'''
Created on 10/07/2013
@author: Mads M. Pedersen (mmpe@dtu.dk)
Wrapper functions and decorators for compiling functions using Cython
'''
import inspect
import os
import re
import shutil
import subprocess
import sys
import numpy as np
import warnings
import imp
def wrap(f, autodeclare, *args, **kwargs):
"""
Wrapper function returned by the cython_compile and cython_compile_autodeclare decorators
:param f: Function to compile
:type f: function
:param py2pyx_func: py2pyx or py2pyx_autodeclare
:type py2pyx_func: function
"""
# Generate name: "c:\documents\project\mymodule.py" -> mymodule_myfunction
# When called from ipython notebooks, filename is an object e.g: "<ipython-input-12-e897f9fefc0c>"
# therefore <,>,- is removed to make it a legal python module name
name = os.path.relpath(inspect.getabsfile(f), os.getcwd()).replace(".py", "")
name = name.replace("<", "").replace(">", "").replace("-", "")
name = "%s_%s" % (name, f.__name__)
if name.startswith(".."):
rel_dir = os.path.dirname(name) + os.path.sep
sys.path.append(rel_dir)
name = name[len(rel_dir):]
pass
module_name = name.replace(os.path.sep, ".")
# import compiled module_name if exists, otherwise compile and import
try:
cmodule = __import__(module_name, fromlist="*")
if cmodule.__name__ != module_name or not hasattr(cmodule, f.__name__):
raise ImportError()
except ImportError:
# Generate pyrex code lines
if autodeclare:
pyx_lines = py2pyx_autodeclare(f, args, kwargs.copy())
else:
# source lines except '@cython_compile'
source_lines = inspect.getsourcelines(f)[0][1:]
indent = source_lines[0].index("def")
pyx_lines = py2pyx([l[indent:] for l in source_lines])
# Write pyrex code lines to .pyx file
pyx_filename = name.replace("\\", "/") + ".pyx"
with open(pyx_filename, 'w') as fid:
fid.writelines(pyx_lines)
# compile, import compiled module_name and delete temporary files
cmodule = compile_and_cleanup(module_name, pyx_filename, module_name)
try:
cf = getattr(cmodule, f.__name__)
if kwargs == {}:
return cf(*args)
else:
return cf(*args, **kwargs)
except AttributeError:
warnings.warn(
"Compilation or import of %s failed. Python function used instead" %
f)
return f(*args, **kwargs)
def cython_compile(f):
"""Decorator for compilation, import and execution of the function, f.
Variables can be declared using Pure or cdef syntax, see module description
Example:
@cython_compile
def my_func(p):
pass
"""
w = lambda *args, **kwargs: wrap(f, False, *args, **kwargs)
w.__name__ = f.__name__
return w
def cython_compile_autodeclare(f):
"""Decorator for autodeclaring, compilation, import and execution of the function, f.
Declared variables using cdef syntax overrides autodeclaration, see module description
Example:
@cython_compile_autocompile
def my_func(p):
pass
"""
w = lambda *args, **kwargs: wrap(f, True, *args, **kwargs)
w.__name__ = f.__name__
return w
def cython_import(import_module_name, compiler=None):
"""Compiles and imports a module. Use it similar to the normal import
Example (import my_func from my_module):
from wetb.utils.cython_compile import cython_import
cython_import('my_module')
import my_module # import must be after cython_import statement
my_module.my_func()
"""
module_name = import_module_name.split(".")[-1]
globals()[module_name] = __import__(import_module_name, fromlist=module_name)
pyd_module = eval(module_name)
if not is_compiled(pyd_module):
# Read py-module
file_name = import_module_name.replace(".", "/") + ".py"
for p in ["."] + sys.path:
if os.path.isfile(os.path.join(p, file_name)):
file_path = os.path.join(p, file_name).replace("\\", "/")
break
else:
raise IOError("Module %s cannot be found" % file_name)
fid = open(file_path)
pylines = fid.readlines()
fid.close()
# write pyrex file
pyx_filename = file_path.replace('.py', '.pyx')
fid = open(pyx_filename, 'w')
pyxlines = py2pyx(pylines)
