void PointCounter::output(const string &fileName) const
{
NcFile file(fileName.c_str(), NcFile::Replace);
if (!file.is_valid()) {
string message = "Failed to open file "+fileName+".";
REPORT_ERROR(message.c_str());
}
NcDim *numLonDim = file.add_dim("lon", counters.extent(0));
NcDim *numLatDim = file.add_dim("lat", counters.extent(1));
NcDim *numBndsDim = file.add_dim("bnds", 2);
//NcDim *numLevDim = file.add_dim("lev", counters.extent(2));
NcVar *lonBndsVar = file.add_var("lon_bnds", ncDouble, numLonDim, numBndsDim);
NcVar *latBndsVar = file.add_var("lat_bnds", ncDouble, numLatDim, numBndsDim);
//NcVar *levVar = file.add_var("lev", ncDouble, numLevDim);
lonBndsVar->add_att("long_name", "longitude bounds");
lonBndsVar->add_att("units", "degree_east");
latBndsVar->add_att("long_name", "latitude bounds");
latBndsVar->add_att("units", "degree_north");
int numLonBnds = mesh[0].getNumLon()-2, numLatBnds = mesh[0].getNumLat()-1;
double lonBnds[numLonBnds][2], latBnds[numLatBnds][2];
for (int i = 0; i < numLonBnds; ++i) {
lonBnds[i][0] = mesh[0].lon(i)*Rad2Deg;
lonBnds[i][1] = mesh[0].lon(i+1)*Rad2Deg;
}
for (int j = 0; j < numLatBnds; ++j) {
latBnds[j][0] = mesh[0].lat(j)*Rad2Deg;
latBnds[j][1] = mesh[0].lat(j+1)*Rad2Deg;
}
lonBndsVar->put(&lonBnds[0][0], numLonBnds, 2);
latBndsVar->put(&latBnds[0][0], numLatBnds, 2);
NcVar *countersVar = file.add_var("counters", ncInt, numLatDim, numLonDim);
countersVar->add_att("long_name", "contained point numbers in grid boxes");
int counters[this->counters.extent(1)][this->counters.extent(0)];
for (int j = 0; j < this->counters.extent(1); ++j)
for (int i = 0; i < this->counters.extent(0); ++i)
counters[j][i] = this->counters(i, j, 0);
countersVar->put(&counters[0][0], this->counters.extent(1), this->counters.extent(0));
}
void RLLMesh::output(const string &fileName) const
{
NcFile file(fileName.c_str(), NcFile::Replace);
if (!file.is_valid()) {
Message message;
message << "Failed to create point counter mesh file \"";
message << fileName << "\"!";
REPORT_ERROR(message.str());
}
NcDim *lonDim = file.add_dim("lon", lon.size());
NcDim *latDim = file.add_dim("lat", lat.size());
NcVar *lonVar = file.add_var("lon", ncDouble, lonDim);
NcVar *latVar = file.add_var("lat", ncDouble, latDim);
double lonTmp[lon.size()], latTmp[lat.size()];
for (int i = 0; i < lon.size(); ++i)
lonTmp[i] = lon(i)*Rad2Deg;
for (int j = 0; j < lat.size(); ++j)
latTmp[j] = lat(j)*Rad2Deg;
lonVar->put(lonTmp, lon.size());
latVar->put(latTmp, lat.size());
file.close();
}
int
main(void)
@{
// This is the data array we will write. It will just be filled
// with a progression of numbers for this example.
int dataOut[NX][NY];
// Create some pretend data. If this wasn't an example program, we
// would have some real data to write, for example, model output.
for(int i = 0; i < NX; i++)
for(int j = 0; j < NY; j++)
dataOut[i][j] = i * NY + j;
// Create the file. The Replace parameter tells netCDF to overwrite
// this file, if it already exists.
NcFile dataFile("simple_xy.nc", NcFile::Replace);
// You should always check whether a netCDF file creation or open
// constructor succeeded.
if (!dataFile.is_valid())
@{
cout << "Couldn't open file!\n";
return NC_ERR;
@}
// For other method calls, the default behavior of the C++ API is
// to exit with a message if there is an error. If that behavior
// is OK, there is no need to check return values in simple cases
// like the following.
// When we create netCDF dimensions, we get back a pointer to an
// NcDim for each one.
NcDim* xDim = dataFile.add_dim("x", NX);
NcDim* yDim = dataFile.add_dim("y", NY);
// Define a netCDF variable. The type of the variable in this case
// is ncInt (32-bit integer).
NcVar *data = dataFile.add_var("data", ncInt, xDim, yDim);
// Write the pretend data to the file. Although netCDF supports
// reading and writing subsets of data, in this case we write all
// the data in one operation.
data->put(&dataOut[0][0], NX, NY);
// The file will be automatically close when the NcFile object goes
// out of scope. This frees up any internal netCDF resources
// associated with the file, and flushes any buffers.
cout << "*** SUCCESS writing example file simple_xy.nc!" << endl;
return 0;
@}
int TestSuite::testVar()
{
try
{
string FILE_NAME = "tst_vars.nc";
int NDIMS = 4;
int NLAT = 6;
int NLON = 12;
// Names of things.
string LAT_NAME = "latitude";
string LON_NAME = "longitude";
int MAX_ATT_LEN = 80;
// These are used to construct some example data.
float START_LAT = 25.0;
float START_LON = -125.0;
string UNITS = "units";
string DEGREES_EAST = "degrees_east";
string DEGREES_NORTH = "degrees_north";
// For the units attributes.
string LAT_UNITS = "degrees_north";
string LON_UNITS = "degrees_east";
// Return this code to the OS in case of failure.
#define NC_ERR 2
// We will write latitude and longitude fields.
float lats[NLAT],lons[NLON];
// create some pretend data. If this wasn't an example program, we
// would have some real data to write for example, model output.
for (int lat = 0; lat < NLAT; lat++)
lats[lat] = START_LAT + 5. * lat;
for (int lon = 0; lon < NLON; lon++)
lons[lon] = START_LON + 5. * lon;
// Create the file.
NcFile test(FILE_NAME, NcFile::Replace);
// Define the dimensions. NetCDF will hand back an ncDim object for
// each.
NcDim* latDim = test.addDim(LAT_NAME, NLAT);
NcDim* lonDim = test.addDim(LON_NAME, NLON);
// Define the coordinate variables.
NcVar* latVar = test.addVar(LAT_NAME, ncFloat, latDim);
NcVar* lonVar = test.addVar(LON_NAME, ncFloat, lonDim);
// Define units attributes for coordinate vars. This attaches a
// text attribute to each of the coordinate variables, containing
// the units.
latVar->addAtt(UNITS,ncString, DEGREES_NORTH);
lonVar->addAtt(UNITS,ncString, DEGREES_EAST);
// Write the coordinate variable data to the file.
latVar->put(lats, NLAT);
lonVar->put(lons, NLON);
NcValues *latVals = latVar->getValues();
cout<<"toString returns lats: "<<latVals->toString()<<endl;
cout<<"toChar returns "<<latVals->toChar(1)<<endl;
cout<<"toShort returns "<<latVals->toShort(1)<<endl;
cout<<"toInt returns "<<latVals->toInt(1)<<endl;
cout<<"toLong returns "<<latVals->toLong(1)<<endl;
latVals->print(cout);
NcValues *lonVals = lonVar->getValues();
cout<<"toString returns lats: "<<lonVals->toString()<<endl;
lonVals->print(cout);
cout<<"no segmentation fault thus far"<<endl;
//test varaibles here
}
catch(NcException e)
{
e.what();
return 1;
}
try
{
cout<<"should test adding a variable with more than 5 dimensions here"<<endl;
// test creating a variable with more than 5 dimensions
}
catch (NcException e)
{
e.what();
return 1;
}
try //write the file with float's b/c that's all NcValues can handle at the moment
{
int NX = 6;
int NY = 12;
float dataOut[NX][NY];
// Create some pretend data. If this wasn't an example program, we
// would have some real data to write, for example, model output.
for(int i = 0; i < NX; i++)
for(int j = 0; j < NY; j++)
dataOut[i][j] = i * NY + j;
// The default behavior of the C++ API is to throw an exception i
// an error occurs. A try catch block in necessary.
// Create the file. The Replace parameter tells netCDF to overwrite
// this file, if it already exists.
string filename ="simples_xy.nc";
NcFile dataFile(filename, NcFile::Replace);
// When we create netCDF dimensions, we get back a pointer to an
// NcDim for each one.
NcDim* xDim = dataFile.addDim("x", NX);
NcDim* yDim = dataFile.addDim("y", NY);
// Define the variable. The type of the variable in this case is
// ncInt (32-bit integer).
NcVar *data = dataFile.addVar("data", ncFloat, xDim, yDim);
// Write the pretend data to the file. Although netCDF supports
// reading and writing subsets of data, in this case we write all
// the data in one operation.
data->put(&dataOut[0][0], NX, NY,0,0,0);
// The file will be automatically close when the NcFile object goes
// out of scope. This frees up any internal netCDF resources
// associated with the file, and flushes any buffers.
cout << "*** SUCCESS writing example file simples_xy.nc!" << endl;
}
catch(std::exception e)
{e.what();}
try
{
int NX = 6;
int NY = 12;
// Return this in event of a problem.
// int NC_ERR = 2;
// This is the array we will read.
float dataIn[NX][NY];
// Open the file. The ReadOnly parameter tells netCDF we want
// read-only access to the file.
NcFile dataFile("simples_xy.nc", NcFile::ReadOnly);
// Retrieve the variable named "data"
NcVar *data = dataFile.getVar("data");
//call getType on data
// Read all the values from the "data" variable into memory.
data->get(&dataIn[0][0], NX, NY);
// Check the values.
for (int i = 0; i < NX; i++)
for (int j = 0; j < NY; j++)
if (dataIn[i][j] != i * NY + j)
return 1;
NcValues* dataVar= data->getValues();
cout<<dataVar->toString()<<endl;;
dataVar->print(cout);
}
catch(NcException e)
{
e.what();
return 1;
}
cout<<"***************** Testing Variables was successful *****************"<<endl;
return 0;
}
int TestSuite::testFile(string fName, NcFile::FileMode fMode)
{
string UNITS = "UNITS:";
cout<<"*** Testing tst_file in tst_suite ";
int NLAT = 6;
int NLON = 12;
int NDIMS = 4;
int NLVL = 2;
int NREC = 2;
/* These are used to construct some example data. */
int SAMPLE_PRESSURE = 900;
float SAMPLE_TEMP = 9.0;
float START_LAT = 25.0;
float START_LON = -125.0;
/* We will write surface temperature and pressure fields. */
float pres_out[NLAT][NLON];
float pres_in[NLAT][NLON];
float temp_out[NLAT][NLON];
float temp_in[NLAT][NLON];
float lats[NLAT], lons[NLON],lats_in[NLAT],lons_in[NLON];
std::string chararray []={"I"," hope"," this"," is"," stored "," properly" };
std::string chararray_in[NLAT];
int outInts[NLAT],outInts_in[NLAT];
/* It's good practice for each netCDF variable to carry a "units"
* attribute. */
char pres_units[] = "hPa";
char temp_units[] = "celsius";
/* Loop indexes. */
int lat, lon;
/* Create some pretend data. If this wasn't an example program, we
* would have some real data to write, for example, model
* output. */
for (lat = 0; lat < NLAT; lat++)
{
lats[lat] = START_LAT + 5.*lat;
}
for(lat = 0; lat < NLAT; lat++)
{
outInts[lat]= 450;
}
for (lon = 0; lon < NLON; lon++)
{
lons[lon] = START_LON + 5.*lon;
}
for (lat = 0; lat < NLAT; lat++)
{
for (lon = 0; lon < NLON; lon++)
{
pres_out[lat][lon] = SAMPLE_PRESSURE + (lon * NLAT + lat);
temp_out[lat][lon] = SAMPLE_TEMP + .25 * (lon * NLAT + lat);
}
}
// nc_set_log_level(3);
try
{
NcFile f("tst_file.nc",NcFile::Replace);
NcGroup *root = f.getRootGroup();
NcDim *latDim = root->addDim(string("lat"),NLAT);
NcDim *lonDim = root->addDim(string("lon"),NLON);
NcVar *latVar = root->addVar(string("latVar"),ncDouble,latDim);
NcVar *lonVar = root->addVar(string("lonVar"),ncFloat,lonDim);
NcVar *outIntsVar = root->addVar(string("outintsVar"),ncInt,latDim);
NcVar *charArrVar = root->addVar(string("CharArray"),ncString,latDim);
latVar->addAtt(string(UNITS),ncChar,string("degrees_north"));
lonVar->addAtt(string(UNITS),ncChar,string("degrees_south"));
outIntsVar->put(&outInts[0],NLAT,0,0,0,0);
charArrVar->put(&chararray[0],NLAT,0,0,0,0);
latVar->put(&lats[0],NLAT,0,0,0,0);
lonVar->put(&lons[0],NLON,0,0,0,0);
NcVar *presVar = root->addVar(string("press"),ncFloat,latDim,lonDim);
NcVar *tempVar = root->addVar(string("temp"),ncFloat,latDim,lonDim);
presVar->addAtt(string("UNITS:"),ncChar,string(pres_units));
tempVar->addAtt(string("UNITS:"),ncChar,string(temp_units));
presVar->put(&pres_out[0][0],NLAT,NLON,0,0,0);
tempVar->put(&temp_out[0][0],NLAT,NLON,0,0,0);
//NcValues *ncvalues = presVar->getValues();
{ //another scope for variables
NcGroup::varIterator variableItr;
variableItr = root->beginVar();
while(variableItr != root->endVar())
{
variableItr++;
}
NcVar::attIterator varAttItr;
varAttItr = latVar->beginAtt();
while(varAttItr != latVar->endAtt())
{
varAttItr++;
}
}
}
catch(NcException e)
{
cout<<"FAILURE***"<<endl;
e.what();
return 1;
}
try
{
NcFile f1("tst_file.nc",NcFile::ReadOnly);
NcGroup * root =f1.getRootGroup();
NcGroup::dimIterator dimItr; //get an iterator to move over the dimensions
dimItr = root->beginDim(); //created in the file
while(dimItr != root->endDim())
dimItr++;
NcGroup::attIterator attItr;
attItr= root->beginAtt();
while(attItr !=root->endAtt())
attItr++;
NcGroup::varIterator variableItr;
NcVar::attIterator varAttItr;
variableItr = root->beginVar();
while(variableItr != root->endVar())
{
varAttItr = variableItr->beginAtt();
while(varAttItr != variableItr->endAtt())
varAttItr++;
variableItr++;
}
}
catch(NcException e)
{
cout<<"FAILURE***"<<endl;
e.what();
return 1;
}
cout<<" OK***"<<endl;
return 0;
}
void PolygonManager::output(const string &fileName)
{
// -------------------------------------------------------------------------
NcFile file(fileName.c_str(), NcFile::Replace);
if (!file.is_valid()) {
string message = "Failed to open file "+fileName+".";
REPORT_ERROR(message.c_str());
}
// -------------------------------------------------------------------------
// time information
if (TimeManager::onLine()) {
file.add_att("time", TimeManager::getSeconds());
file.add_att("time_step", TimeManager::getTimeStep());
file.add_att("steps", TimeManager::getSteps());
}
// -------------------------------------------------------------------------
// dimensions
NcDim *numVertexDim = file.add_dim("num_total_vertex", vertices.size());
NcDim *numEdgeDim = file.add_dim("num_total_edge", edges.size());
NcDim *numPolygonDim = file.add_dim("num_total_polygon", polygons.size());
// -------------------------------------------------------------------------
// vertices part
NcVar *oldVtxLonVar = file.add_var("old_vertex_lon", ncDouble, numVertexDim);
