RAMMatrices: cleanup indexing params in arrays

* introduce ArrayParamsMap type for clarity
* annotate types of the corresp. RAMMatrices fields
* remove cartesian indexing since it is not used
* rename get_parameter_indices() into array_parameters_map()
* use the single pass over the array for performance

Author: alyst

src/additional_functions/parameters.jl

@@ -18,14 +18,20 @@ function fill_A_S_M(A, S, M, A_indices, S_indices, M_indices, parameters)
     end
 end
 
-function get_parameter_indices(parameters, M; linear = true, kwargs...)
-    M_indices = [findall(x -> (x == par), M) for par in parameters]
-
-    if linear
-        M_indices = cartesian2linear.(M_indices, [M])
+# build the map from the index of the parameter to the linear indices
+# of this parameter occurences in M
+# returns ArrayParamsMap object
+function array_parameters_map(parameters::AbstractVector, M::AbstractArray)
+    params_index = Dict(param => i for (i, param) in enumerate(parameters))
+    T = Base.eltype(eachindex(M))
+    res = [Vector{T}() for _ in eachindex(parameters)]
+    for (i, val) in enumerate(M)
+        par_ind = get(params_index, val, nothing)
+        if !isnothing(par_ind)
+            push!(res[par_ind], i)
+        end
     end
-
-    return M_indices
+    return res
 end
 
 function eachindex_lower(M; linear_indices = false, kwargs...)
@@ -49,9 +55,6 @@ function linear2cartesian(ind_lin, dims)
     return ind_cart
 end
 
-cartesian2linear(ind_cart, A::AbstractArray) = cartesian2linear(ind_cart, size(A))
-linear2cartesian(ind_linear, A::AbstractArray) = linear2cartesian(ind_linear, size(A))
-
 function set_constants!(M, M_pre)
     for index in eachindex(M)
         δ = tryparse(Float64, string(M[index]))

src/frontend/specification/RAMMatrices.jl

@@ -2,11 +2,15 @@
 ### Type
 ############################################################################################
 
+# map from parameter index to linear indices of matrix/vector positions where it occurs
+AbstractArrayParamsMap = AbstractVector{<:AbstractVector{<:Integer}}
+ArrayParamsMap = Vector{Vector{Int}}
+
 struct RAMMatrices
-    A_ind::Any
-    S_ind::Any
-    F_ind::Any
-    M_ind::Any
+    A_ind::ArrayParamsMap
+    S_ind::ArrayParamsMap
+    F_ind::Vector{Int}
+    M_ind::Union{ArrayParamsMap, Nothing}
     parameters::Any
     colnames::Any
     constants::Any
@@ -18,9 +22,9 @@ end
 ############################################################################################
 
 function RAMMatrices(; A, S, F, M = nothing, parameters, colnames)
-    A_indices = get_parameter_indices(parameters, A)
-    S_indices = get_parameter_indices(parameters, S)
-    isnothing(M) ? M_indices = nothing : M_indices = get_parameter_indices(parameters, M)
+    A_indices = array_parameters_map(parameters, A)
+    S_indices = array_parameters_map(parameters, S)
+    M_indices = !isnothing(M) ? array_parameters_map(parameters, M) : nothing
     F_indices = findall([any(isone.(col)) for col in eachcol(F)])
     constants = get_RAMConstants(A, S, M)
     return RAMMatrices(