ucar.nc2.internal.dataset.conv.NUWGConvention Maven / Gradle / Ivy
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/*
* Copyright (c) 1998-2020 John Caron and University Corporation for Atmospheric Research/Unidata
* See LICENSE for license information.
*/
package ucar.nc2.internal.dataset.conv;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.List;
import java.util.NoSuchElementException;
import java.util.StringTokenizer;
import ucar.ma2.Array;
import ucar.ma2.DataType;
import ucar.ma2.IndexIterator;
import ucar.nc2.Attribute;
import ucar.nc2.Dimension;
import ucar.nc2.Variable;
import ucar.nc2.constants.AxisType;
import ucar.nc2.constants.CDM;
import ucar.nc2.constants._Coordinate;
import ucar.nc2.dataset.CoordinateAxis;
import ucar.nc2.dataset.CoordinateAxis1D;
import ucar.nc2.dataset.CoordinateTransform;
import ucar.nc2.dataset.NetcdfDataset;
import ucar.nc2.dataset.ProjectionCT;
import ucar.nc2.dataset.VariableDS;
import ucar.nc2.dataset.spi.CoordSystemBuilderFactory;
import ucar.nc2.internal.dataset.CoordSystemBuilder;
import ucar.nc2.units.SimpleUnit;
import ucar.nc2.util.CancelTask;
import ucar.unidata.geoloc.LatLonPoint;
import ucar.unidata.geoloc.ProjectionPoint;
import ucar.unidata.geoloc.projection.LambertConformal;
import ucar.unidata.geoloc.projection.Stereographic;
import ucar.unidata.util.Format;
import ucar.unidata.util.StringUtil2;
/**
* NUWG Convention (ad hoc).
* see https://www.unidata.ucar.edu/software/netcdf/NUWG/
*/
public class NUWGConvention extends CoordSystemBuilder {
private static final String CONVENTION_NAME = "NUWG";
public static class Factory implements CoordSystemBuilderFactory {
@Override
public String getConventionName() {
return CONVENTION_NAME;
}
@Override
public CoordSystemBuilder open(NetcdfDataset.Builder datasetBuilder) {
return new NUWGConvention(datasetBuilder);
}
}
private NavInfoList navInfo = new NavInfoList();
private String xaxisName = "", yaxisName = "";
private Grib1 grib;
private static final boolean dumpNav = false;
NUWGConvention(NetcdfDataset.Builder datasetBuilder) {
super(datasetBuilder);
this.conventionName = CONVENTION_NAME;
}
@Override
protected void augmentDataset(CancelTask cancelTask) throws IOException {
if (null != rootGroup.getAttributeContainer().findAttribute("_enhanced"))
return; // check if its already been done - aggregating enhanced datasets.
rootGroup.getAttributeContainer().addAttribute("_enhanced", "");
// find all variables that have the nav dimension
// put them into a NavInfoList
// make their data into metadata
for (Variable.Builder vb : rootGroup.vbuilders) {
VariableDS.Builder v = (VariableDS.Builder) vb;
if (0 <= v.orgVar.findDimensionIndex("nav")) {
if (dumpNav)
parseInfo.format("NUWG has NAV var = %s%n", v);
try {
navInfo.add(new NavInfo(v));
} catch (IOException ex) {
parseInfo.format("ERROR NUWG reading NAV var = %s%n", v);
}
}
}
navInfo.sort(new NavComparator());
parseInfo.format("%s%n%n", navInfo);
// problem is NUWG doesnt identify the x, y coords.
