- regroup common options (but we still need a cleanup)

- don't create temporary dir if not needed

bin/combine.cpp

@@ -1,32 +1,3 @@
-/** 
-   Generic limit setting, with any model.
-
-
-   Takes as input:
-    - one label for the output root file
-    - one input datacard file
-    - a value of the higgs mass
-    - the name of the statistical method to apply
-    - the number of toys to run (0 means to create a single toy corresponding to the expected signal, the so called Asimov dataset)
-    - the seed for the random number generator
-
-   
-  The datacard can be:
-    - a LandS-like datacard for a generic counting experiment with an arbitrary number of bins, processes and systematical uncertainties
-    - a RooStats model in the "High Level Factory" syntax, that has to define:
-      - a RooRealVar "r" corresponding to the cross section strength
-      - a RooArgSet "obs" with the observables, and a RooArgSet "poi" with the parameters of interest (just "r")
-      - RooAbsPdfs "model_s" and "model_b" for the (S+B) and B-only scenarios (not all statistical methods use both)
-      - if systematical uncertainties are enabled, it must also define a RooArgSet "nuisances" with the nuisance parameters,
-        and a RooAbsPdf "nuisancePdf" with the pdf for those. In this case "model_s" must already be the product of the pdf
-        for the observables and the pdf for the nuisances.
-      - the observed dataset will be constructed taking the default value of the observables as in the model.
-
-  The program will assume that a file ending in ".hlf" is a RooStats model, and anything else is a LandS datacard.
-
-  See higgsCombineSimple.cxx for the documentation of the other input parameters and of the output
-*/
-//#include "higgsCombine_Common.cxx"
 #include "HiggsAnalysis/CombinedLimit/interface/Combine.h"
 #include <TString.h>
 #include <TSystem.h>
@@ -79,28 +50,36 @@ int main(int argc, char **argv) {
     methodsDesc += i->first;
   }
 
-  po::options_description desc("Allowed options");
+  po::options_description desc("Main options");
   desc.add_options()
-    ("help,h", "Produce help message")
-    ("verbose,v",  po::value<int>(&verbose)->default_value(1), "Verbosity level")
-    ("name,n",     po::value<string>(&name)->default_value("Test"), "Name of the job")
-    ("datacard,d", po::value<string>(&datacard), "Datacard file")
-    ("dataset,D",  po::value<string>(&dataset)->default_value("data_obs"), "Dataset for observed limit")
+    ("datacard,d", po::value<string>(&datacard), "Datacard file (can also be specified directly without the -d or --datacard)")
     ("method,M",      po::value<string>(&whichMethod)->default_value("ProfileLikelihood"), methodsDesc.c_str())
-    ("hintMethod,H",  po::value<string>(&whichHintMethod)->default_value(""), "Run first this method to provide a hint on the result")
-    ("mass,m",     po::value<int>(&iMass)->default_value(120), "Higgs mass to store in the output tree")
+    ("verbose,v",  po::value<int>(&verbose)->default_value(1), "Verbosity level (-1 = very quiet; 0 = quiet, 1 = verbose, 2+ = debug)")
+    ("help,h", "Produce help message")
+    ;
+  combiner.statOptions().add_options()
     ("toys,t", po::value<int>(&runToys)->default_value(0), "Number of Toy MC extractions")
     ("seed,s", po::value<int>(&seed)->default_value(123456), "Toy MC random seed")
-    ("saveToys,w", "Save results of toy MC")
-    ("toysFile,f", po::value<string>(&toysFile)->default_value(""), "Toy MC input file")
+    ("hintMethod,H",  po::value<string>(&whichHintMethod)->default_value(""), "Run first this method to provide a hint on the result")
+    ;
+  combiner.ioOptions().add_options()
+    ("name,n",     po::value<string>(&name)->default_value("Test"), "Name of the job, affects the name of the output tree")
+    ("mass,m",     po::value<int>(&iMass)->default_value(120), "Higgs mass to store in the output tree")
+    ("dataset,D",  po::value<string>(&dataset)->default_value("data_obs"), "Name of the dataset for observed limit")
+    ("saveToys",   "Save results of toy MC or other intermediate results")
+    ("toysFile",   po::value<string>(&toysFile)->default_value(""), "Read toy mc or other intermediate results from this file")
+    ;
+  combiner.miscOptions().add_options()
     ("igpMem", "Setup support for memory profiling using IgProf")
     ("LoadLibrary,L", po::value<vector<string> >(&librariesToLoad), "Load library through gSystem->Load(...). Can specify multiple libraries using this option multiple times")
     ;
-  desc.add(combiner.options());
+  desc.add(combiner.statOptions());
+  desc.add(combiner.ioOptions());
   for(map<string, LimitAlgo *>::const_iterator i = methods.begin(); i != methods.end(); ++i) {
     if(i->second->options().options().size() != 0) 
       desc.add(i->second->options());
   }
+  desc.add(combiner.miscOptions());
   po::positional_options_description p;
   p.add("datacard", -1);
   po::variables_map vm;

