/*
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*
* Portions of this software were developed by the Unidata Program at the
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package ucar.nc2.dataset;
import org.junit.Test;
import org.junit.experimental.categories.Category;
import ucar.ma2.ArrayDouble;
import ucar.ma2.InvalidRangeException;
import ucar.ma2.Section;
import ucar.nc2.Dimension;
import ucar.nc2.dt.GridCoordSystem;
import ucar.nc2.dt.grid.GeoGrid;
import ucar.nc2.dt.grid.GridDataset;
import ucar.nc2.units.SimpleUnit;
import ucar.unidata.geoloc.vertical.*;
import ucar.unidata.util.test.category.NeedsCdmUnitTest;
import ucar.unidata.util.test.TestDir;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
/**
* test vertical transforms.
*
* @author caron
*/
@Category(NeedsCdmUnitTest.class)
public class TestTransforms {
private String testDir= TestDir.cdmUnitTestDir + "transforms/";
@Test
public void testHybridSigmaPressure() throws IOException, InvalidRangeException {
String filename = testDir + "HybridSigmaPressure.nc";
test(filename, "lev", "T", "time", VerticalCT.Type.HybridSigmaPressure, HybridSigmaPressure.class, SimpleUnit.pressureUnit);
}
@Test
public void testHybridSigmaPressure2() throws IOException, InvalidRangeException {
String filename = testDir + "climo.cam2.h0.0000-09.nc";
NetcdfDataset ncd = ucar.nc2.dataset.NetcdfDataset.openDataset(filename);
VerticalTransform vt = test(ncd, "lev", "T", "time", VerticalCT.Type.HybridSigmaPressure, HybridSigmaPressure.class, SimpleUnit.pressureUnit, true);
Dimension timeDim = ncd.findDimension("time");
for (int i = 0; i < timeDim.getLength(); i++) {
ucar.ma2.ArrayDouble.D3 coordVals = vt.getCoordinateArray(i);
int[] shape = coordVals.getShape();
assert shape[0] == ncd.findDimension("lev").getLength();
assert shape[1] == ncd.findDimension("lat").getLength();
assert shape[2] == ncd.findDimension("lon").getLength();
}
ncd.close();
}
@Test
public void testHybridSigmaPressure3() throws IOException, InvalidRangeException {
String filename = testDir + "HIRLAMhybrid.ncml";
NetcdfDataset ncd = ucar.nc2.dataset.NetcdfDataset.openDataset(filename);
VerticalTransform vt = test(ncd, "hybrid", "Relative_humidity_hybrid", "time", VerticalCT.Type.HybridSigmaPressure, HybridSigmaPressure.class,
SimpleUnit.pressureUnit, true);
Dimension timeDim = ncd.findDimension("time");
for (int i = 0; i < timeDim.getLength(); i++) {
ucar.ma2.ArrayDouble.D3 coordVals = vt.getCoordinateArray(i);
int[] shape = coordVals.getShape();
assert shape[0] == ncd.findDimension("hybrid").getLength();
assert shape[1] == ncd.findDimension("y").getLength();
assert shape[2] == ncd.findDimension("x").getLength();
}
ncd.close();
}
@Test
public void testOceanS() throws IOException, InvalidRangeException {
String filename = testDir+ "OceanS.nc";
test(filename, "s_rho", "salt", "ocean_time", VerticalCT.Type.OceanS, OceanS.class, SimpleUnit.meterUnit);
}
@Test
public void testOceanS2() throws IOException, InvalidRangeException {
String filename = testDir+ "OceanS2.nc";
test(filename, "s_rho", "temp", "ocean_time", VerticalCT.Type.OceanS, OceanS.class, SimpleUnit.meterUnit);
}
@Test
public void testOceanSigma() throws IOException, InvalidRangeException {
String filename = testDir+ "OceanSigma.nc";
test(filename, "zpos", "salt", "time", VerticalCT.Type.OceanSigma, OceanSigma.class, SimpleUnit.meterUnit);
}
@Test
public void testOceanSigma2() throws IOException, InvalidRangeException {
String filename = testDir+ "erie_test.ncml";
test(filename, "sigma", "temp", "time", VerticalCT.Type.OceanSigma, OceanSigma.class, SimpleUnit.meterUnit);
}
@Test
public void testGomoos() throws IOException, InvalidRangeException {
String filename = testDir+ "gomoos.ncml";
test(filename, "zpos", "temp", "time", VerticalCT.Type.OceanSigma, OceanSigma.class, SimpleUnit.meterUnit);
}
@Test
