phuSrSSKrSSKrSSKrSSKJrJrJrJ r J r SSK J r SSKJ r Jr SSKJrJrJrJrJrJr SSKJr SS KJr SS KJr SS KJrJr SS K Jr \R@"\!5r""S S5r#g)zGRepresents a candidate system for |small_phi| and |big_phi| evaluation.N) Directioncache distributionutilsvalidate)repertoire_distance)max_entropy_distributionrepertoire_shape)ConceptMaximallyIrreducibleCauseMaximallyIrreducibleEffectNullCut RepertoireIrreducibilityAnalysis _null_ria)irreducible_purviews)generate_nodes)mip_partitions) condition_tpmmarginalize_out)time_annotatedcR\rSrSrSrS@Sjr\S5r\RS5r\S5r \S5r \S 5r \S 5r \S 5r \S 5r\S 5r\S5rSrSrSrSrSrSrSrSrSrSrSrSrSrSrSrSr \!RD"S\#RH5S 5r%\!RD"S!\#RH5S"5r&\!RD"S\#RN5S#5r(\!RD"S!\#RN5S$5r)S%r*S&r+S'r,S(r-S)r.SAS*jr/SAS+jr0SAS,jr1S-r2S.r3S/r4SAS0jr5S1r6S2r7S3r8S4r9S5r:S6r;SBS7jr<\!RD"S85SBS9j5r=SBS:jr>SBS;jr?S<r@\S=5rA\BSCS>j5rCS?rDg)D SubsystemaA set of nodes in a network. Args: network (Network): The network the subsystem belongs to. state (tuple[int]): The state of the network. Keyword Args: nodes (tuple[int] or tuple[str]): The nodes of the network which are in this subsystem. Nodes can be specified either as indices or as labels if the |Network| was passed ``node_labels``. If this is ``None`` then the full network will be used. cut (Cut): The unidirectional |Cut| to apply to this subsystem. Attributes: network (Network): The network the subsystem belongs to. tpm (np.ndarray): The TPM conditioned on the state of the external nodes. cm (np.ndarray): The connectivity matrix after applying the cut. state (tuple[int]): The state of the network. node_indices (tuple[int]): The indices of the nodes in the subsystem. cut (Cut): The cut that has been applied to this subsystem. null_cut (Cut): The cut object representing no cut. Nc .[R"U5 XlURUlURR U5Ul[R "X RR5 [U5Ul Uc:[[UR 5[UR 5- 5Ul OXl [URRURUR5Ul UbUO[UR UR5UlURR!UR"5Ul[$R&"X5UlU=(d [$R*"5UlU=(d [$R*"5Ul[1URUR"URUR UR5Ul[R4"U5 gN)r is_networknetwork node_labelscoerce_to_indices node_indices state_lengthsizetuplestatesetexternal_indicesrtpmrcut apply_cutcmr MICECache _mice_cache DictCache_single_node_repertoire_cache_repertoire_cachernodes subsystem) selfrr%r1r) mice_cacherepertoire_cachesingle_node_repertoire_cache_external_indicess I/home/james-whalen/.local/lib/python3.13/site-packages/pyphi/subsystem.py__init__Subsystem.__init__4s G$ "..!,,>>uEe\\%6%675\   $$)G(()C0A0A,BB%DD !%6 !! LL  d33TZZA?C !2!2D4D4DE (($$WZZ0!??4< ) =EOO,= *!1!FU__5F# HHdggtzz4+<+N>NP  4 cUR$)z+tuple[Node]: The nodes in this |Subsystem|.)_nodesr3s r8r1Subsystem.nodesgs{{r;crXlURVs0sHo"RU_M snUlgs snf)zORemap indices to nodes whenever nodes are changed, e.g. in the `macro` module. N)r=index _index2node)r3valuenodes r8r1r?ls.  9=EJJ,EEs4cX[R"URUR5$)ztuple[int]: The state of the subsystem. ``proper_state[i]`` gives the state of the |ith| node **in the subsystem**. Note that this is **not** the state of ``nodes[i]``. )rstate_ofr!r%r>s r8 proper_stateSubsystem.proper_stateus~~d//<s r8connectivity_matrixSubsystem.connectivity_matrix~s wwr;c,[UR5$)z*int: The number of nodes in the subsystem.lenr!r>s r8r#Subsystem.sizes4$$%%r;c8URR(+$)z9bool: ``True`` if this Subsystem has a cut applied to it.)r)is_nullr>s r8is_cutSubsystem.is_cuts88####r;cUR$)ztuple[int]: The nodes of this subsystem to cut for |big_phi| computations. This was added to support ``MacroSubsystem``, which cuts indices other than ``node_indices``. Yields: tuple[int] )r!r>s r8 cut_indicesSubsystem.cut_indicess   r;c6URR5$)z=list[tuple[int]]: The mechanisms that are cut in this system.)r)all_cut_mechanismsr>s r8cut_mechanismsSubsystem.cut_mechanismssxx**,,r;cUR$)zF``NodeLabels``: Labels for the nodes of this system that will be cut. )rr>s r8cut_node_labelsSubsystem.cut_node_labelss r;c4URRS$)z$int: The number of nodes in the TPM.)r(shaper>s r8tpm_sizeSubsystem.tpm_sizesxx~~b!!r;cURR5URR5URR5S.