public void readByte2Short() throws Exception {
Variable t2 = null;
assert (null != (t2 = ncfileRead.findVariable("t2")));
assert (t2.getDataType() == DataType.BYTE);
Attribute att = t2.findAttribute(CDM.SCALE_FACTOR);
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
assert (2 == att.getNumericValue().doubleValue());
assert (DataType.SHORT == att.getDataType());
assert (null != (t2 = dsRead.findVariable("t2")));
assert t2 instanceof VariableEnhanced;
VariableDS vs = (VariableDS) t2;
assert (vs.getDataType() == DataType.SHORT) : vs.getDataType();
assert (!vs.hasMissing());
Array A = vs.read();
assert (A.getElementType() == short.class) : A.getElementType();
Index ima = A.getIndex();
int[] shape = A.getShape();
int i, j;
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getShort(ima.set(i, j)) == (2 * (i * 10 + j) + 77));
}
}
System.out.println("**************TestStandardVar readByte2Short");
}
public void testAggCoordVar(NetcdfFile ncfile) {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1 : time.getRank();
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.INT;
assert time.getDimension(0) == ncfile.findDimension("time");
try {
Array data = time.read();
assert (data instanceof ArrayInt.D1) : data.getClass().getName();
ArrayInt.D1 dataI = (ArrayInt.D1) data;
assert dataI.get(0) == 0;
assert dataI.get(1) == 10;
assert dataI.get(2) == 99;
} catch (IOException io) {
io.printStackTrace();
assert false;
}
}
public void readShortMissing() throws Exception {
Variable v = null;
assert (null != (v = ncfileRead.findVariable("t4")));
assert (v.getDataType() == DataType.SHORT);
// default use of missing_value
assert (null != (v = dsRead.findVariable("t4")));
assert v instanceof VariableEnhanced;
assert v instanceof VariableDS;
VariableDS vs = (VariableDS) v;
assert (vs.getDataType() == DataType.SHORT);
Attribute att = vs.findAttribute(CDM.MISSING_VALUE);
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
System.out.println("missing_value = " + att.getNumericValue().shortValue());
assert (((short) -9999) == att.getNumericValue().shortValue());
assert (DataType.SHORT == att.getDataType());
assert (vs.hasMissing());
assert (vs.hasMissingValue());
assert (vs.isMissing((double) ((short) -9999)));
assert (vs.isMissingValue((double) ((short) -9999)));
Array A = vs.read();
Index ima = A.getIndex();
int[] shape = A.getShape();
int i, j;
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getFloat(ima.set(i, j)) == (i * 10 + j));
}
}
// turn off missing data
vs.setMissingDataIsMissing(false);
assert (vs.getDataType() == DataType.SHORT);
assert (!vs.hasMissing());
assert (vs.hasMissingValue());
assert (!vs.isMissing((double) ((short) -9999)));
assert (vs.isMissingValue((double) ((short) -9999)));
vs.setMissingDataIsMissing(true);
assert (vs.hasMissing());
assert (vs.isMissing((double) ((short) -9999)));
System.out.println("**************TestStandardVar Read readShortMissing");
}
public void testAggCoordVar2(NetcdfFile ncfile) {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1 : time.getRank();
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.INT;
assert time.getDimension(0) == ncfile.findDimension("time");
try {
Array data = time.read();
assert (data instanceof ArrayInt);
IndexIterator dataI = data.getIndexIterator();
assert dataI.getIntNext() == 0 : dataI.getIntCurrent();
assert dataI.getIntNext() == 1 : dataI.getIntCurrent();
assert dataI.getIntNext() == 2 : dataI.getIntCurrent();
} catch (IOException io) {
io.printStackTrace();
assert false;
}
}
private void doWrite2(NetcdfFileWriteable ncfile, String varName) throws Exception {
Variable v = ncfile.findVariable(varName);
int[] w = getWeights(v);
int[] shape = v.getShape();
Array aa = Array.factory(v.getDataType().getPrimitiveClassType(), shape);
Index ima = aa.getIndex();
for (int i = 0; i < shape[0]; i++) {
for (int j = 0; j < shape[1]; j++) {
aa.setDouble(ima.set(i, j), (double) (i * w[0] + j * w[1]));
}
}
ncfile.write(varName, aa);
}
private int[] getWeights(Variable v) {
int rank = v.getRank();
int[] w = new int[rank];
for (int n = 0; n < rank; n++) {
Dimension dim = v.getDimension(n);
String dimName = dim.getName();
if (dimName.equals("time")) w[n] = 1000;
if (dimName.equals("z")) w[n] = 100;
if (dimName.equals("y")) w[n] = 10;
if (dimName.equals("x")) w[n] = 1;
}
return w;
}
private double computeFitness(IGPProgram a_program, Variable vx) {
double error = 0.0f;
Object[] noargs = new Object[0];
// Initialize local stores.
