private void loadNeuralNet(File neuralNetFile) throws IOException, JnnException {
Jnn.setOptimizing(true);
neuralNet = Jnn.readNna(neuralNetFile);
final Logger logger = BeamLogManager.getSystemLogger();
logger.info("Using JNN Neural Net Library, version " + Jnn.VERSION_STRING);
logger.info(neuralNetFile + " loaded");
}
/**
* Copies the given image to the system clipboard.
*
* @param image the image to copy
*/
public static void copyToClipboard(final Image image) {
ImageSelection selection = new ImageSelection(image);
Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
if (clipboard != null) {
clipboard.setContents(selection, null);
} else {
BeamLogManager.getSystemLogger().severe("failed to obtain clipboard instance");
}
}
/**
* Copies the given text to the system clipboard.
*
* @param text the text to copy
*/
public static void copyToClipboard(final String text) {
StringSelection selection = new StringSelection(text == null ? "" : text);
Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
if (clipboard != null) {
clipboard.setContents(selection, selection);
} else {
BeamLogManager.getSystemLogger().severe("failed to obtain clipboard instance");
}
}
private static void initJAI(ClassLoader cl) {
System.setProperty(
"com.sun.media.jai.disableMediaLib", "true"); // disable native libraries for JAI
// Must use a new operation registry in order to register JAI operators defined in Ceres and
// BEAM
OperationRegistry operationRegistry = OperationRegistry.getThreadSafeOperationRegistry();
InputStream is = SystemUtils.class.getResourceAsStream(JAI_REGISTRY_PATH);
if (is != null) {
// Suppress ugly (and harmless) JAI error messages saying that a descriptor is already
// registered.
final PrintStream oldErr = System.err;
try {
setSystemErr(new PrintStream(new ByteArrayOutputStream()));
operationRegistry.updateFromStream(is);
operationRegistry.registerServices(cl);
JAI.getDefaultInstance().setOperationRegistry(operationRegistry);
} catch (IOException e) {
BeamLogManager.getSystemLogger()
.log(
Level.SEVERE,
MessageFormat.format("Error loading {0}: {1}", JAI_REGISTRY_PATH, e.getMessage()),
e);
} finally {
setSystemErr(oldErr);
}
} else {
BeamLogManager.getSystemLogger()
.warning(MessageFormat.format("{0} not found", JAI_REGISTRY_PATH));
}
Integer parallelism =
Integer.getInteger(
BEAM_PARALLELISM_PROPERTY_NAME, Runtime.getRuntime().availableProcessors());
JAI.getDefaultInstance().getTileScheduler().setParallelism(parallelism);
BeamLogManager.getSystemLogger()
.info(MessageFormat.format("JAI tile scheduler parallelism set to {0}", parallelism));
}
@Override
public void parseRecords(int offset, int numRecords) throws IOException {
featureCollection = new ListFeatureCollection(simpleFeatureType);
SimpleFeatureBuilder builder = new SimpleFeatureBuilder(simpleFeatureType);
skipToLine(offset);
String line;
long featureCount = offset;
while ((numRecords == -1 || featureCount < offset + numRecords)
&& (line = stream.readLine()) != null) {
String[] tokens = getTokens(line);
if (tokens == null) {
break;
}
int expectedTokenCount = simpleFeatureType.getAttributeCount();
expectedTokenCount += hasFeatureId ? 1 : 0;
if (tokens.length != expectedTokenCount) {
continue;
}
builder.reset();
String featureId = "" + featureCount++;
for (int i = 0; i < tokens.length; i++) {
String token = tokens[i];
if (i == 0 && hasFeatureId) {
featureId = token;
} else {
try {
Object value = null;
int currentIndex = i;
currentIndex -= hasFeatureId ? 1 : 0;
if (!VectorDataNodeIO.NULL_TEXT.equals(token)) {
