Compute costs matrix from phylogenetic tree and reorganise sources

data/costs.csv

@@ -1,52 +0,0 @@
-name,Ail,Asperge,Ciboulette,Echalote,Oignon,Poireau,Fève,Haricot,Pois,Aneth,Carotte,Celeri,Cerfeuil,Fenouil,Panais,Persil,Aubergine,Poivron,Pomme de terre,Tomate,Chou,Chou rave,Chou rouge,Navet,Radis,Concombre,Cornichon,Cucurbita,Courgette,Melon,Artichaut,Basilic,Bette,Betterave,Capucine,Chicoree,Cresson,Epinard,Fraisier,Laitue,Maïs,Menthe,Oeillet d'inde,Sarriette,Sauge,Scorsonère,Souci,Tétragone,Tournesol,Vigne,Lavande
-Ail,,,,,1,,-1,-1,-1,1,1,1,1,1,1,1,-1,-1,1,1,,,,,,,,,,,,,,1,,,,,1,1,,,,,,,1,,,,
-Asperge,,,,,,1,-1,1,-1,1,1,1,1,1,1,1,-1,-1,-1,1,,,,,,1,1,,,,,,,,,,,,,,,,,,,,,,,,
-Ciboulette,,,,,,,-1,-1,-1,1,1,1,1,1,1,1,-1,-1,-1,-1,,,,,,,,1,1,,,,,,,,,,,,,,,,,,,,,,
-Echalote,,,,,-1,,-1,-1,-1,1,1,1,1,1,1,1,-1,-1,-1,-1,,,,,,,,1,1,,,,,,,,,,1,,,,,,,,,,,,
-Oignon,1,,,-1,,-1,-1,-1,-1,1,1,1,1,1,1,1,-1,-1,-1,1,-1,,,,,1,1,1,1,,1,,1,1,,,,,1,1,,,,,,1,1,,,,
-Poireau,,1,,,-1,1,-1,-1,-1,1,1,1,1,1,1,1,-1,-1,-1,1,,,,,,,,,,1,,,-1,,,,,1,1,1,,,,,,1,1,,,,
-Feve,-1,-1,-1,-1,-1,-1,,,,,,,,,1,,,,,,1,1,1,1,1,1,1,1,1,1,,,,,,,,,,,,,,,,,,,,,
-Haricot,-1,1,-1,-1,-1,-1,,1,-1,,1,1,,,1,,1,,1,,1,1,1,1,1,1,1,1,1,1,,,1,1,,,,1,1,1,2,,,,,,,1,,,
-Pois,-1,-1,-1,-1,-1,-1,,-1,1,,1,1,,,,,,,1,-1,1,1,1,1,1,1,1,1,1,1,,,,,,,,,,1,,,,,,,,,,,
-Aneth,1,1,1,1,1,1,,,,1,1,1,1,1,1,1,,,,,1,1,1,1,1,,,,,,,,,,,,,,,1,,,,,,,,,,,
-Carotte,1,1,1,1,1,1,,1,1,1,1,1,1,1,1,1,,,,1,1,1,1,1,1,,,,,,,,1,-1,,1,,1,,1,,-1,,,,1,,,,,
-Celeri,1,1,1,1,1,1,,1,1,1,1,1,1,1,1,1,,,,1,1,1,1,1,1,,,,,,,,1,,,,,,,,-1,,,,,,,,,,
-Cerfeuil,1,1,1,1,1,1,,,,1,1,1,1,1,1,1,,,,,1,1,1,1,-1,,,,,,,,,,,,,,,1,,,,,,,,,,,
-Fenouil,1,1,1,1,1,1,,,,1,1,1,1,1,1,1,,,,-1,1,1,1,1,1,,,,,,,,,,,,,,,,,,,,,,,,,,
-Panais,1,1,1,1,1,1,1,1,,1,1,1,1,1,1,1,,,,1,1,1,1,1,1,,,,,,,,,,,,,,,-1,,,,,,,,,,,
-Persil,1,1,1,1,1,1,,,,1,1,1,1,1,1,1,,,,1,1,1,1,1,1,,,,,,,,,,,,,,1,-1,,,,,,,,,,,
-Aubergine,-1,-1,-1,-1,-1,-1,,1,,,,,,,,,,1,-1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
-Poivron,-1,-1,-1,-1,-1,-1,,,,,,,,,,,1,,,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
-Pomme de terre,1,-1,-1,-1,-1,-1,,1,1,,,,,,,,-1,,,-1,,,,,-1,,,,-1,,,,,,,,,,,,1,,,,,,1,,,,
-Tomate,1,1,-1,-1,-1,1,,,-1,,1,1,,-1,1,1,,1,-1,1,1,,-1,,1,,,,,,,1,,-1,,,,1,,1,1,,,,,,1,1,,,