NcVar *oldVtxLatVar = file.add_var("old_vertex_lat", ncDouble, numVertexDim);
NcVar *newVtxLonVar = file.add_var("new_vertex_lon", ncDouble, numVertexDim);
NcVar *newVtxLatVar = file.add_var("new_vertex_lat", ncDouble, numVertexDim);
oldVtxLonVar->add_att("long_name", "old vertex longitude");
oldVtxLonVar->add_att("units", "degree_east");
oldVtxLatVar->add_att("long_name", "old vertex latitude");
oldVtxLatVar->add_att("units", "degree_north");
newVtxLonVar->add_att("long_name", "new vertex longitude");
newVtxLonVar->add_att("units", "degree_east");
newVtxLatVar->add_att("long_name", "new vertex latitude");
newVtxLatVar->add_att("units", "degree_north");
double *oldVtxLon = new double[vertices.size()];
double *oldVtxLat = new double[vertices.size()];
double *newVtxLon = new double[vertices.size()];
double *newVtxLat = new double[vertices.size()];
Vertex *vertex = vertices.front();
for (int i = 0; i < vertices.size(); ++i) {
oldVtxLon[i] = vertex->getCoordinate(OldTimeLevel).getLon()*Rad2Deg;
oldVtxLat[i] = vertex->getCoordinate(OldTimeLevel).getLat()*Rad2Deg;
newVtxLon[i] = vertex->getCoordinate(NewTimeLevel).getLon()*Rad2Deg;
newVtxLat[i] = vertex->getCoordinate(NewTimeLevel).getLat()*Rad2Deg;
vertex = vertex->next;
}
oldVtxLonVar->put(oldVtxLon, vertices.size());
oldVtxLatVar->put(oldVtxLat, vertices.size());
newVtxLonVar->put(newVtxLon, vertices.size());
newVtxLatVar->put(newVtxLat, vertices.size());
delete [] oldVtxLon;
delete [] oldVtxLat;
delete [] newVtxLon;
delete [] newVtxLat;
// -------------------------------------------------------------------------
// edges part
NcVar *firstPointVar = file.add_var("first_point_idx", ncInt, numEdgeDim);
NcVar *secondPointVar = file.add_var("second_point_idx", ncInt, numEdgeDim);
firstPointVar->add_att("long_name", "first point index of edge");
secondPointVar->add_att("long_name", "second point index of edge");
int *idx1 = new int[edges.size()];
int *idx2 = new int[edges.size()];
Edge *edge = edges.front();
for (int i = 0; i < edges.size(); ++i) {
idx1[i] = edge->getEndPoint(FirstPoint)->getID();
idx2[i] = edge->getEndPoint(SecondPoint)->getID();
edge = edge->next;
}
firstPointVar->put(idx1, edges.size());
secondPointVar->put(idx2, edges.size());
delete [] idx1;
delete [] idx2;
// test point
NcVar *oldTestLonVar = file.add_var("old_testpoint_lon", ncDouble, numEdgeDim);
NcVar *oldTestLatVar = file.add_var("old_testpoint_lat", ncDouble, numEdgeDim);
NcVar *newTestLonVar = file.add_var("new_testpoint_lon", ncDouble, numEdgeDim);
NcVar *newTestLatVar = file.add_var("new_testpoint_lat", ncDouble, numEdgeDim);
oldTestLonVar->add_att("long_name", "old test point longitude");
oldTestLonVar->add_att("units", "degree_east");
oldTestLatVar->add_att("long_name", "old test point latitude");
oldTestLatVar->add_att("units", "degree_north");
newTestLonVar->add_att("long_name", "new test point longitude");
newTestLonVar->add_att("units", "degree_east");
newTestLatVar->add_att("long_name", "new test point latitude");
newTestLatVar->add_att("units", "degree_north");
#if defined TTS_ONLINE || PREPROCESS
double *oldTestLon = new double[edges.size()];
double *oldTestLat = new double[edges.size()];
double *newTestLon = new double[edges.size()];
double *newTestLat = new double[edges.size()];
edge = edges.front();
for (int i = 0; i < edges.size(); ++i) {
Vertex *testPoint = edge->getTestPoint();
oldTestLon[i] = testPoint->getCoordinate(OldTimeLevel).getLon()*Rad2Deg;
oldTestLat[i] = testPoint->getCoordinate(OldTimeLevel).getLat()*Rad2Deg;
newTestLon[i] = testPoint->getCoordinate(NewTimeLevel).getLon()*Rad2Deg;
newTestLat[i] = testPoint->getCoordinate(NewTimeLevel).getLat()*Rad2Deg;
edge = edge->next;
}
oldTestLonVar->put(oldTestLon, edges.size());
oldTestLatVar->put(oldTestLat, edges.size());
newTestLonVar->put(newTestLon, edges.size());
newTestLatVar->put(newTestLat, edges.size());
delete [] oldTestLon;
delete [] oldTestLat;
delete [] newTestLon;
delete [] newTestLat;
#endif
// -------------------------------------------------------------------------
// polygons part
NcVar *edgeNumVar = file.add_var("edge_num", ncInt, numPolygonDim);
NcVar *areaVar = file.add_var("area", ncDouble, numPolygonDim);
edgeNumVar->add_att("long_name", "edge number of polygon");
areaVar->add_att("long_name", "polygon area");
int edgeNum[polygons.size()];
double area[polygons.size()];
int counter = 0;
Polygon *polygon = polygons.front();
for (int i = 0; i < polygons.size(); ++i) {
edgeNum[i] = polygon->edgePointers.size();
area[i] = polygon->getArea();
counter += edgeNum[i];
polygon = polygon->next;
}
int numEdgeIdx = counter;
NcDim *numEdgeIdxDim = file.add_dim("num_edge_idx", numEdgeIdx);
NcVar *edgeIdxVar = file.add_var("edge_idx", ncInt, numEdgeIdxDim);
NcVar *edgeOntVar = file.add_var("edge_ont", ncInt, numEdgeIdxDim);
edgeIdxVar->add_att("long_name", "edge index of polygon");
edgeOntVar->add_att("long_name", "edge orientation of polygon");
int *edgeIdx = new int[counter];
int *edgeOnt = new int[counter];
counter = 0;
polygon = polygons.front();
for (int i = 0; i < polygons.size(); ++i) {
EdgePointer *edgePointer = polygon->edgePointers.front();
for (int j = 0; j < polygon->edgePointers.size(); ++j) {
edgeIdx[counter] = edgePointer->edge->getID();
edgeOnt[counter] = edgePointer->orient;
counter++;
edgePointer = edgePointer->next;
}
polygon = polygon->next;
}
edgeNumVar->put(edgeNum, polygons.size());
areaVar->put(area, polygons.size());
edgeIdxVar->put(edgeIdx, numEdgeIdx);
edgeOntVar->put(edgeOnt, numEdgeIdx);
delete [] edgeIdx;
delete [] edgeOnt;
// -------------------------------------------------------------------------
file.close();
}
int main(int argc, char** argv) {
NcError error(NcError::verbose_nonfatal);
try {
// Input file
std::string strInputFile;
// Input file list
std::string strInputFileList;
// Input file format
std::string strInputFormat;
// NetCDF file containing latitude and longitude arrays
std::string strLatLonFile;
// Output file (NetCDF)
std::string strOutputFile;
// Output variable name
std::string strOutputVariable;
// Column in which the longitude index appears
int iLonIxCol;
// Column in which the latitude index appears
int iLatIxCol;
// Begin latitude
double dLatBegin;
// End latitude
double dLatEnd;
// Begin longitude
double dLonBegin;
// End longitude
double dLonEnd;
// Number of latitudes in output
int nLat;
// Number of longitudes in output
int nLon;
// Parse the command line
BeginCommandLine()
CommandLineString(strInputFile, "in", "");
CommandLineString(strInputFileList, "inlist", "");
CommandLineStringD(strInputFormat, "in_format", "std", "(std|visit)");
CommandLineString(strOutputFile, "out", "");
CommandLineString(strOutputVariable, "outvar", "density");
CommandLineInt(iLonIxCol, "iloncol", 8);
CommandLineInt(iLatIxCol, "ilatcol", 9);
CommandLineDouble(dLatBegin, "lat_begin", -90.0);
CommandLineDouble(dLatEnd, "lat_end", 90.0);
CommandLineDouble(dLonBegin, "lon_begin", 0.0);
CommandLineDouble(dLonEnd, "lon_end", 360.0);
CommandLineInt(nLat, "nlat", 180);
CommandLineInt(nLon, "nlon", 360);
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
// Check input
if ((strInputFile == "") && (strInputFileList == "")) {
_EXCEPTIONT("No input file (--in) or (--inlist) specified");
}
if ((strInputFile != "") && (strInputFileList != "")) {
_EXCEPTIONT("Only one input file (--in) or (--inlist) allowed");
}
if (strInputFormat != "std") {
_EXCEPTIONT("UNIMPLEMENTED: Only \"--in_format std\" supported");
}
// Check output
if (strOutputFile == "") {
_EXCEPTIONT("No output file (--out) specified");
}
// Check output variable
if (strOutputVariable == "") {
_EXCEPTIONT("No output variable name (--outvar) specified");
}
// Number of latitudes and longitudes
if (nLat == 0) {
_EXCEPTIONT("UNIMPLEMENTED: --nlat must be specified currently");
}
if (nLon == 0) {
_EXCEPTIONT("UNIMPLEMENTED: --nlon must be specified currently");
}
// Input file list
std::vector<std::string> vecInputFiles;
if (strInputFile != "") {
vecInputFiles.push_back(strInputFile);
}
if (strInputFileList != "") {
GetInputFileList(strInputFileList, vecInputFiles);
}
int nFiles = vecInputFiles.size();
// Density
DataMatrix<int> nCounts;
nCounts.Initialize(nLat, nLon);
// Loop through all files in list
AnnounceStartBlock("Processing files");
std::string strBuffer;
strBuffer.reserve(1024);
for (int f = 0; f < nFiles; f++) {
Announce("File \"%s\"", vecInputFiles[f].c_str());
FILE * fp = fopen(vecInputFiles[f].c_str(), "r");
if (fp == NULL) {
_EXCEPTION1("Unable to open input file \"%s\"",
vecInputFiles[f].c_str());
}
for (;;) {
// Read in the next line
fgets(&(strBuffer[0]), 1024, fp);
int nLength = strlen(&(strBuffer[0]));
// Check for end of file
if (feof(fp)) {
break;
}
// Check for comment line
if (strBuffer[0] == '#') {
continue;
}
// Check for new storm
if (strncmp(&(strBuffer[0]), "start", 5) == 0) {
continue;
}
// Parse line
double dLon;
double dLat;
int iCol = 0;
int iLast = 0;
bool fWhitespace = true;
for (int i = 0; i <= nLength; i++) {
if ((strBuffer[i] == ' ') ||
(strBuffer[i] == ',') ||
(strBuffer[i] == '\t') ||
(strBuffer[i] == '\0')
) {
if (!fWhitespace) {
if (iCol == iLonIxCol) {
strBuffer[i] = '\0';
dLon = atof(&(strBuffer[iLast]));
}
if (iCol == iLatIxCol) {
strBuffer[i] = '\0';
dLat = atof(&(strBuffer[iLast]));
}
}
fWhitespace = true;
} else {
if (fWhitespace) {
iLast = i;
iCol++;
}
fWhitespace = false;
}
}
// Latitude and longitude index
int iLon =
static_cast<int>(static_cast<double>(nLon)
* (dLon - dLonBegin) / (dLonEnd - dLonBegin));
int iLat =
static_cast<int>(static_cast<double>(nLat)
* (dLat - dLatBegin) / (dLatEnd - dLatBegin));
if (iLon == (-1)) {
iLon = 0;
}
if (iLon == nLon) {
iLon = nLon - 1;
}
if (iLat == (-1)) {
iLat = 0;
}
if (iLat == nLat) {
iLat = nLat - 1;
}
if ((iLat < 0) || (iLat >= nLat)) {
_EXCEPTION1("Latitude index (%i) out of range", iLat);
}
if ((iLon < 0) || (iLon >= nLon)) {
_EXCEPTION1("Longitude index (%i) out of range", iLon);
}
nCounts[iLat][iLon]++;
}
fclose(fp);
}
AnnounceEndBlock("Done");
// Output results
AnnounceStartBlock("Output results");
// Load the netcdf output file
NcFile ncOutput(strOutputFile.c_str(), NcFile::Replace);
if (!ncOutput.is_valid()) {
_EXCEPTION1("Unable to open output file \"%s\"",
strOutputFile.c_str());
}
// Create output
NcDim * dimLat = ncOutput.add_dim("lat", nLat);
NcDim * dimLon = ncOutput.add_dim("lon", nLon);
NcVar * varLat = ncOutput.add_var("lat", ncDouble, dimLat);
NcVar * varLon = ncOutput.add_var("lon", ncDouble, dimLon);
varLat->add_att("units", "degrees_north");
varLon->add_att("units", "degrees_east");
DataVector<double> dLat(nLat);
DataVector<double> dLon(nLon);
for (int j = 0; j < nLat; j++) {
dLat[j] = dLatBegin
+ (dLatEnd - dLatBegin)
* (static_cast<double>(j) + 0.5)
/ static_cast<double>(nLat);
}
for (int i = 0; i < nLon; i++) {
dLon[i] = dLonBegin
+ (dLonEnd - dLonBegin)
* (static_cast<double>(i) + 0.5)
/ static_cast<double>(nLon);
}
varLat->put(&(dLat[0]), nLat);
varLon->put(&(dLon[0]), nLon);
// Output counts
NcVar * varCount =
ncOutput.add_var(
strOutputVariable.c_str(),
ncInt,
dimLat,
dimLon);
varCount->put(&(nCounts[0][0]), nLat, nLon);
ncOutput.close();
AnnounceEndBlock("Done");
AnnounceBanner();
} catch(Exception & e) {
Announce(e.ToString().c_str());
}
}
void gen(const char* path, NcFile::FileFormat format) // Generate a netCDF file
{
NcFile nc(path, NcFile::Replace, NULL, 0, format); // Create, leave in define mode
// Check if the file was opened successfully
if (! nc.is_valid()) {
cerr << "can't create netCDF file " << path << "\n";
return;
}
// Create dimensions
const int NLATS = 4;
const int NLONS = 3;
const int NFRTIMES = 2;
const int TIMESTRINGLEN = 20;
NcDim* latd = nc.add_dim("lat", NLATS);
NcDim* lond = nc.add_dim("lon", NLONS);
NcDim* frtimed = nc.add_dim("frtime"); // unlimited dimension
NcDim* timelend = nc.add_dim("timelen", TIMESTRINGLEN);
// Create variables and their attributes
NcVar* P = nc.add_var("P", ncFloat, frtimed, latd, lond);
P->add_att("long_name", "pressure at maximum wind");
P->add_att("units", "hectopascals");
static float range[] = {0., 1500.};
P->add_att("valid_range", 2, range);
P->add_att("_FillValue", -9999.0f);
NcVar* lat = nc.add_var("lat", ncFloat, latd);
lat->add_att("long_name", "latitude");
lat->add_att("units", "degrees_north");
NcVar* lon = nc.add_var("lon", ncFloat, lond);
lon->add_att("long_name", "longitude");
lon->add_att("units", "degrees_east");
NcVar* frtime = nc.add_var("frtime", ncLong, frtimed);
frtime->add_att("long_name", "forecast time");
frtime->add_att("units", "hours");
NcVar* reftime = nc.add_var("reftime",ncChar,timelend);
reftime->add_att("long_name", "reference time");
reftime->add_att("units", "text_time");
NcVar* scalar = nc.add_var("scalarv", ncInt);
scalar->add_att("scalar_att", 1);
// Global attributes
nc.add_att("history", "created by Unidata LDM from NPS broadcast");
nc.add_att("title", "NMC Global Product Set: Pressure at Maximum Wind");
// Start writing data, implictly leaves define mode
static float lats[NLATS] = {-90, -87.5, -85, -82.5};
lat->put(lats, NLATS);
static float lons[NLONS] = {-180, -175, -170};
lon->put(lons, NLONS);
static int frtimes[NFRTIMES] = {12, 18};
frtime->put(frtimes, NFRTIMES);
static const char* s = "1992-3-21 12:00" ;
reftime->put(s, strlen(s));
static float P_data[2][4][3] = {
{{950, 951, 952}, {953, 954, 955}, {956, 957, 958}, {959, 960, 961}},
{{962, 963, 964}, {965, 966, 967}, {968, 969, 970}, {971, 972, 973}}
};
// We could write all P data at once with P->put(&P_data[0][0][0], P->edges()),
// but instead we write one record at a time, to show use of setcur().
