org.meteoinfo.data.meteodata.netcdf.NetCDFDataInfo Maven / Gradle / Ivy
/* Copyright 2012 Yaqiang Wang,
* [email protected]
*
* This library is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation; either version 2.1 of the License, or (at
* your option) any later version.
*
* This library is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser
* General Public License for more details.
*/
package org.meteoinfo.data.meteodata.netcdf;
import org.meteoinfo.common.Extent;
import org.meteoinfo.common.MIMath;
import org.meteoinfo.common.util.JDateUtil;
import org.meteoinfo.data.GridData;
import org.meteoinfo.data.StationData;
import org.meteoinfo.data.meteodata.DataInfo;
import org.meteoinfo.ndarray.math.ArrayMath;
import org.meteoinfo.ndarray.math.ArrayUtil;
import org.meteoinfo.ndarray.Dimension;
import org.meteoinfo.ndarray.DimensionType;
import org.meteoinfo.data.meteodata.IGridDataInfo;
import org.meteoinfo.data.meteodata.IStationDataInfo;
import org.meteoinfo.data.meteodata.StationInfoData;
import org.meteoinfo.data.meteodata.StationModelData;
import org.meteoinfo.data.meteodata.Variable;
import java.io.IOException;
import java.text.ParseException;
import java.time.LocalDateTime;
import java.time.format.DateTimeFormatter;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.swing.JOptionPane;
import org.meteoinfo.data.GridArray;
import org.meteoinfo.data.meteodata.MeteoDataType;
import org.meteoinfo.projection.KnownCoordinateSystems;
import org.meteoinfo.projection.ProjectionInfo;
import org.meteoinfo.ndarray.Array;
import org.meteoinfo.ndarray.Index;
import org.meteoinfo.ndarray.IndexIterator;
import org.meteoinfo.ndarray.MAMath;
import org.meteoinfo.data.meteodata.Attribute;
import org.meteoinfo.projection.Reproject;
import ucar.nc2.NetcdfFile;
import ucar.nc2.NetcdfFileWriter;
import ucar.nc2.NetcdfFiles;
import ucar.nc2.iosp.hdf5.H5header;
import ucar.unidata.io.RandomAccessFile;
/**
*
* @author yaqiang
*/
public class NetCDFDataInfo extends DataInfo implements IGridDataInfo, IStationDataInfo {
//
private String _fileTypeStr;
private String _fileTypeId;
private Conventions _convention = Conventions.CF;
private NetcdfFile ncfile = null;
private boolean keepOpen = false;
private List ncVariables = new ArrayList<>();
private List ncDimensions = new ArrayList<>();
private List dimensions = new ArrayList<>();
private List ncAttributes = new ArrayList<>();
//private List attributes = new ArrayList<>();
private ucar.nc2.Variable _xVar = null;
private ucar.nc2.Variable _yVar = null;
private ucar.nc2.Variable _levelVar = null;
private ucar.nc2.Variable _timeVar = null;
private boolean _isHDFEOS = false;
private boolean _isSWATH = false;
private boolean _isPROFILE = false;
//
//
/**
* Constructor
*/
public NetCDFDataInfo() {
this.setDataType(MeteoDataType.NETCDF);
}
//
//
/**
* Get netCDF file
*
* @return NetCDF file
*/
public NetcdfFile getFile() {
return this.ncfile;
}
/**
* Get MeteoInfo dimensions
*
* @return MeteoInfo dimensions
*/
@Override
public List getDimensions() {
return this.dimensions;
}
/**
* Get ucar nc2 dimensions
*
* @return Ucar nc2 dimensions
*/
public List getNCDimensions() {
return this.ncDimensions;
}
/**
* Get global attributes
*
* @return Global attributes
*/
@Override
public List getGlobalAttributes() {
return this.attributes;
}
/**
* Get ucar nc2 variables
*
* @return Ucar nc2 variables
*/
public List getNCVariables() {
return this.ncVariables;
}
/**
* Get file type identifer
*
* @return File type identifer
*/
public String getFileTypeId() {
return _fileTypeId;
}
/**
* Get if is HDF EOS data
*
* @return Boolean
*/
public boolean isHDFEOS() {
return _isHDFEOS;
}
/**
* Get if is SWATH
*
* @return Boolean
*/
public boolean isSWATH() {
if (_isSWATH || _isPROFILE) {
return true;
} else {
return false;
}
}
//
//
//
/**
* Test if the file can be opened.
*
* @param fileName The file name.
* @return Can be opened or not.
* @throws IOException
*/
public static boolean canOpen(String fileName) throws IOException {
boolean r = NetcdfFiles.canOpen(fileName);
if (!r) {
RandomAccessFile raf = RandomAccessFile.acquire(fileName);
r = H5header.isValidFile(raf);
}
return r;
}
/**
* Check if the file is opened or closed.
* @return Boolean
*/
public boolean isOpened() {
return this.ncfile != null;
}
/**
* Reopen data file.
*/
public void reOpen() {
if (ncfile == null) {
try {
ncfile = NetcdfFile.open(this.getFileName());
} catch (IOException e) {
e.printStackTrace();
}
}
}
/**
* Close file
* @throws IOException
*/
public void close() throws IOException {
if (this.ncfile != null) {
this.ncfile.close();
this.ncfile = null;
}
}
@Override
public void readDataInfo(String fileName) {
this.setFileName(fileName);
try {
//ncfile = NetcdfFile.open(fileName);
//ncfile = NetcdfDatasets.openDataset(fileName);
ncfile = NetcdfFile.open(fileName);
readDataInfo(false);
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* Read data info for mixed GRIB-1 and GRIB-2 data file
*
* @param fileName File name
* @param mdt Meteo data type
*/
public void readDataInfo(String fileName, MeteoDataType mdt) {
this.setFileName(fileName);
String iospClassName = "ucar.nc2.grib.collection.Grib2Iosp";
switch (mdt) {
case GRIB1:
iospClassName = "ucar.nc2.grib.collection.Grib1Iosp";
break;
}
try {
ncfile = NetcdfFiles.open(fileName, iospClassName, 0, null, null);
readDataInfo(false);
} catch (ClassNotFoundException | IllegalAccessException | InstantiationException | IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
public void readDataInfo(NetcdfFile nf, boolean keepOpen) {
this.ncfile = nf;
readDataInfo(keepOpen);
}
public void readDataInfo(boolean keepOpen) {
try {
_fileTypeStr = ncfile.getFileTypeDescription();
_fileTypeId = ncfile.getFileTypeId();
// if (_fileTypeId.equals("GRIB2")){
// ncfile.getIosp().
// }
//Read variables
ncVariables = ncfile.getVariables();
//Read dimensions
ncDimensions = ncfile.getDimensions();
if (_fileTypeId.equals("HDF5-EOS") || _fileTypeId.equals("HDF4-EOS")) {
_isHDFEOS = true;
List dimNames = new ArrayList<>();
for (ucar.nc2.Variable var : ncVariables) {
for (ucar.nc2.Dimension dim : var.getDimensions()) {
String dimName = dim.getShortName();
if (dimName == null) {
continue;
}
if (!dimNames.contains(dimName)) {
dimNames.add(dimName);
}
}
}
for (ucar.nc2.Dimension dim : ncDimensions) {
if (dim.getShortName().contains("_")) {
for (String dimName : dimNames) {
if (dim.getShortName().contains(dimName)) {
dim.setShortName(dimName);
}
}
// String newName;
// //int idx = dim.getShortName().lastIndexOf("_");
// int idx = dim.getShortName().indexOf("Data_Fields_");
// if (idx >= 0) {
// newName = dim.getShortName().substring(idx + 12);
// } else {
// idx = dim.getShortName().lastIndexOf("_");
// newName = dim.getShortName().substring(idx + 1);
// }
// dim.setShortName(newName);
}
}
}
this.dimensions = new ArrayList<>();
for (ucar.nc2.Dimension dim : ncDimensions) {
Dimension ndim = NCUtil.convertDimension(dim);
if (dim.getShortName().equals("nXtrack")) {
ndim.setDimType(DimensionType.X_TRACK);
}
this.dimensions.add(ndim);
}
//Read global attribute
ncAttributes = ncfile.getGlobalAttributes();
String featureType = this.getGlobalAttStr("featureType");
switch (featureType) {
case "SWATH":
_isSWATH = true;
break;
case "PROFILE":
_isPROFILE = true;
break;
}
for (ucar.nc2.Attribute ncattr : ncAttributes) {
this.attributes.add(NCUtil.convertAttribute(ncattr));
}
//Get convention
_convention = this.getConvention();
//Get projection
this.getProjection();
//Get dimensions values
getDimensionValues(ncfile);
//Get variables
List vars = new ArrayList<>();
//List coorDims = new ArrayList();
for (ucar.nc2.Variable var : ncVariables) {
Variable nvar = NCUtil.convertVariable(var);
//nvar.setName(var.getShortName());
//nvar.setCoorVar(var.isCoordinateVariable());
nvar.setDimVar(var.getRank() <= 1);
if (_isSWATH || _isPROFILE) {
nvar.setStation(true);
}
nvar.getDimensions().clear();
for (ucar.nc2.Dimension dim : var.getDimensions()) {
//Dimension ndim = this.getCoordDimension(dim);
int idx = this.getDimensionIndex(dim);
if (idx >= 0) {
Dimension ndim = this.dimensions.get(idx);
nvar.addDimension(ndim);
} else {
Dimension ndim = NCUtil.convertDimension(dim);
ndim.setDimType(DimensionType.OTHER);
nvar.addDimension(ndim);
}
}
//nvar.setAttributes(var.getAttributes());
double[] packData = this.getPackData(var);
nvar.setAddOffset(packData[0]);
nvar.setScaleFactor(packData[1]);
nvar.setFillValue(packData[2]);
vars.add(nvar);
}
this.setVariables(vars);
//
//getVariableLevels();
} catch (IOException | ParseException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
} finally {
this.keepOpen = keepOpen;
if (!keepOpen) {
if (null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
//this.keepOpen = true;
}
@Override
public void readDataInfo(String fileName, boolean keepOpen) {
try {
this.setFileName(fileName);
//ncfile = NetcdfDatasets.openDataset(fileName);
ncfile = NetcdfFile.open(fileName);
//ucar.nc2.grib.grib1.tables.Grib1ParamTables.setStrict(true);
//ncfile = NetcdfFiles.open(fileName);
readDataInfo(keepOpen);
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
private int getDimensionIndex(ucar.nc2.Dimension dim) {
String name2 = dim.getShortName();
if (name2 == null) {
return -1;
}
for (int i = 0; i < ncDimensions.size(); i++) {
ucar.nc2.Dimension idim = ncDimensions.get(i);
if (idim.getShortName().equals(name2)) {
return i;
}
}
for (int i = 0; i < ncDimensions.size(); i++) {
ucar.nc2.Dimension idim = ncDimensions.get(i);
if (idim.getLength() == (dim.getLength())) {
String name1 = idim.getShortName();
int len1 = name1.length();
int len2 = name2.length();
if (len1 > len2) {
if (name1.substring(len1 - len2).equals(name2)) {
return i;
}
}
}
}
return -1;
}
/**
* Find netCDF dimension by name
*
* @param dimName Dimension name
* @return NetCDF dimension
*/
public ucar.nc2.Dimension findNCDimension(String dimName) {
for (ucar.nc2.Dimension dim : this.ncDimensions) {
if (dim.getShortName().equalsIgnoreCase(dimName)) {
return dim;
}
}
return null;
}
/**
* Find dimension by name
*
* @param dimName Dimension name
* @return Dimension
*/
public Dimension findDimension(String dimName) {
for (Dimension dim : this.dimensions) {
if (dim.getShortName().equalsIgnoreCase(dimName)) {
return dim;
}
}
return null;
}
/**
* Find global attribute
*
* @param attName Attribute name
* @return Global attribute
*/
public Attribute findGlobalAttribute(String attName) {
for (Attribute att : this.attributes) {
if (att.getShortName().equalsIgnoreCase(attName)) {
return att;
}
}
return null;
}
private Dimension findCoordDimension(ucar.nc2.Dimension dim) {
if (dim.getShortName().equals(this.getXDimension().getShortName())) {
return this.getXDimension();
} else if (dim.getShortName().equals(this.getYDimension().getShortName())) {
return this.getYDimension();
} else if (dim.getShortName().equals(this.getZDimension().getShortName())) {
return this.getZDimension();
} else if (dim.getShortName().equals(this.getTimeDimension().getShortName())) {
return this.getTimeDimension();
} else {
return null;
}
}
private Conventions getConvention() {
Conventions convention = _convention;
boolean isIOAPI = false;
boolean isWRFOUT = false;
//List WRFStrings = new ArrayList();
for (ucar.nc2.Attribute aAtts : ncAttributes) {
if (aAtts.getShortName().toLowerCase().equals("ioapi_version")) {
isIOAPI = true;
break;
}
if (aAtts.getShortName().toUpperCase().equals("TITLE")) {
String title = aAtts.getStringValue();
if (title.toUpperCase().contains("OUTPUT FROM WRF") || title.toUpperCase().contains("OUTPUT FROM GEOGRID")
|| title.toUpperCase().contains("OUTPUT FROM GRIDGEN") || title.toUpperCase().contains("OUTPUT FROM METGRID")) {
isWRFOUT = true;
break;
}
if (title.toUpperCase().contains("OUTPUT FROM") && title.toUpperCase().contains("WRF")) {
isWRFOUT = true;
break;
}
}
if (aAtts.getShortName().toUpperCase().equals("WEST-EAST_GRID_DIMENSION")) {
if (!this.getGlobalAttStr("MAP_PROJ").isEmpty()) {
isWRFOUT = true;
break;
}
}
}
if (isIOAPI) {
convention = Conventions.IOAPI;
}
if (isWRFOUT) {
convention = Conventions.WRFOUT;
}
return convention;
}
private void getProjection() {
ProjectionInfo projInfo = this.getProjectionInfo();
switch (_convention) {
case CF:
projInfo = getProjection_CF();
break;
case IOAPI:
projInfo = getProjection_IOAPI();
break;
case WRFOUT:
projInfo = getProjection_WRFOUT();
break;
}
this.setProjectionInfo(projInfo);
}
private ProjectionInfo getProjection_CF() {
String projStr = this.getProjectionInfo().toProj4String();
if (this._isHDFEOS) {
ucar.nc2.Variable pVar = null;
for (ucar.nc2.Variable aVar : ncVariables) {
if (aVar.getShortName().equals("_HDFEOS_CRS")) {
pVar = aVar;
break;
}
}
if (pVar != null) {
ucar.nc2.Attribute projAtt = pVar.findAttributeIgnoreCase("Projection");
String proj = projAtt.getStringValue();
if (proj.contains("GCTP_GEO")) {
} else {
ucar.nc2.Attribute paraAtt = pVar.findAttributeIgnoreCase("ProjParams");
