Source code for netcontrolz.cacti

"""
This module provides functionality for building, querying, and manipulating the cacti structure of a directed network.

For information cacti structures, see the following reference:
Commault, Dion, Van der Woude. Characterization of generic properties of linear structured systems for efficient computations. Kybernetika, 38(5):503-520, 2002.
"""
from sys import setrecursionlimit
from zen import DiGraph
from zen.algorithms.matching import maximum_matching_
from zen.exceptions import type_check
from lti import controls_idx
from netcontrolz.util import maximum_weight_matching_
from collections import OrderedDict
#from numpy import *
from exceptions import *
import itertools as it
setrecursionlimit(2**27)

__all__ = ['build_cacti','build_cacti_fixed_controls_','build_cacti_fixed_controls','build_cacti_free_controls','build_cacti_from_matching','build_cacti_from_matching_']

[docs]class Stem: """ An instance of :py:class:`Stem` represents a single stem (with reference to any associated buds) in a cacti structure. """ def __init__(self,Gi,node_seq): """ Creates a new :py:class:`Stem` from a sequence of nodes given by ``node_seq``. """ self._node_dict = OrderedDict.fromkeys(node_seq) self._G = Gi def __contains__(self,x): """ Returns ``True`` if ``x`` is a node in the stem (containment doesn't extend to buds). """ return x in self._node_dict def __len__(self): """ Returns the number of nodes in stem (does not include nodes in attached buds). """ return len(self._node_dict) def __iter__(self): """ Iterate over the nodes in the stem (not the attached buds). """ return self._node_dict.iterkeys()
[docs] def origin(self): """ Returns the origin or starting node (object) of the stem. """ return self._G.node_object(self.origin_())
[docs] def origin_(self): """ Returns the origin or starting node (index) of the stem. """ return next(self._node_dict.iterkeys(), None)
[docs] def terminus(self): """ Returns the terminus or end node (object) of the stem. """ return self._G.node_object(self.terminus_())
[docs] def terminus_(self): """ Returns the terminus or end node (index) of the stem. """ x = None for x in self._node_dict.iterkeys(): pass return x
def _extend(self, nodes): """ Extend stem by adding ``nodes`` (``py:iterable``) at the end. Needed when a bud is attached at terminus of the stem, in which case the bud is broken down and stem is extended. """ for u in nodes: self._node_dict[u] = None def _set_bud(self, x, bud): """ Private method to add bud to a node x in this stem. """ self._node_dict[x] = bud
[docs] def length_with_buds(self): """ Returns the length of the stem including the buds attached to it. """ l = len(self._node_dict) for bud in self._node_dict.itervalues(): if bud is not None: l += len(bud) return l
[docs] def buds(self): """ Returns a list of buds (Cycle objects) that are attached to this stem """ return list(self.buds_iter())
[docs] def buds_iter(self): """ Returns an iterator over buds (Cycle objects) that are attached to this stem """ return (x for x in self._node_dict.itervalues() if x is not None)
[docs]class Cycle: """ :py:class:`Cycle` can either be a bud that is connected to a stem by a distinguished node or an independent cycle (no associated stem). """ def __init__(self, Gi, node_seq): """ Creates a new :py:class:`Cycle` from a sequence of nodes given by ``node_seq``. """ self._node_dict = OrderedDict.fromkeys(node_seq) self._G = Gi self.droot = None self._dnode = None def __contains__(self,x): """ Returns ``True`` if ``x`` is a node in the cycle (containment doesn't extend to buds). """ return x in self._node_dict def __len__(self): """ Returns the number of nodes in cycle (does not include nodes in attached buds). """ return len(self._node_dict) def __iter__(self): """ Iterate over nodes in the cycle. """ return self._node_dict.iterkeys()
[docs] def origin(self): """ A starting node (object) of this cycle, in the case of a bud this is the node where the distinguished edge is pointing to. In the case of a non-bud cycle, returns None. """ res = self.origin_() return None if res == -1 else self._G.node_object(res)
[docs] def origin_(self): """ A starting node (index) of this cycle, in the case of a bud this is the node where the distinguished edge is pointing to. In the case of a non-bud cycle, returns -1. """ if not self.is_bud(): return -1 return next(self._node_dict.iterkeys(), -1)
