use of ucar.ma2.DataType in project imageio-ext by geosolutions-it.
the class NCOMConverter method run.
private void run(String fileNameIn, String fileNameOut) {
try {
final File fileIn = new File(fileNameIn);
final NetcdfFile ncFileIn = NetcdfFile.open(fileNameIn);
final File fileOut = new File(fileNameOut);
// keep original name
final File outputFile = File.createTempFile(fileIn.getName(), ".tmp");
final NetcdfFileWriteable ncFileOut = NetcdfFileWriteable.createNew(outputFile.getAbsolutePath());
boolean hasDepth = false;
// input dimensions
final Dimension timeDim0 = ncFileIn.findDimension("time");
final int nTimes = timeDim0.getLength();
final Dimension latDim0 = ncFileIn.findDimension("lat");
final int nLat = latDim0.getLength();
final Dimension lonDim0 = ncFileIn.findDimension("lon");
final int nLon = lonDim0.getLength();
// input VARIABLES
final Variable timeOriginalVar = ncFileIn.findVariable("time");
final Array timeOriginalData = timeOriginalVar.read();
final Index timeOriginalIndex = timeOriginalData.getIndex();
final DataType timeDataType = timeOriginalVar.getDataType();
final Variable lonOriginalVar = ncFileIn.findVariable("lon");
final DataType lonDataType = lonOriginalVar.getDataType();
final Variable latOriginalVar = ncFileIn.findVariable("lat");
final DataType latDataType = latOriginalVar.getDataType();
final Array latOriginalData = latOriginalVar.read();
final Array lonOriginalData = lonOriginalVar.read();
// //
//
// Depth related vars
//
// //
Array depthOriginalData = null;
int nDepths = 0;
Array depth1Data = null;
Dimension depthDim = null;
DataType depthDataType = null;
// Depth
final Variable depthOriginalVar = ncFileIn.findVariable("depth");
if (depthOriginalVar != null) {
nDepths = depthOriginalVar.getDimension(0).getLength();
depthOriginalData = depthOriginalVar.read();
depthDataType = depthOriginalVar.getDataType();
hasDepth = true;
}
Dimension timeDim = ncFileOut.addDimension("time", nTimes);
Dimension latDim = ncFileOut.addDimension(NetCDFUtilities.LAT, nLat);
Dimension lonDim = ncFileOut.addDimension(NetCDFUtilities.LON, nLon);
if (hasDepth)
depthDim = ncFileOut.addDimension(NetCDFUtilities.DEPTH, nDepths);
NetCDFConverterUtilities.copyGlobalAttributes(ncFileOut, ncFileIn.getGlobalAttributes());
// Dimensions
Variable timeVar = ncFileOut.addVariable("time", timeDataType, new Dimension[] { timeDim });
NetCDFConverterUtilities.setVariableAttributes(timeOriginalVar, ncFileOut, new String[] { "long_name" });
ncFileOut.addVariableAttribute("time", "long_name", "time");
ncFileOut.addVariable(NetCDFUtilities.LAT, latDataType, new Dimension[] { latDim });
NetCDFConverterUtilities.setVariableAttributes(latOriginalVar, ncFileOut);
ncFileOut.addVariable(NetCDFUtilities.LON, lonDataType, new Dimension[] { lonDim });
NetCDFConverterUtilities.setVariableAttributes(lonOriginalVar, ncFileOut);
if (hasDepth) {
ncFileOut.addVariable(NetCDFUtilities.DEPTH, depthDataType, new Dimension[] { depthDim });
NetCDFConverterUtilities.setVariableAttributes(depthOriginalVar, ncFileOut);
}
// lat Variable
Array lat1Data = NetCDFConverterUtilities.getArray(nLat, latDataType);
NetCDFConverterUtilities.setData1D(latOriginalData, lat1Data, latDataType, nLat, true);
// lon Variable
Array lon1Data = NetCDFConverterUtilities.getArray(nLon, lonDataType);
NetCDFConverterUtilities.setData1D(lonOriginalData, lon1Data, lonDataType, nLon, false);
if (hasDepth) {
// depth level Variable
depth1Data = NetCDFConverterUtilities.getArray(nDepths, depthDataType);
NetCDFConverterUtilities.setData1D(depthOriginalData, depth1Data, depthDataType, nDepths, false);
