeCount() > 0) {
final Mask[] overlayMasks =
overlayMaskGroup.toArray(new Mask[overlayMaskGroup.getNodeCount()]);
for (final Mask overlayMask : overlayMasks) {
final String expression;
if (overlayMask.getImageType() == Mask.BandMathsType.INSTANCE) {
expression = Mask.BandMathsType.getExpression(overlayMask);
} else if (overlayMask.getImageType() == Mask.RangeType.INSTANCE) {
expression = Mask.RangeType.getExpression(overlayMask);
} else {
expression = null;
}
if (expression != null) {
expressions.add(expression);
}
}
}
if (node instanceof VirtualBand) {
final VirtualBand virtualBand = (VirtualBand) node;
expressions.add(virtualBand.getExpression());
}
final ArrayList<Term> termList = new ArrayList<Term>(10);
for (final String expression : expressions) {
try {
final Term term = product.parseExpression(expression);
if (term != null) {
termList.add(term);
}
} catch (ParseException e) {
// @todo se handle parse exception
Debug.trace(e);
}
}
final Term[] terms = termList.toArray(new Term[termList.size()]);
final RasterDataSymbol[] refRasterDataSymbols = BandArithmetic.getRefRasterDataSymbols(terms);
return BandArithmetic.getRefRasters(refRasterDataSymbols);
}
return new RasterDataNode[0];
}
public void addBandMetadata(Product product) throws ProductIOException {
Group group = ncFile.findGroup("Geophysical_Data");
if (productReader.getProductType() == SeadasProductReader.ProductType.Level2_Aquarius) {
group = ncFile.findGroup("Aquarius_Data");
}
if (productReader.getProductType() == SeadasProductReader.ProductType.Level1B_HICO) {
group = ncFile.findGroup("products");
}
if (group != null) {
final MetadataElement bandAttributes = new MetadataElement("Band_Attributes");
List<Variable> variables = group.getVariables();
for (Variable variable : variables) {
final String name = variable.getShortName();
final MetadataElement sdsElement = new MetadataElement(name + ".attributes");
final int dataType = getProductDataType(variable);
final MetadataAttribute prodtypeattr = new MetadataAttribute("data_type", dataType);
sdsElement.addAttribute(prodtypeattr);
bandAttributes.addElement(sdsElement);
final List<Attribute> list = variable.getAttributes();
for (Attribute varAttribute : list) {
addAttributeToElement(sdsElement, varAttribute);
}
}
final MetadataElement metadataRoot = product.getMetadataRoot();
metadataRoot.addElement(bandAttributes);
}
}
public void addInputParamMetadata(Product product) throws ProductIOException {
Variable inputParams = ncFile.findVariable("Input_Parameters");
if (inputParams != null) {
final MetadataElement inputParamsMeta = new MetadataElement("Input_Parameters");
Array array;
try {
array = inputParams.read();
} catch (IOException e) {
throw new ProductIOException(e.getMessage());
}
String[] lines = array.toString().split("\n");
for (String line : lines) {
String[] parts = line.split("=");
if (parts.length == 2) {
final String name = parts[0].trim();
final String value = parts[1].trim();
final ProductData data = ProductData.createInstance(ProductData.TYPE_ASCII, value);
final MetadataAttribute attribute = new MetadataAttribute(name, data, true);
