diff --git a/Trigger/TrigValidation/TrigUpgradeTest/share/RunMenuTest.ref b/Trigger/TrigValidation/TrigUpgradeTest/share/RunMenuTest.ref
index 82b7e4a12fa73368dc265a485f11b5d47a5362c9..739e534823a1da683ed4ecd43135aac0fb09970d 100644
--- a/Trigger/TrigValidation/TrigUpgradeTest/share/RunMenuTest.ref
+++ b/Trigger/TrigValidation/TrigUpgradeTest/share/RunMenuTest.ref
@@ -1,41 +1,9 @@
 TrigSignatureMoniMT                                INFO Chains passing step (1st row events & 2nd row decision counts
 TrigSignatureMoniMT                                INFO Chain name                   L1,      AfterPS, [... steps ...], Output
 TrigSignatureMoniMT                                INFO All                           20        20        0         0         17        
-TrigSignatureMoniMT                                INFO HLT_2e3_etcut                 20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_2e3_etcut decisions                           0         0         
-TrigSignatureMoniMT                                INFO HLT_2mu6                      20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_2mu6 decisions                                0         0         
-TrigSignatureMoniMT                                INFO HLT_e15mu24                   20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_e15mu24 decisions                             0         0         
 TrigSignatureMoniMT                                INFO HLT_e3_etcut                  20        20        18        17        17        
 TrigSignatureMoniMT                                INFO HLT_e3_etcut decisions                            54        262       
-TrigSignatureMoniMT                                INFO HLT_e3e5_etcut                20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_e3e5_etcut decisions                          0         0         
 TrigSignatureMoniMT                                INFO HLT_e5_etcut                  20        20        17        16        16        
 TrigSignatureMoniMT                                INFO HLT_e5_etcut decisions                            50        251       
-TrigSignatureMoniMT                                INFO HLT_e7_etcut                  20        20        11        11        11        
-TrigSignatureMoniMT                                INFO HLT_e7_etcut decisions                            17        117       
-TrigSignatureMoniMT                                INFO HLT_g5_etcut                  20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_g5_etcut decisions                            0         0         
-TrigSignatureMoniMT                                INFO HLT_j35_gsc45_bmv2c1070       20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_j35_gsc45_bmv2c1070 decisions                    0         0         
-TrigSignatureMoniMT                                INFO HLT_j35_gsc45_bmv2c1070_split 20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_j35_gsc45_bmv2c1070_split decisions                    0         0         
-TrigSignatureMoniMT                                INFO HLT_j35_gsc45_boffperf_split  20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_j35_gsc45_boffperf_split decisions                    0         0         
-TrigSignatureMoniMT                                INFO HLT_j60                       20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_j60 decisions                                 0         0         
-TrigSignatureMoniMT                                INFO HLT_j85                       20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_j85 decisions                                 0         0         
-TrigSignatureMoniMT                                INFO HLT_mu20                      20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_mu20 decisions                                0         0         
-TrigSignatureMoniMT                                INFO HLT_mu6                       20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_mu6 decisions                                 0         0         
-TrigSignatureMoniMT                                INFO HLT_mu6idperf                 20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_mu6idperf decisions                           0         0         
-TrigSignatureMoniMT                                INFO HLT_te15                      20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_te15 decisions                                0         0         
-TrigSignatureMoniMT                                INFO HLT_xe10                      20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_xe10 decisions                                0         0         
-TrigSignatureMoniMT                                INFO HLT_xs20                      20        20        0         0         0         
-TrigSignatureMoniMT                                INFO HLT_xs20 decisions                                0         0         
+TrigSignatureMoniMT                                INFO HLT_e7_etcut                  20        20        15        14        14        
+TrigSignatureMoniMT                                INFO HLT_e7_etcut decisions                            36        205       
diff --git a/Trigger/TrigValidation/TrigUpgradeTest/share/runMenuTest.py b/Trigger/TrigValidation/TrigUpgradeTest/share/runMenuTest.py
index a3e1c38e49794b2b83443caa8484418bca91229d..520d8cb58cc78ecab3c05f23c0cc7540d36c6c8d 100644
--- a/Trigger/TrigValidation/TrigUpgradeTest/share/runMenuTest.py
+++ b/Trigger/TrigValidation/TrigUpgradeTest/share/runMenuTest.py
@@ -5,23 +5,23 @@
 # import flags
 include("TrigUpgradeTest/testHLT_MT.py")
 
+from AthenaCommon.Constants import VERBOSE,INFO,DEBUG
 from TriggerJobOpts.TriggerFlags import TriggerFlags
 TriggerFlags.triggerMenuSetup = "LS2_v1"
 
 from TriggerMenuMT.HLTMenuConfig.Menu.GenerateMenuMT import GenerateMenuMT
-g = GenerateMenuMT()
+menu = GenerateMenuMT(DEBUG)
 
 
 
 # set some flags
-g.doEgammaChains=True
+menu.doEgammaChains      = True
+menu.doJetChains         = False
+menu.doMuonChains        = False
+menu.doCombinedChains    = False
 
-g.generateMT()
-
-#allChainConfigs = g.getChainsFromMenu()
-#EnabledChainNamesToCTP = dict([ (c[0], c[1])  for c in allChainConfigs])
-#topSequence.L1DecoderTest.ChainToCTPMapping = EnabledChainNamesToCTP
- 
+# generate the Chains from the Menu Dictionary
+allChainConfigs = menu.generateMT()
 
