More changes to symbolic

GPy/core/mapping.py

@@ -34,7 +34,7 @@ class Mapping(Parameterized):
         raise NotImplementedError
 
     def df_dtheta(self, dL_df, X):
-        """The gradient of the outputs of the multi-layer perceptron with respect to each of the parameters.
+        """The gradient of the outputs of the mapping with respect to each of the parameters.
 
         :param dL_df: gradient of the objective with respect to the function.
         :type dL_df: ndarray (num_data x output_dim)
@@ -50,7 +50,7 @@ class Mapping(Parameterized):
         """
         Plots the mapping associated with the model.
           - In one dimension, the function is plotted.
-          - In two dimsensions, a contour-plot shows the function
+          - In two dimensions, a contour-plot shows the function
           - In higher dimensions, we've not implemented this yet !TODO!
 
         Can plot only part of the data and part of the posterior functions
@@ -65,6 +65,14 @@ class Mapping(Parameterized):
         else:
             raise NameError, "matplotlib package has not been imported."
 
+class Bijective_mapping(Mapping):
+    """This is a mapping that is bijective, i.e. you can go from X to f and also back from f to X. The inverse mapping is called g()."""
+    def __init__(self, input_dim, output_dim, name='bijective_mapping'):
+        super(Bijective_apping, self).__init__(name=name)
+
+    def g(self, f):
+        """Inverse mapping from output domain of the function to the inputs."""
+        raise NotImplementedError
 
 from model import Model
 

GPy/core/parameterization/param.py

@@ -4,7 +4,7 @@
 import itertools
 import numpy
 from parameter_core import OptimizationHandlable, adjust_name_for_printing
-from array_core import ObsAr
+from observable_array import ObsAr
 
 ###### printing
 __constraints_name__ = "Constraint"

GPy/util/symbolic.py

@@ -7,45 +7,94 @@ def stabilise(e):
     return e #sym.expand(e)
 
 
-def gen_code(expressions, prefix='sub'):
+def gen_code(expressions, cache_prefix = 'cache', sub_prefix = 'sub', prefix='XoXoXoX', cacheable=[]):
-    """Generate code for the list of expressions provided using the common sub-expression eliminator."""
+    """Generate code for the list of expressions provided using the common sub-expression eliminator to separate out portions that are computed multiple times."""
     # First convert the expressions to a list.
     # We should find the following type of expressions: 'function', 'derivative', 'second_derivative', 'third_derivative'. 
 
+    # Helper functions to get data in and out of dictionaries.
+    # this code from http://stackoverflow.com/questions/14692690/access-python-nested-dictionary-items-via-a-list-of-keys
+    def getFromDict(dataDict, mapList):
+        return reduce(lambda d, k: d[k], mapList, dataDict)
+    def setInDict(dataDict, mapList, value):
+        getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value
+
+    # This is the return dictionary that stores all the generated code.
+    code = {}
     expression_list = []
-    expression_keys = []
+    key_list = []
-    function_code = {}
+    order_list = []
-    for key in expressions.key():
+    code['main'] = {}
+    for key in expressions.keys():
         if key == 'function':
             expression_list.append(expressions[key])            
-            expression_keys.append(key)
+            key_list.append([key])
-            function_code[key] = ''
+            order_list.append(1) 
-        elif key[-9:] == 'derivative':
+            code['main'][key] = ''
-            function_code[key] = {}
+        elif key[-10:] == 'derivative':
-            for dkey in expressions[key]:
+            code['main'][key] = {}
+            for dkey in expressions[key].keys():
                 expression_list.append(expressions[key][dkey])
-                expression_keys.append([key, dkey])
+                key_list.append([key, dkey])
-                function_code[key][dkey] = ''
+                if key[:-10] == 'first' or key[:-10] == '':
+                    order_list.append(3) #sym.count_ops(expressions[key][dkey]))
+                elif key[:-10] == 'second':
+                    order_list.append(4) #sym.count_ops(expressions[key][dkey]))
+                elif key[:-10] == 'third':
+                    order_list.append(5) #sym.count_ops(expressions[key][dkey]))
+                code['main'][key][dkey] = ''
+        else:
+            expression_list.append(expressions[key])            
+            key_list.append([key])
+            order_list.append(2) 
+            code['main'][key] = ''
 
-    symbols, functions = sym.cse(expression_list, numbered_symbols(prefix=prefix))
+    # This step may be unecessary.
+    # Not 100% sure if the sub expression elimination is order sensitive. This step orders the list with the 'function' code first and derivatives after.
+    order_list, expression_list, key_list = zip(*sorted(zip(order_list, expression_list, key_list)))
 
+    print expression_list
+
+    subexpressions, expression_substituted_list = sym.cse(expression_list, numbered_symbols(prefix=prefix))
+    cacheable_list = []
     # Create strings that lambda strings from the expressions. 
-    sub_expressions = []
+    code['params_change'] = []
-    for sub, expr in symbols:
+    code['cache'] = []
+    for expr in subexpressions:
+        arg_list = [e for e in expr[1].atoms() if e.is_Symbol]
+        cacheable_symbols = [e for e in arg_list if e in cacheable_list or e in cacheable]
+        if cacheable_symbols:
+            code['cacheable'].append((expr[0],expr2code(arg_list, expr[1])))
+            # list which ensures dependencies are cacheable.
+            cacheable_list.append(expr[0])
+            code['cacheexpressions'].append(expr[0])
+        else:
+            code['params_change'].append((expr[0],expr2code(arg_list, expr[1])))
+            code['subexpressions'].append(expr[0])
+            
+    for expr, keys in zip(expression_substituted_list, key_list):
         arg_list = [e for e in expr.atoms() if e.is_Symbol]
-        sub_code += [lambdastr(sorted(arg_list), expr)]
+        setInDict(code['main'], keys, expr2code(arg_list, expr))
+        setInDict(expressions, keys, expr)
 
-    function_expressions = []
+    sub_dict = {}
-    for expr, keys in zip(functions, expression_keys):
+    for i, sub in enumerate(code['cacheexpressions']):
-        arg_list = [e for e in expr.atoms() if e.is_Symbol]
+        sub_dict[sub.name] = cache_prefix + str(i)
-        function_code += [lambdastr(sorted(arg_list), expr)]
+    for i, sub in enumerate(code['subexpressions']):
+        sub_dict[sub.name] = sub_prefix + str(i)
 
-    for key in function_code.key():
-        if key == 'function':
-            function_code[key] = 
     
-    return sub_code, func_code
     
+    return code
+
+def expr2code(arg_list, expr):
+    """Convert the given symbolic expression into code."""
+    code = lambdastr(arg_list, expr)
+    function_code = code.split(':')[1]
+    for arg in arg_list:
+        function_code = function_code.replace(arg.name, 'self.'+arg.name)
+        
+    return function_code
 
 class logistic(Function):
     """The logistic function as a symbolic function."""