long rec = 0; // start at zero-th
const long nrecs = 1; // # records to write
P->put(&P_data[0][0][0], nrecs, NLATS, NLONS); // write zero-th record
P->set_cur(++rec); // set to next record
P->put(&P_data[1][0][0], nrecs, NLATS, NLONS); // write next record
// close of nc takes place in destructor
}
int main(int argc, char ** argv) {
MPI_Init(&argc, &argv);
try {
// Number of latitudes
int nLat;
// Number of longitudes
int nLon;
// Zonal wavenumber
int nK;
// Meridional power
int nLpow;
// Output file
std::string strOutputFile;
// Parse the command line
BeginCommandLine()
CommandLineInt(nLat, "lat", 40);
CommandLineInt(nLon, "lon", 80);
CommandLineString(strOutputFile, "out", "topo.nc");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
// Generate longitude and latitude arrays
AnnounceBanner();
AnnounceStartBlock("Generating longitude and latitude arrays");
DataVector<double> dLon;
dLon.Initialize(nLon);
Parameters param;
param.GenerateLatituteArray(nLat);
std::vector<double> & dLat = param.vecNode;
double dDeltaLon = 2.0 * M_PI / static_cast<double>(nLon);
for (int i = 0; i < nLon; i++) {
dLon[i] = (static_cast<double>(i) + 0.5) * dDeltaLon;
}
AnnounceEndBlock("Done");
// Open NetCDF output file
AnnounceStartBlock("Writing to file");
NcFile ncdf_out(strOutputFile.c_str(), NcFile::Replace);
// Output coordinates
NcDim * dimLat = ncdf_out.add_dim("lat", nLat);
NcDim * dimLon = ncdf_out.add_dim("lon", nLon);
NcVar * varLat = ncdf_out.add_var("lat", ncDouble, dimLat);
varLat->set_cur((long)0);
varLat->put(&(param.vecNode[0]), nLat);
NcVar * varLon = ncdf_out.add_var("lon", ncDouble, dimLon);
varLon->set_cur((long)0);
varLon->put(&(dLon[0]), nLon);
// Generate topography
DataMatrix<double> dTopo;
dTopo.Initialize(nLat, nLon);
double dK = static_cast<double>(nK);
double dLpow = static_cast<double>(nLpow);
double dA = 6.37122e6;
double dX = 500.0;
double dLatM = 0.0;
double dLonM = M_PI / 4.0;
double dD = 5000.0;
double dH0 = 1.0;
double dXiM = 4000.0;
for (int j = 0; j < nLat; j++) {
for (int i = 0; i < nLon; i++) {
// Great circle distance
double dR = dA / dX * acos(sin(dLatM) * sin(dLat[j])
+ cos(dLatM) * cos(dLat[j]) * cos(dLon[i] - dLonM));
double dCosXi = 1.0; //cos(M_PI * dR / dXiM);
dTopo[j][i] = dH0 * exp(- dR * dR / (dD * dD))
* dCosXi * dCosXi;
}
}
// Write topography
NcVar * varZs = ncdf_out.add_var("Zs", ncDouble, dimLat, dimLon);
varZs->set_cur(0, 0);
varZs->put(&(dTopo[0][0]), nLat, nLon);
AnnounceEndBlock("Done");
Announce("Completed successfully!");
AnnounceBanner();
} catch(Exception & e) {
Announce(e.ToString().c_str());
}
MPI_Finalize();
}
int main(int argc, char** argv)
{
if (!cmdline(argc, argv))
{
printhelp();
return EXIT_FAILURE;
}
NcFile infile(infilename.c_str(), NcFile::ReadOnly);
if (!infile.is_valid())
{
std::cerr << "Error: invalid input file -- '" << infilename << "'" << std::endl;
infile.close();
return EXIT_FAILURE;
}
NcFile outfile(outfilename.c_str(), NcFile::Replace);
if (!outfile.is_valid())
{
std::cerr << "Error: cannot open output file -- '" << outfilename << "'" << std::endl;
outfile.close();
return EXIT_FAILURE;
}
if (varstrings.size() == 0)
{
std::cerr << "Warning: no variables specified" << std::endl;
}
std::vector<NcVar*> invars;
for (std::vector<std::string>::const_iterator it = varstrings.begin();
it != varstrings.end(); ++it)
{
NcVar* var = infile.get_var((*it).c_str());
if (var == NULL)
{
std::cerr << "Error: " << *it << ": no such variable" << std::endl;
infile.close();
outfile.close();
return EXIT_FAILURE;
}
invars.push_back(var);
}
// extract the distinct set of dims
std::map<std::string, NcDim*> indims;
for (std::vector<NcVar*>::const_iterator it = invars.begin();
it != invars.end(); ++it)
{
NcVar* var = *it;
for (int i = 0; i < var->num_dims(); ++i)
{
NcDim* dim = var->get_dim(i);
indims[dim->name()] = dim;
}
}
// add dims to outfile
std::map<std::string, NcDim*> outdims;
for (std::map<std::string, NcDim*>::const_iterator it = indims.begin();
it != indims.end(); ++it)
{
NcDim* dim = (*it).second;
NcDim* outdim = NULL;
if (dim->is_unlimited())
{
outdim = outfile.add_dim(dim->name());
}
else
{
outdim = outfile.add_dim(dim->name(), dim->size());
}
if (outdim != NULL)
{
outdims[outdim->name()] = outdim;
}
}
// create variables
for (std::vector<NcVar*>::const_iterator it = invars.begin();
it != invars.end(); ++it)
{
NcVar* var = *it;
std::vector<const NcDim*> dims(var->num_dims());
for (int i = 0; i < var->num_dims(); ++i)
{
dims[i] = outdims[var->get_dim(i)->name()];
}
NcVar* outvar = outfile.add_var(var->name(), var->type(), var->num_dims(), &dims[0]);
// identify largest dim, if dim (nearly) exceeds main memory, split along that dim
int maxdim = -1;
long maxdimsize = 0;
long totallen = 1;
for (int i = 0; i < var->num_dims(); ++i)
{
NcDim* dim = var->get_dim(i);
if (dim->size() > maxdimsize)
{
maxdim = i;
maxdimsize = dim->size();
}
totallen *= dim->size();
}
// TODO: support other data types
totallen *= sizeof(float);
// TODO: configurable page size
const unsigned long pagesize = 1000000000;
#ifdef __linux__
struct sysinfo info;
sysinfo(&info);
if (pagesize >= info.freeram)
{
std::cerr << "Warning: page size exceeds free memory" << std::endl;
}
#endif
int numpages = 1;
long pagesizedim = var->get_dim(maxdim)->size();
if (totallen < pagesize)
{
}
else
{
long mul = 1;
for (int i = 0; i < var->num_dims(); ++i)
{
if (i != maxdim)
{
NcDim* dim = var->get_dim(i);
mul *= dim->size();
}
}
// TODO: support other data types
mul *= sizeof(float);
pagesizedim = pagesize / mul;
numpages = var->get_dim(maxdim)->size() / pagesizedim;
if (var->get_dim(maxdim)->size() % pagesizedim > 0)
{
++numpages;
}
}
std::vector< std::vector<long> > curvec;
std::vector< std::vector<long> > countsvec;
std::vector<long> lengths;
int pages = numpages > 0 ? numpages : 1;
for (int p = 0; p < pages; ++p)
{
long len = 1;
std::vector<long> cur;
std::vector<long> counts;
for (int i = 0; i < var->num_dims(); ++i)
{
NcDim* dim = var->get_dim(i);
long current = 0;
long count = dim->size();
if (i == maxdim)
{
current = pagesizedim * p;
count = pagesizedim;
if (p == pages -1)
{
if (dim->size() % pagesizedim != 0)
{
count = dim->size() % pagesizedim;
}
}
}
cur.push_back(current);
counts.push_back(count);
len *= count;
}
curvec.push_back(cur);
countsvec.push_back(counts);
lengths.push_back(len);
}
std::vector< std::vector<long> >::const_iterator it1;
std::vector< std::vector<long> >::const_iterator it2;
std::vector<long>::const_iterator it3;
for (it1 = curvec.begin(), it2 = countsvec.begin(), it3 = lengths.begin();
it1 != curvec.end() && it2 != countsvec.end() && it3 != lengths.end(); ++it1, ++it2, ++it3)
{
std::vector<long> cur = *it1;
std::vector<long> counts = *it2;
long len = *it3;
var->set_cur(&cur[0]);
outvar->set_cur(&cur[0]);
switch (outvar->type())
{
case ncByte:
{
ncbyte* barr = new ncbyte[len];
var->get(barr, &counts[0]);
outvar->put(barr, &counts[0]);
delete[] barr;
break;
}
case ncChar:
{
char* carr = new char[len];
var->get(carr, &counts[0]);
outvar->put(carr, &counts[0]);
delete[] carr;
break;
}
case ncShort:
{
short* sarr = new short[len];
var->get(sarr, &counts[0]);
outvar->put(sarr, &counts[0]);
delete[] sarr;
break;
}
case ncInt:
{
long* larr = new long[len];
var->get(larr, &counts[0]);
outvar->put(larr, &counts[0]);
delete[] larr;
break;
}
case ncFloat:
{
float* farr = new float[len];
var->get(farr, &counts[0]);
outvar->put(farr, &counts[0]);
delete[] farr;
break;
}
case ncDouble:
{
double* darr = new double[len];
var->get(darr, &counts[0]);
outvar->put(darr, &counts[0]);
delete[] darr;
break;
}
default:
break;
}
}
}
infile.close();
outfile.close();
return 0;
}
int main(int argc, char ** argv) {
try {
// Parameters
Parameters param;
// Output filename
std::string strOutputFile;
// Horizontal minimum wave number
int nKmin;
// Horizontal maximum wave number
int nKmax;
// Parse the command line
BeginCommandLine()
CommandLineInt(param.nPhiElements, "n", 40);
CommandLineInt(nKmin, "kmin", 1);
CommandLineInt(nKmax, "kmax", 20);
CommandLineDouble(param.dXscale, "X", 1.0);
CommandLineDouble(param.dT0, "T0", 300.0);
CommandLineDouble(param.dU0, "U0", 20.0);
CommandLineDouble(param.dG, "G", 9.80616);
CommandLineDouble(param.dOmega, "omega", 7.29212e-5);
CommandLineDouble(param.dGamma, "gamma", 1.4);
CommandLineString(strOutputFile, "out", "wave.nc");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
// Generate latitude values
param.GenerateLatituteArray(param.nPhiElements);
// Open NetCDF file
NcFile ncdf_out(strOutputFile.c_str(), NcFile::Replace);
NcDim *dimK = ncdf_out.add_dim("k", nKmax - nKmin + 1);
NcDim *dimLat = ncdf_out.add_dim("lat", param.nPhiElements);
NcDim *dimEig = ncdf_out.add_dim("eig", param.nPhiElements);
// Write parameters and latitudes to file
param.WriteToNcFile(ncdf_out, dimLat, dimLatS);
// Wave numbers
NcVar *varK = ncdf_out.add_var("k", ncInt, dimK);
DataVector<int> vecK;
vecK.Initialize(nKmax - nKmin + 1);
for (int nK = nKmin; nK <= nKmax; nK++) {
vecK[nK - nKmin] = nK;
}
varK->set_cur((long)0);
varK->put(vecK, nKmax - nKmin + 1);
// Eigenvalues
NcVar *varMR = ncdf_out.add_var("mR", ncDouble, dimK, dimEig);
NcVar *varMI = ncdf_out.add_var("mI", ncDouble, dimK, dimEig);
NcVar *varUR = ncdf_out.add_var("uR", ncDouble, dimK, dimEig, dimLat);
NcVar *varUI = ncdf_out.add_var("uI", ncDouble, dimK, dimEig, dimLat);
NcVar *varVR = ncdf_out.add_var("vR", ncDouble, dimK, dimEig, dimLatS);
NcVar *varVI = ncdf_out.add_var("vI", ncDouble, dimK, dimEig, dimLatS);
NcVar *varPR = ncdf_out.add_var("pR", ncDouble, dimK, dimEig, dimLat);
NcVar *varPI = ncdf_out.add_var("pI", ncDouble, dimK, dimEig, dimLat);
NcVar *varWR = ncdf_out.add_var("wR", ncDouble, dimK, dimEig, dimLat);
NcVar *varWI = ncdf_out.add_var("wI", ncDouble, dimK, dimEig, dimLat);
NcVar *varRhoR = ncdf_out.add_var("rhoR", ncDouble, dimK, dimEig, dimLat);
NcVar *varRhoI = ncdf_out.add_var("rhoI", ncDouble, dimK, dimEig, dimLat);
// Allocate temporary arrays
DataVector<double> dUR;
dUR.Initialize(param.nPhiElements);
DataVector<double> dUI;
dUI.Initialize(param.nPhiElements);
DataVector<double> dVR;
dVR.Initialize(param.nPhiElements-1);
DataVector<double> dVI;
dVI.Initialize(param.nPhiElements-1);
DataVector<double> dPR;
dPR.Initialize(param.nPhiElements);
DataVector<double> dPI;
dPI.Initialize(param.nPhiElements);
DataVector<double> dWR;
dWR.Initialize(param.nPhiElements);
DataVector<double> dWI;
dWI.Initialize(param.nPhiElements);
DataVector<double> dRhoR;
dRhoR.Initialize(param.nPhiElements);
DataVector<double> dRhoI;
dRhoI.Initialize(param.nPhiElements);
// Loop over all horizontal wave numbers
for (int nK = nKmin; nK <= nKmax; nK++) {
// Build matrices
char szMessage[100];
sprintf(szMessage, "Building evolution matrices (k = %i)", nK);
AnnounceStartBlock(szMessage);
DataMatrix<double> matM;
DataMatrix<double> matB;
GenerateEvolutionMatrix(nK, param, matM, matB);
AnnounceEndBlock("Done");
// Solve the matrices
AnnounceStartBlock("Solving evolution matrices");
DataVector<double> vecAlphaR;
DataVector<double> vecAlphaI;
DataVector<double> vecBeta;
DataMatrix<double> matVR;
vecAlphaR.Initialize(matM.GetRows());
vecAlphaI.Initialize(matM.GetRows());
vecBeta .Initialize(matM.GetRows());
matVR .Initialize(matM.GetRows(), matM.GetColumns());
SolveEvolutionMatrix(
matM,
matB,
vecAlphaR,
vecAlphaI,
vecBeta,
matVR);
// Sort eigenvalues
std::multimap<double, int> mapSortedRows;
for (int i = 0; i < vecBeta.GetRows(); i++) {
if (vecBeta[i] != 0.0) {
double dLambdaR = vecAlphaR[i] / vecBeta[i];
double dLambdaI = vecAlphaI[i] / vecBeta[i];
double dMR = dLambdaI;
double dMI = - dLambdaR - 1.0;
double dEvalMagnitude = fabs(dMR);
//printf("\n%1.5e %1.5e ", dMR, dMI);
// Purely imaginary eigenvalue
if (dMR == 0.0) {
// Wave must decay with height
if (dMI < 0.0) {
continue;
}
// Complex-conjugate pair of eigenvalues
} else {
// Phase propagation must be downward, and energy
// propagation upwards
if (dMR < 0.0) {
continue;
}
}
//printf("(OK)");
mapSortedRows.insert(
std::pair<double, int>(dEvalMagnitude, i));
// Only store one entry for complex-conjugate pairs
if (vecAlphaI[i] != 0.0) {
i++;
}
}
}
Announce("%i eigenmodes found to satisfy entropy condition",
mapSortedRows.size());
/*
if (mapSortedRows.size() != param.nPhiElements) {
_EXCEPTIONT("Mismatch between eigenmode count and latitude count");
}
*/