value = converters[currentIndex].parse(token);
}
builder.set(simpleFeatureType.getDescriptor(currentIndex).getLocalName(), value);
} catch (ConversionException e) {
BeamLogManager.getSystemLogger()
.warning(String.format("Problem in '%s': %s", csv.getPath(), e.getMessage()));
}
}
}
SimpleFeature simpleFeature = builder.buildFeature(featureId);
featureCollection.add(simpleFeature);
bytePositionForOffset.put(featureCount, stream.getStreamPosition());
}
recordsParsed = true;
}
public static void loadAvailableColorPalettes(File palettesDir) {
cpdRasterList = new HashMap<>();
final ArrayList<ColorPaletteDef> newCpdList = new ArrayList<>();
final ArrayList<String> newCpdNames = new ArrayList<>();
final File[] files =
palettesDir.listFiles(
new FilenameFilter() {
@Override
public boolean accept(File dir, String name) {
return name.toLowerCase().endsWith(".cpd");
}
});
for (File file : files) {
try {
final ColorPaletteDef newCpd = ColorPaletteDef.loadColorPaletteDef(file);
newCpdList.add(newCpd);
newCpdNames.add(file.getName());
} catch (IOException e) {
final Logger logger = BeamLogManager.getSystemLogger();
logger.warning(
"Unable to load color palette definition from file '" + file.getAbsolutePath() + "'");
logger.log(Level.INFO, e.getMessage(), e);
}
}
if (cpdList != null) {
for (ColorPaletteDef oldCpd : cpdList) {
if (newCpdList.contains(oldCpd)) {
final int i = newCpdList.indexOf(oldCpd);
final ColorPaletteDef newCpd = newCpdList.get(i);
cpdRasterList.put(newCpd, cpdRasterList.remove(oldCpd));
} else {
final List<RasterDataNode> nodes = cpdRasterList.remove(oldCpd);
if (nodes != null) {
nodes.clear();
}
}
}
cpdNames.clear();
cpdList.clear();
}
cpdNames = newCpdNames;
cpdList = newCpdList;
}
@Deprecated
private static Class<?> loadClassWithNativeDependencies(
Class<?> callerClass, String className, String warningPattern) {
ClassLoader classLoader = callerClass.getClassLoader();
String classResourceName = "/" + className.replace('.', '/') + ".class";
SystemUtils.class.getResource(classResourceName);
if (callerClass.getResource(classResourceName) != null) {
try {
return Class.forName(className, true, classLoader);
} catch (Throwable error) {
BeamLogManager.getSystemLogger()
.warning(
MessageFormat.format(
warningPattern, callerClass, error.getClass(), error.getMessage()));
return null;
}
} else {
return null;
}
}
@Override
public Object[] parseRecords(final int offset, final int numRecords, final String rowName)
throws IOException {
AttributeDescriptor attributeDescriptor = simpleFeatureType.getDescriptor(rowName);
int expectedTokenCount = simpleFeatureType.getAttributeCount();
expectedTokenCount += hasFeatureId ? 1 : 0;
int rowIndex = simpleFeatureType.getAttributeDescriptors().indexOf(attributeDescriptor);
int tokenIndex = rowIndex + (hasFeatureId ? 1 : 0);
List<Object> values = new ArrayList<>(numRecords);
skipToLine(offset);
String line;
long featureCount = offset;
while ((numRecords == -1 || featureCount < offset + numRecords)
&& (line = stream.readLine()) != null) {
String[] tokens = getTokens(line);
if (tokens == null) {
break;
}
if (tokens.length != expectedTokenCount) {
continue;
}
featureCount++;
String token = tokens[tokenIndex];
try {
Object value = null;
if (!VectorDataNodeIO.NULL_TEXT.equals(token)) {
value = converters[rowIndex].parse(token);
}
values.add(value);
} catch (ConversionException e) {
BeamLogManager.getSystemLogger()
.warning(String.format("Problem in '%s': %s", csv.getPath(), e.getMessage()));
}
