//TODO optimize this thing
void writeResultsFile(string dataFileName, string yDimension, vector<double> * pValues)
{
NcFile file(dataFileName.c_str(), NcFile::ReadOnly);
NcVar *geneNames = file.get_var("gene");
int dataYsize = file.get_dim(yDimension.c_str())->size();
FILE * pFile;
pFile = fopen ("results.txt","w");
cout << "Writing results to file.." << endl;
int percentage = dataYsize / 10;
int percentageCount = 10;
for(int i = 0; i < dataYsize; i++){
char * c = geneNames->as_string(i*28);
std::string str;
if(pValues->at(i) > 0.05){
std::ostringstream strs;
strs << pValues->at(i);
str = strs.str();
}else{
str = "NA";
}
fprintf (pFile, "%-20s-%20s", c, str.c_str());
fprintf (pFile, "\n");
if(i == percentage)
{
cout << percentageCount << "% complete" << endl;
percentageCount += 10;
percentage += dataYsize / 10;
}
delete c;
}
fclose(pFile);
}
FieldPtr FileArome::getFieldCore(std::string iVariable, int iTime) const {
// Not cached, retrieve data
NcVar* var = getVar(iVariable);
int nLat = mNLat;
int nLon = mNLon;
int numDims = var->num_dims();
long* count;
long totalCount = nLat*nLon;
if(numDims == 4) {
// Variable has a surface dimension
count = new long[4];
count[0] = 1;
count[1] = 1;
count[2] = nLat;
count[3] = nLon;
var->set_cur(iTime, 0, 0, 0);
}
else if(numDims == 3) {
count = new long[3];
count[0] = 1;
count[1] = nLat;
count[2] = nLon;
var->set_cur(iTime, 0, 0);
}
else {
std::stringstream ss;
ss << "Cannot read variable '" << iVariable << "' from '" << getFilename() << "'";
Util::error(ss.str());
}
float* values = new float[nLat*nLon];
var->get(values, count);
float MV = getMissingValue(var);
float offset = getOffset(var);
float scale = getScale(var);
int index = 0;
FieldPtr field = getEmptyField();
for(int lat = 0; lat < nLat; lat++) {
for(int lon = 0; lon < nLon; lon++) {
float value = values[index];
assert(index < totalCount);
if(value == MV) {
// Field has missing value indicator and the value is missing
// Save values using our own internal missing value indicator
value = Util::MV;
}
else {
value = scale*values[index] + offset;
}
(*field)(lat,lon,0) = value;
index++;
}
}
delete[] values;
delete[] count;
return field;
}
int NetcdfSource::readScalar(double *v, const QString& field)
{
// TODO error handling
QByteArray bytes = field.toLatin1();
NcVar *var = _ncfile->get_var(bytes.constData()); // var is owned by _ncfile
var->get(v);
return 1;
}
void NetCdfConfigureDialog::setVariableSelect()
{
for (int i=0; i<(_currentFile->num_vars()); i++)
{
NcVar *focusedVar = _currentFile->get_var(i);
if (focusedVar->num_dims() > 0) comboBoxVariable->addItem(focusedVar->name());
}
}
Var( const NcVar* var ):
m_var( var )
{
const int ndims = m_var->num_dims();
for ( int i = 0; i < ndims; i++ )
{
m_dims.push_back( new Dim( m_var->get_dim(i) ) );
}
}
std::vector<T> read_vector(NcFile &nc, std::string const &var_name)
{
// Read points vector
NcVar *vpoints = nc.get_var(var_name.c_str());
long npoints = vpoints->get_dim(0)->size();
std::vector<T> points(npoints);
vpoints->get(&points[0], npoints);
return points;
}
void DumpableNcFile::dumpdata( )
{
NcVar* vp;
for (int n = 0; vp = get_var(n); n++) {
cout << " " << vp->name() << " = ";
NcValues* vals = vp->values();
cout << *vals << " ;" << endl ;
delete vals;
}
}
bool ReadAstro::open(const char *path)
{
assert(!m_ncfile);
m_ncfile = new NcFile(path, NcFile::ReadOnly);
if (!m_ncfile->is_valid())
{
close();
sendError("failed to open NetCDF file %s", path);