Array params = NCUtil.convertArray(paraAtt.getValues());
if (proj.contains("GCTP_SNSOID")) {
projStr = "+proj=sinu"
+ "+lon_0=" + params.getObject(4).toString()
+ "+a=" + params.getObject(0).toString()
+ "+b=" + params.getObject(0).toString();
} else if (proj.contains("GCTP_CEA")) {
projStr = "+proj=cea"
+ "+lon_0=" + params.getObject(4).toString()
+ "+lat_ts=" + String.valueOf(params.getDouble(5) / 1000000);
//+ "+x_0=" + params.getObject(6).toString()
//+ "+y_0=" + params.getObject(7).toString();
}
}
ucar.nc2.Attribute ulAtt = pVar.findAttributeIgnoreCase("UpperLeftPointMtrs");
ucar.nc2.Attribute lrAtt = pVar.findAttributeIgnoreCase("LowerRightMtrs");
double xmin = ulAtt.getValues().getDouble(0);
double ymin = ulAtt.getValues().getDouble(1);
double xmax = lrAtt.getValues().getDouble(0);
double ymax = lrAtt.getValues().getDouble(1);
if (proj.contains("GCTP_GEO")) {
if (Math.abs(xmax) > 1000000) {
xmin = xmin / 1000000;
xmax = xmax / 1000000;
ymin = ymin / 1000000;
ymax = ymax / 1000000;
}
}
if (ymin > ymax) {
// double temp = ymax;
// ymax = ymin;
// ymin = temp;
if (this._fileTypeId.equals("HDF5-EOS")) {
this.setYReverse(true);
}
} else if (!this._fileTypeId.equals("HDF5-EOS")) {
this.setYReverse(true);
}
Dimension xDim = this.findDimension("XDim");
Dimension yDim = this.findDimension("YDim");
int xnum = xDim.getLength();
int ynum = yDim.getLength();
double xdelt = (xmax - xmin) / xnum;
double ydelt = (ymax - ymin) / ynum;
double[] X = new double[xnum];
xmin = xmin + xdelt * 0.5;
for (int i = 0; i < xnum; i++) {
X[i] = xmin + xdelt * i;
}
xDim.setDimType(DimensionType.X);
xDim.setValues(X);
this.setXDimension(xDim);
double[] Y = new double[ynum];
ymin = ymin + ydelt * 0.5;
for (int i = 0; i < ynum; i++) {
Y[i] = ymin + ydelt * i;
}
yDim.setDimType(DimensionType.Y);
yDim.setValues(Y);
this.setYDimension(yDim);
}
} else {
ucar.nc2.Variable pVar = null;
int pvIdx = -1;
for (ucar.nc2.Variable aVarS : ncVariables) {
ucar.nc2.Attribute att = aVarS.findAttribute("grid_mapping_name");
if (att != null) {
pVar = aVarS;
pvIdx = aVarS.getAttributes().indexOf(att);
break;
}
}
if (pVar != null) {
if (pVar.findAttribute("proj4") != null) {
projStr = pVar.findAttribute("proj4").getValue(0).toString();
} else {
ucar.nc2.Attribute pAtt = pVar.getAttributes().get(pvIdx);
String attStr = pAtt.getStringValue();
switch (attStr) {
case "albers_conical_equal_area": {
//Two standard parallels condition need to be considered
Array values = NCUtil.convertArray(pVar.findAttribute("standard_parallel").getValues());
String sp1 = String.valueOf(values.getDouble(0));
String sp2 = "";
if (values.getSize() == 2) {
sp2 = String.valueOf(values.getDouble(1));
}
projStr = "+proj=aea"
+ "+lat_1=" + sp1;
if (!sp2.isEmpty()) {
projStr += "+lat_2=" + sp2;
}
projStr += "+lon_0=" + pVar.findAttribute("longitude_of_central_meridian").getValue(0).toString()
+ "+lat_0=" + pVar.findAttribute("latitude_of_projection_origin").getValue(0).toString();
if (pVar.findAttribute("false_easting") != null) {
projStr += "+x_0=" + pVar.findAttribute("false_easting").getValue(0).toString();
}
if (pVar.findAttribute("false_northing") != null) {
projStr += "+y_0=" + pVar.findAttribute("false_northing").getValue(0).toString();
}
break;
}
case "azimuthal_equidistant":
projStr = "+proj=aeqd"
+ "+lon_0=" + pVar.findAttribute("longitude_of_projection_origin").getValue(0).toString()
+ "+lat_0=" + pVar.findAttribute("latitude_of_projection_origin").getValue(0).toString();
if (pVar.findAttribute("false_easting") != null) {
projStr += "+x_0=" + pVar.findAttribute("false_easting").getValue(0).toString();
}
if (pVar.findAttribute("false_northing") != null) {
projStr += "+y_0=" + pVar.findAttribute("false_northing").getValue(0).toString();
}
break;
case "lambert_azimuthal_equal_area":
projStr = "+proj=laea"
+ "+lon_0=" + pVar.findAttribute("longitude_of_projection_origin").getValue(0).toString()
+ "+lat_0=" + pVar.findAttribute("latitude_of_projection_origin").getValue(0).toString();
if (pVar.findAttribute("false_easting") != null) {
projStr += "+x_0=" + pVar.findAttribute("false_easting").getValue(0).toString();
}
if (pVar.findAttribute("false_northing") != null) {
projStr += "+y_0=" + pVar.findAttribute("false_northing").getValue(0).toString();
}
break;
case "lambert_conformal_conic": {
//Two standard parallels condition need to be considered
Array values = NCUtil.convertArray(pVar.findAttribute("standard_parallel").getValues());
String sp1 = String.valueOf(values.getDouble(0));
String sp2 = "";
if (values.getSize() == 2) {
sp2 = String.valueOf(values.getDouble(1));
}
projStr = "+proj=lcc"
+ "+lat_1=" + sp1;
if (!sp2.isEmpty()) {
projStr += "+lat_2=" + sp2;
}
projStr += "+lon_0=" + pVar.findAttribute("longitude_of_central_meridian").getValue(0).toString()
+ "+lat_0=" + pVar.findAttribute("latitude_of_projection_origin").getValue(0).toString();
if (pVar.findAttribute("false_easting") != null) {
projStr += "+x_0=" + pVar.findAttribute("false_easting").getValue(0).toString();
}
if (pVar.findAttribute("false_northing") != null) {
projStr += "+y_0=" + pVar.findAttribute("false_northing").getValue(0).toString();
}
break;
}
case "lambert_cylindrical_equal_area":
projStr = "+proj=cea"
+ "+lon_0=" + pVar.findAttribute("longitude_of_central_meridian").getValue(0).toString();
if (pVar.findAttribute("standard_parallel") != null) {
projStr += "+lat_ts=" + pVar.findAttribute("standard_parallel").getValue(0).toString();
} else if (pVar.findAttribute("scale_factor_at_projection_origin") != null) {
projStr += "+k_0=" + pVar.findAttribute("scale_factor_at_projection_origin").getValue(0).toString();
}
if (pVar.findAttribute("false_easting") != null) {
projStr += "+x_0=" + pVar.findAttribute("false_easting").getValue(0).toString();
}
if (pVar.findAttribute("false_northing") != null) {
projStr += "+y_0=" + pVar.findAttribute("false_northing").getValue(0).toString();
}
break;
case "mercator":
projStr = "+proj=merc"
+ "+lon_0=" + pVar.findAttribute("longitude_of_projection_origin").getValue(0).toString();
if (pVar.findAttribute("standard_parallel") != null) {
projStr += "+lat_ts=" + pVar.findAttribute("standard_parallel").getValue(0).toString();
} else if (pVar.findAttribute("scale_factor_at_projection_origin") != null) {
projStr += "+k_0=" + pVar.findAttribute("scale_factor_at_projection_origin").getValue(0).toString();
}
if (pVar.findAttribute("false_easting") != null) {
projStr += "+x_0=" + pVar.findAttribute("false_easting").getValue(0).toString();
}
if (pVar.findAttribute("false_northing") != null) {
projStr += "+y_0=" + pVar.findAttribute("false_northing").getValue(0).toString();
}
break;
case "orthographic":
projStr = "+proj=ortho"
+ "+lon_0=" + pVar.findAttribute("longitude_of_projection_origin").getValue(0).toString()
+ "+lat_0=" + pVar.findAttribute("latitude_of_projection_origin").getValue(0).toString();
if (pVar.findAttribute("false_easting") != null) {
projStr += "+x_0=" + pVar.findAttribute("false_easting").getValue(0).toString();
}
if (pVar.findAttribute("false_northing") != null) {
projStr += "+y_0=" + pVar.findAttribute("false_northing").getValue(0).toString();
}
break;
case "polar_stereographic":
projStr = "+proj=stere";
if (pVar.findAttribute("longitude_of_projection_origin") != null) {
projStr += "+lon_0=" + pVar.findAttribute("longitude_of_projection_origin").getValue(0).toString();
} else if (pVar.findAttribute("straight_vertical_longitude_from_pole") != null) {
projStr += "+lon_0=" + pVar.findAttribute("straight_vertical_longitude_from_pole").getValue(0).toString();
}
if (pVar.findAttribute("latitude_of_projection_origin") != null) {
projStr += "+lat_0=" + pVar.findAttribute("latitude_of_projection_origin").getValue(0).toString();
}
if (pVar.findAttribute("standard_parallel") != null) {
projStr += "+lat_ts=" + pVar.findAttribute("standard_parallel").getValue(0).toString();
}
if (pVar.findAttribute("scaling_factor") != null) {
projStr += "+k=" + pVar.findAttribute("scaling_factor").getValue(0).toString();
} else if (pVar.findAttribute("standard_parallel") != null) {
String stPs = pVar.findAttribute("standard_parallel").getValue(0).toString();
//projStr += "+lat_ts=" + stPs;
double k0 = ProjectionInfo.calScaleFactorFromStandardParallel(Double.parseDouble(stPs));
projStr += "+k=" + String.format("%1$.2f", k0);
} else if (pVar.findAttribute("scale_factor_at_projection_origin") != null) {
projStr += "+k_0=" + pVar.findAttribute("scale_factor_at_projection_origin").getValue(0).toString();
}
if (pVar.findAttribute("false_easting") != null) {
projStr += "+x_0=" + pVar.findAttribute("false_easting").getValue(0).toString();
}
if (pVar.findAttribute("false_northing") != null) {
projStr += "+y_0=" + pVar.findAttribute("false_northing").getValue(0).toString();
}
break;
case "rotated_latitude_longitude":
break;
case "stereographic":
projStr = "+proj=stere"
+ "+lon_0=" + pVar.findAttribute("longitude_of_projection_origin").getValue(0).toString()
+ "+lat_0=" + pVar.findAttribute("latitude_of_projection_origin").getValue(0).toString()
+ "+k_0=" + pVar.findAttribute("scale_factor_at_projection_origin").getValue(0).toString();
if (pVar.findAttribute("false_easting") != null) {
projStr += "+x_0=" + pVar.findAttribute("false_easting").getValue(0).toString();
}
if (pVar.findAttribute("false_northing") != null) {
projStr += "+y_0=" + pVar.findAttribute("false_northing").getValue(0).toString();
}
break;
case "transverse_mercator":
projStr = "+proj=tmerc"
+ "+lon_0=" + pVar.findAttribute("longitude_of_central_meridian").getValue(0).toString()
+ "+lat_0=" + pVar.findAttribute("latitude_of_projection_origin").getValue(0).toString()
+ "+k_0=" + pVar.findAttribute("scale_factor_at_central_meridian").getValue(0).toString();
if (pVar.findAttribute("false_easting") != null) {
projStr += "+x_0=" + pVar.findAttribute("false_easting").getValue(0).toString();
}
if (pVar.findAttribute("false_northing") != null) {
projStr += "+y_0=" + pVar.findAttribute("false_northing").getValue(0).toString();
}
break;
case "vertical_perspective":
projStr = "+proj=geos"
+ "+lon_0=" + pVar.findAttribute("longitude_of_projection_origin").getValue(0).toString()
+ "+lat_0=" + pVar.findAttribute("latitude_of_projection_origin").getValue(0).toString()
+ "+h=" + pVar.findAttribute("perspective_point_height").getValue(0).toString();
if (pVar.findAttribute("false_easting") != null) {
projStr += "+x_0=" + pVar.findAttribute("false_easting").getValue(0).toString();
}
if (pVar.findAttribute("false_northing") != null) {
projStr += "+y_0=" + pVar.findAttribute("false_northing").getValue(0).toString();
}
break;
}
}
}
}
try {
ProjectionInfo projInfo = ProjectionInfo.factory(projStr);
return projInfo;
} catch (Exception e) {
return KnownCoordinateSystems.geographic.world.WGS1984;
}
}
private ProjectionInfo getProjection_IOAPI() {
String projStr = this.getProjectionInfo().toProj4String();
int gridType = Integer.parseInt(getGlobalAttStr("GDTYP"));
switch (gridType) {
case 1: //Lat-Lon
break;
case 2: //Lambert conformal conic
projStr = "+proj=lcc"
+ "+lon_0=" + getGlobalAttStr("P_GAM")
+ "+lat_0=" + getGlobalAttStr("YCENT")
+ "+lat_1=" + getGlobalAttStr("P_ALP")
+ "+lat_2=" + getGlobalAttStr("P_BET");
break;
case 3: //General Mercator (hotine oblique mercator)
projStr = "+proj=omerc"
+ "+lat_0=" + getGlobalAttStr("P_ALP")
+ "+lonc=" + getGlobalAttStr("P_BET")
+ "+alpha=" + getGlobalAttStr("P_GAM");
break;
case 4: //tangent stereographic
projStr = "+proj=stere"
+ "+lon_0=" + getGlobalAttStr("P_BET")
+ "+lat_0=" + getGlobalAttStr("P_ALP");
break;
case 5: //UTM
projStr = "+proj=utm"
+ "+zone=" + getGlobalAttStr("P_ALP");
break;
case 6: //polar secant stereographic
String lat0 = "90";
if (getGlobalAttStr("P_ALP").substring(0, 1).equals("-")) {
lat0 = "-90";
}
projStr = "+proj=stere"
+ "+lon_0=" + getGlobalAttStr("P_GAM")
+ "+lat_0=" + lat0;
String stPs = getGlobalAttStr("P_BET");
//projStr += "+lat_ts=" + stPs;
double k0 = ProjectionInfo.calScaleFactorFromStandardParallel(Double.parseDouble(stPs));
projStr += "+k=" + String.valueOf(k0);
break;
case 7: //Equatorial Mercator
projStr = "+proj=merc"
+ "+lat_ts=" + getGlobalAttStr("P_ALP")
+ "+lon_0=" + getGlobalAttStr("P_GAM");
break;
case 8: //Transverse Mercator
projStr = "+proj=tmerc"
+ "+lon_0=" + getGlobalAttStr("P_GAM")
+ "+lat_0=" + getGlobalAttStr("P_ALP");
break;
case 9: //Albers Equal-Area Conic
projStr = "+proj=aea"
+ "+lat_1=" + getGlobalAttStr("P_ALP")
+ "+lat_2=" + getGlobalAttStr("P_BET")
+ "+lat_0=" + getGlobalAttStr("YCENT")
+ "+lon_0=" + getGlobalAttStr("P_GAM");
break;
case 10: //Lambert Azimuthal Equal-Area
projStr = "+proj=laea"
+ "+lat_0=" + getGlobalAttStr("P_ALP")
+ "+lon_0=" + getGlobalAttStr("P_GAM");
break;
}
return ProjectionInfo.factory(projStr);
}
private ProjectionInfo getProjection_WRFOUT() {
String projStr = this.getProjectionInfo().toProj4String();
String pstr = this.getGlobalAttStr("MAP_PROJ");
if (pstr.isEmpty()) {
return this.getProjectionInfo();
}
