/usr/lib/python2.7/dist-packages/brian/optimiser.py is in python-brian 1.4.3-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 | # ----------------------------------------------------------------------------------
# Copyright ENS, INRIA, CNRS
# Contributors: Romain Brette (brette@di.ens.fr) and Dan Goodman (goodman@di.ens.fr)
#
# Brian is a computer program whose purpose is to simulate models
# of biological neural networks.
#
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software. You can use,
# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info".
#
# As a counterpart to the access to the source code and rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
# liability.
#
# In this respect, the user's attention is drawn to the risks associated
# with loading, using, modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean that it is complicated to manipulate, and that also
# therefore means that it is reserved for developers and experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
# requirements in conditions enabling the security of their systems and/or
# data to be ensured and, more generally, to use and operate it in the
# same conditions as regards security.
#
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license and that you accept its terms.
# ----------------------------------------------------------------------------------
#
'''
Optimizations for Brian.
'''
import re
import warnings
import parser
from inspection import *
from log import *
try:
import sympy
use_sympy = True
except:
warnings.warn('sympy not installed')
use_sympy = False
#TODO: also insert a global pref?
__all__ = ['freeze', 'simplify_expr', 'symbolic_eval']
def freeze(expr, vars, namespace={}, safe=False):
"""
Replaces all identifiers in expr by their float value.
The variables vars are not changed.
If safe is True, freezing fails if one variable is not a quantity
"""
# Find variables
ids = [name for name in get_identifiers(expr) if name not in vars]
# Check that they are in the namespaces and find their value
value = {}
for id in ids:
if id in namespace:
value[id] = namespace[id]
else:
log_warn('brian.optimizer.freeze', "Freezing impossible because the value of " + id + " is missing")
return None
if not isinstance(value[id], (int, float)): # or unit?
if safe:
log_warn('brian.optimizer.freeze', "Freezing impossible because " + id + " is not a number")
return None
else:
value[id] = id
else:
value[id] = float(value[id]) # downcast Quantity to float
# Substitute
for id in ids:
if isinstance(value[id], float):
strver = repr(value[id])
else:
strver = str(value[id])
expr = re.sub("\\b" + id + "\\b", strver, expr)
# Clean (changes -- to +)
expr = re.sub("--", "+", expr)
#print "freezing:",expr
#return simplify_expr(expr)
return expr
def symbolic_eval(expr):
"""
Evaluates expr as a symbolic expression.
"""
if not use_sympy:
return expr
# TODO: not with all symbols
# Find all symbols
namespace = {}
vars = get_identifiers(expr)
for var in vars:
namespace[var] = sympy.Symbol(var)
return sympy.sympify(eval(expr, namespace))
def simplify_expr(expr):
'''
Simplifies a string expression for an equation.
NB: does not seem to yield any speed up!
'''
return str(symbolic_eval(expr))
#return str(sympy.simplify(symbolic_eval(expr)))
|