Added graphviz dot file creation capability

cfg/parity.yaml

@@ -0,0 +1,21 @@
+# Cambrian.jl settings
+seed: 0
+d_fitness: 1
+n_population: 5
+n_elite: 1
+n_gen: 3000
+log_gen: 10
+save_gen: 10
+m_rate: 0.1
+# CartesianGeneticProgramming.jl settings
+rows: 2
+columns: 16
+recur: 0.0
+n_in: 8
+n_out: 1
+out_m_rate: 0.3
+functions:
+  - f_and
+  - f_or
+  - f_xor
+  - f_not

graphing/graph_utils.jl

@@ -1,10 +1,11 @@
-using CGP
+using CartesianGeneticProgramming
 using LightGraphs
 using MetaGraphs
 using TikzGraphs
 using TikzPictures
 using LaTeXStrings
-using Base.Test
+using Printf
+#using Base.Test
 
 function to_graph(c::Chromosome; active_outputs=trues(c.nout))
     actives = [n.active for n in c.nodes]

graphing/to_dot.jl

@@ -0,0 +1,29 @@
+function walk_nodes(ind::CGPInd)
+    dot_strs = []
+    push!(dot_strs, "digraph cgpgraph {\n")
+    function visit(node_num, current_nd) 
+        if current_nd.active
+            fname = String(Symbol(current_nd.f))
+            visit(current_nd.x, ind.nodes[current_nd.x])
+            if(CGPFunctions.arity[fname] > 1)
+               visit(current_nd.y, ind.nodes[current_nd.y])
+
+            end
+            @show (node_num, current_nd)
+
+            xdotline = "N$(current_nd.x)-> N$node_num ;"
+            push!(dot_strs, "N$node_num [label=\"$fname:$node_num\"];")
+            push!(dot_strs, xdotline)
+            if(CGPFunctions.arity[fname] > 1)
+               ydotline = "N$(current_nd.y)-> N$node_num ;"
+               push!(dot_strs, ydotline)
+            end
+        end
+    end
+    for current_node_num in ind.outputs 
+        current_node     = ind.nodes[current_node_num]
+        visit(current_node_num, current_node)
+    end
+    push!(dot_strs, "}")
+    dot_strs
+end

scripts/parity.jl

@@ -0,0 +1,78 @@
+using CartesianGeneticProgramming
+using Cambrian
+import Cambrian.mutate
+using StatsBase
+using Base.Iterators: repeated
+include("../graphing/to_dot.jl")
+"""
+A simple example  for calculating parity
+"""
+
+ #bitArray parity
+ parity(x) = isodd(sum(x))
+
+ function create_testcases(sz)
+    train_cases = []
+    for i in 0:(2^sz-1)
+      bin = digits(i, base=2, pad=sz)
+      push!(train_cases, (bin, parity(bin)))
+      @show (bin, parity(bin))
+    end
+    return train_cases
+ end
+
+ NUMCLASSES = 10
+ WIDTH = 8 #60
+
+ train = create_testcases(WIDTH)
+ trainX = [ x[1] for x in train ]
+ trainX = hcat(trainX...)
+ trainY = [ x[2] for x in train ]
+
+
+X, Y = trainX, trainY
+
+function evaluate(ind::CGPInd, X::AbstractArray, Y::AbstractArray)
+    accuracy = 0.0
+    for i in 1:size(X, 2)
+        out = process(ind, float(X[:, i]))
+        if out[1] == Int(Y[i])
+            accuracy += 1
+        end
+    end
+    [accuracy / size(X, 1)]
+end
+
+function error_count(e, X::AbstractArray, Y::AbstractArray)
+   failed = 0
+   for i in 1:size(X,2)
+      y_hat = process(e.population[5], float(X[:,i]))
+      if y_hat[1] != Int(Y[i]) 
+           failed += 1
+      end
+   end
+   failed
+end
+
+cfg = get_config("cfg/parity.yaml")
+fit(i::CGPInd) = evaluate(i, X, Y)
+mutate(i::CGPInd) = goldman_mutate(cfg, i)
+e = CGPEvolution(cfg, fit)
+println("run!")
+run!(e)
+
+@show e.population[end].nodes
+errors = error_count(e,X,Y )
+println("$errors errors out of $(size(X,2)) entries")
+
+#generate dot file
+dot_array = walk_nodes(e.population[5])
+dot_file  = "parity_graph.dot"
+open(dot_file, "w") do f
+   for i in dot_array
+      println(f, i)
+   end
+end
+# to view from commandline:
+# $ dot -Tpng parity_graph.dot -o parity_graph.png
+# $ display parity_graph.png