Adds a independent alphabet-translation struct. Adds a thingy I needed for gephi

.gitignore

@@ -1,6 +1,9 @@
+.DS_Store
+
 *.dot
 *.png
 *.pdf
 *_seq
 *splitting_tree
 *test_suite
+

lib/mealy.hpp

@@ -7,11 +7,13 @@
 #include <vector>
 
 /*
- * Structure used for reading mealy files from dot files.
  * Everything is indexed by size_t's, so that we can index vectors
- * in constant time. The maps contain the original values corresponding
+ * in constant time. Can only represent deterministic machines,
- * to these size_t's. Can only represent deterministic machines,
  * but partiality still can occur.
+ *
+ * Note that graph_size == graph.size() and that input_size equals the size
+ * of the biggest row in graph. Finally output_size bounds the number of
+ * outputs. These values are redundant, but nice to have here.
  */
 struct mealy {
 	struct edge {
@@ -19,14 +21,9 @@ struct mealy {
 		output output = -1;
 	};
 
-	std::map<std::string, state> nodes_indices;
-	std::map<std::string, input> input_indices;
-	std::map<std::string, output> output_indices;
-
 	// state -> input -> (output, state)
 	std::vector<std::vector<edge>> graph;
 
-	// these are actually redundant!
 	size_t graph_size = 0;
 	size_t input_size = 0;
 	size_t output_size = 0;
@@ -53,13 +50,3 @@ auto apply(mealy const & m, state state, Iterator b, Iterator e){
 	}
 	return ret;
 }
-
-// Used to invert the input_indices and output_indices maps
-template <typename T>
-std::vector<std::string> create_reverse_map(std::map<std::string, T> const & indices){
-	std::vector<std::string> ret(indices.size());
-	for(auto&& p : indices){
-		ret[p.second.base()] = p.first;
-	}
-	return ret;
-}

lib/read_mealy_from_dot.cpp

@@ -17,13 +17,16 @@ T get(istream& in){
 	return t;
 }
 
-mealy read_mealy_from_dot(istream& in){
+mealy read_mealy_from_dot(std::istream & in, translation & t){
 	mealy m;
 
+	std::map<std::string, state> state_indices;
+	state max_state = 0;
+
 	string line;
 	stringstream ss;
 	while(getline(in, line)){
-		if(line.find("}") != string::npos) return m;
+		if(line.find("}") != string::npos) break;
 
 		const auto i = line.find("->");
 		if(i == string::npos) continue;
@@ -47,18 +50,22 @@ mealy read_mealy_from_dot(istream& in){
 		const auto output = get<string>(ss);
 
 		// make fresh indices, if needed
-		if(m.nodes_indices.count(lh) < 1) m.nodes_indices[lh] = m.graph_size++;
+		if(state_indices.count(lh) < 1) state_indices[lh] = max_state++;
-		if(m.nodes_indices.count(rh) < 1) m.nodes_indices[rh] = m.graph_size++;
+		if(state_indices.count(rh) < 1) state_indices[rh] = max_state++;
-		if(m.input_indices.count(input) < 1) m.input_indices[input] = m.input_size++;
+		if(t.input_indices.count(input) < 1) t.input_indices[input] = t.max_input++;
-		if(m.output_indices.count(output) < 1) m.output_indices[output] = m.output_size++;
+		if(t.output_indices.count(output) < 1) t.output_indices[output] = t.max_output++;
 
 		// add edge
-		m.graph.resize(m.graph_size);
+		m.graph.resize(max_state.base());
-		auto & v = m.graph[m.nodes_indices[lh].base()];
+		auto & v = m.graph[state_indices[lh].base()];
-		v.resize(m.input_size);
+		v.resize(t.max_input.base());
-		v[m.input_indices[input].base()] = {m.nodes_indices[rh], m.output_indices[output]};
+		v[t.input_indices[input].base()] = {state_indices[rh], t.output_indices[output]};
 	}
 
+	m.graph_size = max_state.base();
+	m.input_size = t.max_input.base();
+	m.output_size = t.max_output.base();
+
 	assert(m.graph_size > 0);
 	assert(m.input_size > 0);
 	assert(m.output_size > 0);
@@ -66,7 +73,22 @@ mealy read_mealy_from_dot(istream& in){
 	return m;
 }
 
