NcAtt* NcVar::get_att( NcToken aname ) const
{
NcAtt* att = new NcAtt(the_file, this, aname);
if (! att->is_valid()) {
delete att;
return 0;
}
return att;
}
int NetcdfSource::readString(QString *stringValue, const QString& stringName)
{
// TODO more error handling?
NcAtt *att = _ncfile->get_att((NcToken) stringName.toLatin1().data());
if (att) {
*stringValue = QString(att->as_string(0));
return 1;
}
delete att;
return 0;
}
void DumpableNcFile::dumpgatts( void )
{
NcAtt* ap;
for(int n = 0; ap = get_att(n); n++) {
cout << "\t\t" << ":" << ap->name() << " = " ;
NcValues* vals = ap->values();
cout << *vals << " ;" << endl ;
delete vals;
delete ap;
}
}
void dumpatts(NcVar& var)
{
NcToken vname = var.name();
NcAtt* ap;
for(int n = 0; ap = var.get_att(n); n++) {
cout << "\t\t" << vname << ":" << ap->name() << " = " ;
NcValues* vals = ap->values();
cout << *vals << " ;" << endl ;
delete ap;
delete vals;
}
}
bool NetcdfSource::initFile() {
_ncfile = new NcFile(_filename.toUtf8().data(), NcFile::ReadOnly);
if (!_ncfile->is_valid()) {
qDebug() << _filename << ": failed to open in initFile()" << endl;
return false;
}
KST_DBG qDebug() << _filename << ": building field list" << endl;
_fieldList.clear();
_fieldList += "INDEX";
int nb_vars = _ncfile->num_vars();
KST_DBG qDebug() << nb_vars << " vars found in total" << endl;
_maxFrameCount = 0;
for (int i = 0; i < nb_vars; i++) {
NcVar *var = _ncfile->get_var(i);
if (var->num_dims() == 0) {
_scalarList += var->name();
} else if (var->num_dims() == 1) {
_fieldList += var->name();
int fc = var->num_vals() / var->rec_size();
_maxFrameCount = qMax(_maxFrameCount, fc);
_frameCounts[var->name()] = fc;
} else if (var->num_dims() == 2) {
_matrixList += var->name();
}
}
// Get strings
int globalAttributesNb = _ncfile->num_atts();
for (int i = 0; i < globalAttributesNb; ++i) {
// Get only first value, should be enough for a start especially as strings are complete
NcAtt *att = _ncfile->get_att(i);
if (att) {
QString attrName = QString(att->name());
char *attString = att->as_string(0);
QString attrValue = QString(att->as_string(0));
delete[] attString;
//TODO port
//KstString *ms = new KstString(KstObjectTag(attrName, tag()), this, attrValue);
_stringList += attrName;
}
delete att;
}
// TODO update(); // necessary? slows down initial loading
return true;
}
QMap<QString, QString> DataInterfaceNetCdfVector::metaStrings(const QString& field)
{
QMap<QString, QString> fieldStrings;
QString tmpString;
NcVar *var = netcdf._ncfile->get_var(field.toLatin1().constData());
for (int i=0; i<var->num_atts(); ++i) {
NcAtt *att = var->get_att(i);
// Only handle char/unspecified attributes as fieldStrings, the others as fieldScalars
if (att->type() == NC_CHAR || att->type() == NC_UNSPECIFIED) {
fieldStrings[att->name()] = QString(att->values()->as_string(0));
}
// qDebug() << att->name() << ": " << att->values()->num() << endl;
}
return fieldStrings;
}
string GrabAttribute(const NcVar* dataVar, const int attIndex)
{
if (NULL == dataVar)
{
cerr << "ERROR: Invalid NcVar!\n";
return("");
}
NcAtt* dataAttrib = dataVar->get_att(attIndex);
if (NULL == dataAttrib)
{
cerr << "ERROR: Could not obtain data attribute: index #" << attIndex << endl;
return("");
}
const string returnVal = dataAttrib->as_string(0);
delete dataAttrib;
return(returnVal);
}
QMap<QString, double> DataInterfaceNetCdfVector::metaScalars(const QString& field)
{
QMap<QString, double> fieldScalars;
NcVar *var = netcdf._ncfile->get_var(field.toLatin1().constData());
fieldScalars["NbAttributes"] = var->num_atts();
for (int i=0; i<var->num_atts(); ++i) {
NcAtt *att = var->get_att(i);
// Only handle char attributes as fieldStrings, the others as fieldScalars
if (att->type() == NC_BYTE || att->type() == NC_SHORT || att->type() == NC_INT
|| att->type() == NC_LONG || att->type() == NC_FLOAT || att->type() == NC_DOUBLE) {
// Some attributes may have multiple values => load the first as is, and for the others
// add a -2, -3, etc... suffix as obviously we can have only one value per scalar.
// Do it in two steps to avoid a test in the loop while keeping a "clean" name for the first one
fieldScalars[QString(att->name())] = att->values()->as_double(0);
for (int j=1; j<att->values()->num(); ++j) {
fieldScalars[QString(att->name()) + QString("-") + QString::number(j+1)] = att->values()->as_double(j);
}
}
}
return fieldScalars;
}
void
avtS3DFileFormat::PopulateDatabaseMetaData(avtDatabaseMetaData *md,
int timeState)
{
debug5 << "avtS3DFileFormat::PopulateDatabaseMetaData" << endl;
// Get the metadata from the log file first.
OpenLogFile();
// Mesh
avtMeshMetaData *mesh = new avtMeshMetaData;
mesh->name = "mesh";
mesh->meshType = AVT_RECTILINEAR_MESH;
mesh->numBlocks = procs[0] * procs[1] * procs[2];
mesh->blockOrigin = 1;
mesh->cellOrigin = 0;
mesh->spatialDimension = 3;
mesh->topologicalDimension = 3;
mesh->blockTitle = "blocks";
mesh->blockPieceName = "block";
mesh->hasSpatialExtents = false;
mesh->xUnits = "mm";
mesh->yUnits = "mm";
mesh->zUnits = "mm";
md->Add(mesh);
//
// Look in the NetCDF file for the first block for the list of variables.
//
// Calculate the timestep directory that the data lives in.
char *pathcopy = strdup(mainFilename);
string dir = parse_dirname(pathcopy);
string timestepDir = CreateStringFromDouble(fileTimes[timeState]);
char path[256];
SNPRINTF(path,256,"%s%s%s%sfield.00000",dir.c_str(),VISIT_SLASH_STRING, timestepDir.c_str(), VISIT_SLASH_STRING);
NcError err(NcError::verbose_nonfatal);
NcFile nf(path);
if (!nf.is_valid())
{
EXCEPTION1(InvalidFilesException, path);
}
debug5 << "avtS3DFileFormat::PopulateDatabaseMetaData: Got valid file" << endl;
int nvars = nf.num_vars();
debug5 << "avtS3DFileFormat::PopulateDatabaseMetaData: Found " << nvars << " variables" << endl;
for (int i=0 ; i<nvars; i++)
{
NcVar *v = nf.get_var(i);
if (!v)
continue;
debug4 << "Found variable " << v->name() << endl;
// Check dimensionality
int nvals = v->num_vals();
if (nvals != 1) // Single scalars are useless.