// ------------------------
a_program.getGPConfiguration().clearStack();
a_program.getGPConfiguration().clearMemory();
// Compute fitness for each program.
// ---------------------------------
for (int i = 2; i < 15; i++) {
for (int j = 0; j < a_program.size(); j++) {
vx.set(new Integer(i));
try {
try {
// Only evaluate after whole GP program was run.
// ---------------------------------------------
if (j == a_program.size() - 1) {
double result = a_program.execute_int(j, noargs);
error += Math.abs(result - fib_iter(i));
} else {
a_program.execute_void(j, noargs);
}
} catch (IllegalStateException iex) {
error = Double.MAX_VALUE / 2;
break;
}
} catch (ArithmeticException ex) {
System.out.println("Arithmetic Exception with x = " + i);
System.out.println(a_program.getChromosome(j));
throw ex;
}
}
}
return error;
}
public void readSlice(NetcdfFile ncfile, int[] origin, int[] shape, String name)
throws IOException, InvalidRangeException {
Variable v = ncfile.findVariable(name);
Array data = v.read(origin, shape);
assert data.getRank() == 3;
assert data.getSize() == shape[0] * shape[1] * shape[2];
assert data.getShape()[0] == shape[0] : data.getShape()[0] + " " + shape[0];
assert data.getShape()[1] == shape[1];
assert data.getShape()[2] == shape[2];
assert data.getElementType() == double.class;
Index tIndex = data.getIndex();
for (int i = 0; i < shape[0]; i++)
for (int j = 0; j < shape[1]; j++)
for (int k = 0; k < shape[2]; k++) {
double val = data.getDouble(tIndex.set(i, j, k));
// System.out.println(" "+val);
assert TestUtils.close(val, 100 * (i + origin[0]) + 10 * j + k) : val;
}
}
public void testAggCoordVarScan(NetcdfFile ncfile) throws IOException {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1 : time.getRank();
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.INT : time.getDataType();
assert time.getDimension(0) == ncfile.findDimension("time");
int count = 0;
Array data = time.read();
assert (data instanceof ArrayInt);
while (data.hasNext()) {
int val = data.nextInt();
assert val == count * 10 : val + "!=" + count * 10;
count++;
}
}
public void testAggCoordVar3(NetcdfFile ncfile) throws IOException {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1 : time.getRank();
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.DOUBLE : time.getDataType();
assert time.getDimension(0) == ncfile.findDimension("time");
Array data = time.read();
assert (data instanceof ArrayDouble);
IndexIterator dataI = data.getIndexIterator();
double val = dataI.getDoubleNext();
assert Misc.closeEnough(val, 0.0) : val;
assert Misc.closeEnough(dataI.getDoubleNext(), 10.0) : dataI.getDoubleCurrent();
assert Misc.closeEnough(dataI.getDoubleNext(), 99.0) : dataI.getDoubleCurrent();
}
public void testCoordVar(NetcdfFile ncfile) {
Variable lat = ncfile.findVariable("lat");
assert null != lat;
assert lat.getShortName().equals("lat");
assert lat.getRank() == 1;
assert lat.getSize() == 3;
assert lat.getShape()[0] == 3;
assert lat.getDataType() == DataType.FLOAT;
assert !lat.isUnlimited();
assert lat.getDimension(0).equals(ncfile.findDimension("lat"));
Attribute att = lat.findAttribute("units");
assert null != att;
assert !att.isArray();