$)z#Report repertoire cache statistics.)single_node_repertoire repertoiremice)r/infor0r-r>s r8 cache_infoSubsystem.cache_infosD2277900557$$))+   r;cURR5 URR5 URR5 g)z%Clear the mice and repertoire caches.N)r/clearr0r-r>s r8 clear_cachesSubsystem.clear_cachess8 **002 $$&  r;c`SSR[[UR55-S-$)Nz Subsystem(z, ))joinmapreprr1r>s r8__repr__Subsystem.__repr__s&diiD$**(=>>DDr;c[U5$r)rrr>s r8__str__Subsystem.__str__s Dzr;c,[UR5$)zDReturn ``False`` if the Subsystem has no nodes, ``True`` otherwise. )boolr1r>s r8__bool__Subsystem.__bool__sDJJr;cD[U[5(dg[UR5[UR5:H=(aY URUR:H=(a9 UR UR :H=(a UR UR :H$)zReturn whether this Subsystem is equal to the other object. Two Subsystems are equal if their sets of nodes, networks, and cuts are equal. F) isinstancerr&r!r%rr)r3others r8__eq__Subsystem.__eq__sz %++ !! "c%*<*<&= = " JJ%++ % " LLEMM ) " HH !  r;c.URU5(+$r)rr~s r8__ne__Subsystem.__ne__s;;u%%%r;cX[UR5[UR5:$)z=Return whether this subsystem has fewer nodes than the other.rNr1r~s r8__lt__Subsystem.__lt__4::U[[!111r;cX[UR5[UR5:$)zs r8__len__Subsystem.__len__s4$$%%r;cp[URURURUR45$r)hashrr!r%r)r>s r8__hash__Subsystem.__hash__s(T\\4#4#4djj$((KLLr;c`URURURURS.$)z*Return a JSON-serializable representation.)rr%r1r))rr%r!r)r>s r8to_jsonSubsystem.to_jsons,||ZZ&&88   r;cj[URURURXRS9$)zReturn a cut version of this |Subsystem|. Args: cut (Cut): The cut to apply to this |Subsystem|. Returns: Subsystem: The cut subsystem. )r)r4)rrr%r!r-)r3r)s r8r*Subsystem.apply_cuts.tzz43D3D -=-=? ?r;c^[U5[TR5- (a [S5e[U4SjU55$)zReturn |Nodes| for these indices. Args: indices (tuple[int]): The indices in question. Returns: tuple[Node]: The |Node| objects corresponding to these indices. Raises: ValueError: If requested indices are not in the subsystem. z6`indices` must be a subset of the Subsystem's indices.c3B># UHnTRUv M g7fr)rB).0nr3s r8 *Subsystem.indices2nodes..s:'QT%%a('s)r&r! ValueErrorr$)r3indicess` r8 indices2nodesSubsystem.indices2nodess? w<#d//0 0HJ J:':::r;r/cURUnURSUR4n[URU- U5$)N.)rBr(r%rinputs)r3mechanism_node_indexpurviewmechanism_noder(s r8_single_node_cause_repertoire'Subsystem._single_node_cause_repertoiresL))*>?  n&:&:!:; 5 5 ?#FFr;r0c U(d[R"S/5$U(d[X R5$[ U5n[R "[ X R55nU[R"[RUVs/sHnURXB5PM sn5-n[R"U5$s snf)aReturn the cause repertoire of a mechanism over a purview. Args: mechanism (tuple[int]): The mechanism for which to calculate the cause repertoire. purview (tuple[int]): The purview over which to calculate the cause repertoire. Returns: np.ndarray: The cause repertoire of the mechanism over the purview. .. note:: The returned repertoire is a distribution over purview node states, not the states of the whole network. ?) nparrayr ra frozensetonesr functoolsreducemultiplyrr normalize)r3 mechanismrjointms r8cause_repertoireSubsystem.cause_repertoire!s&88SE? "+G]]C CG$(--@A !! KK#,.#,a< K+22Y>17{{+\-?-?,@,0MM;< Compute the repertoire of a partitioned mechanism and purview.)rerrrrrr)r3r partitionpart repertoiress r8partitioned_repertoire Subsystem.partitioned_repertoiresU" ! OOI~~t|| D!   [99  s0Ac>Ucg[R"U5nUc URn[U5R U5(d [ S5e[ [U5[U5- 5nURX5nX&-n[R"U5$)a)Distribute an effect repertoire over a larger purview. Args: direction (Direction): |CAUSE| or |EFFECT|. repertoire (np.ndarray): The repertoire to expand. Keyword Args: new_purview (tuple[int]): The new purview to expand the repertoire over. If ``None`` (the default), the new purview is the entire network. Returns: np.ndarray: A distribution over the new purview, where probability is spread out over the new nodes. Raises: ValueError: If the expanded purview doesn't contain the original purview. Nz/Expanded purview must contain original purview.) rrr!r&issubsetrr$rr)r3rre new_purviewrnon_purview_indicesucexpanded_repertoires r8expand_repertoireSubsystem.expand_repertoires(  &&z2  ++K7|$$[11NO O$C $4s7|$CD  * *9 J)o%%&9::r;cDUR[RUU5$)zKAlias for |expand_repertoire()| with ``direction`` set to |CAUSE|. )rrrr3rers r8expand_cause_repertoire!Subsystem.expand_cause_repertoires"%%iooz&13 3r;cDUR[RUU5$)zLAlias for |expand_repertoire()| with ``direction`` set to |EFFECT|. )rrrrs r8expand_effect_repertoire"Subsystem.expand_effect_repertoires$%%i&6&6 &13 3r;ct[[RURX5UR U55$)z[UTTTUTUTRS9$)N)rrrrrrerr)rr)rrrrrrrer3s r8_mip Subsystem.find_mip.._mip1s04###%'= ,,  r;rNinf)rrg) rrerrrallfloatrrrr) r3rrrrmiprrrres ```` @r8find_mipSubsystem.find_mipsY 7; ;__Y 7C     (zQ''4& & 9g5<H' 7D# UHnTRTTU5v M g7fr)r )rrrrr3s r8r&Subsystem.find_mice..s(3)1g-- 9gFF)1s #) rrmaxrrr rrrr)r3rrrmax_mips``` r8 find_miceSubsystem.find_mices$**9iJ 9b9G3)133G   ',W5 5 )** *-g6 6!!),,r;c>UR[RXS9$)zxReturn the mechanism's maximally-irreducible cause (|MIC|). Alias for |find_mice()| with ``direction`` set to |CAUSE|. r)r#rrr3rrs r8mic Subsystem.mics ~~iooy~LLr;c>UR[RXS9$)zzReturn the mechanism's maximally-irreducible effect (|MIE|). Alias for |find_mice()| with ``direction`` set to |EFFECT|. r&)r#rrr's r8mie Subsystem.mies ~~i.. ~MMr;c~[URU5RURU5R5$)zqReturn the |small_phi_max| of a mechanism. This is the maximum of |small_phi| taken over all possible purviews. )rr(rr+)r3rs r8phi_maxSubsystem.phi_maxs/ 488I&**DHHY,?,C,CDDr;cURSS5nURSS5n[[[R SSU55n[ [[RSSU55n[SUUUS9$)zReturn the null concept of this subsystem. The null concept is a point in concept space identified with the unconstrained cause and effect repertoire of this subsystem. rrcauseeffectr2) rrr rrrrrr )r3rrr2r3s r8 null_conceptSubsystem.null_concepts 00R8 222r:* ioor2/? @B, i&&B0A BD"$!%' 'r;c [RSU5 U(d![RS5 UR$URX=(d US9nUR X=(d US9n[RSU5 [ XUUS9$)aReturn the concept specified by a mechanism within this subsytem. Args: mechanism (tuple[int]): The candidate set of nodes. Keyword Args: purviews (tuple[tuple[int]]): Restrict the possible purviews to those in this list. cause_purviews (tuple[tuple[int]]): Restrict the possible cause purviews to those in this list. Takes precedence over ``purviews``. effect_purviews (tuple[tuple[int]]): Restrict the possible effect purviews to those in this list. Takes precedence over ``purviews``. Returns: Concept: The pair of maximally irreducible cause/effect repertoires that constitute the concept specified by the given mechanism. zComputing concept %s...z%Empty concept; returning null conceptr&zFound concept %sr1)logdebugr4r(r+r )r3rrcause_purviewseffect_purviewsr2r3s r8conceptSubsystem.concepts, +Y7 II= >$$ $.HJ)/J(L $i0 !%' 'r;)rBr-r=r0r/r+r)r'rr!rr1r%r()NNNNNNr)F)FFF)E__name__ __module__ __qualname____firstlineno____doc__r9propertyr1setterrGrJr#rRrUrYr\rarhrlrsrvrzrrrrrrrrrr*rrmethodrrrrrrrrerrrrrrrrrrrr r rrrrrr#r(r+r.r4rr;__static_attributes__rr;r8rrs0IMEI#'1!f \\FF==&&$$ ! !--  "" ! E  &2233&M  ?;$ \\19??CGDG \\%y7(-8(-V \\193C3CD <E < \\%y'7'78  9  D-07GH:&;P3 3   9'+-<9vBC%%<M. \\- -!->MNE''0@E %('('r;r)$rArloggingnumpyrrrrrrdistancer r r modelsr r rrrrrrrDrrrr(rrr getLoggerr=r7rrr;r8rLsY N==)DBB* %/! !v 'v 'r;