code stringlengths 1 1.49M | vector listlengths 0 7.38k | snippet listlengths 0 7.38k |
|---|---|---|
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from ctypes import *
def setProcName(name):
"""Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differing amounts in differing cases."""
# Call the process control function...
libc = cdll.LoadLibrary('libc.so.6')
libc.prctl(15, c_char_p(name), 0, 0, 0)
# Update argv...
charPP = POINTER(POINTER(c_char))
argv = charPP.in_dll(libc,'_dl_argv')
size = libc.strlen(argv[0])
libc.strncpy(argv[0],c_char_p(name),size)
if __name__=='__main__':
# Quick test that it works...
import os
ps1 = 'ps'
ps2 = 'ps -f'
os.system(ps1)
os.system(ps2)
setProcName('wibble_wobble')
os.system(ps1)
os.system(ps2)
| [
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"from ctypes import *",
"def setProcName(name):\n \"\"\"Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differin... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import multiprocessing as mp
import multiprocessing.synchronize # To make sure we have all the functionality.
import types
import marshal
import unittest
def repeat(x):
"""A generator that repeats the input forever - can be used with the mp_map function to give data to a function that is constant."""
while True: yield x
def run_code(code,args):
"""Internal use function that does the work in each process."""
code = marshal.loads(code)
func = types.FunctionType(code, globals(), '_')
return func(*args)
def mp_map(func, *iters, **keywords):
"""A multiprocess version of the map function. Note that func must limit itself to the data provided - if it accesses anything else (globals, locals to its definition.) it will fail. There is a repeat generator provided in this module to work around such issues. Note that, unlike map, this iterates the length of the shortest of inputs, rather than the longest - whilst this makes it not a perfect substitute it makes passing constant argumenmts easier as they can just repeat for infinity."""
if 'pool' in keywords: pool = keywords['pool']
else: pool = mp.Pool()
code = marshal.dumps(func.func_code)
jobs = []
for args in zip(*iters):
jobs.append(pool.apply_async(run_code,(code,args)))
for i in xrange(len(jobs)):
jobs[i] = jobs[i].get()
return jobs
class TestMpMap(unittest.TestCase):
def test_simple1(self):
data = ['a','b','c','d']
def noop(data):
return data
data_noop = mp_map(noop, data)
self.assertEqual(data, data_noop)
def test_simple2(self):
data = [x for x in xrange(1000)]
data_double = mp_map(lambda a: a*2, data)
self.assertEqual(map(lambda a: a*2,data), data_double)
def test_gen(self):
def gen():
for i in xrange(100): yield i
data_double = mp_map(lambda a: a*2, gen())
self.assertEqual(map(lambda a: a*2,gen()), data_double)
def test_repeat(self):
def mult(a,b):
return a*b
data = [x for x in xrange(50,5000,5)]
data_triple = mp_map(mult, data, repeat(3))
self.assertEqual(map(lambda a: a*3,data),data_triple)
def test_none(self):
data = []
data_sqr = mp_map(lambda x: x*x, data)
self.assertEqual([],data_sqr)
if __name__ == '__main__':
unittest.main()
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"import multiprocessing as mp",
"import multiprocessing.synchronize # To make sure we have all the functionality.",
"import types",
"import marshal",
"import unittest",
"def repeat(x):\n \"\"\"A generator that repeats the input forever - can be used with the mp_map function to give data to a function tha... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from utils.start_cpp import start_cpp
# Defines helper functions for accessing numpy arrays...
numpy_util_code = start_cpp() + """
#ifndef NUMPY_UTIL_CODE
#define NUMPY_UTIL_CODE
float & Float1D(PyArrayObject * arr, int index = 0)
{
return *(float*)(arr->data + index*arr->strides[0]);
}
float & Float2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
float & Float3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
unsigned char & Byte1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index*arr->strides[0]);
}
unsigned char & Byte2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
unsigned char & Byte3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
int & Int1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index*arr->strides[0]);
}
int & Int2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
int & Int3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
#endif
"""
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"from utils.start_cpp import start_cpp",
"numpy_util_code = start_cpp() + \"\"\"\n#ifndef NUMPY_UTIL_CODE\n#define NUMPY_UTIL_CODE\n\nfloat & Float1D(PyArrayObject * arr, int index = 0)\n{\n return *(float*)(arr->data + index*arr->strides[0]);\n}"
] |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import cvarray
import mp_map
import prog_bar
import numpy_help_cpp
import python_obj_cpp
import matrix_cpp
import gamma_cpp
import setProcName
import start_cpp
import make
import doc_gen
# Setup...
doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of miscellaneous stuff - most modules depend on this.')
