Skip to main content
  • Home
  • Development
  • Documentation
  • Donate
  • Operational login
  • Browse the archive

swh logo
SoftwareHeritage
Software
Heritage
Archive
Features
  • Search

  • Downloads

  • Save code now

  • Add forge now

  • Help

https://github.com/uberparagon/mgn
22 June 2021, 16:13:34 UTC
  • Code
  • Branches (5)
  • Releases (0)
  • Visits
    • Branches
    • Releases
    • HEAD
    • refs/heads/master
    • refs/tags/1.1.2
    • refs/tags/v1.0.4
    • refs/tags/v1.0.5
    • refs/tags/v1.0.9
    No releases to show
  • 97085ea
  • /
  • strataalgebra
  • /
  • stratagraph.py
Raw File Download
Take a new snapshot of a software origin

If the archived software origin currently browsed is not synchronized with its upstream version (for instance when new commits have been issued), you can explicitly request Software Heritage to take a new snapshot of it.

Use the form below to proceed. Once a request has been submitted and accepted, it will be processed as soon as possible. You can then check its processing state by visiting this dedicated page.
swh spinner

Processing "take a new snapshot" request ...

Permalinks

To reference or cite the objects present in the Software Heritage archive, permalinks based on SoftWare Hash IDentifiers (SWHIDs) must be used.
Select below a type of object currently browsed in order to display its associated SWHID and permalink.

  • content
  • directory
  • revision
  • snapshot
origin badgecontent badge Iframe embedding
swh:1:cnt:9fb45476006b0386b0dd7e8cc0b87840a36ca9c0
origin badgedirectory badge Iframe embedding
swh:1:dir:81284197a7d7278adc1fe2d2fbd5c72cd401c538
origin badgerevision badge
swh:1:rev:87eacb93177c9d41edb525bb71ae03ae45f18d14
origin badgesnapshot badge
swh:1:snp:6e9d4128140ea9fc091a9d1ff362de9d8be50de2
Citations

This interface enables to generate software citations, provided that the root directory of browsed objects contains a citation.cff or codemeta.json file.
Select below a type of object currently browsed in order to generate citations for them.

  • content
  • directory
  • revision
  • snapshot
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Tip revision: 87eacb93177c9d41edb525bb71ae03ae45f18d14 authored by Drew Johnson on 20 March 2020, 16:48:33 UTC
added a ps and ps_ member to strataalgebra
Tip revision: 87eacb9
stratagraph.py
from __future__ import print_function, absolute_import
import itertools
from sage.all import PolynomialRing, var, factorial, Matrix, ZZ, cached_function, copy, Permutations, SetPartitions, prod, SR, sage, Integer, operator
  

class StrataGraph(object):
  R = PolynomialRing(ZZ,"X",1,order='lex')
  Xvar = R.gen()
  
  def __init__(self,M=None,genus_list=None):
    #print genus_list
    if M:
      self.M = copy(M)
    elif genus_list:
      self.M = Matrix(StrataGraph.R,len(genus_list)+1,1,[-1]+genus_list)
    else:
      self.M = Matrix(StrataGraph.R,1,1,-1)
      
  def __repr__(self):
    """
    Drew added this.
    """
    name = self.nice_name()
    if name == None:
        return repr(self.nice_matrix())
    else:
        return name

  def num_vertices(self):
    return self.M.nrows() - 1

  def num_edges(self):
    return self.M.ncols() - 1

  def h1(self):
    return self.M.ncols()-self.M.nrows()+1

  def add_vertex(self,g):
    self.M = self.M.stack(Matrix(1,self.M.ncols()))
    self.M[-1,0] = g

  def add_edge(self,i1,i2,marking=0):
    self.M = self.M.augment(Matrix(self.M.nrows(),1))
    self.M[0,-1] = marking
    if i1 > 0:
      self.M[i1,-1] += 1
    if i2 > 0:
      self.M[i2,-1] += 1

  def del_vertex(self,i):
    self.M = self.M[:i].stack(self.M[(i+1):])

  def del_edge(self,i):
    self.M = self.M[0:,:i].augment(self.M[0:,(i+1):])