}
// {} Variables
final ArrayList<String> variables = new ArrayList<String>(5);
final HashMap<String, String> updatingValidRange = new HashMap<String, String>(5);
int numVars = 0;
for (int i = 0; i < NUMVARS; i++) {
String varName = (String) VARIABLES.get(i);
Variable var = ncFileIn.findVariable(varName);
if (var != null) {
variables.add(varName);
List<Dimension> dims = var.getDimensions();
boolean hasLocalDepth = false;
for (Dimension dim : dims) {
if (dim.getName().equalsIgnoreCase("depth")) {
hasLocalDepth = true;
break;
}
}
if (hasDepth && hasLocalDepth)
ncFileOut.addVariable(varName, var.getDataType(), new Dimension[] { timeDim, depthDim, latDim, lonDim });
else
ncFileOut.addVariable(varName, var.getDataType(), new Dimension[] { timeDim, latDim, lonDim });
Attribute validRange = var.findAttribute(NetCDFUtilities.DatasetAttribs.VALID_MAX);
if (validRange != null)
validRange = var.findAttribute(NetCDFUtilities.DatasetAttribs.VALID_MIN);
if (validRange == null)
validRange = var.findAttribute(NetCDFUtilities.DatasetAttribs.VALID_RANGE);
if (validRange == null) {
updatingValidRange.put(varName, "");
ArrayShort range = new ArrayShort(new int[] { 2 });
Index index = range.getIndex();
range.setShort(index.set(0), Short.MIN_VALUE);
range.setShort(index.set(1), Short.MAX_VALUE);
ncFileOut.addVariableAttribute(varName, NetCDFUtilities.DatasetAttribs.VALID_RANGE, range);
}
NetCDFConverterUtilities.setVariableAttributes(var, ncFileOut);
numVars++;
}
}
// writing bin data ...
ncFileOut.create();
ArrayFloat timeData = new ArrayFloat(new int[] { timeDim.getLength() });
Index timeIndex = timeData.getIndex();
for (int t = 0; t < timeDim.getLength(); t++) {
timeData.setFloat(timeIndex.set(t), timeOriginalData.getFloat(timeOriginalIndex.set(t)));
}
ncFileOut.write("time", timeData);
timeVar = ncFileOut.findVariable("time");
timeDim.addCoordinateVariable(timeVar);
ncFileOut.write(NetCDFUtilities.LAT, lat1Data);
ncFileOut.write(NetCDFUtilities.LON, lon1Data);
if (hasDepth) {
Variable depthVar = ncFileOut.findVariable("depth");
depthDim.addCoordinateVariable(depthVar);
ncFileOut.write(NetCDFUtilities.DEPTH, depth1Data);
}
for (int i = 0; i < numVars; i++) {
String varName = (String) variables.get(i);
Variable var = ncFileIn.findVariable(varName);
boolean hasLocalDepth = NetCDFConverterUtilities.hasThisDimension(var, "depth");
Array originalVarArray = var.read();
DataType varDataType = var.getDataType();
Array destArray = null;
int[] dimensions = null;
if (hasDepth && hasLocalDepth) {
dimensions = new int[] { timeDim.getLength(), depthDim.getLength(), latDim.getLength(), lonDim.getLength() };
} else {
dimensions = new int[] { timeDim.getLength(), latDim.getLength(), lonDim.getLength() };
}
destArray = NetCDFConverterUtilities.getArray(dimensions, varDataType);
boolean findNewRange = updatingValidRange.containsKey(varName);
final boolean setDepth = hasDepth && hasLocalDepth;
final int[] loopLengths;
if (setDepth)
loopLengths = new int[] { nTimes, nDepths, nLat, nLon };
else
loopLengths = new int[] { nTimes, nLat, nLon };
NetCDFConverterUtilities.writeData(ncFileOut, varName, var, originalVarArray, destArray, findNewRange, false, loopLengths, true);
}
ncFileOut.close();
outputFile.renameTo(fileOut);
} catch (Exception e) {
// something bad happened
if (NetCDFConverterUtilities.LOGGER.isLoggable(Level.INFO))
NetCDFConverterUtilities.LOGGER.log(Level.INFO, e.getLocalizedMessage(), e);
JAI.getDefaultInstance().getTileCache().flush();
}
}
use of ucar.ma2.DataType in project imageio-ext by geosolutions-it.