def _reorder_origin(self, x): """ Private method to make target node of the distinguished edge as the origin of this cycle when this cycle is a bud. """ if x not in self._node_dict.iterkeys(): return toremove = list(it.takewhile(lambda a: a!=x, self._node_dict.iterkeys())) for k in toremove: t = self._node_dict[k] del self._node_dict[k] self._node_dict[k] = t def _set_distinguished_root(self,droot,dnode): """ Private method to set the stem or cycle and distinguished node of this cycle when this cycle is a bud. """ self._droot = droot self._dnode = dnode
[docs] def distinguished_root(self): """ Returns the stem or cycle to which this cycle is attached if it is a bud, otherwise return None. """ if not self.is_bud(): return None return self._droot
[docs] def dist_node(self): """ Returns the distinguished node (object) of the stem to which this cycle is attached if it is a bud, otherwise return None. """ res = self.dist_node_() return None if res == -1 else self._G.node_object(res)
[docs] def dist_node_(self): """ Returns the distinguished node (index) of the stem to which this cycle is attached if it is a bud, otherwise return -1. """ if not self.is_bud(): return -1 return self._dnode
[docs] def dist_edge(self): """ Returns the distinguished edge (u,v) (node objects) where u is in the stem and v is in this cycle/bud of the stem. Returns None if this cycle is not a bud. """ res = self.dist_edge_() return None if res == -1 else self._G.endpoints(res)
[docs] def dist_edge_(self): """ Returns the distinguished edge e (edge index) where src(e) is in the stem and tgt(e) is in this cycle/bud of the stem. Returns -1 if this cycle is not a bud. """ if not self.is_bud(): return -1 return self._G.edge_idx_(self._dnode, self.origin_())
[docs] def is_bud(self): """ Returns ``True`` if this cycle is a bud. """ return self._stem != None
def _set_bud(self, x, bud): """ Private method to add bud to a node x in this cycle. """ self._node_dict[x] = bud
[docs] def length_with_buds(self): """ Returns the length of the cycle including the buds attached to it. """ l = len(self._node_dict) for bud in self._node_dict.itervalues(): if bud is not None: l += len(bud) return l
[docs] def buds(self): """ Returns a list of buds (Cycle objects) that are attached to this cycle """ return list(self.buds_iter())
[docs] def buds_iter(self): """ Returns an iterator over buds (Cycle objects) that are attached to this stem """ return (x for x in self._node_dict.itervalues() if x is not None)
# helper function to construct stems and cycles from a given matching def _stems_cycs_from_matching(Gi, matching, roots=None, origins=[]): outmap = {a:b for a,b in matching} vis = set() indegmap = {} for a,b in matching: indegmap.setdefault(a,0) indegmap[b] = indegmap.get(b, 0) + 1 # if no roots are provided, pick all the unmatched nodes # isolated unmatched nodes would not be captured this way if roots is None: roots = [u for u in indegmap if indegmap[u] == 0] def recur(z,cur,stems,cycs): # already visited this node if z in vis: cycs.append(Cycle(Gi, cur)) return vis.add(z) cur.append(z) # reached the end of the stem if z not in outmap: stems.append(Stem(Gi, cur)) return recur(outmap[z],cur,stems,cycs) stems, cycs = [],[] # starting at the roots, build stems & cycles for r in roots: if r not in vis: recur(r,[],stems,cycs) origins = set(origins) # find everything that wasn't reachable from the original roots roots = [x for x in outmap.iterkeys() if x not in vis] # give preference to any nodes who directly receive a control roots.sort(key=lambda x: 0 if x in origins else 1) # starting at the non-reachable nodes, sorted with controlled nodes first, build stems & cycles # these origins would include nodes controlled in cycles that are not buds for r in roots: if r not in vis: recur(r,[],stems,cycs) return stems, cycs
[docs]def build_cacti_from_matching(G, fixed_ctls, matching, roots=None): """ This method constructs :py:class:`Cacti` for a given directed graph ``G`` and a precomputed matching. This requires the matching, the roots of the matching and the subset of roots that are controlled (the fixed_ctrls). **Args**: see method ``build_cacti_from_matching_`` Only difference here is that fixed_ctls are node objs and not indices. The matching is passed as tuples of node pairs. Returns a :py:class:`Cacti` object. """ type_check(G,DiGraph,'only directed graphs are supported') if fixed_ctls is None: raise ValueError, "fixed_ctls cannot be None." if matching is None: raise ValueError, "matching cannot be None." fixed_ctls_obj = control_idx(fixed_ctls) matching_obj = [G.endpoints(eidx) for eidx in matching] roots_obj = None if roots: roots_obj = [G.node_idx(a) for a in roots] return build_cacti_from_matching_(G, fixed_ctls_obj, matching_obj, roots_obj)
