Tagging remastered

bin/ma5

@@ -67,8 +67,8 @@ sys.path.insert(0, servicedir)
 
 # Release version
 # Do not touch it !!!!!  
-version = "2.0.0"
-date = "2022/05/24"
+version = "2.0.1"
+date = "2022/07/04"
 
 # Loading the MadAnalysis session
 import madanalysis.core.launcher

doc/releases/changelog-v2.0.md

@@ -1,13 +1,55 @@
-# Release 2.0-dev (development release)
+# Release 2.0.0-dev (development release)
 
 ## New features since last release
 
+* A module allowing for jet substructure studies has been implemented in
+  MadAnalysis 5. [(#13)](https://github.com/MadAnalysis/madanalysis5/pull/13)
+  * It includes the following fastjet-contrib functionalities:
+    * VariableR: normal and expert mode
+    * SoftDrop: expert mode
+    * Clusterer: expert mode
+    * Jet Filtering: expert mode
+    * Reclustering: expert mode
+    * Nsubjettiness: expert mode
+    * Pruner: expert mode
+    * Energy Correlator: expert mode
+    * HEPTopTagger: expert mode
+  * `RecJetFormat` has been wrapped with a `PseudoJet` structure to accommodate
+     dynamic transition between two objects.
+
+  All these methods can be used through the SFS interface.
+
+* Substructure and HEPTopTagger has been redesigned to be shared libraries, so
+  that MadAnalysis could be compiled without these modules as well.
+  [(#63)](https://github.com/MadAnalysis/madanalysis5/pull/63)
+
+* The tagger module has been redesigned to accommodate the features of
+  substructure module.
+  [(#86)](https://github.com/MadAnalysis/madanalysis5/pull/86)
+
+* Multi-level object tagging has been enabled through the SFS framework.
+  ([#97](https://github.com/MadAnalysis/madanalysis5/pull/97))
+  * Option to activate charm-jet tagging has been introduced.
+  * Option to use jet-based hadronic tau matching has been introduced.
+
 ## Improvements
 
+* The SFS libraries are now included in the file `analysisList.h`, instead of in
+  the main analysis file. This leads to much cleaner and independent analysis
+  construction. [(#86)](https://github.com/MadAnalysis/madanalysis5/pull/86)
+
+* Compilation time testing has been added for the jet Substructure and
+  HEPTopTagger interfaces 
+  ([#86](https://github.com/MadAnalysis/madanalysis5/pull/86)).
+
 ## Bug fixes
 
+* Various bugfixes for matching the numeric results to MA5 v1.10.
+  ([#97](https://github.com/MadAnalysis/madanalysis5/pull/97))
+
 ## Contributors
 
 This release contains contributions from (in alphabetical order):
 
-Jack Y. Araz, Benjamin Fuks
+[Jack Y. Araz](https://github.com/jackaraz), 
+[Benjamin Fuks](https://github.com/BFuks)

madanalysis/IOinterface/job_writer.py

@@ -471,11 +471,11 @@ def CreateMainFct(self,file,analysisName,outputName):
             file.write('  std::map<std::string, std::string> parametersC1;\n')
             parameters = self.main.fastsim.SampleAnalyzerConfigString()
             for k,v in sorted(six.iteritems(parameters),key=lambda k_v: (k_v[0],k_v[1])):
-                file.write('  parametersC1["'+k+'"]="'+v+'";\n')
+                file.write('  parametersC1["' + (k + '"').ljust(30, " ") + '] = "' + v + '";\n')
             for obj in ["electron","muon","track","photon"]:
                 if len(getattr(self.main.superfastsim, obj+"_isocone_radius")) != 0:
                     file.write(
-                        '  parametersC1["isolation.'+obj+'.radius"]="'+ ','.join(
+                        '  parametersC1[' + ('"isolation.' + obj + '.radius"').ljust(30, " ") + '] = "' + ','.join(
                         [str(x) for x in getattr(self.main.superfastsim, obj+"_isocone_radius")]
                         )+'";\n'
                     )
@@ -491,7 +491,7 @@ def CreateMainFct(self,file,analysisName,outputName):
                     file.write('  std::map<std::string, std::string> '+map_name+';\n')
                     for opt, val in item.__dict__.items():
                         if opt in ['JetID','algorithm']:
-                            file.write('  '+map_name+'["'+(opt+'"').ljust(18,' ') + '] = "'+str(val)+'";\n')
+                            file.write('  '+map_name+'["'+(opt+'"').ljust(20,' ') + '] = "'+str(val)+'";\n')
                         else:
                             # To follow old syntax add "cluster.". 
                             # This is not necessary but makes sense for unified syntax
@@ -507,7 +507,8 @@ def CreateMainFct(self,file,analysisName,outputName):
                 file.write('  cluster1->LoadSmearer(mySmearer);\n\n')
             if self.main.superfastsim.isTaggerOn():
                 file.write('  // Declaration of a generic tagger\n')
-                file.write('  NewTagger* tagger = new NewTagger();\n\n')
+                file.write('  NewTagger* myTagger = new NewTagger();\n')
+                file.write('  cluster1->LoadTagger(myTagger);\n\n')
 
