Fixes made to both MATLAB and Python div and log implementations

* The tests are still giving bad results when using the Python
  evaluation of individuals. Look into the code and check that the
  problem related with the failure of tests is the well-known precision
  bug #27

Author: Ezetowers

MLC/Common/Lisp_Tree_Expr/Operation_Nodes.py

@@ -98,6 +98,7 @@ def op_compute(self, arg_list):
 
 class Division_Node(Internal_Node):
     PROTECTION = 0.001
+    SIMPLIFY_PROTECTION = 0.01
 
     def __init__(self):
         Internal_Node.__init__(self, "/", 1)
@@ -107,9 +108,8 @@ def formal(self):
 
     def _process_division(self, dividend, divisor):
         if type(divisor) == np.ndarray:
-            # Check if at least one element is below the protection value
-            if [x for x in divisor if abs(x) < Division_Node.PROTECTION] != []:
-                return np.sign(divisor) * dividend / np.repeat(Division_Node.PROTECTION, len(divisor))
+            divisor = [Division_Node.PROTECTION if abs(x) < Division_Node.PROTECTION else x for x in divisor]
+            return np.sign(divisor) * dividend / np.asarray(divisor)
         else:
             if abs(divisor) < Division_Node.PROTECTION:
                 return dividend / Division_Node.PROTECTION
@@ -127,7 +127,7 @@ def op_simplify(self):
 
         if not self._nodes[0].is_sensor() and not self._nodes[1].is_sensor():
             # FIXME: Harcoded number. Change it
-            if abs(float(self._nodes[1].to_string())) < 0.01:
+            if abs(float(self._nodes[1].to_string())) < Division_Node.SIMPLIFY_PROTECTION:
                 return Leaf_Node(process_float(0))
             else:
                 arg = float(self._nodes[0].to_string()) / float(self._nodes[1].to_string())
@@ -179,6 +179,7 @@ def op_compute(self, arg_list):
 
 class Logarithm_Node(Internal_Node):
     PROTECTION = 0.00001
+    SIMPLIFY_PROTECTION = 0.01
 
     def __init__(self):
         Internal_Node.__init__(self, "log", 5)
@@ -188,9 +189,7 @@ def formal(self):
 
     def _process_arg(self, arg):
         if type(arg) == np.ndarray:
-            # Check if at least one element is below the protection value
-            if [x for x in arg if abs(x) < Logarithm_Node.PROTECTION] != []:
-                return np.repeat(Logarithm_Node.PROTECTION, len(arg))
+            return [Logarithm_Node.PROTECTION if abs(x) < Logarithm_Node.PROTECTION else abs(x) for x in arg]
         else:
             if abs(arg) < Logarithm_Node.PROTECTION:
                 return Logarithm_Node.PROTECTION
@@ -199,8 +198,8 @@ def _process_arg(self, arg):
 
     def op_simplify(self):
         if not self._nodes[0].is_sensor():
-            if float(self._nodes[0].to_string()) < 0.01:
-                arg = math.log(0.01)
+            if float(self._nodes[0].to_string()) < Logarithm_Node.SIMPLIFY_PROTECTION:
+                arg = math.log(Logarithm_Node.SIMPLIFY_PROTECTION)
             else:
                 arg = math.log(float(self._nodes[0].to_string()))
 

MLC/individual/Individual.py

@@ -461,7 +461,6 @@ def __change_const_tree(self, tree_expression, leaf_value_generator):
 
     def __str__(self):
         return "value: %s\n" % self.get_value() + \
-               "type: %s\n" % self.get_type() + \
                "cost_history: %s\n" % self.get_cost_history() + \
                "evaluation_time: %s\n" % self.get_evaluation_time() + \
                "appearences: %s\n" % self.get_appearences() + \

matlab_code/MLC_tools/my_div.m

@@ -1,8 +1,24 @@
 function b=my_div(arg1,arg2)
-    protec=0.001;
-    if abs(arg2)>protec
-        b=arg1./arg2;
+    protection = 0.001;
+    sign_array = sign(arg2);
+    protect_array = abs(arg2) < protection;
+    elements_to_modify = sum(protect_array);
+
+    if elements_to_modify == 0
+        b=arg1 ./ arg2;
     else
-        b=sign(arg2).*arg1./protec;
+        inverse_protect_array = ~protect_array;
+        valid_elements = arg2 .* inverse_protect_array;
+        non_valid_elements = protect_array .* protection;
+        new_arg2 = valid_elements + non_valid_elements;
+        b = sign_array .* arg1 ./ new_arg2;
     end
-end
+
+% function b=my_div(arg1,arg2)
+%     protec=0.001;
+%     if abs(arg2)>protec
+%         b=arg1./arg2;
+%     else
+%         b=sign(arg2).*arg1./protec;
+%     end
+% end

matlab_code/MLC_tools/my_log.m

@@ -1,8 +1,25 @@
 function b=my_log(arg1)
-    protec=0.00001;
-    if abs(arg1)>protec
-        b=log(abs(arg1));
+    protection = 0.00001;
+    sign_array = sign(arg1);
+    protect_array = abs(arg1) < protection;
+    elements_to_modify = sum(protect_array);
+
+    if elements_to_modify == 0
+        b = log(abs(arg1));
     else
-        b=log(protec);
+        inverse_protect_array = ~protect_array;
+        valid_elements = arg1 .* inverse_protect_array;
+        non_valid_elements = protect_array .* protection;
+        new_arg1 = valid_elements + non_valid_elements;
+        b = log(abs(new_arg1));
     end
-end
+end
+
+% function b=my_log(arg1)
+%     protec=0.00001;
+%     if abs(arg1)>protec
+%         b=log(abs(arg1));
+%     else
+%         b=log(protec);
+%     end
+% end

tests/integration_tests/integration_tests.py

@@ -1,3 +1,5 @@
+import sys, os
+sys.path.append("../..")
 import unittest
 import matlab.engine
 import numpy as np
@@ -8,7 +10,6 @@
 from MLC.mlc_table.MLCTable import MLCTable
 from MLC.db.mlc_repository import MLCRepository
 from MLC.Simulation import Simulation
-import sys, os
 import yaml
 
 """
@@ -239,4 +240,4 @@ def execute_integration_test(test_name, integration_test):
                 print "'%s'? there is no integration test with that name!" % test_name
 
     for test_dir, integration_test in test_to_run.iteritems():
-        execute_integration_test(test_dir, integration_test)
+        execute_integration_test(test_dir, integration_test)

tests/integration_tests/test_basic/configuration.ini

@@ -51,7 +51,8 @@ cascade = 1,1
 # evaluation_method = standalone_function
 # evaluation_method = standalone_files
 evaluation_method = mfile_standalone
-evaluation_function = toy_problem
+# evaluation_function = toy_problem
+evaluation_function = toy_problem_python_ev
 indfile = ind.dat
 Jfile = J.dat
 # exchangedir = fullfile(pwd,evaluator0)