AnnounceEndBlock("Done");
// Write the matrices to a file
AnnounceStartBlock("Writing results");
int iKix = nK - nKmin;
int iWave = 0;
std::map<double, int>::const_iterator it;
for (it = mapSortedRows.begin(); it != mapSortedRows.end(); it++) {
int i = it->second;
double dLambdaR = vecAlphaR[i] / vecBeta[i];
double dLambdaI = vecAlphaI[i] / vecBeta[i];
double dMR = dLambdaI;
double dMI = - dLambdaR - 1.0;
// Dump eigenvalue to NetCDF file
varMR->set_cur(iKix, iWave);
varMR->put(&dMR, 1, 1);
varMI->set_cur(iKix, iWave);
varMI->put(&dMI, 1, 1);
// Store real part of eigenfunction
for (int j = 0; j < param.nPhiElements; j++) {
dUR [j] = matVR[i][4*j ];
dPR [j] = matVR[i][4*j+1];
dWR [j] = matVR[i][4*j+2];
dRhoR[j] = matVR[i][4*j+3];
}
for (int j = 0; j < param.nPhiElements-1; j++) {
dVR[j] = matVR[i][4 * param.nPhiElements + j];
}
// Complex eigenvalue / eigenfunction pair
if (dLambdaI != 0.0) {
// Eigenvalue Lambda is complex conjugate
dMR = -dMR;
// Dump eigenvalue to NetCDF file
varMR->set_cur(iKix, iWave+1);
varMR->put(&dMR, 1, 1);
varMI->set_cur(iKix, iWave+1);
varMI->put(&dMI, 1, 1);
// Store imaginary component of vector
for (int j = 0; j < param.nPhiElements; j++) {
dUI [j] = matVR[i+1][4*j ];
dPI [j] = matVR[i+1][4*j+1];
dWI [j] = matVR[i+1][4*j+2];
dRhoI[j] = matVR[i+1][4*j+3];
}
for (int j = 0; j < param.nPhiElements-1; j++) {
dVI[j] = matVR[i+1][4 * param.nPhiElements + j];
}
// Real eigenvalue / eigenvector pair
} else {
dUI.Zero();
dPI.Zero();
dWI.Zero();
dRhoI.Zero();
dVI.Zero();
}
// Dump the first eigenfunction to the file
varUR->set_cur(iKix, iWave, 0);
varUR->put(dUR, 1, 1, param.nPhiElements);
varVR->set_cur(iKix, iWave, 0);
varVR->put(dVR, 1, 1, param.nPhiElements-1);
varPR->set_cur(iKix, iWave, 0);
varPR->put(dPR, 1, 1, param.nPhiElements);
varWR->set_cur(iKix, iWave, 0);
varWR->put(dWR, 1, 1, param.nPhiElements);
varRhoR->set_cur(iKix, iWave, 0);
varRhoR->put(dRhoR, 1, 1, param.nPhiElements);
varUI->set_cur(iKix, iWave, 0);
varUI->put(dUI, 1, 1, param.nPhiElements);
varVI->set_cur(iKix, iWave, 0);
varVI->put(dVI, 1, 1, param.nPhiElements-1);
varPI->set_cur(iKix, iWave, 0);
varPI->put(dPI, 1, 1, param.nPhiElements);
varWI->set_cur(iKix, iWave, 0);
varWI->put(dWI, 1, 1, param.nPhiElements);
varRhoI->set_cur(iKix, iWave, 0);
varRhoI->put(dRhoI, 1, 1, param.nPhiElements);
// Complex eigenvalue / eigenvector pair
if (dLambdaI != 0.0) {
for (int j = 0; j < param.nPhiElements; j++) {
dUI [j] = - dUI [j];
dPI [j] = - dPI [j];
dWI [j] = - dWI [j];
dRhoI[j] = - dRhoI[j];
}
for (int j = 0; j < param.nPhiElements-1; j++) {
dVI[j] = - dVI[j];
}
varUR->set_cur(iKix, iWave+1, 0);
varUR->put(dUR, 1, 1, param.nPhiElements);
varVR->set_cur(iKix, iWave+1, 0);
varVR->put(dVR, 1, 1, param.nPhiElements-1);
varPR->set_cur(iKix, iWave+1, 0);
varPR->put(dPR, 1, 1, param.nPhiElements);
varWR->set_cur(iKix, iWave+1, 0);
varWR->put(dWR, 1, 1, param.nPhiElements);
varRhoR->set_cur(iKix, iWave+1, 0);
varRhoR->put(dRhoR, 1, 1, param.nPhiElements);
varUI->set_cur(iKix, iWave+1, 0);
varUI->put(dUI, 1, 1, param.nPhiElements);
varVI->set_cur(iKix, iWave+1, 0);
varVI->put(dVI, 1, 1, param.nPhiElements-1);
varPI->set_cur(iKix, iWave+1, 0);
varPI->put(dPI, 1, 1, param.nPhiElements);
varWI->set_cur(iKix, iWave+1, 0);
varWI->put(dWI, 1, 1, param.nPhiElements);
varRhoI->set_cur(iKix, iWave+1, 0);
varRhoI->put(dRhoI, 1, 1, param.nPhiElements);
}
// Increment wave index
iWave++;
if (dLambdaI != 0.0) {
iWave++;
}
}
AnnounceEndBlock("Done");
AnnounceBanner();
}
} catch(Exception & e) {
Announce(e.ToString().c_str());
}
}
int main(int argc, char ** argv) {
MPI_Init(&argc, &argv);
NcError error(NcError::silent_nonfatal);
try {
// Input filename
std::string strInputFile;
// Output filename
std::string strOutputFile;
// Separate topography file
std::string strTopographyFile;
// List of variables to extract
std::string strVariables;
// Extract geopotential height
bool fGeopotentialHeight;
// Pressure levels to extract
std::string strPressureLevels;
// Height levels to extract
std::string strHeightLevels;
// Extract variables at the surface
bool fExtractSurface;
// Extract total energy
bool fExtractTotalEnergy;
// Parse the command line
BeginCommandLine()
CommandLineString(strInputFile, "in", "");
CommandLineString(strOutputFile, "out", "");
CommandLineString(strVariables, "var", "");
CommandLineBool(fGeopotentialHeight, "output_z");
CommandLineBool(fExtractTotalEnergy, "output_energy");
CommandLineString(strPressureLevels, "p", "");
CommandLineString(strHeightLevels, "z", "");
CommandLineBool(fExtractSurface, "surf");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
// Check command line arguments
if (strInputFile == "") {
_EXCEPTIONT("No input file specified");
}
if (strOutputFile == "") {
_EXCEPTIONT("No output file specified");
}
if (strVariables == "") {
_EXCEPTIONT("No variables specified");
}
// Parse variable string
std::vector< std::string > vecVariableStrings;
ParseVariableList(strVariables, vecVariableStrings);
// Check variables
if (vecVariableStrings.size() == 0) {
_EXCEPTIONT("No variables specified");
}
// Parse pressure level string
std::vector<double> vecPressureLevels;
ParseLevelArray(strPressureLevels, vecPressureLevels);
int nPressureLevels = (int)(vecPressureLevels.size());
for (int k = 0; k < nPressureLevels; k++) {
if (vecPressureLevels[k] <= 0.0) {
_EXCEPTIONT("Non-positive pressure values not allowed");
}
}
// Parse height level string
std::vector<double> vecHeightLevels;
ParseLevelArray(strHeightLevels, vecHeightLevels);
int nHeightLevels = (int)(vecHeightLevels.size());
// Check pressure levels
if ((nPressureLevels == 0) &&
(nHeightLevels == 0) &&
(!fExtractSurface)
) {
_EXCEPTIONT("No pressure / height levels to process");
}
// Open input file
AnnounceStartBlock("Loading input file");
NcFile ncdf_in(strInputFile.c_str(), NcFile::ReadOnly);
if (!ncdf_in.is_valid()) {
_EXCEPTION1("Unable to open file \"%s\" for reading",
strInputFile.c_str());
}
// Load time array
Announce("Time");
NcVar * varTime = ncdf_in.get_var("time");
if (varTime == NULL) {
_EXCEPTION1("File \"%s\" does not contain variable \"time\"",
strInputFile.c_str());
}
int nTime = varTime->get_dim(0)->size();
DataArray1D<double> dTime(nTime);
varTime->set_cur((long)0);
varTime->get(&(dTime[0]), nTime);
// Load latitude array
Announce("Latitude");
NcVar * varLat = ncdf_in.get_var("lat");
if (varLat == NULL) {
_EXCEPTION1("File \"%s\" does not contain variable \"lat\"",
strInputFile.c_str());
}
int nLat = varLat->get_dim(0)->size();
DataArray1D<double> dLat(nLat);
varLat->set_cur((long)0);
varLat->get(&(dLat[0]), nLat);
// Load longitude array
Announce("Longitude");
NcVar * varLon = ncdf_in.get_var("lon");
if (varLon == NULL) {
_EXCEPTION1("File \"%s\" does not contain variable \"lon\"",
strInputFile.c_str());
}
int nLon = varLon->get_dim(0)->size();
DataArray1D<double> dLon(nLon);
varLon->set_cur((long)0);
varLon->get(&(dLon[0]), nLon);
// Load level array
Announce("Level");
NcVar * varLev = ncdf_in.get_var("lev");
if (varLev == NULL) {
_EXCEPTION1("File \"%s\" does not contain variable \"lev\"",
strInputFile.c_str());
}
int nLev = varLev->get_dim(0)->size();
DataArray1D<double> dLev(nLev);
varLev->set_cur((long)0);
varLev->get(&(dLev[0]), nLev);
// Load level interface array
Announce("Interface");
NcVar * varILev = ncdf_in.get_var("ilev");
int nILev = 0;
DataArray1D<double> dILev;
if (varILev == NULL) {
Announce("Warning: Variable \"ilev\" not found");
} else {
nILev = varILev->get_dim(0)->size();
if (nILev != nLev + 1) {
_EXCEPTIONT("Variable \"ilev\" must have size lev+1");
}
dILev.Allocate(nILev);
varILev->set_cur((long)0);
varILev->get(&(dILev[0]), nILev);
}
// Load topography
Announce("Topography");
NcVar * varZs = ncdf_in.get_var("Zs");
if (varZs == NULL) {
_EXCEPTION1("File \"%s\" does not contain variable \"Zs\"",
strInputFile.c_str());
}
DataArray2D<double> dZs(nLat, nLon);
varZs->set_cur((long)0, (long)0);
varZs->get(&(dZs[0][0]), nLat, nLon);
AnnounceEndBlock("Done");
// Open output file
AnnounceStartBlock("Constructing output file");
NcFile ncdf_out(strOutputFile.c_str(), NcFile::Replace);
if (!ncdf_out.is_valid()) {
_EXCEPTION1("Unable to open file \"%s\" for writing",
strOutputFile.c_str());
}
CopyNcFileAttributes(&ncdf_in, &ncdf_out);
// Output time array
Announce("Time");
NcDim * dimOutTime = ncdf_out.add_dim("time");
NcVar * varOutTime = ncdf_out.add_var("time", ncDouble, dimOutTime);
varOutTime->set_cur((long)0);
varOutTime->put(&(dTime[0]), nTime);
CopyNcVarAttributes(varTime, varOutTime);
// Output pressure array
NcDim * dimOutP = NULL;
NcVar * varOutP = NULL;
if (nPressureLevels > 0) {
Announce("Pressure");
dimOutP = ncdf_out.add_dim("p", nPressureLevels);
varOutP = ncdf_out.add_var("p", ncDouble, dimOutP);
varOutP->set_cur((long)0);
varOutP->put(&(vecPressureLevels[0]), nPressureLevels);
}
// Output height array
NcDim * dimOutZ = NULL;
NcVar * varOutZ = NULL;
if (nHeightLevels > 0) {
Announce("Height");
dimOutZ = ncdf_out.add_dim("z", nHeightLevels);
varOutZ = ncdf_out.add_var("z", ncDouble, dimOutZ);
varOutZ->set_cur((long)0);
varOutZ->put(&(vecHeightLevels[0]), nHeightLevels);
}
// Output latitude and longitude array
Announce("Latitude");
NcDim * dimOutLat = ncdf_out.add_dim("lat", nLat);
NcVar * varOutLat = ncdf_out.add_var("lat", ncDouble, dimOutLat);
varOutLat->set_cur((long)0);
varOutLat->put(&(dLat[0]), nLat);
CopyNcVarAttributes(varLat, varOutLat);
Announce("Longitude");
NcDim * dimOutLon = ncdf_out.add_dim("lon", nLon);
NcVar * varOutLon = ncdf_out.add_var("lon", ncDouble, dimOutLon);
varOutLon->set_cur((long)0);
varOutLon->put(&(dLon[0]), nLon);
CopyNcVarAttributes(varLon, varOutLon);
// Output topography
Announce("Topography");
NcVar * varOutZs = ncdf_out.add_var(
"Zs", ncDouble, dimOutLat, dimOutLon);
varOutZs->set_cur((long)0, (long)0);
varOutZs->put(&(dZs[0][0]), nLat, nLon);
AnnounceEndBlock("Done");
// Done
AnnounceEndBlock("Done");
// Load all variables
Announce("Loading variables");
std::vector<NcVar *> vecNcVar;
for (int v = 0; v < vecVariableStrings.size(); v++) {
vecNcVar.push_back(ncdf_in.get_var(vecVariableStrings[v].c_str()));
if (vecNcVar[v] == NULL) {
_EXCEPTION1("Unable to load variable \"%s\" from file",
vecVariableStrings[v].c_str());
}
}
// Physical constants
Announce("Initializing thermodynamic variables");
NcAtt * attEarthRadius = ncdf_in.get_att("earth_radius");
double dEarthRadius = attEarthRadius->as_double(0);
NcAtt * attRd = ncdf_in.get_att("Rd");
double dRd = attRd->as_double(0);
NcAtt * attCp = ncdf_in.get_att("Cp");
double dCp = attCp->as_double(0);
double dGamma = dCp / (dCp - dRd);
NcAtt * attP0 = ncdf_in.get_att("P0");
double dP0 = attP0->as_double(0);
double dPressureScaling = dP0 * std::pow(dRd / dP0, dGamma);
NcAtt * attZtop = ncdf_in.get_att("Ztop");
double dZtop = attZtop->as_double(0);
// Input data
DataArray3D<double> dataIn(nLev, nLat, nLon);
DataArray3D<double> dataInt(nILev, nLat, nLon);
// Output data
DataArray2D<double> dataOut(nLat, nLon);
// Pressure in column
DataArray1D<double> dataColumnP(nLev);
// Height in column
DataArray1D<double> dataColumnZ(nLev);
DataArray1D<double> dataColumnIZ(nILev);
// Column weights
DataArray1D<double> dW(nLev);
DataArray1D<double> dIW(nILev);
// Loop through all times, pressure levels and variables
AnnounceStartBlock("Interpolating");
// Add energy variable
NcVar * varEnergy;
if (fExtractTotalEnergy) {
varEnergy = ncdf_out.add_var("TE", ncDouble, dimOutTime);
}
// Create output pressure variables
std::vector<NcVar *> vecOutNcVarP;
if (nPressureLevels > 0) {
for (int v = 0; v < vecVariableStrings.size(); v++) {
vecOutNcVarP.push_back(
ncdf_out.add_var(
vecVariableStrings[v].c_str(), ncDouble,
dimOutTime, dimOutP, dimOutLat, dimOutLon));
// Copy attributes
CopyNcVarAttributes(vecNcVar[v], vecOutNcVarP[v]);
}
}
// Create output height variables
std::vector<NcVar *> vecOutNcVarZ;
if (nHeightLevels > 0) {
for (int v = 0; v < vecVariableStrings.size(); v++) {
std::string strVarName = vecVariableStrings[v];
if (nPressureLevels > 0) {
strVarName += "z";
}
vecOutNcVarZ.push_back(
ncdf_out.add_var(
strVarName.c_str(), ncDouble,
dimOutTime, dimOutZ, dimOutLat, dimOutLon));
// Copy attributes
CopyNcVarAttributes(vecNcVar[v], vecOutNcVarZ[v]);
}
}
// Create output surface variable
std::vector<NcVar *> vecOutNcVarS;
if (fExtractSurface) {