int mapProj = Integer.parseInt(pstr);
String lon_0 = getGlobalAttStr("STAND_LON");
if (lon_0.isEmpty()) {
lon_0 = getGlobalAttStr("CEN_LON");
}
switch (mapProj) {
case 1: //Lambert conformal
projStr = "+proj=lcc"
+ "+lon_0=" + lon_0
+ "+lat_0=" + getGlobalAttStr("CEN_LAT")
+ "+lat_1=" + getGlobalAttStr("TRUELAT1")
+ "+lat_2=" + getGlobalAttStr("TRUELAT2");
break;
case 2: //Polar Stereographic
String lat0 = "90";
if (getGlobalAttStr("POLE_LAT").substring(0, 1).equals("-")) {
lat0 = "-90";
}
projStr = "+proj=stere"
+ "+lon_0=" + lon_0
+ "+lat_0=" + lat0;
String stPs = getGlobalAttStr("CEN_LAT");
//projStr += "+lat_ts=" + stPs;
double k0 = ProjectionInfo.calScaleFactorFromStandardParallel(Double.parseDouble(stPs));
projStr += "+k=" + String.valueOf(k0);
break;
case 3: //Mercator
projStr = "+proj=merc"
+ "+lat_ts=" + getGlobalAttStr("CEN_LAT")
+ "+lon_0=" + lon_0;
break;
}
ProjectionInfo projInfo = ProjectionInfo.factory(projStr);
//double clon = Double.parseDouble(this.getGlobalAttStr("CEN_LON"));
//double clat = Double.parseDouble(this.getGlobalAttStr("CEN_LAT"));
//projInfo.setCenterLat(clat);
//projInfo.setCenterLon(clon);
return projInfo;
}
private String getGlobalAttStr(String attName) {
String attStr = "";
for (ucar.nc2.Attribute aAttS : this.ncAttributes) {
if (aAttS.getShortName().equals(attName)) {
attStr = aAttS.getValue(0).toString();
break;
}
}
return attStr;
}
private List getTimes(ucar.nc2.Variable aVar, Array values) {
//Get start time
String unitsStr;
int i;
List times = new ArrayList<>();
ucar.nc2.Attribute unitAtt = aVar.findAttribute("units");
if (unitAtt == null) {
LocalDateTime sTime = LocalDateTime.of(1985, 1, 1, 0, 0);
IndexIterator ii = values.getIndexIterator();
while (ii.hasNext()) {
times.add(sTime.plusHours(ii.getIntNext()));
}
return times;
}
unitsStr = unitAtt.getStringValue();
if (unitsStr.contains("as")) {
if (unitsStr.contains("%")) {
return null;
}
//Get data time
DateTimeFormatter format = DateTimeFormatter.ofPattern("yyyyMMdd");
for (i = 0; i < values.getSize(); i++) {
String md = String.valueOf(values.getInt(i));
if (md.length() <= 3) {
md = "0" + md;
}
times.add(LocalDateTime.parse(md, format));
}
} else {
TimeUnit aTU;
LocalDateTime sTime = LocalDateTime.now();
if (unitsStr.equalsIgnoreCase("month")) {
sTime = LocalDateTime.of(sTime.getYear(), 1, 1, 0, 0, 0);
aTU = TimeUnit.Month;
} else {
aTU = this.getTimeUnit(unitsStr);
sTime = this.getStartTime(unitsStr);
}
//getPSDTimeInfo(unitsStr, sTime, aTU);
//Get data time
for (i = 0; i < values.getSize(); i++) {
switch (aTU) {
case Year:
times.add(sTime.plusYears(values.getInt(i)));
break;
case Month:
// if (unitsStr.equalsIgnoreCase("month")) {
// cal.add(Calendar.MONTH, values.getInt(i) - 1);
// } else {
// cal.add(Calendar.MONTH, values.getInt(i));
// }
times.add(sTime.plusMonths(values.getInt(i)));
break;
case Day:
times.add(sTime.plusDays(values.getInt(i)));
break;
case Hour:
if (sTime.getYear() == 1 && sTime.getMonthValue() == 1
&& sTime.getDayOfMonth() == 1 && values.getInt(i) > 48) {
times.add(sTime.plusHours(values.getInt(i) - 48));
} else {
times.add(sTime.plusHours(values.getInt(i)));
}
break;
case Minute:
times.add(sTime.plusMinutes(values.getInt(i)));
break;
case Second:
times.add(sTime.plusSeconds(values.getInt(i)));
break;
}
}
}
return times;
}
private boolean getDimensionValues(NetcdfFile ncfile) throws IOException, ParseException {
switch (_convention) {
case CF:
if (this._isHDFEOS) {
getDimValues_HDFEOS_SWATH();
} else {
getDimValues_CF();
if (this.getXDimension() == null || this.getYDimension() == null) {
if (this.findNCVariable("Longitude") != null && this.findNCVariable("Latitude") != null) {
this._isSWATH = true;
}
}
}
break;
case IOAPI:
getDimValues_IOAPI();
break;
case WRFOUT:
getDimValues_WRF(ncfile);
break;
default:
return false;
}
return true;
}
private void getDimValues_HDFEOS_SWATH() throws IOException {
if (this._isSWATH || this._isPROFILE) {
ucar.nc2.Variable var = this.findNCVariable("Pressure");
if (var != null) {
Array darray = NCUtil.convertArray(var.read());
int n = (int) darray.getSize();
double[] values = new double[n];
for (int i = 0; i < n; i++) {
values[i] = darray.getDouble(i);
}
Dimension zDim = this.findDimension(var.getDimension(0).getShortName());
zDim.setDimType(DimensionType.Z);
zDim.setValues(values);
this.setZDimension(zDim);
} else {
//var = this.getNCVariable("")
}
var = this.findNCVariable("Time");
if (var != null && var.getDimensions().size() == 1) {
Array darray = NCUtil.convertArray(var.read());
List times = this.getTimes(var, darray);
List ts = new ArrayList<>();
for (LocalDateTime t : times) {
ts.add(JDateUtil.toOADate(t));
}
Dimension tDim = this.findDimension(var.getDimension(0).getShortName());
if (tDim != null) {
tDim.setDimType(DimensionType.T);
tDim.setValues(ts);
this.setTimeDimension(tDim);
}
}
}
}
private void getDimValues_CF() throws IOException {
for (ucar.nc2.Variable var : ncVariables) {
if (var.getRank() == 1) {
if (!var.getDataType().isNumeric()) {
continue;
}
int idx = this.getDimensionIndex(var.getDimension(0));
if (idx == -1) {
continue;
}
Dimension dim = this.dimensions.get(idx);
if (dim.getDimType() != DimensionType.OTHER) {
continue;
}
DimensionType dimType = getDimType(var);
dim.setDimType(dimType);
Array values = NCUtil.convertArray(var.read());
if (values.getSize() > 1) {
if (values.getDouble(0) > values.getDouble(1)) {
switch (dimType) {
case X:
this.setXReverse(true);
dim.setReverse(true);
//values = values.flip(0);
break;
case Y:
this.setYReverse(true);
dim.setReverse(true);
//values = values.flip(0);
break;
}
}
}
//aDim.setValues(values);
switch (dimType) {
case X:
double[] X = (double[]) ArrayUtil.copyToNDJavaArray_Double(values);
if (X.length > 1) {
double XDelt = X[1] - X[0];
if (this.getProjectionInfo().isLonLat()) {
if (X[X.length - 1] + XDelt
- X[0] == 360) {
this.setGlobal(true);
}
}
}
if (!this.getProjectionInfo().isLonLat()) {
ucar.nc2.Attribute unitAtt = var.findAttribute("units");
if (unitAtt != null) {
if (unitAtt.getStringValue().trim().toLowerCase().equals("km")) {
for (int i = 0; i < X.length; i++) {
X[i] = X[i] * 1000;
}
}
}
}
dim.setValues(X);
this.setXDimension(dim);
break;
case Y:
double[] Y = (double[]) ArrayUtil.copyToNDJavaArray_Double(values);
if (!this.getProjectionInfo().isLonLat()) {
ucar.nc2.Attribute unitAtt = var.findAttribute("units");
if (unitAtt != null) {
if (unitAtt.getStringValue().trim().toLowerCase().equals("km")) {
for (int i = 0; i < Y.length; i++) {
Y[i] = Y[i] * 1000;
}
}
}
}
dim.setValues(Y);
this.setYDimension(dim);
break;
case Z:
double[] levels = (double[]) ArrayUtil.copyToNDJavaArray_Double(values);
dim.setValues(levels);
this.setZDimension(dim);
break;
case T:
List times = this.getTimes(var, values);
if (times != null) {
List ts = new ArrayList<>();
for (LocalDateTime t : times) {
ts.add(JDateUtil.toOADate(t));
}
dim.setValues(ts);
}
this.setTimeDimension(dim);
break;
default:
dim.setValues((double[]) ArrayUtil.copyToNDJavaArray_Double(values));
break;
}
}
}
}
private void getDimValues_IOAPI() {
int i;
//Get times
String sDateStr = getGlobalAttStr("SDATE");
String sTimeStr = getGlobalAttStr("STIME");
int len = sTimeStr.length();
LocalDateTime tt = LocalDateTime.now();
try {
tt = LocalDateTime.of(Integer.parseInt(sDateStr.substring(0, 4)), 1, 1, 0, 0, 0);
if (MIMath.isNumeric(sDateStr.substring(4))) {
tt = tt.plusDays(Integer.parseInt(sDateStr.substring(4)) - 1);
}
} catch (NumberFormatException e) {
e.printStackTrace();
}
if (sTimeStr.length() <= 2) {
tt = tt.plusSeconds(Integer.parseInt(sTimeStr));
} else if (sTimeStr.length() <= 4) {
tt = tt.plusMinutes(Integer.parseInt(sTimeStr.substring(0, len - 2)));
tt = tt.plusSeconds(Integer.parseInt(sTimeStr.substring(len - 2)));
} else {
tt = tt.plusHours(Integer.parseInt(sTimeStr.substring(0, len - 4)));
tt = tt.plusMinutes(Integer.parseInt(sTimeStr.substring(len - 4, len - 2)));
tt = tt.plusSeconds(Integer.parseInt(sTimeStr.substring(len - 2)));
}
int tNum = getDimensionLength("TSTEP");
sTimeStr = getGlobalAttStr("TSTEP");
len = sTimeStr.length();
List times = new ArrayList<>();
times.add(tt);
for (i = 1; i < tNum; i++) {
if (sTimeStr.length() <= 2) {
tt = tt.plusSeconds(Integer.parseInt(sTimeStr));
} else if (sTimeStr.length() <= 4) {
tt = tt.plusMinutes(Integer.parseInt(sTimeStr.substring(0, len - 2)));
tt = tt.plusSeconds(Integer.parseInt(sTimeStr.substring(len - 2)));
} else {
tt = tt.plusHours(Integer.parseInt(sTimeStr.substring(0, len - 4)));
tt = tt.plusMinutes(Integer.parseInt(sTimeStr.substring(len - 4, len - 2)));
tt = tt.plusSeconds(Integer.parseInt(sTimeStr.substring(len - 2)));
}
times.add(tt);
}
List values = new ArrayList<>();
for (LocalDateTime t : times) {
values.add(JDateUtil.toOADate(t));
}
Dimension tDim = this.findDimension("TSTEP");
if (tDim != null) {
tDim.setDimType(DimensionType.T);
tDim.setValues(values);
this.setTimeDimension(tDim);
}
//Get levels
Attribute levAtt = this.findGlobalAttribute("VGLVLS");
Array array = levAtt.getValues();
int znum = (int) array.getSize() - 1;
double[] levels = new double[znum];
for (i = 0; i < znum; i++) {
levels[i] = (array.getDouble(i) + array.getDouble(i + 1)) / 2;
}
// String[] levStrs = levStr.split(",");
// for (i = 0; i < levStrs.length - 1; i++) {
// levels[i] = (Double.parseDouble(levStrs[i].trim()) + Double.parseDouble(levStrs[i + 1].trim())) / 2;
// }
Dimension zDim = this.findDimension("LAY");
if (zDim != null) {
zDim.setDimType(DimensionType.Z);
zDim.setValues(levels);
this.setZDimension(zDim);
}
//Get X array
int xNum = Integer.parseInt(getGlobalAttStr("NCOLS"));
double[] X = new double[xNum];
double sx = Double.parseDouble(getGlobalAttStr("XORIG"));
double XDelt = Double.parseDouble(getGlobalAttStr("XCELL"));
for (i = 0; i < xNum; i++) {
X[i] = sx + XDelt * i;
}
Dimension xDim = this.findDimension("COL");
if (xDim != null) {
xDim.setDimType(DimensionType.X);
xDim.setValues(X);
this.setXDimension(xDim);
}
//Get Y array
int yNum = Integer.parseInt(getGlobalAttStr("NROWS"));
double[] Y = new double[yNum];
double sy = Double.parseDouble(getGlobalAttStr("YORIG"));
double YDelt = Double.parseDouble(getGlobalAttStr("YCELL"));
for (i = 0; i < yNum; i++) {
Y[i] = sy + YDelt * i;
}
Dimension yDim = this.findDimension("ROW");
if (yDim != null) {
yDim.setDimType(DimensionType.Y);
yDim.setValues(Y);
this.setYDimension(yDim);
}
}
private void getDimValues_WRF(NetcdfFile ncfile) throws ParseException, IOException {
int dimLen, i;
double orgLon, orgLat, orgX, orgY;
Dimension xDim = this.findDimension("west_east");
Dimension yDim = this.findDimension("south_north");
if (xDim != null && yDim != null) {
xDim.setDimType(DimensionType.X);
yDim.setDimType(DimensionType.Y);
int xNum = xDim.getLength();
int yNum = yDim.getLength();
//List varNameList = this.getVariableNames();
_yVar = ncfile.findVariable("XLAT");
if (_yVar == null) {
_yVar = ncfile.findVariable("XLAT_M");
}
_xVar = ncfile.findVariable("XLONG");
if (_xVar == null) {
_xVar = ncfile.findVariable("XLONG_M");
}
_levelVar = ncfile.findVariable("ZNU");
//Get X/Y Array
double dx = Double.parseDouble(getGlobalAttStr("DX"));
double dy = Double.parseDouble(getGlobalAttStr("DY"));
ProjectionInfo fromProj = KnownCoordinateSystems.geographic.world.WGS1984;
double[][] points = new double[1][];
if (_yVar != null && _xVar != null) {
dimLen = yNum;
Array yarray = NCUtil.convertArray(_yVar.read().reduce());
double[] xlat = new double[dimLen];
for (i = 0; i < dimLen; i++) {
xlat[i] = yarray.getDouble(i);
}
orgLat = xlat[0];
dimLen = xNum;
Array xarray = NCUtil.convertArray(_xVar.read().reduce());
double[] xlon = new double[dimLen];
for (i = 0; i < dimLen; i++) {
xlon[i] = xarray.getDouble(i);
}
orgLon = xlon[0];
points[0] = new double[]{orgLon, orgLat};
Reproject.reprojectPoints(points, fromProj, this.getProjectionInfo(), 0, 1);
orgX = points[0][0];
orgY = points[0][1];
} else {
double clon = Double.parseDouble(getGlobalAttStr("CEN_LON"));
double clat = Double.parseDouble(getGlobalAttStr("CEN_LAT"));
points[0] = new double[]{clon, clat};
Reproject.reprojectPoints(points, fromProj, this.getProjectionInfo(), 0, 1);
double cx = points[0][0];
double cy = points[0][1];
orgX = cx - dx * xNum * 0.5;
orgY = cy - dy * yNum * 0.5;
}
double[] X = new double[xNum];
for (i = 0; i < xNum; i++) {
X[i] = orgX + dx * i;
}
xDim.setValues(X);
this.setXDimension(xDim);
double[] Y = new double[yNum];
for (i = 0; i < yNum; i++) {
Y[i] = orgY + dy * i;
}
yDim.setValues(Y);
this.setYDimension(yDim);
Dimension xsdim = findDimension("west_east_stag");
Dimension ysdim = findDimension("south_north_stag");
if (xsdim != null && ysdim != null) {
xsdim.setDimType(DimensionType.X);
double[] nX = new double[xNum + 1];
double norgX = orgX - dx * 0.5;
for (i = 0; i <= xNum; i++) {
nX[i] = norgX + dx * i;
}
xsdim.setValues(nX);
ysdim.setDimType(DimensionType.Y);
double[] nY = new double[yNum + 1];
double norgY = orgY - dx * 0.5;
for (i = 0; i <= yNum; i++) {
nY[i] = norgY + dy * i;
}