-mealy read_mealy_from_dot(const string& filename){
+
+mealy read_mealy_from_dot(const string & filename, translation & t){
 	ifstream file(filename);
-	return read_mealy_from_dot(file);
+	return read_mealy_from_dot(file, t);
+}
+
+
+std::pair<mealy, translation> read_mealy_from_dot(istream & in){
+	translation t;
+	const auto m = read_mealy_from_dot(in, t);
+	return {move(m), move(t)};
+}
+
+
+std::pair<mealy, translation> read_mealy_from_dot(const string & filename){
+	translation t;
+	const auto m = read_mealy_from_dot(filename, t);
+	return {move(m), move(t)};
 }

lib/read_mealy_from_dot.hpp

@@ -1,7 +1,38 @@
 #pragma once
 
+#include "types.hpp"
+
 #include <iosfwd>
+#include <map>
+#include <utility>
+
+/*
+ * These maps record the translation used while reading.
+ */
+struct translation {
+	std::map<std::string, input> input_indices;
+	input max_input = 0;
+
+	std::map<std::string, output> output_indices;
+	output max_output = 0;
+};
 
 struct mealy;
-mealy read_mealy_from_dot(const std::string & filename);
+
-mealy read_mealy_from_dot(std::istream & input);
+// Read a mealy machine while extending the translation
+mealy read_mealy_from_dot(std::istream & in, translation & t);
+mealy read_mealy_from_dot(const std::string & filename, translation & t);
+
+// Read a mealy machine, starting with the empty translation
+std::pair<mealy, translation> read_mealy_from_dot(std::istream & in);
+std::pair<mealy, translation> read_mealy_from_dot(const std::string & filename);
+
+// Used to invert the input_indices and output_indices maps
+template <typename T>
+std::vector<std::string> create_reverse_map(std::map<std::string, T> const & indices){
+	std::vector<std::string> ret(indices.size());
+	for(auto&& p : indices){
+		ret[p.second.base()] = p.first;
+	}
+	return ret;
+}

lib/splitting_tree.cpp

@@ -27,8 +27,8 @@ splitting_tree &lca_impl2(splitting_tree & node){
 
 result create_splitting_tree(const mealy& g, options opt){
 	const auto N = g.graph.size();
-	const auto P = g.input_indices.size();
+	const auto P = g.input_size;
-	const auto Q = g.output_indices.size();
+	const auto Q = g.output_size;
 
 	result r(N);
 	auto & root = r.root;

src/conf-hyp.cpp

@@ -1,106 +0,0 @@
-#include <mealy.hpp>
-#include <read_mealy_from_dot.hpp>
-
-#include <io.hpp>
-
-#include <fstream>
-#include <iostream>
-#include <string>
-
-using namespace std;
-
-template <typename T>
-vector<T> resize_new(vector<T> const & in, size_t N){
-	vector<T> ret(N);
-	copy_n(in.begin(), N, ret.begin());
-	return ret;
-}
-
-vector<string> conform(mealy const & spec, vector<string> const & spec_o_map, mealy const & impl, vector<string> const & impl_o_map, vector<vector<string>> const & suite){
-	for(auto && test : suite){
-		state s = 0;
-		state t = 0;
-
-		size_t count = 0;
-		for(auto && i : test){
-			const auto i1 = spec.input_indices.at(i);
-			const auto r1 = apply(spec, s, i1);
-			const auto o1 = spec_o_map[r1.output.base()];
-			s = r1.to;
-
-			const auto i2 = spec.input_indices.at(i);
-			const auto r2 = apply(impl, t, i2);
-			const auto o2 = impl_o_map[r2.output.base()];
-			t = r2.to;
-
-			if(o1 != o2){
-				return resize_new(test, count+1);
-			}
-			count++;
-		}
-	}
-
-	return {};
-}
-
-vector<vector<string>> open_suite(string suite_filename){
-	boost::iostreams::filtering_istream suite_file;
-	suite_file.push(boost::iostreams::gzip_decompressor());
-	suite_file.push(boost::iostreams::file_descriptor_source(suite_filename));
-	boost::archive::text_iarchive archive(suite_file);
-
-	vector<vector<string>> suite;
-	archive >> suite;
-	return suite;
-}
-
-int main(int argc, char *argv[]){
-	const size_t N = 136;
-	vector< pair<mealy, vector<string>> > machines_and_maps(N);
-	vector< vector<vector<string>>      > suites(N);
-	for(int i = 0; i < N; ++i){
-		cout << "reading " << i << "\r" << flush;
-
-		const string filename = "hyp." + to_string(i) + ".obf.dot";
-		machines_and_maps[i].first = read_mealy_from_dot(filename);
-		machines_and_maps[i].second = create_reverse_map(machines_and_maps[i].first.output_indices);
-
-		const string suite_filename = filename + "test_suite";
-		suites[i] = open_suite(suite_filename);
-	}
-	cout << "done reading" << endl;
-
-	const string red = "\x1b[31m";
-	const string yellow = "\x1b[33m";
-	const string cyan = "\x1B[36m";
-	const string reset = "\033[0m";
-
-	size_t fails = 0;
-	for(int i = 0; i < N; ++i){
-		for(int j = 0; j < N; ++j){
-			cout << "checking " << i << " against " << j << "\r" << flush;
-			const auto & spec = machines_and_maps[i];
-			const auto & impl = machines_and_maps[j];
-			const auto & suite = suites[i];
-			const auto result = conform(spec.first, spec.second, impl.first, impl.second, suite);
-
-			if(i == j && !result.empty()){
-				cout << cyan << "FAIL: " << i << " " << j << " is the same machine" << reset << endl;
-				fails++;
-			}
-
-			if(i < j && result.empty()){
-				cout << red << "FAIL: " << i << " " << j << " no flaw detected" << reset << endl;
-				fails++;
-			}
-
-			if(i > j && result.empty()){
-				cout << yellow << "FAIL: " << i << " " << j << " no flaw detected" << reset << endl;
-				fails++;
-			}
-		}
-	}
-	cout << "done checking" << endl;
-	cout << "total of " << fails << " fails out of " << N*N << endl;
-}
-