 
         # + Case Delphes
@@ -596,8 +597,6 @@ def CreateMainFct(self,file,analysisName,outputName):
             file.write('      if (!analyzer2->Execute(mySample,myEvent)) continue;\n')
         if self.main.fastsim.package=="fastjet":
             file.write('      cluster1->Execute(mySample,myEvent);\n')
-            if self.main.superfastsim.isTaggerOn():
-                file.write('      tagger->Execute(mySample,myEvent);\n')
         elif self.main.fastsim.package=="delphes":
             file.write('      fastsim1->Execute(mySample,myEvent);\n')
         elif self.main.fastsim.package=="delphesMA5tune":
@@ -696,6 +695,10 @@ def WriteSelectionSource(self,main):
         file.write('#include "SampleAnalyzer/Process/Analyzer/AnalyzerManager.h"\n')
         file.write('#include "SampleAnalyzer/User/Analyzer/user.h"\n')
         file.write('#include "SampleAnalyzer/Commons/Service/LogStream.h"\n')
+        if self.main.superfastsim.isTaggerOn():
+            file.write('#include "new_tagger.h"\n')
+        if self.main.superfastsim.isNewSmearerOn():
+            file.write('#include "new_smearer_reco.h"\n')
         file.write('\n')
         file.write('// ------------------------------------------' +\
                    '-----------------------------------\n')

madanalysis/IOinterface/library_writer.py

@@ -121,6 +121,8 @@ def WriteMakefileForInterfaces(self,package):
             filename = self.path+"/SampleAnalyzer/Test/Makefile_zlib"
         elif package=='test_fastjet':
             filename = self.path+"/SampleAnalyzer/Test/Makefile_fastjet"
+        elif package=='test_substructure':
+            filename = self.path+"/SampleAnalyzer/Test/Makefile_substructure"
         elif package=='test_htt':
             filename = self.path+"/SampleAnalyzer/Test/Makefile_htt"
         elif package=='test_delphes':
@@ -146,6 +148,8 @@ def WriteMakefileForInterfaces(self,package):
             title='*zlib-interface* test'
         elif package=='test_fastjet':
             title='*fastjet-interface* test'
+        elif package=='test_substructure':
+            title='*substructure-interface* test'
         elif package=='test_htt':
             title='*htt-interface* test'
         elif package=='test_delphes':
@@ -186,6 +190,19 @@ def WriteMakefileForInterfaces(self,package):
                  'cleanup_substructure.log',
                  'mrproper_substructure.log']
             )
+        elif package == "test_substructure":
+            options.has_commons = True
+            options.has_fastjet_inc = True
+            options.has_fastjet_lib = True
+            options.ma5_fastjet_mode = True
+            options.has_fastjet_ma5lib = True
+            options.has_substructure = True
+            toRemove.extend(
+                ['compilation_test_substructure.log',
+                 'linking_test_substructure.log',
+                 'cleanup_test_substructure.log',
+                 'mrproper_test_substructure.log']
+            )
         elif package == "HEPTopTagger":
             options.has_commons=True
             options.has_fastjet_inc=True
@@ -203,7 +220,7 @@ def WriteMakefileForInterfaces(self,package):
         elif package == "test_htt":
             options.has_commons=True
             options.has_fastjet_inc=True
-            # options.has_fastjet_lib=True
+            options.has_fastjet_lib=True
             # @JACK: To be able to use fastjet in Ma5 data structure
             options.ma5_fastjet_mode=True
             options.has_fastjet_ma5lib = True
@@ -342,9 +359,12 @@ def WriteMakefileForInterfaces(self,package):
         elif package=='test_fastjet':
             cppfiles = ['Fastjet/*.cpp']
             hfiles   = ['Fastjet/*.h']
+        elif package=='test_substructure':
+            cppfiles = ['Substructure/*.cpp']
+            hfiles   = []
         elif package=='test_htt':
             cppfiles = ['HEPTopTagger/*.cpp']
-            hfiles   = ['HEPTopTagger/*.h']
+            hfiles   = []
         elif package=='test_delphes':
             cppfiles = ['Delphes/*.cpp']
             hfiles   = ['Delphes/*.h']
@@ -379,6 +399,10 @@ def WriteMakefileForInterfaces(self,package):
             isLibrary=False
             ProductName='TestFastjet'
             ProductPath='../Bin/'
+        elif package=='test_substructure':
+            isLibrary=False
+            ProductName='TestSubstructure'
+            ProductPath='../Bin/'
         elif package=='test_htt':
             isLibrary=False
             ProductName='TestHEPTopTagger'
@@ -416,16 +440,18 @@ def Compile(self,ncores,package,folder):
         # log file name
         if package in ['process','commons','test','configuration']:
             logfile = folder+'/compilation.log'
-        elif package in ['test_process','test_commons','test_zlib','test_fastjet', "test_htt", 'test_root','test_delphes','test_delphesMA5tune']:
-            logfile = folder+'/compilation_'+package[5:]+'.log'
+        elif package in ['test_process', 'test_commons', 'test_zlib', 'test_fastjet', "test_substructure", "test_htt",
+                         'test_root', 'test_delphes', 'test_delphesMA5tune']:
+            logfile = folder + '/compilation_' + package[5:] + '.log'
         else:
             logfile = folder+'/compilation_'+package+'.log'
 