ysdim.setValues(nY);
}
}
//Get levels
Dimension zDim = this.findDimension("bottom_up");
if (zDim == null) {
zDim = this.findDimension("bottom_top");
}
if (zDim != null) {
int lNum = zDim.getLength();
if (_levelVar != null) {
dimLen = lNum;
Array larray = NCUtil.convertArray(_levelVar.read().reduce());
double[] levels = new double[lNum];
for (i = 0; i < lNum; i++) {
if (i < dimLen) {
levels[i] = larray.getDouble(i);
} else {
break;
}
}
zDim.setDimType(DimensionType.Z);
//zDim.setDimName(_levelVar.getShortName());
zDim.setValues(levels);
this.setZDimension(zDim);
}
}
zDim = this.findDimension("bottom_up_stag");
if (zDim == null) {
zDim = this.findDimension("bottom_top_stag");
}
if (zDim != null) {
int lNum = zDim.getLength();
ucar.nc2.Variable levelVar = ncfile.findVariable("ZNW");
if (levelVar != null) {
dimLen = lNum;
Array larray = NCUtil.convertArray(levelVar.read().reduce());
double[] levels = new double[lNum];
for (i = 0; i < lNum; i++) {
if (i < dimLen) {
levels[i] = larray.getDouble(i);
} else {
break;
}
}
zDim.setDimType(DimensionType.Z);
//zDim.setDimName(_levelVar.getShortName());
zDim.setValues(levels);
//this.setZDimension(zDim);
}
}
zDim = this.findDimension("soil_layers_stag");
if (zDim != null) {
int lNum = zDim.getLength();
ucar.nc2.Variable levelVar = ncfile.findVariable("ZS");
if (levelVar != null) {
dimLen = lNum;
Array larray = NCUtil.convertArray(levelVar.read().reduce());
double[] levels = new double[lNum];
for (i = 0; i < lNum; i++) {
if (i < dimLen) {
levels[i] = larray.getDouble(i);
} else {
break;
}
}
zDim.setDimType(DimensionType.Z);
//zDim.setDimName(_levelVar.getShortName());
zDim.setValues(levels);
//this.setZDimension(zDim);
}
}
for (ucar.nc2.Variable aVarS : ncVariables) {
//dimLen = aVarS.getShape(0);
//Get times
if (aVarS.getShortName().toLowerCase().equals("times") && aVarS.getRank() == 2) {
Dimension tDim = this.findDimension("Time");
int tNum = tDim.getLength();
List times = new ArrayList<>();
ucar.nc2.Dimension tsDim = ncfile.findDimension("DateStrLen");
int strLen = tsDim.getLength();
char[] charData = new char[tNum * strLen];
Array tArray = NCUtil.convertArray(aVarS.read());
if (tArray.getSize() == 0) {
times.add(LocalDateTime.now());
} else {
for (i = 0; i < tNum * strLen; i++) {
charData[i] = tArray.getChar(i);
}
String tStr;
DateTimeFormatter format;
if (strLen == 19)
format = DateTimeFormatter.ofPattern("yyyy-MM-dd_HH:mm:ss");
else
format = DateTimeFormatter.ofPattern("yyyyMMdd_HHmmss");
for (i = 0; i < tNum; i++) {
StringBuilder timeStr = new StringBuilder();
for (int j = 0; j < strLen; j++) {
timeStr.append(charData[i * strLen + j]);
}
tStr = timeStr.toString();
if (tStr.contains("0000-00-00")) {
tStr = "0001-01-01_00:00:00";
}
times.add(LocalDateTime.parse(tStr, format));
}
}
List values = new ArrayList<>();
for (LocalDateTime t : times) {
values.add(JDateUtil.toOADate(t));
}
tDim.setDimType(DimensionType.T);
//tDim.setDimName("times");
tDim.setValues(values);
this.setTimeDimension(tDim);
break;
}
}
}
private int getDimensionLength(String dimName) {
for (ucar.nc2.Dimension aDimS : ncDimensions) {
if (aDimS.getShortName().equals(dimName)) {
return aDimS.getLength();
}
}
return -1;
}
private int getVarLength(Variable aVarS) {
int dataLen = 1;
for (int i = 0; i < aVarS.getDimNumber(); i++) {
dataLen = dataLen * aVarS.getDimensions().get(i).getLength();
}
return dataLen;
}
/**
* Find netCDF variable by name
*
* @param name Variable name
* @return NetCDF variable
*/
public ucar.nc2.Variable findNCVariable(String name) {
for (ucar.nc2.Variable var : this.ncVariables) {
if (var.getShortName().equalsIgnoreCase(name)) {
return var;
}
}
return null;
}
private DimensionType getDimType(ucar.nc2.Variable aVar) {
String sName;
DimensionType dimType = DimensionType.OTHER;
if (_fileTypeId.equals("HDF5-EOS")) {
sName = aVar.getShortName().toLowerCase();
switch (sName) {
case "longitude":
dimType = DimensionType.X;
break;
case "latitude":
dimType = DimensionType.Y;
break;
case "pressure":
dimType = DimensionType.Z;
break;
case "time":
dimType = DimensionType.T;
break;
}
} else {
if (aVar.findAttributeIgnoreCase("standard_name") != null) {
ucar.nc2.Attribute axisAtt = aVar.findAttributeIgnoreCase("standard_name");
sName = axisAtt.getStringValue().trim().toLowerCase();
switch (sName) {
case "longitude":
case "projection_x_coordinate":
case "longitude_east":
dimType = DimensionType.X;
break;
case "latitude":
case "projection_y_coordinate":
case "latitude_north":
dimType = DimensionType.Y;
break;
case "time":
dimType = DimensionType.T;
break;
case "level":
dimType = DimensionType.Z;
break;
}
}
if (dimType == DimensionType.OTHER) {
if (aVar.findAttributeIgnoreCase("long_name") != null) {
ucar.nc2.Attribute axisAtt = aVar.findAttributeIgnoreCase("long_name");
sName = axisAtt.getStringValue().trim().toLowerCase();
switch (sName) {
case "longitude":
case "coordinate longitude":
case "x":
dimType = DimensionType.X;
break;
case "latitude":
case "coordinate latitude":
case "y":
dimType = DimensionType.Y;
break;
case "time":
case "initial time":
dimType = DimensionType.T;
break;
case "level":
case "pressure":
case "pressure_level":
case "isobaric surface":
dimType = DimensionType.Z;
break;
default:
if (sName.contains("level") || sName.contains("depths")) {
dimType = DimensionType.Z;
}
break;
}
}
}
if (dimType == DimensionType.OTHER) {
if (aVar.findAttributeIgnoreCase("axis") != null) {
ucar.nc2.Attribute axisAtt = aVar.findAttributeIgnoreCase("axis");
sName = axisAtt.getStringValue().trim().toLowerCase();
switch (sName) {
case "x":
dimType = DimensionType.X;
break;
case "y":
dimType = DimensionType.Y;
break;
case "z":
dimType = DimensionType.Z;
break;
case "t":
dimType = DimensionType.T;
break;
}
}
}
if (dimType == DimensionType.OTHER) {
if (aVar.findAttributeIgnoreCase("GRIB_level_type") != null) {
dimType = DimensionType.Z;
}
}
if (dimType == DimensionType.OTHER) {
if (aVar.findAttributeIgnoreCase("Grib2_level_type") != null) {
dimType = DimensionType.Z;
}
}
if (dimType == DimensionType.OTHER) {
if (aVar.findAttributeIgnoreCase("hybrid_layer") != null) {
dimType = DimensionType.Z;
}
}
if (dimType == DimensionType.OTHER) {
if (aVar.findAttributeIgnoreCase("unitsCategory") != null) {
sName = aVar.findAttributeIgnoreCase("unitsCategory").getStringValue().trim().toLowerCase();
switch (sName) {
case "longitude":
dimType = DimensionType.X;
break;
case "latitude":
dimType = DimensionType.Y;
break;
}
}
}
if (dimType == DimensionType.OTHER) {
String vName = aVar.getShortName().toLowerCase();
switch (vName) {
case "lon":
case "longitude":
case "x":
dimType = DimensionType.X;
break;
case "lat":
case "latitude":
case "y":
dimType = DimensionType.Y;
break;
case "time":
dimType = DimensionType.T;
break;
case "level":
case "lev":
case "height":
case "isobaric":
case "pressure":
case "depth":
dimType = DimensionType.Z;
break;
}
}
}
return dimType;
}
private TimeUnit getTimeUnit(String tStr) {
TimeUnit aTU = TimeUnit.Second;
tStr = tStr.trim();
String tu;
String[] dataArray;
int i;
dataArray = tStr.split("\\s+");
if (dataArray.length < 2) {
return aTU;
}
//Get time unit
tu = dataArray[0];
if (tu.toLowerCase().contains("second")) {
aTU = TimeUnit.Second;
} else if (tu.length() == 1) {
String str = tu.toLowerCase();
switch (str) {
case "y":
aTU = TimeUnit.Year;
break;
case "d":
aTU = TimeUnit.Day;
break;
case "h":
aTU = TimeUnit.Hour;
break;
case "s":
aTU = TimeUnit.Second;
break;
}
} else {
String str = tu.toLowerCase().substring(0, 2);
switch (str) {
case "yr":
case "ye":
aTU = TimeUnit.Year;
break;
case "mo":
aTU = TimeUnit.Month;
break;
case "da":
aTU = TimeUnit.Day;
break;
case "hr":
case "ho":
aTU = TimeUnit.Hour;
break;
case "mi":
aTU = TimeUnit.Minute;
break;
case "se":
aTU = TimeUnit.Second;
break;
}
}
return aTU;
}
private LocalDateTime getStartTime(String tStr) {
LocalDateTime sTime = LocalDateTime.now();
tStr = tStr.trim();
String[] dataArray;
dataArray = tStr.split("\\s+");
if (dataArray.length < 3) {
return sTime;
}
//Get start time
String ST;
ST = dataArray[2];
if (ST.contains("T")) {
dataArray = Arrays.copyOf(dataArray, dataArray.length + 1);
dataArray[dataArray.length - 1] = ST.split("T")[1];
ST = ST.split("T")[0];
}
int year = 2000, month = 1, day = 1;
int hour = 0, min = 0, sec = 0;
if (ST.contains("-")) {
String[] darray1 = ST.split("-");
year = Integer.parseInt(darray1[0]);
month = Integer.parseInt(darray1[1]);
if (darray1[2].length() > 2) {
darray1[2] = darray1[2].substring(0, 2);
}
day = Integer.parseInt(darray1[2]);
if (dataArray.length >= 4) {
String hmsStr = dataArray[3];
hmsStr = hmsStr.replace("0.0", "00");
try {
String[] hms = hmsStr.split(":");
hour = Integer.parseInt(hms[0]);
if (hms.length > 1) {
min = Integer.parseInt(hms[1]);
}
if (hms.length > 2) {
sec = Integer.parseInt(hms[2]);
}
} catch (NumberFormatException e) {
}
}
} else if (ST.contains(":")) {
String hmsStr = ST;
hmsStr = hmsStr.replace("0.0", "00");
try {
String[] hms = hmsStr.split(":");
hour = Integer.parseInt(hms[0]);
if (hms.length > 1) {
min = Integer.parseInt(hms[1]);
}
if (hms.length > 2) {
sec = Integer.parseInt(hms[2]);
}
} catch (Exception e) {
}
}
if (year == 0) {
year = 1;
}
sTime = LocalDateTime.of(year, month, day, hour, min, sec);
return sTime;
}
@Override
public String generateInfoText() {
String dataInfo;
int i, j;
ucar.nc2.Attribute aAttS;
dataInfo = "File Name: " + this.getFileName();
dataInfo += System.getProperty("line.separator") + "File type: " + _fileTypeStr + " (" + _fileTypeId + ")";
dataInfo += System.getProperty("line.separator") + "Dimensions: " + ncDimensions.size();
for (i = 0; i < ncDimensions.size(); i++) {
dataInfo += System.getProperty("line.separator") + "\t" + ncDimensions.get(i).getShortName() + " = "
+ String.valueOf(ncDimensions.get(i).getLength()) + ";";
}
Dimension xdim = this.getXDimension();
if (xdim != null) {
dataInfo += System.getProperty("line.separator") + "X Dimension: Xmin = " + String.valueOf(xdim.getMinValue())
+ "; Xmax = " + String.valueOf(xdim.getMaxValue()) + "; Xsize = "
+ String.valueOf(xdim.getLength()) + "; Xdelta = " + String.valueOf(xdim.getDeltaValue());
}
Dimension ydim = this.getYDimension();
if (ydim != null) {
dataInfo += System.getProperty("line.separator") + "Y Dimension: Ymin = " + String.valueOf(ydim.getMinValue())
+ "; Ymax = " + String.valueOf(ydim.getMaxValue()) + "; Ysize = "
+ String.valueOf(ydim.getLength()) + "; Ydelta = " + String.valueOf(ydim.getDeltaValue());
}
dataInfo += System.getProperty("line.separator") + "Global Attributes: ";
for (i = 0; i < ncAttributes.size(); i++) {
aAttS = ncAttributes.get(i);
dataInfo += System.getProperty("line.separator") + "\t: " + aAttS.toString();
}
dataInfo += System.getProperty("line.separator") + "Variations: " + ncVariables.size();
for (i = 0; i < ncVariables.size(); i++) {
dataInfo += System.getProperty("line.separator") + "\t" + ncVariables.get(i).getDataType().toString()
+ " " + ncVariables.get(i).getFullName() + "(";
List dims = ncVariables.get(i).getDimensions();
for (j = 0; j < dims.size(); j++) {
dataInfo += dims.get(j).getShortName() + ",";
}
dataInfo = dataInfo.substring(0, dataInfo.length() - 1);
dataInfo += ");";
List atts = ncVariables.get(i).getAttributes();
for (j = 0; j < atts.size(); j++) {
aAttS = atts.get(j);
dataInfo += System.getProperty("line.separator") + "\t" + "\t" + ncVariables.get(i).getShortName()
+ ": " + aAttS.toString();
}
}
for (ucar.nc2.Dimension dim : ncDimensions) {
if (dim.isUnlimited()) {
dataInfo += System.getProperty("line.separator") + "Unlimited dimension: " + dim.getShortName();
}
break;
}
return dataInfo;
}
private int getTrueVarIndex(int varIdx) {
int tVarIdx = varIdx;
for (int i = 0; i < this.getVariables().size(); i++) {
Variable var = this.getVariables().get(i);
if (tVarIdx > i || (tVarIdx == i && var.isPlottable())) {
break;
}
if (!var.isPlottable()) {
tVarIdx += 1;
}
}
return tVarIdx;
}
private double[] getPackData(ucar.nc2.Variable var) {
double add_offset, scale_factor, missingValue = this.getMissingValue();
add_offset = 0;
scale_factor = 1;
for (int i = 0; i < var.getAttributes().size(); i++) {
ucar.nc2.Attribute att = var.getAttributes().get(i);
String attName = att.getShortName();
if (attName.equals("add_offset")) {
add_offset = Double.parseDouble(att.getValue(0).toString());
}
if (attName.equals("scale_factor")) {
scale_factor = Double.parseDouble(att.getValue(0).toString());
}
if (attName.equals("missing_value")) {
try {
missingValue = Double.parseDouble(att.getValue(0).toString());
} catch (NumberFormatException e) {
e.printStackTrace();
}
}
//MODIS NetCDF data
if (attName.equals("_FillValue")) {
try {
missingValue = Double.parseDouble(att.getValue(0).toString());
} catch (NumberFormatException e) {
e.printStackTrace();
}
}
}
// //Adjust undefine data
// if (Double.isNaN(missingValue)) {
// missingValue = this.getMissingValue();
// } else {
// missingValue = missingValue * scale_factor + add_offset;
// }