-Chou,,,,,-1,,1,1,1,1,1,1,1,1,1,1,,,,1,,,,,,1,1,,,,1,,,,,,,1,-1,1,,,,1,,,,,,,
-Chou rave,,,,,,,1,1,1,1,1,1,1,1,1,1,,,,,,,,,,,,,,,,,1,,,,,,,,,,,,,1,,,,,
-Chou rouge,,,,,,,1,1,1,1,1,1,1,1,1,1,,,,-1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
-Navet,,,,,,,1,1,1,1,1,1,1,1,1,1,,,,,,,,,,,,,,,,,1,,,,,1,,,,,,,,,,,,,
-Radis,,,,,,,1,1,1,1,1,1,-1,1,1,1,,,-1,1,,,,,,-1,-1,,,,1,,1,,,,1,1,,1,,,,,,1,,,,,
-Concombre,,1,,,1,,1,1,1,,,,,,,,,,,,1,,,,-1,,,-1,-1,,,1,,,,,,,,1,1,,1,,,,,,,,
-Cornichon,,1,,,1,,1,1,1,,,,,,,,,,,,1,,,,-1,,,-1,-1,,,1,,,,,,,,1,1,,1,,,,,,,,
-Cucurbita,,,1,1,1,,1,1,1,,,,,,,,,,,,,,,,,-1,-1,,,,,,,,,,,,,,1,,,,,,,,,,
-Courgette,,,1,1,1,,1,1,1,,,,,,,,,,-1,,,,,,,-1,-1,,,,,,,,,,,,,,,,,,,,,1,,,
-Melon,,,,,,1,1,1,1,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,1,1,,,,,,,,,,
-Artichaut,,,,,1,,1,1,1,,,,,,,,,,,,1,,,,1,,,,,,,,,,,,,,,1,,,,,,,,,,,
-Basilic,,,,,,,1,1,1,,,,,,,,,,,1,,,,,,1,1,,,,,,,,,,,,,,,,,,,,,,,,
-Bette,,,,,1,-1,1,1,,,1,1,,,,,,,,,,1,,1,1,,,,,,,,,,,,,,,1,,,,,,,,,,,
-Betterave,1,,,,1,,1,1,,,-1,,,,,,,,,-1,,,,,,,,,,,,,,,,,,1,,1,-1,,,,,,,,,,
-Capucine,,,,,,,1,1,1,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,,,,,,,,,,,,,,
-Chicorée,,,,,,,1,1,1,,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,
-Cresson,,,,,,,1,1,1,,,,,,,,,,,,,,,,1,,,,,,,,,,,,,,,,,,,,,,,,,,
-Epinard,,,,,,1,1,1,1,,1,,,,,,,,,1,1,,,1,1,,,,,,,,,1,,,,,1,1,,,,,,,,,,,
-Fraisier,1,,,1,1,1,1,1,1,,,,,,,1,,,,,-1,,,,,,,,,,,,,,,,,1,,1,,,,,1,,,,,,
-Laitue,1,,,,1,1,1,1,1,1,1,,1,,-1,-1,,,,1,1,,,,1,1,1,,,1,1,,1,1,,,,1,1,1,,,,,,1,,,-1,,
-Maïs,,,,,,,1,2,1,,,-1,,,,,,,1,1,,,,,,1,1,1,,1,,,,-1,,,,,,,,,,,,,,,,,
-Menthe,,,,,,,1,1,1,,-1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
-Oeillet d'inde,,,,,,,1,1,1,,,,,,,,,,,,,,,,,1,1,,,,,,,,,,,,,,,,,,,,,,,,
-Sarriette,,,,,,,1,1,1,,,,,,,,,,,,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
-Sauge,,,,,,,1,1,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,,,,,
-Scorsonère,,,,,1,1,1,1,1,,1,,,,,,,,,,,1,,,1,,,,,,,,,,,,,,,1,,,,,,,,,,,
-Souci,1,,,,1,1,1,1,1,,,,,,,,,,1,1,,,,,,,,,,,,,,,,1,,,,,,,,,,,,,,,
-Tétragone,,,,,,,1,1,1,,,,,,,,,,,1,,,,,,,,,1,,,,,,,,,,,,,,,,,,,,,,
-Tournesol,,,,,,,1,1,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,-1,,,,,,,,,,,
-Vigne,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
-Lavande,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,

