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Merge pull request #5 from AlgebraicJulia/cleancode
clean and refactor codebase, and also start adding networks
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,278 +1,14 @@ | ||
| """ Some description of ths package | ||
| """ | ||
| module StateCharts | ||
| using Reexport | ||
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| export StateChartF, TheoryStateChart, AbstractStateChart, StateChart, | ||
| ns, nt, ne, neal, nal, sname, snames, tname, tnames, ename, enames, eaname, eanames, aname, anames, texpr, | ||
| ttype, ealsource, ealsources, ealtarget, ealtargets, tsource, ttarget, etarget, alsource, alsources, altarget, altargets, | ||
| Graph | ||
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| using Catlab | ||
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| using Catlab.CategoricalAlgebra | ||
| using Catlab.Graphics.Graphviz | ||
| import Catlab.Graphics.Graphviz: Graph, Subgraph | ||
| using Catlab.Graphics | ||
| import Base.Iterators: flatten | ||
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| vectorify(n::Vector) = collect(n) | ||
| vectorify(n::Tuple) = length(n) == 1 ? [n] : collect(n) | ||
| vectorify(n::SubArray) = collect(n) | ||
| vectorify(n) = [n] | ||
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| state_dict(n) = Dict(s=>i for (i, s) in enumerate(n)) | ||
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| # define the schema of state charts | ||
| @present TheoryStateChart(FreeSchema) begin | ||
| S::Ob #state | ||
| T::Ob #transitions | ||
| ALT::Ob #alternative branches | ||
| E::Ob # start transition (in this statechart schema, it can have multiple start transitions -- with multiple state chart in parallel) | ||
| EALT::Ob # alternative branches for the start transition | ||
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| ts::Hom(T,S) | ||
| tt::Hom(T,S) | ||
| abs::Hom(ALT,T) | ||
| abt::Hom(ALT,S) | ||
| es::Hom(E,S) | ||
| eabs::Hom(EALT,E) | ||
| eabt::Hom(EALT,S) | ||
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| Name::AttrType | ||
| Expr::AttrType | ||
| TT::AttrType # type of the non-start transitions | ||
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| ttype::Attr(T, TT) | ||
| texpr::Attr(T, Expr) | ||
| aexpr::Attr(ALT, Expr) | ||
| eaexpr::Attr(EALT, Expr) | ||
| aname::Attr(ALT, Name) | ||
| eaname::Attr(EALT, Name) | ||
| sname::Attr(S, Name) | ||
| tname::Attr(T, Name) | ||
| ename::Attr(E, Name) | ||
| end | ||
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| @abstract_acset_type AbstractStateChart | ||
| @acset_type StateChartUntype(TheoryStateChart) <: AbstractStateChart | ||
| #const StateChart = StateChartUntype{Symbol,Union{Float16,Sampleable},Symbol} | ||
| const StateChart = StateChartUntype{Symbol,Float16,Symbol} | ||
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| # define functions of adding components of state charts | ||
| add_transition!(ss::AbstractStateChart,s,t;kw...) = add_part!(ss,:T;ts=s,tt=t,kw...) | ||
| add_transitions!(ss::AbstractStateChart,s,t,n;kw...) = add_parts!(ss,:T,n;ts=s,tt=t,kw...) | ||
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| add_state!(ss::AbstractStateChart;kw...) = add_part!(ss,:S;kw...) | ||
| add_states!(ss::AbstractStateChart,n;kw...) = add_parts!(ss,:S,n;kw...) | ||
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| add_alternative!(ss::AbstractStateChart,s,t;kw...) = add_part!(ss,:ALT;abs=s,abt=t,kw...) | ||
| add_alternatives!(ss::AbstractStateChart,s,t,n;kw...) = add_parts!(ss,:ALT,n;abs=s,abt=t,kw...) | ||
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| add_startTransition!(ss::AbstractStateChart,t;kw...) = add_part!(ss,:E;es=t,kw...) | ||
| add_startTransitions!(ss::AbstractStateChart,t,n;kw...) = add_parts!(ss,:E,n;es=t,kw...) | ||
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| add_startAlternative!(ss::AbstractStateChart,s,t;kw...) = add_part!(ss,:EALT;eabs=s,eabt=t,kw...) | ||
| add_startAlternatives!(ss::AbstractStateChart,s,t,n;kw...) = add_parts!(ss,:EALT,n;eabs=s,eabt=t,kw...) | ||
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| """ StateCharts(name::String) | ||
| StateCharts(s::Tuple, t::Tuple, alt::Tuple, e::Tuple, ealt::Tuple) | ||
| Returns an instance of State Charts | ||
| """ | ||
| StateChartF(s, t, alt, e, ealt) = begin | ||
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| ss = StateChart() | ||
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| # add states | ||
| states=vectorify(s) | ||
| add_states!(ss,length(states),sname=states) | ||
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| # add non-start transitions | ||
| transitions=vectorify(t) | ||
| tns=map(first,transitions) | ||
| tst=map(first,map(last,transitions)) | ||
| tnr=map(last,map(last,transitions)) | ||
