Move MCMC code to its own source file

src/GardenOptim.jl

@@ -15,93 +15,7 @@ export update!, randomgardenevolution!, outputgarden
 
 include("classification.jl")
 include("loaddata.jl")
-
+include("mcmc.jl")
-"Return a random index to be filled from the garden mask."
-function randomindex(mask::Matrix{Bool})::Int
-    while true
-        i = rand(1:length(mask))
-        if mask[i]
-            return i
-        end
-    end
-end
-
-"Swap to the elements corresponding to the two provided indices."
-function swap!(garden::Matrix{Int}, i::Int, j::Int)
-    t = garden[i]
-    garden[i] = garden[j]
-    garden[j] = t
-    garden
-end
-
-"Return the neighbours to be filled of the cell at the given index."
-function neighbours(garden::Matrix{Int}, idx::Int)::Vector{Int}
-    m, n = size(garden)
-    j, i = divrem(idx - 1, m)
-    i += 1
-    j += 1
-    neighbourindices = [(i, j-1), (i, j+1), (i-1, j), (i+1, j)]
-    # cells filled with 0 are not part of the garden
-    [
-        garden[k, l] for (k, l) in neighbourindices
-        if 0 < k <= m && 0 < l <= n && garden[k, l] != 0
-    ]
-end
-
-"Compute the cost difference when swapping the two provided indices."
-function deltacost(garden::Matrix{Int}, costs::Matrix{Float64}, i::Int, j::Int)::Float64
-    cost = 0
-    for k in neighbours(garden, i)
-        cost += costs[k, garden[j]] - costs[k, garden[i]]
-    end
-    for k in neighbours(garden, j)
-        cost += costs[k, garden[i]] - costs[k, garden[j]]
-    end
-    cost
-end
-
-"Update the garden using Metropolis-Hastings, using the inverse temperature beta."
-function update!(
-    garden::Matrix{Int},
-    mask::Matrix{Bool},
-    costs::Matrix{Float64},
-    beta::Float64 = 10.0
-)
-    N = length(garden)
-    i = randomindex(mask)
-    j = randomindex(mask)
-    while i == j
-        j = randomindex(mask)
-    end
-    d = deltacost(garden, costs, i, j)
-    @debug "cost difference $d"
-    if rand() < exp(- beta * d)
-        @debug "swapping indices $i and $j"
-        return swap!(garden, i, j)
-    end
-    garden
-end
-
-"Fill the garden randomly with a predefined number of plants."
-function randomfillgarden!(garden::Matrix{Int}, mask::Matrix{Bool}, plantcount::Int)
-    garden[mask] = rand(1:plantcount, sum(mask))
-    garden
-end
-
-"Update the garden for a given number of steps, starting from a random initialisation."
-function randomgardenevolution!(
-    garden::Matrix{Int},
-    mask::Matrix{Bool},
-    costs::Matrix{Float64};
-    steps::Int = 10000
-)
-    m = size(costs, 1)
-    garden = randomfillgarden!(garden, mask, m)
-    for i = 1:steps
-        update!(garden, mask, costs, 10.0)
-    end
-    garden
-end
 
 "Save the garden to a CSV file."
 function outputgarden(garden::Matrix{Int}, plants::Vector{String})

src/mcmc.jl

@@ -0,0 +1,88 @@
+using Logging
+
+"Return a random index to be filled from the garden mask."
+function randomindex(mask::Matrix{Bool})::Int
+    while true
+        i = rand(1:length(mask))
+        if mask[i]
+            return i
+        end
+    end
+end
+
+"Swap to the elements corresponding to the two provided indices."
+function swap!(garden::Matrix{Int}, i::Int, j::Int)
+    t = garden[i]
+    garden[i] = garden[j]
+    garden[j] = t
+    garden
+end
+
+"Return the neighbours to be filled of the cell at the given index."
+function neighbours(garden::Matrix{Int}, idx::Int)::Vector{Int}
+    m, n = size(garden)
+    j, i = divrem(idx - 1, m)
+    i += 1
+    j += 1
+    neighbourindices = [(i, j-1), (i, j+1), (i-1, j), (i+1, j)]
+    # cells filled with 0 are not part of the garden
+    [
+        garden[k, l] for (k, l) in neighbourindices
+        if 0 < k <= m && 0 < l <= n && garden[k, l] != 0
+    ]
+end
+
+"Compute the cost difference when swapping the two provided indices."
+function deltacost(garden::Matrix{Int}, costs::Matrix{Float64}, i::Int, j::Int)::Float64
+    cost = 0
+    for k in neighbours(garden, i)
+        cost += costs[k, garden[j]] - costs[k, garden[i]]
+    end
+    for k in neighbours(garden, j)
+        cost += costs[k, garden[i]] - costs[k, garden[j]]
+    end
+    cost
+end
+
+"Update the garden using Metropolis-Hastings, using the inverse temperature beta."
+function update!(
+    garden::Matrix{Int},
+    mask::Matrix{Bool},
+    costs::Matrix{Float64},
+    beta::Float64 = 10.0
+)
+    N = length(garden)
+    i = randomindex(mask)
+    j = randomindex(mask)
+    while i == j
+        j = randomindex(mask)
+    end
+    d = deltacost(garden, costs, i, j)
+    @debug "cost difference $d"
+    if rand() < exp(- beta * d)
+        @debug "swapping indices $i and $j"
+        return swap!(garden, i, j)
+    end
+    garden
+end
+
+"Fill the garden randomly with a predefined number of plants."
+function randomfillgarden!(garden::Matrix{Int}, mask::Matrix{Bool}, plantcount::Int)
+    garden[mask] = rand(1:plantcount, sum(mask))
+    garden
+end
+
+"Update the garden for a given number of steps, starting from a random initialisation."
+function randomgardenevolution!(
+    garden::Matrix{Int},
+    mask::Matrix{Bool},
+    costs::Matrix{Float64};
+    steps::Int = 10000
+)
+    m = size(costs, 1)
+    garden = randomfillgarden!(garden, mask, m)
+    for i = 1:steps
+        update!(garden, mask, costs, 10.0)
+    end
+    garden
+end