// so we get to hack it in here
int mode = 3; // default is LambertConformal
try {
mode = navInfo.getInt("grid_type_code");
} catch (NoSuchElementException e) {
log.warn("No mode in navInfo - assume 3");
}
try {
if (mode == 0) {
xaxisName = navInfo.getString("i_dim");
yaxisName = navInfo.getString("j_dim");
} else {
xaxisName = navInfo.getString("x_dim");
yaxisName = navInfo.getString("y_dim");
}
} catch (NoSuchElementException e) {
log.warn("No mode in navInfo - assume = 1");
// LOOK could match variable grid_type, data = "tangential lambert conformal "
}
grib = new Grib1(mode);
if (!rootGroup.findVariableLocal(xaxisName).isPresent()) {
grib.makeXCoordAxis(xaxisName);
parseInfo.format("Generated x axis from NUWG nav= %s%n", xaxisName);
} else if (xaxisName.equalsIgnoreCase("lon")) {
try {
// check monotonicity
boolean ok = true;
VariableDS.Builder dc = (VariableDS.Builder) rootGroup.findVariableLocal(xaxisName).get();
Array coordVal = dc.orgVar.read();
IndexIterator coordIndex = coordVal.getIndexIterator();
double coord1 = coordIndex.getDoubleNext();
double coord2 = coordIndex.getDoubleNext();
boolean increase = coord1 > coord2;
coord1 = coord2;
while (coordIndex.hasNext()) {
coord2 = coordIndex.getDoubleNext();
if ((coord1 > coord2) ^ increase) {
ok = false;
break;
}
coord1 = coord2;
}
if (!ok) {
parseInfo.format("ERROR lon axis is not monotonic, regen from nav%n");
grib.makeXCoordAxis(xaxisName);
}
} catch (IOException ioe) {
log.warn("IOException when reading xaxis = " + xaxisName);
}
}
if (!rootGroup.findVariableLocal(yaxisName).isPresent()) {
grib.makeYCoordAxis(yaxisName);
parseInfo.format("Generated y axis from NUWG nav=%s%n", yaxisName);
}
// "referential" variables
for (Dimension dim : rootGroup.getDimensions()) {
String dimName = dim.getShortName();
if (rootGroup.findVariableLocal(dimName).isPresent())
continue; // already has coord axis
List ncvars = searchAliasedDimension(dim);
if ((ncvars == null) || (ncvars.isEmpty())) // no alias
continue;
if (ncvars.size() == 1) {
Variable.Builder ncvar = ncvars.get(0);
if (ncvar.dataType == DataType.STRUCTURE)
continue; // cant be a structure
if (makeCoordinateAxis(ncvar, dim)) {
parseInfo.format("Added referential coordAxis = %s%n", ncvar.shortName);
} else {
parseInfo.format("Couldnt add referential coordAxis = %s%n", ncvar.shortName);
}
} else if (ncvars.size() == 2) {
if (dimName.equals("record")) {
Variable.Builder ncvar0 = ncvars.get(0);
Variable.Builder ncvar1 = ncvars.get(1);
VariableDS.Builder ncvar =
(VariableDS.Builder) (ncvar0.shortName.equalsIgnoreCase("valtime") ? ncvar0 : ncvar1);
if (makeCoordinateAxis(ncvar, dim)) {
parseInfo.format("Added referential coordAxis (2) = %s%n", ncvar.shortName);
// the usual crap - clean up time units
String units = ncvar.getUnits();
if (units != null) {
units = StringUtil2.remove(units, '(');
units = StringUtil2.remove(units, ')');
ncvar.addAttribute(new Attribute(CDM.UNITS, units));
ncvar.setUnits(units);
}
} else {
parseInfo.format("Couldnt add referential coordAxis = %s%n", ncvar.shortName);
}
} else {
// lower(?) bound
Variable.Builder ncvar = ncvars.get(0);
if (ncvar.dataType == DataType.STRUCTURE)
continue; // cant be a structure
if (makeCoordinateAxis(ncvar, dim)) {
parseInfo.format("Added referential boundary coordAxis (2) = %s%n", ncvar.shortName);
} else {