doc.addFile('readme.txt', 'Overview')
# Variables...
doc.addVariable('numpy_help_cpp.numpy_util_code', 'Assorted utility functions for accessing numpy arrays within scipy.weave C++ code.')
doc.addVariable('python_obj_cpp.python_obj_code', 'Assorted utility functions for interfacing with python objects from scipy.weave C++ code.')
doc.addVariable('matrix_cpp.matrix_code', 'Matrix manipulation routines for use in scipy.weave C++')
doc.addVariable('gamma_cpp.gamma_code', 'Gamma and related functions for use in scipy.weave C++')
# Functions...
doc.addFunction(make.make_mod)
doc.addFunction(cvarray.cv2array)
doc.addFunction(cvarray.array2cv)
doc.addFunction(mp_map.repeat)
doc.addFunction(mp_map.mp_map)
doc.addFunction(setProcName.setProcName)
doc.addFunction(start_cpp.start_cpp)
doc.addFunction(make.make_mod)
# Classes...
doc.addClass(prog_bar.ProgBar)
doc.addClass(doc_gen.DocGen)
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"import cvarray",
"import mp_map",
"import prog_bar",
"import numpy_help_cpp",
"import python_obj_cpp",
"import matrix_cpp",
"import gamma_cpp",
"import setProcName",
"import start_cpp",
"import make",
"import doc_gen",
"doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of misc... |
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import unittest
import random
import math
from scipy.special import gammaln, psi, polygamma
from scipy import weave
from utils.start_cpp import start_cpp
# Provides various gamma-related functions...
gamma_code = start_cpp() + """
#ifndef GAMMA_CODE
#define GAMMA_CODE
#include <cmath>
// Returns the natural logarithm of the Gamma function...
// (Uses Lanczos's approximation.)
double lnGamma(double z)
{
static const double coeff[9] = {0.99999999999980993, 676.5203681218851, -1259.1392167224028, 771.32342877765313, -176.61502916214059, 12.507343278686905, -0.13857109526572012, 9.9843695780195716e-6, 1.5056327351493116e-7};
if (z<0.5)
{
// Use reflection formula, as approximation doesn't work down here...
return log(M_PI) - log(sin(M_PI*z)) - lnGamma(1.0-z);
}
else
{
double x = coeff[0];
for (int i=1;i<9;i++) x += coeff[i]/(z+i-1);
double t = z + 6.5;
return log(sqrt(2.0*M_PI)) + (z-0.5)*log(t) - t + log(x);
}
}
// Calculates the Digamma function, i.e. the derivative of the log of the Gamma function - uses a partial expansion of an infinite series to 4 terms that is good for high values, and an identity to express lower values in terms of higher values...
double digamma(double z)
{
static const double highVal = 13.0; // A bit of fiddling shows that the last term with this is of the order 1e-10, so we can expect at least 9 digits of accuracy past the decimal point.
double ret = 0.0;
while (z<highVal)
{
ret -= 1.0/z;
z += 1.0;
}
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz4 = iz2*iz2;
double iz6 = iz4*iz2;
ret += log(z) - iz1/2.0 - iz2/12.0 + iz4/120.0 - iz6/252.0;
return ret;
}
// Calculates the trigamma function - uses a partial expansion of an infinite series that is accurate for large values, and then uses an identity to express lower values in terms of higher values - same approach as for the digamma function basically...