{
avtScalarMetaData *scalar = new avtScalarMetaData();
scalar->name = v->name();
scalar->meshName = "mesh";
scalar->centering = AVT_NODECENT;
scalar->hasDataExtents = false;
scalar->treatAsASCII = false;
NcAtt *units = v->get_att(NcToken("units"));
if (units)
{
long nv = units->num_vals();
if (nv == 0)
{
scalar->hasUnits = false;
} else {
char *unitString = units->as_string(0);
scalar->units = unitString;
scalar->hasUnits = true;
}
} else
scalar->hasUnits = false;
md->Add(scalar);
} else {
debug4 << "Unable to process variable " << v->name() <<
" since it is a single scalar" << endl;
}
}
#if 0
// Expressions
Expression tempGradient_expr;
tempGradient_expr.SetName("Temperature_gradient");
tempGradient_expr.SetDefinition("gradient(Temperature)");
tempGradient_expr.SetType(Expression::VectorMeshVar);
tempGradient_expr.SetHidden(true);
md->AddExpression(&tempGradient_expr);
Expression tempUnit_expr;
tempUnit_expr.SetName("Temperature_grad_unit");
//tempUnit_expr.SetDefinition("(Temperature_gradient + {1e-6,0,0})/(magnitude(Temperature_gradient) + 1e-6)");
//tempUnit_expr.SetDefinition("Temperature_gradient/(magnitude(Temperature_gradient) + 1e-6)");
tempUnit_expr.SetDefinition("normalize(Temperature_gradient)");
tempUnit_expr.SetType(Expression::VectorMeshVar);
tempUnit_expr.SetHidden(true);
md->AddExpression(&tempUnit_expr);
Expression tempCurv_expr;
tempCurv_expr.SetName("Temperature_curvature");
tempCurv_expr.SetDefinition("divergence(Temperature_grad_unit)");
tempCurv_expr.SetType(Expression::ScalarMeshVar);
tempUnit_expr.SetHidden(false);
md->AddExpression(&tempCurv_expr);
#endif
}
RadarData_t ReadRadarFile(const string &filename,
const float latmin, const float latmax,
const float lonmin, const float lonmax)
{
RadarData_t inputData;
// Sets the internal netcdf error handling to nonfatal for this scope
NcError error_handler(NcError::verbose_nonfatal);
NcFile radarFile(filename.c_str());
if (!radarFile.is_valid())
{
cerr << "ERROR: Could not open radar file: " << filename << " for reading.\n";
// Error is indicated by the lack of initialization of
// the filename member of the struct.
return(inputData);
}
NcVar* latVar = radarFile.get_var("lat");
if (NULL == latVar)
{
cerr << "ERROR: invalid data file. No variable called 'lat'!\n";
radarFile.close();
return(inputData);
}
long latCnt = latVar->num_vals();
double* latVals = new double[latCnt];
latVar->get(latVals, latCnt);
inputData.latUnits = GrabAttribute(latVar, 0);
inputData.latSpacing = strtod(GrabAttribute(latVar, 1).c_str(), NULL);
const long minLatIndex = lower_bound(latVals, latmin, latCnt);
const long maxLatIndex = upper_bound(latVals, latmax, latCnt);
delete latVals;
latCnt = (maxLatIndex - minLatIndex) + 1;
latVar->set_cur(minLatIndex);
inputData.latVals = new double[latCnt];
latVar->get(inputData.latVals, latCnt);
NcVar* lonVar = radarFile.get_var("lon");
if (NULL == lonVar)
{
cerr << "ERROR: invalid data file. No variable called 'lon'!\n";
radarFile.close();
return(inputData);
}
long lonCnt = lonVar->num_vals();
double* lonVals = new double[lonCnt];
lonVar->get(lonVals, lonCnt);
inputData.lonUnits = GrabAttribute(lonVar, 0);
inputData.lonSpacing = strtod(GrabAttribute(lonVar, 1).c_str(), NULL);
const long minLonIndex = lower_bound(lonVals, lonmin, lonCnt);
const long maxLonIndex = upper_bound(lonVals, lonmax, lonCnt);
delete lonVals;
lonCnt = (maxLonIndex - minLonIndex) + 1;
lonVar->set_cur(minLonIndex);
inputData.lonVals = new double[lonCnt];
lonVar->get(inputData.lonVals, lonCnt);
NcVar* reflectVar = NULL;
reflectVar = radarFile.get_var("value");
if ( reflectVar == NULL )
{
// Try this variable name
reflectVar = radarFile.get_var("Reflectivity");
}
if (reflectVar == NULL)
{
cerr << "ERROR: invalid data file. No variable called 'value'!\n";
radarFile.close();
return(inputData);
}
inputData.dataEdges = reflectVar->edges(); // [0] - time, [1] - lat, [2] - lon
inputData.dataEdges[1] = latCnt;
inputData.dataEdges[2] = lonCnt;
inputData.dataVals = new double[inputData.dataEdges[0] * inputData.dataEdges[1] * inputData.dataEdges[2]];
reflectVar->set_cur(0, minLatIndex, minLonIndex);
reflectVar->get(inputData.dataVals, inputData.dataEdges);
inputData.var_LongName = GrabAttribute(reflectVar, 0);
inputData.var_Units = "dBZ";//GrabAttribute(reflectVar, 1);
NcVar* timeVar = radarFile.get_var("time");
if (NULL == timeVar)
{
cerr << "ERROR: invalid data file. No variable called 'time'!\n";
radarFile.close();
return(inputData);
}
inputData.scanTime = timeVar->as_long(0);
inputData.timeUnits = GrabAttribute(timeVar, 0);
NcAtt* titleAttrib = radarFile.get_att("title");
inputData.fileTitle = (NULL == titleAttrib ? "" : titleAttrib->as_string(0));
delete titleAttrib;
radarFile.close();
// Success!
