Jet Substructure

.gitignore

@@ -0,0 +1,14 @@
+*/*.pyc
+*/*/*.pyc
+*/*/*/*.pyc
+*/*/*/*.log
+tools/SampleAnalyzer/Interfaces/Makefile_*
+tools/SampleAnalyzer/Test/Makefile_*
+*/*/*.aux
+*/*/*.bbl
+*/*/*.blg
+*/*/*.toc
+*/*/*.out
+*/*/*.log
+doc/??????_mode.log
+doc/??????_mode.pdf

README.md

@@ -2,10 +2,11 @@
 
 [![PAD](https://img.shields.io/static/v1?style=plastic&label=Recasting&message=PublicAnalysisDatabase&color=blue)](http://madanalysis.irmp.ucl.ac.be/wiki/PublicAnalysisDatabase)
 [![TUTO](https://img.shields.io/static/v1?style=plastic&label=Tutorials&message=@HomePage&color=red)](https://madanalysis.irmp.ucl.ac.be/wiki/tutorials)
+[![Talks](https://img.shields.io/static/v1?style=plastic&label=Talks&message=@HomePage&color=red)](http://madanalysis.irmp.ucl.ac.be/wiki/Talks)
 [![FAQ](https://img.shields.io/static/v1?style=plastic&label=FAQ&message=NormalMode&color=orange)](http://madanalysis.irmp.ucl.ac.be/wiki/FAQNormalMode)
 
-![Python v3.8](https://img.shields.io/badge/python-3670A0?style=plastic&logo=python&logoColor=ffdd54&label=3.6|3.7|3.8&color=brightgreen)
-![C++](https://img.shields.io/badge/c++-%2300599C.svg?style=plastic&logo=c%2B%2B&logoColor=white&label=98|11)
+![Python v3.8](https://img.shields.io/badge/python-3670A0?style=plastic&logo=python&logoColor=ffdd54&label=3.8&color=brightgreen)
+![C++](https://img.shields.io/badge/c++-%2300599C.svg?style=plastic&logo=c%2B%2B&logoColor=white&label=11)
 ## Outline
  - [What is MadAnalysis 5?](#what-is-madanalysis-5)
  - [Requirements](#requirements)
@@ -14,6 +15,7 @@
  - [Description of the package](#description-of-the-package)
  - [Very first steps with MadAnalysis 5](#very-first-steps-with-madanalysis-5)
  - [Troubleshootings and bug reports](#troubleshootings-and-bug-reports)
+ - [Supported third party software](#supported-third-party-software)
  - [Authors](#authors)
  - [Our famous last words](#our-famous-last-words)
  - [Credits](#credits)
@@ -44,7 +46,7 @@ More details can be found on the [MadAnalysis 5 website](https://madanalysis.irm
 
 MadAnalysis 5 requires several external libraries in order to properly run:
 
- - Python 3.6 or a more recent version that can be downloaded from [this website](http://www.python.org/)
+ - Python 3.8 or a more recent version that can be downloaded from [this website](http://www.python.org/)
    In order to check the installed version of Python on a system, it is
    sufficient to issue in a shell `$ python --version`.
 
@@ -225,6 +227,16 @@ suggested to create a report on [GitHub Issues](https://github.com/MadAnalysis/m
 In this way, you also participate to the improvement of MadAnalysis 5 and the
 authors thank you for this.
 
+### Supported third party software
+
+In the following you can find supported third party software that can be used within MadAnalysis 5.
+The [latest release](https://github.com/MadAnalysis/madanalysis5/releases) of MadAnalysis 5 has been tested with enlisted versions.
+
+- [FastJet](http://fastjet.fr) v3.3.3
+- [Delphes](https://github.com/delphes/delphes) v3.4.3
+- [ROOT](https://root.cern) v6.04.08
+- [pyhf](https://github.com/scikit-hep/pyhf) v0.6.3
+
 ### Authors
 
 MadAnalysis 5 is openly developed by the core dev team consisting of:

bin/ma5

@@ -33,19 +33,17 @@ and call immediately the command line interface scripts"""
 
 # Checking if the correct release of Python is installed
 import sys
-if  (sys.version_info[0] == 2 and sys.version_info[1] < 7) or (sys.version_info[0] == 3 and sys.version_info[1] < 6):
+if  sys.version_info[0] != 3 or sys.version_info[1] <= 6:
     sys.exit('Python release '+ sys.version + ' is detected.\n' + \
-    'MadAnalysis 5 works only with python 2.7 ' + \
-    'or  python 3.6 and later.\n' + \
-    'Please upgrade your version of python.')
+    'MadAnalysis 5 works only with Python version 3.7 and more recent version.\n' + \
+    'Please upgrade your Python installation.')
 