assert att.isString();
assert att.getDataType() == DataType.STRING;
assert att.getStringValue().equals("degrees_north");
assert att.getNumericValue() == null;
assert att.getNumericValue(3) == null;
try {
Array data = lat.read();
assert data.getRank() == 1;
assert data.getSize() == 3;
assert data.getShape()[0] == 3;
assert data.getElementType() == float.class;
IndexIterator dataI = data.getIndexIterator();
assert TestUtils.close(dataI.getDoubleNext(), 41.0);
assert TestUtils.close(dataI.getDoubleNext(), 40.0);
assert TestUtils.close(dataI.getDoubleNext(), 39.0);
} catch (IOException io) {
}
}
public void readByte() throws Exception {
Variable v = null;
assert (null != (v = ncfileRead.findVariable("t3")));
assert (v.getDataType() == DataType.BYTE);
assert (null != (v = dsRead.findVariable("t3")));
assert v instanceof VariableEnhanced;
assert v instanceof VariableDS;
VariableDS vs = (VariableDS) v;
assert (vs.getDataType() == DataType.BYTE);
Attribute att = vs.findAttribute("_FillValue");
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
System.out.println("_FillValue = " + att.getNumericValue().byteValue());
assert (((byte) 255) == att.getNumericValue().byteValue());
assert (DataType.BYTE == att.getDataType());
assert (vs.hasMissing());
assert (vs.hasFillValue());
assert (vs.isMissing((double) ((byte) 255)));
assert (vs.isFillValue((double) ((byte) 255)));
Array A = vs.read();
assert (A.getElementType() == byte.class) : A.getElementType();
Index ima = A.getIndex();
int[] shape = A.getShape();
int i, j;
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getFloat(ima.set(i, j)) == (i * 10 + j));
}
}
System.out.println("**************TestStandardVar ReadByte");
}
public void testAggCoordVarNoCoordsDir(NetcdfFile ncfile) throws IOException {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1 : time.getRank();
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.STRING : time.getDataType();
assert time.getDimension(0) == ncfile.findDimension("time");
Array data = time.read();
assert (data instanceof ArrayObject);
IndexIterator dataI = data.getIndexIterator();
String coordName = (String) dataI.getObjectNext();
assert coordName.equals("time0Dir.nc") : coordName;
coordName = (String) dataI.getObjectNext();
assert coordName.equals("time1Dir.nc") : coordName;
coordName = (String) dataI.getObjectNext();
assert coordName.equals("time2Dir.nc") : coordName;
}
public void readDouble() throws Exception {
Variable t1 = null;
assert (null != (t1 = ncfileRead.findVariable("t1")));
assert (t1.getDataType() == DataType.DOUBLE);
Attribute att = t1.findAttribute(CDM.SCALE_FACTOR);
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
assert (2.0 == att.getNumericValue().doubleValue());
assert (DataType.DOUBLE == att.getDataType());
// read
Array A = t1.read();
int i, j;
Index ima = A.getIndex();
int[] shape = A.getShape();
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getDouble(ima.set(i, j)) == (double) (i * 10.0 + j));
}
}
assert (null != (t1 = dsRead.findVariable("t1")));
assert t1 instanceof VariableEnhanced;
VariableEnhanced dsVar = (VariableEnhanced) t1;
assert (dsVar.getDataType() == DataType.DOUBLE);
A = dsVar.read();