inputData.inputFilename = filename;
return(inputData);
}
void ReadCFTimeDataFromNcFile(
NcFile * ncfile,
const std::string & strFilename,
std::vector<Time> & vecTimes,
bool fWarnOnMissingCalendar
) {
// Empty existing Time vector
vecTimes.clear();
// Get time dimension
NcDim * dimTime = ncfile->get_dim("time");
if (dimTime == NULL) {
_EXCEPTION1("Dimension \"time\" not found in file \"%s\"",
strFilename.c_str());
}
// Get time variable
NcVar * varTime = ncfile->get_var("time");
if (varTime == NULL) {
_EXCEPTION1("Variable \"time\" not found in file \"%s\"",
strFilename.c_str());
}
if (varTime->num_dims() != 1) {
_EXCEPTION1("Variable \"time\" has more than one dimension in file \"%s\"",
strFilename.c_str());
}
if (strcmp(varTime->get_dim(0)->name(), "time") != 0) {
_EXCEPTION1("Variable \"time\" does not have dimension \"time\" in file \"%s\"",
strFilename.c_str());
}
// Calendar attribute
NcAtt * attTimeCal = varTime->get_att("calendar");
std::string strCalendar;
if (attTimeCal == NULL) {
if (fWarnOnMissingCalendar) {
Announce("WARNING: Variable \"time\" is missing \"calendar\" attribute; assuming \"standard\"");
}
strCalendar = "standard";
} else {
strCalendar = attTimeCal->as_string(0);
}
Time::CalendarType eCalendarType =
Time::CalendarTypeFromString(strCalendar);
// Units attribute
NcAtt * attTimeUnits = varTime->get_att("units");
if (attTimeUnits == NULL) {
_EXCEPTION1("Variable \"time\" is missing \"units\" attribute in file \"%s\"",
strFilename.c_str());
}
std::string strTimeUnits = attTimeUnits->as_string(0);
// Load in time data
DataVector<int> vecTimeInt;
DataVector<float> vecTimeFloat;
DataVector<double> vecTimeDouble;
DataVector<ncint64> vecTimeInt64;
if (varTime->type() == ncInt) {
vecTimeInt.Initialize(dimTime->size());
varTime->set_cur((long)0);
varTime->get(&(vecTimeInt[0]), dimTime->size());
} else if (varTime->type() == ncFloat) {
vecTimeFloat.Initialize(dimTime->size());
varTime->set_cur((long)0);
varTime->get(&(vecTimeFloat[0]), dimTime->size());
} else if (varTime->type() == ncDouble) {
vecTimeDouble.Initialize(dimTime->size());
varTime->set_cur((long)0);
varTime->get(&(vecTimeDouble[0]), dimTime->size());
} else if (varTime->type() == ncInt64) {
vecTimeInt64.Initialize(dimTime->size());
varTime->set_cur((long)0);
varTime->get(&(vecTimeInt64[0]), dimTime->size());
} else {
_EXCEPTION1("Variable \"time\" has invalid type "
"(expected \"int\", \"int64\", \"float\" or \"double\")"
" in file \"%s\"", strFilename.c_str());
}
for (int t = 0; t < dimTime->size(); t++) {
Time time(eCalendarType);
if (varTime->type() == ncInt) {
time.FromCFCompliantUnitsOffsetInt(
strTimeUnits,
vecTimeInt[t]);
} else if (varTime->type() == ncFloat) {
time.FromCFCompliantUnitsOffsetDouble(
strTimeUnits,
static_cast<double>(vecTimeFloat[t]));
} else if (varTime->type() == ncDouble) {
time.FromCFCompliantUnitsOffsetDouble(
strTimeUnits,
vecTimeDouble[t]);
} else if (varTime->type() == ncInt64) {
time.FromCFCompliantUnitsOffsetInt(
strTimeUnits,
(int)(vecTimeInt64[t]));
}
vecTimes.push_back(time);
}
}
void CopyNcVarAttributes(
NcVar * varIn,
NcVar * varOut
) {
for (int a = 0; a < varIn->num_atts(); a++) {
NcAtt * att = varIn->get_att(a);
long num_vals = att->num_vals();
NcValues * pValues = att->values();
if (att->type() == ncByte) {
varOut->add_att(att->name(), num_vals,
(const ncbyte*)(pValues->base()));
} else if (att->type() == ncChar) {
varOut->add_att(att->name(), num_vals,
(const char*)(pValues->base()));
} else if (att->type() == ncShort) {
varOut->add_att(att->name(), num_vals,
(const short*)(pValues->base()));
} else if (att->type() == ncInt) {
varOut->add_att(att->name(), num_vals,
(const int*)(pValues->base()));
} else if (att->type() == ncFloat) {
varOut->add_att(att->name(), num_vals,
(const float*)(pValues->base()));
} else if (att->type() == ncDouble) {
varOut->add_att(att->name(), num_vals,
(const double*)(pValues->base()));
} else {
_EXCEPTIONT("Invalid attribute type");
}
delete pValues;
}
}
//
// Reads variable data from dump file
//
bool DataVar::initFromFile(const string& filename, const_DomainChunk_ptr dom)
{
cleanup();
#if ESYS_HAVE_NETCDF
NcError ncerr(NcError::silent_nonfatal);
NcFile* input = new NcFile(filename.c_str());
if (!input->is_valid()) {
cerr << "Could not open input file " << filename << "." << endl;
delete input;
return false;
}
NcDim* dim;
NcAtt* att;
att = input->get_att("type_id");
int typeID = att->as_int(0);
if (typeID != 2) {
cerr << "WARNING: Only expanded data supported!" << endl;
delete input;
return false;
}
att = input->get_att("rank");
rank = att->as_int(0);
dim = input->get_dim("num_data_points_per_sample");
ptsPerSample = dim->size();
att = input->get_att("function_space_type");
funcSpace = att->as_int(0);
centering = dom->getCenteringForFunctionSpace(funcSpace);
dim = input->get_dim("num_samples");
numSamples = dim->size();
#ifdef _DEBUG
cout << varName << ":\t" << numSamples << " samples, "
<< ptsPerSample << " pts/s, rank: " << rank << endl;
#endif
domain = dom;
NodeData_ptr nodes = domain->getMeshForFunctionSpace(funcSpace);
if (nodes == NULL) {
delete input;
return false;
}
meshName = nodes->getName();
siloMeshName = nodes->getFullSiloName();
initialized = true;
size_t dimSize = 1;
vector<long> counts;
if (rank > 0) {
dim = input->get_dim("d0");
int d = dim->size();
shape.push_back(d);
counts.push_back(d);
dimSize *= d;
}
if (rank > 1) {
dim = input->get_dim("d1");
int d = dim->size();
shape.push_back(d);
counts.push_back(d);
dimSize *= d;
}
if (rank > 2) {
cerr << "WARNING: Rank " << rank << " data is not supported!\n";
initialized = false;
}
if (initialized && numSamples > 0) {
sampleID.insert(sampleID.end(), numSamples, 0);
NcVar* var = input->get_var("id");
var->get(&sampleID[0], numSamples);
size_t dataSize = dimSize*numSamples*ptsPerSample;
counts.push_back(ptsPerSample);
counts.push_back(numSamples);
float* tempData = new float[dataSize];
var = input->get_var("data");
var->get(tempData, &counts[0]);
const float* srcPtr = tempData;
for (size_t i=0; i < dimSize; i++, srcPtr++) {
float* c = averageData(srcPtr, dimSize);
dataArray.push_back(c);
}
delete[] tempData;
initialized = reorderSamples();
}
delete input;
#endif // ESYS_HAVE_NETCDF
return initialized;
}
int main(void)
{
// These will hold our pressure and temperature data.