  def compute_degree_vec(self):
    self.degree_vec = [sum(self.M[i,j][0] for j in range(1,self.M.ncols())) for i in range(1,self.M.nrows())]

  def degree(self,i):
    return self.degree_vec[i-1]

  def split_vertex(self,i,row1,row2):
    self.M = self.M.stack(Matrix(2,self.M.ncols(),row1+row2))
    self.add_edge(self.M.nrows()-2, self.M.nrows()-1)
    self.del_vertex(i)

  def compute_parity_vec_original(self):
    X = StrataGraph.Xvar
    self.parity_vec = [(ZZ(1+self.M[i,0][0]+sum(self.M[i,k][1] for k in range(1,self.M.ncols()))+sum(self.M[i,k][2] for k in range(1,self.M.ncols()))+self.M[i,0].derivative(X).substitute(X=1)) % 2) for i in range(1,self.M.nrows())]
    
  def compute_parity_vec(self):
    self.parity_vec = [(ZZ(1+self.M[i,0][0]+sum(self.M[i,k][1] for k in range(1,self.M.ncols()))+sum(self.M[i,k][2] for k in range(1,self.M.ncols()))+self.last_parity_summand(i)) % 2) for i in range(1,self.M.nrows())]
    
  def last_parity_summand(self,i):
    return sum(( expon[0] * coef for expon, coef in self.M[i,0].dict().items() ))

  def parity(self,i):
    return self.parity_vec[i-1]

  def replace_vertex_with_graph(self,i,G):
    X = StrataGraph.Xvar
    nv = self.num_vertices()
    ne = self.num_edges()
    #i should have degree d, there should be no classes near i, and G should have markings 1,...,d and genus equal to the genus of i
    hedge_list = []
    for k in range(1,self.M.ncols()):
      for j in range(ZZ(self.M[i,k])):
        hedge_list.append(k)
    self.del_vertex(i)
    for j in range(G.num_edges() - len(hedge_list)):
      self.add_edge(0,0)
    for j in range(G.num_vertices()):
      self.add_vertex(G.M[j+1,0])
    col = ne+1
    for k in range(1,G.M.ncols()):
      if G.M[0,k] > 0:
        mark = ZZ(G.M[0,k])
        for j in range(G.num_vertices()):
          if self.M[nv+j,hedge_list[mark-1]] == 0:
            self.M[nv+j,hedge_list[mark-1]] = G.M[j+1,k]
          elif G.M[j+1,k] != 0:
            a = self.M[nv+j,hedge_list[mark-1]][1]
            b = G.M[j+1,k][1]
            self.M[nv+j,hedge_list[mark-1]] = 2 + max(a,b)*X + min(a,b)*X**2
      else:
        for j in range(G.num_vertices()):
          self.M[nv+j,col] = G.M[j+1,k]
        col += 1

  def compute_invariant(self):
    self.compute_parity_vec()
    self.compute_degree_vec()
    nr,nc = self.M.nrows(),self.M.ncols()
    self.invariant = [[self.M[i,0], [], [], [[] for j in range(1,nr)]] for i in range(1,nr)]
    for k in range(1,nc):
      L = [i for i in range(1,nr) if self.M[i,k] != 0]
      if len(L) == 1:
        if self.M[0,k] != 0:
          self.invariant[L[0]-1][2].append([self.M[0,k],self.M[L[0],k]])
        else:
          self.invariant[L[0]-1][1].append(self.M[L[0],k])
      else:
        self.invariant[L[0]-1][3][L[1]-1].append([self.M[L[0],k],self.M[L[1],k]])
        self.invariant[L[1]-1][3][L[0]-1].append([self.M[L[1],k],self.M[L[0],k]])
    for i in range(1,nr):
      self.invariant[i-1][3] = [term for term in self.invariant[i-1][3] if len(term) > 0]
      for term in self.invariant[i-1][3]:
        term.sort()
      self.invariant[i-1][3].sort()
      self.invariant[i-1][2].sort()
      self.invariant[i-1][1].sort()
    vertex_invariants = [[i,self.invariant[i-1]] for i in range(1,nr)]
    self.invariant.sort()
    vertex_invariants.sort(key=lambda x: x[1])
    self.vertex_groupings = []
    for i in range(nr-1):
      if i == 0 or vertex_invariants[i][1] != vertex_invariants[i-1][1]:
        self.vertex_groupings.append([])
      self.vertex_groupings[-1].append(vertex_invariants[i][0])
    