bytePositionForOffset.put(featureCount, stream.getStreamPosition());
}
return values.toArray();
}
@Override
protected Product readProductNodesImpl() throws IOException {
final String s = getInput().toString();
final File file0 = new File(s);
final File dir = file0.getParentFile();
final S2FilenameInfo fni0 = S2FilenameInfo.create(file0.getName());
if (fni0 == null) {
throw new IOException();
}
Header metadataHeader = null;
final Map<Integer, BandInfo> fileMap = new HashMap<Integer, BandInfo>();
if (dir != null) {
File[] files =
dir.listFiles(
new FilenameFilter() {
@Override
public boolean accept(File dir, String name) {
return name.endsWith(Sentinel2ProductReaderPlugIn.JP2_EXT);
}
});
if (files != null) {
for (File file : files) {
int bandIndex = fni0.getBand(file.getName());
if (bandIndex >= 0 && bandIndex < WAVEBAND_INFOS.length) {
final S2WavebandInfo wavebandInfo = WAVEBAND_INFOS[bandIndex];
BandInfo bandInfo =
new BandInfo(
file, bandIndex, wavebandInfo, imageLayouts[wavebandInfo.resolution.id]);
fileMap.put(bandIndex, bandInfo);
}
}
}
File[] metadataFiles =
dir.listFiles(
new FilenameFilter() {
@Override
public boolean accept(File dir, String name) {
return name.startsWith("MTD_") && name.endsWith(".xml");
}
});
if (metadataFiles != null && metadataFiles.length > 0) {
File metadataFile = metadataFiles[0];
try {
metadataHeader = Header.parseHeader(metadataFile);
} catch (JDOMException e) {
BeamLogManager.getSystemLogger()
.warning("Failed to parse metadata file: " + metadataFile);
}
} else {
BeamLogManager.getSystemLogger().warning("No metadata file found");
}
}
final ArrayList<Integer> bandIndexes = new ArrayList<Integer>(fileMap.keySet());
Collections.sort(bandIndexes);
if (bandIndexes.isEmpty()) {
throw new IOException("No valid bands found.");
}
String prodType = "S2_MSI_" + fni0.procLevel;
final Product product =
new Product(
String.format("%s_%s_%s", prodType, fni0.orbitNo, fni0.tileId),
prodType,
imageLayouts[S2Resolution.R10M.id].width,
imageLayouts[S2Resolution.R10M.id].height);
try {
product.setStartTime(ProductData.UTC.parse(fni0.start, "yyyyMMddHHmmss"));
} catch (ParseException e) {
// warn
}
try {
product.setEndTime(ProductData.UTC.parse(fni0.stop, "yyyyMMddHHmmss"));
} catch (ParseException e) {
// warn
}
if (metadataHeader != null) {
SceneDescription sceneDescription = SceneDescription.create(metadataHeader);
int tileIndex = sceneDescription.getTileIndex(fni0.tileId);
Envelope2D tileEnvelope = sceneDescription.getTileEnvelope(tileIndex);
Header.Tile tile = metadataHeader.getTileList().get(tileIndex);
try {
product.setGeoCoding(
new CrsGeoCoding(
tileEnvelope.getCoordinateReferenceSystem(),
imageLayouts[S2Resolution.R10M.id].width,
imageLayouts[S2Resolution.R10M.id].height,
tile.tileGeometry10M.upperLeftX,
tile.tileGeometry10M.upperLeftY,
tile.tileGeometry10M.xDim,
-tile.tileGeometry10M.yDim,
0.0,
0.0));
} catch (FactoryException e) {
// todo - handle e
} catch (TransformException e) {
// todo - handle e
}
}
for (Integer bandIndex : bandIndexes) {
final BandInfo bandInfo = fileMap.get(bandIndex);
final Band band = product.addBand(bandInfo.wavebandInfo.bandName, ProductData.TYPE_UINT16);
band.setSpectralWavelength((float) bandInfo.wavebandInfo.centralWavelength);
band.setSpectralBandwidth((float) bandInfo.wavebandInfo.bandWidth);
band.setSpectralBandIndex(bandIndex);
band.setSourceImage(new DefaultMultiLevelImage(new Jp2MultiLevelSource(bandInfo)));
}
product.setNumResolutionLevels(imageLayouts[0].numResolutions);
return product;
}
