void cmd_nlls()
{
Real *work, *y, *bounds, *covar, *p;
int nQ = count_data();
int ndim = fit[0].pars.n;
int i;
/* Allocate storage: y, covar, bounds, p */
work = (Real *)malloc(sizeof(Real)*(nQ + ndim*ndim + 3*ndim));
assert(work != NULL);
y = work;
bounds = y + nQ;
covar = bounds + 2*ndim;
p = covar + ndim*ndim;
write_pop(&set); /* In case fit crashes */
/* Record what we are doing */
if (parFD != NULL) {
fprintf(parFD,"# %15d Starting Levenberg-Marquardt\n", GetGen(&set));
fflush(parFD);
}
/* Copy normalized data values */
copy_normalized_data(y);
/* Set bounds */
for (i=0; i < ndim; i++) {
bounds[i] = 0.;
bounds[i+ndim] = 1.;
}
/* Get best into p */
pars_set(&fit[0].pars, bestpars);
pars_get01(&fit[0].pars, p);
/* Call nlls */
tic();
#if 1
box_nlls(step_nlls, ndim, nQ, fit, y, bounds, p, covar);
#else
nlls(step_nlls, ndim, nQ, fit, y, p, covar);
#endif
printf("Done LM\n");fflush(stdout);
toc();
print_covar(ndim,covar);
/* Record LM results */
log_best();
/* Inject new p into the GA */
setChromosome(&set, 0, p);
/* Done */
free(work);
}
const CAuth_list& CPub::GetAuthors (void) const
{
switch (Which()) {
case CPub::e_Gen :
return (GetGen().GetAuthors());
case CPub::e_Sub :
return (GetSub().GetAuthors());
case CPub::e_Article :
return (GetArticle().GetAuthors());
case CPub::e_Book :
return (GetBook().GetAuthors());
case CPub::e_Proc :
return (GetProc().GetBook().GetAuthors());
case CPub::e_Patent :
return (GetPatent().GetAuthors());
case CPub::e_Man :
return (GetMan().GetCit().GetAuthors());
default :
NCBI_THROW(CSerialException, eNotImplemented,
"CPub::GetAuthors: unsupported entry type "
+ SelectionName(Which()));
}
}
bool CPub::IsSetAuthors(void) const
{
switch (Which()) {
case CPub::e_Gen :
return (GetGen().IsSetAuthors());
case CPub::e_Sub :
return (GetSub().IsSetAuthors());
case CPub::e_Article :
return (GetArticle().IsSetAuthors());
case CPub::e_Book :
return (GetBook().IsSetAuthors());
case CPub::e_Proc :
return (GetProc().IsSetBook() && GetProc().GetBook().IsSetAuthors());
case CPub::e_Patent :
return (GetPatent().IsSetAuthors());
case CPub::e_Man :
return (GetMan().IsSetCit() && GetMan().GetCit().IsSetAuthors());
default :
break;
}
return false;
}
void ZShape2dMC(){
double signal_weight = 3531.89/30459500.;//3504
if (!doMG) signal_weight = 1966.7 / 42705454.; //
TH1D* mc_truegen;
vector<TH1D*> mc_truegen_cteq, mc_truegen_fsr_pileup;
GetGen(signal_weight, mc_truegen, mc_truegen_cteq, mc_truegen_fsr_pileup);
cout<<"Get MC distribution"<<endl;
vector<TGraphAsymmErrors*> g_MC_phistar;
TGraphAsymmErrors* g_MC_phistar_temp1=ConvertToTGraph(mc_truegen);
g_MC_phistar.push_back(g_MC_phistar_temp1);
vector<TGraphAsymmErrors*> g_MC_phistar_cteq;
for (size_t u=0; u<mc_truegen_cteq.size(); u++){
TGraphAsymmErrors* g_MC_phistar_temp=ConvertToTGraph(mc_truegen_cteq[u]);
g_MC_phistar_cteq.push_back(g_MC_phistar_temp);
}
vector<TGraphAsymmErrors*> g_MC_phistar_fsr_pileup;
for (size_t u=0; u<mc_truegen_fsr_pileup.size(); u++){