float presIn[NLAT][NLON];
float tempIn[NLAT][NLON];
// These will hold our latitudes and longitudes.
float latsIn[NLAT];
float lonsIn[NLON];
// Change the error behavior of the netCDF C++ API by creating an
// NcError object. Until it is destroyed, this NcError object will
// ensure that the netCDF C++ API silently returns error codes on
// any failure, and leaves any other error handling to the calling
// program. In the case of this example, we just exit with an
// NC_ERR error code.
NcError err(NcError::silent_nonfatal);
// Open the file and check to make sure it's valid.
NcFile dataFile("sfc_pres_temp.nc", NcFile::ReadOnly);
if(!dataFile.is_valid())
return NC_ERR;
// There are a number of inquiry functions in netCDF which can be
// used to learn about an unknown netCDF file. In this case we know
// that there are 2 netCDF dimensions, 4 netCDF variables, no
// global attributes, and no unlimited dimension.
if (dataFile.num_dims() != 2 || dataFile.num_vars() != 4 ||
dataFile.num_atts() != 0 || dataFile.rec_dim() != 0)
return NC_ERR;
// We get back a pointer to each NcVar we request. Get the
// latitude and longitude coordinate variables.
NcVar *latVar, *lonVar;
if (!(latVar = dataFile.get_var("latitude")))
return NC_ERR;
if (!(lonVar = dataFile.get_var("longitude")))
return NC_ERR;
// Read the latitude and longitude coordinate variables into arrays
// latsIn and lonsIn.
if (!latVar->get(latsIn, NLAT))
return NC_ERR;
if (!lonVar->get(lonsIn, NLON))
return NC_ERR;
// Check the coordinate variable data.
for(int lat = 0; lat < NLAT; lat++)
if (latsIn[lat] != START_LAT + 5. * lat)
return NC_ERR;
// Check longitude values.
for (int lon = 0; lon < NLON; lon++)
if (lonsIn[lon] != START_LON + 5. * lon)
return NC_ERR;
// We get back a pointer to each NcVar we request.
NcVar *presVar, *tempVar;
if (!(presVar = dataFile.get_var("pressure")))
return NC_ERR;
if (!(tempVar = dataFile.get_var("temperature")))
return NC_ERR;
// Read the data. Since we know the contents of the file we know
// that the data arrays in this program are the correct size to
// hold all the data.
if (!presVar->get(&presIn[0][0], NLAT, NLON))
return NC_ERR;
if (!tempVar->get(&tempIn[0][0], NLAT, NLON))
return NC_ERR;
// Check the data.
for (int lat = 0; lat < NLAT; lat++)
for (int lon = 0; lon < NLON; lon++)
if (presIn[lat][lon] != SAMPLE_PRESSURE + (lon * NLAT + lat)
|| tempIn[lat][lon] != SAMPLE_TEMP + .25 * (lon * NLAT + lat))
return NC_ERR;
// Each of the netCDF variables has a "units" attribute. Let's read
// them and check them.
NcAtt *att;
char *units;
if (!(att = latVar->get_att("units")))
return NC_ERR;
units = att->as_string(0);
if (strncmp(units, "degrees_north", strlen("degrees_north")))
return NC_ERR;
// Attributes and attribute values should be deleted by the caller
// when no longer needed, to prevent memory leaks.
delete units;
delete att;
if (!(att = lonVar->get_att("units")))
return NC_ERR;
units = att->as_string(0);
if (strncmp(units, "degrees_east", strlen("degrees_east")))
return NC_ERR;
delete units;
delete att;
if (!(att = presVar->get_att("units")))
return NC_ERR;
units = att->as_string(0);
if (strncmp(units, "hPa", strlen("hPa")))
return NC_ERR;
delete units;
delete att;
if (!(att = tempVar->get_att("units")))
return NC_ERR;
units = att->as_string(0);
if (strncmp(units, "celsius", strlen("celsius")))
return NC_ERR;
delete units;
delete att;
// The file will be automatically closed by the destructor. This
// frees up any internal netCDF resources associated with the file,
// and flushes any buffers.
cout << "*** SUCCESS reading example file sfc_pres_temp.nc!" << endl;
return 0;
}
bool
RemapWidget::getVolumeInfo(QString volfile,
int &skipheaderbytes,
uchar &voxelType,
int &voxelUnit,
float &vx, float &vy, float &vz,
QString &description,
QList<float> &rawMap,
QList<uchar> &pvlMap,
int &depth,
int &width,
int &height)
{
NcError err(NcError::verbose_nonfatal);
NcFile pvlFile(volfile.toAscii().data(), NcFile::ReadOnly);
if (!pvlFile.is_valid())
{
QMessageBox::information(0, "Error",
QString("%1 is not a valid preprocessed volume file").arg(volfile));
return false;
}
int i;
NcAtt *att;
char *attval;
QString pvalue;
att = pvlFile.get_att("description");
if (att)
{
attval = att->as_string(0);
description = attval;
delete [] attval;
}
att = pvlFile.get_att("voxeltype");
if (att)
{
attval = att->as_string(0);
pvalue = attval;
if (pvalue == "unsigned char")
voxelType = Raw2Pvl::_UChar;
if (pvalue == "char")
voxelType = Raw2Pvl::_Char;
if (pvalue == "unsigned short")
voxelType = Raw2Pvl::_UShort;
if (pvalue == "short")
voxelType = Raw2Pvl::_Short;
if (pvalue == "int")
voxelType = Raw2Pvl::_Int;
if (pvalue == "float")
voxelType = Raw2Pvl::_Float;
delete [] attval;
}
att = pvlFile.get_att("voxelunit");
if (att)
{
attval = att->as_string(0);
pvalue = attval;
voxelUnit = Raw2Pvl::_Nounit;
if (pvalue == "angstrom")
voxelUnit = Raw2Pvl::_Angstrom;
else if (pvalue == "nanometer")
voxelUnit = Raw2Pvl::_Nanometer;
else if (pvalue == "micron")
voxelUnit = Raw2Pvl::_Micron;
else if (pvalue == "millimeter")
voxelUnit = Raw2Pvl::_Millimeter;
else if (pvalue == "centimeter")
voxelUnit = Raw2Pvl::_Centimeter;
else if (pvalue == "meter")
voxelUnit = Raw2Pvl::_Meter;
else if (pvalue == "kilometer")
voxelUnit = Raw2Pvl::_Kilometer;
else if (pvalue == "parsec")
voxelUnit = Raw2Pvl::_Parsec;
else if (pvalue == "kiloparsec")
voxelUnit = Raw2Pvl::_Kiloparsec;
delete [] attval;
}
att = pvlFile.get_att("gridsize");
if (att)
{
depth = att->as_int(0);
width = att->as_int(1);
height = att->as_int(2);
}
att = pvlFile.get_att("voxelsize");
if (att)
{
vx = att->as_float(0);
vy = att->as_float(1);
vz = att->as_float(2);
}
att = pvlFile.get_att("skipheaderbytes");
if (att)
skipheaderbytes = att->as_int(0);
att = pvlFile.get_att("mapraw");
if (att)
{
for(i=0; i<att->num_vals(); i++)
rawMap.append(att->as_float(i));
att = pvlFile.get_att("mappvl");
for(i=0; i<att->num_vals(); i++)
pvlMap.append(att->as_ncbyte(i));
}
pvlFile.close();
return true;
}
vtkDataArray *
avtS3DFileFormat::GetVar(int timeState, int domain, const char *varname)
{
debug5 << "avtS3DFileFormat::GetVar( timeState=" << timeState << ", domain="
<< domain << ", varname=" << varname << ")" << endl;
// Calculate the timestep directory that the data lives in.