return new double[]{add_offset, scale_factor, missingValue};
}
/**
* Get grid data
*
* @param varName Variable name
* @return Grid data
*/
@Override
public GridArray getGridArray(String varName) {
return null;
}
@Override
public GridData getGridData_LonLat(int timeIdx, String varName, int levelIdx) {
try {
if (ncfile == null) {
//ncfile = NetcdfDatasets.openFile(this.getFileName(), null);
ncfile = NetcdfFile.open(this.fileName);
}
int i, j;
ucar.nc2.Variable var = ncfile.findVariable(varName);
//Get pack info
double add_offset, scale_factor, missingValue;
double[] packData = this.getPackData(var);
add_offset = packData[0];
scale_factor = packData[1];
missingValue = packData[2];
//Read grid data
Variable nvar = this.getVariable(varName);
int xNum, yNum;
xNum = nvar.getXDimension().getLength();
yNum = nvar.getYDimension().getLength();
double[][] gridData = new double[yNum][xNum];
int rank = var.getRank();
int[] origin = new int[rank];
int[] size = new int[rank];
int xdimIdx = 0;
int ydimIdx = 0;
for (i = 0; i < rank; i++) {
ucar.nc2.Dimension dim = var.getDimension(i);
Dimension ndim = (Dimension) nvar.getDimension(i);
switch (ndim.getDimType()) {
case T:
origin[i] = timeIdx;
size[i] = 1;
break;
case Z:
origin[i] = levelIdx;
size[i] = 1;
break;
case Y:
origin[i] = 0;
size[i] = yNum;
ydimIdx = i;
break;
case X:
origin[i] = 0;
size[i] = xNum;
xdimIdx = i;
break;
default:
origin[i] = 0;
size[i] = 1;
break;
}
}
Array data2D = NCUtil.convertArray(var.read(origin, size).reduce());
double v;
if (ydimIdx < xdimIdx) {
for (i = 0; i < yNum; i++) {
for (j = 0; j < xNum; j++) {
v = data2D.getDouble(i * xNum + j);
if (v == missingValue) {
gridData[i][j] = v;
} else {
gridData[i][j] = v * scale_factor + add_offset;
}
}
}
} else {
for (i = 0; i < yNum; i++) {
for (j = 0; j < xNum; j++) {
v = data2D.getDouble(j * yNum + i);
if (v == missingValue) {
gridData[i][j] = v;
} else {
gridData[i][j] = v * scale_factor + add_offset;
}
}
}
}
GridData aGridData = new GridData(gridData, nvar.getXDimension().getValues(),
nvar.getYDimension().getValues(), missingValue);
if (this._convention == Conventions.WRFOUT) {
if (nvar.getName().equals("U")) {
aGridData.setXStagger(true);
}
if (nvar.getName().equals("V")) {
aGridData.setYStagger(true);
}
}
return aGridData;
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (!this.keepOpen && null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
@Override
public GridData getGridData_TimeLat(int lonIdx, String varName, int levelIdx) {
try {
if (ncfile == null) {
//ncfile = NetcdfDataset.openFile(this.getFileName(), null);
ncfile = NetcdfFile.open(this.fileName);
}
int i, j;
ucar.nc2.Variable var = ncfile.findVariable(varName);
//Get pack info
double add_offset, scale_factor, missingValue;
double[] packData = this.getPackData(var);
add_offset = packData[0];
scale_factor = packData[1];
missingValue = packData[2];
//Read grid data
Variable nvar = this.getVariable(varName);
int xNum, yNum;
xNum = nvar.getYDimension().getLength();
yNum = nvar.getTDimension().getLength();
double[][] gridData = new double[yNum][xNum];
int rank = var.getRank();
int[] origin = new int[rank];
int[] size = new int[rank];
for (i = 0; i < rank; i++) {
Dimension ndim = (Dimension) nvar.getDimension(i);
switch (ndim.getDimType()) {
case T:
origin[i] = 0;
size[i] = yNum;
break;
case Z:
origin[i] = levelIdx;
size[i] = 1;
break;
case Y:
origin[i] = 0;
size[i] = xNum;
break;
case X:
origin[i] = lonIdx;
size[i] = 1;
break;
default:
origin[i] = 0;
size[i] = 1;
break;
}
}
Array data2D = NCUtil.convertArray(var.read(origin, size).reduce());
double v;
for (i = 0; i < yNum; i++) {
for (j = 0; j < xNum; j++) {
v = data2D.getDouble(i * xNum + j);
if (v == missingValue) {
gridData[i][j] = v;
} else {
gridData[i][j] = v * scale_factor + add_offset;
}
}
}
GridData aGridData = new GridData(gridData, nvar.getYDimension().getValues(),
nvar.getTDimension().getValues(), missingValue);
return aGridData;
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (null != ncfile) {
try {
ncfile.close();
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
@Override
public GridData getGridData_TimeLon(int latIdx, String varName, int levelIdx) {
try {
if (ncfile == null) {
//ncfile = NetcdfDataset.openFile(this.getFileName(), null);
ncfile = NetcdfFile.open(this.fileName);
}
int i, j;
ucar.nc2.Variable var = ncfile.findVariable(varName);
//Get pack info
double add_offset, scale_factor, missingValue;
double[] packData = this.getPackData(var);
add_offset = packData[0];
scale_factor = packData[1];
missingValue = packData[2];
//Read grid data
Variable nvar = this.getVariable(varName);
int xNum, yNum;
xNum = nvar.getXDimension().getLength();
yNum = nvar.getTDimension().getLength();
double[][] gridData = new double[yNum][xNum];
int rank = var.getRank();
int[] origin = new int[rank];
int[] size = new int[rank];
for (i = 0; i < rank; i++) {
Dimension ndim = (Dimension) nvar.getDimension(i);
switch (ndim.getDimType()) {
case T:
origin[i] = 0;
size[i] = yNum;
break;
case Z:
origin[i] = levelIdx;
size[i] = 1;
break;
case Y:
origin[i] = latIdx;
size[i] = 1;
break;
case X:
origin[i] = 0;
size[i] = xNum;
break;
default:
origin[i] = 0;
size[i] = 1;
break;
}
}
Array data2D = NCUtil.convertArray(var.read(origin, size).reduce());
double v;
for (i = 0; i < yNum; i++) {
for (j = 0; j < xNum; j++) {
v = data2D.getDouble(i * xNum + j);
if (v == missingValue) {
gridData[i][j] = v;
} else {
gridData[i][j] = v * scale_factor + add_offset;
}
}
}
GridData aGridData = new GridData(gridData, nvar.getXDimension().getValues(),
nvar.getTDimension().getValues(), missingValue);
return aGridData;
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (!this.keepOpen && null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
@Override
public GridData getGridData_LevelLat(int lonIdx, String varName, int timeIdx) {
try {
if (ncfile == null) {
//ncfile = NetcdfDataset.openFile(this.getFileName(), null);
ncfile = NetcdfFile.open(this.fileName);
}
int i, j;
ucar.nc2.Variable var = ncfile.findVariable(varName);
//Get pack info
double add_offset, scale_factor, missingValue;
double[] packData = this.getPackData(var);
add_offset = packData[0];
scale_factor = packData[1];
missingValue = packData[2];
//Read grid data
Variable nvar = this.getVariable(varName);
int xNum, yNum;
xNum = nvar.getYDimension().getLength();
yNum = nvar.getZDimension().getLength();
double[][] gridData = new double[yNum][xNum];
int rank = var.getRank();
int[] origin = new int[rank];
int[] size = new int[rank];
for (i = 0; i < rank; i++) {
Dimension ndim = (Dimension) nvar.getDimension(i);
switch (ndim.getDimType()) {
case T:
origin[i] = timeIdx;
size[i] = 1;
break;
case Z:
origin[i] = 0;
size[i] = yNum;
break;
case Y:
origin[i] = 0;
size[i] = xNum;
break;
case X:
origin[i] = lonIdx;
size[i] = 1;
break;
default:
origin[i] = 0;
size[i] = 1;
break;
}
}
Array data2D = NCUtil.convertArray(var.read(origin, size).reduce());
double v;
for (i = 0; i < yNum; i++) {
for (j = 0; j < xNum; j++) {
v = data2D.getDouble(i * xNum + j);
if (v == missingValue) {
gridData[i][j] = v;
} else {
gridData[i][j] = v * scale_factor + add_offset;
}
}
}
GridData aGridData = new GridData(gridData, nvar.getYDimension().getValues(),
nvar.getZDimension().getValues(), missingValue);
return aGridData;
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (!this.keepOpen && null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
@Override
public GridData getGridData_LevelLon(int latIdx, String varName, int timeIdx) {
try {
if (ncfile == null) {
//ncfile = NetcdfDataset.openFile(this.getFileName(), null);
ncfile = NetcdfFile.open(this.fileName);
}
int i, j;
ucar.nc2.Variable var = ncfile.findVariable(varName);
//Get pack info
double add_offset, scale_factor, missingValue;
double[] packData = this.getPackData(var);
add_offset = packData[0];
scale_factor = packData[1];
missingValue = packData[2];
//Read grid data
Variable nvar = this.getVariable(varName);
int xNum, yNum;
xNum = nvar.getXDimension().getLength();
yNum = nvar.getZDimension().getLength();
double[][] gridData = new double[yNum][xNum];
int rank = var.getRank();
int[] origin = new int[rank];
int[] size = new int[rank];
for (i = 0; i < rank; i++) {
Dimension ndim = (Dimension) nvar.getDimension(i);
switch (ndim.getDimType()) {
case T:
origin[i] = timeIdx;
size[i] = 1;
break;
case Z:
origin[i] = 0;
size[i] = yNum;
break;
case Y:
origin[i] = latIdx;
size[i] = 1;
break;
case X:
origin[i] = 0;
size[i] = xNum;
break;
default:
origin[i] = 0;
size[i] = 1;
break;
}
}
Array data2D = NCUtil.convertArray(var.read(origin, size).reduce());
double v;
for (i = 0; i < yNum; i++) {
for (j = 0; j < xNum; j++) {
v = data2D.getDouble(i * xNum + j);
if (v == missingValue) {
gridData[i][j] = v;
} else {
gridData[i][j] = v * scale_factor + add_offset;
}
}
}
GridData aGridData = new GridData(gridData, nvar.getXDimension().getValues(),
nvar.getZDimension().getValues(), missingValue);
return aGridData;
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (!this.keepOpen && null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
@Override
public GridData getGridData_LevelTime(int latIdx, String varName, int lonIdx) {
try {
if (ncfile == null) {
//ncfile = NetcdfDataset.openFile(this.getFileName(), null);
ncfile = NetcdfFile.open(this.fileName);
}
int i, j;
ucar.nc2.Variable var = ncfile.findVariable(varName);
//Get pack info
double add_offset, scale_factor, missingValue;
double[] packData = this.getPackData(var);
add_offset = packData[0];
scale_factor = packData[1];
missingValue = packData[2];
//Read grid data
Variable nvar = this.getVariable(varName);
int xNum, yNum;
xNum = nvar.getTDimension().getLength();
yNum = nvar.getZDimension().getLength();
double[][] gridData = new double[yNum][xNum];
int rank = var.getRank();
int[] origin = new int[rank];
int[] size = new int[rank];
for (i = 0; i < rank; i++) {
Dimension ndim = (Dimension) nvar.getDimension(i);
switch (ndim.getDimType()) {
case T:
origin[i] = 0;
size[i] = xNum;
break;
case Z:
origin[i] = 0;
size[i] = yNum;
break;
case Y:
origin[i] = latIdx;
size[i] = 1;
break;
case X:
origin[i] = lonIdx;
size[i] = 1;
break;
default:
origin[i] = 0;
size[i] = 1;
break;
}
}
Array data2D = NCUtil.convertArray(var.read(origin, size).reduce());
if (data2D.getShape()[0] == xNum) {
data2D = data2D.transpose(0, 1);
}
Index index = data2D.getIndex();
double v;
for (i = 0; i < yNum; i++) {
for (j = 0; j < xNum; j++) {
v = data2D.getDouble(index);
if (v == missingValue) {
gridData[i][j] = v;
} else {
gridData[i][j] = v * scale_factor + add_offset;
}
index.incr();
}
}
GridData aGridData = new GridData(gridData, nvar.getTDimension().getValues(),
nvar.getZDimension().getValues(), missingValue);
return aGridData;
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (!this.keepOpen && null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
@Override
public GridData getGridData_Time(int lonIdx, int latIdx, String varName, int levelIdx) {
try {
if (ncfile == null) {
//ncfile = NetcdfDataset.openFile(this.getFileName(), null);
ncfile = NetcdfFile.open(this.fileName);
}
int i;
ucar.nc2.Variable var = ncfile.findVariable(varName);
//Get pack info
double add_offset, scale_factor, missingValue;
double[] packData = this.getPackData(var);
add_offset = packData[0];
scale_factor = packData[1];
missingValue = packData[2];
//Read grid data
Variable nvar = this.getVariable(varName);
int dNum = nvar.getTDimension().getLength();
double[][] gridData = new double[1][dNum];
int rank = var.getRank();
int[] origin = new int[rank];
int[] size = new int[rank];
for (i = 0; i < rank; i++) {
Dimension ndim = (Dimension) nvar.getDimension(i);
switch (ndim.getDimType()) {
case T:
origin[i] = 0;
size[i] = dNum;
break;
case Z:
origin[i] = levelIdx;
size[i] = 1;
break;
case Y:
origin[i] = latIdx;
size[i] = 1;
break;
case X:
origin[i] = lonIdx;
size[i] = 1;
break;
default:
origin[i] = 0;
size[i] = 1;
break;
}
}
Array data1D = NCUtil.convertArray(var.read(origin, size).reduce());
double v;
for (i = 0; i < dNum; i++) {
v = data1D.getDouble(i);
if (v == missingValue) {
gridData[0][1] = v;
} else {
gridData[0][i] = v * scale_factor + add_offset;
}
}
GridData aGridData = new GridData(gridData, nvar.getTDimension().getValues(),
new double[1], missingValue);
return aGridData;
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (!this.keepOpen && null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
@Override
public GridData getGridData_Level(int lonIdx, int latIdx, String varName, int timeIdx) {
try {
if (ncfile == null) {
//ncfile = NetcdfDataset.openFile(this.getFileName(), null);
ncfile = NetcdfFile.open(this.fileName);
}
int i;
ucar.nc2.Variable var = ncfile.findVariable(varName);
//Get pack info
double add_offset, scale_factor, missingValue;
double[] packData = this.getPackData(var);
add_offset = packData[0];
scale_factor = packData[1];
missingValue = packData[2];
//Read grid data
Variable nvar = this.getVariable(varName);