for (int v = 0; v < vecVariableStrings.size(); v++) {
std::string strVarName = vecVariableStrings[v];
strVarName += "S";
vecOutNcVarS.push_back(
ncdf_out.add_var(
strVarName.c_str(), ncDouble,
dimOutTime, dimOutLat, dimOutLon));
// Copy attributes
CopyNcVarAttributes(vecNcVar[v], vecOutNcVarS[v]);
}
}
// Loop over all times
for (int t = 0; t < nTime; t++) {
char szAnnounce[256];
sprintf(szAnnounce, "Time %i", t);
AnnounceStartBlock(szAnnounce);
// Rho
DataArray3D<double> dataRho(nLev, nLat, nLon);
NcVar * varRho = ncdf_in.get_var("Rho");
if (varRho == NULL) {
_EXCEPTIONT("Unable to load variable \"Rho\" from file");
}
varRho->set_cur(t, 0, 0, 0);
varRho->get(&(dataRho[0][0][0]), 1, nLev, nLat, nLon);
// Pressure
DataArray3D<double> dataP(nLev, nLat, nLon);
if (nPressureLevels != 0) {
NcVar * varP = ncdf_in.get_var("P");
if (varP == NULL) {
_EXCEPTIONT("Unable to load variable \"P\" from file");
}
varP->set_cur(t, 0, 0, 0);
varP->get(&(dataP[0][0][0]), 1, nLev, nLat, nLon);
}
/*
// Populate pressure array
if (nPressureLevels > 0) {
// Calculate pointwise pressure
for (int k = 0; k < nLev; k++) {
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
dataP[k][i][j] = dPressureScaling
* exp(log(dataRho[k][i][j] * dataP[k][i][j]) * dGamma);
}
}
}
}
*/
// Height everywhere
DataArray3D<double> dataZ(nLev, nLat, nLon);
DataArray3D<double> dataIZ;
if (nILev != 0) {
dataIZ.Allocate(nILev, nLat, nLon);
}
// Populate height array
if ((nHeightLevels > 0) || (fGeopotentialHeight)) {
for (int k = 0; k < nLev; k++) {
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
dataZ[k][i][j] = dZs[i][j] + dLev[k] * (dZtop - dZs[i][j]);
}
}
}
for (int k = 0; k < nILev; k++) {
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
dataIZ[k][i][j] = dZs[i][j] + dILev[k] * (dZtop - dZs[i][j]);
}
}
}
}
// Loop through all pressure levels and variables
for (int v = 0; v < vecNcVar.size(); v++) {
bool fOnInterfaces = false;
// Load in the data array
vecNcVar[v]->set_cur(t, 0, 0, 0);
if (vecNcVar[v]->get_dim(1)->size() == nLev) {
vecNcVar[v]->get(&(dataIn[0][0][0]), 1, nLev, nLat, nLon);
Announce("%s (n)", vecVariableStrings[v].c_str());
} else if (vecNcVar[v]->get_dim(1)->size() == nILev) {
vecNcVar[v]->get(&(dataInt[0][0][0]), 1, nILev, nLat, nLon);
fOnInterfaces = true;
Announce("%s (i)", vecVariableStrings[v].c_str());
} else {
_EXCEPTION1("Variable \"%s\" has invalid level dimension",
vecVariableStrings[v].c_str());
}
// At the physical surface
if (fExtractSurface) {
if (fOnInterfaces) {
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
dataOut[i][j] = dataInt[0][i][j];
}
}
} else {
int kBegin = 0;
int kEnd = 3;
PolynomialInterp::LagrangianPolynomialCoeffs(
3, dLev, dW, 0.0);
// Loop thorugh all latlon indices
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
// Interpolate in the vertical
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dW[k] * dataIn[k][i][j];
}
}
}
}
// Write variable
vecOutNcVarS[v]->set_cur(t, 0, 0);
vecOutNcVarS[v]->put(&(dataOut[0][0]), 1, nLat, nLon);
}
// Loop through all pressure levels
for (int p = 0; p < nPressureLevels; p++) {
// Loop thorugh all latlon indices
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
// Store column pressure
for (int k = 0; k < nLev; k++) {
dataColumnP[k] = dataP[k][i][j];
}
// Find weights
int kBegin = 0;
int kEnd = 0;
// On a pressure surface
InterpolationWeightsLinear(
vecPressureLevels[p],
dataColumnP,
kBegin,
kEnd,
dW);
// Interpolate in the vertical
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dW[k] * dataIn[k][i][j];
}
}
}
// Write variable
vecOutNcVarP[v]->set_cur(t, p, 0, 0);
vecOutNcVarP[v]->put(&(dataOut[0][0]), 1, 1, nLat, nLon);
}
// Loop through all height levels
for (int z = 0; z < nHeightLevels; z++) {
// Loop thorugh all latlon indices
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
// Find weights
int kBegin = 0;
int kEnd = 0;
// Interpolate from levels to z surfaces
if (!fOnInterfaces) {
for (int k = 0; k < nLev; k++) {
dataColumnZ[k] = dataZ[k][i][j];
}
InterpolationWeightsLinear(
vecHeightLevels[z],
dataColumnZ,
kBegin,
kEnd,
dW);
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dW[k] * dataIn[k][i][j];
}
// Interpolate from interfaces to z surfaces
} else {
for (int k = 0; k < nILev; k++) {
dataColumnIZ[k] = dataIZ[k][i][j];
}
InterpolationWeightsLinear(
vecHeightLevels[z],
dataColumnIZ,
kBegin,
kEnd,
dIW);
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dIW[k] * dataInt[k][i][j];
}
}
}
}
// Write variable
vecOutNcVarZ[v]->set_cur(t, z, 0, 0);
vecOutNcVarZ[v]->put(&(dataOut[0][0]), 1, 1, nLat, nLon);
}
}
// Output geopotential height
if (fGeopotentialHeight) {
Announce("Geopotential height");
// Output variables
NcVar * varOutZ;
NcVar * varOutZs;
if (nPressureLevels > 0) {
varOutZ = ncdf_out.add_var(
"PHIZ", ncDouble, dimOutTime, dimOutP, dimOutLat, dimOutLon);
}
if (fExtractSurface) {
varOutZs = ncdf_out.add_var(
"PHIZS", ncDouble, dimOutTime, dimOutLat, dimOutLon);
}
// Interpolate onto pressure levels
for (int p = 0; p < nPressureLevels; p++) {
// Loop thorugh all latlon indices
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
int kBegin = 0;
int kEnd = 0;
for (int k = 0; k < nLev; k++) {
dataColumnP[k] = dataP[k][i][j];
}
InterpolationWeightsLinear(
vecPressureLevels[p],
dataColumnP,
kBegin,
kEnd,
dW);
// Interpolate in the vertical
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dW[k] * dataZ[k][i][j];
}
}
}
// Write variable
varOutZ->set_cur(t, p, 0, 0);
varOutZ->put(&(dataOut[0][0]), 1, 1, nLat, nLon);
}
// Interpolate onto the physical surface
if (fExtractSurface) {
int kBegin = 0;
int kEnd = 3;
PolynomialInterp::LagrangianPolynomialCoeffs(
3, dLev, dW, 0.0);
// Loop thorugh all latlon indices
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
// Interpolate in the vertical
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dW[k] * dataZ[k][i][j];
}
}
}
// Write variable
varOutZs->set_cur(t, 0, 0);
varOutZs->put(&(dataOut[0][0]), 1, nLat, nLon);
}
}
// Extract total energy
if (fExtractTotalEnergy) {
Announce("Total Energy");
// Zonal velocity
DataArray3D<double> dataU(nLev, nLat, nLon);
NcVar * varU = ncdf_in.get_var("U");
varU->set_cur(t, 0, 0, 0);
varU->get(&(dataU[0][0][0]), 1, nLev, nLat, nLon);
// Meridional velocity
DataArray3D<double> dataV(nLev, nLat, nLon);
NcVar * varV = ncdf_in.get_var("V");
varV->set_cur(t, 0, 0, 0);
varV->get(&(dataV[0][0][0]), 1, nLev, nLat, nLon);
// Vertical velocity
DataArray3D<double> dataW(nLev, nLat, nLon);
NcVar * varW = ncdf_in.get_var("W");
varW->set_cur(t, 0, 0, 0);
varW->get(&(dataW[0][0][0]), 1, nLev, nLat, nLon);
// Calculate total energy
double dTotalEnergy = 0.0;
double dElementRefArea =
dEarthRadius * dEarthRadius
* M_PI / static_cast<double>(nLat)
* 2.0 * M_PI / static_cast<double>(nLon);
for (int k = 0; k < nLev; k++) {
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
double dKineticEnergy =
0.5 * dataRho[k][i][j] *
( dataU[k][i][j] * dataU[k][i][j]
+ dataV[k][i][j] * dataV[k][i][j]
+ dataW[k][i][j] * dataW[k][i][j]);
double dInternalEnergy =
dataP[k][i][j] / (dGamma - 1.0);
dTotalEnergy +=
(dKineticEnergy + dInternalEnergy)
* std::cos(M_PI * dLat[i] / 180.0) * dElementRefArea
* (dZtop - dZs[i][j]) / static_cast<double>(nLev);
}
}
}
// Put total energy into file
varEnergy->set_cur(t);
varEnergy->put(&dTotalEnergy, 1);
}
AnnounceEndBlock("Done");
}
AnnounceEndBlock("Done");
} catch(Exception & e) {
Announce(e.ToString().c_str());
}
// Finalize MPI
MPI_Finalize();
}
//
// Creates NetCDF product
//
bool NetCDFProduct(MSG_header *PRO_head, MSG_data* PRO_data,
int totalsegs, int *segsindexes,
MSG_header *header, MSG_data *msgdat)
{
struct tm *tmtime;
char NcName[1024];
char reftime[64];
char projname[16];
int wd, hg;
int bpp;
int ncal;
float *cal;
NcVar *ivar;
NcVar *tvar;
NcDim *tdim;
NcDim *ldim;
NcDim *cdim;
NcDim *caldim;
int npix = header[0].image_structure->number_of_columns;
int nlin = header[0].image_structure->number_of_lines;
size_t npixperseg = npix*nlin;
size_t total_size = totalsegs*npixperseg;
MSG_SAMPLE *pixels = new MSG_SAMPLE[total_size];
memset(pixels, 0, total_size*sizeof(MSG_SAMPLE));
size_t pos = 0;
for (int i = 0; i < totalsegs; i ++)
{
if (segsindexes[i] >= 0)
memcpy(pixels+pos, msgdat[segsindexes[i]].image->data,
npixperseg*sizeof(MSG_SAMPLE));
pos += npixperseg;
}
nlin = nlin*totalsegs;
// Manage subarea
if (is_subarea)
{
if (AreaLinStart < 0 ||
AreaLinStart > nlin - AreaNlin ||
AreaNlin > nlin - AreaLinStart)
{
std::cerr << "Wrong Subarea in lines...." << std::endl;
throw;
}
if (AreaPixStart < 0 ||
AreaPixStart > npix - AreaNpix ||
AreaNpix > npix - AreaPixStart)
{
std::cerr << "Wrong Subarea in Pixels...." << std::endl;
throw;
}
size_t newsize = AreaNpix * AreaNlin;
MSG_SAMPLE *newpix = new MSG_SAMPLE[newsize];
memset(newpix, 0, newsize*sizeof(MSG_SAMPLE));
for (int i = 0; i < AreaNlin; i ++)
memcpy(newpix + i * AreaNpix,
pixels + (AreaLinStart + i) * npix + AreaPixStart,
AreaNpix * sizeof(MSG_SAMPLE));
delete [ ] pixels;
pixels = newpix;
total_size = newsize;
}
else
{
AreaNpix = npix;
AreaNlin = nlin;
}
tmtime = PRO_data->prologue->image_acquisition.PlannedAquisitionTime.TrueRepeatCycleStart.get_timestruct( );
t_enum_MSG_spacecraft spc = header[0].segment_id->spacecraft_id;
uint_1 chn = header[0].segment_id->spectral_channel_id;
float sublon = header[0].image_navigation->subsatellite_longitude;
int cfac = header[0].image_navigation->column_scaling_factor;
int lfac = header[0].image_navigation->line_scaling_factor;
int coff = header[0].image_navigation->column_offset;
int loff = header[0].image_navigation->line_offset;
float sh = header[0].image_navigation->satellite_h;
char *channelstring = strdup(MSG_channel_name(spc, chn).c_str( ));
char *channel = chname(channelstring, strlen(channelstring) + 1);
// Build up output NetCDF file name and open it
sprintf( NcName, "%s_%4d%02d%02d_%02d%02d.nc", channel,
tmtime->tm_year + 1900, tmtime->tm_mon + 1, tmtime->tm_mday,
tmtime->tm_hour, tmtime->tm_min );
NcFile ncf ( NcName , NcFile::Replace );
if (! ncf.is_valid()) return false;
// Fill arrays on creation
ncf.set_fill(NcFile::Fill);
// Add Global Attributes
if (! ncf.add_att("Satellite", MSG_spacecraft_name(spc).c_str()))
return false;
sprintf(reftime, "%04d-%02d-%02d %02d:%02d:00 UTC",
tmtime->tm_year + 1900, tmtime->tm_mon + 1, tmtime->tm_mday,
tmtime->tm_hour, tmtime->tm_min);
if (! ncf.add_att("Antenna", "Fixed") ) return false;
if (! ncf.add_att("Receiver", "HIMET") ) return false;
if (! ncf.add_att("Time", reftime) ) return false;
if (! ncf.add_att("Area_Name", "SpaceView" ) ) return false;
sprintf(projname, "GEOS(%3.1f)", sublon);
if (! ncf.add_att("Projection", projname) ) return false;
if (! ncf.add_att("Columns", AreaNpix ) ) return false;
if (! ncf.add_att("Lines", AreaNlin ) ) return false;
if (! ncf.add_att("SampleX", 1.0 ) ) return false;
if (! ncf.add_att("SampleY", 1.0 ) ) return false;
if (! ncf.add_att("AreaStartPix", AreaPixStart ) ) return false;
if (! ncf.add_att("AreaStartLin", AreaLinStart ) ) return false;
if (! ncf.add_att("Column_Scale_Factor", cfac) ) return false;
if (! ncf.add_att("Line_Scale_Factor", lfac) ) return false;
if (! ncf.add_att("Column_Offset", coff) ) return false;
if (! ncf.add_att("Line_Offset", loff) ) return false;
if (! ncf.add_att("Orbit_Radius", sh) ) return false;
if (! ncf.add_att("Longitude", sublon) ) return false;
if (! ncf.add_att("NortPolar", 1) ) return false;
if (! ncf.add_att("NorthSouth", 1) ) return false;
if (! ncf.add_att("title", TITLE) ) return false;
if (! ncf.add_att("Institution", INSTITUTION) ) return false;
if (! ncf.add_att("Type", TYPE) ) return false;
if (! ncf.add_att("Version", HIMET_VERSION) ) return false;
if (! ncf.add_att("Conventions", "COARDS") ) return false;
if (! ncf.add_att("history", "Created from raw data") ) return false;
// Dimensions
wd = AreaNpix;
hg = AreaNlin;
bpp = header[0].image_structure->number_of_bits_per_pixel;
ncal = (int) pow(2.0, bpp);
tdim = ncf.add_dim("time");
if (!tdim->is_valid()) return false;
ldim = ncf.add_dim("line", hg);
if (!ldim->is_valid()) return false;
cdim = ncf.add_dim("column", wd);
if (!cdim->is_valid()) return false;
caldim = ncf.add_dim("calibration", ncal);
if (!caldim->is_valid()) return false;
// Get calibration values
cal = PRO_data->prologue->radiometric_proc.get_calibration((int) chn, bpp);