    #Drew added this
    self.invariant = tupleit(self.invariant)
    self.hash = hash(self.invariant)
    
  def __eq__(self,other):
        """
        Drew added this.
        """
        return graph_isomorphic(self, other)
        
  def __hash__(self):
        """
        Drew added this.
        Note that it returns a value stored when "compute_invariant" is called.
        """
        try:
            return self.hash
        except:
            self.compute_invariant()
            return self.hash
            
        
  def codim(self):
    codim = 0
    for v in range(1, self.num_vertices()+1):
        for expon, coef in self.M[v,0].dict().items():
            codim += expon[0]*coef
        for e in range(1, self.num_edges()+1):
            for expon, coef in self.M[v,e].dict().items():
                if expon[0] > 0:
                    codim += coef
    for e in range(1, self.num_edges()+1):
        if self.M[0,e] == 0:
            codim +=1   
    return codim
    
  def codim_undecorated(self):
    codim = 0
    for e in range(1, self.num_edges()+1):
        if self.M[0,e] == 0:
            codim +=1   
    return codim

    print("not implemented!!!!!!")
    return 1

        
  def kappa_on_v(self,v):
    """
    Drew added this.
    
    """
    #print "kappa",self.M[v,0].dict()
    
    for ex, coef in self.M[v,0].dict().items():
        if ex[0] != 0:
            yield ex[0], coef
            
                
  def psi_no_loop_on_v(self,v):
    for edge in range(1,self.num_edges()+1):
        if self.M[v,edge][0] == 1:
            psi_expon = self.M[v,edge][1]
            if psi_expon > 0:
                yield edge, psi_expon
                
  def psi_loop_on_v(self,v):
    for edge in range(1,self.num_edges()+1):
        if self.M[v,edge][0] == 2:
            psi_expon1 = self.M[v,edge][1]
            psi_expon2 = self.M[v,edge][2]
            if psi_expon1 > 0:
                yield edge, psi_expon1, psi_expon2
                    
  def moduli_dim_v(self,v):
    """
    Drew added this.
    """
    return 3*self.M[v,0][0]-3 + sum(( self.M[v,j][0] for j in range(1, self.num_edges()+1 ) ))
   
  def num_loops(self):
    count = 0
    for edge in range(1, self.num_edges()+1):
        for v in range(1, self.num_vertices()+1):
            if self.M[v,edge][0] == 2:
                count+=1
                break
                
    return count
    
  def num_undecorated_loops(self):
    count = 0
    for edge in range(1, self.num_edges()+1):
        for v in range(1, self.num_vertices()+1):
            if self.M[v,edge] == 2:
                count+=1
                break
                
    return count

  def num_full_edges(self):
      count = 0
      for edge in range(1, self.num_edges()+1):
          if sum(( self.M[v,edge][0] for v in range(1, self.num_vertices()+1 ))) == 2:
              count += 1
      return count
    
  def forget_kappas(self):
    M = copy(self.M)
    for v in range(1, self.num_vertices()+1):
        M[v,0] = M[v,0][0]
    return StrataGraph(M)
    
  def forget_decorations(self):
    M = Matrix(StrataGraph.R,[[self.M[r,c][0] for c in range(self.M.ncols())] for r in range(self.M.nrows())] )
    Gnew = StrataGraph(M)
    #Gnew.compute_invariant()
    return Gnew
    
  def is_loop(self,edge):
    for v in range(1, self.num_vertices()+1):
      if self.M[v,edge][0] == 2:
        return True
      if self.M[v,edge][0] == 1:
        return False
        
    raise Exception("Unexpected!")