 
 ##########################################  
diff --git a/Trigger/TriggerCommon/TriggerMenuMT/python/HLTMenuConfig/Menu/GenerateMenuMT.py b/Trigger/TriggerCommon/TriggerMenuMT/python/HLTMenuConfig/Menu/GenerateMenuMT.py
index e0acb90930cac7017fffaded7ed530a7a92e887b..93b72656577a3da73707680c16429f55bc85c1f9 100755
--- a/Trigger/TriggerCommon/TriggerMenuMT/python/HLTMenuConfig/Menu/GenerateMenuMT.py
+++ b/Trigger/TriggerCommon/TriggerMenuMT/python/HLTMenuConfig/Menu/GenerateMenuMT.py
@@ -13,6 +13,7 @@ AlgScheduler.ShowDataFlow( True )
 
 from AthenaCommon.CFElements import parOR, seqAND, stepSeq
 from AthenaCommon.AlgSequence import AlgSequence, AthSequencer
+from AthenaCommon.Constants import VERBOSE,INFO,DEBUG
 
 from TriggerMenuMT.HLTMenuConfig.Menu.TriggerConfigHLT  import TriggerConfigHLT
 from TriggerMenuMT.HLTMenuConfig.Menu.HLTCFConfig import *
@@ -28,12 +29,14 @@ import os, traceback, operator, commands, time
 from AthenaCommon.Logging import logging
 log = logging.getLogger( 'TriggerMenuMT.HLTMenuConfig.Menu.GenerateMenuMT' )
 
+
 _func_to_modify_the_menu = None
 _func_to_modify_signatures = None
 
 class GenerateMenuMT:   
     
-    def __init__(self):
+    def __init__(self, logLevel=DEBUG):
+        log.setLevel(logLevel)
         self.triggerConfigHLT = None
         self.chains = []
         self.chainDefs = []
@@ -253,4 +256,5 @@ class GenerateMenuMT:
                 print step
 
         makeHLTTree(finalListOfChainConfigs)
+        return finalListOfChainConfigs
             
diff --git a/Trigger/TriggerCommon/TriggerMenuMT/python/HLTMenuConfig/Menu/HLTCFConfig.py b/Trigger/TriggerCommon/TriggerMenuMT/python/HLTMenuConfig/Menu/HLTCFConfig.py
index c93b3db116deb2c27eaa012a0e020cb67b676b98..63a50bfe2a16ad2874af3a2fed67d720dc506b9d 100644
--- a/Trigger/TriggerCommon/TriggerMenuMT/python/HLTMenuConfig/Menu/HLTCFConfig.py
+++ b/Trigger/TriggerCommon/TriggerMenuMT/python/HLTMenuConfig/Menu/HLTCFConfig.py
@@ -107,43 +107,50 @@ def createCFTree(CFseq):
 
 def makeHLTTree(HLTChains):
     """ creates the full HLT tree"""
-    #    TopHLTRootSeq = seqAND("TopHLTRoot") # Root
-    # main HLT top sequence
-    hltTop = seqOR("hltTop")
+
+    # lock flags
+    from AthenaConfiguration.AllConfigFlags import ConfigFlags
+    ConfigFlags.lock()
+
+    # get totpSequnece
+    from AthenaCommon.AlgSequence import AlgSequence
+    topSequence = AlgSequence()
 
     #add the L1Upcacking
-#    TopHLTRootSeq += L1UnpackingSeq
+    #    TopHLTRootSeq += L1UnpackingSeq
+
+    # connect to L1Decoder
+    l1decoder = [ d for d in topSequence.getChildren() if d.getType() == "L1Decoder" ]
+    if len(l1decoder)  != 1 :
+        raise RuntimeError(" Can't find 1 instance of L1Decoder in topSequence, instead found this in topSequence "+str(topSequence.getChildren()) )
+
+
+    # set CTP chains before creating the full tree (and the monitor)
+    EnabledChainNamesToCTP = dict([ (c.name, c.seed)  for c in HLTChains])
+    l1decoder[0].ChainToCTPMapping = EnabledChainNamesToCTP
 
+    # main HLT top sequence
+    hltTop = seqOR("hltTop")
+ 
     # add the HLT steps Node
     steps = seqAND("HLTAllSteps")
     hltTop +=  steps
     
     # make CF tree
     finalDecisions = decisionTree_From_Chains(steps, HLTChains)
-    EnabledChainNames = [c.name for c in HLTChains]
     
-
+    # make Summary
     flatDecisions=[]
     for step in finalDecisions: flatDecisions.extend (step)
     summary= makeSummary("TriggerSummaryFinal", flatDecisions)
     #from TrigOutputHandling.TrigOutputHandlingConf import HLTEDMCreator
-    #edmCreator = HLTEDMCreator()
-    
+    #edmCreator = HLTEDMCreator()    
     #edmCreator.TrigCompositeContainer = flatDecisions
     #summary.OutputTools= [ edmCreator ]
     hltTop += summary
 
-    from AthenaCommon.AlgSequence import AlgSequence
-    topSequence = AlgSequence()
-
+    # add some more monitor
     from TriggerJobOpts.TriggerConfig import collectHypos, triggerMonitoringCfg, triggerSummaryCfg
-    from AthenaConfiguration.AllConfigFlags import ConfigFlags
-    ConfigFlags.lock()
-    
-    l1decoder = [ d for d in topSequence.getChildren() if d.getType() == "L1Decoder" ]
-    if len(l1decoder)  != 1 :
-        raise RuntimeError(" Can't find 1 instance of L1Decoder in topSequence, instead found this in topSequence "+str(topSequence.getChildren()) )
-
     hypos = collectHypos(steps)
     summaryAcc, summaryAlg = triggerSummaryCfg( ConfigFlags, hypos )
     hltTop += summaryAlg