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 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));
}
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 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();
}
//
// 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 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
}