TGraphAsymmErrors* g_MC_phistar_temp=ConvertToTGraph(mc_truegen_fsr_pileup[u]);
g_MC_phistar_fsr_pileup.push_back(g_MC_phistar_temp);
}
vector<TGraphAsymmErrors *> g_MC_norm = CreateCopy(g_MC_phistar);
vector<TGraphAsymmErrors *> g_MC_norm_cteq = CreateCopy(g_MC_phistar_cteq);
vector<TGraphAsymmErrors *> g_MC_norm_fsr_pileup = CreateCopy(g_MC_phistar_fsr_pileup);
NormalizeGraph(g_MC_phistar, 0);
NormalizeGraph(g_MC_phistar_cteq, 0);
NormalizeGraph(g_MC_phistar_fsr_pileup, 0);
NormalizeGraph(g_MC_norm, 1);
NormalizeGraph(g_MC_norm_cteq, 1);
NormalizeGraph(g_MC_norm_fsr_pileup, 1);
TGraphAsymmErrors* g_syst_mc_cteq = CalcTotalSysU_updown(g_MC_phistar_cteq,g_MC_phistar_cteq[0],1,1);
TGraphAsymmErrors* g_syst_mc_fsr = CalcTotalSysU_fsr(g_MC_phistar_fsr_pileup[0],g_MC_phistar[0]);
TGraphAsymmErrors* g_syst_norm_mc_cteq = CalcTotalSysU_updown(g_MC_norm_cteq,g_MC_norm_cteq[0],1,1);
TGraphAsymmErrors* g_syst_norm_mc_fsr = CalcTotalSysU_fsr(g_MC_norm_fsr_pileup[0],g_MC_norm[0]);
vector<TGraphAsymmErrors *> g_mc_syst;
g_mc_syst.push_back(g_MC_phistar[0]);
g_mc_syst.push_back(g_syst_mc_fsr);
if (!doMG) g_mc_syst.push_back(g_syst_mc_cteq);
vector<std::string> syst_mc_list;
syst_mc_list.push_back("unfolding");
syst_mc_list.push_back("fsr");
if (!doMG) syst_mc_list.push_back("cteq");
TGraphAsymmErrors* g_mc_final=GetMCFinal(g_mc_syst, syst_mc_list, 0);
vector<TGraphAsymmErrors *> g_mc_syst_norm;
g_mc_syst_norm.push_back(g_MC_norm[0]);
g_mc_syst_norm.push_back(g_syst_norm_mc_fsr);
if (!doMG) g_mc_syst_norm.push_back(g_syst_norm_mc_cteq);
vector<std::string> syst_mc_list_norm;
syst_mc_list_norm.push_back("unfolding");
syst_mc_list_norm.push_back("fsr");
if (!doMG) syst_mc_list_norm.push_back("cteq");
TGraphAsymmErrors* g_mc_final_norm=GetMCFinal(g_mc_syst_norm, syst_mc_list_norm, 1);
string textn="Output/TESTMC_Graph_Abs_";
if (doMG) textn+="MG_";
else textn+="PH_";
if (elec==0)textn+="Dressed.root";
if (elec==1)textn+="Born.root";
if (elec==2)textn+="Naked.root";
TFile tr2(textn.c_str(),"RECREATE");
g_mc_final->Write();
textn="Output/TESTMC_Graph_Norm_";
if (doMG) textn+="MG_";
else textn+="PH_";
if (elec==0)textn+="Dressed.root";
if (elec==1)textn+="Born.root";
if (elec==2)textn+="Naked.root";
TFile tr3(textn.c_str(),"RECREATE");
g_mc_final_norm->Write();
}
// Appends a label to "label"
bool CPub::GetLabel(string* label,
ELabelType type,
TLabelFlags flags,
ELabelVersion version) const
{
static const char* s_PubTypes[14] = {
"Unknown",
"Generic",
"Submit",
"Medline",
"MUID",
"Article",
"Journal",
"Book",
"Proceedings",
"Patent",
"PatID",
"Manuscript",
"Equiv",
"PMID" };
// Check that label exists
if (!label) {
return false;
}
// Get the index into the s_PubTypes array corresponding to pub type
int idx = static_cast<int>(Which());
idx = idx >= 0 && idx < 14 ? idx : 0;
if (type == eType) {
// Append pub type to label and return
*label += s_PubTypes[idx];
return true;
}
if (type == eBoth) {
// Append pub type to label
*label += string(s_PubTypes[idx]) + ": ";
}
switch (Which()) {
