add option to include CRs and VRs in the full likelihood

Option introduced in the `.info` file of the analysis e.g.
```
  <pyhf id="RegionC">
    <name>atlas_susy_2018_31_SRC.json</name>
    <regions>
      <channel name="CRtt_cuts"> </channel>
      <channel name="SR_metsigST">
      SRC_22
      SRC_24
      SRC_26
      SRC_28
      </channel>
      <channel name="VRzAlt_cuts" is_included="True"> </channel>
      <channel name="CRz_cuts" is_included="True"> </channel>
      <channel name="VRtt_cuts"> </channel>
      <channel name="VRz_cuts"> </channel>
    </regions>
  </pyhf>
```
If there is no data present in the channel code will look for `is_included`
tag which can be "True", "yes", "1". If true the channel will be included
in the likelihood calculation if not it will be removed. If `is_included`
is not present and channel does not have any data, it will be removed by
default.

madanalysis/misc/histfactory_reader.py

@@ -34,19 +34,15 @@ def __init__(self,pyhf_config):
         self.path        = pyhf_config.get('path', 'missing_path')
         self.name        = pyhf_config.get('name', 'missing_name')
         self.logger      = logging.getLogger('MA5')
-        if type(self) == HF_Background:
+        if isinstance(self, HF_Background):
             self.hf             = {}
             self.global_config  = self.pyhf_config
-        elif type(self) == HF_Signal:
+        elif isinstance(self, HF_Signal):
             self.hf      = []
 
     def __call__(self,lumi):
         return self.extrapolate(lumi)
 
-    @classmethod
-    def __type__(self):
-        return self.__name__
-
     def extrapolate(self,lumi):
         """ To calculate the HL variables HF needs to be extrapolated. Expected
             observables will be extrapolated and summed, summation is superseeded
@@ -107,7 +103,7 @@ def extrapolate(self,lumi):
                         if item != []:
                             HF['observations'][iobs]['data'] = item
 
-        elif isinstance(self,HF_Signal):#type(self) == HF_Signal:
+        elif isinstance(self, HF_Signal):#type(self) == HF_Signal:
             # Signal extrapolation
             for i in range(len(HF)):
                 if HF[i]['op'] == 'remove':
@@ -214,23 +210,27 @@ class HF_Signal(HistFactory):
         is failed and correct pyhf_config is needed.
     """
     def __init__(self,pyhf_config, regiondata, xsection=-1, **kwargs):
-        super(HF_Signal,self).__init__(pyhf_config)
+        super(HF_Signal, self).__init__(pyhf_config)
         self.signal_config = {}
 
         with open(os.path.join(self.path, self.name), 'r') as json_file:
             tmp_bkg = json.load(json_file)
 
+        bin_sizes = [len(x.get('data', [])) for x in tmp_bkg.get('observations',[])]
+
         for key, item in self.pyhf_config.items():
             if key != 'lumi':
                 self.signal_config[key] = {}
-                if item['data'] == []:
+                if not item['is_included']:
                     self.signal_config[key]['op'] = 'remove'
                     self.signal_config[key]["path"] = '/channels/' + str(item['channels'])
                 else:
                     self.signal_config[key]['op'] = 'add'
                     self.signal_config[key]["path"] = \
                         '/channels/' + str(item['channels']) + '/samples/' + \
                         str(len(tmp_bkg["channels"][int(item['channels'])]["samples"])-1)
+                    self.signal_config[key]["bin_size"] = \
+                        bin_sizes[int(self.signal_config[key]["path"].split('/')[2])]
 
                 self.signal_config[key]['data'] = []
                 for SRname in item['data']:
@@ -247,7 +247,7 @@ def __init__(self,pyhf_config, regiondata, xsection=-1, **kwargs):
                                         add_normsys  = kwargs.get('add_normsys', []),
                                         add_histosys = kwargs.get('add_histosys',[]),)
 
-    def set_HF(self,xsection,**kwargs):
+    def set_HF(self, xsection, **kwargs):
         HF = []
         if xsection<=0.:
             return HF
@@ -269,6 +269,8 @@ def set_HF(self,xsection,**kwargs):
                         ]
                     }
                 }
+                if len(SR_tmp["value"]["data"]) == 0:
+                    SR_tmp["value"]["data"] = [0.0] * self.signal_config[SR]['bin_size']
                 HF.append(SR_tmp)
             else:
                 toRemove.append(
@@ -287,13 +289,13 @@ def set_HF(self,xsection,**kwargs):
             HF = self.add_normsys(HF,sys['hi_data'],sys['lo_data'],sys['name'])
 
         background = kwargs.get('background',{})
-        if type(background) == HF_Background:
-            if not self.validate_bins(background,HF):
+        if isinstance(background, HF_Background):
+            if not self.validate_bins(background, HF):
                 self.logger.warning('Signal HistFactory validation failed.')
                 return []
         return HF
 
-    def validate_bins(self,background,HF=[]):
+    def validate_bins(self, background, HF = []):
         if HF == []:
             HF = self.hf
         bkg_bins    = background.size()

madanalysis/misc/run_recast.py

@@ -923,11 +923,10 @@ def parse_info_file(self, etree, analysis, extrapolated_lumi):
             return -1,-1, -1
         ## Getting the XML information
         try:
-            info_input = open(filename)
-            info_tree = etree.parse(info_input)
-            info_input.close()
+            with open(filename, "r") as info_input:
+                info_tree = etree.parse(info_input)
         except Exception as err:
-            self.logger.warning("Error during HMTL parsing: "+str(err))
+            self.logger.warning("Error during XML parsing: "+str(err))
             self.logger.warning('Cannot parse the info file')
             return -1,-1, -1
 
@@ -1251,9 +1250,15 @@ def pyhf_info_file(self,info_root):
                                     if channel.text != None:
                                         data = channel.text.split()
                                     pyhf_config[likelihood_profile]['SR'][channel.attrib['name']] = {
-                                        'channels' : channel.attrib.get('id',-1),
-                                        'data'     : data
+                                        "channels"    : channel.get('id', default = -1),
+                                        "data"        : data,
                                     }
+                                    is_included = (
+                                            channel.get("is_included", default = 0) in ["True", "1", "yes"]
+                                    ) if len(data) == 0 else True
+                                    pyhf_config[likelihood_profile]['SR'][channel.attrib['name']].update(
+                                        {"is_included" : is_included}
+                                    )
                                     if pyhf_config[likelihood_profile]['SR'][channel.attrib['name']]['channels'] == -1:
                                         file = os.path.join(
                                             pyhf_config[likelihood_profile]['path'],
@@ -1276,7 +1281,7 @@ def pyhf_info_file(self,info_root):
                 continue
             # validat pyhf config
             background = HF_Background(config)
-            signal     = HF_Signal(config,{},xsection=1.,
+            signal     = HF_Signal(config, {}, xsection=1.,
                                    background = background,
                                    validate   = True)