// Add Calibration values
NcVar *cvar = ncf.add_var("calibration", ncFloat, caldim);
if (!cvar->is_valid()) return false;
cvar->add_att("long_name", "Calibration coefficients");
cvar->add_att("variable", channel);
if (chn > 3 && chn < 12)
cvar->add_att("units", "K");
else
cvar->add_att("units", "mW m^-2 sr^-1 (cm^-1)^-1");
if (!cvar->put(cal, ncal)) return false;
tvar = ncf.add_var("time", ncDouble, tdim);
if (!tvar->is_valid()) return false;
tvar->add_att("long_name", "Time");
tvar->add_att("units", "seconds since 2000-01-01 00:00:00 UTC");
double atime;
time_t ttime;
extern long timezone;
ttime = mktime(tmtime);
atime = ttime - 946684800 - timezone;
if (!tvar->put(&atime, 1)) return false;
ivar = ncf.add_var(channel, ncShort, tdim, ldim, cdim);
if (!ivar->is_valid()) return false;
if (!ivar->add_att("add_offset", 0.0)) return false;
if (!ivar->add_att("scale_factor", 1.0)) return false;
if (!ivar->add_att("chnum", chn)) return false;
// Write output values
if (!ivar->put((const short int *) pixels, 1, hg, wd)) return false;
// Close NetCDF output
(void) ncf.close( );
delete [ ] pixels;
delete [ ] cal;
return( true );
}
void TracerManager::output(const string &fileName)
{
// -------------------------------------------------------------------------
// output polygon stuffs
polygonManager.output(fileName);
#ifdef TTS_REMAP
// -------------------------------------------------------------------------
NcFile file(fileName.c_str(), NcFile::Write);
if (!file.is_valid()) {
Message message;
message << "Failed to open tracer output file \"";
message << fileName << "\" for appending meshed density field!";
REPORT_ERROR(message.str());
}
// -------------------------------------------------------------------------
// output tracer densities on the polygons
NcDim *numPolygonDim = file.get_dim("num_total_polygon");
double q0[polygonManager.polygons.size()];
for (int l = 0; l < tracerNames.size(); ++l) {
char varName[30];
sprintf(varName, "q%d", l);
NcVar *qVar = file.add_var(varName, ncDouble, numPolygonDim);
Polygon *polygon = polygonManager.polygons.front();
for (int i = 0; i < polygonManager.polygons.size(); ++i) {
q0[i] = polygon->tracers[l].getDensity();
polygon = polygon->next;
}
qVar->put(q0, polygonManager.polygons.size());
}
// -------------------------------------------------------------------------
// output tracer densities on the mesh
const RLLMesh &mesh = tracerDensities[0].getMesh();
int numLon = mesh.getNumLon()-2;
int numLat = mesh.getNumLat();
double lon[numLon], lat[numLat];
for (int i = 0; i < numLon; ++i)
lon[i] = mesh.lon(i+1)*Rad2Deg;
for (int j = 0; j < numLat; ++j)
lat[j] = mesh.lat(j)*Rad2Deg;
NcDim *lonDim = file.add_dim("lon", numLon);
NcDim *latDim = file.add_dim("lat", numLat);
NcVar *lonVar = file.add_var("lon", ncDouble, lonDim);
lonVar->add_att("long_name", "longitude");
lonVar->add_att("units", "degrees_east");
lonVar->put(lon, numLon);
NcVar *latVar = file.add_var("lat", ncDouble, latDim);
latVar->add_att("long_name", "latitude");
latVar->add_att("units", "degrees_north");
latVar->put(lat, numLat);
NcVar *areaVar = file.add_var("area_mesh", ncDouble, latDim, lonDim);
areaVar->add_att("long_name", "area of fixed mesh cell");
areaVar->add_att("units", "m2");
double area[numLat][numLon];
for (int i = 0; i < numLon; ++i)
for (int j = 0; j < numLat; ++j)
area[j][i] = tracerDensities[0].getMesh(Field::Bound).area(i, j);
areaVar->put(&area[0][0], numLat, numLon);
double q[numLat][numLon];
for (int l = 0; l < tracerNames.size(); ++l) {
char varName[30];
sprintf(varName, "q%d_mesh", l);
NcVar *qVar = file.add_var(varName, ncDouble, latDim, lonDim);
qVar->add_att("long_name", tracerNames[l].c_str());
for (int i = 0; i < numLon; ++i)
for (int j = 0; j < numLat; ++j)
q[j][i] = tracerDensities[l].values(i+1, j, 0).getNew();
qVar->put(&q[0][0], numLat, numLon);
}
// -------------------------------------------------------------------------
file.close();
#endif
NOTICE("TracerManager", fileName+" is generated.");
}
bool OutputManagerReference::OpenFile(
const std::string & strFileName
) {
#ifdef TEMPEST_NETCDF
// Determine processor rank; only proceed if root node
int nRank = 0;
#ifdef TEMPEST_MPIOMP
MPI_Comm_rank(MPI_COMM_WORLD, &nRank);
#endif
// The active model
const Model & model = m_grid.GetModel();
// Open NetCDF file on root process
if (nRank == 0) {
// Check for existing NetCDF file
if (m_pActiveNcOutput != NULL) {
_EXCEPTIONT("NetCDF file already open");
}
// Append .nc extension to file
std::string strNcFileName = strFileName + ".nc";
// Open new NetCDF file
m_pActiveNcOutput = new NcFile(strNcFileName.c_str(), NcFile::Replace);
if (m_pActiveNcOutput == NULL) {
_EXCEPTION1("Error opening NetCDF file \"%s\"",
strNcFileName.c_str());
}
if (!m_pActiveNcOutput->is_valid()) {
_EXCEPTION1("Error opening NetCDF file \"%s\"",
strNcFileName.c_str());
}
// Create nodal time dimension
NcDim * dimTime = m_pActiveNcOutput->add_dim("time");
if (dimTime == NULL) {
_EXCEPTIONT("Error creating \"time\" dimension");
}
m_varTime = m_pActiveNcOutput->add_var("time", ncDouble, dimTime);
if (m_varTime == NULL) {
_EXCEPTIONT("Error creating \"time\" variable");
}
std::string strUnits =
"days since " + model.GetStartTime().ToDateString();
std::string strCalendarName = model.GetStartTime().GetCalendarName();
m_varTime->add_att("long_name", "time");
m_varTime->add_att("units", strUnits.c_str());
m_varTime->add_att("calendar", strCalendarName.c_str());
m_varTime->add_att("bounds", "time_bnds");
// Create levels dimension
NcDim * dimLev =
m_pActiveNcOutput->add_dim("lev", m_dREtaCoord.GetRows());
// Create interfaces dimension
NcDim * dimILev =
m_pActiveNcOutput->add_dim("ilev", m_grid.GetRElements()+1);
// Create latitude dimension
NcDim * dimLat =
m_pActiveNcOutput->add_dim("lat", m_nYReference);
// Create longitude dimension
NcDim * dimLon =
m_pActiveNcOutput->add_dim("lon", m_nXReference);
// Output physical constants
const PhysicalConstants & phys = model.GetPhysicalConstants();
m_pActiveNcOutput->add_att("earth_radius", phys.GetEarthRadius());
m_pActiveNcOutput->add_att("g", phys.GetG());
m_pActiveNcOutput->add_att("omega", phys.GetOmega());
m_pActiveNcOutput->add_att("alpha", phys.GetAlpha());
m_pActiveNcOutput->add_att("Rd", phys.GetR());
m_pActiveNcOutput->add_att("Cp", phys.GetCp());
m_pActiveNcOutput->add_att("T0", phys.GetT0());
m_pActiveNcOutput->add_att("P0", phys.GetP0());
m_pActiveNcOutput->add_att("rho_water", phys.GetRhoWater());
m_pActiveNcOutput->add_att("Rvap", phys.GetRvap());
m_pActiveNcOutput->add_att("Mvap", phys.GetMvap());
m_pActiveNcOutput->add_att("Lvap", phys.GetLvap());
// Output grid parameters
m_pActiveNcOutput->add_att("Ztop", m_grid.GetZtop());
// Output equation set
const EquationSet & eqn = model.GetEquationSet();
m_pActiveNcOutput->add_att("equation_set", eqn.GetName().c_str());
// Create variables
for (int c = 0; c < eqn.GetComponents(); c++) {
if ((m_fOutputAllVarsOnNodes) ||
(m_grid.GetVarLocation(c) == DataLocation_Node)
) {
m_vecComponentVar.push_back(
m_pActiveNcOutput->add_var(
eqn.GetComponentShortName(c).c_str(),
ncDouble, dimTime, dimLev, dimLat, dimLon));
} else {
m_vecComponentVar.push_back(
m_pActiveNcOutput->add_var(
eqn.GetComponentShortName(c).c_str(),
ncDouble, dimTime, dimILev, dimLat, dimLon));
}
}
for (int c = 0; c < eqn.GetTracers(); c++) {
m_vecTracersVar.push_back(
m_pActiveNcOutput->add_var(
eqn.GetTracerShortName(c).c_str(),
ncDouble, dimTime, dimLev, dimLat, dimLon));
}
// Vorticity variable
if (m_fOutputVorticity) {
m_varVorticity =
m_pActiveNcOutput->add_var(
"ZETA", ncDouble, dimTime, dimLev, dimLat, dimLon);
}
// Divergence variable
if (m_fOutputDivergence) {
m_varDivergence =
m_pActiveNcOutput->add_var(
"DELTA", ncDouble, dimTime, dimLev, dimLat, dimLon);
}
// Temperature variable
if (m_fOutputTemperature) {
m_varTemperature =
m_pActiveNcOutput->add_var(
"T", ncDouble, dimTime, dimLev, dimLat, dimLon);
}
// Surface pressure variable
if (m_fOutputSurfacePressure) {
m_varSurfacePressure =
m_pActiveNcOutput->add_var(
"PS", ncDouble, dimTime, dimLat, dimLon);
}
// Richardson number variable
if (m_fOutputRichardson) {
m_varRichardson =
m_pActiveNcOutput->add_var(
"Ri", ncDouble, dimTime, dimLev, dimLat, dimLon);
}
// User data variables
const UserDataMeta & metaUserData = model.GetUserDataMeta();
m_vecUserData2DVar.resize(metaUserData.GetUserData2DItemCount());
for (int i = 0; i < metaUserData.GetUserData2DItemCount(); i++) {
m_vecUserData2DVar[i] =
m_pActiveNcOutput->add_var(
metaUserData.GetUserData2DItemName(i).c_str(),
ncDouble, dimTime, dimLat, dimLon);
}
// Output longitudes and latitudes
NcVar * varLon = m_pActiveNcOutput->add_var("lon", ncDouble, dimLon);
NcVar * varLat = m_pActiveNcOutput->add_var("lat", ncDouble, dimLat);
varLon->put(m_dXCoord, m_dXCoord.GetRows());
varLat->put(m_dYCoord, m_dYCoord.GetRows());
varLon->add_att("long_name", "longitude");
varLon->add_att("units", "degrees_east");
varLat->add_att("long_name", "latitude");
varLat->add_att("units", "degrees_north");
// Output levels
NcVar * varLev =
m_pActiveNcOutput->add_var("lev", ncDouble, dimLev);
varLev->put(
m_dREtaCoord,
m_dREtaCoord.GetRows());
varLev->add_att("long_name", "level");
varLev->add_att("units", "level");
// Output interface levels
NcVar * varILev =
m_pActiveNcOutput->add_var("ilev", ncDouble, dimILev);
varILev->put(
m_grid.GetREtaStretchInterfaces(),
m_grid.GetREtaStretchInterfaces().GetRows());
varILev->add_att("long_name", "interface level");
varILev->add_att("units", "level");
// Topography variable
m_varTopography =
m_pActiveNcOutput->add_var("Zs", ncDouble, dimLat, dimLon);
// Fresh output file
m_fFreshOutputFile = true;
}
#ifdef TEMPEST_MPIOMP
// Wait for all processes to complete
MPI_Barrier(MPI_COMM_WORLD);
#endif
#endif
return true;
}
int TestSuite::testExamples()
{
#define FILE_NAME "pres_temp_4D.nc"
// We are writing 4D data, a 2 x 6 x 12 lvl-lat-lon grid, with 2
// timesteps of data.
#define NDIMS 4
#define NLVL 2
#define NLAT 6
#define NLON 12
#define NREC 2
// Names of things.
#define LVL_NAME "level"
#define LAT_NAME "latitude"
#define LON_NAME "longitude"
#define REC_NAME "time"
#define PRES_NAME "pressure"
#define TEMP_NAME "temperature"
#define MAX_ATT_LEN 80
// These are used to construct some example data.
#define SAMPLE_PRESSURE 900
#define SAMPLE_TEMP 9.0
#define START_LAT 25.0
#define START_LON -125.0
string UNITS = "units";
string DEGREES_EAST = "degrees_east";
string DEGREES_NORTH = "degrees_north";
// For the units attributes.
string PRES_UNITS = "hPa";
string TEMP_UNITS = "celsius";
string LAT_UNITS = "degrees_north";
string LON_UNITS = "degrees_east";
// Return this code to the OS in case of failure.
#define NC_ERR 2
// We will write latitude and longitude fields.
float lats[NLAT],lons[NLON];
// Program variables to hold the data we will write out. We will
// only need enough space to hold one timestep of data; one record.
float pres_out[NLVL][NLAT][NLON];
float temp_out[NLVL][NLAT][NLON];
int i=0; //used in the data generation loop
// create some pretend data. If this wasn't an example program, we
// would have some real data to write for example, model output.
for (int lat = 0; lat < NLAT; lat++)
lats[lat] = START_LAT + 5. * lat;
for (int lon = 0; lon < NLON; lon++)
lons[lon] = START_LON + 5. * lon;
for (int lvl = 0; lvl < NLVL; lvl++)
for (int lat = 0; lat < NLAT; lat++)
for (int lon = 0; lon < NLON; lon++)
{
pres_out[lvl][lat][lon] = SAMPLE_PRESSURE + i;
temp_out[lvl][lat][lon] = SAMPLE_TEMP + i++;
}
try
{
// Create the file.
NcFile test(FILE_NAME, NcFile::Replace);
// Define the dimensions. NetCDF will hand back an ncDim object for
// each.
NcDim* lvlDim = test.addDim(LVL_NAME, NLVL);
NcDim* latDim = test.addDim(LAT_NAME, NLAT);
NcDim* lonDim = test.addDim(LON_NAME, NLON);
NcDim* recDim = test.addDim(REC_NAME); //adds an unlimited dimension
// Define the coordinate variables.
NcVar* latVar = test.addVar(LAT_NAME, ncFloat, latDim);
NcVar* lonVar = test.addVar(LON_NAME, ncFloat, lonDim);
// Define units attributes for coordinate vars. This attaches a
// text attribute to each of the coordinate variables, containing
// the units.
latVar->addAtt(UNITS,ncChar, DEGREES_NORTH);
lonVar->addAtt(UNITS,ncChar, DEGREES_EAST);
// Define the netCDF variables for the pressure and temperature
// data.