  ps_name = "ps"
  ps2_name = "ps_"

  def nice_matrix(self):
      Mnice = Matrix(SR, self.M.nrows(), self.M.ncols())
      for edge in range(1, self.num_edges()+1):
          Mnice[0,edge] = self.M[0,edge]
      for v in range(1, self.num_vertices()+1):
          kappas = 1
          for expon, coef in self.M[v,0].dict().items():
              if expon[0]==0:
                  Mnice[v,0] += coef
              else:
                  kappas *= var("ka{0}".format(expon[0]))**coef
          if kappas != 1:
              Mnice[v,0] += kappas

          for edge in range(1, self.num_edges()+1):
              psis = 1
              for expon, coef in self.M[v,edge].dict().items():
                  if expon[0]==0:
                      Mnice[v,edge] += coef
                  elif expon[0]==1:
                      psis *= var(StrataGraph.ps_name)**coef
                  elif expon[0]==2:
                      psis *= var(StrataGraph.ps2_name)**coef
              if psis != 1:
                  Mnice[v,edge] += psis
      return Mnice

  @staticmethod
  def from_nice_matrix(lists):
      Mx = Matrix(StrataGraph.R, len(lists), len(lists[0]))
      Mx[0,0]=-1
      Mx[0,:] = Matrix([lists[0]])
      for v in range(1, len(lists)):
          if lists[v][0] in ZZ:
              Mx[v,0]=lists[v][0]
              continue
          if lists[v][0].operator() == sage.symbolic.operators.add_vararg:
              operands = lists[v][0].operands()
              if len(operands) != 2:
                  raise Exception("Input error!")
              genus = operands[1] #the genus
              kappas = operands[0]
          else:
              kappas = lists[v][0]
              genus = 0


          if kappas.operator() == sage.symbolic.operators.mul_vararg:
              for operand in kappas.operands():
                  Mx[v,0] += StrataGraph._kappaSR_monom_to_X(operand)
              Mx[v,0] += genus
          else:
              Mx[v,0] = StrataGraph._kappaSR_monom_to_X(kappas) + genus

      X = StrataGraph.Xvar
      for v in range(1, len(lists)):
          for edge in range(1, len(lists[0])):
              if lists[v][edge] in ZZ:
                  Mx[v,edge] = lists[v][edge]
              else:
                  for operand in lists[v][edge].operands():
                      if operand in ZZ:
                          Mx[v,edge] += operand
                      elif operand.operator() is None:
                          #it is a ps or ps2
                          Mx[v,edge] += X
                      elif operand.operator() == operator.pow:
                          #it is ps^n or ps2^n
                          Mx[v,edge] += X * operand.operands()[1]
                      elif operand.operator() == sage.symbolic.operators.mul_vararg:
                          #it is a ps^n*ps2^m
                          op1,op2 = operand.operands()
                          if op1.operator() is None:
                              exp1 = 1
                          else:
                              exp1 = op1.operand()[1]
                          if op2.operator() == None:
                              exp2 = 1
                          else:
                              exp2 = op2.operand()[1]

                          if exp1 >= exp2:
                              Mx[v,edge] += exp1*X + exp2*X**2
                          else:
                              Mx[v,edge] += exp1*X**2 + exp2*X
      return StrataGraph(Mx)





  @staticmethod
  def _kappaSR_monom_to_X(expr):
      X = StrataGraph.Xvar
      if expr in ZZ:
          return expr
      elif expr.operator() == None:
          ka_subscript = Integer(str(expr)[2:])
          return  X ** ka_subscript
      elif expr.operator() == operator.pow:
          ops = expr.operands()
          expon = ops[1]
          ka = ops[0]
          ka_subscript = Integer(str(ka)[2:])
          return  expon * X ** ka_subscript