public void testWrf() throws IOException, InvalidRangeException {
String filename = TestDir.cdmUnitTestDir + "conventions/wrf/global.nc";
test(filename, "z", "T", "Time", VerticalCT.Type.WRFEta, WRFEta.class, SimpleUnit.pressureUnit);
test(filename, "z", "U", "Time", VerticalCT.Type.WRFEta, WRFEta.class, SimpleUnit.pressureUnit);
test(filename, "z", "V", "Time", VerticalCT.Type.WRFEta, WRFEta.class, SimpleUnit.pressureUnit);
test(filename, "z_stag", "W", "Time", VerticalCT.Type.WRFEta, WRFEta.class, SimpleUnit.meterUnit);
}
@Test
public void testWrf2() throws IOException, InvalidRangeException {
String filename = TestDir.cdmUnitTestDir + "conventions/wrf/wrfout_mercator.nc";
test(filename, "z", "T", "Time", VerticalCT.Type.WRFEta, WRFEta.class, SimpleUnit.pressureUnit);
test(filename, "z", "U", "Time", VerticalCT.Type.WRFEta, WRFEta.class, SimpleUnit.pressureUnit);
test(filename, "z", "V", "Time", VerticalCT.Type.WRFEta, WRFEta.class, SimpleUnit.pressureUnit);
test(filename, "z_stag", "W", "Time", VerticalCT.Type.WRFEta, WRFEta.class, SimpleUnit.meterUnit);
}
// LOOK these are failing
// needs COnvention = CF
public void testOceanSigmaNcml() throws IOException, InvalidRangeException {
String filename = "http://coast-enviro.er.usgs.gov/models/share/glos_test.ncml";
test(filename, "sigma", "temp", "time", VerticalCT.Type.OceanSigma, OceanSigma.class, SimpleUnit.meterUnit);
}
/* btestOceanS3
problem is that u is
float u(ocean_time=1, s_rho=6, eta_u=120, xi_u=155);
:coordinates = "lon_u lat_u s_rho ocean_time";
double s_rho(s_rho=6);
:long_name = "S-coordinate at RHO-points";
:positive = "up";
:standard_name = "ocean_s_coordinate";
:formula_terms = "s: s_rho eta: zeta depth: h a: theta_s b: theta_b depth_c: hc";
which uses zeta:
float zeta(ocean_time=1, eta_rho=120, xi_rho=156);
which is 120 x 126 instead of 120 x 125.
seems to be an rsignell file. may be motivation for staggered convention
OceanS_Transform_s_rho type=Vertical
standard_name = ocean_s_coordinate
formula_terms = s: s_rho eta: zeta depth: h a: theta_s b: theta_b depth_c: hc
height_formula = height(x,y,z) = depth_c*s(z) + (depth(x,y)-depth_c)*C(z) + eta(x,y) * (1 + (depth_c*s(z) + (depth(x,y)-depth_c)*C(z))/depth(x,y)
C_formula = C(z) = (1-b)*sinh(a*s(z))/sinh(a) + b*(tanh(a*(s(z)+0.5))/(2*tanh(0.5*a))-0.5)
Eta_variableName = zeta
S_variableName = s_rho
Depth_variableName = h
Depth_c_variableName = hc
A_variableName = theta_s
B_variableName = theta_b
*/
@Test
public void btestOceanS3() throws IOException, InvalidRangeException {
String filename = testDir+ "ocean_his.nc";
_test(filename, "s_rho", "u", "ocean_time", VerticalCT.Type.OceanS, OceanS.class, SimpleUnit.meterUnit, false);
}
@Test
public void btestOceanG1() throws IOException, InvalidRangeException {
String filename = testDir+ "ocean_his_g1.nc";
_test(filename, "s_rho", "u", "ocean_time", VerticalCT.Type.OceanSG1, OceanSG1.class, SimpleUnit.meterUnit, false);
}
@Test
public void btestOceanG2() throws IOException, InvalidRangeException {
String filename = testDir+ "ocean_his_g2.nc";
_test(filename, "s_rho", "u", "ocean_time", VerticalCT.Type.OceanSG2, OceanSG2.class, SimpleUnit.meterUnit, false);
}
@Test
public void testSigma() throws IOException, InvalidRangeException {
String filename = testDir+ "Sigma_LC.nc";
test(filename, "level", "Temperature", null, VerticalCT.Type.Sigma, AtmosSigma.class, SimpleUnit.pressureUnit);
}
@Test
public void testExisting3D() throws IOException, InvalidRangeException {
String filename = testDir+ "VExisting3D_NUWG.nc";
test(filename, "VerticalTransform", "rhu_hybr", "record", VerticalCT.Type.Existing3DField, VTfromExistingData.class,
null);
}
private VerticalTransform test(String filename, String levName, String varName, String timeName,
VerticalCT.Type vtype, Class vclass, SimpleUnit unit)
throws IOException, InvalidRangeException {
