GeneDc.kexpression and its simplification

geppy/core/entity.py

@@ -13,7 +13,7 @@
 """
 import copy
 from ..tools.generator import *
-from ..core.symbol import Function, TerminalRNC
+from ..core.symbol import Function, TerminalRNC, Terminal
 
 
 _DEBUG = False
@@ -411,6 +411,36 @@ def __str__(self):
             return str(self.rnc_array[self.dc[0]])
         return expr[0].format()    # only contains a normal terminal
 
+    @property
+    def kexpression(self):
+        """
+        Get the K-expression of type :class:`KExpression` represented by this gene. The involved RNC terminal will be
+        replaced by a constant terminal with its value retrived from the :meth:`rnc_array` according to the GEP-RNC
+        algorithm.
+        """
+        n_rnc = 0
+
+        def convert_RNC(p):
+            nonlocal n_rnc
+            if isinstance(p, TerminalRNC):
+                index = self.dc[n_rnc]
+                value = self.rnc_array[index]
+                n_rnc += 1
+                t = Terminal(str(value), value)
+                return t
+            return p
+
+        # level-order
+        expr = KExpression([convert_RNC(self[0])])
+        i = 0
+        j = 1
+        while i < len(expr):
+            for _ in range(expr[i].arity):
+                expr.append(convert_RNC(self[j]))
+                j += 1
+            i += 1
+        return expr
+
     def __repr__(self):
         return super().__repr__() + ', rnc_array=[' + ', '.join(str(num) for num in self.rnc_array) + ']'
 

geppy/support/simplification.py

@@ -6,15 +6,16 @@
 This module :mod:`simplification` provides utility functions for symbolic simplification of GEP individuals, which may
 be used in postprocessing.
 """
-
+import math
 import operator
 from geppy.core.entity import KExpression, Chromosome, Gene
 from geppy.core.symbol import Function, Terminal
 
 import sympy as sp
 
-#: the default symbolic function map for the :func:`simplify` function, which includes common arithmetic operations,
-#: Boolean operations.
+#: The default symbolic function map for the :func:`simplify` function, which includes common arithmetic operations and
+#: Boolean operations. Note that generally normal Python functions cannot work with symbolic variables directly. Thus,
+#: such a map is required.
 DEFAULT_SYMBOLIC_FUNCTION_MAP = {
     operator.and_.__name__: sp.And,
     operator.or_.__name__: sp.Or,
@@ -24,7 +25,8 @@
     operator.mul.__name__: operator.mul,
     operator.neg.__name__: operator.neg,
     operator.floordiv.__name__: operator.floordiv,
-    operator.truediv.__name__: operator.truediv
+    operator.truediv.__name__: operator.truediv,
+    math.log.__name__: sp.log
 }
 
 
@@ -98,6 +100,11 @@ def simplify(genome, symbolic_function_map=None):
     elif isinstance(genome, Chromosome):
         if len(genome) == 1:
             return _simplify_kexpression(genome[0].kexpression, symbolic_function_map)
+        else:   # multigenic chromosome
+            simplified_exprs = [_simplify_kexpression(g.kexpression, symbolic_function_map) for g in genome]
+            # combine these sub-expressions into a single one with the linking function
+            linker = symbolic_function_map[genome.linker.__name__]
+            return sp.simplify(linker(*simplified_exprs))
     else:
         raise TypeError('Only an argument of type KExpression, Gene, and Chromosome is acceptable. The provided '
                         'genome type is {}.'.format(type(genome)))