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);
}
}
/**
* 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);
}
}
private static void readCalibrationLUT(
final File file, final String lutName, final MetadataElement root, final boolean flipLUT)
throws IOException {
if (!file.exists()) return;
final org.jdom.Document xmlDoc = XMLSupport.LoadXML(file.getAbsolutePath());
final Element rootElement = xmlDoc.getRootElement();
final Element offsetElem = rootElement.getChild("offset");
final double offset = Double.parseDouble(offsetElem.getValue());
final Element gainsElem = rootElement.getChild("gains");
double[] gainsArray = StringUtils.toDoubleArray(gainsElem.getValue().trim(), " ");
if (flipLUT) {
double tmp;
for (int i = 0; i < gainsArray.length / 2; i++) {
tmp = gainsArray[i];
gainsArray[i] = gainsArray[gainsArray.length - i - 1];
gainsArray[gainsArray.length - i - 1] = tmp;
}
}
final MetadataElement lut = new MetadataElement(lutName);
root.addElement(lut);
final MetadataAttribute offsetAttrib =
new MetadataAttribute("offset", ProductData.TYPE_FLOAT64);
offsetAttrib.getData().setElemDouble(offset);
lut.addAttribute(offsetAttrib);
final MetadataAttribute gainsAttrib =
new MetadataAttribute("gains", ProductData.TYPE_FLOAT64, gainsArray.length);
gainsAttrib.getData().setElems(gainsArray);
lut.addAttribute(gainsAttrib);
}
public void addGlobalMetadata(Product product) {
final MetadataElement globalElement = new MetadataElement("Global_Attributes");
addAttributesToElement(globalAttributes, globalElement);
final MetadataElement metadataRoot = product.getMetadataRoot();
metadataRoot.addElement(globalElement);
}
private void handleMetadataGroup(Group group, MetadataElement metadataElement)
throws ProductIOException {
List<Variable> variables = group.getVariables();
for (Variable variable : variables) {
final String name = variable.getShortName();
final int dataType = getProductDataType(variable);
Array array;
try {
array = variable.read();
} catch (IOException e) {
throw new ProductIOException(e.getMessage());
}
final ProductData data = ProductData.createInstance(dataType, array.getStorage());
final MetadataAttribute attribute = new MetadataAttribute("data", data, true);
final MetadataElement sdsElement = new MetadataElement(name);
sdsElement.addAttribute(attribute);
metadataElement.addElement(sdsElement);
final List<Attribute> list = variable.getAttributes();
for (Attribute hdfAttribute : list) {
final String attribName = hdfAttribute.getShortName();
if ("units".equals(attribName)) {
attribute.setUnit(hdfAttribute.getStringValue());
} else if ("long_name".equals(attribName)) {
attribute.setDescription(hdfAttribute.getStringValue());
} else {
addAttributeToElement(sdsElement, hdfAttribute);
}
}
}
}
/**
* Used to save a model entry
*
* @param model
* @throws Exception
*/
ModelElement(final DynamicModel model) throws Exception {
super();
name = model.getName();
type = model.getModelType().toString();
visible = model.isVisible();
path = null; // Not used by dynamic vdbs
if (model.getDescription() != null && !model.getDescription().isEmpty()) {
description = model.getDescription();
}
getComments().add(model.getComments());
for (VdbSource source : model.getSources()) {
getSources().add(new SourceElement(source));
}
if (model.isMultiSource())
getProperties()
.add(new PropertyElement(MULTI_SOURCE, Boolean.toString(model.isMultiSource())));
if (model.doAddColumn())
getProperties()
.add(new PropertyElement(MULTI_SOURCE_ADD_COLUMN, Boolean.toString(model.doAddColumn())));
String alias = model.getColumnAlias();
if (alias != null && alias.length() > 0)
getProperties().add(new PropertyElement(MULTI_SOURCE_COLUMN_ALIAS, alias));
for (Map.Entry<Object, Object> entry : model.getProperties().entrySet()) {
getProperties()
.add(new PropertyElement(entry.getKey().toString(), entry.getValue().toString()));
}
// Append any comments to the property elements
for (PropertyElement propElement : getProperties()) {
CommentSets propertyComments = model.getPropertyComments(propElement.getName());
propElement.getComments().add(propertyComments);
}
Metadata metadata = model.getMetadata();
if (metadata != null && metadata.getSchemaText() != null) {
MetadataElement metadataElement =
new MetadataElement(metadata.getSchemaText(), metadata.getType().name());
metadataElement.getComments().add(metadata.getComments());
getMetadata().add(metadataElement);
}
}
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());
}
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 void writeMetadataElement(int locationID, MetadataElement element) throws IOException {
int groupID = createH5G(locationID, element.getName());
try {
for (int i = 0; i < element.getNumAttributes(); i++) {
MetadataAttribute attribute = element.getAttributeAt(i);
writeMetadataAttribute(groupID, attribute);
}
for (int i = 0; i < element.getNumElements(); i++) {
MetadataElement subElement = element.getElementAt(i);
writeMetadataElement(groupID, subElement);
}
} catch (IOException e) {
throw e;
} finally {
closeH5G(groupID);
}
}
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);
}
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);
}
}
/**
* Read the LUT for use in calibration
*
* @param product the target product
* @param folder the folder containing the input
* @throws IOException if can't read lut
*/
private static void addCalibrationLUT(final Product product, final File folder)
throws IOException {
final MetadataElement absRoot = AbstractMetadata.getAbstractedMetadata(product);
final boolean isAscending =
absRoot.getAttributeString(AbstractMetadata.PASS).equals("ASCENDING");
final boolean isAntennaPointingRight =
absRoot.getAttributeString(AbstractMetadata.antenna_pointing).equals("right");
final boolean flipLUT =
flipToSARGeometry
&& ((isAscending && !isAntennaPointingRight)
|| (!isAscending && isAntennaPointingRight));
final File sigmaLUT = new File(folder, lutsigma + ".xml");
final File gammaLUT = new File(folder, lutgamma + ".xml");
final File betaLUT = new File(folder, lutbeta + ".xml");
final MetadataElement origProdRoot = AbstractMetadata.getOriginalProductMetadata(product);
readCalibrationLUT(sigmaLUT, lutsigma, origProdRoot, flipLUT);
readCalibrationLUT(gammaLUT, lutgamma, origProdRoot, flipLUT);
readCalibrationLUT(betaLUT, lutbeta, origProdRoot, flipLUT);
}
/**
* Adds an attribute to this node. If an attribute with the same name already exists, the method
* does nothing.
*
* @param attribute the attribute to be added
* @throws IllegalArgumentException if the attribute added is not an integer or does not have a
* scalar value
*/
@Override
public void addAttribute(MetadataAttribute attribute) {
if (!attribute.getData().isInt()) {
throw new IllegalArgumentException("attribute value is not a integer");
}
if (attribute.getData().getNumElems() == 0) {
throw new IllegalArgumentException("attribute value is missing");
}
/*
if (!attribute.getData().isScalar()) {
throw new IllegalArgumentException("attribute value is not a scalar");
}
*/
super.addAttribute(attribute);
}
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);
}
public Metadata putElement(MetadataElement element) {
jsonObject.put(element.getName(), element.getJsonObject());
return this;
}
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);
}
}
}
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 addAttributeToElement(final MetadataElement element, final Attribute attribute) {
final MetadataAttribute metadataAttribute = attributeToMetadata(attribute);
element.addAttribute(metadataAttribute);
}