NcVar* pressVar = test.addVar(PRES_NAME, ncFloat, recDim, lvlDim,
latDim, lonDim);
NcVar* tempVar = test.addVar(TEMP_NAME, ncFloat, recDim, lvlDim,
latDim, lonDim);
// Define units attributes for coordinate vars. This attaches a
// text attribute to each of the coordinate variables, containing
// the units.
pressVar->addAtt(UNITS,ncChar, PRES_UNITS);
tempVar->addAtt(UNITS,ncChar ,TEMP_UNITS);
// Write the coordinate variable data to the file.
latVar->put(lats, NLAT);
lonVar->put(lons, NLON);
// Write the pretend data. This will write our surface pressure and
// surface temperature data. The arrays only hold one timestep
// worth of data. We will just rewrite the same data for each
// timestep. In a real application, the data would change between
// timesteps.
for (int rec = 0; rec < NREC; rec++)
{
pressVar->putRec(&pres_out[0][0][0], rec);
tempVar->putRec(&temp_out[0][0][0], rec);
}
//NcValues * pressVals = pressVar->getValues();
//pressVals->print(cout);
// The file is automatically closed by the destructor. This frees
// up any internal netCDF resources associated with the file, and
// flushes any buffers.
cout << "*** SUCCESS writing example file " << FILE_NAME << "!" << endl;
}
catch(NcException e)
{
e.what();
return 1;
}
return 0;
}
void CCohortdriver::createSoilClimate(BgcData *bd, EnvData *ed, Vegetation_Env *ve,
string& datadir){
string file = datadir+ "calirestart.nc";
NcFile* resFile = new NcFile(file.c_str(), NcFile::Replace);
NcDim * chtD = resFile->add_dim("CHTID", 1);
NcDim * monD = resFile->add_dim("MON", 12);
NcDim * layD = resFile->add_dim("LAYER", MAX_SOI_LAY);
NcVar* drgV = resFile->add_var("DRG",ncInt, chtD);
NcVar* vegV = resFile->add_var("VEG",ncInt, chtD);
NcVar* numslV = resFile->add_var("NUMSL",ncInt, chtD);
NcVar* rsoilcV = resFile->add_var("RSOILC", ncDouble, layD);
NcVar* nsoilcV = resFile->add_var("NSOILC", ncDouble, layD);
NcVar* dzV = resFile->add_var("DZ", ncDouble, layD);
NcVar* typeV = resFile->add_var("TYPE", ncDouble, layD);
NcVar* poroV = resFile->add_var("PORO", ncDouble, layD);
NcVar* rootfracV = resFile->add_var("ROOTFRAC", ncDouble, layD);
NcVar* taV = resFile->add_var("TA",ncDouble, monD);
NcVar* growV = resFile->add_var("GROW",ncDouble, monD);
NcVar* co2V = resFile->add_var("CO2",ncDouble, monD);
NcVar* petV = resFile->add_var("PET",ncDouble, monD);
NcVar* eetV = resFile->add_var("EET",ncDouble, monD);
NcVar* parV = resFile->add_var("PAR",ncDouble, monD);
NcVar* envlaiV = resFile->add_var("ENVLAI",ncFloat, monD);
NcVar* tsV = resFile->add_var("TS", ncDouble, monD, layD);
NcVar* ch4V = resFile->add_var("CH4",ncDouble, monD, layD);
NcVar* liqV = resFile->add_var("LIQ",ncDouble, monD, layD);
NcVar* vwcV = resFile->add_var("VSM",ncDouble, monD, layD);
NcVar* swsV = resFile->add_var("SWS",ncDouble, monD, layD);
NcVar* iceV = resFile->add_var("ICE",ncDouble, monD, layD);
NcVar* yreetV = resFile->add_var("YREET",ncDouble, chtD);
NcVar* yrpetV = resFile->add_var("YRPET",ncDouble, chtD);
NcVar* yrco2V = resFile->add_var("YRCO2",ncDouble, chtD);
NcVar* prveetmxV = resFile->add_var("PRVEETMX",ncDouble, chtD);
NcVar* prvpetmxV = resFile->add_var("PRVPETMX",ncDouble, chtD);
numslV->put(&ed->m_soid.actual_num_soil, 1);
drgV->put(&ed->cd->drgtype, 1);
vegV->put(&ed->cd->vegtype, 1);
poroV->put(&ed->m_sois.por[0], MAX_SOI_LAY);
typeV->put(&ed->m_sois.type[0], MAX_SOI_LAY);
dzV->put(&ed->m_sois.dz[0], MAX_SOI_LAY);
rsoilcV->put(&bd->m_sois.reac[0], MAX_SOI_LAY);
nsoilcV->put(&bd->m_sois.nonc[0], MAX_SOI_LAY);
rootfracV->put(&ed->m_sois.rootfrac[0], MAX_SOI_LAY);
tsV->put(&ed->eq_ts[0][0], 12, MAX_SOI_LAY);
ch4V->put(&ed->eq_ch4[0][0], 12, MAX_SOI_LAY);
liqV->put(&ed->eq_liq[0][0], 12, MAX_SOI_LAY);
iceV->put(&ed->eq_ice[0][0], 12, MAX_SOI_LAY);
vwcV->put(&ed->eq_vwc[0][0], 12, MAX_SOI_LAY);
swsV->put(&ed->eq_sws[0][0], 12, MAX_SOI_LAY);
taV->put(&ed->eq_ta[0], 12);
petV->put(&ed->eq_pet[0], 12);
eetV->put(&ed->eq_eet[0], 12);
co2V->put(&ed->eq_co2[0], 12);
parV->put(&ed->eq_par[0], 12);
growV->put(&ed->eq_grow[0], 12);
envlaiV->put(&ve->envlaiall[0], 12);
yreetV->put(&ed->eq_y_eet, 1);
yrpetV->put(&ed->eq_y_pet, 1);
yrco2V->put(&ed->eq_y_co2, 1);
prveetmxV->put(&ed->eq_prveetmx);
prvpetmxV->put(&ed->eq_prvpetmx);
resFile->close();
delete resFile; //Yuan: if not, memory leaking may occur
// exit(0);
};
int TestSuite::testTypes()
{
try
{
NcFile f("tst_types.nc",NcFile::Replace);
NcEnumType *state;
NcGroup * root;
root = f.getRootGroup();
state =f.addEnumType("state");
state->addMember("sitting",10);
state->addMember("standing",11);
state->addMember("walking",12);
state->addMember("running",13);
enum estuff{sitting =10, standing =11, walking =12,running = 13};
estuff s;
s = standing;
NcVar *var = root->addVar("enumVar",state);
var->put(&s);// how do I store and variable that is of enumaration type
cout<<" done with enum stuff*****************************************************"<<endl;
NcCompoundType *myStruct;
struct s1
{
int i1;
int i2;
};
myStruct = f.addCompoundType("basicCompoundType",sizeof(s1));
myStruct->addMember("i1",NC_INT);
myStruct->addMember("i2",NC_INT);
s1 tempStruct;
tempStruct.i1= 23;
tempStruct.i2= 15;
NcVar *var1= root->addVar("basicCompoundVariable",myStruct);
var1->put(&tempStruct);
//var1->addAtt("basicCompoundAtt",myStruct,&tempStruct);
cout<<"done with basic compound stuff *********************************************"<<endl;
struct cs
{
s1 s;
int j;
string k;
};
NcCompoundType * compStruct;
compStruct= f.addCompoundType("mediumCompoundType",sizeof(cs));
compStruct->addMember("s",myStruct);
compStruct->addMember("j",NC_INT);
compStruct->addMember("k",NC_STRING);
cs struct2;
struct2.s = tempStruct;
struct2.j =15;
struct2.k = "it works";
NcVar *var2= root->addVar("mediumCompoundVariable",compStruct);
var2->put(&struct2);
cout<<"*******************done with medium compund stuff*******************"<<endl;
struct cs3
{
s1 a;
s1 b;
estuff k;
int i;
};
NcCompoundType *compStruct2 = f.addCompoundType("complexCompoundType",sizeof(cs3));
compStruct2->addMember("a",myStruct);
compStruct2->addMember("b",myStruct);
compStruct2->addMember("k",state);
compStruct2->addMember("i",NC_INT);
cs3 comps2v;
comps2v.a = tempStruct;
comps2v.b = tempStruct;
comps2v.k = s;
comps2v.i = 1985;
NcVar *var3= root->addVar("complexCompoundVariable",compStruct2);
var3->put(&comps2v);
cout<<"*********************done with complex compound stuff***************************************"<<endl;
cout<<"****************************now doing variable length stuff****************************"<<endl;
nc_vlen_t data1[3];
int *phoney;
/* Create phoney data. */
for (int i=0; i<3; i++)
{
if (!(phoney = new int[i+1]))
return NC_ENOMEM;
for (int j=0; j<i+1; j++)
phoney[j] = -99;
data1[i].p = phoney;
data1[i].len = i+1;
}
NcVLenType *vlen;
vlen=f.addVLenType("variableLengthType",ncInt);
//NcVar *vlenVar = root->addVar("variableLengthVariable",vlen);
string stuff = "hello world";
//vlenVar->addAtt("vlenatt",vlen,data1);
cout<<"about to call put for variable vlenvar"<<endl;
//vlenVar->put(&data1);
cout<<"I just called put for the variable lenght data. I'm in the tst_...cpp file, hopefully it works"<<endl;
cout<<"*********************now dealing with opaque stuff*************************"<<endl;
unsigned char data[5][5];
for(int i = 0;i < 5; i++)
{
for(int j =0; j<5; j++)
{
data[i][j]= 'a';
}
}
NcOpaqueType *opaque;
opaque = f.addOpaqueType("opaqueType",sizeof(data));
NcVar *ovar = root->addVar("opaqueVar",opaque);
//ovar->put(&data);
cout<<"********************done with opaque stuff ******************************"<<endl;
}
catch(NcException e)
{
e.what();
return 1;
}
try
{
cout<<"I'm going to try reading now"<<endl;
NcFile f("tst_types.nc",NcFile::ReadOnly);
cout<<"hopefully all the stuff has been read correctly"<<endl;
}
catch(NcException e)
{
e.what();
return 1;
}
return 0;
}
void InputNetcdf::writeCore(const Data& iData, int iDate, int iInit, const std::vector<float>& iOffsets, const std::vector<Location>& iLocations, const std::vector<Member>& iMembers, const std::vector<std::string>& iVariables) const {
// Set up file
Key::Input key;
key.date = iDate;
key.init = iInit;
key.location = 0;
std::string filename = getFilename(key);
// Global::createDirectory(filename);
NcFile ncfile(filename.c_str(), NcFile::Replace);
if(!ncfile.is_valid()) {
std::stringstream ss;
ss << " InputNetcdf: Could not write file: " << filename;
Global::logger->write(ss.str(), Logger::error);
}
// Write dimensions
NcDim* dimOffset = ncfile.add_dim("Offset", (long) iOffsets.size());
NcDim* dimLocation = ncfile.add_dim("Location", (long) iLocations.size());
NcDim* dimMember = ncfile.add_dim("Member", (long) iMembers.size());
// Write offsets
NcVar* varOffsets = ncfile.add_var("Offset", ncFloat, dimOffset);
writeVariable(varOffsets, iOffsets);
// Write lat/lons
NcVar* varLats = ncfile.add_var("Lat", ncFloat, dimLocation);
NcVar* varLons = ncfile.add_var("Lon", ncFloat, dimLocation);
NcVar* varElevs = ncfile.add_var("Elev", ncFloat, dimLocation);
NcVar* varIds = ncfile.add_var("Id", ncInt, dimLocation);
std::vector<float> lats;
std::vector<float> lons;
std::vector<float> elevs;
std::vector<float> ids;
for(int i = 0; i < (int) iLocations.size(); i++) {
lats.push_back(iLocations[i].getLat());
lons.push_back(iLocations[i].getLon());
elevs.push_back(iLocations[i].getElev());
ids.push_back(iLocations[i].getId());
}
writeVariable(varLats, lats);
writeVariable(varLons, lons);
writeVariable(varElevs, elevs);
writeVariable(varIds, ids);
// Write resolution
NcVar* varRes = ncfile.add_var("Resolution", ncFloat, dimMember);
std::vector<float> resolutions;
for(int i = 0; i < (int) iMembers.size(); i++) {
resolutions.push_back(iMembers[i].getResolution());
}
writeVariable(varRes, resolutions);
// Preallocate
int N = iOffsets.size() * iLocations.size() * iMembers.size();
float* values = new float[N];
std::vector<std::string> localVariables;
// Write each variable
for(int v = 0; v < (int) iVariables.size(); v++) {
for(int i = 0; i < N; i++)
values[i] = Global::MV;
std::string variable = iVariables[v];
std::string localVariable = variable;
//bool found = getLocalVariableName(variable, localVariable);
//if(!found) {
// std::stringstream ss;
// ss << "InputNetcdf::write: Do not know what to map " << variable << " to. Skipping.";
// Global::logger->write(ss.str(), Logger::message);
// }
if(std::find(localVariables.begin(), localVariables.end(), localVariable) != localVariables.end()) {
std::cout << "Variable " << localVariable << " has already been written once. Discarding duplicate." << std::endl;
}
else {
localVariables.push_back(localVariable);
// Populate values;
for(int l = 0; l < (int) iLocations.size(); l++) {
for(int o = 0; o < (int) iOffsets.size(); o++) {
float offset = iOffsets[o];
for(int m = 0; m < (int) iMembers.size(); m++) {
float value = iData.getValue(iDate, iInit, offset, iLocations[l], iMembers[m], variable);
int index = o*iLocations.size()*iMembers.size() + l*iMembers.size() + m;
assert(index < N);
values[index] = value;
}
}
}
// Write values
long count[3] = {iOffsets.size(), iLocations.size(), iMembers.size()};
NcVar* ncvar = ncfile.add_var(localVariable.c_str(), ncFloat, dimOffset, dimLocation, dimMember);
ncvar->put(values, count);
}
}
delete[] values;
ncfile.close();
}
void CopyNcVar(
NcFile & ncIn,
NcFile & ncOut,
const std::string & strVarName,
bool fCopyAttributes,
bool fCopyData
) {
if (!ncIn.is_valid()) {
_EXCEPTIONT("Invalid input file specified");
}
if (!ncOut.is_valid()) {
_EXCEPTIONT("Invalid output file specified");
}
NcVar * var = ncIn.get_var(strVarName.c_str());
if (var == NULL) {
_EXCEPTION1("NetCDF file does not contain variable \"%s\"",
strVarName.c_str());
}
NcVar * varOut;
std::vector<NcDim *> dimOut;
dimOut.resize(var->num_dims());
std::vector<long> counts;
counts.resize(var->num_dims());
long nDataSize = 1;
for (int d = 0; d < var->num_dims(); d++) {
NcDim * dimA = var->get_dim(d);
dimOut[d] = ncOut.get_dim(dimA->name());
if (dimOut[d] == NULL) {
if (dimA->is_unlimited()) {
dimOut[d] = ncOut.add_dim(dimA->name());
} else {
dimOut[d] = ncOut.add_dim(dimA->name(), dimA->size());
}
if (dimOut[d] == NULL) {
_EXCEPTION2("Failed to add dimension \"%s\" (%i) to file",
dimA->name(), dimA->size());
}
}
if (dimOut[d]->size() != dimA->size()) {
if (dimA->is_unlimited() && !dimOut[d]->is_unlimited()) {
_EXCEPTION2("Mismatch between input file dimension \"%s\" and "
"output file dimension (UNLIMITED / %i)",
dimA->name(), dimOut[d]->size());
} else if (!dimA->is_unlimited() && dimOut[d]->is_unlimited()) {
_EXCEPTION2("Mismatch between input file dimension \"%s\" and "
"output file dimension (%i / UNLIMITED)",
dimA->name(), dimA->size());
} else if (!dimA->is_unlimited() && !dimOut[d]->is_unlimited()) {
_EXCEPTION3("Mismatch between input file dimension \"%s\" and "
"output file dimension (%i / %i)",
dimA->name(), dimA->size(), dimOut[d]->size());
}
}
counts[d] = dimA->size();
nDataSize *= counts[d];
}
// ncByte / ncChar type
if ((var->type() == ncByte) || (var->type() == ncChar)) {
DataVector<char> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
// ncShort type
if (var->type() == ncShort) {
DataVector<short> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
if (fCopyData) {
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
}
// ncInt type
if (var->type() == ncInt) {
DataVector<int> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
if (fCopyData) {
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
}
// ncFloat type
if (var->type() == ncFloat) {
DataVector<float> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
if (fCopyData) {
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
}
// ncDouble type
if (var->type() == ncDouble) {
DataVector<double> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
if (fCopyData) {
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
}
// ncInt64 type
if (var->type() == ncInt64) {
DataVector<ncint64> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
if (fCopyData) {
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
}
// Check output variable exists
if (varOut == NULL) {
_EXCEPTION1("Unable to create output variable \"%s\"",
var->name());
}
// Copy attributes
if (fCopyAttributes) {
CopyNcVarAttributes(var, varOut);
}
}
int main(int argc, const char* argv[]) {
string fileName;
int maxDataSavePts, boundHandlingMethod;
double stoppingTol;
if (argc == 8) {
for (int i = 0; i < argc; i++) {
if (argv[i][0] == '-') {
