updated include dependencies

eo/contrib/mathsym/GNUmakefile

@@ -19,7 +19,7 @@ CXXSOURCES=FunDef.cpp Sym.cpp SymImpl.cpp SymOps.cpp sym_compile.cpp TreeBuilder
 	Dataset.cpp ErrorMeasure.cpp Scaling.cpp TargetInfo.cpp BoundsCheck.cpp util.cpp NodeSelector.cpp\
 	eoSymCrossover.cpp sym_operations.cpp eoSymMutate.cpp eoSymLambdaMutate.cpp MultiFunction.cpp
 
-TESTPROGRAMS=test/test_compile test/testeo test/test_simplify test/test_diff test/test_lambda test/test_mf
+TESTPROGRAMS=test/test_compile test/testeo test/test_simplify test/test_diff test/test_lambda test/test_mf test/test_interval
 
 OBJS= $(CXXSOURCES:.cpp=.o) c_compile.o
 
@@ -40,7 +40,7 @@ libsym.a: $(OBJS)
 	rm libsym.a; ar cq $(SYMLIB) $(OBJS) 
 
 check: $(TESTPROGRAMS)
-	test/test_compile && test/testeo && test/test_simplify && test/test_diff && test/test_lambda && echo "all tests succeeded"
+	test/test_compile && test/test_interval && test/testeo && test/test_simplify && test/test_diff && test/test_lambda && echo "all tests succeeded"
 
 test/test_compile: test/test_compile.o ${SYMLIB}
 	$(CXX) -o test/test_compile test/test_compile.o $(SYMLIB) ${LIBS}
@@ -60,6 +60,10 @@ test/test_lambda: test/test_lambda.o $(SYMLIB)
 test/test_mf: test/test_mf.o $(SYMLIB)
 	$(CXX) -o test/test_mf test/test_mf.o  $(SYMLIB) ${LIBS}
 
+test/test_interval: test/test_interval.o
+	$(CXX) -o test/test_interval test/test_interval.o  $(SYMLIB) ${LIBS}
+
+
 # eo
 ../../src/libeo.a:
 	make -C ../../src libeo.a

eo/contrib/mathsym/eo_interface/eoSym.h

@@ -19,8 +19,8 @@
 #define EOSYM_H_
 
 #include <EO.h>
-#include <Sym.h>
+#include <sym/Sym.h>
-#include <FunDef.h>
+#include <fun/FunDef.h>
 
 
 template <class Fitness>

eo/contrib/mathsym/eo_interface/eoSymCrossover.cpp

@@ -21,6 +21,9 @@
 
 #include <eoSymCrossover.h>
 #include <utils/eoRNG.h>
+#include <vector>
+
+using namespace std;
 
 bool subtree_quad(Sym& a, Sym& b, NodeSelector& select) {
     NodeSelector::NodeSelection sel_a = select.select_node(a);
@@ -75,4 +78,46 @@ bool homologous_bin(Sym& a, const Sym& b) {
     return org != a;
 }
 
+void set_size_levels(Sym sym, vector<unsigned>& l, vector<unsigned>& s, unsigned level = 1) {
+    l.push_back(level);
+    s.push_back(sym.size());
+    
+    for (unsigned i = 0; i < sym.args().size(); ++i) {
+        set_size_levels(sym.args()[i], l, s, level+1);
+    }
+}
+
+
+bool size_level_xover(Sym& a, const Sym& b) {
+    
+    Sym org = a;
+        
+    vector<unsigned> levela;
+    vector<unsigned> sizesa;
+    vector<unsigned> levelb;
+    vector<unsigned> sizesb;
+
+    set_size_levels(a, levela, sizesa);
+    set_size_levels(b, levelb, sizesb);
+
+    unsigned p0;
+    unsigned p1;
+    
+    for (unsigned tries = 0;; ++tries) {
+        p0 = rng.random(a.size());
+        p1 = rng.random(b.size());
+        
+        if (tries < 5 && (sizesa[p0] != sizesb[p1] && levela[p0] != levelb[p1])) {
+            continue;   
+        }
+
+        break;
+    }
+
+    a = insert_subtree(a, p0, get_subtree(b, p1));
+
+    return org != a;
+    
+}
+
 

eo/contrib/mathsym/eo_interface/eoSymCrossover.h

@@ -60,5 +60,14 @@ class eoBinHomologousCrossover : public eoBinOp<EoType> {
 };
 
