void listener(char* fifo,char writeTo[],char readFrom[]){
int rec,id;
rec=open(fifo,O_RDONLY);
read(rec,&id,sizeof(int));
close(rec);
makeNames(id,writeTo,readFrom);
}
MComponent::MComponent( MProject* project, MRule* rule, const WString& mask, const char* target )
: _dirty( true )
, _needsMake( true )
, _project( project )
, _filename( NULL )
, _relFilename( target )
, _target( NULL )
, _mask( mask )
, _autodepend( rule->autodepend() )
, _autotrack( rule->autotrack() )
, _mode( SWMODE_DEBUG )
, _batchMode( false )
{
WFileName targ;
makeNames( target, _filename, _relFilename, targ );
_target = new MItem( targ, this, rule, true );
}
bool MComponent::renameComponent( WFileName& fn, MRule* rule, WString& mask )
{
WFileName filename;
WFileName relname;
WFileName targ;
makeNames( fn, filename, relname, targ );
if( _target->rename( targ, rule ) ) {
_filename = filename;
_relFilename = relname;
_mask = mask;
// MRule* nilRule = _config->nilRule();
for( int i=0; i<_items.count(); i++ ) {
MItem* m = (MItem*)_items[i];
MRule* r = _config->findMatchingRule( *m, _target->rule(), _mask );
m->setRule( r );
}
refresh();
setDirty();
return( true );
}
return( false );
}
/**
* Executes the algorithm
*/
void PlotPeakByLogValue::exec()
{
// Create a list of the input workspace
const std::vector<InputData> wsNames = makeNames();
std::string fun = getPropertyValue("Function");
//int wi = getProperty("WorkspaceIndex");
std::string logName = getProperty("LogValue");
bool sequential = getPropertyValue("FitType") == "Sequential";
bool isDataName = false; // if true first output column is of type string and is the data source name
ITableWorkspace_sptr result = WorkspaceFactory::Instance().createTable("TableWorkspace");
if (logName == "SourceName")
{
result->addColumn("str","Source name");
isDataName = true;
}
else if (logName.empty())
{
result->addColumn("double","axis-1");
}
else
{
result->addColumn("double",logName);
}
// Create an instance of the fitting function to obtain the names of fitting parameters
IFitFunction* ifun = FunctionFactory::Instance().createInitialized(fun);
if (!ifun)
{
throw std::invalid_argument("Fitting function failed to initialize");
}
for(size_t iPar=0;iPar<ifun->nParams();++iPar)
{
result->addColumn("double",ifun->parameterName(iPar));
result->addColumn("double",ifun->parameterName(iPar)+"_Err");
}
result->addColumn("double","Chi_squared");
delete ifun;
setProperty("OutputWorkspace",result);
double dProg = 1./static_cast<double>(wsNames.size());
double Prog = 0.;
for(int i=0;i<static_cast<int>(wsNames.size());++i)
{
InputData data = getWorkspace(wsNames[i]);
if (!data.ws)
{
g_log.warning() << "Cannot access workspace " << wsNames[i].name << '\n';
continue;
}
if (data.i < 0 && data.indx.empty())
{
g_log.warning() << "Zero spectra selected for fitting in workspace " << wsNames[i].name << '\n';
continue;
}
int j,jend;
if (data.i >= 0)
{
j = data.i;
jend = j + 1;
}
else
{// no need to check data.indx.empty()
j = data.indx.front();
jend = data.indx.back() + 1;
}
dProg /= abs(jend - j);
for(;j < jend;++j)
{
// Find the log value: it is either a log-file value or simply the workspace number
double logValue;
if (logName.empty())
{
API::Axis* axis = data.ws->getAxis(1);
logValue = (*axis)(j);
}
else if (logName != "SourceName")
{
Kernel::Property* prop = data.ws->run().getLogData(logName);
if (!prop)
{
throw std::invalid_argument("Log value "+logName+" does not exist");
}
TimeSeriesProperty<double>* logp =
dynamic_cast<TimeSeriesProperty<double>*>(prop);
logValue = logp->lastValue();
}
std::string resFun = fun;
std::vector<double> errors;
double chi2;
try
{
// Fit the function
API::IAlgorithm_sptr fit = createSubAlgorithm("Fit");
fit->initialize();
fit->setProperty("InputWorkspace",data.ws);
//fit->setPropertyValue("InputWorkspace",data.ws->getName());
fit->setProperty("WorkspaceIndex",j);
fit->setPropertyValue("Function",fun);
fit->setPropertyValue("StartX",getPropertyValue("StartX"));
fit->setPropertyValue("EndX",getPropertyValue("EndX"));
fit->setPropertyValue("Minimizer",getPropertyValue("Minimizer"));
fit->setPropertyValue("CostFunction",getPropertyValue("CostFunction"));
fit->execute();
resFun = fit->getPropertyValue("Function");
errors = fit->getProperty("Errors");
chi2 = fit->getProperty("OutputChi2overDoF");
}
catch(...)