ima = A.getIndex();
shape = A.getShape();
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getDouble(ima.set(i, j)) == (2.0 * (i * 10.0 + j) + 77.0));
}
}
assert (null == t1.findAttribute(CDM.SCALE_FACTOR));
assert (null == t1.findAttribute("add_offset"));
System.out.println("**************TestStandardVar ReadDouble");
}
public void testRandomInitialize_0() throws Exception {
Variable vx;
Class[] types = {CommandGene.VoidClass, CommandGene.VoidClass, CommandGene.IntegerClass};
Class[][] argTypes = {{}, {}, {}};
int[] minDepths = new int[] {3, 4, 1};
int[] maxDepths = new int[] {3, 4, 1};
CommandGene[][] nodeSets = {
{
CMD_SUB_V_V, // 0
CMD_CONST1, // 1
new StoreTerminal(m_gpconf, "mem0", CommandGene.IntegerClass), // 2
new StoreTerminal(m_gpconf, "mem1", CommandGene.IntegerClass), // 3
},
{
vx = Variable.create(m_gpconf, "X", CommandGene.IntegerClass), // 0
new AddAndStore(m_gpconf, CommandGene.IntegerClass, "mem2"), // 1
CMD_FOR, // 2
new TransferMemory(m_gpconf, "mem2", "mem1"), // 3
new TransferMemory(m_gpconf, "mem1", "mem0"), // 4
new ReadTerminal(m_gpconf, CommandGene.IntegerClass, "mem0"), // 5
new ReadTerminal(m_gpconf, CommandGene.IntegerClass, "mem1"), // 6
CMD_SUB_V_V_V, // 7
new Increment(m_gpconf, CommandGene.IntegerClass, -1), // 8
},
{}
};
// Add commands working with internal memory.
// ------------------------------------------
nodeSets[2] =
CommandFactory.createReadOnlyCommands(
nodeSets[2], m_gpconf, CommandGene.IntegerClass, "mem", 1, 2, !true);
// Execute the functionality to test.
// ----------------------------------
rn.setNextIntSequence(new int[] {0, 2, 1, 3, 1, 2, 8, 0, 7, 1, 5, 6, 4, 3});
m_gpconf.setPopulationSize(1);
GPGenotype gen =
GPGenotype.randomInitialGenotype(
m_gpconf,
types,
argTypes,
nodeSets,
minDepths,
maxDepths,
200,
new boolean[] {true, true, false},
false);
GPPopulation pop = gen.getGPPopulation();
assertEquals(m_gpconf.getPopulationSize(), pop.size());
// Evaluate program 1
// ------------------
IGPProgram p = pop.getGPProgram(0);
assertEquals(8, p.getChromosome(0).size());
assertEquals(CMD_SUB_V_V, p.getChromosome(0).getNode(0));
assertEquals(StoreTerminal.class, p.getChromosome(0).getNode(1).getClass());
assertSame(CMD_CONST1, p.getChromosome(0).getNode(2));
assertEquals(SubProgram.class, p.getChromosome(0).getNode(3).getClass());
// assertEquals(StoreTerminal.class, p.getChromosome(0).getNode(3).getClass());
assertSame(CMD_CONST1, p.getChromosome(0).getNode(4));
// Evaluate program 2
// ------------------
int node = 0;
assertEquals(9, p.getChromosome(1).size());
assertEquals(CMD_FOR, p.getChromosome(1).getNode(node++));
assertEquals(Increment.class, p.getChromosome(1).getNode(node++).getClass());
assertEquals(Variable.class, p.getChromosome(1).getNode(node++).getClass());
assertEquals(CMD_SUB_V_V_V, p.getChromosome(1).getNode(node++));
assertEquals(AddAndStore.class, p.getChromosome(1).getNode(node++).getClass());
assertEquals(ReadTerminal.class, p.getChromosome(1).getNode(node++).getClass());
assertEquals(ReadTerminal.class, p.getChromosome(1).getNode(node++).getClass());
assertEquals(TransferMemory.class, p.getChromosome(1).getNode(node++).getClass());