char *pathcopy = strdup(mainFilename);
string dir = parse_dirname(pathcopy);
string timestepDir = CreateStringFromDouble(fileTimes[timeState]);
debug4 << "Timestep directory is <" << timestepDir << ">" << endl;
// Figure out how big this piece is.
CalculateSubpiece(domain);
// Open up the NetCDF file.
char path[256];
SNPRINTF(path,256,"%s%s%s%sfield.%05d",dir.c_str(),VISIT_SLASH_STRING, timestepDir.c_str(), VISIT_SLASH_STRING, domain);
debug5 << "avtS3DFileFormat::GetVar: Full path to data file is " << path << endl;
NcFile nf(path);
if (!nf.is_valid())
{
debug1 << nc_strerror(NcError().get_err()) << endl;
EXCEPTION1(InvalidFilesException, path);
}
debug5 << "avtS3DFileFormat::GetVar: Got valid file." << endl;
// Pull out the appropriate variable.
NcVar *v = nf.get_var(varname);
if (!v)
{
debug1 << nc_strerror(NcError().get_err()) << endl;
EXCEPTION1(InvalidVariableException, varname);
}
// Check if it fits the size of the mesh. Always node-centered, remember.
int ntuples = localDims[0] * localDims[1] * localDims[2];
debug5 << "ntuples:" << ntuples << endl;
int nvals = v->num_vals();
if (ntuples != nvals)
{
debug1 << "The variable " << v->name() <<
" does not conform to its mesh (" << nvals << " != " <<
ntuples << ")" << endl;
EXCEPTION1(InvalidVariableException, v->name());
}
// Set up the VTK dataset.
vtkFloatArray *rv = vtkFloatArray::New();
rv->SetNumberOfTuples(ntuples);
float *p = (float*)rv->GetVoidPointer(0);
NcValues *input = v->values();
if (!input)
{
debug1 << nc_strerror(NcError().get_err()) << endl;
EXCEPTION1(InvalidVariableException, v->name());
}
// Get the scaling factor.
NcAtt *scaling = v->get_att(NcToken("scale_factor"));
float scaling_factor = 1;
if (scaling)
{
scaling_factor = scaling->as_float(0);
debug5 << "avtS3DFileFormat::GetVar: Set the scaling factor as " << scaling_factor << endl;
}
// Process the variable into the returned data.
float *base = (float*)input->base();
for(int i=0;i<ntuples;i++)
{
p[i] = *(base + i) * scaling_factor;
}
return rv;
}
int main(int argc, char** argv) {
NcError error(NcError::silent_nonfatal);
try {
// Input filename
std::string strInputFile;
// Output mesh filename
std::string strOutputFile;
// Polynomial degree per element
int nP = 2;
// Parse the command line
BeginCommandLine()
CommandLineString(strInputFile, "in", "");
CommandLineString(strOutputFile, "out", "");
//CommandLineInt(nP, "np", 2);
//CommandLineBool(fCGLL, "cgll");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
// Check file names
if (strInputFile == "") {
std::cout << "ERROR: No input file specified" << std::endl;
return (-1);
}
if (strOutputFile == "") {
std::cout << "ERROR: No output file specified" << std::endl;
return (-1);
}
if (nP < 1) {
std::cout << "ERROR: --np must be >= 2" << std::endl;
return (-1);
}
AnnounceBanner();
// Load input mesh
AnnounceStartBlock("Loading input mesh");
Mesh meshIn(strInputFile);
meshIn.RemoveZeroEdges();
AnnounceEndBlock("Done");
// Construct edge map
AnnounceStartBlock("Constructing edge map");
meshIn.ConstructEdgeMap();
AnnounceEndBlock("Done");
// Build connectivity vector using edge map
AnnounceStartBlock("Constructing connectivity");
std::vector< std::set<int> > vecConnectivity;
int err = GenerateConnectivityData(meshIn, vecConnectivity);
if (err) return err;
AnnounceEndBlock("Done");
// Open output file
AnnounceStartBlock("Writing connectivity file");
NcFile ncmesh(strInputFile.c_str(), NcFile::ReadOnly);
NcVar * varLat = ncmesh.get_var("grid_center_lat");
NcVar * varLon = ncmesh.get_var("grid_center_lon");
// Check if center latitudes and longitudes are already available
DataArray1D<double> dAllLats;
DataArray1D<double> dAllLons;
bool fConvertLatToDegrees = true;
bool fConvertLonToDegrees = true;
if ((varLat == NULL) || (varLon == NULL)) {
Announce("grid_center_lat not found, recalculating face centers");
} else {
Announce("grid_center_lat found in file, loading values");
if (varLat->get_dim(0)->size() != vecConnectivity.size()) {
_EXCEPTIONT("grid_center_lat dimension mismatch");
}
if (varLon->get_dim(0)->size() != vecConnectivity.size()) {
_EXCEPTIONT("grid_center_lon dimension mismatch");
}
dAllLats.Allocate(vecConnectivity.size());
varLat->set_cur((long)0);
varLat->get(dAllLats, vecConnectivity.size());
NcAtt * attLatUnits = varLat->get_att("units");
std::string strLatUnits = attLatUnits->as_string(0);
if (strLatUnits == "degrees") {
fConvertLatToDegrees = false;
}