 
+extern bool size_level_xover(Sym& a, const Sym& b);
+template <class EoType>
+class eoSizeLevelCrossover : public eoBinOp<EoType> {
+    public:
+	bool operator()(EoType& a, const EoType& b) {
+	    return size_level_xover(a,b);
+	}
+};
+
 #endif
 

eo/contrib/mathsym/eo_interface/eoSymInit.h

@@ -19,7 +19,7 @@
 #define EOSYMINIT_H
 
 #include <eoInit.h>
-#include <TreeBuilder.h>
+#include <gen/TreeBuilder.h>
 
 /** Default initializer, Koza style */
 template <class EoType>

eo/contrib/mathsym/eo_interface/eoSymMutate.cpp

@@ -63,11 +63,10 @@ bool mutate_constants(Sym& sym, double stdev) {
     }
     
     for (unsigned i = 0; i < values.size(); ++i) {
-	values[i] += rng.normal() * stdev;
+	values[i] += rng.normal() * stdev / values.size();
     }
     
     sym = set_constants(sym, values);
-
     return true;
 }
 

eo/contrib/mathsym/eo_interface/eoSymMutate.h

@@ -18,8 +18,8 @@
 #ifndef SYMMUTATE_H
 #define SYMMUTATE_H
 
-#include <TreeBuilder.h>
+#include <gen/TreeBuilder.h>
-#include <NodeSelector.h>
+#include <gen/NodeSelector.h>
 
 #include <eoSym.h>
 #include <eoOp.h>

eo/contrib/mathsym/eval/Interval.h

@@ -77,39 +77,6 @@ std::ostream& operator<<(std::ostream& os, const Interval& val) {
 }
 
 #ifdef TEST_INTERVAL
-using namespace std;
-using namespace boost::numeric;
-
-int main() {
-    Interval a(0, 10);
-    Interval b(-1.5, 2);
-    cout << "a       = " << a << endl;
-    cout << "b       = " << b << endl;
-    cout << "a + b   = " << a + b << endl;
-    cout << "a - b   = " << a - b << endl;
-    cout << "b - a   = " << b - a << endl;
-    cout << "-a      = " << -a << endl;
-    cout << "a * b   = " << a * b << endl;
-    cout << "b/(a+1) = " << b / (a + 1.0) << endl;
-    cout << "b * a   = " << b * a << endl;
-
-    cout << "b / a   = " << b/a << endl;
-    
-    cout << "cos(a)  = " << cos(a) << endl;
-    cout << "cos(b)  = " << cos(b) << endl;
-   
-    cout << "log(b)  = " << log(b) << endl;
-    
-    cout << "sqrt(b) = " << sqrt(b) << endl;
-    cout << "sqrt(a) = " << sqrt(a) << endl;
-    cout << "sqr(b)  = " << sqr(b) << endl;
-   
-    cout << "exp(b*a)= " << exp(b*a) << endl;
-   
-    cout << "atan(a) = " << atan(a) << endl;
-    cout << "cosh(b) = " << cosh(b) << endl;
-    
-}
 #endif
 
 #endif

eo/contrib/mathsym/eval/sym_compile.h

@@ -19,7 +19,7 @@
 #define SYMCOMPILE_H_
 
 #include <vector>
-
+#include <sym/Sym.h>
 
 typedef double (*single_function)(const double []);
 typedef double (*multi_function)(const double[], double[]);

eo/contrib/mathsym/fun/FunDef.cpp

@@ -247,8 +247,6 @@ class Const : public FunDef {
 	}
 	
 	Interval eval(const vector<Interval>& _, const vector<Interval>& inputs) const { 
-	    // Profil/Bias seems to have a problem with 0 * inf when the Interval is exact zero (fpe)
-	    //if (value == 0.0) return Interval(-BiasEpsilon,BiasEpsilon);
 	    return Interval(value); 
 	}
 

eo/contrib/mathsym/fun/FunDef.h

@@ -23,8 +23,8 @@
 #include <memory>
 #include <iostream>
 
-#include "Sym.h"
+#include "sym/Sym.h"
-#include "Interval.h"
+#include "eval/Interval.h"
 
 class FunDef {
     public:

eo/contrib/mathsym/fun/SymOps.h

@@ -18,7 +18,7 @@
 #ifndef SYMOPS_H
 #define SYMOPS_H
 
-#include "Sym.h"
+#include "sym/Sym.h"
 
 extern Sym operator+(Sym a, Sym b);
 extern Sym operator*(Sym a, Sym b);

eo/contrib/mathsym/gen/LanguageTable.h

@@ -18,7 +18,7 @@
 #ifndef LANGUAGE_TABLE_H
 #define LANGUAGE_TABLE_H
 
-#include "token.h"
+#include <sym/token.h>
 
 class LanguageImpl;
 class Sym;

