MenuAlignmentTools.MenuAlignment Class Reference

Collaboration diagram for MenuAlignmentTools.MenuAlignment:

Public Member Functions
def	__init__ (self, combinations_in_menu, groups_to_align, length_of_configs)
def	analyse_combinations (self)
def	alignment_group_is_alone (self, alignment_grp)
def	alignment_group_is_first (self, alignment_grp)
def	get_groups_to_align (self, alignment_grp)
def	single_align (self, chainDict, chainConfig)
def	multi_align (self, chainDict, chainConfig, lengthOfChainConfigs)

Public Attributes
	combinations_in_menu
	length_of_configs
	groups_to_align
	signature_dict
	inverse_sig_dict
	sets_to_align

Detailed Description

Class to hold/calculate chain alignment 

Definition at line 79 of file MenuAlignmentTools.py.

Constructor & Destructor Documentation

__init__()

def MenuAlignmentTools.MenuAlignment.__init__	(		self,
			combinations_in_menu,
			groups_to_align,
			length_of_configs
	)

Definition at line 81 of file MenuAlignmentTools.py.

    def __init__(self, combinations_in_menu, groups_to_align, length_of_configs):
    
        self.combinations_in_menu = combinations_in_menu
        self.length_of_configs = length_of_configs
        self.groups_to_align = groups_to_align
        
        self.signature_dict = {}
        self.inverse_sig_dict ={}
        
        self.sets_to_align = {}
 
        # first we make a dictionary of the ordering, based on the_signature_grouping 
        # e.g. 1 electron+photon, 2 muon, 3 tau, 4 jet/met/b-jet, 5 noL1 muons
        igrp = 0
        for value in the_signature_grouping.values():
            if value not in self.signature_dict:
                self.signature_dict[value] = igrp
                igrp += 1
        
        self.inverse_sig_dict = {v: k for k, v in self.signature_dict.items()}
 

Member Function Documentation

alignment_group_is_alone()

def MenuAlignmentTools.MenuAlignment.alignment_group_is_alone	(		self,
			alignment_grp
	)

Definition at line 182 of file MenuAlignmentTools.py.

    def alignment_group_is_alone(self, alignment_grp):
        # no need to align lonely alignment groups
        # the latter condition should never happen, because we only put in alignment groups that are 
        # in combined chains, and thus will need *some* aligning. but good to check in any case.
        if alignment_grp not in self.sets_to_align:
            return True
        elif len(self.sets_to_align[alignment_grp]) == 1:
            return True
        return False
        

alignment_group_is_first()

def MenuAlignmentTools.MenuAlignment.alignment_group_is_first	(		self,
			alignment_grp
	)

Definition at line 192 of file MenuAlignmentTools.py.

    def alignment_group_is_first(self, alignment_grp):
    
        # if it's the first chain in the set to be aligned, again - nothing to do here.
        if alignment_grp == self.sets_to_align[alignment_grp][0]:
            return True
        return False
 

analyse_combinations()

def MenuAlignmentTools.MenuAlignment.analyse_combinations

(

self

)

Definition at line 123 of file MenuAlignmentTools.py.

    def analyse_combinations(self): #combinations_in_menu, alignmentGroups_in_combinations):
    
        # need to find out of if an alignment group, or anything in combination with that
        # aligment group, is in combination with any other alignment group.
        
        the_matrix = np.eye((len(self.signature_dict)))
        
        for comb in self.combinations_in_menu:
            for comb_pair in list(itertools.combinations(comb,2)):
                the_matrix[self.signature_dict[comb_pair[0]]][self.signature_dict[comb_pair[1]]] = 1  
                the_matrix[self.signature_dict[comb_pair[1]]][self.signature_dict[comb_pair[0]]] = 1
 
        _,eigenvecs = np.linalg.eig(the_matrix)
        # eigenvecs: The normalized (unit length) eigenvectors, such that the column v[:,i] 
        # is the eigenvector corresponding to the eigenvalue w[i].
        # so we do the transpose!
        eigenvecs = np.transpose(eigenvecs)
        
        # find the indices filled by each eigenvector, and make a unique list of these
        pre_unique_sets = list(set([tuple(np.nonzero(eigenvec)[0]) for eigenvec in eigenvecs]))
        
        # remove any that are subsets of another (e.g. because something like (1,1,1), (1,-1,1),(0,1,1)
        # could be an answer but (0,1,1) clearly is not spanning a unique subspace from (1,1,1))
        unique_sets = []
        for aset in pre_unique_sets:
            if len(unique_sets) == 0 : 
                unique_sets +=[aset]
            else: 
                inlist = True
                for ibset,bset in enumerate(unique_sets):
                    if aset == bset:
                        inlist = True
                        break
                    elif set(aset).issubset(set(bset)):
                        inlist = True
                        break
                    elif set(bset).issubset(set(aset)):
                        unique_sets.pop(ibset)
                        unique_sets += [aset]
                        inlist = True
                        break
                    else:
                        inlist = False
                if not inlist:
                    unique_sets +=[aset]
 