 # Checking that the 'six' package is present
 try:
     import six
 except:
-    sys.exit('The python "six" module is not found on your system and it is required for MadAnalysis 5 for ' +\
-    'a question of Python 2/3 compatibility. Please install it with the following command:\n' +\
-    'pip install six')  
+    sys.exit('The python "six" module is not found on your system. ' +\
+             'Please install it with by typing in a shell:\n  python -m pip install six')
 
 # Getting the parent directory (ma5 root dir) of the script real path (bin)
 import os
@@ -69,8 +67,8 @@ sys.path.insert(0, servicedir)
 
 # Release version
 # Do not touch it !!!!!  
-version = "1.10.0"
-date = "2022/01/12"
+version = "1.10.2"
+date = "2022/02/15"
 
 # Loading the MadAnalysis session
 import madanalysis.core.launcher

madanalysis/IOinterface/job_writer.py

@@ -23,13 +23,17 @@
 
 
 from __future__ import absolute_import
-from madanalysis.selection.instance_name      import InstanceName
-from madanalysis.IOinterface.folder_writer    import FolderWriter
-from shell_command                            import ShellCommand
+
 import logging
-import shutil
 import os
+import shutil
+
 import six
+from shell_command import ShellCommand
+
+from madanalysis.IOinterface.folder_writer import FolderWriter
+from madanalysis.selection.instance_name import InstanceName
+
 
 class JobWriter(object):
 
@@ -459,14 +463,13 @@ def CreateMainFct(self,file,analysisName,outputName):
 
         # Fast-Simulation detector
         # + Case Fastsim
+        # + Case extra jet definitions
         if self.main.fastsim.package=="fastjet":
             file.write('  //Getting pointer to the clusterer\n')
             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])):
+            for k,v in sorted(six.iteritems(parameters),key=lambda k_v: (k_v[0],k_v[1])):
                 file.write('  parametersC1["'+k+'"]="'+v+'";\n')
-
             for obj in ["electron","muon","track","photon"]:
                 if len(getattr(self.main.superfastsim, obj+"_isocone_radius")) != 0:
                     file.write(
@@ -478,6 +481,24 @@ def CreateMainFct(self,file,analysisName,outputName):
             file.write('      manager.InitializeJetClusterer("'+\
                        self.main.fastsim.clustering.algorithm+'",parametersC1);\n')
             file.write('  if (cluster1==0) return 1;\n\n')
+            if len(self.main.jet_collection) > 0:
+                # Write configuration for other jets
+                for ix, (key, item) in enumerate(self.main.jet_collection.collection.items()):
+                    map_name = "JetConfiguration"+str(ix+1)
+                    file.write('  //Adding new jet with ID ' + key + '\n')
+                    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')
+                        else:
+                            # To follow old syntax add "cluster.". 
+                            # This is not necessary but makes sense for unified syntax
+                            opt = opt.replace('radius','R')
+                            opt = opt.replace('ptmin','PTmin')
+                            valule = val if type(val) != bool else val*(1)
+                            file.write('  '+map_name+'["'+('cluster.'+opt+'"').ljust(18,' ') +\
+                                                       '] = "'+str(valule)+'";\n')
+                    file.write('  cluster1->LoadJetConfiguration('+map_name+');\n\n')
             if self.main.superfastsim.isNewSmearerOn():
                 file.write('  // Declaration of the smearer\n')
                 file.write('  SmearerBase* mySmearer = new NewSmearer();\n')
@@ -486,14 +507,16 @@ def CreateMainFct(self,file,analysisName,outputName):
                 file.write('  // Declaration of a generic tagger\n')
                 file.write('  NewTagger* tagger = new NewTagger();\n\n')
 
+
         # + Case Delphes
         if self.main.fastsim.package in ["delphes","delphesMA5tune"]:
             file.write('  //Getting pointer to fast-simulation package\n')
             file.write('  std::map<std::string, std::string> parametersD1;\n')
-            if self.fastsim.package=="delphesMA5tune":
-                cfg=self.main.fastsim.delphesMA5tune
-            else:
-                cfg=self.main.fastsim.delphes
+            #@JACK: This variable is not used
+            #if self.fastsim.package=="delphesMA5tune":
+            #    cfg=self.main.fastsim.delphesMA5tune
+            #else:
+            #    cfg=self.main.fastsim.delphes
             parameters = self.main.fastsim.SampleAnalyzerConfigString()
             for k,v in sorted(six.iteritems(parameters),\
                               key=lambda k_v1: (k_v1[0],k_v1[1])):
@@ -667,44 +690,10 @@ def WriteSelectionSource(self,main):
         file.close()
         return True
 