  def nice_name(self):
      """
      :return:
      """
      if self.num_vertices() == 1:
          num_loops = self.num_loops()
          if num_loops >1:
              return None
          elif num_loops == 1:
              if self.codim() == 1:
                  return "D_irr"
              else:
                  return None
          #else, there are no loops
          var_strs = []
          for expon, coef in self.M[1,0].dict().items():
              if expon[0] == 0 or coef == 0:
                  continue
              if coef == 1:
                  var_strs.append("ka{0}".format(expon[0]))
              else:
                  var_strs.append("ka{0}^{1}".format(expon[0],coef))
          for he in range(1,self.num_edges()+1): #should only be half edges now
              if self.M[1,he][1] > 1:
                  var_strs.append("ps{0}^{1}".format(self.M[0,he],self.M[1,he][1]))
              elif self.M[1,he][1] ==  1:
                  var_strs.append("ps{0}".format(self.M[0,he]))
          if len(var_strs) > 0:
              return "*".join(var_strs)
          else:
              return "one"
      if self.num_vertices() == 2 and self.num_full_edges() == 1 and self.codim() == 1:
          #it is a boundary divisor
          v1_marks = [self.M[0,j] for j in range(1, self.num_edges()+1) if self.M[1,j] == 1 and self.M[0,j] != 0]
          v1_marks.sort()
          v2_marks = [self.M[0,j] for j in range(1, self.num_edges()+1) if self.M[2,j] == 1 and self.M[0,j] != 0]
          v2_marks.sort()
          if v1_marks < v2_marks:
              g = self.M[1,0]
          elif v1_marks == v2_marks:
              if self.M[1,0] <= self.M[2,0]:
                  g = self.M[1,0]
              else:
                  g = self.M[2,0]
          else:
              g = self.M[2,0]
              #temp = v1_marks
              v1_marks = v2_marks
              #v2_marks = temp
          if len(v1_marks) == 0:
              return "Dg{0}".format(g)
          else:
              return "Dg{0}m".format(g) + "_".join([str(m) for m in v1_marks])



         
def tupleit(t):
  """
  Drew added this.
  Changes a nested list into a nested tuple.
  Needed so that we can hash the invariant.
  """
  return tuple(map(tupleit, t)) if isinstance(t, list) else t

def graph_isomorphic(G1,G2):
  if "invariant" not in G1.__dict__.keys():
    G1.compute_invariant()
  if "invariant" not in G2.__dict__.keys():
    G2.compute_invariant()
  if G1.invariant != G2.invariant:
    return False
  else:
    return isomorphic(G1.M,G2.M,G1.vertex_groupings,G2.vertex_groupings)

def isomorphic(M1,M2,group1,group2):
  nr,nc = M1.nrows(),M1.ncols()
  PermList = [Permutations(list(range(len(group)))) for group in group1]
  for sigma_data in itertools.product(*PermList):
    sigma = [0 for i in range(nr-1)]
    for i in range(len(group1)):
      for j in range(len(group1[i])):
        sigma[group1[i][j]-1] = group2[i][sigma_data[i][j]]
    good = True
    for i in range(1,nr):
      ii = sigma[i-1]
      for j in range(1,i):
        jj = sigma[j-1]
        L1 = []
        for k in range(1,nc):
          if M1[i,k] != 0 and M1[j,k] != 0:
            L1.append([M1[i,k],M1[j,k]])
        L1.sort()
        L2 = []
        for k in range(1,nc):
          if M2[ii,k] != 0 and M2[jj,k] != 0:
            L2.append([M2[ii,k],M2[jj,k]])
        L2.sort()
        if L1 != L2:
          good = False
          break
      if good == False:
        break     
    if good:
      return True
  return False

@cached_function
def graph_count_automorphisms(G,vertex_orbits=False):
  return count_automorphisms(G.M,G.vertex_groupings,vertex_orbits)

def count_automorphisms(M,grouping,vertex_orbits=False):
  nr,nc = M.nrows(),M.ncols()
  count = 0
  PermList = [Permutations(list(range(len(group)))) for group in grouping]
  if vertex_orbits:
    isom_list = []
  for sigma_data in itertools.product(*PermList):
    sigma = [0 for i in range(nr-1)]
    for i in range(len(grouping)):
      for j in range(len(grouping[i])):
        sigma[grouping[i][j]-1] = grouping[i][sigma_data[i][j]]
    good = True
    for i in range(1,nr):
      ii = sigma[i-1]
      for j in range(1,i):
        jj = sigma[j-1]
        L1 = []
        for k in range(1,nc):
          if M[i,k] != 0 and M[j,k] != 0:
            L1.append([M[i,k],M[j,k]])
        L1.sort()
        L2 = []
        for k in range(1,nc):
          if M[ii,k] != 0 and M[jj,k] != 0:
            L2.append([M[ii,k],M[jj,k]])
        L2.sort()
        if L1 != L2:
          good = False
          break
      if good == False:
        break     
    if good:
      count += 1
      if vertex_orbits:
        isom_list.append(sigma)

