ucar.nc2.dataset.conv.NUWGConvention Maven / Gradle / Ivy
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/*
* Copyright (c) 1998-2018 John Caron and University Corporation for Atmospheric Research/Unidata
* See LICENSE for license information.
*/
package ucar.nc2.dataset.conv;
import ucar.ma2.*;
import ucar.nc2.*;
import ucar.nc2.constants.CDM;
import ucar.nc2.constants._Coordinate;
import ucar.nc2.constants.AxisType;
import ucar.nc2.util.CancelTask;
import ucar.nc2.dataset.*;
import ucar.nc2.units.SimpleUnit;
import ucar.unidata.geoloc.*;
import ucar.unidata.geoloc.projection.LambertConformal;
import ucar.unidata.geoloc.projection.Stereographic;
import ucar.unidata.util.Format;
import ucar.unidata.util.StringUtil2;
import java.io.IOException;
import java.util.*;
/**
* NUWG Convention (ad hoc).
* see https://www.unidata.ucar.edu/software/netcdf/NUWG/
*
* @author caron
*/
public class NUWGConvention extends CoordSysBuilder {
private NavInfoList navInfo = new NavInfoList();
private String xaxisName = "", yaxisName = "";
private Grib1 grib;
private static final boolean dumpNav = false;
public NUWGConvention() {
this.conventionName = "NUWG";
}
public void augmentDataset(NetcdfDataset ds, CancelTask cancelTask) {
if (null != ds.findGlobalAttribute("_enhanced"))
return; // check if its already been done - aggregating enhanced datasets.
ds.addAttribute(null, new Attribute("_enhanced", "")); // LOOK
// find all variables that have the nav dimension
// put them into a NavInfoList
// make their data into metadata
List vars = ds.getVariables();
for (Variable v : vars) {
if (0 <= v.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 (null == ds.findVariable(xaxisName)) {
grib.makeXCoordAxis(ds, xaxisName);
parseInfo.format("Generated x axis from NUWG nav= %s%n", xaxisName);
} else if (xaxisName.equalsIgnoreCase("lon")) {
try {
// check monotonicity
boolean ok = true;
Variable dc = ds.findVariable(xaxisName);
Array coordVal = dc.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(ds, xaxisName);
}
} catch (IOException ioe) {
log.warn("IOException when reading xaxis = " + xaxisName);
}
}
if (null == ds.findVariable(yaxisName)) {
grib.makeYCoordAxis(ds, yaxisName);
parseInfo.format("Generated y axis from NUWG nav=%s%n", yaxisName);
}
// "referential" variables
List dims = ds.getRootGroup().getDimensions();
for (Dimension dim : dims) {
String dimName = dim.getShortName();
if (null != ds.findVariable(dimName)) // already has a coord axis
continue;
List ncvars = searchAliasedDimension(ds, dim);
if ((ncvars == null) || (ncvars.isEmpty())) // no alias
continue;
if (ncvars.size() == 1) {
Variable ncvar = ncvars.get(0);
if (!(ncvar instanceof VariableDS))
continue; // cant be a structure
if (makeCoordinateAxis(ncvar, dim)) {
parseInfo.format("Added referential coordAxis = ");
ncvar.getNameAndDimensions(parseInfo, true, false);
parseInfo.format("%n");
} else {
parseInfo.format("Couldnt add referential coordAxis = %s%n", ncvar.getFullName());
}
} else if (ncvars.size() == 2) {
if (dimName.equals("record")) {
Variable ncvar0 = ncvars.get(0);
Variable ncvar1 = ncvars.get(1);
Variable ncvar = ncvar0.getShortName().equalsIgnoreCase("valtime") ? ncvar0 : ncvar1;
if (makeCoordinateAxis(ncvar, dim)) {
parseInfo.format("Added referential coordAxis (2) = ");
ncvar.getNameAndDimensions(parseInfo, true, false);
parseInfo.format("%n");
// the usual crap - clean up time units