dAllLons.Allocate(vecConnectivity.size());
varLon->set_cur((long)0);
varLon->get(dAllLons, vecConnectivity.size());
NcAtt * attLonUnits = varLon->get_att("units");
std::string strLonUnits = attLonUnits->as_string(0);
if (strLonUnits == "degrees") {
fConvertLonToDegrees = false;
}
}
// Write connectiivty file
FILE * fp = fopen(strOutputFile.c_str(), "w");
fprintf(fp, "%lu\n", vecConnectivity.size());
for (size_t f = 0; f < vecConnectivity.size(); f++) {
double dLon;
double dLat;
if ((varLat == NULL) || (varLon == NULL)) {
Node nodeCentroid;
for (int i = 0; i < meshIn.faces[f].edges.size(); i++) {
nodeCentroid.x += meshIn.nodes[meshIn.faces[f][i]].x;
nodeCentroid.y += meshIn.nodes[meshIn.faces[f][i]].y;
nodeCentroid.z += meshIn.nodes[meshIn.faces[f][i]].z;
}
double dMagnitude = nodeCentroid.Magnitude();
nodeCentroid.x /= dMagnitude;
nodeCentroid.y /= dMagnitude;
nodeCentroid.z /= dMagnitude;
dLon = atan2(nodeCentroid.y, nodeCentroid.x);
dLat = asin(nodeCentroid.z);
if (dLon < 0.0) {
dLon += 2.0 * M_PI;
}
} else {
dLon = dAllLons[f];
dLat = dAllLats[f];
}
if (fConvertLonToDegrees) {
dLon *= 180.0 / M_PI;
}
if (fConvertLatToDegrees) {
dLat *= 180.0 / M_PI;
}
fprintf(fp, "%1.14f,", dLon);
fprintf(fp, "%1.14f,", dLat);
fprintf(fp, "%lu", vecConnectivity[f].size());
std::set<int>::const_iterator iter = vecConnectivity[f].begin();
for (; iter != vecConnectivity[f].end(); iter++) {
fprintf(fp, ",%i", *iter);
}
if (f != vecConnectivity.size()-1) {
fprintf(fp,"\n");
}
}
fclose(fp);
AnnounceEndBlock("Done");
// Announce
AnnounceBanner();
return (0);
} catch(Exception & e) {
Announce(e.ToString().c_str());
return (-1);
} catch(...) {
return (-2);
}
}
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();
}
void PolygonManager::init()
{
string fileName;
ConfigTools::read("parcel_polygon_file", fileName);
NOTICE("PolygonManager::init", "Reading polygons from \""+fileName+"\" ...");
NcFile file(fileName.c_str(), NcFile::ReadOnly);
if (!file.is_valid()) {
REPORT_ERROR(string("Failed to open file "+fileName+"."))
}
NcError ncError(NcError::silent_nonfatal);
if (TimeManager::onLine()) {
NcAtt *timeAtt = file.get_att("time");
NcAtt *timeStepAtt = file.get_att("time_step");
NcAtt *stepsAtt = file.get_att("steps");
if (timeAtt != NULL && timeStepAtt != NULL && stepsAtt != NULL) {
TimeManager::reset();
double dt = timeStepAtt->as_double(0);
double second = timeAtt->as_double(0);
double steps = stepsAtt->as_int(0);
TimeManager::setClock(dt, second, steps);
}
}
NcDim *numVertexDim = file.get_dim("num_total_vertex");
if (numVertexDim == NULL) {
Message message;
message << "Failed to find \"num_total_vertex\" dimension in file \"";
message << fileName << "\"!";
REPORT_ERROR(message.str());
}
NcDim *numEdgeDim = file.get_dim("num_total_edge");
if (numEdgeDim == NULL) {
Message message;
message << "Failed to find \"num_total_edge\" dimension in file \"";
message << fileName << "\"!";
REPORT_ERROR(message.str());
}
NcDim *numPolygonDim = file.get_dim("num_total_polygon");
if (numPolygonDim == NULL) {
Message message;
message << "Failed to find \"num_total_polygon\" dimension in file \"";
message << fileName << "\"!";
REPORT_ERROR(message.str());
}
int numVertex = static_cast<int>(numVertexDim->size());
int numEdge = static_cast<int>(numEdgeDim->size());
int numPolygon = static_cast<int>(numPolygonDim->size());
// -------------------------------------------------------------------------
// vertices part
vertices.create(numVertex);
double *oldVtxLon = new double[numVertex];
double *oldVtxLat = new double[numVertex];
double *oldVtxLev = new double[numVertex];
double *newVtxLon = new double[numVertex];
double *newVtxLat = new double[numVertex];
double *newVtxLev = new double[numVertex];
file.get_var("old_vertex_lon")->get(oldVtxLon, numVertex);
file.get_var("old_vertex_lat")->get(oldVtxLat, numVertex);
file.get_var("new_vertex_lon")->get(newVtxLon, numVertex);
file.get_var("new_vertex_lat")->get(newVtxLat, numVertex);
if (file.get_var("old_vertex_lev") != NULL) {
file.get_var("old_vertex_lev")->get(oldVtxLev, numVertex);
file.get_var("new_vertex_lev")->get(newVtxLev, numVertex);
} else {
for (int i = 0; i < vertices.size(); ++i) {
oldVtxLev[i] = 0.0;
newVtxLev[i] = 0.0;
}
}
// change the units from degree to rad
for (int i = 0; i < numVertex; ++i) {
oldVtxLon[i] /= Rad2Deg;
oldVtxLat[i] /= Rad2Deg;
newVtxLon[i] /= Rad2Deg;
newVtxLat[i] /= Rad2Deg;
}
Vertex *vertexMap[vertices.size()];