return false;
}
if (m_ncfile->get_format() == NcFile::BadFormat)
{
close();
sendError("bad NetCDF file");
return false;
}
fprintf(stderr, "dims=%d, vars=%d, attrs=%d\n",
m_ncfile->num_dims(), m_ncfile->num_vars(), m_ncfile->num_atts());
for (int i = 0; i < m_ncfile->num_dims(); ++i)
{
fprintf(stderr, "%s: %ld\n",
m_ncfile->get_dim(i)->name(),
m_ncfile->get_dim(i)->size());
}
for (int i = 0; i < m_ncfile->num_vars(); ++i)
{
fprintf(stderr, "%s: dims=%d atts=%d vals=%ld type=%d\n",
m_ncfile->get_var(i)->name(),
m_ncfile->get_var(i)->num_dims(),
m_ncfile->get_var(i)->num_atts(),
m_ncfile->get_var(i)->num_vals(),
m_ncfile->get_var(i)->type());
//int dims = m_ncfile->get_var(i)->num_dims();
NcVar *var = m_ncfile->get_var(i);
for (int j = 0; j < var->num_dims(); ++j)
{
fprintf(stderr, " %s: %ld edge=%ld\n",
var->get_dim(j)->name(),
var->get_dim(j)->size(),
var->edges()[j]);
}
}
for (int i = 0; i < m_ncfile->num_atts(); ++i)
{
fprintf(stderr, "%s\n", m_ncfile->get_att(i)->name());
}
return true;
}
vector<string>
eavlNetCDFImporter::GetFieldList(const string &mesh)
{
vector<string> retval;
for (unsigned int v=0; v<vars.size(); v++)
{
NcVar *var = vars[v];
retval.push_back(var->name());
}
return retval;
}
int NetcdfSource::samplesPerFrame(const QString& field) {
if (field.toLower() == "index") {
return 1;
}
QByteArray bytes = field.toLatin1();
NcVar *var = _ncfile->get_var(bytes.constData());
if (!var) {
return 0;
}
return var->rec_size();
}
int NetCdfConfigureDialog::getTimeStep()
{
NcVar* timeVar = _currentFile->get_var(comboBoxDim2->currentIndex());
const double datesToMinutes = convertDateToMinutes(_currentInitialDateTime,dateTimeEditDim3->date(),dateTimeEditDim3->time());
double timeArray[1] = {datesToMinutes};
double currentTime = timeVar->get_index(timeArray);
if (currentTime < 0) currentTime=0; //if the value isn't found in the array, set it to 0 as default...
return currentTime;
}
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;
}
}
int main(int argc, char *argv[])
{
NcFile at(atpath, NcFile::ReadOnly);
if(!at.is_valid() || at.num_dims() != 3 || at.num_vars() != 4) {
fprintf(stderr, "failed reading file: %s\n", atpath);
return 1;
}
NcVar* data = at.get_var("rhum");
if(!data->is_valid() || data->num_dims() != 3) {
fprintf(stderr, "rhum has incorrect dimensions");
return 1;
}
NcDim* time = data->get_dim(0);
int timecnt = time->size();
float *rhumd = new float[timecnt*LATS*LONS];
data->get(rhumd, timecnt, LATS, LONS);
float rhumdmon[12][LATS][LONS];
for(int i = 0; i<LATS; i++)
for(int j = 0; j<LONS; j++) {
float rhumdmoncnt[12];
for(int k = 0; k<12; k++) {
rhumdmon[k][i][j] = 0;
rhumdmoncnt[k] = 0;
}
for(int k = 0; k<timecnt; k++) {
double v = rhumd[(k*LATS+i)*LONS+j]*.1 + 3276.5;
if(v >= 0 && v <= 100) {
rhumdmon[k%12][i][j] += v;
rhumdmoncnt[k%12]++;
}
}
for(int k = 0; k<12; k++)
rhumdmon[k][i][j] /= rhumdmoncnt[k];
}
delete [] rhumd;
/* use a single byte instead of 2 to save memory,
resolution of 1/5th of a mm/day resolution */
uint8_t rhumbyte[12][LATS][LONS];
for(int i = 0; i<12; i++)
for(int j = 0; j<LATS; j++)
for(int k = 0; k<LONS; k++)
if(isnan(rhumdmon[i][j][k]) || fabs(rhumdmon[i][j][k]) > 100)
rhumbyte[i][j][k] = 255;
else
rhumbyte[i][j][k] = rhumdmon[i][j][k]*2.0;
fwrite(rhumbyte, sizeof rhumbyte, 1, stdout);
return 0;
}
void ConstantSet::read_from_netcdf(NcFile &nc, std::string const &vname)
{
NcVar *ncvar = giss::get_var_safe(nc, vname.c_str(), true);
if (!ncvar) {