String units = ncvar.getUnitsString();
if (units != null) {
units = StringUtil2.remove(units, '(');
units = StringUtil2.remove(units, ')');
((VariableDS) ncvar).setUnitsString(units);
}
} else {
parseInfo.format("Couldnt add referential coordAxis = %s%n", ncvar.getFullName());
}
// ncvar = (Variable) ncvars.get(0);
// CoordinateAxis refTime = ds.addCoordinateAxis( ncvar);
// vaidTime.setAuxilary( refTime);
// parseInfo.append("Added referential record coordAxis = "+ncvar.getNameAndDimensions()+"%n");
} else {
// lower(?) bound
Variable ncvar = ncvars.get(0);
if (!(ncvar instanceof VariableDS))
continue; // cant be a structure
if (makeCoordinateAxis(ncvar, dim)) {
parseInfo.format("Added referential boundary coordAxis (2) = ");
ncvar.getNameAndDimensions(parseInfo, true, false);
parseInfo.format("%n");
} else {
parseInfo.format("Couldnt add referential coordAxis = %s%n", ncvar.getFullName());
}
/*
* CoordinateAxis bound1 = ds.addCoordinateAxis( (VariableDS) ncvar);
* parseInfo.append("Added referential boundary coordAxis = ");
* ncvar.getNameAndDimensions(parseInfo, true, false);
* parseInfo.append("%n");
*
* // upper(?) bound
* ncvar = (Variable) ncvars.get(1);
* if (!(ncvar instanceof VariableDS)) continue; // cant be a structure
* CoordinateAxis bound2 = ds.addCoordinateAxis( (VariableDS) ncvar);
* //bound1.setAuxilary( bound2);
*
* parseInfo.append("Added referential boundary coordAxis = ");
* ncvar.getNameAndDimensions(parseInfo, true, false);
* parseInfo.append("%n");
*
* /* DimCoordAxis dc = addCoordAxisFromTopBotVars( dim, (Variable) ncvars.get(0),
* (Variable) ncvars.get(1));
* if (null != dc)
* dc.isReferential = true;
*/
}
} // 2
} // loop over dims
if (grib.ct != null) {
VariableDS v = makeCoordinateTransformVariable(ds, grib.ct);
v.addAttribute(new Attribute(_Coordinate.Axes, xaxisName + " " + yaxisName));
ds.addVariable(null, v);
}
ds.finish();
}
private boolean makeCoordinateAxis(Variable ncvar, Dimension dim) {
if (ncvar.getRank() != 1)
return false;
Dimension vdim = ncvar.getDimension(0);
if (!vdim.equals(dim))
return false;
if (!dim.getShortName().equals(ncvar.getShortName())) {
ncvar.addAttribute(new Attribute(_Coordinate.AliasForDimension, dim.getShortName()));
}
/*
* if (dim.getCoordinateVariables().size() == 1) {
* dim.addCoordinateVariable( ncvar);
* ncvar.setIsCoordinateAxis( true);
* }
*/
return true;
}
/*
* private int getDimensionIndex( Variable v, String dimName) {
* Iterator iter = v.getDimensions().iterator();
* int count = 0;
* while (iter.hasNext()) {
* Dimension dim = (Dimension) iter.next();
* if (dimName.equalsIgnoreCase( dim.getShortName()))
* return count;
* count++;
* }
* return -1;
* }
*/
/**
* Search for an aliased coord that may have multiple variables
* :dimName = alias1, alias2;
* Variable alias1(dim);
* Variable alias2(dim);
*
* @param ds search in this dataset
* @param dim: look for this dimension name
* @return Collection of nectdf variables, or null if none
*/
private List searchAliasedDimension(NetcdfDataset ds, Dimension dim) {
String dimName = dim.getShortName();
String alias = ds.findAttValueIgnoreCase(null, dimName, null);
if (alias == null)
return null;
List vars = new ArrayList<>();
StringTokenizer parser = new StringTokenizer(alias, " ,");
while (parser.hasMoreTokens()) {
String token = parser.nextToken();
Variable ncvar = ds.findVariable(token);
if (ncvar == null)
continue;
if (ncvar.getRank() != 1)
continue;