Vertex *vertex = vertices.front();
for (int i = 0; i < vertices.size(); ++i) {
vertexMap[i] = vertex;
vertex->setCoordinate(newVtxLon[i], newVtxLat[i], newVtxLev[i], NewTimeLevel);
vertex->setCoordinate(oldVtxLon[i], oldVtxLat[i], oldVtxLev[i], OldTimeLevel);
vertex = vertex->next;
}
delete [] newVtxLon;
delete [] newVtxLat;
delete [] newVtxLev;
delete [] oldVtxLon;
delete [] oldVtxLat;
delete [] oldVtxLev;
// -------------------------------------------------------------------------
// edges part
edges.create(numEdge);
int *firstPoint = new int[numEdge];
int *secondPoint = new int[numEdge];
file.get_var("first_point_idx")->get(firstPoint, numEdge);
file.get_var("second_point_idx")->get(secondPoint, numEdge);
Edge *edgeMap[edges.size()];
Edge *edge = edges.front();
for (int i = 0; i < edges.size(); ++i) {
edgeMap[i] = edge;
edge->linkEndPoint(FirstPoint, vertexMap[firstPoint[i]-1]);
edge->linkEndPoint(SecondPoint, vertexMap[secondPoint[i]-1]);
edge->calcNormVector();
edge = edge->next;
}
delete [] firstPoint;
delete [] secondPoint;
// test point
double *oldTestLon = new double[numEdge];
double *oldTestLat = new double[numEdge];
double *newTestLon = new double[numEdge];
double *newTestLat = new double[numEdge];
file.get_var("old_testpoint_lon")->get(oldTestLon, numEdge);
file.get_var("old_testpoint_lat")->get(oldTestLat, numEdge);
file.get_var("new_testpoint_lon")->get(newTestLon, numEdge);
file.get_var("new_testpoint_lat")->get(newTestLat, numEdge);
for (int i = 0; i < numEdge; ++i) {
oldTestLon[i] /= Rad2Deg;
oldTestLat[i] /= Rad2Deg;
newTestLon[i] /= Rad2Deg;
newTestLat[i] /= Rad2Deg;
}
edge = edges.front();
for (int i = 0; i < numEdge; ++i) {
Vertex *testPoint = edge->getTestPoint();
testPoint->setCoordinate(oldTestLon[i], oldTestLat[i], OldTimeLevel);
testPoint->setCoordinate(newTestLon[i], newTestLat[i], NewTimeLevel);
edge = edge->next;
}
delete [] oldTestLon;
delete [] oldTestLat;
delete [] newTestLon;
delete [] newTestLat;
// -------------------------------------------------------------------------
// polygons part
polygons.create(numPolygon);
int edgeNum[numPolygon];
file.get_var("edge_num")->get(edgeNum, numPolygon);
int numEdgeIdx = static_cast<int>(file.get_dim("num_edge_idx")->size());
int *edgeIdx = new int[numEdgeIdx];
int *edgeOnt = new int[numEdgeIdx];
file.get_var("edge_idx")->get(edgeIdx, numEdgeIdx);
file.get_var("edge_ont")->get(edgeOnt, numEdgeIdx);
Polygon *polygon = polygons.front();
int counter = 0;
for (int i = 0; i < polygons.size(); ++i) {
for (int j = 0; j < edgeNum[i]; ++j) {
OrientStatus orient;
if (edgeOnt[counter] == 0) {
orient = OrientLeft;
} else if (edgeOnt[counter] == 1) {
orient = OrientRight;
} else {
string message = "Invalid edge_ont in file "+fileName+".";
REPORT_ERROR(message.c_str());
}
edgeMap[edgeIdx[counter]-1]->linkPolygon(orient, polygon);
counter++;
}
polygon->edgePointers.ring();
// calculate the angles
EdgePointer *edgePointer = polygon->edgePointers.front();
for (int j = 0; j < polygon->edgePointers.size(); ++j) {
edgePointer->calcAngle();
edgePointer = edgePointer->next;
}
polygon->calcArea();
polygon = polygon->next;
}
delete [] edgeIdx;
delete [] edgeOnt;
// -------------------------------------------------------------------------
file.close();
}
eavlNetCDFImporter::eavlNetCDFImporter(const string &filename)
{
file = new NcFile(filename.c_str(), NcFile::ReadOnly);
if (!file->is_valid())
{
THROW(eavlException,"Couldn't open file!\n");
}
if (debugoutput) cerr << "num_dims="<<file->num_dims()<<endl;
if (debugoutput) cerr << "num_vars="<<file->num_vars()<<endl;
if (debugoutput) cerr << "num_atts="<<file->num_atts()<<endl;
for (int i=0; i<file->num_dims(); i++)
{
NcDim *d = file->get_dim(i);
if (debugoutput) cerr << " dim["<<i<<"]: name="<<d->name()<<" size="<<d->size()<<endl;
}
for (int i=0; i<file->num_atts(); i++)
{
NcAtt *a = file->get_att(i);
if (debugoutput) cerr << " att["<<i<<"]: name="<<a->name()<<" numvals="<<a->num_vals()<<endl;
}
bool found_grid = false;
for (int i=0; i<file->num_vars(); i++)
{
NcVar *v = file->get_var(i);
if (debugoutput)
{
cerr << " var["<<i<<"]: name="<<v->name();
cerr << " ndims="<<v->num_dims();
cerr << " dims = ";
for (int j=0; j<v->num_dims(); j++)
{
cerr << v->get_dim(j)->name();
if (j<v->num_dims()-1)
cerr << "*";
}
cerr << endl;
}
// Here's the condition for what we're going to use;
// we only support one mesh for the moment, so we're picking one.