inputParamsMeta.addAttribute(attribute);
}
}
final MetadataElement metadataRoot = product.getMetadataRoot();
metadataRoot.addElement(inputParamsMeta);
}
}
public void addGlobalMetadata(Product product) {
final MetadataElement globalElement = new MetadataElement("Global_Attributes");
addAttributesToElement(globalAttributes, globalElement);
final MetadataElement metadataRoot = product.getMetadataRoot();
metadataRoot.addElement(globalElement);
}
protected void addTiePointGridsToProduct(final Product product) {
final GeoCoding geoCoding = getSourceProduct().getGeoCoding();
final String latGridName;
final String lonGridName;
if (geoCoding instanceof TiePointGeoCoding) {
final TiePointGeoCoding tiePointGeoCoding = (TiePointGeoCoding) geoCoding;
final TiePointGrid latGrid = tiePointGeoCoding.getLatGrid();
final TiePointGrid lonGrid = tiePointGeoCoding.getLonGrid();
latGridName = latGrid.getName();
lonGridName = lonGrid.getName();
} else {
latGridName = null;
lonGridName = null;
}
for (int i = 0; i < getSourceProduct().getNumTiePointGrids(); i++) {
final TiePointGrid sourceTiePointGrid = getSourceProduct().getTiePointGridAt(i);
final String gridName = sourceTiePointGrid.getName();
if (isNodeAccepted(gridName)
|| (gridName.equals(latGridName) || gridName.equals(lonGridName))) {
final TiePointGrid tiePointGrid =
TiePointGrid.createSubset(sourceTiePointGrid, getSubsetDef());
if (isFullScene(getSubsetDef()) && sourceTiePointGrid.isStxSet()) {
copyStx(sourceTiePointGrid, tiePointGrid);
}
product.addTiePointGrid(tiePointGrid);
copyImageInfo(sourceTiePointGrid, tiePointGrid);
}
}
}
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 initGeoCoding(Product product) throws IOException {
float pixelX = 0.0f;
float pixelY = 0.0f;
float easting = -180f;
float northing = +90f;
float pixelSizeX = 360.0f / sceneWidth;
float pixelSizeY = 180.0f / sceneHeight;
try {
product.setGeoCoding(
new CrsGeoCoding(
DefaultGeographicCRS.WGS84,
sceneWidth,
sceneHeight,
easting,
northing,
pixelSizeX,
pixelSizeY,
pixelX,
pixelY));
} catch (FactoryException e) {
throw new IOException(e);
} catch (TransformException e) {
throw new IOException(e);
}
}
private static void setLatLongMetadata(
final Product product,
final MetadataElement absRoot,
final String tagLat,
final String tagLon,
final float x,
final float y) {
final PixelPos pixelPos = new PixelPos(x, y);
final GeoPos geoPos = new GeoPos();
if (product.getGeoCoding() == null) return;
product.getGeoCoding().getGeoPos(pixelPos, geoPos);
final MetadataAttribute lat = absRoot.getAttribute(tagLat);
if (lat != null) lat.getData().setElemDouble(geoPos.getLat());
final MetadataAttribute lon = absRoot.getAttribute(tagLon);
if (lon != null) lon.getData().setElemDouble(geoPos.getLon());
}
protected void setSpectralBand(Product product) {
int spectralBandIndex = 0;
for (String name : product.getBandNames()) {
Band band = product.getBandAt(product.getBandIndex(name));
if (name.matches("\\w+_\\d{3,}")) {
String[] parts = name.split("_");
String wvlstr = parts[parts.length - 1].trim();
// Some bands have the wvl portion in the middle...
