]hG@SrSSKrSSKrSSKrSSKJrJrJrJrJ r J r J r SSK r SSKrSSKJrJrJr S$S\S\S\ \S\ \S \S \ \S \\\44S jjrS%S\S\S \\\44S jjrS%S\S\S \\\44SjjrS\S \\\44SjrS\S \\\44SjrS\ S\\\4S\S \4SjrS\ S\\\4S\S \4SjrS\ S\\\4S\S \4SjrS\S \4SjrS\\S \\4Sjr S\ S\\\4S\S \4Sjr!S\ S\\\4S\S\S \4 Sjr"S\S \\4Sjr#S\S \\4Sjr$S \S \ \\\ \\%\ RL444S!jr'S"\S \ \\%\ RL44S#jr(g)&z3 Utility functions for reading the Stan CSV format N)AnyDictListMutableMappingOptionalTextIOUnion)_CMDSTAN_SAMPLING _CMDSTAN_THIN_CMDSTAN_WARMUPpathis_fixed_param iter_sampling iter_warmup save_warmupthinreturnc~[X5nUc[nOQU[:aGSU;a[SRX55eUSU:wa[SRXUS55eUnUc[nUnUc[ n[ [R"X- 55n[ [R"Xu- 55nUSU:wa[SRXUS55eU(aPSU;a USS;d[SRU55eUS U:wa[S RXUS 55eU$) z3Capture essential config, shape from stan_csv file.rz6bad Stan CSV file {}, config error, expected thin = {}z@bad Stan CSV file {}, config error, expected thin = {}, found {}draws_samplingz1bad Stan CSV file {}, expected {} draws, found {}r)truez  #N*L& tyy!456L>#89:N / ? F Fd+;&<   %$}*=*L99?   < /55;V^(<6  Kc(0nSn[US5n[XBU5n[XBU5nU(d[XBU5n[ XBU5n[ XBX15nSSS5 U$![ an[ SU-5UeSnAff=f!,(df  U$=f)z2Process sampler stan_csv output file line by line.rrzError in reading csv file: N)open scan_configscan_column_namesscan_warmup_itersscan_hmc_paramsscan_sampling_itersr)r rdictlinenofdes r rrFsD F dCB J 62F&r8F!*2V<(6:(6JF  K J:TAB I J  Ks)BAA!! A?+A::A??B B save_itersc :0nSn[US5n[XBU5n[XBU5nSnUHnUS- nM SSS5 U(a([R"W[ US54[ SS9n[US5n[U5HnUR5 M [W5HnUR5R5n[ U5S:a[SRXU-55eURS 5n U(a#U V s/sHn [ U 5PM sn WUSS24'XS- :XdM[R"U [ S 9n M SSS5 W US 'U(aWUS 'U$!,(df  GNB=fs sn f!,(df  N8=f) z4Process optimizer stan_csv output file line by line.rr$rN column_namesF)dtypeorderz*cannot parse CSV file {}, error at line {},)r3mle all_iters)r%r&r'npemptylenfloatrangereadlinestriprrsplitarray) r r/r+r,r-itersliner7ixsxr6s r scan_optimize_csvrFWsiD F dCBRv."2V4D QJE   " C^,- .e3!  dCBvA KKMuA;;=&&(D4y1} @GGqj CB57"8R58R"8 !Q$AI~"$((2U"; "DK%[ K? 0#9 s0)E5=BF F)F =F 5 FF  Fc0nSn[US5n[X1U5n[X1U5nSSS5 U$!,(df  U$=f)z2Process laplace stan_csv output file line by line.rr$N)r%r&r')r r+r,r-s r scan_generic_csvrH~sJD F dCBRv."2V4  K  Ks 4 Ac 40nSn[US5n[X1U5n[X1U5nUR5R S5R 5nUS- nUR S5(aUR5R S5nUS- nUR S5(d[SRX$55eURS 5upV[U5US'UR5R S5nUS- nURS 5nUVs/sHn[U5PM n n[R"U 5US '[R"US US SS9R5US'S S S 5 U$s snf!,(df  U$=f)z/Process advi stan_csv output file line by line.rr$ # rzStepsize adaptation complete.z # etaz%line {}: expecting eta, found: "{}"=r5variational_mean#Nhigh)commentskiprowsheaderfloat_precisionvariational_sample)r%r&r'r=lstriprstrip startswithrrr?r;r8r@pdread_csvto_numpy) r r+r,r-rB_rKrDrErMs r scan_variational_csvr\szD F dCBRv."2V4{{}##F+224!  ??: ; ;;;=''1D aKF??5)) =DD ZZ_FA*DK;;=''1D aKF ZZ_.01bE!Hb1#%88,<#=  %'[[ " & (* !"