fprintf(stderr, "ConstantSet::read_from_netcdf() cannot find variable %s\n", vname.c_str());
throw std::exception();
}
int n = ncvar->num_atts();
// Read through the attributes, getting units and names separately
std::map<std::string, std::string> units;
std::map<std::string, double> consts;
std::map<std::string, std::string> descriptions;
for (int i=0; i<n; ++i) {
auto att = giss::get_att(ncvar, i);
std::string att_name(att->name());
if (giss::ends_with(att_name, "_description")) {
descriptions.insert(std::make_pair(
att_name.substr(0, att_name.size() - std::strlen("_description")),
std::string(att->as_string(0))));
} else if (giss::ends_with(att_name, "_units")) {
units.insert(std::make_pair(
att_name.substr(0, att_name.size() - std::strlen("_units")),
std::string(att->as_string(0))));
} else {
consts.insert(std::make_pair(
att_name, att->as_double(0)));
}
}
// Now go through them again, matching up constants and units
for (auto ii = consts.begin(); ii != consts.end(); ++ii) {
std::string const &name = ii->first;
double const val = ii->second;
auto ui = units.find(name);
if (ui == units.end()) {
fprintf(stderr, "Could not find _units attribute for %s\n", name.c_str());
}
auto di = descriptions.find(name);
if (di == descriptions.end()) {
fprintf(stderr, "Could not find _description attribute for %s\n", name.c_str());
}
std::string const &u = units.find(name)->second;
std::string const &d = descriptions.find(name)->second;
set(name, val, u, d);
}
}
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;
@}
void LoadMetaDataFile(
const std::string & strInputMeta,
DataMatrix3D<int> & dataGLLNodes,
DataMatrix3D<double> & dataGLLJacobian
) {
NcFile ncMeta(strInputMeta.c_str(), NcFile::ReadOnly);
NcDim * dimNp = ncMeta.get_dim("np");
if (dimNp == NULL) {
_EXCEPTIONT("Dimension \"np\" missing from metadata file");
}
NcDim * dimNelem = ncMeta.get_dim("nelem");
if (dimNelem == NULL) {
_EXCEPTIONT("Dimension \"nelem\" missing from metadata file");
}
NcVar * varGLLNodes = ncMeta.get_var("GLLnodes");
if (dimNelem == NULL) {
_EXCEPTIONT("Variable \"GLLnodes\" missing from metadata file");
}
NcVar * varGLLJacobian = ncMeta.get_var("J");
if (dimNelem == NULL) {
_EXCEPTIONT("Variable \"J\" missing from metadata file");
}
int nP = dimNp->size();
int nElem = dimNelem->size();
DataMatrix3D<int> dataGLLNodes_tmp;
DataMatrix3D<double> dataGLLJacobian_tmp;
dataGLLNodes.Initialize(nP, nP, nElem);
dataGLLJacobian.Initialize(nP, nP, nElem);
dataGLLNodes_tmp.Initialize(nP, nP, nElem);
dataGLLJacobian_tmp.Initialize(nP, nP, nElem);
varGLLNodes->get(&(dataGLLNodes_tmp[0][0][0]), nP, nP, nElem);
varGLLJacobian->get(&(dataGLLJacobian_tmp[0][0][0]), nP, nP, nElem);
for (int i = 0; i < nP; i++) {
for (int j = 0; j < nP; j++) {
for (int k = 0; k < nElem; k++) {
dataGLLNodes[i][j][k] = dataGLLNodes_tmp[j][i][k];
dataGLLJacobian[i][j][k] = dataGLLJacobian_tmp[j][i][k];
}
}
}
}
//YUAN: recid - the order (from ZERO) in the .nc file, chtid - the cohort id
int SiteinInputer::getRecID(const int &siteid){
NcError err(NcError::silent_nonfatal);
NcFile siteFile(siteinfname.c_str(), NcFile::ReadOnly);
NcVar* siteidV = siteFile.get_var("CHTID");
int id = -1;
for (int i=0; i<(int)siteidV->num_vals(); i++){
siteidV->set_cur(i);
siteidV->get(&id, 1);
if(id==siteid) return i;
}
return -1;
}
FileArome::FileArome(std::string iFilename, bool iReadOnly) : FileNetcdf(iFilename, iReadOnly) {
// Set dimensions
NcDim* dTime = getDim("time");
NcDim* dLon = getDim("x");