[docs]def build_cacti_from_matching_(G, fixed_ctls, matching, roots=None): """ This method constructs :py:class:`Cacti` for a given directed graph ``G`` and a precomputed matching. This requires the matching, the roots of the matching and the subset of roots that are controlled (the fixed_ctrls). **Args**: * ``fixed_ctls`` (``LIST_OF_TUPLES``) * ``LIST_OF_TUPLES``: Represents control nodes that are attached to the nodes in G. e.g., ``[(1,),(3,)]`` represents two controls that are attached to node indices 1 and 3 in ``G``. These indices should be a subset of the roots of the matching or part of a cycle. * ``matching`` (:py:class:`list`) The list of edge indices that indicate the edges belonging to a maximum-matching for the graph. * ``roots`` (:py:class:`list`) The roots of the matching (the indices of the nodes at the base of the stems of the matching); if none, the roots are identified automatically. **Raises**: ``ValueError``: if fixed_ctls or matching is None. Returns a :py:class:`Cacti` object. """ type_check(G,DiGraph,'only directed graphs are supported') if fixed_ctls is None: raise ValueError, "fixed_ctls cannot be None." if matching is None: raise ValueError, "matching cannot be None." cact = Cacti(G) cact._from_matching_case(fixed_ctls, matching, roots) cact._build_cacti_from_stemscycles() return cact
[docs]def build_cacti_fixed_controls(G, fixed_ctls, **kwargs): """ This method constructs :py:class:`Cacti` for a given directed graph ``G`` and set of controls that are fixed to some nodes in G. Maximum perfect weighted matching is used to calculate reachable/controllable nodes given the fixed controls. **Args**: see method ``build_cacti_fixed_controls_`` Only difference here is that fixed_ctls are node objs and not indices. Returns a :py:class:`Cacti` object. """ type_check(G,DiGraph,'only directed graphs are supported') if fixed_ctls is None: raise ValueError, "fixed_ctls cannot be None." ctls = controls_idx(fixed_ctls) return build_cacti_fixed_controls_(G, ctls, **kwargs)
[docs]def build_cacti_fixed_controls_(G, fixed_ctls, **kwargs): """ This method constructs :py:class:`Cacti` for a given directed graph ``G`` and set of controls that are fixed to some nodes in G. Maximum perfect weighted matching is used to calculate reachable/controllable nodes given the fixed controls. **Args**: * ``fixed_ctls`` (``LIST_OF_TUPLES``) * ``LIST_OF_TUPLES``: Represents control nodes that are attached to the nodes in G. e.g., ``[(1,),(3,)]`` represents two controls that are attached to node indices 1 and 3 in ``G``. **KwArgs**: * ``randomize[=False]`` (``Boolean``). Indicates whether the matching should be randomized. * ``with_cycles[=False]`` (``Boolean``). Indicates whether cycles not reachable from the ``fixed_ctls`` should be included in the matching/cacti. **Raises**: ``ValueError``: if fixed_ctls is None. Returns a :py:class:`Cacti` object. """ type_check(G,DiGraph,'only directed graphs are supported') if fixed_ctls is None: raise ValueError, "fixed_ctls cannot be None." cact = Cacti(G) cact._fixed_control_case(fixed_ctls, **kwargs) cact._build_cacti_from_stemscycles() return cact
[docs]def build_cacti_free_controls(G, num_ctls, **kwargs): """ This method constructs :py:class:`Cacti` for a given directed graph ``G`` and a fixed number of controls that can be assigned to any nodes in G. Maximum perfect weighted matching is used to calculate reachable/controllable nodes given the number of controls. **Args**: * ``num_ctls`` (``int``): Number of control nodes (must be greater than one) that are to be attached to the nodes in G. If num_ctls was 0, a degenerate matching of only cycles would be found. **KwArgs**: * ``randomize[=False]`` (``Boolean``). Indicates whether the matching should be randomized. Returns a :py:class:`Cacti` object. """ type_check(G,DiGraph,'only directed graphs are supported') if num_ctls < 1: raise ValueError, "num_ctls cannot be less than one." cact = Cacti(G) cact._free_control_case(num_ctls, **kwargs) cact._build_cacti_from_stemscycles() return cact