int dNum = nvar.getZDimension().getLength();
double[][] gridData = new double[1][dNum];
int rank = var.getRank();
int[] origin = new int[rank];
int[] size = new int[rank];
for (i = 0; i < rank; i++) {
Dimension ndim = (Dimension) nvar.getDimension(i);
switch (ndim.getDimType()) {
case T:
origin[i] = timeIdx;
size[i] = 1;
break;
case Z:
origin[i] = 0;
size[i] = dNum;
break;
case Y:
origin[i] = latIdx;
size[i] = 1;
break;
case X:
origin[i] = lonIdx;
size[i] = 1;
break;
default:
origin[i] = 0;
size[i] = 1;
break;
}
}
Array data1D = NCUtil.convertArray(var.read(origin, size).reduce());
double v;
for (i = 0; i < dNum; i++) {
v = data1D.getDouble(i);
if (v == missingValue) {
gridData[0][1] = v;
} else {
gridData[0][i] = v * scale_factor + add_offset;
}
}
GridData aGridData = new GridData(gridData, nvar.getZDimension().getValues(),
new double[1], missingValue);
return aGridData;
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (!this.keepOpen && null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
@Override
public GridData getGridData_Lon(int timeIdx, int latIdx, String varName, int levelIdx) {
try {
if (ncfile == null) {
//ncfile = NetcdfDataset.openFile(this.getFileName(), null);
ncfile = NetcdfFile.open(this.fileName);
}
int i;
ucar.nc2.Variable var = ncfile.findVariable(varName);
//Get pack info
double add_offset, scale_factor, missingValue;
double[] packData = this.getPackData(var);
add_offset = packData[0];
scale_factor = packData[1];
missingValue = packData[2];
//Read grid data
Variable nvar = this.getVariable(varName);
int dNum = nvar.getXDimension().getLength();
double[][] gridData = new double[1][dNum];
int rank = var.getRank();
int[] origin = new int[rank];
int[] size = new int[rank];
for (i = 0; i < rank; i++) {
Dimension ndim = (Dimension) nvar.getDimension(i);
switch (ndim.getDimType()) {
case T:
origin[i] = timeIdx;
size[i] = 1;
break;
case Z:
origin[i] = levelIdx;
size[i] = 1;
break;
case Y:
origin[i] = latIdx;
size[i] = 1;
break;
case X:
origin[i] = 0;
size[i] = dNum;
break;
default:
origin[i] = 0;
size[i] = 1;
break;
}
}
Array data1D = NCUtil.convertArray(var.read(origin, size).reduce());
double v;
for (i = 0; i < dNum; i++) {
v = data1D.getDouble(i);
if (v == missingValue) {
gridData[0][i] = v;
} else {
gridData[0][i] = v * scale_factor + add_offset;
}
}
GridData aGridData = new GridData(gridData, nvar.getXDimension().getValues(),
new double[1], missingValue);
return aGridData;
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (!this.keepOpen && null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
@Override
public GridData getGridData_Lat(int timeIdx, int lonIdx, String varName, int levelIdx) {
try {
if (ncfile == null) {
//ncfile = NetcdfDataset.openFile(this.getFileName(), null);
ncfile = NetcdfFile.open(this.fileName);
}
int i;
ucar.nc2.Variable var = ncfile.findVariable(varName);
//Get pack info
double add_offset, scale_factor, missingValue;
double[] packData = this.getPackData(var);
add_offset = packData[0];
scale_factor = packData[1];
missingValue = packData[2];
//Read grid data
Variable nvar = this.getVariable(varName);
int dNum = nvar.getYDimension().getLength();
double[][] gridData = new double[1][dNum];
int rank = var.getRank();
int[] origin = new int[rank];
int[] size = new int[rank];
for (i = 0; i < rank; i++) {
Dimension ndim = (Dimension) nvar.getDimension(i);
switch (ndim.getDimType()) {
case T:
origin[i] = timeIdx;
size[i] = 1;
break;
case Z:
origin[i] = levelIdx;
size[i] = 1;
break;
case Y:
origin[i] = 0;
size[i] = dNum;
break;
case X:
origin[i] = lonIdx;
size[i] = 1;
break;
default:
origin[i] = 0;
size[i] = 1;
break;
}
}
Array data1D = NCUtil.convertArray(var.read(origin, size).reduce());
double v;
for (i = 0; i < dNum; i++) {
v = data1D.getDouble(i);
if (v == missingValue) {
gridData[0][i] = v;
} else {
gridData[0][i] = v * scale_factor + add_offset;
}
}
GridData aGridData = new GridData(gridData, nvar.getYDimension().getValues(),
new double[1], missingValue);
return aGridData;
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (!this.keepOpen && null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
@Override
public StationData getStationData(int timeIdx, String varNmae, int levelIdx) {
try {
if (ncfile == null) {
ncfile = NetcdfFile.open(this.getFileName());
}
int i;
ucar.nc2.Variable var = ncfile.findVariable(varNmae);
//Get long/lat data
//ucar.nc2.Variable lonvar = ncfile.findVariable("Longitude");
ucar.nc2.Variable lonvar = this.findNCVariable("Longitude");
//ucar.nc2.Variable latvar = ncfile.findVariable("Latitude");
ucar.nc2.Variable latvar = this.findNCVariable("Latitude");
lonvar = ncfile.getVariables().get(this.ncVariables.indexOf(lonvar));
latvar = ncfile.getVariables().get(this.ncVariables.indexOf(latvar));
Array lonarray = NCUtil.convertArray(lonvar.read());
Array latarray = NCUtil.convertArray(latvar.read());
int stNum = (int) lonarray.getSize();
List lldims = lonvar.getDimensions();
//Get pack info
double add_offset, scale_factor, missingValue;
double[] packData = this.getPackData(var);
add_offset = packData[0];
scale_factor = packData[1];
missingValue = packData[2];
//Read data
Variable nvar = this.getVariable(varNmae);
int rank = var.getRank();
int[] origin = new int[rank];
int[] size = new int[rank];
if (rank == lonvar.getRank()) {
for (i = 0; i < rank; i++) {
ucar.nc2.Dimension dim = var.getDimension(i);
origin[i] = 0;
size[i] = dim.getLength();
}
} else {
for (i = 0; i < rank; i++) {
Dimension ndim = (Dimension) nvar.getDimension(i);
ucar.nc2.Dimension dim = var.getDimension(i);
switch (ndim.getDimType()) {
case T:
if (this._isPROFILE) {
origin[i] = timeIdx;
size[i] = ndim.getLength();
} else {
origin[i] = timeIdx;
size[i] = 1;
}
break;
case X_TRACK:
origin[i] = levelIdx;
size[i] = dim.getLength();
break;
default:
if (lldims.contains(dim)) {
origin[i] = 0;
size[i] = dim.getLength();
} else {
origin[i] = levelIdx;
size[i] = 1;
}
break;
}
}
}
Array darray = NCUtil.convertArray(var.read(origin, size).reduce());
double minx, maxx, miny, maxy;
minx = maxx = lonarray.getDouble(0);
miny = maxy = latarray.getDouble(0);
double lon, lat, value;
double[][] discretedData = new double[stNum][3];
StationData stData = new StationData();
//int n = 1;
double v;
for (i = 0; i < stNum; i++) {
lon = lonarray.getDouble(i);
lat = latarray.getDouble(i);
v = darray.getDouble(i);
if (v == missingValue) {
value = v;
} else {
value = v * scale_factor + add_offset;
}
// if (MIMath.doubleEquals(value, missingValue)){
// continue;
// }
// stData.addData(String.valueOf(n), lon, lat, value);
discretedData[i][0] = lon;
discretedData[i][1] = lat;
discretedData[i][2] = value;
if (minx > lon) {
minx = lon;
} else if (maxx < lon) {
maxx = lon;
}
if (miny > lat) {
miny = lat;
} else if (maxy < lat) {
maxy = lat;
}
}
stData.data = discretedData;
stData.dataExtent = new Extent(minx, maxx, miny, maxy);
stData.missingValue = missingValue;
List stations = new ArrayList<>();
for (i = 0; i < stNum; i++) {
stations.add((String.valueOf(i + 1)));
}
stData.stations = stations;
return stData;
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (!this.keepOpen && null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
@Override
public StationInfoData getStationInfoData(int timeIdx, int levelIdx) {
throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
}
@Override
public StationModelData getStationModelData(int timeIdx, int levelIdx) {
throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
}
/**
* Read array data of the variable
*
* @param varName Variable name
* @return Array data
*/
@Override
public Array read(String varName) {
return read(varName, true);
}
/**
* Read array data of the variable
*
* @param varName Variable name
* @param unpack Unpack data or not
* @return Array data
*/
public Array read(String varName, boolean unpack) {
try {
if (ncfile == null) {
ncfile = NetcdfFile.open(this.getFileName());
}
ucar.nc2.Variable var = ncfile.findVariable(varName);
if (var == null) {
List vars = ncfile.getVariables();
for (ucar.nc2.Variable v : vars) {
if (v.getShortName().equals(varName)) {
var = v;
break;
}
}
}
if (var == null) {
System.out.println("Variable not exist: " + varName);
return null;
}
Array data = NCUtil.convertArray(var.read());
if (unpack) {
//Get pack info
double add_offset, scale_factor, missingValue;
double[] packData = this.getPackData(var);
add_offset = packData[0];
scale_factor = packData[1];
missingValue = packData[2];
if (add_offset != 0 || scale_factor != 1) {
//ArrayMath.fill_value = missingValue;
data = ArrayMath.add(ArrayMath.mul(data, scale_factor), add_offset);
}
}
return data;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (!this.keepOpen && null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
/**
* Read array data of the variable
*
* @param varName Variable name
* @param origin The origin array
* @param size The size array
* @param stride The stride array
* @return Array data
*/
@Override
public Array read(String varName, int[] origin, int[] size, int[] stride) {
return read(varName, origin, size, stride, true);
}
/**
* Read array data of the variable
*
* @param varName Variable name
* @param origin The origin array
* @param size The size array
* @param stride The stride array
* @param unpack Unpack data or not
* @return Array data
*/
public Array read(String varName, int[] origin, int[] size, int[] stride, boolean unpack) {
try {
if (ncfile == null) {
//ncfile = NetcdfDataset.openFile(this.getFileName(), null);
//ncfile = NetcdfFiles.open(this.fileName);
ncfile = NetcdfFile.open(this.fileName);
}
ucar.nc2.Variable var = ncfile.findVariable(varName);
if (var == null) {
List vars = ncfile.getVariables();
for (ucar.nc2.Variable v : vars) {
if (v.getShortName().equals(varName)) {
var = v;
break;
}
}
}
if (var == null) {
System.out.println("Variable not exist: " + varName);
return null;
}
boolean negStride = false;
for (int s : stride) {
if (s < 0) {
negStride = true;
break;
}
}
Array data;
if (negStride) {
int[] pStride = new int[stride.length];
List flips = new ArrayList<>();
for (int i = 0; i < stride.length; i++) {
pStride[i] = Math.abs(stride[i]);
if (stride[i] < 0) {
flips.add(i);
}
}
ucar.ma2.Section section = new ucar.ma2.Section(origin, size, pStride);
Array r = NCUtil.convertArray(var.read(section));
for (int i : flips) {
r = r.flip(i);
}
data = Array.factory(r.getDataType(), r.getShape());
MAMath.copy(data, r);
} else {
ucar.ma2.Section section = new ucar.ma2.Section(origin, size, stride);
data = NCUtil.convertArray(var.read(section));
}
if (unpack) {
//Get pack info
double add_offset, scale_factor, missingValue;
double[] packData = this.getPackData(var);
add_offset = packData[0];
scale_factor = packData[1];
missingValue = packData[2];
if (add_offset != 0 || scale_factor != 1) {
//ArrayMath.fill_value = missingValue;
data = ArrayMath.add(ArrayMath.mul(data, scale_factor), add_offset);
}
}
return data;
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (!this.keepOpen && null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
/**
* Read array data of the variable
*
* @param varName Variable name
* @param origin The origin array
* @param size The size array
* @return Array data
*/
public Array read(String varName, int[] origin, int[] size) {
return read(varName, origin, size, true);
}
/**
* Read array data of the variable
*
* @param varName Variable name
* @param origin The origin array
* @param size The size array
* @param unpack Unpack data or not
* @return Array data
*/
public Array read(String varName, int[] origin, int[] size, boolean unpack) {
try {
if (ncfile == null) {
ncfile = NetcdfFile.open(this.getFileName());
}
ucar.nc2.Variable var = ncfile.findVariable(varName);
ucar.ma2.Section section = new ucar.ma2.Section(origin, size);
Array data = NCUtil.convertArray(var.read(section));
if (unpack) {
//Get pack info
double add_offset, scale_factor, missingValue;
double[] packData = this.getPackData(var);
add_offset = packData[0];
scale_factor = packData[1];
missingValue = packData[2];
if (add_offset != 0 || scale_factor != 1) {
//ArrayMath.fill_value = missingValue;
data = ArrayMath.add(ArrayMath.mul(data, scale_factor), add_offset);
}
}
return data;
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (!this.keepOpen && null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
/**
* Read array data of the variable
*
* @param varName Variable name
* @param origin The origin array
* @param size The size array
* @return Array data
*/
public Array read_pack(String varName, int[] origin, int[] size) {
try {
if (ncfile == null) {
ncfile = NetcdfFile.open(this.getFileName());
}
ucar.nc2.Variable var = ncfile.findVariable(varName);
ucar.ma2.Section section = new ucar.ma2.Section(origin, size);
Array data = NCUtil.convertArray(var.read(section));
//Get pack info
double add_offset, scale_factor, missingValue;
double[] packData = this.getPackData(var);
add_offset = packData[0];
scale_factor = packData[1];
