cSc@sdZddlZddlZddlZddlZddlmZddlZddl m Z ddl Z ddl Tddl Z e jdddd Zejstejd d efd YZd efdYZdefdYZdefdYZdS(sa This Module contains the definitions of objects for spatial simulation on geo reference spaces. iN(tbinomial(t json_graph(t*thostt localhosttportii tsiteobjcBseZdZddZdZddgdddZedZdZ dZ d Z d Z d Z d Zd ZdZdZdZdZdZdZdZdZdZRS(s] Basic site object containing attributes and methods common to all site objects. c Cs||_d|_||_t||_g|_g|_t|_d|_ ||_ ||_ d|_ d|_d|_d|_d|_g|_g|_g|_g|_g|_d|_ggg|_d|_d|_d|_tjdg|_d|_||_ d|_!d|_"g|_#g|_$g|_%g|_&ddddddddddddg |_'t(j)dj*|j ddS(s  Set initial values for site attributes. -name: name of the locality -coords: site coordinates. -initpop: total population size. -geocode: integer id code for site -values: Tuple containing adicional values from the sites file is {}:totalcasesN(+tidt stochtransptpostfloatttotpopttst incidencetFalsetinfectedtNonetinfectortsitenametvaluest centralityt betweenesstthidxtdegreet parentGraphtedgest neighborst thetalistt thetahisttpasslistt totalcasest vaccinationt vaccineNowtvaccovt nVaccinatedtsystmaxintt quarantinet nQuarantinedtgeocodetpaintedtmodtypetmigInftinedgestoutedgestpdesttinfectedvisitingt redisclienttsettformat(tselftnametinitpoptcoordsR'R((sL/home/fccoelho/Documentos/Projects_Software/epigrass-code/Epigrass/simobj.pyt__init__#sH                               -cCs-tj}|jdGtj|GH|S(s- For multiprocessing to work sTime to runModel: (ttimetrunModel(R2tt0((sL/home/fccoelho/Documentos/Projects_Software/epigrass-code/Epigrass/simobj.pyt__call__Xs  ttmodel1c Cs|j}||_||_||_||_tj|j||_tj ||_ y |j j t |jWnjt k r}|j dddgkrgdddgD]}||^qg|_ qt d|nXd|jd  0  &5     *- cCstj}|jdj|jdjdj|jjdj|jj\}}}|jjt |t |}t |}|j |7_ |j j||j s|dkr|jj|_ |jjj|jj|j|jfqn|jj|dS(Ns{}:tsis{}:Lposs {}:migInfi(R/RWtlindexR1R'tgetRZR RItevalR RR RRRQtepipathRR*(R2RdRbt last_statetLposR*((sL/home/fccoelho/Documentos/Projects_Software/epigrass-code/Epigrass/simobj.pyR]s $    .cCs|\}}}|jj||j|7_|jj||js|dkr|jj|_|jjj|jj|j|j fqn|j j|dS(s Processes the output of a step updating simulation statistics :param res: Tuple with the output of the simulation model iN( R RIRR RRRQRhR'RR*(R2RdtstateRjR*((sL/home/fccoelho/Documentos/Projects_Software/epigrass-code/Epigrass/simobj.pyt handle_olds  .cCs@|jdd||_|jddd||jdds  + cCs|jsgS|jr |jSi}xW|jD]L}|j|j|jg}|j|}|j||d||dscSs |jjS(N(t edge_dictR(R2((sL/home/fccoelho/Documentos/Projects_Software/epigrass-code/Epigrass/simobj.pyRsiiid(+R3tdigraphRtpropertyRzRt edge_listRRQtmaxstepRht graphdictRRtzerosRRtcyclestwienerDtmeanDtdiameterRtweighttiotaidxtpiidxtbetaidxtalphaidxtgammaidxt connmatrixtshortDistMatrixtepisizetepispeedtinfectedcitiest spreadtimetmediansurvivalt totVaccinatedttotQuarantinedtdmaptprintedtmultiprocessingtPoolt cpu_countR[(R2t graph_nameR((sL/home/fccoelho/Documentos/Projects_Software/epigrass-code/Epigrass/simobj.pyR6sJ                                 cCs8t|tstdn||j|j<||_dS(s Adds a site object to the graph. It takes a siteobj object as its only argument and returns None. s,add_site received a non siteobj class objectN(RRtErrorRR'R(R2tsitio((sL/home/fccoelho/Documentos/Projects_Software/epigrass-code/Epigrass/simobj.pytaddSites c Csi}i}t}d||w, G[v][w] is the length of the edge. This is related to the representation in where Guido van Rossum suggests representing graphs as dictionaries mapping vertices to lists of neighbors, however dictionaries of edges have many advantages over lists: they can store extra information (here, the lengths), they support fast existence tests, and they allow easy modification of the graph by edge insertion and removal. Such modifications are not needed here but are important in other graph algorithms. Since dictionaries obey iterator protocol, a graph represented as described here could be handed without modification to an algorithm using Guido's representation. Of course, G and G[v] need not be Python dict objects; they can be any other object that obeys dict protocol, for instance a wrapper in which vertices are URLs and a call to G[v] loads the web page and finds its links. The output is a pair (D,P) where D[v] is the distance from start to v and P[v] is the predecessor of v along the shortest path from s to v. Dijkstra's algorithm is only guaranteed to work correctly when all edge lengths are positive. This code does not verify this property for all edges (only the edges seen before the end vertex is reached), but will correctly compute shortest paths even for some graphs with negative edges, and will raise an exception if it discovers that a negative edge has caused it to make a mistake. is3Dijkstra: found better path to already-final vertex(tpriorityDictionaryRt( R2tGtstarttendtDtPtQRLtwtvwLength((sL/home/fccoelho/Documentos/Projects_Software/epigrass-code/Epigrass/simobj.pytdijkstras$+       cCslg|jD]$}|jt|kr |^q }t|}|dkrT|dS|dkrd|SdSdS(sERetrieved a site from the graph. Given a site's name the corresponding Siteobj instance will be returned. If multiple sites exist with that name, a list of Siteobj instances is returned. If only one site exists, the instance is returned. None is returned otherwise. iiN(RzR3tstrRrR(R2R3Rtmatchtl((sL/home/fccoelho/Documentos/Projects_Software/epigrass-code/Epigrass/simobj.pytgetSite,s 4   cCst|tstdn|jj|jkrBtdn|jj|jkrftdn||j|jj|jjf<||_ |j dS(syAdds an edge object to the graph. It takes a edge object as its only argument and returns None. s)add_edge received a non edge class objects(Edge source does not belong to the graphs-Edge destination does not belong to the graphN( RRRRR'RRKRRRR(R2t graph_edge((sL/home/fccoelho/Documentos/Projects_Software/epigrass-code/Epigrass/simobj.pytaddEdgeDs cCs=i}x'|jjD]}|j||eZdZdZdZdZdZdZRS(cCsg|_tj|dS(so by David Eppstein. Initialize priorityDictionary by creating binary heap of pairs (value,key). Note that changing or removing a dict entry will not remove the old pair from the heap until it is found by smallest() or until the heap is rebuilt. N(t_priorityDictionary__heapRVR6(R2((sL/home/fccoelho/Documentos/Projects_Software/epigrass-code/Epigrass/simobj.pyR6_s cCst|dkrtdn|j}x|dd|ks^||dd|ddkr|j}d}xd|d}|dt|kr||||dkr|d7}n|t|ks|||kr|||s.         X@