         # makefile
         if package in ['process','commons','test','configuration']:
             makefile = 'Makefile'
-        elif package in ['test_process','test_commons','test_zlib','test_fastjet', "test_htt", 'test_root','test_delphes','test_delphesMA5tune']:
-            makefile = 'Makefile_'+package[5:]
+        elif package in ['test_process', 'test_commons', 'test_zlib', 'test_fastjet', "test_substructure", "test_htt",
+                         'test_root', 'test_delphes', 'test_delphesMA5tune']:
+            makefile = 'Makefile_' + package[5:]
         else:
             makefile = 'Makefile_'+package
 
@@ -451,15 +477,17 @@ def Link(self,package,folder):
         # log file name
         if package in ['process','commons','test','configuration']:
             logfile = folder+'/linking.log'
-        elif package in ['test_process','test_commons','test_zlib','test_fastjet',"test_htt",'test_root','test_delphes','test_delphesMA5tune']:
+        elif package in ['test_process', 'test_commons', 'test_zlib', 'test_fastjet', "test_substructure", "test_htt",
+                         'test_root', 'test_delphes', 'test_delphesMA5tune']:
             logfile = folder+'/linking_'+package[5:]+'.log'
         else:
             logfile = folder+'/linking_'+package+'.log'
 
         # makefile
         if package in ['process','commons','test','configuration']:
             makefile = 'Makefile'
-        elif package in ['test_process','test_commons','test_zlib','test_fastjet',"test_htt",'test_root','test_delphes','test_delphesMA5tune']:
+        elif package in ['test_process', 'test_commons', 'test_zlib', 'test_fastjet', "test_substructure", "test_htt",
+                         'test_root', 'test_delphes', 'test_delphesMA5tune']:
             makefile = 'Makefile_'+package[5:]
         else:
             makefile = 'Makefile_'+package
@@ -483,15 +511,17 @@ def Clean(self,package,folder):
         # log file name
         if package in ['process','commons','configuration','test']:
             logfile = folder+'/cleanup.log'
-        elif package in ['test_process','test_commons','test_zlib','test_fastjet',"test_htt",'test_root','test_delphes','test_delphesMA5tune']:
+        elif package in ['test_process', 'test_commons', 'test_zlib', 'test_fastjet', "test_substructure", "test_htt",
+                         'test_root', 'test_delphes', 'test_delphesMA5tune']:
             logfile = folder+'/cleanup_'+package[5:]+'.log'
         else:
             logfile = folder+'/cleanup_'+package+'.log'
 
         # makefile
         if package in ['process','commons','test','configuration']:
             makefile = 'Makefile'
-        elif package in ['test_process','test_commons','test_zlib','test_fastjet',"test_htt",'test_root','test_delphes','test_delphesMA5tune']:
+        elif package in ['test_process', 'test_commons', 'test_zlib', 'test_fastjet', "test_substructure", "test_htt",
+                         'test_root', 'test_delphes', 'test_delphesMA5tune']:
             makefile = 'Makefile_'+package[5:]
         else:
             makefile = 'Makefile_'+package
@@ -515,7 +545,8 @@ def MrProper(self,package,folder):
         # log file name
         if package in ['process','commons','configuration']:
             logfile = folder+'/mrproper.log'
-        elif package in ['test_process','test_commons','test_zlib','test_root','test_fastjet',"test_htt",'test_delphes','test_delphesMA5tune']:
+        elif package in ['test_process', 'test_commons', 'test_zlib', 'test_root', 'test_fastjet', "test_substructure",
+                         "test_htt", 'test_delphes', 'test_delphesMA5tune']:
             logfile = folder+'/mrproper_'+package[5:]+'.log'
         else:
             logfile = folder+'/mrproper_'+package+'.log'
@@ -525,7 +556,8 @@ def MrProper(self,package,folder):
         # makefile
         if package in ['process','commons','test','configuration']:
             makefile = 'Makefile'
-        elif package in ['test_process','test_commons','test_zlib','test_root','test_fastjet',"test_htt",'test_delphes','test_delphesMA5tune']:
+        elif package in ['test_process', 'test_commons', 'test_zlib', 'test_root', 'test_fastjet', "test_substructure",
+                         "test_htt", 'test_delphes', 'test_delphesMA5tune']:
             makefile = 'Makefile_'+package[5:]
         else:
             makefile = 'Makefile_'+package