// Also, the netcdf files we have have the time dim size as "1"
if (v->num_dims() == 4 && string(v->get_dim(0)->name())=="time")
{
if (!found_grid)
{
dims.push_back(v->get_dim(1));
dims.push_back(v->get_dim(2));
dims.push_back(v->get_dim(3));
found_grid = true;
vars.push_back(v);
if (debugoutput) cerr << " * using as first real var\n";
}
else
{
if (string(v->get_dim(1)->name()) == dims[0]->name() &&
string(v->get_dim(2)->name()) == dims[1]->name() &&
string(v->get_dim(3)->name()) == dims[2]->name())
{
vars.push_back(v);
if (debugoutput) cerr << " * using as another var; matches the first real one's dims\n";
}
}
}
}
}
bool
NetworkObject::loadNetCDF(QString flnm)
{
m_fileName = flnm;
NcError err(NcError::verbose_nonfatal);
NcFile ncfFile(flnm.toLatin1().data(), NcFile::ReadOnly);
NcAtt *att;
NcVar *var;
// ---- get gridsize -----
att = ncfFile.get_att("gridsize");
m_nX = att->as_int(0);
m_nY = att->as_int(1);
m_nZ = att->as_int(2);
//------------------------
// ---- get vertex centers -----
var = ncfFile.get_var("vertex_centers");
if (!var)
var = ncfFile.get_var("vertex_center");
if (!var)
var = ncfFile.get_var("vertex_centres");
if (!var)
var = ncfFile.get_var("vertex_centre");
int nv = var->get_dim(0)->size();
float *vc = new float [3*nv];
var->get(vc, nv, 3);
m_vertexCenters.resize(nv);
for(int i=0; i<nv; i++)
m_vertexCenters[i] = Vec(vc[3*i+0], vc[3*i+1], vc[3*i+2]);
delete [] vc;
//------------------------
// ---- get edges -----
var = ncfFile.get_var("edge_neighbours");
int ne = var->get_dim(0)->size();
int *ed = new int [2*ne];
var->get(ed, ne, 2);
m_edgeNeighbours.resize(ne);
for(int i=0; i<ne; i++)
m_edgeNeighbours[i] = qMakePair(ed[2*i], ed[2*i+1]);
delete [] ed;
//------------------------
Vec bmin = m_vertexCenters[0];
Vec bmax = m_vertexCenters[0];
for(int i=0; i<m_vertexCenters.count(); i++)
{
bmin = StaticFunctions::minVec(bmin, m_vertexCenters[i]);
bmax = StaticFunctions::maxVec(bmax, m_vertexCenters[i]);
}
m_centroid = (bmin + bmax)/2;
m_enclosingBox[0] = Vec(bmin.x, bmin.y, bmin.z);
m_enclosingBox[1] = Vec(bmax.x, bmin.y, bmin.z);
m_enclosingBox[2] = Vec(bmax.x, bmax.y, bmin.z);
m_enclosingBox[3] = Vec(bmin.x, bmax.y, bmin.z);
m_enclosingBox[4] = Vec(bmin.x, bmin.y, bmax.z);
m_enclosingBox[5] = Vec(bmax.x, bmin.y, bmax.z);
m_enclosingBox[6] = Vec(bmax.x, bmax.y, bmax.z);
m_enclosingBox[7] = Vec(bmin.x, bmax.y, bmax.z);
// QStringList vatt, eatt;
int nvars = ncfFile.num_vars();
// for (int i=0; i < nvars; i++)
// {
// var = ncfFile.get_var(i);
// QString attname = var->name();
// attname.toLower();
// if (attname.contains("vertex_") &&
// ( attname != "vertex_centers" ||
// attname != "vertex_centres"))
// vatt.append(attname);
// else if (attname.contains("edge_") &&
// attname != "edge_neighbours")
// eatt.append(attname);
// }
m_vertexAttribute.clear();
m_edgeAttribute.clear();
m_vertexRadiusAttribute = -1;
m_edgeRadiusAttribute = -1;
int vri = 0;
int eri = 0;
for (int i=0; i < nvars; i++)
{
var = ncfFile.get_var(i);
QString attname = var->name();
attname.toLower();
if (attname.contains("vertex_") &&
attname != "vertex_center" &&
attname != "vertex_centre" &&
attname != "vertex_centers" &&
attname != "vertex_centres")
{
if (attname == "vertex_radius")
m_vertexRadiusAttribute = vri;
vri++;
QVector<float> val;
val.clear();
if (var->type() == ncByte || var->type() == ncChar)
{
uchar *v = new uchar[nv];
var->get((ncbyte *)v, nv);
for(int j=0; j<nv; j++)
val.append(v[j]);
delete [] v;
}
else if (var->type() == ncShort)
{
short *v = new short[nv];
var->get((short *)v, nv);
for(int j=0; j<nv; j++)
val.append(v[j]);
delete [] v;
}
else if (var->type() == ncInt)
{
int *v = new int[nv];
var->get((int *)v, nv);
for(int j=0; j<nv; j++)
val.append(v[j]);
delete [] v;
}
else if (var->type() == ncFloat)
{
float *v = new float[nv];
var->get((float *)v, nv);
for(int j=0; j<nv; j++)
val.append(v[j]);
delete [] v;
}
if (val.count() > 0)
m_vertexAttribute.append(qMakePair(attname, val));
}
else if (attname.contains("edge_") &&
attname != "edge_neighbours")
{
if (attname == "edge_radius")
m_edgeRadiusAttribute = eri;
eri++;
QVector<float> val;
val.clear();
if (var->type() == ncByte || var->type() == ncChar)
{
uchar *v = new uchar[ne];
var->get((ncbyte *)v, ne);
for(int j=0; j<ne; j++)
val.append(v[j]);
delete [] v;
}
else if (var->type() == ncShort)
{
short *v = new short[ne];
var->get((short *)v, ne);
for(int j=0; j<ne; j++)
val.append(v[j]);
delete [] v;
}
else if (var->type() == ncInt)
{
int *v = new int[ne];
var->get((int *)v, ne);
for(int j=0; j<ne; j++)
val.append(v[j]);
delete [] v;
}
else if (var->type() == ncFloat)
{
float *v = new float[ne];
var->get((float *)v, ne);
for(int j=0; j<ne; j++)
val.append(v[j]);
delete [] v;
}
if (val.count() > 0)
m_edgeAttribute.append(qMakePair(attname, val));
}
}
ncfFile.close();
if (!Global::batchMode())
{
QString str;
str = QString("Grid Size : %1 %2 %3\n").arg(m_nX).arg(m_nY).arg(m_nZ);
str += QString("Vertices : %1\n").arg(m_vertexCenters.count());
str += QString("Edges : %1\n").arg(m_edgeNeighbours.count());
str += QString("\n");
str += QString("Vertex Attributes : %1\n").arg(m_vertexAttribute.count());
for(int i=0; i<m_vertexAttribute.count(); i++)
str += QString(" %1\n").arg(m_vertexAttribute[i].first);
str += QString("\n");
str += QString("Edge Attributes : %1\n").arg(m_edgeAttribute.count());
for(int i=0; i<m_edgeAttribute.count(); i++)
str += QString(" %1\n").arg(m_edgeAttribute[i].first);
QMessageBox::information(0, "Network loaded", str);
}
m_Vatt = 0;
m_Eatt = 0;
m_Vminmax.clear();
m_Eminmax.clear();
m_userVminmax.clear();
m_userEminmax.clear();
for(int i=0; i<m_vertexAttribute.count(); i++)
{
float vmin = m_vertexAttribute[i].second[0];
float vmax = m_vertexAttribute[i].second[0];
for(int j=1; j<m_vertexAttribute[i].second.count(); j++)
{
vmin = qMin((float)m_vertexAttribute[i].second[j], vmin);
vmax = qMax((float)m_vertexAttribute[i].second[j], vmax);
}
m_Vminmax.append(qMakePair(vmin, vmax));
m_userVminmax.append(qMakePair((vmin+vmax)/2, vmax));
}
for(int i=0; i<m_edgeAttribute.count(); i++)
{
float emin = m_edgeAttribute[i].second[0];
float emax = m_edgeAttribute[i].second[0];
for(int j=1; j<m_edgeAttribute[i].second.count(); j++)
{
emin = qMin((float)m_edgeAttribute[i].second[j], emin);
emax = qMax((float)m_edgeAttribute[i].second[j], emax);
}
m_Eminmax.append(qMakePair(emin, emax));
m_userEminmax.append(qMakePair((emin+emax)/2, emax));
}
return true;
}