+ 8 K2' 8 KsDF F5AFF Fr- config_dictr,cUR5nUR5R5n[U5S:Ga]UR S5(GaFUS- nUR S5(aUR SS5nURS5nURS5n[U5S:XaUSR5S :Xa0USR S 5(dUSR5US 'OKUSR5S :wa4USR5n[U5nXqUSR5'UR5nUR5R5n[U5S:aUR S5(aGMFURU5 U$![a8 [U5nN![a US :XaSnNUS :XaSnNUnNf=ff=f)zj Scan initial stan_csv file comments lines and save non-default configuration information to config_dict. rrNrz (Default)rJrLfilecsv data_filerfalse) tellr=r>r:rWendswithreplacerUr?rrr;seek)r-r]r,cur_posrBkey_valraw_valvals r r&r&s ggiG ;;=   D d)a-DOOC00!  == % %<< R0D{{6"**S/ w<1 qz!V+GAJ4G4G4N4N+21:+;+;+= K(!!#v-!!***, *g,C36GAJ,,./''){{}""$5 d)a-DOOC006GGG M" **#Gn%*"f,"#C$/"#C")C * *sB& F// G1: GG-G1G-$G1'G-)G1,G--G1cSU;aU$UR5nUR5R5nSn[U5S:auUR S5(d_US- nUS- nUR5nUR5R5n[U5S:aUR S5(dM_UR U5 XQS'U$)z" Check warmup iterations, if any. rrrNrr)rer=r>r:rWrh)r-r]r,rirB draws_founds r r(r(s K' ggiG ;;=   DK d)a- 4 4! q ''){{}""$ d)a- 4 4 GGG"- Mr"cUR5R5nUS- nUR5US'URS5n[[ U55US'U$)z> Process columns header, add to config_dict as 'column_names' r raw_headerr5r1)r=r>r?tuplemunge_varnames)r-r]r,rBnamess r r'r'sW ;;=   D aKF $ K  JJsOE"'u(=">K Mr"namecSU;aSU;aU$URS5n[U5H;up#SU;aM URSSS5nURSS5nUS- nX1U'M= SRU5$)N.:[rr5])r? enumeratergjoin)rt tuple_partsrCparts r munge_varnamer~s $3d? **S/K[) d? ||Ca(||C%  A * 88K  r"rsc`Uc [S5eUVs/sHn[U5PM sn$s snf)z Change formatting for indices of container var elements from use of dot separator to array-like notation, e.g., rewrite label ``y_forecast.2.4`` to ``y_forecast[2,4]``. zmissing argument "names")rr~)rsrts r rrrrs2  }344,1 2EDM$ E 22 2s+cUSnUR5R5nUS- nUS:Xd[SRX$55eUR5R5nUS- nUR S5upVUR S5(d[SRX$55e[ UR55 UR5nUR5R5nUS- nUS :Xa.UR S 5(aU$URU5 US- $US :XaUS :Xd&US:XaUS:Xd[SRU55eUR5RS5nUS- n[UR S55n US :XaU$[SU 5H_n UR5RS5nUS- n[UR S55U :wdMG[SRU55e U$![a n[SRX&55UeS nAff=f)z; Scan step size, metric from stan_csv file comment lines. metricrz# Adaptation terminatedz(line {}: expecting metric, found: "{}"rLz # Step sizez+line {}: expecting step size, found: "{}"zline {}: invalid step size: {}Nunit_ez# No free parametersdiag_ez+# Diagonal elements of inverse mass matrix:dense_ez"# Elements of inverse mass matrix:z5line {}: invalid or missing mass matrix specificationrJr5) r=r>rrr?rWr;rerhrUr:r<) r-r]r,rrBlabel step_sizer. before_metricnum_unconstrained_paramsr[s r r)r)s9  "F ;;=   D aKF , , 8 ? ? M   ;;=   D aKFzz#E   M * * $fV2   ioo GGIM ;;=   D aKF  ??1 2 2M GGM "A:  h EE i D,P$P "F6N   ;;=   'D aKF"4::c?3  q23A;;=''/D aKF4::c?