missingValue = packData[2];
if (add_offset != 0 || scale_factor != 1) {
//ArrayMath.fill_value = missingValue;
data = ArrayMath.add(ArrayMath.mul(data, scale_factor), add_offset);
}
return data;
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (!this.keepOpen && null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
public Array read(String varName, String key) {
try {
if (ncfile == null) {
ncfile = NetcdfFile.open(this.getFileName());
}
ucar.nc2.Variable var = ncfile.findVariable(varName);
Array data = NCUtil.convertArray(var.read(key));
return data;
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
return null;
} finally {
if (!this.keepOpen && null != ncfile) {
try {
ncfile.close();
ncfile = null;
} catch (IOException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
}
/**
* Convert Array to GridData
*
* @param array The Array
* @param xdim X dimension
* @param ydim Y dimension
* @return The grid data
*/
public static GridData arrayToGrid(Array array, Dimension xdim, Dimension ydim) {
int yNum = ydim.getLength();
int xNum = xdim.getLength();
double[][] gridData = new double[yNum][xNum];
for (int i = 0; i < yNum; i++) {
for (int j = 0; j < xNum; j++) {
gridData[i][j] = array.getDouble(j * yNum + i);
}
}
return new GridData(gridData, xdim.getValues(), ydim.getValues());
}
/**
* Convert grid data to NetCDF array 2D
*
* @param gData Grid data
* @return NetCDF array 2D
*/
public static Array gridToArray2D(GridData gData) {
Array a = Array.factory(gData.getData());
int[] shape = new int[2];
shape[0] = gData.getYNum();
shape[1] = gData.getXNum();
a = a.reshape(shape);
return a;
}
/**
* Convert grid data to NetCDF array 3D
*
* @param gData Grid data
* @return NetCDF array 3D
*/
public static Array gridToArray3D(GridData gData) {
Array a = Array.factory(gData.getData());
int[] shape = new int[3];
shape[0] = 1;
shape[1] = gData.getYNum();
shape[2] = gData.getXNum();
a = a.reshape(shape);
return a;
}
/**
* Convert grid data to NetCDF array 4D
*
* @param gData Grid data
* @return NetCDF array 4D
*/
public static Array gridToArray4D(GridData gData) {
Array a = Array.factory(gData.getData());
int[] shape = new int[4];
shape[0] = 1;
shape[1] = 1;
shape[2] = gData.getYNum();
shape[3] = gData.getXNum();
a = a.reshape(shape);
return a;
}
//
//
/**
* Create netCDF file
*
* @param fileName File name
* @return NetcdfFileWriter
* @throws IOException
*/
public NetcdfFileWriter createNCFile(String fileName) throws IOException {
NetcdfFileWriter ncfilew = NetcdfFileWriter.createNew(NetcdfFileWriter.Version.netcdf3, fileName);
//Define dimensions
for (Dimension dim : this.dimensions) {
ncfilew.addDimension(null, dim.getShortName(), dim.getLength(),
dim.isUnlimited(), dim.isVariableLength());
}
//Define global attributes
for (ucar.nc2.Attribute attr : this.ncAttributes) {
ncfilew.addGroupAttribute(null, attr);
}
//Define variables
for (ucar.nc2.Variable var : this.ncVariables) {
ucar.nc2.Variable nvar = ncfilew.addVariable(null, var.getShortName(), var.getDataType(), var.getDimensions());
for (ucar.nc2.Attribute attr : var.getAttributes()) {
nvar.addAttribute(attr);
}
}
//Create netCDF file
ncfilew.create();
return ncfilew;
}
/**
* Join netCDF data files
*
* @param inFiles Input netCDF data files
* @param outFile Output netCDF data file
* @param tDimName Time dimension name
*/
public static void joinDataFiles(List inFiles, String outFile, String tDimName) {
//Check number of selected files
int fNum = inFiles.size();
if (fNum < 2) {
JOptionPane.showMessageDialog(null, "There should be at least two files!", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
//Check top two files to decide joining time or variables
String aFile = inFiles.get(0);
String bFile = inFiles.get(1);
NetCDFDataInfo aDataInfo = new NetCDFDataInfo();
NetCDFDataInfo bDataInfo = new NetCDFDataInfo();
aDataInfo.readDataInfo(aFile);
bDataInfo.readDataInfo(bFile);
//If can be joined
int dataJoinType = getDataJoinType(aDataInfo, bDataInfo, tDimName);
if (dataJoinType == 0) {
JOptionPane.showMessageDialog(null, "Data dimensions are not same!", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
//Join data
if (dataJoinType == 2) //Join variables
{
try {
joinDataFiles_Variable(inFiles, outFile);
} catch (IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
} else //Join time
{
try {
if (dataJoinType == 1) {
joinDataFiles_Time(inFiles, outFile, tDimName);
} else {
joinDataFiles_Time_pack(inFiles, outFile, tDimName);
}
} catch (IOException | ucar.ma2.InvalidRangeException | ParseException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
/**
* Join data files by time
*
* @param inFiles Input nc files
* @param outFile Output nc file
* @param timeDimStr Time dimension name
* @throws IOException
* @throws ucar.ma2.InvalidRangeException
* @throws ParseException
*/
public static void joinDataFiles_Time(List inFiles, String outFile, String timeDimStr) throws IOException, ucar.ma2.InvalidRangeException, ParseException {
//Check number of selected files
int fNum = inFiles.size();
if (fNum < 2) {
JOptionPane.showMessageDialog(null, "There should be at least two files!", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
//Open the first file
int i;
String aFile = inFiles.get(0);
NetCDFDataInfo aDataInfo = new NetCDFDataInfo();
aDataInfo.readDataInfo(aFile);
switch (aDataInfo.getConvention()) {
case WRFOUT:
timeDimStr = "Time";
break;
}
//Change time dimension as unlimit
for (i = 0; i < aDataInfo.getDimensions().size(); i++) {
Dimension aDimS = aDataInfo.getDimensions().get(i);
if (aDimS.getShortName().equals(timeDimStr)) {
aDimS.setUnlimited(true);
break;
}
}
List varNames = new ArrayList<>();
for (Variable var : aDataInfo.getVariables()) {
if (MIMath.isNumeric(var.getName().substring(0, 1))) {
var.setName('V' + var.getName());
}
varNames.add(var.getName());
}
//Create output nc file and write the data of the first file
NetcdfFileWriter ncfilew = NetcdfFileWriter.createNew(NetcdfFileWriter.Version.netcdf3, outFile);
//Define dimensions
List dims = new ArrayList<>();
for (Dimension dim : aDataInfo.dimensions) {
if (dim.getShortName().equals(timeDimStr)) {
dims.add(ncfilew.addUnlimitedDimension(dim.getShortName()));
} else {
dims.add(ncfilew.addDimension(null, dim.getShortName(), dim.getLength()));
}
}
//Define global attributes
for (ucar.nc2.Attribute attr : aDataInfo.ncAttributes) {
ncfilew.addGroupAttribute(null, attr);
}
//Define variables
for (ucar.nc2.Variable var : aDataInfo.ncVariables) {
List vdims = new ArrayList<>();
for (ucar.nc2.Dimension dim : var.getDimensions()) {
for (ucar.nc2.Dimension vdim : dims) {
if (vdim.getShortName().equals(dim.getShortName())) {
vdims.add(vdim);
break;
}
}
}
ucar.nc2.Variable nvar = ncfilew.addVariable(null, var.getShortName(), var.getDataType(), vdims);
if (var.getDimensions().size() == 1 && var.getDimensions().get(0).getShortName().equals(timeDimStr)) {
nvar.addAttribute(new ucar.nc2.Attribute("units", "hours since 1800-1-1 00:00:00"));
nvar.addAttribute(new ucar.nc2.Attribute("long_name", "Time"));
nvar.addAttribute(new ucar.nc2.Attribute("standard_name", "time"));
nvar.addAttribute(new ucar.nc2.Attribute("axis", "T"));
} else {
for (ucar.nc2.Attribute attr : var.getAttributes()) {
nvar.addAttribute(attr);
}
}
}
LocalDateTime sTime = LocalDateTime.of(1800, 1, 1, 0, 0, 0);
//Create netCDF file
ncfilew.create();
//Join data
//Add data
int tDimNum = 0;
for (i = 0; i < fNum; i++) {
aFile = inFiles.get(i);
aDataInfo = new NetCDFDataInfo();
aDataInfo.readDataInfo(aFile);
if (i == 0) {
for (ucar.nc2.Variable var : ncfilew.getNetcdfFile().getVariables()) {
List dimNames = new ArrayList<>();
for (ucar.nc2.Dimension dim : var.getDimensions()) {
dimNames.add(dim.getShortName());
}
if (!dimNames.contains(timeDimStr)) {
Array varaData = aDataInfo.read(var.getShortName(), false);
ncfilew.write(var, NCUtil.convertArray(varaData));
}
}
}
for (ucar.nc2.Variable var : ncfilew.getNetcdfFile().getVariables()) {
if (!varNames.contains(var.getShortName())) {
continue;
}
List dimNames = new ArrayList<>();
for (ucar.nc2.Dimension dim : var.getDimensions()) {
dimNames.add(dim.getShortName());
}
if (!dimNames.contains(timeDimStr)) {
continue;
}
ucar.nc2.Variable dvar = aDataInfo.findNCVariable(var.getShortName());
int tDimIdx = dimNames.indexOf(timeDimStr);
int dimNum = var.getDimensions().size();
int[] start = new int[dimNum];
int[] count = new int[dimNum];
if (dimNum == 4) {
start[2] = 0;
count[2] = dvar.getDimensions().get(2).getLength();
start[3] = 0;
count[3] = dvar.getDimensions().get(3).getLength();
for (int d1 = 0; d1 < dvar.getDimensions().get(0).getLength(); d1++) {
start[0] = d1;
count[0] = 1;
for (int d2 = 0; d2 < dvar.getDimensions().get(1).getLength(); d2++) {
start[0] = d1;
start[1] = d2;
count[1] = 1;
Array varaData = aDataInfo.read(dvar.getShortName(), start, count, false);
start[tDimIdx] += tDimNum;
ncfilew.write(var, start, NCUtil.convertArray(varaData));
}
}
} else if (dimNum == 3) {
start[1] = 0;
count[1] = dvar.getDimensions().get(1).getLength();
start[2] = 0;
count[2] = dvar.getDimensions().get(2).getLength();
for (int d1 = 0; d1 < dvar.getDimensions().get(0).getLength(); d1++) {
start[0] = d1;
count[0] = 1;
Array varaData = aDataInfo.read(dvar.getShortName(), start, count, false);
start[tDimIdx] += tDimNum;
ncfilew.write(var, start, NCUtil.convertArray(varaData));
}
} else {
for (int v = 0; v < dvar.getDimensions().size(); v++) {
start[v] = 0;
count[v] = dvar.getDimension(v).getLength();
}
Array varaData = aDataInfo.read(dvar.getShortName());
start[tDimIdx] += tDimNum;
if (dimNum == 1) {
List times = aDataInfo.getTimeValues(sTime, "hours");
varaData = Array.factory(NCUtil.convertDataType(dvar.getDataType()), dvar.getShape());
for (int j = 0; j < times.size(); j++) {
varaData.setDouble(j, times.get(j));
}
if (i > 0) {
var.getDimension(0).setLength(var.getDimension(0).getLength() + varaData.getShape()[0]);
}
}
ncfilew.write(var, start, NCUtil.convertArray(varaData));
}
}
tDimNum += aDataInfo.findDimension(timeDimStr).getLength();
}
//Close data file
ncfilew.flush();
ncfilew.close();
}
/**
* Join data files by time
*
* @param inFiles Input nc files
* @param outFile Output nc file
* @param timeDimStr Time dimension name
* @throws IOException
* @throws ucar.ma2.InvalidRangeException
* @throws ParseException
*/
public static void joinDataFiles_Time_pack(List inFiles, String outFile, String timeDimStr) throws IOException, ucar.ma2.InvalidRangeException, ParseException {
//Check number of selected files
int fNum = inFiles.size();
if (fNum < 2) {
JOptionPane.showMessageDialog(null, "There should be at least two files!", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
//Open the first file
int i;
String aFile = inFiles.get(0);
NetCDFDataInfo aDataInfo = new NetCDFDataInfo();
aDataInfo.readDataInfo(aFile);
switch (aDataInfo.getConvention()) {
case WRFOUT:
timeDimStr = "Time";
break;
}
//Change time dimension as unlimit
for (i = 0; i < aDataInfo.getDimensions().size(); i++) {
Dimension aDimS = aDataInfo.getDimensions().get(i);
if (aDimS.getShortName().equals(timeDimStr)) {
aDimS.setUnlimited(true);
break;
}
}
List varNames = new ArrayList<>();
for (Variable var : aDataInfo.getVariables()) {
if (MIMath.isNumeric(var.getName().substring(0, 1))) {
var.setName('V' + var.getName());
}
varNames.add(var.getName());
}
//Create output nc file and write the data of the first file
NetcdfFileWriter ncfilew = NetcdfFileWriter.createNew(NetcdfFileWriter.Version.netcdf3, outFile);
//Define dimensions
List dims = new ArrayList<>();
for (Dimension dim : aDataInfo.dimensions) {
if (dim.getShortName().equals(timeDimStr)) {
dims.add(ncfilew.addUnlimitedDimension(dim.getShortName()));
} else {
dims.add(ncfilew.addDimension(null, dim.getShortName(), dim.getLength()));
}
}
//Define global attributes
for (ucar.nc2.Attribute attr : aDataInfo.ncAttributes) {
ncfilew.addGroupAttribute(null, attr);
}
//Define variables
for (ucar.nc2.Variable var : aDataInfo.ncVariables) {
List vdims = new ArrayList<>();
for (ucar.nc2.Dimension dim : var.getDimensions()) {
for (ucar.nc2.Dimension vdim : dims) {
if (vdim.getShortName().equals(dim.getShortName())) {
vdims.add(vdim);
break;
}
}
}
ucar.nc2.Variable nvar;
if (var.findAttribute("add_offset") != null || var.findAttribute("scale_factor") != null) {
nvar = ncfilew.addVariable(null, var.getShortName(), ucar.ma2.DataType.DOUBLE, vdims);
} else {
nvar = ncfilew.addVariable(null, var.getShortName(), var.getDataType(), vdims);
}
if (var.getDimensions().size() == 1 && var.getDimensions().get(0).getShortName().equals(timeDimStr)) {
nvar.addAttribute(new ucar.nc2.Attribute("units", "hours since 1800-1-1 00:00:00"));
nvar.addAttribute(new ucar.nc2.Attribute("long_name", "Time"));
nvar.addAttribute(new ucar.nc2.Attribute("standard_name", "time"));
nvar.addAttribute(new ucar.nc2.Attribute("axis", "T"));
} else {
for (ucar.nc2.Attribute attr : var.getAttributes()) {