| s_idx=state_dict(states) | ||
| t_idx=state_dict(tns) | ||
| ts=map(x->s_idx[x], map(first,tst)) | ||
| tt=map(x->s_idx[x], map(last,tst)) | ||
| add_transitions!(ss,ts,tt,length(tns),tname=tns,ttype=map(first,tnr),texpr=map(last,tnr)) | ||
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| # add start transitions | ||
| es=vectorify(e) | ||
| esname=map(first,es) | ||
| esstates=map(last,es) | ||
| e_idx=state_dict(esname) | ||
| tes=map(x->s_idx[x], map(last,es)) | ||
| add_startTransitions!(ss,tes,length(esname),ename=esname) | ||
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| # add branches of start transitions | ||
| if length(ealt)>0 # if have branches | ||
| for (i,(tn,rps)) in enumerate(vectorify(ealt)) | ||
| rps = vectorify(rps) | ||
| t = e_idx[tn] | ||
| ps = map(first,rps) | ||
| an = map(first,ps) | ||
| p = map(last,ps) | ||
| sns = map(last,rps) | ||
| s = map(x->s_idx[x],sns) | ||
| add_startAlternatives!(ss,repeat([t], length(s)),s,length(s),eaexpr=p,eaname=an) | ||
| end | ||
| end | ||
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| # add branches of non-start transitions | ||
| if length(alt)>0 # if have branches | ||
| for (i,(tn,rps)) in enumerate(vectorify(alt)) | ||
| rps = vectorify(rps) | ||
| t = t_idx[tn] | ||
| ps = map(first,rps) | ||
| an = map(first,ps) | ||
| p = map(last,ps) | ||
| sns = map(last,rps) | ||
| s = map(x->s_idx[x],sns) | ||
| add_alternatives!(ss,repeat([t], length(s)),s,length(s),aexpr=p,aname=an) | ||
| end | ||
| end | ||
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| ss | ||
| end | ||
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| ns(ss::AbstractStateChart) = nparts(ss,:S) | ||
| nt(ss::AbstractStateChart) = nparts(ss,:T) | ||
| ne(ss::AbstractStateChart) = nparts(ss,:E) | ||
| neal(ss::AbstractStateChart) = nparts(ss,:EALT) # return the numbers of start branch alternatives -- one branch counts to one alternative | ||
| nal(ss::AbstractStateChart) = nparts(ss,:ALT) # return the numbers of non-start branch alternatives -- one branch counts to one alternative | ||
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| sname(ss::AbstractStateChart,s) = subpart(ss,s,:sname) | ||
| snames(ss::AbstractStateChart) = [sname(ss, s) for s in 1:ns(ss)] | ||
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| tname(ss::AbstractStateChart,t) = subpart(ss,t,:tname) | ||
| tnames(ss::AbstractStateChart) = [tname(ss, t) for t in 1:nt(ss)] | ||
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| ename(ss::AbstractStateChart,e) = subpart(ss,e,:ename) | ||
| enames(ss::AbstractStateChart) = [ename(ss, e) for e in 1:ne(ss)] | ||
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| eaname(ss::AbstractStateChart,eal) = subpart(ss,eal,:eaname) | ||
| eanames(ss::AbstractStateChart) = [eaname(ss, eal) for eal in 1:neal(ss)] | ||
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| aname(ss::AbstractStateChart,al) = subpart(ss,al,:aname) | ||
| anames(ss::AbstractStateChart) = [aname(ss, al) for al in 1:nal(ss)] | ||
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| ttype(ss::AbstractStateChart,t) = subpart(ss,t,:ttype) | ||
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| ealsource(ss::AbstractStateChart,eal) = subpart(ss,eal,:eabs) | ||
| ealsources(ss::AbstractStateChart) = [ealsource(ss, eal) for eal in 1:neal(ss)] | ||
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| ealtarget(ss::AbstractStateChart,eal) = subpart(ss,eal,:eabt) | ||
| ealtargets(ss::AbstractStateChart) = [ealtarget(ss, eal) for eal in 1:neal(ss)] | ||
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| # return a transition's source state | ||
| tsource(ss::AbstractStateChart,t) = subpart(ss,t,:ts) | ||
| # return a transition's target state | ||
| ttarget(ss::AbstractStateChart,t) = subpart(ss,t,:tt) | ||
| # return a start transition's target state | ||
| etarget(ss::AbstractStateChart,e) = subpart(ss,e,:es) | ||
| # return an alternative's source transition | ||
| alsource(ss::AbstractStateChart,al) = subpart(ss,al,:abs) | ||
| alsources(ss::AbstractStateChart) = [alsource(ss, al) for al in 1:nal(ss)] | ||
| # return an alternative's target state | ||
| altarget(ss::AbstractStateChart,al) = subpart(ss,al,:abt) | ||
| altargets(ss::AbstractStateChart) = [altarget(ss, al) for al in 1:nal(ss)] | ||
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| texpr(ss::AbstractStateChart,t) = subpart(ss,t,:texpr) | ||
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| # visualization | ||
| TTYPE=Dict(:Rate=>"📉", :TimeOut=>"⏰", :Conditional=>"❓", :Pattern=>"🚩") | ||
| # for Pattern, it indicates pattern match. User will provide the pattern match rule, and the state chart schema structure only | ||
| # capture the index of the array of the user-defined pattern match rule. | ||