#'?? $$*F6N 4 S  , 3 3F F  s0H I#H>>Ic PSn[US5nU(d1USRS5nUSRS5nUSnSn Sn UR5n UR5R 5n [U 5S:aU R S5(dUS- nUS- nU R S5n [U 5U:wa6[S RX%[U R S555S -5eUR5n UR5R 5n U(d(W [U W5- n [U W5W:XaW S- n [U 5S:aU R S5(dMURU 5 XAS 'U(d W US 'W US 'U$)zy Parse sampling iteration, save number of iterations to config_dict. Also save number of divergences, max_treedepth hits rr1 divergent__ treedepth__ max_depthrNrr5z0line {}: bad draw, expecting {} items, found {} zThis error could be caused by running out of disk space. Try clearing up TEMP or setting output_dir to a path on another drive.rct_divergencesct_max_treedepth) r:indexrer=r>rWr?rrrrh)r-r]r,rrnnum_cols idx_divergent idx_treedepth max_treedepthrrrirBdatas r r*r*RsK;~./H #N399-H #N399-H #K0 ggiG ;;=   D d)a- 4 4! q zz# t9 CJJc$**S/&:%% ''){{}""$ c$}"56 6N4 &'=8 A% % d)a- 4 4(GGG$/ ! (6 $%*: &' Mr"cURS5(ay[US5n[R"U5nSSS5 SW;a.[R "US5n[ UR5$[SRU55e[ [U55nUc[SRU55eU$!,(df  N=f)zT Read metric file in JSON or Rdump format. Return dimensions of entry "inv_metric". z.jsonr$N inv_metric1metric file {}, bad or missing entry "inv_metric") rfr%jsonloadr8asarraylistshaperrread_rdump_metric)r r- metric_dictdims_npdimss r read_metricrs  }}W $_))B-K ; &"$**[-F"GG & &&&,fTl  %d+, <&&,fTl  #_s C Cc[U5nUb(SU;a"[US[R5(d[ SR U55e[ USR5$)zD Find dimensions of variable named 'inv_metric' in Rdump data file. rr)rload isinstancer8ndarrayrrrr)r rs r rrsd+K # {<0"** = = ? F Ft L    L)// 00r"fnamec0n[US5nUR5nSSS5 SnU[W5:a&SX4;aUS- nU[U5:a SX4;aMU[U5:XagUnUS- nU[U5:a&SX4;aUS- nU[U5:a SX4;aMUnSRX5U5R SS5nUR S5Vs/sHoR 5PM snupU R SS5n U R S S5n [U 5X'U[U5:XaU$UnUS- nM!,(df  GN5=fs snf) zParse data and parameter variable values from an R dump format file. This parser only supports the subset of R dump data as described in the "Dump Data Format" section of the CmdStan manual, i.e., scalar, vector, matrix, and array data types. r$Nrz<-rr_ "L)r% readlinesr:r{rgr?r>parse_rdump_value) r data_dictr-linesidx start_idxnext_varvar_dataitemlhsrhss r rrsf I eS R   C E t5:5 q E t5:5 c%jI1HC CJ4uz#9 1HCCJ4uz#9775845==dBG-5^^D-AB-ATJJL-ABkk#r"kk#r"*3/  #e*     q   CsE$E  Erc[R"S5nURS5(aURU5nUbUR S5c [ U5eUR S5R S5Vs/sHn[U5PM nn[R"USS9nUR S5b]UR S5R S5Vs/sHn[U5PM nn[R"U5RUSS9nU$URS 5(aZURS 5(aD[R"US S R S5Vs/sHn[U5PM sn5nU$S U;dSU;a [U5nU$[U5nU$s snfs snfs snf![a n[ SRU55UeSnAff=f)zProcess right hand side of Rdump variable assignment statement. Value is either scalar, vector, or multi-dim structure. Use regex to capture structure values, dimensions. zQstructure\(\s*c\((?P[^)]*)\)(,\s*\.Dim\s*=\s*c\s*\((?P[^)]*)\s*\))?\) structureNvalsr5r2)r4rzc()r`rvr.zbad value in Rdump file: {})recompilerWmatchgrouprr?r;r8r@rreshaperf TypeErrorr) rpatparsevrrlrrr.s r rrs ** ; C K >>+ & &IIcNE} F 3 ; o%&+kk&&9&?&?&DE&DE!H&DDE((4s+C{{6".(- F(;(A(A#(FG(F1A(FGhhtn,,T,= J^^D ! !cll3&7&7((C"IOOC4HI4HDE$K4HIJC J CZ3#:*C Jc(C JFHJ K6==cBCJKsVA)GF5A G!F:6&GAG0F?GG' G5G G.G))G.)FNNFN)F))__doc__rrrtypingrrrrrrr numpyr8pandasrX cmdstanpyr r r strboolrr!rrFrHr\r&r(r'r~rrr)r*rrr;rrrr"r rs KKKGG !#'!% 4 44C=4# 4  4 3- 4 #s(^4n3c3h"$C$T$d38n$N34S> s tCH~ F#F#c3h###L!#s(^58*  +CH5 ?B   ! ! ! 3$s)3S 3@@!#s(^@58@@F++!#s(^+58+JN++\cd3i4 1C 1DI 1$sE#ubjj2H,I'I"JKB35eRZZ)?#@r"