case e_Muid:
*label += "NLM" + NStr::IntToString(GetMuid());
return true;
case e_Pmid:
*label += "PM" + NStr::IntToString(GetPmid().Get());
return true;
case e_Equiv:
return GetEquiv().GetLabel(label, flags, version);
case e_Medline:
return GetMedline().GetLabel(label, flags, version);
case e_Article:
return GetArticle().GetLabel(label, flags, version);
case e_Journal:
return GetJournal().GetLabel(label, flags, version);
case e_Book:
return GetBook().GetLabel(label, flags, version);
case e_Proc:
return GetProc().GetLabel(label, flags, version);
case e_Man:
return GetMan().GetLabel(label, flags, version);
case e_Sub:
return GetSub().GetLabel(label, flags, version);
case e_Patent:
return GetPatent().GetLabel(label, flags, version);
case e_Pat_id:
return GetPat_id().GetLabel(label, flags, version);
case e_Gen:
return GetGen().GetLabel(label, flags, version);
default:
return false;
}
}
void CPub::GetTitles(
TOneTitleRefVec & out_title,
size_t iMaxToGet ) const
{
// this "if" lets us assume below this point that
// we have room for at least one
if( iMaxToGet <= 0 ) {
return;
}
switch( Which() ) {
case CPub::e_not_set:
case CPub::e_Medline:
case CPub::e_Pmid:
case CPub::e_Pat_id:
// these types don't have titles, so nothing to do
break;
case CPub::e_Gen:
if( GetGen().IsSetTitle() ) {
out_title.push_back(
xs_GetTitleFromPlainString(
GetGen().GetTitle()) );
}
break;
case CPub::e_Sub:
if( GetSub().IsSetDescr() ) {
out_title.push_back(
xs_GetTitleFromPlainString(
GetSub().GetDescr()) );
}
break;
case CPub::e_Article:
if( GetArticle().IsSetTitle() && GetArticle().GetTitle().IsSet() ) {
xs_AppendTitles( out_title, iMaxToGet, GetArticle().GetTitle() );
}
break;
case CPub::e_Journal:
if( GetJournal().IsSetTitle() ) {
xs_AppendTitles( out_title, iMaxToGet, GetJournal().GetTitle() );
}
break;
case CPub::e_Book:
if( GetBook().IsSetTitle() ) {
xs_AppendTitles( out_title, iMaxToGet, GetBook().GetTitle() );
}
break;
case CPub::e_Proc:
// what to do here? It has a book and meeting
// It's not entirely clear if this is the best course of action
if( FIELD_CHAIN_OF_2_IS_SET(GetProc(), Book, Title) ) {
xs_AppendTitles( out_title, iMaxToGet,
GetProc().GetBook().GetTitle() );
}
break;
case CPub::e_Patent:
if( GetPatent().IsSetTitle() ) {
out_title.push_back(
xs_GetTitleFromPlainString(
GetPatent().GetTitle()) );
}
break;
case CPub::e_Man:
if( FIELD_CHAIN_OF_2_IS_SET(GetMan(), Cit, Title) ) {
xs_AppendTitles( out_title, iMaxToGet,
GetMan().GetCit().GetTitle() );
}
break;
case CPub::e_Equiv:
{
size_t iMaxTitleSizeAllowed = ( out_title.size() + iMaxToGet );
if( iMaxTitleSizeAllowed < out_title.size() ) {
// integer overflowed
iMaxTitleSizeAllowed =
std::numeric_limits<std::size_t>::max();
}
FOR_EACH_PUB_ON_PUBEQUIV(pub_it, GetEquiv()) {
if( out_title.size() >= iMaxTitleSizeAllowed ) {
break;
}
// dig down recursively
(*pub_it)->GetTitles(out_title,
(iMaxTitleSizeAllowed - out_title.size()) );
}
}
break;
default:
NCBI_THROW(CException, eUnknown, "unhandled pub type");
}
}