  if vertex_orbits:
    orbit_list = []
    vertices_used = []
    while len(vertices_used) < nr-1:
      i = [ii for ii in range(1,nr) if ii not in vertices_used][0]
      orbit = []
      for sigma in isom_list:
        if sigma[i-1] not in orbit:
          orbit.append(sigma[i-1])
          vertices_used.append(sigma[i-1])
      orbit.sort()
      orbit_list.append(orbit)
    return orbit_list

  for i in range(1,nr):
    for k in range(1,nc):
      if M[i,k][0] == 2 and M[i,k][1] == M[i,k][2]:
        count *= 2
    L = []
    for k in range(1,nc):
      if M[i,k] != 0:
        if sum(1 for j in range(1,nr) if M[j,k] != 0) == 1:
          L.append([M[0,k],M[i,k]])
    count *= aut(L)

    for j in range(1,i):
      L = []
      for k in range(1,nc):
        if M[i,k] != 0 and M[j,k] != 0:
          L.append([M[i,k],M[j,k]])
      count *= aut(L)
  return count

def aut(L):
  if len(L) == 0:
    return 1
  L.sort()
  total = 1
  n = 1
  last = L[0]
  for l in L[1:]:
    if l == last:
      n += 1
    else:
      n = 1
    total *= n
    last = l
  return total


def PsiKappaVars(A, kappa_only = False):  
    kappa_names = ["kappa{0}_{1}".format(a,v) for v in range(1,A.num_vertices()+1) for a in range(1,A.moduli_dim_v(v)+1)]
    
    if kappa_only:
        PsiKappaRing = PolynomialRing(ZZ,  kappa_names, len(kappa_names) )
    else:
        psi_names = ["psi{0}_{1}".format(e,v) for v in range(1,A.num_vertices()+1) for e in range(1,A.num_edges()+1) if A.M[v,e][0] > 0]
    
        psi_names += ["psi{0}_{1}_2".format(e,v) for v in range(1,A.num_vertices()+1) for e in range(1,A.num_edges()+1) if A.M[v,e][0] == 2] 
    
        PsiKappaRing = PolynomialRing(ZZ,  kappa_names +psi_names)
        
    kappa = {(a,v) : PsiKappaRing.gens_dict()["kappa{0}_{1}".format(a,v)] for v in range(1,A.num_vertices()+1) for a in range(1,A.moduli_dim_v(v)+1) } 
    
    #print PsiKappaRing
    if kappa_only:
        return PsiKappaRing, kappa
    else:
        psi = {(e,v) : PsiKappaRing.gens_dict()["psi{0}_{1}".format(e,v)] for v in range(1,A.num_vertices()+1) for e in range(1,A.num_edges()+1) if A.M[v,e][0] > 0 }
    
        psi2 = {(e,v) : PsiKappaRing.gens_dict()["psi{0}_{1}_2".format(e,v)] for v in range(1,A.num_vertices()+1) for e in range(1,A.num_edges()+1) if A.M[v,e][0] == 2 }
        
        return PsiKappaRing, kappa, psi, psi2
        

def X_to_kappa(f,kappa):
    """
    f -- A polynomial in X. The constant term is ignored.
    kappa -- A function so that kappa(a) is kappa_a.
    
    Returns::
        A polynomial in kappas, converting ...
    """
    psi_list = []
    for expon,coef in f.dict().items():
        #print expon[0], coef
        if expon[0] !=0:
            psi_list += [expon[0]]*coef
        
    #print psi_list
    result = 0 
    for p in SetPartitions(list(range(len(psi_list)))):   
        #print p  
        #print [ kappa( sum((psi_list[i] for i in s)) ) for s in p]
        result +=   prod((factorial(len(s) - 1) for s in p)) * prod(( kappa( sum((psi_list[i] for i in s)) ) for s in p ))
    return result

Software Heritage — Copyright (C) 2015–2025, The Software Heritage developers. License: GNU AGPLv3+.
The source code of Software Heritage itself is available on our development forge.
The source code files archived by Software Heritage are available under their own copyright and licenses.
Terms of use: Archive access, API— Contact— JavaScript license information— Web API

back to top