the class NetCDFConverterUtilities method setData1D.
public static void setData1D(Array originalData, Array destinationData, final DataType navLatDataType, final int maxIndex, final boolean flipData) {
Index originalDataIndex = originalData.getIndex();
Index destinationDataIndex = flipData ? destinationData.getIndex() : originalDataIndex;
if (navLatDataType == DataType.FLOAT) {
for (int pos = 0; pos < maxIndex; pos++) {
float f = originalData.getFloat(originalDataIndex.set(pos));
// Flipping latitudes
if (flipData) {
destinationDataIndex.set(maxIndex - pos - 1);
}
destinationData.setFloat(destinationDataIndex, f);
}
} else if (navLatDataType == DataType.DOUBLE) {
for (int pos = 0; pos < maxIndex; pos++) {
double d = originalData.getDouble(originalDataIndex.set(pos));
// Flipping latitudes
if (flipData) {
destinationDataIndex.set(maxIndex - pos - 1);
}
destinationData.setDouble(destinationDataIndex, d);
}
} else if (navLatDataType == DataType.BYTE) {
for (int pos = 0; pos < maxIndex; pos++) {
byte b = originalData.getByte(originalDataIndex.set(pos));
// Flipping latitudes
if (flipData) {
destinationDataIndex.set(maxIndex - pos - 1);
}
destinationData.setByte(destinationDataIndex, b);
}
} else if (navLatDataType == DataType.SHORT) {
for (int pos = 0; pos < maxIndex; pos++) {
short s = originalData.getShort(originalDataIndex.set(pos));
// Flipping latitudes
if (flipData) {
destinationDataIndex.set(maxIndex - pos - 1);
}
destinationData.setShort(destinationDataIndex, s);
}
} else if (navLatDataType == DataType.INT) {
for (int pos = 0; pos < maxIndex; pos++) {
int i = originalData.getInt(originalDataIndex.set(pos));
// Flipping latitudes
if (flipData) {
destinationDataIndex.set(maxIndex - pos - 1);
}
destinationData.setInt(destinationDataIndex, i);
}
}
}
use of ucar.ma2.DataType in project imageio-ext by geosolutions-it.
the class NetCDFConverterUtilities method isFillValueOutsideValidRange.
public static boolean isFillValueOutsideValidRange(Attribute validRange, Attribute fillValue, DataType dataType) {
Array range = validRange.getValues();
Index index = range.getIndex();
if (dataType == DataType.FLOAT) {
final float min = range.getFloat(index.set(0));
final float max = range.getFloat(index.set(1));
final float fill = fillValue.getNumericValue().floatValue();
if (fill == min || fill == max)
return false;
else
return true;
} else if (dataType == DataType.DOUBLE) {
final double min = range.getDouble(index.set(0));
final double max = range.getDouble(index.set(1));
final double fill = fillValue.getNumericValue().doubleValue();
if (fill == min || fill == max)
return false;
else
return true;
} else if (dataType == DataType.BYTE) {
final byte min = range.getByte(index.set(0));
final byte max = range.getByte(index.set(1));
final byte fill = fillValue.getNumericValue().byteValue();
if (fill == min || fill == max)
return false;
else
return true;
} else if (dataType == DataType.SHORT) {
final short min = range.getShort(index.set(0));
final short max = range.getShort(index.set(1));
final short fill = fillValue.getNumericValue().shortValue();
if (fill == min || fill == max)
return false;
else
return true;
} else if (dataType == DataType.INT) {
final int min = range.getInt(index.set(0));
final int max = range.getInt(index.set(1));
final int fill = fillValue.getNumericValue().intValue();
if (fill == min || fill == max)
return false;
else
return true;
}
throw new IllegalArgumentException("Actually unsupported Datatype");
}
use of ucar.ma2.DataType in project imageio-ext by geosolutions-it.