parseInfo.format("Couldnt add referential coordAxis = %s%n", ncvar.shortName);
}
}
} // 2
} // loop over dims
if (grib.projectionCT != null) {
VariableDS.Builder v = makeCoordinateTransformVariable(grib.projectionCT);
v.addAttribute(new Attribute(_Coordinate.Axes, xaxisName + " " + yaxisName));
rootGroup.addVariable(v);
}
}
private boolean makeCoordinateAxis(Variable.Builder ncvar, Dimension dim) {
if (ncvar.getRank() != 1)
return false;
String vdimName = ncvar.getFirstDimensionName();
if (!vdimName.equals(dim.getShortName()))
return false;
if (!dim.getShortName().equals(ncvar.shortName)) {
ncvar.addAttribute(new Attribute(_Coordinate.AliasForDimension, dim.getShortName()));
}
return true;
}
/**
* Search for an aliased coord that may have multiple variables
* :dimName = alias1, alias2;
* Variable alias1(dim);
* Variable alias2(dim);
*
* @param dim: look for this dimension name
* @return Collection of nectdf variables, or null if none
*/
private List searchAliasedDimension(Dimension dim) {
String dimName = dim.getShortName();
String alias = rootGroup.getAttributeContainer().findAttributeString(dimName, null);
if (alias == null)
return null;
List vars = new ArrayList<>();
StringTokenizer parser = new StringTokenizer(alias, " ,");
while (parser.hasMoreTokens()) {
String token = parser.nextToken();
if (!rootGroup.findVariableLocal(token).isPresent()) {
continue;
}
Variable.Builder ncvar = rootGroup.findVariableLocal(token).get();
if (ncvar.getRank() != 1)
continue;
String firstDimName = ncvar.getFirstDimensionName();
if (dimName.equals(firstDimName)) {
vars.add(ncvar);
}
}
return vars;
}
private StringBuilder buf = new StringBuilder(2000);
public String extraInfo() {
buf.setLength(0);
buf.append(navInfo).append("%n");
return buf.toString();
}
@Override
protected void makeCoordinateTransforms() {
if ((grib != null) && (grib.projectionCT != null)) {
VarProcess vp = findVarProcess(grib.projectionCT.getName(), null);
if (vp != null) {
vp.isCoordinateTransform = true;
vp.ct = CoordinateTransform.builder().setPreBuilt(grib.projectionCT);
coords.addCoordinateTransform(vp.ct);
}
}
super.makeCoordinateTransforms();
}
@Override
protected AxisType getAxisType(VariableDS.Builder v) {
String vname = v.shortName;
if (vname.equalsIgnoreCase("lat"))
return AxisType.Lat;
if (vname.equalsIgnoreCase("lon"))
return AxisType.Lon;
if (vname.equalsIgnoreCase(xaxisName))
return AxisType.GeoX;
if (vname.equalsIgnoreCase(yaxisName))
return AxisType.GeoY;
if (vname.equalsIgnoreCase("record"))
return AxisType.Time;
String dimName = v.getFirstDimensionName();
if ((dimName != null) && dimName.equalsIgnoreCase("record")) { // wow thats bad!
return AxisType.Time;
}
String unit = v.getUnits();
if (unit != null) {
if (SimpleUnit.isCompatible("millibar", unit))
return AxisType.Pressure;
if (SimpleUnit.isCompatible("m", unit))
return AxisType.Height;
if (SimpleUnit.isCompatible("sec", unit))
return null;
}
return AxisType.GeoZ; // AxisType.GeoZ;
}
/**
* @return "up" if this is a Vertical (z) coordinate axis which goes up as coords get bigger
* @param v for this axis
*/
public String getZisPositive(CoordinateAxis v) {
// gotta have a length unit
String unit = v.getUnitsString();
if ((unit != null) && SimpleUnit.isCompatible("m", unit))
return "up";
return "down";
// lame NUWG Conventions! units of millibar might be "millibars above ground" !