[docs]def build_cacti(G): """ This method constructs :py:class:`Cacti` for a given directed graph ``G`` using maximum unweighted matching. The resulting matching forms a cacti which also gives the minimum number (and one possible set of locations/configuration) of controls required for the full control of the network. The degeneracy of the matching and the ambiguity/flexibility of attaching buds to stems and other cycles means that there are many ways to map the mapping into a collection of Cactus structures. In this implementation, we opportunistically (whichever comes first) attach cycles as buds to stems, then opportunistically attach cycles as buds to existing buds, then opportunistically attach cycles to other non-bud cycles. This serves to minimize the number of connections that the controls need to make in the network. There could be a variety of other strategies. This may effect energy quantifications or robustness qualities of the network, especially if the control properties are largely determined by the cycles in the network. Returns a :py:class:`Cacti` object. """ type_check(G,DiGraph,'only directed graphs are supported') cact = Cacti(G) cact._min_controls_case() cact._build_cacti_from_stemscycles() return cact
[docs]class Cacti: """ The Cacti class represents the cacti control structure of a given network. It can be used to find the location (and number) of inputs required to control the network as well as to access the underlying cacti structure. It can also be used to find the extent to which a network can be controlled by a specified set of controls and the related constrained cacti. """ def __init__(self,G): """ Private constructor. Should not be used directly. build_cacti methods should be used, which return Cacti object. """ self._G = G self._stems = [] self._cycles = [] self._matching = [] self._controls = [] self._controllable_nodes=set()
[docs] def num_controls(self): """ Returns the number of controls/inputs used to control the network. """ return len(self._controls)
[docs] def stems(self): """ Returns a list of stems comprising the cacti. """ return list(self._stems)
[docs] def cycles(self): """ Returns a lit of cycles contained in the cacti. Some cycles may be buds connected to either the stem or another bud via a distinguished edge. """ return list(self._cycles)
[docs] def non_bud_cycles(self): """ Returns the non-bud (independent cycles without distinguished edges). """ return filter(lambda x: not x.is_bud(), self._cycles)
# helper function to build cacti from stems and cycles def _build_cacti_from_stemscycles(self): self._stems.sort(key=lambda x:len(x), reverse=True) self._cycles.sort(key=lambda x:len(x), reverse=True) # for every node in each stem, check if any of the nbrs are part of a cycle (that isn't already a bud) for stem in self._stems: for u in stem: for v in self._G.out_neighbors_(u): for icyc,cyc in enumerate(self._cycles): if cyc and not cyc.is_bud() and v in cyc: cyc._reorder_origin(v) if u == stem.terminus_(): stem._extend(cyc) self._cycles[icyc] = None else: stem._set_bud(u, cyc) cyc._set_distinguished_root(stem, u) # remove any cycles we extended into a stem self._cycles = [c for c in self._cycles if c is not None and len(c) > 0] # loop over all the nodes in the bud cycles to see if their out nbrs are part of a cycle (that isn't already a bud). nonbud_cycles = [c for c in self._cycles if not c.is_bud()] new_bud_cycles = [c for c in self._cycles if c.is_bud()] while len(new_bud_cycles) > 0: bud_cycles = new_bud_cycles new_bud_cycles = [] for cycle in bud_cycles: for u in cycle: for v in self._G.out_neighbors_(u): for icyc,cyc in enumerate(nonbud_cycles): if cyc and not cyc.is_bud() and v in cyc: cyc._reorder_origin(v) cycle._set_bud(u, cyc) cyc._set_distinguished_root(cycle, u) new_bud_cycles.append(cyc) # Any remaining non-bud cycles have no distinguished edges from the stems or any existing buds. Now check to see if any of the non-bud cycles have distinguished edges between each other nonbud_cycles = [c for c in self._cycles if not c.is_bud()] for cycle in nonbud_cycles: for u in cycle: for v in self._G.out_neighbors_(u): for icyc,cyc in enumerate(nonbud_cycles): if cyc and not cyc.is_bud() and v in cyc: cyc._reorder_origin(v) cycle._set_bud(u, cyc) cyc._set_distinguished_root(cycle, u) # the location of the controls are the base of the stems controls = [ [stem.origin_()] for stem in self._stems ] # assign the remaining, non-bud cycles to the stems one at a time, looping through the stems as many times as needed # if there are no stems, then attach all cycles to a single control if controls: idx = 0 for cyc in self._cycles: if not cyc.is_bud(): controls[idx].append(list(cyc)[0]) idx = (idx+1) % len(controls) controls = [tuple(a) for