double trigamma(double z)
{
static const double highVal = 8.0;
double ret = 0.0;
while (z<highVal)
{
ret += 1.0/(z*z);
z += 1.0;
}
z -= 1.0;
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz3 = iz1*iz2;
double iz5 = iz3*iz2;
double iz7 = iz5*iz2;
double iz9 = iz7*iz2;
ret += iz1 - 0.5*iz2 + iz3/6.0 - iz5/30.0 + iz7/42.0 - iz9/30.0;
return ret;
}
#endif
"""
def lnGamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns the logorithm of the gamma function"""
code = start_cpp(gamma_code) + """
return_val = lnGamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def digamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the digamma function"""
code = start_cpp(gamma_code) + """
return_val = digamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def trigamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the trigamma function"""
code = start_cpp(gamma_code) + """
return_val = trigamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
class TestFuncs(unittest.TestCase):
"""Test code for the assorted gamma-related functions."""
def test_compile(self):
code = start_cpp(gamma_code) + """
"""
weave.inline(code, support_code=gamma_code)
def test_error_lngamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = lnGamma(z)
good = gammaln(z)
assert(math.fabs(own-good)<1e-12)
def test_error_digamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = digamma(z)
good = psi(z)
assert(math.fabs(own-good)<1e-9)
def test_error_trigamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = trigamma(z)
good = polygamma(1,z)
assert(math.fabs(own-good)<1e-9)
# If this file is run do the unit tests...
if __name__ == '__main__':
unittest.main()
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"import unittest",
"import random",
"import math",
"from scipy.special import gammaln, psi, polygamma",
"from scipy import weave",
"from utils.start_cpp import start_cpp",
"gamma_code = start_cpp() + \"\"\"\n#ifndef GAMMA_CODE\n#define GAMMA_CODE\n\n#include <cmath>\n\n// Returns the natural logarithm o... |
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import inspect
import hashlib
def start_cpp(hash_str = None):
"""This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for working around the fact the scipy.weave only recompiles if the hash of the code changes, but ignores the support_code - passing the support_code into start_cpp avoids this problem by putting its hash into the code and forcing a recompile when that code changes. Usage is <code variable> = start_cpp([support_code variable]) + <3 quotations to start big comment with code in, typically going over many lines.>"""
frame = inspect.currentframe().f_back
info = inspect.getframeinfo(frame)
if hash_str==None:
return '#line %i "%s"\n'%(info[1],info[0])
else:
h = hashlib.md5()
h.update(hash_str)
hash_val = h.hexdigest()
return '#line %i "%s" // %s\n'%(info[1],info[0],hash_val)
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"import inspect",
"import hashlib",
"def start_cpp(hash_str = None):\n \"\"\"This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for work... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import sys
import os.path
import tempfile
import shutil
from distutils.core import setup, Extension
import distutils.ccompiler
import distutils.dep_util
try:
__default_compiler = distutils.ccompiler.new_compiler()
except:
__default_compiler = None
def make_mod(name, base, source, openCL = False):
"""Uses distutils to compile a python module - really just a set of hacks to allow this to be done 'on demand', so it only compiles if the module does not exist or is older than the current source, and after compilation the program can continue on its merry way, and immediatly import the just compiled module. Note that on failure erros can be thrown - its your choice to catch them or not. name is the modules name, i.e. what you want to use with the import statement. base is the base directory for the module, which contains the source file - often you would want to set this to 'os.path.dirname(__file__)', assuming the .py file that imports the module is in the same directory as the code. It is this directory that the module is output to. source is the filename of the source code to compile, or alternativly a list of filenames. openCL indicates if OpenCL is used by the module, in which case it does all the necesary setup - done like this so these setting can be kept centralised, so when they need to be different for a new platform they only have to be changed in one place."""
if __default_compiler==None: raise Exception('No compiler!')