fid.writelines(pyxlines)
fid.close()
# compile, import compiled module and delete temporary files
module_relname = os.path.relpath(eval(module_name).__file__, os.getcwd()).replace(os.path.sep, ".")[:-3]
return compile_and_cleanup(import_module_name, pyx_filename, module_relname, compiler)
return eval(module_name)
def compile_and_cleanup(module, pyx_filename, module_relname, compiler=None):
"""compile, import compiled module and delete temporary files"""
# Generate setup.py script
fid = open('setup.py', 'w')
setup_str = """from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
import numpy
ext_modules = [Extension("%s", ["%s"], include_dirs = [numpy.get_include()])]
setup(
name = 'name',
cmdclass = {'build_ext': build_ext},
ext_modules = ext_modules
)""" % (module_relname, pyx_filename)
fid.write(setup_str)
fid.close()
if hasattr(sys, 'frozen'):
raise Exception ("Trying to compile %s in frozen application" % str(module))
# create compile command
import platform
if compiler is not None:
compiler_str = "--compiler=%s" % compiler
elif platform.architecture()[0] == "32bit" and os.name == 'nt' and "mingw" in os.environ['path'].lower():
compiler_str = "--compiler=mingw32"
else:
compiler_str = ""
bin_python = sys.executable
cmd = "%s setup.py build_ext --inplace %s" % (bin_python, compiler_str)
# compile
print ("compiling %s: %s" % (module, cmd))
proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True)
(out, err) = proc.communicate()
# Reload and check that module is compiled
try:
try:
del sys.modules[module]
except KeyError:
pass
cmodule = __import__(module, fromlist=module.split(".")[-1])
imp.reload(cmodule)
except ImportError:
cmodule = None
if cmodule is None or is_compiled(cmodule) == False:
line = '\n' + '=' * 79 + '\n'
sys.stderr.write("%s was not compiled correctly. It may result in slower execution" % module)
sys.stderr.write('%sstdout:\n%s' % (line, out.decode()))
sys.stderr.write('%sstderr:%s%s' % (line, line, err))
else:
print ("Compiling succeeded")
for f in ['setup.py', pyx_filename, pyx_filename.replace(".pyx", '.c')]:
if os.path.isfile(f):
os.remove(f)
# Clean up. Remove temporary files and folders
if os.path.isdir("build"):
try:
shutil.rmtree("build")
except:
pass
return cmodule
def py2pyx_autodeclare(f, args, kwargs):
"""Generate pyrex code of function f and its input arguments
This function invokes py2pyx and extends with autodeclarations:
- arguments: input arguments are declared based their values in args and kwargs
- cdef: Variables declared by cdef, overrides autodeclaration, e.g:
"def func(a): #cpdef func(int a):" -> "cpdef func(int a):" (independent of type of a)
"#cdef int a" - "cdef int a" (independent of type of a)
- assignment: Variables assigned in function, e.g.
"a = xxx"
are declared based on the type of eval(xxx)
- in: variables returned by iterators, e.g:
"for a in range(5)",
"for a,b in [(1,.2)]:"
are declared base on the type of the first element in eval(iterator), e.g. "type(eval(range(5)[0]))"
"""
arg_names, _, _, defaults = inspect.getargspec(f)
# update kwargs with defaults
if defaults:
for k, v in zip(arg_names[::-1], defaults[::-1]):
if k not in kwargs:
kwargs[k] = v
kwargs.update(dict(zip(arg_names, args)))
# get pyx code lines using py2pyx
lines = inspect.getsourcelines(f)[0]
if lines[0].strip() == "@cython_compile_autodeclare":
lines = lines[1:]
lines = py2pyx(lines)
# prepare regular expressions
var_name = "(?:_*[a-zA-Z][a-zA-Z0-9_]*)" # optional "_" + one alpha + [0..n] x alphanum. "?:" = no group
reg_args = re.compile("[ \t]*def +(?:%s) *\(([^:]*)\) *:" % (var_name))
reg_import = re.compile("[ \t]*c?import *(%s)(?: +as +(%s))?" % (var_name, var_name))
reg_cdef = re.compile("[ \t]*cdef +(?:(?:signed|unsigned|int|long|float|double|np\.ndarray\[.*\]) *)*(%s)" % var_name)
reg_assign = re.compile('[ \t]*(%s) *=(.*)' % var_name)