NcDim* dLat = getDim("y");
mNTime = dTime->size();
mNLat = dLat->size();
mNLon = dLon->size();
mNEns = 1;
mLats = getLatLonVariable("latitude");
mLons = getLatLonVariable("longitude");
if(hasVariableCore("surface_geopotential")) {
FieldPtr elevField = getFieldCore("surface_geopotential", 0);
mElevs.resize(getNumLat());
for(int i = 0; i < getNumLat(); i++) {
mElevs[i].resize(getNumLon());
for(int j = 0; j < getNumLon(); j++) {
float value = (*elevField)(i,j,0) / 9.81;
mElevs[i][j] = value;
}
}
std::cout << "Deriving altitude from geopotential height in " << getFilename() << std::endl;
}
else {
mElevs = getLatLonVariable("altitude");
}
if(hasVar("time")) {
NcVar* vTime = getVar("time");
double* times = new double[mNTime];
vTime->get(times , mNTime);
setTimes(std::vector<double>(times, times+mNTime));
delete[] times;
}
else {
std::vector<double> times;
times.resize(getNumTime(), Util::MV);
setTimes(times);
}
if(hasVar("forecast_reference_time")) {
NcVar* vReferenceTime = getVar("forecast_reference_time");
double referenceTime = getReferenceTime();
vReferenceTime->get(&referenceTime, 1);
setReferenceTime(referenceTime);
}
Util::status( "File '" + iFilename + " 'has dimensions " + getDimenionString());
}
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;
}
int main()
{
// 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;
// The default behavior of the C++ API is to throw an exception i
// an error occurs. A try catch block is necessary.
try
{
// Create the file. The Replace parameter tells netCDF to overwrite
// this file, if it already exists.
NcFile dataFile("simple_xy.nc", NcFile::replace);
// Create netCDF dimensions
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).
vector<NcDim> dims;
dims.push_back(xDim);
dims.push_back(yDim);
NcVar data = dataFile.addVar("data", ncInt, dims);
// Write the 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.putVar(dataOut);
// 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;
}
catch(NcException& e)
{e.what();
return NC_ERR;
}
}
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;
}
void Regioner::createCohorList4Run(){
// read in a list of cohorts to run
//netcdf error
NcError err(NcError::silent_nonfatal);
//open file and check if valid
string filename = md.runchtfile;
NcFile runFile(filename.c_str(), NcFile::ReadOnly);
if(!runFile.is_valid()){
string msg = filename+" is not valid";
char* msgc = const_cast< char* > ( msg.c_str());
throw Exception(msgc, I_NCFILE_NOT_EXIST);
}
NcDim* chtD = runFile.get_dim("CHTID");
if(!chtD->is_valid()){
string msg="CHT Dimension is not valid in createCohortList4Run";
char* msgc = const_cast<char*> (msg.c_str());
throw Exception(msgc, I_NCDIM_NOT_EXIST);
}
NcVar* chtV = runFile.get_var("CHTID");
if(chtV==NULL){
string msg="Cannot get CHTID in createCohortList4Run ";
char* msgc = const_cast<char*> (msg.c_str());
throw Exception(msgc, I_NCVAR_NOT_EXIST);
}
int numcht = chtD->size();
int chtid = -1;
int chtid0 = -1;
int chtidx = -1;
for (int i=0; i<numcht; i++){
chtV->set_cur(i);
chtV->get(&chtid, 1);
runchtlist.push_back(chtid);
if (i==0) chtid0=chtid;
if (i==numcht-1) chtidx=chtid;
}
cout <<md.casename << ": " <<numcht <<" cohorts to be run @" <<md.runstages<< "\n";
cout <<" from: " <<chtid0<<" to: " <<chtidx <<"\n";
};
int main(void)
{
try
{
// This is the array we will read.
int dataIn[NX][NY];
// Open the file. The ReadOnly parameter tells netCDF we want
// read-only access to the file.