a in controls] else: controls = [ tuple(list(cyc)[0] for cyc in self._cycles) ] self._controls = controls ctlable_nodes = set() ctlable_nodes.update([a for s in self._stems for a in s]) ctlable_nodes.update([a for c in self._cycles for a in c]) self._controllable_nodes = ctlable_nodes # To find minimum controls required to fully control a network using # Unweighted maximum Matching def _min_controls_case(self): #TODO Randomize matching G = self._G matching = set(maximum_matching_(G)) matching = [G.endpoints_(eidx) for eidx in matching] stems, cycles = _stems_cycs_from_matching(G, matching) # in the min controls case, any remaining unmatched nodes (isolated nodes), we need to add a stem and control for u in set(G.nodes_iter_()).difference(set(x for y in matching for x in y)) : stems.append(Stem(G, [u])) # ??? Do we need to add these nodes to the self._controllable_nodes set? self._matching, self._stems, self._cycles = matching, stems, cycles # To find cacti and hence controllable nodes given a fixed set of controls # (fixed_ctls) using maximum weighted matching def _fixed_control_case(self, fixed_ctls, **kwargs): kwargs['controls'] = fixed_ctls G = self._G origins = [a for b in fixed_ctls for a in b] matching,roots = maximum_weight_matching_(G, **kwargs)[1:3] matching = [G.endpoints_(eidx) for eidx in matching] self._stems, self._cycles = _stems_cycs_from_matching(G, matching, roots, origins) self._matching = matching # To find cacti and hence controllable nodes given a fixed number of # controls that can be assigned anywhere for maximum control possible def _free_control_case(self, num_ctls, **kwargs): G = self._G ctls = [ tuple(G.nodes_()) for x in xrange(num_ctls) ] kwargs['controls'] = ctls matching,roots = maximum_weight_matching_(G, **kwargs)[1:3] matching = [ G.endpoints_(eidx) for eidx in matching ] self._stems, self._cycles = _stems_cycs_from_matching(G, matching, roots=roots) self._matching = matching # Builds the cacti directly from the matching # fixed_ctls contains a subset of the roots, since some roots may not be attached to a control def _from_matching_case(self, fixed_ctls, matching, roots): origins = [a for b in fixed_ctls for a in b] matching = [self._G.endpoints_(eidx) for eidx in matching] self._stems, self._cycles = _stems_cycs_from_matching(self._G, matching, roots, origins) self._matching = matching
[docs] def controls(self): """ Returns list of nodes (objects) where controls are attached. In case of unweighted matching, it is the minimum number of controls required for full control of the network. In case of weighted matching (when fixed set of controls are given), this method returns the controls that are sufficient for controlling the maximum possible nodes of the network. """ ctls = self.controls_() return [tuple(self._G.node_object(x) for x in t) for t in ctls]
[docs] def controls_(self): """ Returns list of nodes (indices) where controls should be attached. In case of unweighted matching, it is the minimum number of controls required for full control of the network. In case of weighted matching (when fixed set of controls are given), this method returns the controls that are sufficient for controlling the maximum possible nodes of the network. """ return list(self._controls)
[docs] def controllable_nodes(self): """ Returns the set of nodes (objects) that are controllable. """ return set([self._G.node_object(a) for a in self._controllable_nodes])
[docs] def controllable_nodes_(self): """ Returns the set of nodes (indices) that are controllable. """ return set(self._controllable_nodes)
[docs] def num_controllable_nodes(self): """ Returns the number of nodes that are controllable. """ return len(self._controllable_nodes)
[docs] def matching(self): """ Returns the matching used to create this :py:class:`Cacti` object, in form of a list of edges (u,v) where u and v are node objects, as calculated by the maximum matching algorithm (unweighted or weighted as the case maybe). Note that there is degeneracy in the matching, so this may be just one possible matching. """ return [self._G.endpoints(e) for e in self.matching_()]
[docs] def matching_(self): """ Returns the matching used to create this :py:class:`Cacti` object, in form of a list of edge indices, as calculated by the maximum matching algorithm (unweighted or weighted as the case maybe). Note that there is degeneracy in the matching, so this may be just one possible matching. """ return [self._G.edge_idx_(u,v) for u,v in self._matching]