-    def WriteSampleAnalyzerMakefile(self,option=""):
-
-        from madanalysis.build.makefile_writer import MakefileWriter
-        options=MakefileWriter.MakefileOptions()
-
-        # Name of the Makefile
-        filename = self.path+"/Build/SampleAnalyzer/Makefile"
-
-        # Header
-        title='User package'
-        toRemove = []
-
-        # Options
-        option.has_commons   = True
-        options.has_process  = True
-        if self.main.archi_info.has_root:
-            options.has_root_inc = True
-            options.has_root_lib = True
-        toRemove.extend(['compilation.log','linking.log','cleanup.log','mrproper.log'])
-
-        # File to compile
-        cppfiles = package+'/*.cpp'
-        hfiles   = package+'/*.h'
-
-        # Files to produce
-        isLibrary=True
-        ProductName='libUserPackage_for_ma5.so'
-        ProductPath='../../Build/Lib/'
-
-        # write makefile
-        MakefileWriter.Makefile(filename,title,ProductName,ProductPath,isLibrary,cppfiles,hfiles,options,self.main.archi_info,toRemove)
-
-        # Ok
-        return True
-
-
-    def WriteMakefiles(self,option=""):
 
+    def WriteMakefiles(self,option="",**kwargs):
+        # kwargs: keyword arguments regarding additional mode options such as `ma5_fastjet_mode`
+        # this will protect Delphes based analyses in PAD
         from madanalysis.build.makefile_writer import MakefileWriter
         options=MakefileWriter.MakefileOptions()
 
@@ -717,9 +706,20 @@ def WriteMakefiles(self,option=""):
         # Options
         options.has_commons  = True
         options.has_process  = True
-        if self.main.archi_info.has_root:
-            options.has_root_inc = True
-            options.has_root_lib = True
+        # @JACK enable usage of fastjet
+        # If there are any root files, fastjet clusterer should not run with MA5_FASTJET_MODE Flag
+        options.ma5_fastjet_mode   = (
+            all([all([('root' not in x) for x in dataset.filenames]) for dataset in self.main.datasets]) 
+            and self.main.archi_info.has_fastjet 
+            and kwargs.get('ma5_fastjet_mode',True)
+            and self.main.fastsim.package == 'fastjet'
+        )
+        options.has_fastjet_lib    = self.main.archi_info.has_fastjet
+        options.has_fastjet_ma5lib = self.main.archi_info.has_fastjet
+        # @JACK: fastjet_inc is required to be able to use the FJ files when FJ mode is on
+        options.has_fastjet_inc    = self.main.archi_info.has_fastjet
+        options.has_root_inc       = self.main.archi_info.has_root
+        options.has_root_lib       = self.main.archi_info.has_root
         #options.has_userpackage = True
         toRemove=['Log/compilation.log','Log/linking.log','Log/cleanup.log','Log/mrproper.log']
 

madanalysis/IOinterface/library_writer.py

@@ -164,15 +164,23 @@ def WriteMakefileForInterfaces(self,package):
             options.has_commons=True
             options.has_fastjet_inc=True
             options.has_fastjet_lib=True
+            # @JACK: To be able to use fastjet in Ma5 data structure
+            options.ma5_fastjet_mode=True
             toRemove.extend(['compilation_fastjet.log','linking_fastjet.log','cleanup_fastjet.log','mrproper_fastjet.log'])
         elif package=='test_fastjet':
             options.has_commons=True
             options.has_fastjet_ma5lib=True
+            options.has_fastjet_inc=True
           #  options.has_fastjet_lib=True
             toRemove.extend(['compilation_fastjet.log','linking_fastjet.log','cleanup_fastjet.log','mrproper_fastjet.log','../Bin/TestFastjet.log'])
         elif package=='configuration':
             toRemove.extend(['compilation.log','linking.log','cleanup.log','mrproper.log'])
         elif package=='commons':
+            # @JACK: This will allow us to dynamically use the FJ libraries in commons
+            options.ma5_fastjet_mode   = self.main.archi_info.has_fastjet
+            options.has_fastjet_inc    = self.main.archi_info.has_fastjet
+            options.has_fastjet_lib    = self.main.archi_info.has_fastjet
+            # options.has_fastjet_ma5lib = self.main.archi_info.has_fastjet
             toRemove.extend(['compilation.log','linking.log','cleanup.log','mrproper.log'])
         elif package=='test_commons':
             options.has_commons  = True
@@ -252,6 +260,11 @@ def WriteMakefileForInterfaces(self,package):
             options.has_zlib_tag              = self.main.archi_info.has_zlib
             options.has_root_tag              = self.main.archi_info.has_root
             options.has_root_ma5lib           = self.main.archi_info.has_root
+            # @JACK: For fastjet to be accessible through ma5 datastructure
+            options.has_fastjet_inc    = self.main.archi_info.has_fastjet
+            options.has_fastjet_lib    = self.main.archi_info.has_fastjet
+            options.ma5_fastjet_mode   = self.main.archi_info.has_fastjet
+
             toRemove.extend(['compilation.log','linking.log','cleanup.log','mrproper.log'])
         elif package=='test_process':
             options.has_commons               = True