if (!attr.getShortName().equals("add_offset") && !attr.getShortName().equals("scale_factor")) {
nvar.addAttribute(attr);
}
}
}
}
LocalDateTime sTime = LocalDateTime.of(1800, 1, 1, 0, 0, 0);
//Create netCDF file
ncfilew.create();
//Join data
//Add data
int tDimNum = 0;
for (i = 0; i < fNum; i++) {
aFile = inFiles.get(i);
aDataInfo = new NetCDFDataInfo();
aDataInfo.readDataInfo(aFile);
if (i == 0) {
for (ucar.nc2.Variable var : ncfilew.getNetcdfFile().getVariables()) {
List dimNames = new ArrayList<>();
for (ucar.nc2.Dimension dim : var.getDimensions()) {
dimNames.add(dim.getShortName());
}
if (!dimNames.contains(timeDimStr)) {
Array varaData = aDataInfo.read(var.getShortName());
ncfilew.write(var, NCUtil.convertArray(varaData));
}
}
}
for (ucar.nc2.Variable var : ncfilew.getNetcdfFile().getVariables()) {
if (!varNames.contains(var.getShortName())) {
continue;
}
List dimNames = new ArrayList<>();
for (ucar.nc2.Dimension dim : var.getDimensions()) {
dimNames.add(dim.getShortName());
}
if (!dimNames.contains(timeDimStr)) {
continue;
}
ucar.nc2.Variable dvar = aDataInfo.findNCVariable(var.getShortName());
int tDimIdx = dimNames.indexOf(timeDimStr);
int dimNum = var.getDimensions().size();
int[] start = new int[dimNum];
int[] count = new int[dimNum];
if (dimNum == 4) {
start[2] = 0;
count[2] = dvar.getDimensions().get(2).getLength();
start[3] = 0;
count[3] = dvar.getDimensions().get(3).getLength();
for (int d1 = 0; d1 < dvar.getDimensions().get(0).getLength(); d1++) {
start[0] = d1;
count[0] = 1;
for (int d2 = 0; d2 < dvar.getDimensions().get(1).getLength(); d2++) {
start[0] = d1;
start[1] = d2;
count[1] = 1;
Array varaData;
if (dvar.findAttribute("add_offset") != null || dvar.findAttribute("scale_factor") != null) {
varaData = aDataInfo.read_pack(dvar.getShortName(), start, count);
} else {
varaData = aDataInfo.read(dvar.getShortName(), start, count);
}
start[tDimIdx] += tDimNum;
ncfilew.write(var, start, NCUtil.convertArray(varaData));
}
}
} else if (dimNum == 3) {
start[1] = 0;
count[1] = dvar.getDimensions().get(1).getLength();
start[2] = 0;
count[2] = dvar.getDimensions().get(2).getLength();
for (int d1 = 0; d1 < dvar.getDimensions().get(0).getLength(); d1++) {
start[0] = d1;
count[0] = 1;
Array varaData;
if (dvar.findAttribute("add_offset") != null || dvar.findAttribute("scale_factor") != null) {
varaData = aDataInfo.read_pack(dvar.getShortName(), start, count);
} else {
varaData = aDataInfo.read(dvar.getShortName(), start, count);
}
start[tDimIdx] += tDimNum;
ncfilew.write(var, start, NCUtil.convertArray(varaData));
}
} else {
for (int v = 0; v < dvar.getDimensions().size(); v++) {
start[v] = 0;
count[v] = dvar.getDimension(v).getLength();
}
Array varaData = aDataInfo.read(dvar.getShortName());
start[tDimIdx] += tDimNum;
if (dimNum == 1) {
List times = aDataInfo.getTimeValues(sTime, "hours");
varaData = Array.factory(NCUtil.convertDataType(dvar.getDataType()), dvar.getShape());
for (int j = 0; j < times.size(); j++) {
varaData.setDouble(j, times.get(j));
}
if (i > 0) {
var.getDimension(0).setLength(var.getDimension(0).getLength() + varaData.getShape()[0]);
}
}
ncfilew.write(var, start, NCUtil.convertArray(varaData));
}
}
tDimNum += aDataInfo.findDimension(timeDimStr).getLength();
}
//Close data file
ncfilew.flush();
ncfilew.close();
}
/**
* Join data files by variable
*
* @param inFiles Input nc files
* @param outFile Output nc file
* @throws IOException
* @throws ucar.ma2.InvalidRangeException
*/
public static void joinDataFiles_Variable(List inFiles, String outFile) throws IOException, ucar.ma2.InvalidRangeException {
//Check number of selected files
int fNum = inFiles.size();
if (fNum < 2) {
JOptionPane.showMessageDialog(null, "There should be at least two files!", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
//Open a file
String aFile = inFiles.get(0);
NetCDFDataInfo aDataInfo = new NetCDFDataInfo();
aDataInfo.readDataInfo(aFile);
//Create nc file writer
NetcdfFileWriter ncfile = NetcdfFileWriter.createNew(NetcdfFileWriter.Version.netcdf3, outFile);
//Define dimensions
for (Dimension dim : aDataInfo.dimensions) {
ncfile.addDimension(null, dim.getShortName(), dim.getLength(),
dim.isUnlimited(), dim.isVariableLength());
}
//Define global attributes
for (ucar.nc2.Attribute attr : aDataInfo.ncAttributes) {
ncfile.addGroupAttribute(null, attr);
}
//Define variables
List nvars = new ArrayList<>();
for (ucar.nc2.Variable var : aDataInfo.ncVariables) {
ucar.nc2.Variable nvar = ncfile.addVariable(null, var.getShortName(), var.getDataType(), var.getDimensions());
for (ucar.nc2.Attribute attr : var.getAttributes()) {
nvar.addAttribute(attr);
}
nvars.add(nvar);
}
//Add variables from more files
List> mvars = new ArrayList<>();
List mncf = new ArrayList<>();
List varNames = aDataInfo.getVariableNames();
for (int i = 1; i < fNum; i++) {
NetCDFDataInfo df = new NetCDFDataInfo();
df.readDataInfo(inFiles.get(i));
List vars = new ArrayList<>();
for (ucar.nc2.Variable var : df.ncVariables) {
if (!varNames.contains(var.getShortName())) {
ucar.nc2.Variable nvar = ncfile.addVariable(null, var.getShortName(), var.getDataType(), var.getDimensions());
for (ucar.nc2.Attribute attr : var.getAttributes()) {
nvar.addAttribute(attr);
}
vars.add(nvar);
varNames.add(var.getShortName());
}
}
mncf.add(df);
mvars.add(vars);
}
//Create netCDF file
ncfile.create();
//Write variable data of first NC file
for (ucar.nc2.Variable nvar : nvars) {
int ndim = nvar.getDimensions().size();
if (ndim < 4) {
ncfile.write(nvar, NCUtil.convertArray(aDataInfo.read(nvar.getShortName(), false)));
} else {
int[] start = new int[ndim];
int[] count = new int[ndim];
for (int j = 1; j < ndim; j++) {
start[j] = 0;
count[j] = nvar.getDimension(j).getLength();
}
int n = nvar.getDimension(0).getLength();
for (int i = 0; i < n; i++) {
start[0] = i;
count[0] = 1;
ncfile.write(nvar, start, NCUtil.convertArray(aDataInfo.read(nvar.getShortName(), start, count, false)));
}
}
}
//Add data in more files
for (int i = 0; i < mncf.size(); i++) {
List vars = mvars.get(i);
if (vars.isEmpty()) {
continue;
}
NetCDFDataInfo df = mncf.get(i);
for (ucar.nc2.Variable nvar : vars) {
int ndim = nvar.getDimensions().size();
if (ndim < 4) {
ncfile.write(nvar, NCUtil.convertArray(df.read(nvar.getShortName(), false)));
} else {
int[] start = new int[ndim];
int[] count = new int[ndim];
int n = nvar.getDimension(0).getLength();
for (int j = 1; j < ndim; j++) {
start[j] = 0;
count[j] = nvar.getDimension(j).getLength();
}
for (int k = 0; k < n; k++) {
start[0] = k;
count[0] = 1;
ncfile.write(nvar, start, NCUtil.convertArray(df.read(nvar.getShortName(), start, count, false)));
}
}
}
}
//Close data file
ncfile.flush();
ncfile.close();
}
private static int getDataJoinType(NetCDFDataInfo aDataInfo, NetCDFDataInfo bDataInfo, String tDimName) {
//If same dimension number
int ndims = aDataInfo.getDimensions().size();
if (ndims != bDataInfo.getDimensions().size()) {
return 0; //Can't be joined
}
//If same dimensions
int i;
boolean IsSame = true;
boolean IsJoinVar = true;
for (i = 0; i < ndims; i++) {
Dimension aDim = aDataInfo.getDimensions().get(i);
Dimension bDim = bDataInfo.getDimensions().get(i);
if (!aDim.getShortName().equals(bDim.getShortName())) {
IsSame = false;
break;
}
if (aDim.getShortName().toLowerCase().equals(tDimName)) {
if (aDim.getLength() != bDim.getLength()) {
IsJoinVar = false;
}
double t1, t2;
for (int j = 0; j < aDataInfo.getTimeNum(); j++) {
t1 = aDataInfo.getTimeValue(j);
t2 = bDataInfo.getTimeValue(j);
if (t1 != t2) {
IsJoinVar = false;
break;
}
}
} else if (aDim.getLength() != bDim.getLength()) {
IsSame = false;
break;
}
}
if (!IsSame) {
return 0; //Can't be joined
}
if (IsJoinVar) {
return 2; //Can join variable
} else {
if (aDataInfo.getVariableNum() != bDataInfo.getVariableNum()) {
return 0;
}
IsSame = true;
boolean unpack = false;
for (i = 0; i < aDataInfo.getVariableNum(); i++) {
Variable aVarS = aDataInfo.getVariables().get(i);
Variable bVarS = bDataInfo.getVariables().get(i);
if (!aVarS.getName().equals(bVarS.getName()) || aVarS.getDimNumber() != bVarS.getDimNumber()) {
IsSame = false;
break;
}
if (unpack == false) {
Attribute aao = aVarS.findAttribute("add_offset");
Attribute asf = aVarS.findAttribute("scale_factor");
Attribute bao = bVarS.findAttribute("add_offset");
Attribute bsf = bVarS.findAttribute("scale_factor");
if (aao != null) {
if (bao == null) {
unpack = true;
} else {
double vaao = Double.parseDouble(aao.getValue(0).toString());
double vbao = Double.parseDouble(bao.getValue(0).toString());
if (vaao != vbao) {
unpack = true;
}
}
} else {
if (bao != null) {
unpack = true;
}
}
if (asf != null) {
if (bsf == null) {
unpack = true;
} else {
double vasf = Double.parseDouble(asf.getValue(0).toString());
double vbsf = Double.parseDouble(bsf.getValue(0).toString());
if (vasf != vbsf) {
unpack = true;
}
}
} else {
if (bsf != null) {
unpack = true;
}
}
}
}
if (IsSame) {
if (unpack) {
return 3;
} else {
return 1; //Can join time
}
} else {
return 0;
}
}
}
/**
* Add time dimension
*
* @param inFile Input nc file
* @param outFile Output nc file
* @param aTime Time
*/
public static void addTimeDimension(String inFile, String outFile, LocalDateTime aTime) {
try {
addTimeDimension(inFile, outFile, aTime, "days");
} catch (ParseException | IOException | ucar.ma2.InvalidRangeException ex) {
Logger.getLogger(NetCDFDataInfo.class.getName()).log(Level.SEVERE, null, ex);
}
}
/**
* Add time dimension
*
* @param inFile Input nc file
* @param outFile Output nc file
* @param aTime Time
* @param timeUnit Time unit (days, hours, minutes, seconds)
* @throws ParseException
* @throws IOException
* @throws ucar.ma2.InvalidRangeException
*/
public static void addTimeDimension(String inFile, String outFile, LocalDateTime aTime, String timeUnit) throws ParseException, IOException, ucar.ma2.InvalidRangeException {
//Set data info
NetCDFDataInfo aDataInfo = new NetCDFDataInfo();
aDataInfo.readDataInfo(inFile);
//Check variables if time included
List varList = aDataInfo.getVariableNames();
if (varList.contains("time")) {
return;
}
//set start time of the data
LocalDateTime sTime = LocalDateTime.of(1800, 1, 1, 0, 0, 0);
int tvalue = DataInfo.getTimeValue(aTime, sTime, timeUnit.toLowerCase());
NetcdfFileWriter ncfilew = NetcdfFileWriter.createNew(NetcdfFileWriter.Version.netcdf3, outFile);
//Define dimensions
for (Dimension dim : aDataInfo.dimensions) {
ncfilew.addDimension(null, dim.getShortName(), dim.getLength(),
dim.isUnlimited(), dim.isVariableLength());
}
ucar.nc2.Dimension tdim = ncfilew.addDimension(null, "time", 1);
//Define global attributes
for (ucar.nc2.Attribute attr : aDataInfo.ncAttributes) {
ncfilew.addGroupAttribute(null, attr);
}
//Define variables
for (ucar.nc2.Variable var : aDataInfo.ncVariables) {
List dims = var.getDimensions();
if (dims.size() > 1) {
dims.add(0, tdim);
}
ucar.nc2.Variable nvar = ncfilew.addVariable(null, var.getShortName(), var.getDataType(), dims);
for (ucar.nc2.Attribute attr : var.getAttributes()) {
nvar.addAttribute(attr);
}
}
List dims = new ArrayList<>();
dims.add(tdim);
ucar.nc2.Variable tvar = ncfilew.addVariable(null, "time", ucar.ma2.DataType.INT, dims);
tvar.addAttribute(new ucar.nc2.Attribute("units", timeUnit.toLowerCase() + " since 1800-1-1 00:00:00"));
tvar.addAttribute(new ucar.nc2.Attribute("long_name", "Time"));
tvar.addAttribute(new ucar.nc2.Attribute("standard_name", "time"));
tvar.addAttribute(new ucar.nc2.Attribute("axis", "T"));
//Create netCDF file
ncfilew.create();
//Add data
for (ucar.nc2.Variable var : aDataInfo.ncVariables) {
int dimNum = var.getDimensions().size();
int[] start = new int[dimNum];
int[] count = new int[dimNum];
if (dimNum == 4) {
start[2] = 0;
count[2] = var.getDimensions().get(2).getLength();
start[3] = 0;
count[3] = var.getDimensions().get(3).getLength();
for (int d1 = 0; d1 < var.getDimensions().get(0).getLength(); d1++) {
start[0] = d1;
count[0] = 1;
for (int d2 = 0; d2 < var.getDimensions().get(1).getLength(); d2++) {
start[0] = d1;
start[1] = d2;
count[1] = 1;
Array varaData = aDataInfo.read(var.getShortName(), start, count);
ncfilew.write(var, start, NCUtil.convertArray(varaData));
}
}
} else if (dimNum == 3) {
start[1] = 0;
count[1] = var.getDimensions().get(1).getLength();
start[2] = 0;
count[2] = var.getDimensions().get(2).getLength();
for (int d1 = 0; d1 < var.getDimensions().get(0).getLength(); d1++) {
start[0] = d1;
count[0] = 1;
Array varaData = aDataInfo.read(var.getShortName(), start, count);
ncfilew.write(var, start, NCUtil.convertArray(varaData));
}
} else {
for (int v = 0; v < var.getDimensions().size(); v++) {
start[v] = 0;
count[v] = var.getDimension(v).getLength();
}
Array varaData = aDataInfo.read(var.getShortName(), start, count);
ncfilew.write(var, start, NCUtil.convertArray(varaData));
}
}
ucar.ma2.Array timeValue = new ucar.ma2.ArrayInt.D1(tvalue, false);
ncfilew.write(tvar, timeValue);
//Close data file
ncfilew.flush();
ncfilew.close();
}
//
//
}
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