src/conf.cpp

@@ -5,6 +5,7 @@
 
 #include <fstream>
 #include <iostream>
+#include <map>
 #include <string>
 
 using namespace std;
@@ -16,21 +17,27 @@ vector<T> resize_new(vector<T> const & in, size_t N){
 	return ret;
 }
 
-vector<string> conform(mealy const & spec, vector<string> const & spec_o_map, mealy const & impl, vector<string> const & impl_o_map, vector<vector<string>> const & suite){
+struct mealy_with_maps {
+	mealy machine;
+	map<string, input> inputs;
+	vector<string> outputs;
+};
+
+vector<string> conform(mealy_with_maps const & spec, mealy_with_maps const & impl, vector<vector<string>> const & suite){
 	for(auto && test : suite){
 		state s = 0;
 		state t = 0;
 
 		size_t count = 0;
 		for(auto && i : test){
-			const auto i1 = spec.input_indices.at(i);
+			const auto i1 = spec.inputs.at(i);
-			const auto r1 = apply(spec, s, i1);
+			const auto r1 = apply(spec.machine, s, i1);
-			const auto o1 = spec_o_map[r1.output.base()];
+			const auto o1 = spec.outputs[r1.output.base()];
 			s = r1.to;
 
-			const auto i2 = spec.input_indices.at(i);
+			const auto i2 = impl.inputs.at(i);
-			const auto r2 = apply(impl, t, i2);
+			const auto r2 = apply(impl.machine, t, i2);
-			const auto o2 = impl_o_map[r2.output.base()];
+			const auto o2 = impl.outputs[r2.output.base()];
 			t = r2.to;
 
 			if(o1 != o2){
@@ -58,14 +65,14 @@ int main(int argc, char *argv[]){
 	if(argc != 3) return 1;
 
 	const auto spec = read_mealy_from_dot(argv[1]);
-	const auto spec_o_map = create_reverse_map(spec.output_indices);
+	const auto spec_o_map = create_reverse_map(spec.second.output_indices);
 
 	const auto impl = read_mealy_from_dot(argv[2]);
-	const auto impl_o_map = create_reverse_map(impl.output_indices);
+	const auto impl_o_map = create_reverse_map(impl.second.output_indices);
 
 	const auto suite = open_suite(argv[1] + string("test_suite"));
 
-	const auto counter_example = conform(spec, spec_o_map, impl, impl_o_map, suite);
+	const auto counter_example = conform({spec.first, spec.second.input_indices, spec_o_map}, {impl.first, impl.second.input_indices, impl_o_map}, suite);
 	if(counter_example.empty()){
 		cerr << "No counter example found" << endl;
 	}

src/main.cpp

@@ -38,7 +38,7 @@ int main(int argc, char *argv[]){
 	const bool randomize_hopcroft = true;
 	const bool randomize_lee_yannakakis = true;
 
-	const auto machine = [&]{
+	const auto machine_and_translation = [&]{
 		time_logger t("reading file " + filename);
 		if(use_stdio){
 			return read_mealy_from_dot(cin);
@@ -47,6 +47,9 @@ int main(int argc, char *argv[]){
 		}
 	}();
 