if (!wvlstr.matches("^\\d{3,}")) {
wvlstr = parts[parts.length - 2].trim();
}
final float wavelength = Float.parseFloat(wvlstr);
band.setSpectralWavelength(wavelength);
band.setSpectralBandIndex(spectralBandIndex++);
}
}
}
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 boolean checkFlagDatasetIncluded() {
final String[] nodeNames = productSubsetDef.getNodeNames();
final List<String> flagDsNameList = new ArrayList<String>(10);
boolean flagDsInSubset = false;
for (int i = 0; i < product.getNumBands(); i++) {
Band band = product.getBandAt(i);
if (band.getFlagCoding() != null) {
flagDsNameList.add(band.getName());
if (StringUtils.contains(nodeNames, band.getName())) {
flagDsInSubset = true;
}
break;
}
}
final int numFlagDs = flagDsNameList.size();
boolean ok = true;
if (numFlagDs > 0 && !flagDsInSubset) {
int status =
JOptionPane.showConfirmDialog(
getJDialog(),
"No flag dataset selected.\n\n"
+ "If you do not include a flag dataset in the subset,\n"
+ "you will not be able to create bitmask overlays.\n\n"
+ "Do you wish to include the available flag dataset(s)\n"
+ "in the current subset?\n",
"No Flag Dataset Selected",
JOptionPane.YES_NO_CANCEL_OPTION);
if (status == JOptionPane.YES_OPTION) {
productSubsetDef.addNodeNames(flagDsNameList.toArray(new String[numFlagDs]));
ok = true;
} else if (status == JOptionPane.NO_OPTION) {
/* OK, no flag datasets wanted */
ok = true;
} else if (status == JOptionPane.CANCEL_OPTION) {
ok = false;
}
}
return ok;
}
private Product createProduct() {
Product sourceProduct = getSourceProduct();
Debug.assertNotNull(sourceProduct);
Debug.assertTrue(getSceneRasterWidth() > 0);
Debug.assertTrue(getSceneRasterHeight() > 0);
final String newProductName;
if (this.newProductName == null || this.newProductName.length() == 0) {
newProductName = sourceProduct.getName();
} else {
newProductName = this.newProductName;
}
final Product product =
new Product(
newProductName,
sourceProduct.getProductType(),
getSceneRasterWidth(),
getSceneRasterHeight(),
this);
product.setPointingFactory(sourceProduct.getPointingFactory());
if (newProductDesc == null || newProductDesc.length() == 0) {
product.setDescription(sourceProduct.getDescription());
} else {
product.setDescription(newProductDesc);
}
if (!isMetadataIgnored()) {
ProductUtils.copyMetadata(sourceProduct, product);
addTiePointGridsToProduct(product);
addFlagCodingsToProduct(product);
addIndexCodingsToProduct(product);
}
addBandsToProduct(product);
if (!isMetadataIgnored()) {
addGeoCodingToProduct(product);
}
ProductUtils.copyVectorData(sourceProduct, product);
ProductUtils.copyMasks(sourceProduct, product);
ProductUtils.copyOverlayMasks(sourceProduct, product);
ProductUtils.copyPreferredTileSize(sourceProduct, product);
setSceneRasterStartAndStopTime(product);
addSubsetInfoMetadata(product);
return product;
}
private void updateMemDisplay() {
if (product != null) {
long storageMem = product.getRawStorageSize(productSubsetDef);
double factor = 1.0 / (1024 * 1024);
double megas = MathUtils.round(factor * storageMem, 10);
if (megas > memWarnLimit) {
memLabel.setForeground(MEM_LABEL_WARN_COLOR);
} else {
memLabel.setForeground(MEM_LABEL_NORM_COLOR);
}
memLabel.setText(MEM_LABEL_TEXT + megas + "M");
} else {
memLabel.setText(" ");
}
}
private boolean checkReferencedRastersIncluded() {
final Set<String> notIncludedNames = new TreeSet<String>();
final List<String> includedNodeNames = Arrays.asList(productSubsetDef.getNodeNames());
for (final String nodeName : includedNodeNames) {
final RasterDataNode rasterDataNode = product.getRasterDataNode(nodeName);
if (rasterDataNode != null) {
collectNotIncludedReferences(rasterDataNode, notIncludedNames);
}
}
boolean ok = true;
if (!notIncludedNames.isEmpty()) {
StringBuilder nameListText = new StringBuilder();