the class HDF4APSImageReader method initializeProfile.
/**
* Initialize main properties for this <code>HDF4APSImageReader</code>
*/
protected void initializeProfile() throws IOException {
final NetcdfDataset dataset = reader.getDataset();
if (dataset == null) {
throw new IOException("Unable to initialize profile due to a null dataset");
}
final List<Variable> variables = dataset.getVariables();
final List<Attribute> attributes = dataset.getGlobalAttributes();
final int numVars = variables.size();
reader.setNumGlobalAttributes(attributes.size());
// //
//
// Getting projection dataset name
//
// //
final String navAttrib = NetCDFUtilities.getGlobalAttributeAsString(dataset, HDF4APSProperties.PFA_NA_MAPPROJECTION);
if (navAttrib != null && navAttrib.length() > 0) {
projectionDatasetName = navAttrib;
}
final String prodAttrib = NetCDFUtilities.getGlobalAttributeAsString(dataset, HDF4APSProperties.PRODLIST);
int numImages = 0;
if (prodAttrib != null && prodAttrib.length() > 0) {
String[] products = prodAttrib.split(",");
productList = HDF4APSProperties.refineProductList(products);
numImages = productList.length;
} else {
numImages = numVars;
}
setNumImages(numImages);
reader.setNumImages(numImages);
final Map<Range, APSDatasetWrapper> indexMap = new HashMap<Range, APSDatasetWrapper>(numImages);
Variable varProjection;
// //
//
// Setting spatial domain
//
// //
// getting map dataset
varProjection = dataset.findVariable(projectionDatasetName);
if (varProjection != null && varProjection.getName().equalsIgnoreCase(projectionDatasetName)) {
// TODO: All projection share the same dataset
// structure?
Array data = varProjection.read();
final int datatype = NetCDFUtilities.getRawDataType(varProjection);
if (projectionMap == null) {
projectionMap = buildProjectionAttributesMap(data, datatype);
// Force UoM of MapBoundary product as the last element in
// the map
}
}
try {
// Scanning all the datasets
for (Variable var : variables) {
final String name = var.getName();
for (int j = 0; j < numImages; j++) {
// Checking if the actual dataset is a product.
if (name.equals(productList[j])) {
// Updating the subDatasetsMap map
indexMap.put(new Range(j, j + 1), new APSDatasetWrapper(var));
break;
}
}
}
} catch (InvalidRangeException e) {
throw new IllegalArgumentException("Error occurred during NetCDF file parsing", e);
}
reader.setIndexMap(indexMap);
}
use of ucar.ma2.DataType in project imageio-ext by geosolutions-it.
the class SWANConverter method run.