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| def_state(ss, s) = ("s$s", Attributes(:label=>"$(sname(ss, s))", | ||
| :shape=>"square", | ||
| :color=>"black", | ||
| :style=>"filled", | ||
| :fillcolor=>"gold2")) | ||
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| def_start(ss, se) = ("se$se", Attributes(:label=>"$(ename(ss, se))", | ||
| :shape=>"point")) | ||
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| def_branchNode(ss, b, isStartTransition=true) = (isStartTransition ? "eb$b" : "b$b", Attributes(:label=>"", | ||
| :shape=>"diamond", | ||
| :height=>"0.2", | ||
| :width=>"0.2", | ||
| :color=>"black", | ||
| :fillcolor=>"white")) | ||
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| def_transition(ss, s, t, f, ttype) = ([s, t],Attributes(:taillabel=>ttype, | ||
| :label=>"$(tname(ss,f))", | ||
| :taillabelfontsize=>"4", | ||
| :labeldistance=>"1.7", | ||
| :labelangle=>"0")) | ||
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| def_start_transition(ss, s, t) = ([s, t],Attributes(:label=>"")) | ||
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| def_default_branch(ss, s, t) = ([s, t],Attributes(:label=>"", | ||
| :style=>"dashed")) | ||
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| def_alternative(ss, s, t, e, isStartTransition=true) = ([s, t], isStartTransition ? Attributes(:label=>"$(eaname(ss,e))") : Attributes(:label=>"$(aname(ss,e))")) | ||
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| function Graph(ss::StateChart) | ||
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| stateNodes = [Node(def_state(ss,s)...) for s in 1:ns(ss)] | ||
| startPoints = [Node(def_start(ss,es)...) for es in 1:ne(ss)] | ||
| eBranchNodes = [Node(def_branchNode(ss,eb,true)...) for eb in unique(ealsources(ss))] | ||
| branchNodes = [Node(def_branchNode(ss,b,false)...) for b in unique(alsources(ss))] | ||
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| smts_Noes=vcat(stateNodes,startPoints,eBranchNodes,branchNodes) | ||
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| edges_T=map(1:nt(ss)) do k | ||
| state_idx_outfrom = tsource(ss,k) | ||
| state_idx_into = ttarget(ss,k) | ||
| t_type=ttype(ss,k) | ||
| if k in alsources(ss) | ||
| branch_idx_into = k | ||
| [Edge(def_transition(ss,"s$state_idx_outfrom","b$branch_idx_into", k, TTYPE[t_type])...), | ||
| Edge(def_default_branch(ss,"b$branch_idx_into","s$state_idx_into")...)] | ||
| else | ||
| [Edge(def_transition(ss,"s$state_idx_outfrom", "s$state_idx_into", k, TTYPE[t_type])...)] | ||
| end | ||
| end |> flatten |> collect | ||
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| edges_E = map(1:ne(ss)) do k | ||
| start_p = k | ||
| state_idx_into = etarget(ss,k) | ||
| if k in ealsources(ss) | ||
| branch_idx_into = k | ||
| [Edge(def_start_transition(ss,"se$start_p","eb$branch_idx_into")...), | ||
| Edge(def_default_branch(ss,"eb$branch_idx_into","s$state_idx_into")...)] | ||
| else | ||
| [Edge(def_start_transition(ss,"se$start_p","s$state_idx_into")...)] | ||
| end | ||
| end |> flatten |> collect | ||
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| edges_ealternatives = map(1:neal(ss)) do k | ||
| start_branch = ealsource(ss,k) | ||
| state_idx_into = ealtarget(ss,k) | ||
| [Edge(def_alternative(ss,"eb$start_branch","s$state_idx_into", k, true)...)] | ||
| end |> flatten |> collect | ||
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| edges_alternatives = map(1:nal(ss)) do k | ||
| start_branch = alsource(ss,k) | ||
| state_idx_into = altarget(ss,k) | ||
| [Edge(def_alternative(ss,"b$start_branch","s$state_idx_into", k, false)...)] | ||
| end |> flatten |> collect | ||
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| smts_edges=vcat(edges_T,edges_E,edges_ealternatives,edges_alternatives) | ||
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| smts=vcat(smts_Noes,smts_edges) | ||
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| graph_attrs = Attributes(:rankdir=>"TB") | ||
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| g = Graphviz.Digraph("G", smts; graph_attrs=graph_attrs) | ||
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| return g | ||
| end | ||
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| end | ||
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| include("StateChartsSchema.jl") | ||
| include("Visualization.jl") | ||
| include("interfacesToAMBs/NetworkSchemaInterfaces.jl") | ||
| include("interfacesToAMBs/StateChartsABMsInterfaces.jl") | ||
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| @reexport using .StateChartsSchema | ||
| @reexport using .Visualization | ||
| @reexport using .NetworkSchemaInterfaces | ||
| @reexport using .StateChartsABMsInterfaces | ||
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| end |
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