NcFile dataFile("simple_xy.nc", NcFile::ReadOnly);
// You should always check whether a netCDF file open or creation
// 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.
// Retrieve the variable named "data"
NcVar *data = dataFile.getVar("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 NC_ERR;
// The netCDF file is automatically closed by the NcFile destructor
cout << "*** SUCCESS reading example file simple_xy.nc!" << endl;
return 0;
}catch(NcException e)
{
e.what();
cout<<"FAILURE*************************************"<<endl;
return 1;
}
}
void ConstantSet::netcdf_define(NcFile &nc, std::string const &vname)
{
// Create the variable to store our constants
NcVar *ncvar = giss::get_var_safe(nc, vname.c_str(), false);
if (!ncvar) {
auto oneDim = giss::get_or_add_dim(nc, "one", 1);
ncvar = nc.add_var(vname.c_str(), ncDouble, oneDim);
}
// Store the constants as attributes
for (int i=0; i<fields.size_withunit(); ++i) {
CoupledField const &field(fields.field(i));
ncvar->add_att(field.name.c_str(), vals[i]);
ncvar->add_att((field.name + "_units").c_str(), field.units.c_str());
ncvar->add_att((field.name + "_description").c_str(), field.description.c_str());
}
}
void NetCdfConfigureDialog::getDimEdges(int dimId, unsigned &size, double &firstValue, double &lastValue)
{
if ((_currentFile->get_var(_currentVar->get_dim(dimId)->name())) != NULL)
{
NcVar *tmpVarOfDim = _currentFile->get_var(_currentVar->get_dim(dimId)->name());
if ((tmpVarOfDim->num_dims()) == 1)
{
int sizeOfDim = tmpVarOfDim->get_dim(0)->size();
size = sizeOfDim;
double arrayOfDimStart[1] = {0};
size_t edgeOfArray[1] = {1};
long edgeOrigin[1] = {0};
tmpVarOfDim->set_cur(edgeOrigin);
tmpVarOfDim->get(arrayOfDimStart,edgeOfArray);
firstValue = arrayOfDimStart[0];
double arrayOfDimEnd[1] = {0};
edgeOrigin[0] = sizeOfDim - 1;
tmpVarOfDim->set_cur(edgeOrigin);
tmpVarOfDim->get(arrayOfDimEnd,edgeOfArray);
lastValue = arrayOfDimEnd[0];
}
} else {
size = 0;
firstValue = 0;
lastValue = 0;
}
}
template<class T> static bool load_nc_array(const NcFile& ncf, const string& name, vector<T>& dest, bool required = true, int offset = 0, int count = -1)
{
NcVar *v = load_nc_variable(ncf, name.c_str(), required);
if (v)
{
vector<long> offsets = list_of(offset).repeat(v->num_dims()-1, 0);
v->set_cur(&offsets.front());
vector<long> counts (v->num_dims());
long* shape = v->edges();
transform(shape, shape + v->num_dims(), offsets.begin(), counts.begin(), minus<long>());
delete shape;
if (count > 0)
{
counts[0] = count;
}
dest.resize(product(counts));
bool success = v->get(&dest.front(), &counts.front());
if (!success)
{
dest.resize(0);
check(!required, string("NetcdfDataset::load_nc_array<") + typeid(T).name() + "> " + name + '\n' + "failed with offset " + str(offsets) + ", counts " + str(counts));
}
return success;
}
return false;
}
void DumpableNcFile::dumpvars( void )
{
int n;
static const char* types[] =
{"","byte","char","short","long","float","double"};
NcVar* vp;
for(n = 0; vp = get_var(n); n++) {
cout << "\t" << types[vp->type()] << " " << vp->name() ;
if (vp->num_dims() > 0) {
cout << "(";
for (int d = 0; d < vp->num_dims(); d++) {