private void run(String fileNameIn, String fileNameOut) {
try {
final File fileIn = new File(fileNameIn);
final NetcdfFile ncFileIn = NetcdfFile.open(fileNameIn);
final File fileOut = new File(fileNameOut);
// keep original name
final File outputFile = File.createTempFile(fileIn.getName(), ".tmp");
final NetcdfFileWriteable ncFileOut = NetcdfFileWriteable.createNew(outputFile.getAbsolutePath());
boolean hasZeta = false;
// input dimensions
final Dimension timeDim0 = ncFileIn.findDimension("time");
final int nTimes = timeDim0.getLength();
final Dimension latDim0 = ncFileIn.findDimension(NetCDFUtilities.LATITUDE);
final int nLat = latDim0.getLength();
final Dimension lonDim0 = ncFileIn.findDimension(NetCDFUtilities.LONGITUDE);
final int nLon = lonDim0.getLength();
// input VARIABLES
final Variable timeOriginalVar = ncFileIn.findVariable("time");
final Array timeOriginalData = timeOriginalVar.read();
final Index timeOriginalIndex = timeOriginalData.getIndex();
final DataType timeDataType = timeOriginalVar.getDataType();
final Variable lonOriginalVar = ncFileIn.findVariable(NetCDFUtilities.LONGITUDE);
final DataType lonDataType = lonOriginalVar.getDataType();
final Variable latOriginalVar = ncFileIn.findVariable(NetCDFUtilities.LATITUDE);
final DataType latDataType = latOriginalVar.getDataType();
final Array latOriginalData = latOriginalVar.read();
final Array lonOriginalData = lonOriginalVar.read();
// //
//
// Depth related vars
//
// //
Array levelOriginalData = null;
int nZeta = 0;
Array zeta1Data = null;
Dimension zDim = null;
DataType zetaDataType = null;
// Depth
final Variable levelOriginalVar = ncFileIn.findVariable("z");
if (levelOriginalVar != null) {
nZeta = levelOriginalVar.getDimension(0).getLength();
levelOriginalData = levelOriginalVar.read();
zetaDataType = levelOriginalVar.getDataType();
hasZeta = true;
}
Dimension timeDim = ncFileOut.addDimension("time", nTimes);
Dimension latDim = ncFileOut.addDimension(NetCDFUtilities.LAT, nLat);
Dimension lonDim = ncFileOut.addDimension(NetCDFUtilities.LON, nLon);
if (hasZeta)
zDim = ncFileOut.addDimension(NetCDFUtilities.HEIGHT, nZeta);
NetCDFConverterUtilities.copyGlobalAttributes(ncFileOut, ncFileIn.getGlobalAttributes());
// Dimensions
Variable timeVar = ncFileOut.addVariable("time", timeDataType, new Dimension[] { timeDim });
NetCDFConverterUtilities.setVariableAttributes(timeOriginalVar, ncFileOut, new String[] { "long_name" });
ncFileOut.addVariableAttribute("time", "long_name", "time");
ncFileOut.addVariable(NetCDFUtilities.LAT, latDataType, new Dimension[] { latDim });
NetCDFConverterUtilities.setVariableAttributes(latOriginalVar, ncFileOut, NetCDFUtilities.LAT);
ncFileOut.addVariable(NetCDFUtilities.LON, lonDataType, new Dimension[] { lonDim });
NetCDFConverterUtilities.setVariableAttributes(lonOriginalVar, ncFileOut, NetCDFUtilities.LON);
if (hasZeta) {
ncFileOut.addVariable(NetCDFUtilities.HEIGHT, zetaDataType, new Dimension[] { zDim });
NetCDFConverterUtilities.setVariableAttributes(levelOriginalVar, ncFileOut, NetCDFUtilities.HEIGHT, new String[] { "long_name" });
ncFileOut.addVariableAttribute(NetCDFUtilities.HEIGHT, "positive", "up");
ncFileOut.addVariableAttribute(NetCDFUtilities.HEIGHT, "long_name", NetCDFUtilities.HEIGHT);
}
// lat Variable
Array lat1Data = NetCDFConverterUtilities.getArray(nLat, latDataType);
NetCDFConverterUtilities.setData1D(latOriginalData, lat1Data, latDataType, nLat, true);