eo/contrib/mathsym/gen/NodeSelector.h

@@ -18,7 +18,7 @@
 #ifndef NODESELECTOR_H
 #define NODESELECTOR_H
 
-#include <Sym.h>
+#include <sym/Sym.h>
 
 /** Base class for selecting nodes */
 class NodeSelector {

eo/contrib/mathsym/gen/TreeBuilder.h

@@ -18,7 +18,7 @@
 #ifndef TREEBUILDER_H_
 #define TREEBUILDER_H_
 
-#include "Sym.h"
+#include "sym/Sym.h"
 #include "LanguageTable.h"
 
 class TreeBuilder {

eo/contrib/mathsym/sym/Sym.h

@@ -38,6 +38,9 @@ struct UniqueNodeStats { virtual ~UniqueNodeStats(){} };
 #else
 #define USE_TR1 0
 #endif
+// TR1 is buggy at times
+#undef USE_TR1
+#define USE_TR1 0
 
 #if USE_TR1
 #include <tr1/unordered_map>

eo/contrib/mathsym/sym/SymImpl.cpp

@@ -47,7 +47,7 @@ SymArgs::SymArgs(const SymArgs& args) : pimpl(0), args_ptr(args.args_ptr) {
     } 
 }
 
-const SymArgs& SymArgs::operator=(const SymArgs& args) {
+SymArgs& SymArgs::operator=(const SymArgs& args) {
     if (args.pimpl && args.args_ptr == &args.pimpl->owned_args) {
 	pimpl = new SymArgsImpl(*args.pimpl);
 	args_ptr = &pimpl->owned_args;

eo/contrib/mathsym/sym/SymImpl.h

@@ -47,7 +47,7 @@ class SymArgs {
     ~SymArgs();
 
     SymArgs(const SymArgs& args);
-    const SymArgs& SymArgs::operator=(const SymArgs& other);
+    SymArgs& operator=(const SymArgs& other);
 
     size_t len() const;
     const std::vector<Sym>& vec() const { return *args_ptr; }

eo/contrib/mathsym/symreg.cpp

@@ -115,7 +115,7 @@ int main(int argc, char* argv[]) {
     
     /* Population */
 
-    unsigned pop_size = parser.createParam(1500u, "population-size", "Population Size", 'p', string("Population")).value();
+    unsigned pop_size = parser.createParam(500u, "population-size", "Population Size", 'p', string("Population")).value();
   
     uint32_t seed = parser.createParam( uint32_t(time(0)), "random-seed", "Seed for rng", 'D').value();
 
@@ -274,7 +274,7 @@ int main(int argc, char* argv[]) {
     genetic_operator.add( submutate, subtree_mut_prob);
    
     // todo, make this parameter, etc
-    double std = 0.01;
+    double std = 1.0;
     eoSymConstantMutate<EoType> constmutate(std);
     genetic_operator.add(constmutate, constant_mut_prob);
     
@@ -285,7 +285,8 @@ int main(int argc, char* argv[]) {
 //    genetic_operator.add(lambda_mutate, lambda_mut_prob); // TODO: prob should be settable
     
     //eoQuadSubtreeCrossover<EoType> quad(node_selector);
-    eoBinSubtreeCrossover<EoType> bin(node_selector);
+    eoSizeLevelCrossover<EoType> bin;//(node_selector);
+    //eoBinSubtreeCrossover<EoType> bin(node_selector);
     genetic_operator.add(bin, subtree_xover_prob);
     
     eoBinHomologousCrossover<EoType> hom;
@@ -298,7 +299,7 @@ int main(int argc, char* argv[]) {
     eoSymPopEval<EoType> evaluator(check, measure, maximumSize);
     
     eoDetTournamentSelect<EoType> selectOne(tournamentsize);
-    eoGeneralBreeder<EoType> breeder(selectOne, genetic_operator);
+    eoGeneralBreeder<EoType> breeder(selectOne, genetic_operator,1);
     eoPlusReplacement<EoType> replace;
 
     // Terminators

eo/contrib/mathsym/test/test_compile.cpp

@@ -109,7 +109,9 @@ int main() {
 	multi_function f = compile(pop);
 	compile_time = time(0);
 	vector<double> out(pop.size());
-	
+        
+        cout << "Compiled" << endl;
+        	
 	for (unsigned j = 0; j < dataset.n_records(); ++j) {
 	    f(&dataset.get_inputs(j)[0], &out[0]);
 	}

eo/contrib/mathsym/test_data.txt

@@ -1,5 +1,5 @@
 # 101 2 nan nan
- 0 -0
+ 0.0 -0
  0.1 -8.89903723981037e-05
  0.2 -0.00122598240763888
  0.3 -0.00517587564272387