NcDim* dim = vp->get_dim(d);
cout << dim->name();
if (d < vp->num_dims()-1)
cout << ", ";
}
cout << ")";
}
cout << " ;\n";
// now dump each of this variable's attributes
dumpatts(*vp);
}
}
int NetcdfSource::readMatrix(double *v, const QString& field)
{
/* For a variable from the netCDF file */
QByteArray bytes = field.toLatin1();
NcVar *var = _ncfile->get_var(bytes.constData()); // var is owned by _ncfile
if (!var) {
KST_DBG qDebug() << "Queried field " << field << " which can't be read" << endl;
return -1;
}
int xSize = var->get_dim(0)->size();
int ySize = var->get_dim(1)->size();
var->get(v, xSize, ySize);
return xSize * ySize;
}
void InputNetcdf::getLocationsCore(std::vector<Location>& iLocations) const {
iLocations.clear();
std::string filename = getLocationFilename();
NcFile ncfile(filename.c_str());
if(ncfile.is_valid()) {
NcDim* ncLocationDim = ncfile.get_dim("Location");
int numLocations = ncLocationDim->size();
NcVar* ncLats = ncfile.get_var("Lat");
NcVar* ncLons = ncfile.get_var("Lon");
NcError q(NcError::silent_nonfatal);
NcVar* ncElevs = ncfile.get_var("Elev");
NcVar* ncIds = ncfile.get_var("Id");
bool hasId = false;
bool hasElev = false;
if(ncIds)
hasId = true;
if(ncElevs)
hasElev = true;
float* lats = new float[numLocations];
float* lons = new float[numLocations];
float* elevs = new float[numLocations];
int* ids = new int[numLocations];
long count[1] = {numLocations};
ncLats->get(lats, count);
ncLons->get(lons, count);
if(hasId)
ncIds->get(ids, count);
if(hasElev)
ncElevs->get(elevs, count);
for(int i = 0; i < numLocations; i++) {
int id = i;
if(hasId)
id = ids[i];
float lat = lats[i];
float lon = lons[i];
float elev = Global::MV;
if(hasElev)
elev = elevs[i];
Location loc(getName(), id, lat, lon);
loc.setElev(elev);
iLocations.push_back(loc);
}
delete[] lats;
delete[] lons;
delete[] elevs;
delete[] ids;
ncfile.close();
}
else {
notifyInvalidSampleFile();
}
}
const kvs::AnyValueArray data(
const size_t offset = 0,
const size_t dim1 = 1,
const size_t dim2 = 1,
const size_t dim3 = 1 ) const
{
const void* head = m_var->values()->base();
const size_t nvalues = dim1 * dim2 * dim3;
switch ( m_var->type() )
{
case ncByte:
{
kvs::UInt8* values = (kvs::UInt8*)( head ) + offset;
return( kvs::AnyValueArray( this->flip( dim1, dim2, dim3, values ), nvalues ) );
}
case ncChar:
{
kvs::Int8* values = (kvs::Int8*)( head ) + offset;
return( kvs::AnyValueArray( this->flip( dim1, dim2, dim3, values ), nvalues ) );
}
case ncShort:
{
kvs::Int16* values = (kvs::Int16*)( head ) + offset;
return( kvs::AnyValueArray( this->flip( dim1, dim2, dim3, values ), nvalues ) );
}
case ncInt:
{
kvs::Int32* values = (kvs::Int32*)( head ) + offset;
return( kvs::AnyValueArray( this->flip( dim1, dim2, dim3, values ), nvalues ) );
}
case ncFloat:
{
kvs::Real32* values = (kvs::Real32*)( head ) + offset;
return( kvs::AnyValueArray( this->flip( dim1, dim2, dim3, values ), nvalues ) );
}
case ncDouble:
{
kvs::Real64* values = (kvs::Real64*)( head ) + offset;
return( kvs::AnyValueArray( this->flip( dim1, dim2, dim3, values ), nvalues ) );
}
default: return( kvs::AnyValueArray() );
}
}