// heres a kludge that should work
// return v.getName().equalsIgnoreCase("fhg") ? "up" : "down";
}
private static class NavComparator implements Comparator {
public int compare(NavInfo n1, NavInfo n2) {
return n1.getName().compareTo(n2.getName());
}
}
private class NavInfo {
VariableDS.Builder vb;
Variable orgVar;
DataType valueType;
String svalue;
byte bvalue;
int ivalue;
double dvalue;
NavInfo(VariableDS.Builder vb) throws IOException {
this.vb = vb;
this.orgVar = vb.orgVar;
valueType = vb.dataType;
try {
if ((valueType == DataType.CHAR) || (valueType == DataType.STRING))
svalue = orgVar.readScalarString();
else if (valueType == DataType.BYTE)
bvalue = orgVar.readScalarByte();
else if ((valueType == DataType.INT) || (valueType == DataType.SHORT))
ivalue = orgVar.readScalarInt();
else
dvalue = orgVar.readScalarDouble();
} catch (UnsupportedOperationException e) {
parseInfo.format("Nav variable %s not a scalar%n", getName());
}
}
public String getName() {
return vb.shortName;
}
public String getDescription() {
Attribute att = vb.getAttributeContainer().findAttributeIgnoreCase(CDM.LONG_NAME);
return (att == null) ? getName() : att.getStringValue();
}
public String getStringValue() {
if ((valueType == DataType.CHAR) || (valueType == DataType.STRING))
return svalue;
else if (valueType == DataType.BYTE)
return Byte.toString(bvalue);
else if ((valueType == DataType.INT) || (valueType == DataType.SHORT))
return Integer.toString(ivalue);
else
return Double.toString(dvalue);
}
private StringBuilder buf = new StringBuilder(200);
public String toString() {
buf.setLength(0);
buf.append(getName());
buf.append(" ");
Format.tab(buf, 15, true);
buf.append(getStringValue());
buf.append(" ");
Format.tab(buf, 35, true);
buf.append(getDescription());
return buf.toString();
}
}
private static class NavInfoList extends ArrayList {
public NavInfo findInfo(String name) {
for (NavInfo nav : this) {
if (name.equalsIgnoreCase(nav.getName()))
return nav;
}
return null;
}
public double getDouble(String name) throws NoSuchElementException {
NavInfo nav = findInfo(name);
if (nav == null)
throw new NoSuchElementException("GRIB1 " + name);
if ((nav.valueType == DataType.DOUBLE) || (nav.valueType == DataType.FLOAT))
return nav.dvalue;
else if ((nav.valueType == DataType.INT) || (nav.valueType == DataType.SHORT))
return (double) nav.ivalue;
else if (nav.valueType == DataType.BYTE)
return (double) nav.bvalue;
throw new IllegalArgumentException("NUWGConvention.GRIB1.getDouble " + name + " type = " + nav.valueType);
}
public int getInt(String name) throws NoSuchElementException {
NavInfo nav = findInfo(name);
if (nav == null)
throw new NoSuchElementException("GRIB1 " + name);
if ((nav.valueType == DataType.INT) || (nav.valueType == DataType.SHORT))
return nav.ivalue;
else if ((nav.valueType == DataType.DOUBLE) || (nav.valueType == DataType.FLOAT))
return (int) nav.dvalue;
else if (nav.valueType == DataType.BYTE)
return (int) nav.bvalue;
throw new IllegalArgumentException("NUWGConvention.GRIB1.getInt " + name + " type = " + nav.valueType);
}
public String getString(String name) throws NoSuchElementException {
NavInfo nav = findInfo(name);
if (nav == null)
throw new NoSuchElementException("GRIB1 " + name);
return nav.svalue;
}
public String toString() {
StringBuilder buf = new StringBuilder(2000);
buf.append("\nNav Info\n");
buf.append("Name___________Value_____________________Description\n");
for (NavInfo nava : this) {
buf.append(nava).append("\n");
}
buf.append("\n");
return buf.toString();
}
}
// encapsolates GRIB-specific processing
private class Grib1 {
private String grid_name;
private int grid_code;
private ProjectionCT projectionCT;