Iterator dimIter = ncvar.getDimensions().iterator();
Dimension dim2 = (Dimension) dimIter.next();
if (dimName.equals(dim2.getShortName())) {
vars.add(ncvar);
if (debug)
System.out.print(" " + token);
}
}
if (debug)
System.out.println();
return vars;
}
private StringBuilder buf = new StringBuilder(2000);
public String extraInfo() {
buf.setLength(0);
buf.append(navInfo).append("%n");
return buf.toString();
}
protected void makeCoordinateTransforms(NetcdfDataset ds) {
if ((grib != null) && (grib.ct != null)) {
VarProcess vp = findVarProcess(grib.ct.getName(), null);
vp.isCoordinateTransform = true;
vp.ct = grib.ct;
}
super.makeCoordinateTransforms(ds);
}
protected AxisType getAxisType(NetcdfDataset ds, VariableEnhanced ve) {
Variable v = (Variable) ve;
String vname = v.getShortName();
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;
Dimension dim = v.getDimension(0);
if ((dim != null) && dim.getShortName().equalsIgnoreCase("record")) { // wow thats bad!
return AxisType.Time;
}
String unit = ve.getUnitsString();
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 java.util.Comparator {
public int compare(NavInfo n1, NavInfo n2) {
return n1.getName().compareTo(n2.getName());
}
}
private class NavInfo {
Variable ncvar;
DataType valueType;
String svalue;
byte bvalue;
int ivalue;
double dvalue;
NavInfo(Variable ncvar) throws IOException {
this.ncvar = ncvar;
valueType = ncvar.getDataType();
try {
if ((valueType == DataType.CHAR) || (valueType == DataType.STRING))
svalue = ncvar.readScalarString();
else if (valueType == DataType.BYTE)
bvalue = ncvar.readScalarByte();
else if ((valueType == DataType.INT) || (valueType == DataType.SHORT))
ivalue = ncvar.readScalarInt();
else
dvalue = ncvar.readScalarDouble();
} catch (java.lang.UnsupportedOperationException e) {
parseInfo.format("Nav variable %s not a scalar%n", getName());
}
// List values = new ArrayList();
// values.add( getStringValue());
// ncDataset.setValues( ncvar, values); // WHY?
}
public String getName() {
return ncvar.getShortName();
}
public String getDescription() {
Attribute att = ncvar.attributes().findAttributeIgnoreCase(CDM.LONG_NAME);
return (att == null) ? getName() : att.getStringValue();
}
public DataType getValueType() {
return valueType;
}
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 ct;
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)
ct = makeLCProjection();
else if (5 == grid_code)
ct = makePSProjection();
else
throw new IllegalArgumentException("NUWGConvention: unknown grid_code= " + grid_code);
// vertical system
}
CoordinateAxis makeXCoordAxis(NetcdfDataset ds, String xname) {
CoordinateAxis v = new CoordinateAxis1D(ds, null, xname, DataType.DOUBLE, xname,
(0 == grid_code) ? CDM.LON_UNITS : "km", "synthesized X coord");
v.addAttribute(
new Attribute(_Coordinate.AxisType, (0 == grid_code) ? AxisType.Lon.toString() : AxisType.GeoX.toString()));
v.setValues(nx, startx, dx);
ds.addCoordinateAxis(v);
return v;
}
CoordinateAxis makeYCoordAxis(NetcdfDataset ds, String yname) {
CoordinateAxis v = new CoordinateAxis1D(ds, null, yname, DataType.DOUBLE, yname,
((0 == grid_code) ? CDM.LAT_UNITS : "km"), "synthesized Y coord");
v.addAttribute(
new Attribute(_Coordinate.AxisType, (0 == grid_code) ? AxisType.Lat.toString() : AxisType.GeoY.toString()));
v.setValues(ny, starty, dy);
ds.addCoordinateAxis(v);
return 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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