+	const auto & machine = machine_and_translation.first;
+	const auto & translation = machine_and_translation.second;
+
 	auto all_pair_seperating_sequences_fut = async([&]{
 		const auto splitting_tree_hopcroft = [&]{
 			time_logger t("creating hopcroft splitting tree");
@@ -85,7 +88,7 @@ int main(int argc, char *argv[]){
 	});
 
 	auto inputs_fut = std::async([&]{
-		return create_reverse_map(machine.input_indices);
+		return create_reverse_map(translation.input_indices);
 	});
 
 	auto relevant_inputs_fut = std::async([&]{
@@ -191,6 +194,7 @@ int main(int argc, char *argv[]){
 
 	if(random_part){
 		time_logger t("outputting all random tests");
+		cerr << "*** K > " << k_max << endl;
 
 		std::random_device rd;
 		std::mt19937 generator(rd());

src/metrics.cpp

@@ -34,7 +34,9 @@ int main(int argc, char *argv[]){
 	if(argc != 2) return 1;
 	const string filename = argv[1];
 
-	const auto machine = read_mealy_from_dot(filename);
+	const auto result = read_mealy_from_dot(filename);
+	const auto & machine = result.first;
+	const auto & translation = result.second;
 
 //	vector<vector<bool>> table(machine.input_size);
 //	for(input i = 0; i < machine.input_size; ++i){
@@ -45,7 +47,7 @@ int main(int argc, char *argv[]){
 	for(state s = 0; s < machine.graph_size; ++s){
 		size_t scores[3] = {0, 0, 0};
 		for(input i = 0; i < machine.input_size; ++i){
-			const auto test1 = apply(machine, s, i).output != machine.output_indices.at("quiescence");
+			const auto test1 = apply(machine, s, i).output != translation.output_indices.at("quiescence");
 			const auto test2 = apply(machine, s, i).to != s;
 
 			scores[test1 + test2]++;

src/pre_gephi_tool.cpp

@@ -0,0 +1,64 @@
+#include <read_mealy_from_dot.hpp>
+#include <mealy.hpp>
+#include <transfer_sequences.hpp>
+
+#include <cassert>
+#include <string>
+#include <fstream>
+#include <iostream>
+#include <queue>
+#include <vector>
+
+using namespace std;
+
+int main(int argc, char *argv[]){
+	if(argc != 3) return 1;
+
+	const string hypo_filename = argv[1];
+	const string mach_filename = argv[2];
+
+	translation t;
+
+	const auto hypothesis = read_mealy_from_dot(hypo_filename, t);
+	const auto machine = read_mealy_from_dot(mach_filename, t);
+
+	auto input_to_string = create_reverse_map(t.input_indices);
+	auto output_to_string = create_reverse_map(t.output_indices);
+
+	vector<bool> visited(machine.graph_size, false);
+	{
+		const auto state_cover = create_transfer_sequences(hypothesis, 0);
+		for(auto && p : state_cover){
+			state s = 0;
+			for(auto && i : p){
+				visited[s.base()] = true;
+				s = apply(machine, s, i).to;
+			}
+			visited[s.base()] = true;
+		}
+	}
+
+	{
+		ofstream out("gephi.dot");
+		out << "digraph g {\n";
+
+		for(state s = 0; s < machine.graph_size; ++s){
+			out << "\t" << "s" << s << " [";
+			out << "visited=\"" << (visited[s.base()] ? "1" : "0") << "\"";
+			out << "]\n";
+		}
+
+		for(state s = 0; s < machine.graph_size; ++s){
+			for(input i = 0; i < machine.input_size; ++i){
+				const auto ret = apply(machine, s, i);
+				out << "\t" << "s" << s << " -> " << "s" << ret.to << " [";
+				out << "input=\"" << input_to_string[i.base()] << "\", ";
+				out << "output=\"" << output_to_string[ret.output.base()] << "\"";
+				out << "]\n";
+			}
+		}
+
+		out << "}" << endl;
+	}
+}
+

src/stats.cpp

@@ -10,7 +10,7 @@
 using namespace std;
 
 void print_stats_for_machine(string filename){
-	const auto machine = read_mealy_from_dot(filename);
+	const auto machine = read_mealy_from_dot(filename).first;
 
 	cout << "machine " << filename << " has\n";
 	cout << '\t' << machine.graph_size << " states\n";