{
g_log.error("Error in Fit subalgorithm");
throw;
}
if (sequential)
{
fun = resFun;
}
// Extract the fitted parameters and put them into the result table
TableRow row = result->appendRow();
if (isDataName)
{
row << wsNames[i].name;
}
else
{
row << logValue;
}
ifun = FunctionFactory::Instance().createInitialized(resFun);
for(size_t iPar=0;iPar<ifun->nParams();++iPar)
{
row << ifun->getParameter(iPar) << errors[iPar];
}
row << chi2;
delete ifun;
Prog += dProg;
progress(Prog);
interruption_point();
} // for(;j < jend;++j)
}
}
SEXP runModel(SEXP m_, SEXP iterations, SEXP burn_in, SEXP adapt, SEXP thin) {
const int eval_limit = 10;
SEXP env_ = Rf_getAttrib(m_,Rf_install("env"));
if(env_ == R_NilValue || TYPEOF(env_) != ENVSXP) {
throw std::logic_error("ERROR: bad environment passed to deterministic.");
}
vpArmaMapT armaMap;
vpMCMCMapT mcmcMap;
std::vector<cppbugs::MCMCObject*> mcmcObjects;
arglistT arglist;
std::vector<const char*> argnames;
initArgList(m_, arglist, 1);
for(size_t i = 0; i < arglist.size(); i++) {
// capture arg name
// FIXME: check class of args to make sure it's mcmc
if(TYPEOF(arglist[i])==SYMSXP) {
argnames.push_back(CHAR(PRINTNAME(arglist[i])));
}
// force eval of late bindings
arglist[i] = forceEval(arglist[i],env_,eval_limit);
try {
ArmaContext* ap = mapOrFetch(arglist[i], armaMap);
cppbugs::MCMCObject* node = createMCMC(arglist[i],armaMap);
mcmcMap[rawAddress(arglist[i])] = node;
mcmcObjects.push_back(node);
} catch (std::logic_error &e) {
releaseMap(armaMap);
releaseMap(mcmcMap);
UNPROTECT(armaMap.size());
REprintf("%s\n",e.what());
return R_NilValue;
}
}
int iterations_ = Rcpp::as<int>(iterations);
int burn_in_ = Rcpp::as<int>(burn_in);
int adapt_ = Rcpp::as<int>(adapt);
int thin_ = Rcpp::as<int>(thin);
SEXP ar;
PROTECT(ar = Rf_allocVector(REALSXP,1));
try {
cppbugs::RMCModel m(mcmcObjects);
m.sample(iterations_, burn_in_, adapt_, thin_);
//std::cout << "acceptance_ratio: " << m.acceptance_ratio() << std::endl;
REAL(ar)[0] = m.acceptance_ratio();
} catch (std::logic_error &e) {
releaseMap(armaMap);
releaseMap(mcmcMap);
UNPROTECT(armaMap.size());
UNPROTECT(1); // ar
REprintf("%s\n",e.what());
return R_NilValue;
}
SEXP ans;
PROTECT(ans = createTrace(arglist,armaMap,mcmcMap));
releaseMap(armaMap);
releaseMap(mcmcMap);
UNPROTECT(armaMap.size());
Rf_setAttrib(ans, R_NamesSymbol, makeNames(argnames));
Rf_setAttrib(ans, Rf_install("acceptance.ratio"), ar);
UNPROTECT(2); // ans + ar
return ans;
}
