void bi::ParticleMCMCNetCDFBuffer::map(const long P, const long T) {
std::string name;
int id, i;
VarType type;
Var* var;
Dim* dim;
/* dimensions */
BI_ERROR_MSG(hasDim("nr"), "File must have nr dimension");
nrDim = mapDim("nr", T);
for (i = 0; i < m.getNumDims(); ++i) {
dim = m.getDim(i);
BI_ERROR_MSG(hasDim(dim->getName().c_str()), "File must have " <<
dim->getName() << " dimension");
nDims.push_back(mapDim(dim->getName().c_str(), dim->getSize()));
}
BI_ERROR_MSG(hasDim("np"), "File must have np dimension");
npDim = mapDim("np", P);
/* time variable */
tVar = ncFile->get_var("time");
BI_ERROR_MSG(tVar != NULL && tVar->is_valid(),
"File does not contain variable time");
BI_ERROR_MSG(tVar->num_dims() == 1, "Variable time has " << tVar->num_dims() <<
" dimensions, should have 1");
BI_ERROR_MSG(tVar->get_dim(0) == nrDim, "Dimension 0 of variable time should be nr");
/* other variables */
for (i = 0; i < NUM_VAR_TYPES; ++i) {
type = static_cast<VarType>(i);
if (type == D_VAR || type == R_VAR || type == P_VAR) {
vars[type].resize(m.getNumVars(type), NULL);
for (id = 0; id < m.getNumVars(type); ++id) {
var = m.getVar(type, id);
if (hasVar(var->getOutputName().c_str())) {
vars[type][id] = mapVar(m.getVar(type, id));
}
}
}
}
llVar = ncFile->get_var("loglikelihood");
BI_ERROR_MSG(llVar != NULL && llVar->is_valid(),
"File does not contain variable loglikelihood");
BI_ERROR_MSG(llVar->num_dims() == 1, "Variable loglikelihood has " <<
llVar->num_dims() << " dimensions, should have 1");
BI_ERROR_MSG(llVar->get_dim(0) == npDim,
"Dimension 0 of variable loglikelihood should be np");
lpVar = ncFile->get_var("logprior");
BI_ERROR_MSG(lpVar != NULL && lpVar->is_valid(),
"File does not contain variable logprior");
BI_ERROR_MSG(lpVar->num_dims() == 1, "Variable logprior has " <<
lpVar->num_dims() << " dimensions, should have 1");
BI_ERROR_MSG(lpVar->get_dim(0) == npDim,
"Dimension 0 of variable logprior should be np");
}
void bi::ParticleMCMCNetCDFBuffer::create(const long P, const long T) {
int id, i;
VarType type;
Var* var;
Dim* dim;
ncFile->add_att(PACKAGE_TARNAME "_schema", "ParticleMCMC");
ncFile->add_att(PACKAGE_TARNAME "_schema_version", 1);
ncFile->add_att(PACKAGE_TARNAME "_version", PACKAGE_VERSION);
/* dimensions */
nrDim = createDim("nr", T);
for (i = 0; i < m.getNumDims(); ++i) {
dim = m.getDim(i);
nDims.push_back(createDim(dim->getName().c_str(), dim->getSize()));
}
npDim = createDim("np", P);
/* time variable */
tVar = ncFile->add_var("time", netcdf_real, nrDim);
BI_ERROR_MSG(tVar != NULL && tVar->is_valid(), "Could not create time variable");
/* other variables */
for (i = 0; i < NUM_VAR_TYPES; ++i) {
type = static_cast<VarType>(i);
vars[type].resize(m.getNumVars(type), NULL);
if (type == D_VAR || type == R_VAR || type == P_VAR) {
for (id = 0; id < (int)vars[type].size(); ++id) {
var = m.getVar(type, id);
if (var->hasOutput()) {
if (type == P_VAR) {
vars[type][id] = createVar(var, false, true);
} else {
vars[type][id] = createVar(var, !var->getOutputOnce(), true);
}
}
}
}
}
llVar = ncFile->add_var("loglikelihood", netcdf_real, npDim);
BI_ERROR_MSG(llVar != NULL && llVar->is_valid(),
"Could not create loglikelihood variable");
lpVar = ncFile->add_var("logprior", netcdf_real, npDim);
BI_ERROR_MSG(lpVar != NULL && lpVar->is_valid(),
"Could not create logprior variable");
}
std::pair<int,int> bi::InputNetCDFBuffer::mapVarDim(const Var* var) {
/* pre-condition */
BI_ASSERT(var != NULL);
const VarType type = var->getType();
Dim* dim;
int ncVar, ncDim, i, j = 0, k = -1;
std::vector<int> dimids;
BI_UNUSED bool canHaveTime, canHaveP;
canHaveTime = type == D_VAR || type == R_VAR || type == F_VAR
|| type == O_VAR;
ncVar = nc_inq_varid(ncid, var->getInputName());
if (ncVar >= 0) {
dimids = nc_inq_vardimid(ncid, ncVar);
/* check for ns-dimension */
if (nsDim >= 0 && j < static_cast<int>(dimids.size())
&& dimids[j] == nsDim) {
++j;
}
/* check for record dimension */
if (j < static_cast<int>(dimids.size())) {
BOOST_AUTO(iter, std::find(recDims.begin(), recDims.end(), dimids[j]));
if (iter != recDims.end()) {
k = std::distance(recDims.begin(), iter);
++j;
}
}
/* check for np-dimension */
if (npDim >= 0 && j < static_cast<int>(dimids.size())
&& dimids[j] == npDim) {
++j;
} else if (j < static_cast<int>(dimids.size())) {
/* check for model dimensions */
for (i = var->getNumDims() - 1;
i >= 0 && j < static_cast<int>(dimids.size()); --i, ++j) {
dim = var->getDim(i);
ncDim = dimids[j];
BI_ERROR_MSG(dim->getName().compare(nc_inq_dimname(ncid, ncDim)) == 0,
"Dimension " << j << " of variable " << var->getName() << " should be " << dim->getName() << " not " << nc_inq_dimname(ncid, ncDim) << ", in file " << file);
BI_ERROR_MSG(k < 0 || coordVars[k] < 0,
"Variable " << nc_inq_varname(ncid, ncVar) << " has both dense and sparse definitions, in file " << file);
}
BI_ERROR_MSG(i == -1,
"Variable " << nc_inq_varname(ncid, ncVar) << " is missing one or more dimensions, in file " << file);
/* check again for np dimension */
if (npDim >= 0 && j < static_cast<int>(dimids.size())
&& dimids[j] == npDim) {
++j;
}
}
BI_ERROR_MSG(j == static_cast<int>(dimids.size()),
"Variable " << nc_inq_varname(ncid, ncVar) << " has extra dimensions, in file " << file);
}
return std::make_pair(k, ncVar);
}