for (String notIncludedName : notIncludedNames) {
nameListText.append(" '").append(notIncludedName).append("'\n");
}
final String pattern =
"The following dataset(s) are referenced but not included\n"
+ "in your current subset definition:\n"
+ "{0}\n"
+ "If you do not include these dataset(s) into your selection,\n"
+ "you might get unexpected results while working with the\n"
+ "resulting product.\n\n"
+ "Do you wish to include the referenced dataset(s) into your\n"
+ "subset definition?\n"; /*I18N*/
final MessageFormat format = new MessageFormat(pattern);
int status =
JOptionPane.showConfirmDialog(
getJDialog(),
format.format(new Object[] {nameListText.toString()}),
"Incomplete Subset Definition", /*I18N*/
JOptionPane.YES_NO_CANCEL_OPTION);
if (status == JOptionPane.YES_OPTION) {
final String[] nodenames = notIncludedNames.toArray(new String[notIncludedNames.size()]);
productSubsetDef.addNodeNames(nodenames);
ok = true;
} else if (status == JOptionPane.NO_OPTION) {
ok = true;
} else if (status == JOptionPane.CANCEL_OPTION) {
ok = false;
}
}
return ok;
}
public void addSmiMetadata(final Product product) {
// Variable l3mvar = ncFile.findVariable("l3m_data");
final MetadataElement bandAttributes = new MetadataElement("Band_Attributes");
List<Variable> variables = ncFile.getVariables();
for (Variable variable : variables) {
final String name = variable.getShortName();
final MetadataElement sdsElement = new MetadataElement(name);
final int dataType = getProductDataType(variable);
final MetadataAttribute prodtypeattr = new MetadataAttribute("data_type", dataType);
sdsElement.addAttribute(prodtypeattr);
bandAttributes.addElement(sdsElement);
final List<Attribute> list = variable.getAttributes();
for (Attribute varAttribute : list) {
addAttributeToElement(sdsElement, varAttribute);
}
}
final MetadataElement metadataRoot = product.getMetadataRoot();
metadataRoot.addElement(bandAttributes);
}
private ProductNodeSubsetPane createAnnotationSubsetPane() {
final MetadataElement metadataRoot = product.getMetadataRoot();
final MetadataElement[] metadataElements = metadataRoot.getElements();
final String[] metaNodes;
if (metadataElements.length == 0) {
return null;
}
// metadata elements must be added to includeAlways list
// to ensure that they are selected if isIgnoreMetada is set to false
if (givenProductSubsetDef != null && !givenProductSubsetDef.isIgnoreMetadata()) {
metaNodes = new String[metadataElements.length];
for (int i = 0; i < metadataElements.length; i++) {
final MetadataElement metadataElement = metadataElements[i];
metaNodes[i] = metadataElement.getName();
}
} else {
metaNodes = new String[0];
}
final String[] includeNodes = StringUtils.addToArray(metaNodes, Product.HISTORY_ROOT_NAME);
return new ProductNodeSubsetPane(metadataElements, includeNodes, true);
}
// Don't do this...it hurts. Too much of a memory hog...
private void addBandsBinMap(Product product) throws IOException, InvalidRangeException {
String[] bandList = product.getBandNames();
if (rowInfo == null) {
rowInfo = createRowInfos();
}
final int height = sceneHeight;
final int width = sceneWidth;
final ISINGrid grid = this.grid;
// loop over lines
try {
int[] lineOffsets = new int[1];
int[] lineLengths = new int[1];
int[] stride = new int[1];
stride[0] = 1;
// for (int y = sourceOffsetY; y < sourceOffsetY + sourceHeight; y++) {
for (String name : bandList) {
if (name.endsWith("mean") || name.endsWith("stdev")) continue;
Band band = product.getBand(name);
ProductData buffer;
final Variable variable = variableMap.get(band);
DataType prodtype = variable.getDataType();
float[] fbuffer = new float[width * height];
short[] sbuffer = new short[width * height];
int[] ibuffer = new int[width * height];
byte[] bbuffer = new byte[width * height];
if (prodtype == DataType.FLOAT) {