data/plants.txt

@@ -1,51 +0,0 @@
-Ail
-Asperge
-Ciboulette
-Echalote
-Oignon
-Poireau
-Feve
-Haricot
-Pois
-Aneth
-Carotte
-Celeri
-Cerfeuil
-Fenouil
-Panais
-Persil
-Aubergine
-Poivron
-Pomme de terre
-Tomate
-Chou
-Chou rave
-Chou rouge
-Navet
-Radis
-Concombre
-Cornichon
-Cucurbita
-Courgette
-Melon
-Artichaut
-Basilic
-Bette
-Betterave
-Capucine
-Chicorée
-Cresson
-Epinard
-Fraisier
-Laitue
-Maïs
-Menthe
-Oeillet d'inde
-Sarriette
-Sauge
-Scorsonère
-Souci
-Tétragone
-Tournesol
-Vigne
-Lavande

src/GardenOptim.jl

@@ -1,15 +1,10 @@
 module GardenOptim
 
 using Logging
-using Unicode
 
-using DataFrames
 using DocStringExtensions
-using CSV
-using JSON
-using Tables
 
-export loadclassification, loadplants, loadgarden, loadcosts
+export loadplants, loadgarden, loadclassification, loadcosts
 export update!, randomgardenevolution!, outputgarden
 
 @template (FUNCTIONS, METHODS, MACROS) =
@@ -18,112 +13,8 @@ export update!, randomgardenevolution!, outputgarden
     $(DOCSTRING)
     """
 
-mutable struct Classification
+include("classification.jl")
-    type::Symbol
+include("loaddata.jl")
-    name::Symbol
-    bio::String
-    children::Vector{Classification}
-    parent::Classification
-
-    function Classification(classif::Dict{String, Any})
-        children = [Classification(d) for d in get(classif, "children", [])]
-        type = Symbol(Unicode.normalize(classif["type"], casefold=true, stripmark=true))
-        name = Symbol(Unicode.normalize(classif["name"], casefold=true, stripmark=true))
-        classif = new(type, name, get(classif, "bio", ""), children)
-        for child in children
-            child.parent = classif
-        end
-        classif
-    end
-end
-
-function loadclassification()
-    clf = JSON.parsefile("data/classification.json")
-    clf = Classification(clf)
-    @debug "loaded classification of type $(clf.type)"
-    clf
-end
-
-function loadplants()::DataFrame
-    plants = CSV.read("data/plants.csv")
-    @info "loaded $(size(plants, 1)) plants"
-    plants.name = Symbol.(plants.name)
-    plants
-end
-
-function loadgarden(plants::Vector{String})::Tuple{Matrix{Int}, Matrix{Bool}}
-    garden = CSV.read("data/garden.csv")
-    garden = coalesce.(garden, "")
-    mask = convert(Matrix, garden .== "empty")
-    garden = indexin(convert(Matrix, garden), plants)
-    garden = replace(garden, nothing=>0)
-    @assert size(garden) == size(mask)
-    @info "loaded garden of size $(size(garden))"
-    garden, mask
-end
-
-function loadcosts()::DataFrame
-    df = CSV.read("data/associations.csv", copycols=true)
-    colnames = String.(names(df))
-    colnames = Symbol.(Unicode.normalize.(colnames, casefold=true, stripmark=true))
-    rename!(df, colnames)
-    df.name = colnames[2:end]
-    # df = coalesce.(df, 0.0)
-    @info "loaded cost matrix for $(size(df, 1)) plants"
-    df
-end
-
-# function loadcosts()::Matrix{Float64}
-#     df = CSV.read("data/costs.csv")
-#     df = coalesce.(df, 0)  # replace missing values by 0
-#     costs = convert(Matrix, df[:, 2:end])
-#     @info "loaded cost matrix of size $(size(costs))"
-#     # ensure the matrix is symmetric: keep the max of itself and its transpose
-#     costs = Float64.(max.(costs, permutedims(costs)))
-# end
-
-function getparent(name::Symbol, classification::Classification)
-    if classification.name == name
-        return classification.parent
-    else
-        for child in classification.children
-            parent = getparent(name, child)
-            if !isnothing(parent)
-                return parent
-            end
-        end
-    end
-end
-
-function computecost(costs::DataFrame, plant1::Symbol, plant2::Symbol, classification::Classification)::Float64
-    @debug "$plant1 and $plant2"
-    if plant1 in names(costs) && plant2 in names(costs)
-        cost = costs[costs.name .== plant1, plant2][1]
-    else
-        @debug "$plant1 and $plant2 not in costs"
-        cost = missing
-    end
-
-    if !ismissing(cost)
-        return cost
-    end
-
-    @debug "missing"
-    try
-        parent1 = getparent(plant1, classification).name
-        computecost(costs, parent1, plant2, classification)
-    catch UndefRefError
-        return missing
-    end
-
-    try
-        parent2 = getparent(plant2, classification).name
-        computecost(costs, plant1, parent2, classification)
-    catch UndefRefError
-        return missing
-    end
-
-end
 
