phhSrSSKJr SSKrSSKJrJr SSKJ r Sr Sr S r S r S rS rS rSrg)z= Functions for manipulating transition probability matrices. )chainNOFFON) all_statesc [[R"[R"URSS5S:H5S5$)z'Return the indices of nodes in the TPM.Nr)tuplenpwherearrayshapetpms C/home/james-whalen/.local/lib/python3.13/site-packages/pyphi/tpm.py tpm_indicesrs3 "((399Sb>2a78; <<clURS:H=(a URSURS:H$)zKReturn ``True`` if ``tpm`` is in state-by-state form, otherwise ``False``. r rr)ndimrrs ris_state_by_staters, 88q= 9SYYq\SYYq\99rc[S5//[U5-nUHnX$[R/X4'M [ [ R "U55nU[U5$)apReturn a TPM conditioned on the given fixed node indices, whose states are fixed according to the given state-tuple. The dimensions of the new TPM that correspond to the fixed nodes are collapsed onto their state, making those dimensions singletons suitable for broadcasting. The number of dimensions of the conditioned TPM will be the same as the unconditioned TPM. N)slicelenr newaxislistr from_iterabler )r fixed_nodesstateconditioning_indicesis r condition_tpmr#se#4[M?SZ7 #(8RZZ"8  3 34H IJ u)* ++rcz[R"S/URS- -URS/-5nX-$)z_Broadcast a state-by-node TPM so that singleton dimensions are expanded over the full network. r rr )r onesrr)r unconstraineds r expand_tpmr'1s9GGQC388a<0CIIbM?BCM  rcUR[U5SS9[R"UR5[ U5R 5- $)aMarginalize out nodes from a TPM. Args: node_indices (list[int]): The indices of nodes to be marginalized out. tpm (np.ndarray): The TPM to marginalize the node out of. Returns: np.ndarray: A TPM with the same number of dimensions, with the nodes marginalized out. T)keepdims)sumr r rrrprod) node_indicesrs rmarginalize_outr-9sF 775&7 6 D./446 88rcR^^^^^U4SjmUUU4Sjm[U4SjU55$)a/Infer the presence or absence of an edge from node A to node B. Let |S| be the set of all nodes in a network. Let |A' = S - {A}|. We call the state of |A'| the context |C| of |A|. There is an edge from |A| to |B| if there exists any context |C(A)| such that |Pr(B | C(A), A=0) != Pr(B | C(A), A=1)|. Args: tpm (np.ndarray): The TPM in state-by-node, multidimensional form. a (int): The index of the putative source node. b (int): The index of the putative sink node. Returns: bool: ``True`` if the edge |A -> B| exists, ``False`` otherwise. cR>UST[-UTS-nUST[-UTS-nX4$)z\Given a context C(A), return the states of the full system with A OFF and ON, respectively. Nr)contexta_offa_onas r a_in_context infer_edge..a_in_contextXsC c!GABK/r{R'!"+-}rc:>T"U5upTUTTUT:g$)z9Return ``True`` if A has an effect on B, given a context.)r0r1r2r4brs ra_affects_b_in_context*infer_edge..a_affects_b_in_context`s*"7+ 5z!}D ! ,,rc34># UH nT"U5v M g7f)Nr7).0r0r9s r infer_edge..esGh7%g..hs)any)rr3r8contextsr9r4s``` @@r infer_edgerAHs - GhG GGrcURSn[[US- 55n[R"X4[ S9n[R "UR5HupE[XXR5X4U'M U$)z\Infer the connectivity matrix associated with a state-by-node TPM in multidimensional form. r r)dtype)rr rr emptyintndindexrA)r network_size all_contextscmr3r8s rinfer_cmrJhsh99R=LL1$456L <.c :B 288$ca6a% IrclURVs/sHoRSPM nnUVs/sHnURURS9PM nnUVs/sHn[R "US5PM nn[ [[U55n[R"USS9$s snfs snfs snf)zCReconstitute the TPM of a subsystem using the individual node TPMs.).r)axisr ) nodesrsqueezeexternal_indicesr expand_dimsrmapr' concatenate) subsystemnode node_tpmsrs rreconstitute_tpmrVts /8oo>od&!oI>C 33 45>>ISR(II>SY/0I >>)" --??sB'#B,!B1)__doc__ itertoolsrnumpyr constantsrrutilsrrrr#r'r-rArJrVr7rrr\sB = :,( 8H@ .r