assertEquals(TransferMemory.class, p.getChromosome(1).getNode(node++).getClass());
// Evaluate program 3
// ------------------
assertEquals(1, p.getChromosome(2).size());
assertEquals(ReadTerminal.class, p.getChromosome(2).getNode(0).getClass());
assertEquals(0.0, computeFitness(p, vx), DELTA);
}
public void testNC3Read() throws IOException {
NetcdfFile ncfile = TestDir.openFileLocal("testWrite.nc");
assert (null != ncfile.findDimension("lat"));
assert (null != ncfile.findDimension("lon"));
Variable temp = null;
assert (null != (temp = ncfile.findVariable("temperature")));
// read entire array
Array A;
try {
A = temp.read();
} catch (IOException e) {
System.err.println("ERROR reading file");
assert (false);
return;
}
assert (A.getRank() == 2);
int i, j;
Index ima = A.getIndex();
int[] shape = A.getShape();
assert shape[0] == 64;
assert shape[1] == 128;
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
double dval = A.getDouble(ima.set(i, j));
assert (dval == (double) (i * 1000000 + j * 1000)) : dval;
}
}
// read part of array
int[] origin2 = new int[2];
int[] shape2 = new int[2];
shape2[0] = 1;
shape2[1] = temp.getShape()[1];
try {
A = temp.read(origin2, shape2);
} catch (InvalidRangeException e) {
System.err.println("ERROR reading file " + e);
assert (false);
return;
} catch (IOException e) {
System.err.println("ERROR reading file");
assert (false);
return;
}
assert (A.getRank() == 2);
for (j = 0; j < shape2[1]; j++) {
assert (A.getDouble(ima.set(0, j)) == (double) (j * 1000));
}
// rank reduction
Array Areduce = A.reduce();
Index ima2 = Areduce.getIndex();
assert (Areduce.getRank() == 1);
for (j = 0; j < shape2[1]; j++) {
assert (Areduce.getDouble(ima2.set(j)) == (double) (j * 1000));
}
// read char variable
Variable c = null;
assert (null != (c = ncfile.findVariable("svar")));
try {
A = c.read();
} catch (IOException e) {
assert (false);
}
assert (A instanceof ArrayChar);
ArrayChar ac = (ArrayChar) A;
String val = ac.getString(ac.getIndex());
assert val.equals("Testing 1-2-3") : val;
// System.out.println( "val = "+ val);
// read char variable 2
Variable c2 = null;
assert (null != (c2 = ncfile.findVariable("svar2")));
try {
A = c2.read();
} catch (IOException e) {
assert (false);
}
assert (A instanceof ArrayChar);
ArrayChar ac2 = (ArrayChar) A;
assert (ac2.getString().equals("Two pairs of ladies stockings!"));
// read String Array
Variable c3 = null;
assert (null != (c3 = ncfile.findVariable("names")));
try {
A = c3.read();
} catch (IOException e) {
assert (false);
}
assert (A instanceof ArrayChar);
ArrayChar ac3 = (ArrayChar) A;
ima = ac3.getIndex();
assert (ac3.getString(ima.set(0)).equals("No pairs of ladies stockings!"));
assert (ac3.getString(ima.set(1)).equals("One pair of ladies stockings!"));
assert (ac3.getString(ima.set(2)).equals("Two pairs of ladies stockings!"));
// read String Array - 2
Variable c4 = null;
assert (null != (c4 = ncfile.findVariable("names2")));
try {
A = c4.read();
} catch (IOException e) {
assert (false);
}
assert (A instanceof ArrayChar);
ArrayChar ac4 = (ArrayChar) A;
ima = ac4.getIndex();
assert (ac4.getString(0).equals("0 pairs of ladies stockings!"));
assert (ac4.getString(1).equals("1 pair of ladies stockings!"));