# Work out the various file names - check if we actually need to do anything...
if not isinstance(source, list): source = [source]
source_path = map(lambda s: os.path.join(base, s), source)
library_path = os.path.join(base, __default_compiler.shared_object_filename(name))
if reduce(lambda a,b: a or b, map(lambda s: distutils.dep_util.newer(s, library_path), source_path)):
try:
print 'b'
# Backup the argv variable and create a temporary directory to do all work in...
old_argv = sys.argv[:]
temp_dir = tempfile.mkdtemp()
# Prepare the extension...
sys.argv = ['','build_ext','--build-lib', base, '--build-temp', temp_dir]
comp_path = filter(lambda s: not s.endswith('.h'), source_path)
depends = filter(lambda s: s.endswith('.h'), source_path)
if openCL:
ext = Extension(name, comp_path, include_dirs=['/usr/local/cuda/include', '/opt/AMDAPP/include'], libraries = ['OpenCL'], library_dirs = ['/usr/lib64/nvidia', '/opt/AMDAPP/lib/x86_64'], depends=depends)
else:
ext = Extension(name, comp_path, depends=depends)
# Compile...
setup(name=name, version='1.0.0', ext_modules=[ext])
finally:
# Cleanup the argv variable and the temporary directory...
sys.argv = old_argv
shutil.rmtree(temp_dir, True)
| [
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[
1,
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[
1,
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0,
0.6... | [
"import sys",
"import os.path",
"import tempfile",
"import shutil",
"from distutils.core import setup, Extension",
"import distutils.ccompiler",
"import distutils.dep_util",
"try:\n __default_compiler = distutils.ccompiler.new_compiler()\nexcept:\n __default_compiler = None",
" __default_compiler... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import pydoc
import inspect
class DocGen:
"""A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code."""
def __init__(self, name, title = None, summary = None):
"""name is the module name - primarilly used for the file names. title is the title used as applicable - if not provide it just uses the name. summary is an optional line to go below the title."""
if title==None: title = name
if summary==None: summary = title
self.doc = pydoc.HTMLDoc()
self.html = open('%s.html'%name,'w')
self.html.write('<html>\n')
self.html.write('<head>\n')
self.html.write('<title>%s</title>\n'%title)
self.html.write('</head>\n')
self.html.write('<body>\n')
self.html_variables = ''
self.html_functions = ''
self.html_classes = ''
self.wiki = open('%s.wiki'%name,'w')
self.wiki.write('#summary %s\n\n'%summary)
self.wiki.write('= %s= \n\n'%title)
self.wiki_variables = ''
self.wiki_functions = ''
self.wiki_classes = ''
def __del__(self):
if self.html_variables!='':
self.html.write(self.doc.bigsection('Synonyms', '#ffffff', '#8d50ff', self.html_variables))
if self.html_functions!='':
self.html.write(self.doc.bigsection('Functions', '#ffffff', '#eeaa77', self.html_functions))
if self.html_classes!='':
self.html.write(self.doc.bigsection('Classes', '#ffffff', '#ee77aa', self.html_classes))
self.html.write('</body>\n')
self.html.write('</html>\n')
self.html.close()
if self.wiki_variables!='':
self.wiki.write('= Variables =\n\n')
self.wiki.write(self.wiki_variables)
self.wiki.write('\n')
if self.wiki_functions!='':
self.wiki.write('= Functions =\n\n')
self.wiki.write(self.wiki_functions)
self.wiki.write('\n')
if self.wiki_classes!='':
self.wiki.write('= Classes =\n\n')
self.wiki.write(self.wiki_classes)
self.wiki.write('\n')
self.wiki.close()
def addFile(self, fn, title, fls = True):
"""Given a filename and section title adds the contents of said file to the output. Various flags influence how this works."""
html = []
wiki = []
for i, line in enumerate(open(fn,'r').readlines()):
hl = line.replace('\n', '')
if i==0 and fls:
hl = '<strong>' + hl + '</strong>'
for ext in ['py','txt']:
if '.%s - '%ext in hl:
s = hl.split('.%s - '%ext, 1)
hl = '<i>' + s[0] + '.%s</i> - '%ext + s[1]
html.append(hl)
wl = line.strip()
if i==0 and fls:
wl = '*%s*'%wl
for ext in ['py','txt']:
if '.%s - '%ext in wl:
s = wl.split('.%s - '%ext, 1)
wl = '`' + s[0] + '.%s` - '%ext + s[1] + '\n'
wiki.append(wl)
self.html.write(self.doc.bigsection(title, '#ffffff', '#7799ee', '<br/>'.join(html)))
self.wiki.write('== %s ==\n'%title)
self.wiki.write('\n'.join(wiki))
self.wiki.write('----\n\n')
def addVariable(self, var, desc):
"""Adds a variable to the documentation. Given the nature of this you provide it as a pair of strings - one referencing the variable, the other some kind of description of its use etc.."""