switch(argv[i][1]) {
case 'n':
maxDataSavePts = atoi(argv[i+1]);
i++;
break;
case 'e':
stoppingTol = atof(argv[i+1]);
i++;
break;
case 'b':
boundHandlingMethod = atof(argv[i+1]);
i++;
break;
}
} else {
fileName = argv[i];
}
}
} else {
fprintf(stderr, "\nUsage: ./FilePrep <fileName> -n <maxDataSavePts> -e <stoppingTol> -b <boundHandlingMethod>\n");
fprintf(stderr, " <fileName> Name of the NetCDF file to be prepared for simulation.\n");
fprintf(stderr, " -n <maxDataSavePts> Maximum number of initial states to be held in the file.\n");
fprintf(stderr, " -e <stoppingTol> Maximum allowable L2 distance between successive probability distributions.\n\n");
fprintf(stderr, " -b <boundHandlingMethod> 1 for deletion. 2 for resampling.");
abort();
}
NcFile file(fileName.c_str(), NcFile::Write);
if (!file.is_valid()) {
fprintf(stderr, "Error: %s could not be opened.\n", fileName.c_str());
abort();
}
NcDim* dim = file.add_dim("maxDataSavePts", maxDataSavePts);
NcVar* stoppingTolVar = file.add_var("stoppingTol", ncDouble);
NcVar* numDataSavePtsVar = file.add_var("numDataSavePts", ncInt, file.get_dim("numMdls"));
NcVar* boundHandlingMethodVar = file.add_var("boundHandlingMethod", ncInt, file.get_dim("numMdls"));
file.add_var("numBoundedSpeciesStates", ncInt, file.get_dim("numMdls"));
file.add_var("speciesStateBounded", ncInt, file.get_dim("numMdls"), file.get_dim("maxSpecies"));
file.add_var("speciesStateLowerBounds", ncDouble, file.get_dim("numMdls"), file.get_dim("maxSpecies"));
file.add_var("speciesStateUpperBounds", ncDouble, file.get_dim("numMdls"), file.get_dim("maxSpecies"));
file.add_var("dataSavePts", ncInt, file.get_dim("numMdls"), dim);
file.add_var("speciesStateChanges", ncInt, file.get_dim("numMdls"), file.get_dim("maxSpecies"));
file.get_var("state")->rename("initFwdData");
file.add_var("initRevData", ncDouble, file.get_dim("numMdls"), file.get_dim("maxTrials"), file.get_dim("maxTimePts"), file.get_dim("maxSaveSpecies"));
file.add_var("fwdData", ncDouble, file.get_dim("numMdls"), dim, file.get_dim("maxTrials"), file.get_dim("maxTimePts"), file.get_dim("maxSaveSpecies"));
file.add_var("revData", ncDouble, file.get_dim("numMdls"), dim, file.get_dim("maxTrials"), file.get_dim("maxTimePts"), file.get_dim("maxSaveSpecies"));
file.add_var("initFwdAbsCurr", ncInt, file.get_dim("numMdls"), file.get_dim("maxTimePts"), file.get_dim("maxSaveSpecies"));
file.add_var("initRevAbsCurr", ncInt, file.get_dim("numMdls"), file.get_dim("maxTimePts"), file.get_dim("maxSaveSpecies"));
file.add_var("fwdAbsCurr", ncInt, file.get_dim("numMdls"), dim, file.get_dim("maxTimePts"), file.get_dim("maxSaveSpecies"));
file.add_var("revAbsCurr", ncInt, file.get_dim("numMdls"), dim, file.get_dim("maxTimePts"), file.get_dim("maxSaveSpecies"));
stoppingTolVar->put(&stoppingTol, 1);
int numMdls = (int) file.get_dim("numMdls")->size();
for (int i = 0; i < numMdls; i++) {
numDataSavePtsVar->set_cur(i);
numDataSavePtsVar->put(&maxDataSavePts, 1);
}
boundHandlingMethodVar->put(&boundHandlingMethod, 1);
}
int main(int argc, char ** argv){
NcError error(NcError::verbose_nonfatal);
try{
std::string inFile;
std::string outFile;
std::string varName;
std::string inList;
// bool calcStdDev;
BeginCommandLine()
CommandLineString(inFile, "in", "");
CommandLineString(inList, "inlist","");
CommandLineString(varName, "var", "");
CommandLineString(outFile, "out", "");
// CommandLineBool(calcStdDev, "std");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
if ((inFile != "") && (inList != "")){
_EXCEPTIONT("Can only open one file (--in) or list (--inlist).");
}
//file list vector
std::vector<std::string> vecFiles;
if (inFile != ""){
vecFiles.push_back(inFile);
}
if (inList != ""){
GetInputFileList(inList,vecFiles);
}
//open up first file
NcFile readin(vecFiles[0].c_str());
if (!readin.is_valid()){
_EXCEPTION1("Unable to open file %s for reading",\
vecFiles[0].c_str());
}
int tLen,latLen,lonLen;
NcDim * time = readin.get_dim("time");
tLen = time->size();
NcVar * timeVar = readin.get_var("time");
NcDim * lat = readin.get_dim("lat");
latLen = lat->size();
NcVar * latVar = readin.get_var("lat");
NcDim * lon = readin.get_dim("lon");
lonLen = lon->size();
NcVar * lonVar = readin.get_var("lon");
//read input variable
NcVar * inVar = readin.get_var(varName.c_str());
//Create output matrix
DataMatrix<double> outMat(latLen,lonLen);
densCalc(inVar,outMat);
//Option for calculating the yearly standard deviation
/* if (calcStdDev){
for (int a=0; a<latLen; a++){
for (int b=0; b<lonLen; b++){
storeMat[0][a][b] = outMat[a][b];
}
}
}
*/
//If multiple files, add these values to the output
if (vecFiles.size()>1){
DataMatrix<double> addMat(latLen,lonLen);
std::cout<<"There are "<<vecFiles.size()<<" files."<<std::endl;
for (int v=1; v<vecFiles.size(); v++){
NcFile addread(vecFiles[v].c_str());
NcVar * inVar = addread.get_var(varName.c_str());
densCalc(inVar,addMat);
for (int a=0; a<latLen; a++){
for (int b=0; b<lonLen; b++){
outMat[a][b]+=addMat[a][b];
}
}
/* if (calcStdDev){
for (int a=0; a<latLen; a++){
for (int b=0; b<lonLen; b++){
storeMat[v][a][b] = addMat[a][b];
}
}
}*/
addread.close();
}
//Divide output by number of files
double div = 1./((double) vecFiles.size());
for (int a=0; a<latLen; a++){
for (int b=0; b<lonLen; b++){
outMat[a][b]*=div;
}
}
}
NcFile readout(outFile.c_str(),NcFile::Replace, NULL,0,NcFile::Offset64Bits);
NcDim * outLat = readout.add_dim("lat", latLen);
NcDim * outLon = readout.add_dim("lon", lonLen);
NcVar * outLatVar = readout.add_var("lat",ncDouble,outLat);
NcVar * outLonVar = readout.add_var("lon",ncDouble,outLon);
std::cout<<"Copying dimension attributes."<<std::endl;
copy_dim_var(latVar,outLatVar);
copy_dim_var(lonVar,outLonVar);
std::cout<<"Creating density variable."<<std::endl;
NcVar * densVar = readout.add_var("dens",ncDouble,outLat,outLon);
densVar->set_cur(0,0);
densVar->put((&outMat[0][0]),latLen,lonLen);
/* if (calcStdDev){
NcVar * stdDevVar = readout.add_var("stddev", ncDouble,outLat,outLon);
DataMatrix<double> stdDevMat(latLen,lonLen);
yearlyStdDev(storeMat,vecFiles.size(),latLen,lonLen,stdDevMat);
stdDevVar->set_cur(0,0);
stdDevVar->put(&(stdDevMat[0][0]),latLen,lonLen);
std::cout<<" created sd variable"<<std::endl;
}
*/
readout.close();
readin.close();
}
catch (Exception &e){
std::cout<<e.ToString()<<std::endl;
}
}
int main(void)
{
// We will write surface temperature and pressure fields.
float presOut[NLAT][NLON];
float tempOut[NLAT][NLON];
float lats[NLAT];
float lons[NLON];
// In addition to the latitude and longitude dimensions, we will
// also create latitude and longitude netCDF variables which will
// hold the actual latitudes and longitudes. Since they hold data
// about the coordinate system, the netCDF term for these is:
// "coordinate variables."
for(int lat = 0;lat < NLAT; lat++)
lats[lat] = START_LAT + 5.*lat;
for(int lon = 0; lon < NLON; lon++)
lons[lon] = START_LON + 5.*lon;
// Create some pretend data. If this wasn't an example program, we
// would have some real data to write, for example, model
// output.
for (int lat = 0; lat < NLAT; lat++)
for(int lon = 0;lon < NLON; lon++)
{
presOut[lat][lon] = SAMPLE_PRESSURE + (lon * NLAT + lat);
tempOut[lat][lon] = SAMPLE_TEMP + .25 * (lon * NLAT +lat);
}
try
{
// Create the file. The Replace parameter tells netCDF to overwrite
// this file, if it already exists.
NcFile sfc(FILE_NAME, NcFile::Replace);
// Define the dimensions. NetCDF will hand back an ncDim object for
// each.
NcDim* latDim = sfc.addDim(LAT_NAME, NLAT);
NcDim* lonDim = sfc.addDim(LON_NAME, NLON);
// Define coordinate netCDF variables. They will hold the
// coordinate information, that is, the latitudes and
// longitudes. An pointer to a NcVar object is returned for
// each.
NcVar *latVar = sfc.addVar(LAT_NAME, ncFloat, latDim);//creates variable
NcVar *lonVar = sfc.addVar(LON_NAME, ncFloat, lonDim);
// Write the coordinate variable data. This will put the latitudes
// and longitudes of our data grid into the netCDF file.
latVar->put(&lats[0], NLAT, 0, 0, 0, 0);
lonVar->put(&lons[0], NLON, 0, 0, 0, 0);
// Define units attributes for coordinate vars. This attaches a
// text attribute to each of the coordinate variables, containing
// the units. Note that we are not writing a trailing NULL, just
// "units", because the reading program may be fortran which does
// not use null-terminated strings. In general it is up to the
// reading C program to ensure that it puts null-terminators on
// strings where necessary.
lonVar->addAtt(UNITS,ncChar, DEGREES_EAST);
latVar->addAtt(UNITS,ncChar ,DEGREES_NORTH);
// Define the netCDF data variables.
NcVar *presVar = sfc.addVar(PRES_NAME, ncFloat, latDim, lonDim);
NcVar *tempVar = sfc.addVar(TEMP_NAME, ncFloat, latDim, lonDim);
// Define units attributes for vars.
presVar->addAtt(UNITS,ncString, string("hPa"));
tempVar->addAtt(UNITS,ncString ,string("celsius"));
// Write the pretend data. This will write our surface pressure and
// surface temperature data. The arrays of data are the same size
// as the netCDF variables we have defined.
presVar->put(&presOut[0][0], NLAT, NLON, 0, 0, 0);
tempVar->put(&tempOut[0][0], NLAT, NLON, 0, 0, 0);
// The file is automatically closed by the destructor. This frees
// up any internal netCDF resources associated with the file, and
// flushes any buffers.
cout << "*** SUCCESS writing example file " << FILE_NAME << "!" << endl;
}
catch(NcException e)
{
e.what();
}
return 0;
}
bool OutputClusters(const string &filename, const vector<Cluster> &theClusters,
const RadarData_t &radarInfo, const ClustParams_t &clustParam)
{
NcFile clusterFile(filename.c_str(), NcFile::Replace);
if (!clusterFile.is_valid())
{
cerr << "Could not create file: " << filename << "\n";
return(false);
}
size_t pixelCnt = 0;
for (vector<Cluster>::const_iterator aClust = theClusters.begin();
aClust != theClusters.end();
aClust++)
{
pixelCnt += aClust->size();
}
NcDim* pixelDim = clusterFile.add_dim("pixel_index", pixelCnt);
NcDim* latDim = clusterFile.add_dim("lat", radarInfo.dataEdges[1]);
NcDim* lonDim = clusterFile.add_dim("lon", radarInfo.dataEdges[2]);
NcVar* clustMember = clusterFile.add_var("clusterIndex", ncInt, pixelDim);
clustMember->add_att("Description", "pixel cluster membership");
NcVar* xLoc = clusterFile.add_var("pixel_xLoc", ncInt, pixelDim);
xLoc->add_att("Description", "x-index of pixel in domain (lat,lon)");
NcVar* yLoc = clusterFile.add_var("pixel_yLoc", ncInt, pixelDim);
yLoc->add_att("Description", "y-index of pixel in domain (lat,lon)");
NcVar* lats = clusterFile.add_var("lat", ncDouble, latDim);
lats->add_att("units", radarInfo.latUnits.c_str());
lats->add_att("spacing", radarInfo.latSpacing);
NcVar* lons = clusterFile.add_var("lon", ncDouble, lonDim);
lons->add_att("units", radarInfo.lonUnits.c_str());
lons->add_att("spacing", radarInfo.lonSpacing);
clusterFile.add_att("title", "SPA Cluster Results of Radar Reflectivities");
clusterFile.add_att("data_source", radarInfo.inputFilename.c_str());
clusterFile.add_att("time", radarInfo.scanTime);
// Need to do type-casting to double because the netcdf libraries can't seem to properly save a float.
// Also, the truncf() is used to -- somewhat -- handle mantisa issues.
clusterFile.add_att("Upper_Sensitivity", (double) (truncf(100.0 * clustParam.upperSensitivity)/100.0));
clusterFile.add_att("Lower_Sensitivity", (double) (truncf(100.0 * clustParam.lowerSensitivity)/100.0));
clusterFile.add_att("Padding_Level", (double) (truncf(100.0 * clustParam.paddingLevel)/100.0));
clusterFile.add_att("Reach", (double) (truncf(100.0 * clustParam.reach)/100.0));
clusterFile.add_att("Subcluster_Depth", clustParam.subClustDepth);
int* clustIndicies = new int[pixelCnt];
int* xPixels = new int[pixelCnt];
int* yPixels = new int[pixelCnt];
size_t pixelIndex = 0;
for (size_t clustIndex = 0; clustIndex < theClusters.size(); clustIndex++)
{
for (Cluster::const_iterator aMember = theClusters[clustIndex].begin();
aMember != theClusters[clustIndex].end();
aMember++, pixelIndex++)
{
clustIndicies[pixelIndex] = clustIndex;
xPixels[pixelIndex] = aMember->XLoc;
yPixels[pixelIndex] = aMember->YLoc;
}
}
clustMember->put(clustIndicies, pixelCnt);
xLoc->put(xPixels, pixelCnt);
yLoc->put(yPixels, pixelCnt);
lats->put(radarInfo.latVals, radarInfo.dataEdges[1]);
lons->put(radarInfo.lonVals, radarInfo.dataEdges[2]);
clusterFile.close();
delete [] clustIndicies;
delete [] xPixels;
delete [] yPixels;
return(true);
}
void FileArome::writeCore(std::vector<Variable::Type> iVariables) {
writeTimes();
writeReferenceTime();
writeGlobalAttributes();
for(int v = 0; v < iVariables.size(); v++) {
Variable::Type varType = iVariables[v];
std::string variable = getVariableName(varType);
NcVar* var;
if(hasVariableCore(varType)) {
var = getVar(variable);
}
else {
// Create variable
if(0) {
NcDim* dTime = getDim("time");
NcDim* dSurface = getDim("height0");
NcDim* dLon = getDim("x");
NcDim* dLat = getDim("y");
var = mFile.add_var(variable.c_str(), ncFloat, dTime, dSurface, dLat, dLon);
}
else {
NcDim* dTime = getDim("time");
NcDim* dLon = getDim("x");
NcDim* dLat = getDim("y");
var = mFile.add_var(variable.c_str(), ncFloat, dTime, dLat, dLon);
}
}
float MV = getMissingValue(var); // The output file's missing value indicator
for(int t = 0; t < mNTime; t++) {
float offset = getOffset(var);
float scale = getScale(var);
FieldPtr field = getField(varType, t);
if(field != NULL) { // TODO: Can't be null if coming from reference
float* values = new float[mNLat*mNLon];
int index = 0;
for(int lat = 0; lat < mNLat; lat++) {
for(int lon = 0; lon < mNLon; lon++) {
float value = (*field)(lat,lon,0);
if(!Util::isValid(value)) {
// Field has missing value indicator and the value is missing
// Save values using the file's missing indicator value
value = MV;
}
else {
value = ((*field)(lat,lon,0) - offset)/scale;
}
values[index] = value;
index++;
}
}
int numDims = var->num_dims();
if(numDims == 4) {
var->set_cur(t, 0, 0, 0);
var->put(values, 1, 1, mNLat, mNLon);
}
else if(numDims == 3) {
var->set_cur(t, 0, 0);
var->put(values, 1, mNLat, mNLon);
}
else {
std::stringstream ss;
ss << "Cannot write variable '" << variable << "' from '" << getFilename() << "'";
Util::error(ss.str());
}
setAttribute(var, "coordinates", "longitude latitude");
setAttribute(var, "units", Variable::getUnits(varType));
setAttribute(var, "standard_name", Variable::getStandardName(varType));
delete[] values;
}
}
setMissingValue(var, MV);
}
}