// lon Variable
Array lon1Data = NetCDFConverterUtilities.getArray(nLon, lonDataType);
NetCDFConverterUtilities.setData1D(lonOriginalData, lon1Data, lonDataType, nLon, false);
if (hasZeta) {
// depth level Variable
zeta1Data = NetCDFConverterUtilities.getArray(nZeta, zetaDataType);
NetCDFConverterUtilities.setData1D(levelOriginalData, zeta1Data, zetaDataType, nZeta, false);
}
// {} Variables
final ArrayList<String> variables = new ArrayList<String>(5);
int numVars = 0;
List<Variable> findVariables = ncFileIn.getVariables();
for (Variable var : findVariables) {
if (var != null) {
String varName = var.getName();
if (varName.equalsIgnoreCase(NetCDFUtilities.LATITUDE) || varName.equalsIgnoreCase(NetCDFUtilities.LONGITUDE) || varName.equalsIgnoreCase(NetCDFUtilities.TIME) || varName.equalsIgnoreCase(NetCDFUtilities.ZETA))
continue;
variables.add(varName);
List<Dimension> dims = var.getDimensions();
boolean hasLocalZeta = false;
for (Dimension dim : dims) {
if (dim.getName().equalsIgnoreCase(NetCDFUtilities.ZETA)) {
hasLocalZeta = true;
break;
}
}
if (hasZeta && hasLocalZeta)
ncFileOut.addVariable(varName, var.getDataType(), new Dimension[] { timeDim, zDim, latDim, lonDim });
else
ncFileOut.addVariable(varName, var.getDataType(), new Dimension[] { timeDim, latDim, lonDim });
NetCDFConverterUtilities.setVariableAttributes(var, ncFileOut, new String[] { "missing_value" });
numVars++;
}
}
// writing bin data ...
ncFileOut.create();
ArrayFloat timeData = new ArrayFloat(new int[] { timeDim.getLength() });
Index timeIndex = timeData.getIndex();
for (int t = 0; t < timeDim.getLength(); t++) {
timeData.setFloat(timeIndex.set(t), timeOriginalData.getFloat(timeOriginalIndex.set(t)));
}
ncFileOut.write("time", timeData);
timeVar = ncFileOut.findVariable("time");
timeDim.addCoordinateVariable(timeVar);
ncFileOut.write(NetCDFUtilities.LAT, lat1Data);
ncFileOut.write(NetCDFUtilities.LON, lon1Data);
if (hasZeta) {
Variable heightVar = ncFileOut.findVariable(NetCDFUtilities.HEIGHT);
zDim.addCoordinateVariable(heightVar);
ncFileOut.write(NetCDFUtilities.HEIGHT, zeta1Data);
}
for (int i = 0; i < numVars; i++) {
String varName = (String) variables.get(i);
Variable var = ncFileIn.findVariable(varName);
boolean hasLocalZeta = NetCDFConverterUtilities.hasThisDimension(var, NetCDFUtilities.ZETA);
Array originalVarArray = var.read();
DataType varDataType = var.getDataType();
Array destArray = null;
int[] dimensions = null;
if (hasZeta && hasLocalZeta) {
dimensions = new int[] { timeDim.getLength(), zDim.getLength(), latDim.getLength(), lonDim.getLength() };
} else {
dimensions = new int[] { timeDim.getLength(), latDim.getLength(), lonDim.getLength() };
}
destArray = NetCDFConverterUtilities.getArray(dimensions, varDataType);
final boolean setZeta = hasZeta && hasLocalZeta;
final int[] loopLengths;
if (setZeta)
loopLengths = new int[] { nTimes, nZeta, nLat, nLon };
else
loopLengths = new int[] { nTimes, nLat, nLon };
NetCDFConverterUtilities.writeData(ncFileOut, varName, var, originalVarArray, destArray, false, false, loopLengths, true);
}
ncFileOut.close();
outputFile.renameTo(fileOut);
} catch (Exception e) {
// something bad happened
if (NetCDFConverterUtilities.LOGGER.isLoggable(Level.INFO))
NetCDFConverterUtilities.LOGGER.log(Level.INFO, e.getLocalizedMessage(), e);
JAI.getDefaultInstance().getTileCache().flush();
}
}
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