 "Return a random index to be filled from the garden mask."
 function randomindex(mask::Matrix{Bool})::Int

src/classification.jl

@@ -0,0 +1,50 @@
+using Unicode
+
+mutable struct Classification
+    type::Symbol
+    name::Symbol
+    bio::String
+    children::Vector{Classification}
+    parent::Classification
+
+    function Classification(classif::Dict{String, Any})
+        children = [Classification(d) for d in get(classif, "children", [])]
+        type = Symbol(Unicode.normalize(classif["type"], casefold=true, stripmark=true))
+        name = Symbol(Unicode.normalize(classif["name"], casefold=true, stripmark=true))
+        classif = new(type, name, get(classif, "bio", ""), children)
+        for child in children
+            child.parent = classif
+        end
+        classif
+    end
+end
+
+function Base.show(io::IO, clf::Classification)
+    if length(clf.children) < 2
+        childrentext = " with $(length(clf.children)) child"
+    else
+        childrentext = " with $(length(clf.children)) children"
+    end
+    biotext = ""
+    if clf.bio != ""
+        biotext = " ($(clf.bio))"
+    end
+    print("Classification(", clf.type, " ", clf.name, biotext, childrentext, ")")
+end
+
+function getfirstparent(name::Symbol, classification::Classification)
+    if classification.name == name
+        parent = classification
+        while parent.parent.name != :god
+            parent = parent.parent
+        end
+        return parent
+    else
+        for child in classification.children
+            parent = getfirstparent(name, child)
+            if !isnothing(parent)
+                return parent
+            end
+        end
+    end
+end

src/loaddata.jl

@@ -0,0 +1,83 @@
+using Logging
+using Unicode
+
+using DataFrames
+using CSV
+using JSON
+
+function loadplants()::DataFrame
+    plants = CSV.read("data/plants.csv")
+    @info "loaded $(size(plants, 1)) plants"
+    plants.name = Symbol.(plants.name)
+    plants
+end
+
+function loadgarden(plants::Vector{Symbol})::Tuple{Matrix{Int}, Matrix{Bool}}
+    garden = CSV.read("data/garden.csv")
+    garden = coalesce.(garden, "")
+    mask = convert(Matrix, garden .== "empty")
+    garden = Unicode.normalize.(garden, casefold=true, stripmark=true)
+    garden = indexin(convert(Matrix, garden), String.(plants))
+    garden = replace(garden, nothing=>0)
+    @assert size(garden) == size(mask)
+    @info "loaded garden of size $(size(garden))"
+    garden, mask
+end
+
+function loadclassification()::Classification
+    clf = JSON.parsefile("data/classification.json")
+    clf = Classification(clf)
+    @debug "loaded classification of type $(clf.type)"
+    clf
+end
+
+function loadcostsdf()::DataFrame
+    df = CSV.read("data/associations.csv", copycols=true)
+    colnames = String.(names(df))
+    colnames = Symbol.(Unicode.normalize.(colnames, casefold=true, stripmark=true))
+    rename!(df, colnames)
+    df.name = colnames[2:end]
+    # df = coalesce.(df, 0.0)
+    @info "loaded cost matrix for $(size(df, 1)) plants"
+    df
+end
+
+function computecost(plant1::Symbol, plant2::Symbol, costs_df::DataFrame, classification::Classification)::Float64
+    @debug "computecost($plant1, $plant2)"
+    if plant1 in names(costs_df) && plant2 in names(costs_df)
+        cost = costs_df[costs_df.name .== plant1, plant2][1]
+    else
+        cost = missing
+    end
+
+    if !ismissing(cost)
+        return cost
+    end
+
+    parent1 = getfirstparent(plant1, classification)
+    parent2 = getfirstparent(plant2, classification)
+    if isnothing(parent1) || isnothing(parent2)
+        return 0.0
+    end
+    @debug "computecost($(parent1.name), $(parent2.name))"
+    if parent1.name in names(costs_df) && parent2.name in names(costs_df)
+        cost = costs_df[costs_df.name .== parent1.name, parent2.name][1]
+    end
+
+    if !ismissing(cost)
+        return cost
+    end
+
+    return 0.0
+end
+
+function costsmatrix(plants::Vector{Symbol}, costs_df::DataFrame, classification::Classification)::Matrix{Float64}
+    [computecost(plant1, plant2, costs_df, classification) for plant1 in plants, plant2 in plants]
+end
+
+function loadcosts()
+    plants = loadplants()
+    clf = loadclassification()
+    costs_df = loadcostsdf()
+    costs = costsmatrix(plants.name, costs_df, clf)
+end