Arrays.fill(fbuffer, Float.NaN);
buffer = ProductData.createInstance(fbuffer);
} else if (prodtype == DataType.SHORT) {
Arrays.fill(sbuffer, (short) -999);
buffer = ProductData.createInstance(sbuffer);
} else if (prodtype == DataType.BYTE) {
Arrays.fill(bbuffer, (byte) 255);
buffer = ProductData.createInstance(bbuffer);
} else {
Arrays.fill(ibuffer, -999);
buffer = ProductData.createInstance(ibuffer);
}
for (int y = 0; y < height; y++) {
final int rowIndex = (height - 1) - y;
final RowInfo rowInfo = this.rowInfo[rowIndex];
if (rowInfo != null) {
final Array bindata;
final int lineOffset = rowInfo.offset;
final int lineLength = rowInfo.length;
lineOffsets[0] = lineOffset;
lineLengths[0] = lineLength;
synchronized (ncFile) {
bindata =
variable
.read()
.section(lineOffsets, lineLengths, stride); // .copyTo1DJavaArray();
}
int lineIndex0 = 0;
for (int x = 0; x < width; x++) {
final double lon = x * 360.0 / width;
final int binIndex = grid.getBinIndex(rowIndex, lon);
int lineIndex = -1;
for (int i = lineIndex0; i < lineLength; i++) {
int binidx = bins[lineOffset + i];
if (binidx >= binIndex) {
if (binidx == binIndex) {
lineIndex = i;
}
lineIndex0 = i;
break;
}
}
if (lineIndex >= 0) {
final int rasterIndex = width * y + x;
final Array elem;
elem = Array.factory(bindata.copyTo1DJavaArray());
for (int i = 0; i < elem.getSize(); i++) {
if (prodtype == DataType.FLOAT) {
buffer.setElemFloatAt(rasterIndex, elem.getFloat(i));
} else {
buffer.setElemIntAt(rasterIndex, elem.getInt(i));
}
// System.arraycopy(bindata, lineIndex, buffer,
// rasterIndex, 1);
}
}
}
}
}
band.setDataElems(buffer);
}
} catch (IOException e) {
throw new IOException("Could not map product " + product.getName(), e);
}
}
@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));
}
}
@Override
public Product createProduct() throws ProductIOException {
int[] dims;
int sceneHeight = 0;
int sceneWidth = 0;
Group geodata = ncFile.findGroup("geophysical_data");
if (productReader.getProductType() == SeadasProductReader.ProductType.OISST) {
dims = ncFile.getVariables().get(4).getShape();
sceneHeight = dims[2];
sceneWidth = dims[3];
mustFlipY = true;
} else if (productReader.getProductType() == SeadasProductReader.ProductType.ANCCLIM) {
List<Variable> vars = ncFile.getVariables();
for (Variable v : vars) {
if (v.getRank() == 2) {
dims = v.getShape();
sceneHeight = dims[0];
sceneWidth = dims[1];
}
}
} else {
if (geodata != null) {
dims = geodata.getVariables().get(0).getShape();
sceneHeight = dims[0];
sceneWidth = dims[1];
} else {
ucar.nc2.Dimension latdim = ncFile.findDimension("lat");
ucar.nc2.Dimension londim = ncFile.findDimension("lon");
if (latdim != null) {
sceneHeight = latdim.getLength();
sceneWidth = londim.getLength();
} else {
dims = ncFile.getVariables().get(0).getShape();
sceneHeight = dims[0];
sceneWidth = dims[1];
}
}
}
String productName = productReader.getInputFile().getName();
try {
productName = getStringAttribute("Product_Name");
} catch (Exception ignored) {
}
SeadasProductReader.ProductType productType = productReader.getProductType();
Product product = new Product(productName, productType.toString(), sceneWidth, sceneHeight);
product.setDescription(productName);
product.setFileLocation(productReader.getInputFile());
product.setProductReader(productReader);
addGlobalMetadata(product);
addSmiMetadata(product);
// variableMap = addBands(product, ncFile.getVariables());
variableMap = addSmiBands(product, ncFile.getVariables());
try {
addGeocoding(product);
} catch (Exception ignored) {
}
addFlagsAndMasks(product);
if (productReader.getProductType() == SeadasProductReader.ProductType.Bathy) {
mustFlipY = true;
Dimension tileSize = new Dimension(640, 320);
product.setPreferredTileSize(tileSize);
}
return product;
}
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);
}
}
}