private int nx, ny;
private double startx, starty;
private double dx, dy;
Grib1(int mode) {
// horiz system
grid_name = "Projection";
if (grid_name.isEmpty())
grid_name = "grid_var";
grid_code = mode;
if (0 == grid_code)
processLatLonProjection();
else if (3 == grid_code)
projectionCT = makeLCProjection();
else if (5 == grid_code)
projectionCT = makePSProjection();
else
throw new IllegalArgumentException("NUWGConvention: unknown grid_code= " + grid_code);
// vertical system
}
void makeXCoordAxis(String xname) {
CoordinateAxis.Builder v = CoordinateAxis1D.builder().setName(xname).setDataType(DataType.DOUBLE)
.setParentGroupBuilder(rootGroup).setDimensionsByName(xname).setUnits((0 == grid_code) ? CDM.LON_UNITS : "km")
.setDesc("synthesized X coord");
v.addAttribute(
new Attribute(_Coordinate.AxisType, (0 == grid_code) ? AxisType.Lon.toString() : AxisType.GeoX.toString()));
v.setAutoGen(startx, dx);
datasetBuilder.replaceCoordinateAxis(rootGroup, v);
}
void makeYCoordAxis(String yname) {
CoordinateAxis.Builder v = CoordinateAxis1D.builder().setName(yname).setDataType(DataType.DOUBLE)
.setParentGroupBuilder(rootGroup).setDimensionsByName(yname).setUnits((0 == grid_code) ? CDM.LAT_UNITS : "km")
.setDesc("synthesized Y coord");
v.addAttribute(
new Attribute(_Coordinate.AxisType, (0 == grid_code) ? AxisType.Lat.toString() : AxisType.GeoY.toString()));
v.setAutoGen(starty, dy);
datasetBuilder.replaceCoordinateAxis(rootGroup, v);
}
private ProjectionCT makeLCProjection() throws NoSuchElementException {
double latin1 = navInfo.getDouble("Latin1");
double latin2 = navInfo.getDouble("Latin2");
double lov = navInfo.getDouble("Lov");
double la1 = navInfo.getDouble("La1");
double lo1 = navInfo.getDouble("Lo1");
// we have to project in order to find the origin
LambertConformal lc = new LambertConformal(latin1, lov, latin1, latin2);
ProjectionPoint start = lc.latLonToProj(LatLonPoint.create(la1, lo1));
if (debug)
System.out.println("start at proj coord " + start);
startx = start.getX();
starty = start.getY();
nx = navInfo.getInt("Nx");
ny = navInfo.getInt("Ny");
dx = navInfo.getDouble("Dx") / 1000.0; // need to be km : unit conversion LOOK;
dy = navInfo.getDouble("Dy") / 1000.0; // need to be km : unit conversion LOOK;
return new ProjectionCT(grid_name, "FGDC", lc);
}
// polar stereographic
private ProjectionCT makePSProjection() throws NoSuchElementException {
double lov = navInfo.getDouble("Lov");
double la1 = navInfo.getDouble("La1");
double lo1 = navInfo.getDouble("Lo1");
// Why the scale factor?. accordining to GRID docs:
// "Grid lengths are in units of meters, at the 60 degree latitude circle nearest to the pole"
// since the scale factor at 60 degrees = k = 2*k0/(1+sin(60)) [Snyder,Working Manual p157]
// then to make scale = 1 at 60 degrees, k0 = (1+sin(60))/2 = .933
Stereographic ps = new Stereographic(90.0, lov, .933);
// we have to project in order to find the origin
ProjectionPoint start = ps.latLonToProj(LatLonPoint.create(la1, lo1));
if (debug)
System.out.println("start at proj coord " + start);
startx = start.getX();
starty = start.getY();
nx = navInfo.getInt("Nx");
ny = navInfo.getInt("Ny");
dx = navInfo.getDouble("Dx") / 1000.0;
dy = navInfo.getDouble("Dy") / 1000.0;
return new ProjectionCT(grid_name, "FGDC", ps);
}
private void processLatLonProjection() throws NoSuchElementException {
// get stuff we need to construct axes
starty = navInfo.getDouble("La1");
startx = navInfo.getDouble("Lo1");
nx = navInfo.getInt("Ni");
ny = navInfo.getInt("Nj");
dx = navInfo.getDouble("Di");
dy = navInfo.getDouble("Dj");
}
} // GRIB1 */
}
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