interface/Combine.h

@@ -24,25 +24,33 @@ class Combine {
 public:
   Combine() ;
 
-  const boost::program_options::options_description & options() const { return options_; }    
+  boost::program_options::options_description & statOptions() { return statOptions_; }    
+  boost::program_options::options_description & ioOptions() { return ioOptions_; }    
+  boost::program_options::options_description & miscOptions() { return miscOptions_; }    
   void applyOptions(const boost::program_options::variables_map &vm) ;
 
   void run(TString hlfFile, const std::string &dataset, double &limit, double &limitErr, int &iToy, TTree *tree, int nToys);
 
 private:
   bool mklimit(RooWorkspace *w, RooAbsData &data, double &limit, double &limitErr) ;
 
-  boost::program_options::options_description options_;
-
-  bool unbinned_; 
+  boost::program_options::options_description statOptions_, ioOptions_, miscOptions_;
+
+  // statistics-related variables
+  bool unbinned_, generateBinnedWorkaround_; 
   float rMin_, rMax_;
-  bool compiledExpr_;
   std::string prior_;
   bool hintUsesStatOnly_;
+  bool toysNoSystematics_;
+
+  // input-output related variables
   bool saveWorkspace_;
   std::string workspaceName_;
   std::string modelConfigName_;
-  bool toysNoSystematics_;
+
+  // implementation-related variables
+  bool compiledExpr_;
+  bool makeTempDir_;
 };
 
 #endif

src/Combine.cc

@@ -63,25 +63,33 @@ float cl = 0.95;
 