        # convert the indices back to actual signature names
        unique_by_sig = [[ self.inverse_sig_dict[sig_int] for sig_int in setlist ] for setlist in unique_sets]
 
        sig_to_set = {}
        for sig in self.groups_to_align:
            for aset in unique_by_sig:
                if sig in aset:
                    sig_to_set[sig] = aset
         
        self.sets_to_align = sig_to_set
        
        return
 

get_groups_to_align()

def MenuAlignmentTools.MenuAlignment.get_groups_to_align	(		self,
			alignment_grp
	)

Definition at line 199 of file MenuAlignmentTools.py.

    def get_groups_to_align(self, alignment_grp):
 
        all_groups_to_align = self.sets_to_align[alignment_grp]
        index_of_chain_group = self.sets_to_align[alignment_grp].index(alignment_grp)
 
        # we don't need to add empty steps for alignment groups that happen *after* the
        # one our chain belongs to - so just cut off at the chain's alignment group here.        
        return all_groups_to_align[:index_of_chain_group]
 
 

multi_align()

def MenuAlignmentTools.MenuAlignment.multi_align	(		self,
			chainDict,
			chainConfig,
			lengthOfChainConfigs
	)

Definition at line 239 of file MenuAlignmentTools.py.

    def multi_align(self, chainDict, chainConfig, lengthOfChainConfigs):
    
        lengthOfChainConfigs = remove_duplicates(lengthOfChainConfigs)
    
        alignment_grps = chainDict['alignmentGroups']
 
        #check for a few bad conditions first:
        if not set(alignment_grps).issubset(self.sets_to_align):
            log.error(" one of the alignmentGroups in %s is not available in the sets to align dictionary!", alignment_grps)
            raise Exception("MenuAlignment.analyse_combinations() needs checking, this should never happen.")
        elif len(set([tuple(self.sets_to_align[x]) for x in alignment_grps])) != 1:
            log.error(" the alignmentGroups %s point to different sets in the sets to align dictionary", alignment_grps)
            for x in alignment_grps:
                log.error("     Set: %s, group %s", self.sets_to_align[x] , x)
            raise Exception("MenuAlignment.analyse_combinations() needs checking, this should never happen.")
                
        #now we know that all alignmentGroups points to the same set, so just use the first entry
        if len(self.sets_to_align[alignment_grps[0]]) == 2:
 
           # if the pair is on its own, then we just make sure the first signature's number
           # of steps is equal to the max in that signature (so the next signature starts at the right step)
      
           # not a dictionary because we could have a chain mu_jet_munoL1? Not sure. But don't want to
           # overwrite duplicates yet. 
           # probably, at some point, will need to divide this beyond signature but instead as unique sequence within a signature. 
           # munoL1 is already one case...
           length_firstgrp = 0
           max_length_firstgrp = self.length_of_configs[self.sets_to_align[alignment_grps[0]][0]]
 
           for config_length,config_grp in lengthOfChainConfigs:
               if config_grp == self.sets_to_align[alignment_grps[0]][0]:
                   length_firstgrp = config_length
 
           if length_firstgrp < max_length_firstgrp:
               #too short! need to add padding steps between two alignment groups...
               needed_steps = max_length_firstgrp - length_firstgrp
               chainConfig.insertEmptySteps('Empty'+self.sets_to_align[alignment_grps[0]][0]+'Align',needed_steps,length_firstgrp) 
    
           elif length_firstgrp > max_length_firstgrp:
               log.error("%s first signature length %d is greater than the max calculated, %d",chainDict.name,length_firstgrp, max_length_firstgrp)     
               raise Exception("Probably something went wrong in GenerateMenuMT.generateChains()!")
 
        #this should probably work for signatures > 2, but might be a few gotchas (and errors need updating)
        #Can't properly test until ATR-22206 is resolved.
        elif len(self.sets_to_align[alignment_grps[0]]) > 2:
            if not set(alignment_grps).issubset(self.sets_to_align):
                log.error(" one of the alignmentGroups in %s is not available in the sets to align dictionary!", alignment_grps)
                raise Exception("MenuAlignment.analyse_combinations() needs checking, this should never happen.")
            elif len(set([tuple(self.sets_to_align[x]) for x in alignment_grps])) != 1:
                log.error(" the alignmentGroups %s point to different sets in the sets to align dictionary", alignment_grps)
                for x in alignment_grps:
                    log.error("     Set: %s, group %s", self.sets_to_align[x] , x)
                raise Exception("MenuAlignment.analyse_combinations() needs checking, this should never happen.")
            
            # first, we need to convert alignment_grps from the order it is based on the chain naming
            # convention into the order it needs to be for the alignment
            # these are not always the same thing!
            