return _test(filename, levName, varName, timeName, vtype, vclass, unit, true);
}
private VerticalTransform _test(String filename, String levName, String varName, String timeName,
VerticalCT.Type vtype, Class vclass, SimpleUnit unit, boolean varsMatch)
throws IOException, InvalidRangeException {
NetcdfDataset ncd = ucar.nc2.dataset.NetcdfDataset.openDataset(filename);
test(ncd, levName, varName, timeName, vtype, vclass, unit, varsMatch);
ncd.close();
if (varsMatch) testGrid(filename, varName);
return null;
}
private VerticalTransform test(NetcdfDataset ncd, String levName, String varName, String timeName,
VerticalCT.Type vtype, Class vclass, SimpleUnit vunit, boolean varsMatch)
throws IOException, InvalidRangeException {
System.out.printf("file= %s%n", ncd.getLocation());
VariableDS lev = (VariableDS) ncd.findVariable(levName);
assert lev != null;
System.out.println(" dump of ctv = \n" + lev);
VariableDS v = (VariableDS) ncd.findVariable(varName);
assert v != null;
System.out.printf(" data variable = %s%n", v);
Section varSection = new Section(v.getShapeAsSection());
List cList = v.getCoordinateSystems();
assert cList != null;
assert cList.size() == 1;
CoordinateSystem csys = (CoordinateSystem) cList.get(0);
List<CoordinateTransform> vList = new ArrayList<CoordinateTransform>();
for (CoordinateTransform ct : csys.getCoordinateTransforms()) {
if (ct.getTransformType() == TransformType.Vertical)
vList.add(ct);
}
assert vList.size() == 1 : vList.size();
CoordinateTransform ct = (CoordinateTransform) vList.get(0);
assert ct.getTransformType() == TransformType.Vertical;
assert ct instanceof VerticalCT;
VerticalCT vct = (VerticalCT) ct;
assert vct.getVerticalTransformType() == vtype : vct.getVerticalTransformType();
VariableDS ctv = CoordTransBuilder.makeDummyTransformVariable(ncd, ct);
System.out.println(" dump of equivilent ctv = \n" + ctv);
VerticalTransform vt = null;
if (timeName == null) {
vt = vct.makeVerticalTransform(ncd, null);
assert !vt.isTimeDependent();
ucar.ma2.Array coordVals = vt.getCoordinateArray(0);
assert (null != coordVals);
Section cSection = new Section(coordVals.getShape());
System.out.printf(" coordVal shape = %s %n", cSection);
assert varSection.computeSize() == cSection.computeSize();
} else {
Dimension timeDim = ncd.findDimension(timeName);
assert null != timeDim;
vt = vct.makeVerticalTransform(ncd, timeDim);
assert vt.isTimeDependent();
varSection = varSection.removeRange(0); // remove time dependence for comparision
for (int i = 0; i < timeDim.getLength(); i++) {
ucar.ma2.ArrayDouble.D3 coordVals = vt.getCoordinateArray(i);
assert (null != coordVals);
Section cSection = new Section(coordVals.getShape());
System.out.printf("%s: varSection shape = %s %n", v.getFullName(), varSection);
System.out.printf("%s: coordVal shape = %s %n", v.getFullName(), cSection);
if (varSection.computeSize() != cSection.computeSize())
System.out.println("HEY");
if (varsMatch) assert varSection.computeSize() == cSection.computeSize();
}
}
assert vt != null;
assert vclass.isInstance(vt);
// should be compatible with vunit
if (vunit != null) {
String vertCoordUnit = vt.getUnitString();
assert vunit.isCompatible(vertCoordUnit) : vertCoordUnit + " not udunits compatible with " + vunit.getUnitString();
}
return vt;
}
private void testGrid(String uri, String var) throws IOException, InvalidRangeException {
GridDataset ds = null;
try {
ds = GridDataset.open(uri);
GeoGrid grid = ds.findGridByName(var);
Section s = new Section(grid.getShape());
System.out.printf("var = %s %n", s);
GridCoordSystem GridCoordS = grid.getCoordinateSystem();
VerticalTransform vt = GridCoordS.getVerticalTransform();
ArrayDouble.D3 z = vt.getCoordinateArray(0);
Section sv = new Section(z.getShape());
System.out.printf("3dcoord = %s %n", sv);
if (vt.isTimeDependent())
s = s.removeRange(0);
assert s.equals(sv);
} finally {
if (ds != null) ds.close();
}
}
}