reg_in = re.compile('[ \t]*for +(%s(?:, *%s)*) +in +(.*):' % (var_name, var_name))
def declare_str(var_name, var_value):
"""Generate declaration string '<type(var_value)> <var_name>' e.g:
declare_str('a',1) -> "long a"
"""
if isinstance(var_value, (int)):
return "long long %s" % var_name
if isinstance(var_value, float):
return "double %s" % var_name
elif isinstance(var_value, np.ndarray):
return "np.ndarray[np.%s_t,ndim=%d] %s" % (var_value.dtype, len(var_value.shape), var_name)
else:
raise NotImplementedError(type(var_value))
defs = {} # dict for known local variables
def_line = None # line nr of "def func():". Autodeclaration of local field inserted below this line
for i, line in enumerate(lines):
if def_line is None and 'def' in line:
# first line containing "def" = function declaration line
def_line = i
match = reg_args.match(line)
if match is not None:
args = match.group(1).strip() # line=" def func(xxx):#comment" -> args='xxx'
arg_strs = []
if args != "":
for arg in args.split(','):
arg_name = arg.split('=')[0].strip()
arg_value = kwargs[arg_name]
try:
arg_strs.append(arg.strip().replace(arg_name, declare_str(arg_name, arg_value), 1))
except NotImplementedError:
arg_strs.append(arg)
# replace function declaration line
lines[i] = '%scpdef %s(%s):\n' % (" " * line.index('def'), f.__name__, ", ".join(arg_strs))
else:
#Import: import x as y
match = reg_import.match(line)
if match is not None:
# add imported moduled to kwargs -> enable evaluation of variables
import_module = match.group(1)
if match.group(2) is None:
kwargs[import_module] = __import__(import_module)
else:
# import xxx as y
kwargs[match.group(2)] = __import__(import_module)
continue
#Cdef: cdef int x
match = reg_cdef.match(line)
if match is not None:
# line contains a 'cdef' declaration.
# Add to defs to avoid redeclaration
var_name = match.group(1)
if var_name not in defs:
defs[var_name] = None
continue
#Assignment: x = y
match = reg_assign.match(line)
if match is not None:
# line contains an assignment, e.g. a = xxx.
# Try to evaluate xxx and declare a as type of eval(xxx)
try:
var_name = match.group(1)
if var_name not in defs:
var_value = eval(match.group(2), globals(), kwargs)
defs[var_name] = declare_str(
var_name.strip(), var_value)
kwargs[var_name] = var_value
except NotImplementedError:
pass
continue
#In: For x in y
match = reg_in.match(line)
if match is not None:
# line contains 'for xxx in yyy:'.
# Try to evaluate yyy and declare xxx as type of first element
# of eval(yyy)
var_names = [v.strip() for v in match.group(1).split(",")]
var_values = eval(match.group(2), globals(), kwargs)[0]
if not isinstance(var_values, (list, tuple)):
var_values = (var_values,)
for var_name, var_value in zip(var_names, var_values):
try:
if var_name not in defs:
defs[var_name] = declare_str(var_name, var_value)
kwargs[var_name] = var_value
except NotImplementedError:
pass
indent = lines[def_line + 1].replace(lines[def_line + 1].lstrip(), "")
# Insert declaration of local fields ordered by name just below function
# declaration
for key in sorted(defs.keys(), reverse=True):
if defs[key] is not None:
lines.insert(def_line + 1, "%scdef %s\n" % (indent, defs[key]))
return lines
def py2pyx(pylines):
"""Generate pyrex code lines from python code lines
- Adds import of cython and numpy
- searches every line for "#c". If found text before "#c" is replaced with text after "#c", e.g:
"def func(a): #cpdef func(int a):" -> "cpdef func(int a):
"#cdef int b" -> "cdef int b"
"""
pyxlines = ['import cython\n', 'import numpy as np\n', 'cimport numpy as np\n']
for l in pylines:
if "#c" in l:
indent = l[:len(l) - len(l.lstrip())]
cdef = l[l.index("#c") + 1:]
l = indent + cdef
pyxlines.append(l)
return pyxlines
def is_compiled(module):
return module.__file__.lower()[-4:] == ".pyd" or module.__file__.lower()[-3:] == ".so"