            # takes the values of the ordering dictionary and creates a list of unique values
            # so it isn't just e.g. [egamma, egamma, egamma, JetMET, JetMET] but actually
            # [egamma, JetMET]
            alignment_grp_ordering = get_alignment_group_ordering()            
            alignment_grps_ordered = [x for x in alignment_grp_ordering if x in alignment_grps]
 
            # we need to know which alignment_grps are in the chain in which order. Assume this is always stored correctly.
            # (this should be true, once it is sorted! If not, there is a bug.)
            # never need to add empty steps to the last leg - it can end at a different
            # time (be a different number of steps) - no problem.
            # ignore any signatures after the end of those in this chain
            aligngroups_set = self.get_groups_to_align(alignment_grps_ordered[-1])
            aligngroups_set.reverse()
            grp_masks = [x in alignment_grps_ordered for x in aligngroups_set]
            grp_lengths = []
            for align_grp,grp_in_chain in zip(aligngroups_set,grp_masks):
                if grp_in_chain:
                  for config_length,config_grp in lengthOfChainConfigs:
                    if config_grp == align_grp: 
                        grp_lengths += [config_length]
                else:
                  grp_lengths += [0]
 
            for istep,(align_grp,grp_in_chain,length_in_chain) in enumerate(zip(aligngroups_set,grp_masks,grp_lengths)):
                # We're working our way backwards through the chain 
                # need to know how many steps are already before us!
                n_steps_before_grp = 0
                if istep < len(grp_lengths)-1: 
                    n_steps_before_grp = sum(grp_lengths[istep+1:])
                max_length_grp = self.length_of_configs[align_grp]
                if grp_in_chain:
                    if length_in_chain < max_length_grp:
                        #too short! gotta add padding steps between two alignmentGroups...
                        needed_steps = max_length_grp - length_in_chain
                        start_step = n_steps_before_grp + length_in_chain
                        chainConfig.insertEmptySteps('Empty'+align_grp+'Align',needed_steps,start_step) 
                else:
                    # this sig isn't in the chain, but we still will need empty steps for it
                    # always add them to the start, because we're running in reverse order
                    chainConfig.insertEmptySteps('Empty'+align_grp+'Align',self.length_of_configs[align_grp],n_steps_before_grp) 
        else:
             log.error("Should never reach this point. Ordered alignmentGroups: %s, sets_to_align: %s",alignment_grps_ordered,self.sets_to_align)
             raise Exception("MenuAlignment.multi_align() needs checking, this should never happen.")
 
        log.debug("Finished with retrieving chain configuration for chain %s", chainDict['chainName']) 
        chainConfig.numberAllSteps()
        
        return chainConfig

single_align()

def MenuAlignmentTools.MenuAlignment.single_align	(		self,
			chainDict,
			chainConfig
	)

Definition at line 209 of file MenuAlignmentTools.py.

    def single_align(self, chainDict, chainConfig):
      
      if len(set(chainDict['alignmentGroups'])) != 1:
          log.error("Cannot call single_align on chain %s with alignment groups %s",
                    chainDict['chainName'], ",".join(chainDict['alignmentGroups']))
          raise Exception("Will not proceed, the chain is not suitable for single alignment.")
 
      alignment_grp = chainDict['alignmentGroups'][0]
 
      if self.alignment_group_is_alone(alignment_grp):
        log.debug("Finished with retrieving chain configuration for chain %s", chainDict['chainName'])
        chainConfig.numberAllSteps()
      elif self.alignment_group_is_first(alignment_grp):
        # if it's the first chain in the set to be aligned, again - nothing to do here,
        # since this is single_align
        log.debug("Finished with retrieving chain configuration for chain %s", chainDict['chainName']) 
        chainConfig.numberAllSteps()
      else:
        # now we know that empty steps are necessary before this chain. we can loop through and add accordingly
        aligngroups_set = self.get_groups_to_align(alignment_grp)
        # but we want to do this in reverse
        aligngroups_set.reverse()
                      
        for align_grp_to_align in aligngroups_set:
            chainConfig.insertEmptySteps('Empty'+align_grp_to_align+'Align',self.length_of_configs[align_grp_to_align],0)         
            log.debug("Finished with retrieving chain configuration for chain %s", chainDict['chainName'])
            chainConfig.numberAllSteps()
 
      return chainConfig
      

Member Data Documentation

combinations_in_menu

MenuAlignmentTools.MenuAlignment.combinations_in_menu

Definition at line 83 of file MenuAlignmentTools.py.

groups_to_align

MenuAlignmentTools.MenuAlignment.groups_to_align

Definition at line 85 of file MenuAlignmentTools.py.

inverse_sig_dict

MenuAlignmentTools.MenuAlignment.inverse_sig_dict

Definition at line 88 of file MenuAlignmentTools.py.

length_of_configs

MenuAlignmentTools.MenuAlignment.length_of_configs

Definition at line 84 of file MenuAlignmentTools.py.

sets_to_align

MenuAlignmentTools.MenuAlignment.sets_to_align

Definition at line 90 of file MenuAlignmentTools.py.

signature_dict

MenuAlignmentTools.MenuAlignment.signature_dict

Definition at line 87 of file MenuAlignmentTools.py.

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The documentation for this class was generated from the following file:

• MenuAlignmentTools.py