 
 Combine::Combine() :
-    options_("Common options"), 
+    statOptions_("Common statistics options"),
+    ioOptions_("Common input-output options"),
+    miscOptions_("Common miscellaneous options"),
     rMin_(std::numeric_limits<float>::quiet_NaN()), 
     rMax_(std::numeric_limits<float>::quiet_NaN()) {
     namespace po = boost::program_options;
-    options_.add_options()
+    statOptions_.add_options() 
       ("systematics,S", po::value<bool>(&withSystematics)->default_value(true), "Add systematic uncertainties")
       ("cl,C",   po::value<float>(&cl)->default_value(0.95), "Confidence Level")
       ("rMin",   po::value<float>(&rMin_), "Override minimum value for signal strength")
       ("rMax",   po::value<float>(&rMax_), "Override maximum value for signal strength")
       ("prior",  po::value<std::string>(&prior_)->default_value("flat"), "Prior to use, for methods that require it and if it's not already in the input file: 'flat' (default), '1/sqrt(r)'")
-      ("unbinned,U", "Generate unbinned datasets instead of binned ones (works only for extended pdfs)")
-      ("compile", "Compile expressions instead of interpreting them")
       ("significance", "Compute significance instead of upper limit")
       ("hintStatOnly", "Ignore systematics when computing the hint")
-      ("saveWorkspace", "Save workspace to output root file")
       ("toysNoSystematics", "Generate all toys with the central value of the nuisance parameters, without fluctuating them")
+      ("unbinned,U", "Generate unbinned datasets instead of binned ones (works only for extended pdfs)")
+      ("generateBinnedWorkaround", "Make binned datasets generating unbinned ones and then binnning them. Workaround for a bug in RooFit.")
+      ;
+    ioOptions_.add_options()
+      ("saveWorkspace", "Save workspace to output root file")
       ("workspaceName,w", po::value<std::string>(&workspaceName_)->default_value("w"), "Workspace name, when reading it from or writing it to a rootfile.")
-      ("modelConfigName,w", po::value<std::string>(&modelConfigName_)->default_value("ModelConfig"), "ModelConfig name, when reading it from or writing it to a rootfile.")
+      ("modelConfigName", po::value<std::string>(&modelConfigName_)->default_value("ModelConfig"), "ModelConfig name, when reading it from or writing it to a rootfile.")
       ;
+    miscOptions_.add_options()
+      ("compile", "Compile expressions instead of interpreting them")
+      ("tempDir", po::value<bool>(&makeTempDir_)->default_value(false), "Run the program from a temporary directory (automatically on if 'compile' is activated)")
+      ; 
 }
 
 void Combine::applyOptions(const boost::program_options::variables_map &vm) {
@@ -91,7 +99,9 @@ void Combine::applyOptions(const boost::program_options::variables_map &vm) {
     std::cout << ">>> no systematics included" << std::endl;
   } 
   unbinned_ = vm.count("unbinned");
-  compiledExpr_ = vm.count("compile");
+  generateBinnedWorkaround_ = vm.count("generateBinnedWorkaround");
+  if (unbinned_ && generateBinnedWorkaround_) throw std::logic_error("You can't set generateBinnedWorkaround and unbinned options at the same time");
+  compiledExpr_ = vm.count("compile"); if (compiledExpr_) makeTempDir_ = true;
   doSignificance_ = vm.count("significance");
   hintUsesStatOnly_ = vm.count("hintStatOnly");
   saveWorkspace_ = vm.count("saveWorkspace");
@@ -131,10 +141,12 @@ bool Combine::mklimit(RooWorkspace *w, RooAbsData &data, double &limit, double &
 }
 
 void Combine::run(TString hlfFile, const std::string &dataset, double &limit, double &limitErr, int &iToy, TTree *tree, int nToys) {
-  TString pwd(gSystem->pwd());
-  TString tmpDir = "roostats-XXXXXX"; 
-  mkdtemp(const_cast<char *>(tmpDir.Data()));
-  gSystem->cd(tmpDir.Data());
+  TString tmpDir = "", pwd(gSystem->pwd());
+  if (makeTempDir_) {
+      tmpDir = "roostats-XXXXXX"; 
+      mkdtemp(const_cast<char *>(tmpDir.Data()));
+      gSystem->cd(tmpDir.Data());
+  }
 
   bool isTextDatacard = false, isBinary = false;
   TString fileToLoad = (hlfFile[0] == '/' ? hlfFile : pwd+"/"+hlfFile);
@@ -449,13 +461,13 @@ void Combine::run(TString hlfFile, const std::string &dataset, double &limit, do
   }
 
   } catch (std::logic_error &le) {
-      boost::filesystem::remove_all(tmpDir.Data());
+      if (tmpDir) boost::filesystem::remove_all(tmpDir.Data());
       throw le;
   } catch (std::runtime_error &re) {
-      boost::filesystem::remove_all(tmpDir.Data());
+      if (tmpDir) boost::filesystem::remove_all(tmpDir.Data());
       throw re;
   }
 
-  boost::filesystem::remove_all(tmpDir.Data());
+  if (tmpDir) boost::filesystem::remove_all(tmpDir.Data()); 
 }