assert (ac4.getString(2).equals("2 pairs of ladies stockings!"));
// System.out.println( "ncfile = "+ ncfile);
ncfile.close();
System.out.println("**************TestRead done");
}
public void readShort2FloatMissing() throws Exception {
Variable v = null;
assert (null != (v = ncfileRead.findVariable("t5")));
assert (v.getDataType() == DataType.SHORT);
// standard convert with missing data
assert (null != (v = dsRead.findVariable("t5")));
assert v instanceof VariableEnhanced;
assert v instanceof VariableDS;
VariableDS vs = (VariableDS) v;
assert (vs.getDataType() == DataType.FLOAT);
assert (vs.hasMissing());
assert (vs.hasMissingValue());
double mv = 2 * (-9999) + 77;
assert (vs.isMissing((double) mv));
assert (vs.isMissingValue((double) mv));
Array A = vs.read();
Index ima = A.getIndex();
int[] shape = A.getShape();
int i, j;
assert (vs.isMissing(A.getFloat(ima.set(0, 0))));
for (i = 0; i < shape[0]; i++) {
for (j = 1; j < shape[1]; j++) {
float val = A.getFloat(ima.set(i, j));
float want = 2 * (i * 10 + j) + 77;
if (val != want) System.out.println(i + " " + j + " " + val + " " + want);
assert (val == want);
}
}
// useNaNs
vs.setUseNaNs(true);
assert (vs.getDataType() == DataType.FLOAT);
assert (vs.hasMissing());
assert (vs.hasMissingValue());
double mv2 = 2 * (-9999) + 77;
assert (vs.isMissing((double) mv2));
assert (vs.isMissingValue((double) mv2));
Array A2 = vs.read();
Index ima2 = A2.getIndex();
int[] shape2 = A2.getShape();
double mval = A2.getFloat(ima2.set(0, 0));
assert vs.isMissing(mval);
assert Double.isNaN(mval);
for (i = 0; i < shape2[0]; i++) {
for (j = 1; j < shape2[1]; j++) {
float val = A2.getFloat(ima2.set(i, j));
float want = 2 * (i * 10 + j) + 77;
if (val != want) System.out.println(i + " " + j + " " + val + " " + want);
assert (val == want) : val + " != " + want;
}
}
assert (null == vs.findAttribute(CDM.SCALE_FACTOR));
assert (null == vs.findAttribute("add_offset"));
assert (null == vs.findAttribute(CDM.MISSING_VALUE));
System.out.println("**************TestStandardVar Read readShort2FloatMissing");
}
public void testReadData(NetcdfFile ncfile, String name) throws IOException {
Variable v = ncfile.findVariable(name);
assert null != v;
assert v.getShortName().equals(name);
assert v.getRank() == 3;
assert v.getSize() == 36 : v.getSize();
assert v.getShape()[0] == 3;
assert v.getShape()[1] == 3;
assert v.getShape()[2] == 4;
assert v.getDataType() == DataType.DOUBLE;
assert !v.isCoordinateVariable();
assert v.getDimension(0) == ncfile.findDimension("time");
assert v.getDimension(1) == ncfile.findDimension("lat");
assert v.getDimension(2) == ncfile.findDimension("lon");
Array data = v.read();
assert data.getRank() == 3;
assert data.getSize() == 36;
assert data.getShape()[0] == 3;
assert data.getShape()[1] == 3;
assert data.getShape()[2] == 4;
assert data.getElementType() == double.class;
int[] shape = data.getShape();
Index tIndex = data.getIndex();
for (int i = 0; i < shape[0]; i++)
for (int j = 0; j < shape[1]; j++)
for (int k = 0; k < shape[2]; k++) {
double val = data.getDouble(tIndex.set(i, j, k));
// System.out.println(" "+val);
assert TestUtils.close(val, 100 * i + 10 * j + k) : val;
}
}