self.html_variables += '<strong>%s</strong><br/>'%var
self.html_variables += '%s<br/><br/>\n'%desc
self.wiki_variables += '*`%s`*\n'%var
self.wiki_variables += ' %s\n\n'%desc
def addFunction(self, func):
"""Adds a function to the documentation. You provide the actual function instance."""
self.html_functions += self.doc.docroutine(func).replace(' ',' ')
self.html_functions += '\n'
name = func.__name__
args, varargs, keywords, defaults = inspect.getargspec(func)
doc = inspect.getdoc(func)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
self.wiki_functions += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_functions += ' %s\n\n'%doc
def addClass(self, cls):
"""Adds a class to the documentation. You provide the actual class object."""
self.html_classes += self.doc.docclass(cls).replace(' ',' ')
self.html_classes += '\n'
name = cls.__name__
parents = filter(lambda a: a!=cls, inspect.getmro(cls))
doc = inspect.getdoc(cls)
par_str = ''
if len(parents)!=0:
par_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda p: p.__name__, parents))
self.wiki_classes += '== %s(%s) ==\n'%(name, par_str)
self.wiki_classes += ' %s\n\n'%doc
methods = inspect.getmembers(cls, inspect.ismethod)
def method_key(pair):
if pair[0]=='__init__': return '___'
else: return pair[0]
methods.sort(key=method_key)
for name, method in methods:
if not name.startswith('_%s'%cls.__name__):
args, varargs, keywords, defaults = inspect.getargspec(method)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
def fetch_doc(cls, name):
try:
method = getattr(cls, name)
if method.__doc__!=None: return inspect.getdoc(method)
except: pass
for parent in filter(lambda a: a!=cls, inspect.getmro(cls)):
ret = fetch_doc(parent, name)
if ret!=None: return ret
return None
doc = fetch_doc(cls, name)
self.wiki_classes += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_classes += ' %s\n\n'%doc
variables = inspect.getmembers(cls, lambda x: isinstance(x, int) or isinstance(x, str) or isinstance(x, float))
for name, var in variables:
if not name.startswith('__'):
self.wiki_classes += '*`%s`* = %s\n\n'%(name, str(var))
| [
[
1,
0,
0.0634,
0.0049,
0,
0.66,
0,
291,
0,
1,
0,
0,
291,
0,
0
],
[
1,
0,
0.0683,
0.0049,
0,
0.66,
0.5,
878,
0,
1,
0,
0,
878,
0,
0
],
[
3,
0,
0.5439,
0.9171,
0,
0.6... | [
"import pydoc",
"import inspect",
"class DocGen:\n \"\"\"A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code.\"\"\"\n def __init__(self, name, ... |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from ctypes import *
def setProcName(name):
"""Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differing amounts in differing cases."""
# Call the process control function...
libc = cdll.LoadLibrary('libc.so.6')
libc.prctl(15, c_char_p(name), 0, 0, 0)
# Update argv...
charPP = POINTER(POINTER(c_char))
argv = charPP.in_dll(libc,'_dl_argv')
size = libc.strlen(argv[0])
libc.strncpy(argv[0],c_char_p(name),size)
if __name__=='__main__':
# Quick test that it works...
import os
ps1 = 'ps'
ps2 = 'ps -f'
os.system(ps1)
os.system(ps2)
setProcName('wibble_wobble')
os.system(ps1)
os.system(ps2)
| [
[
1,
0,
0.3636,
0.0227,
0,
0.66,
0,
182,
0,
1,
0,
0,
182,
0,
0
],
[
2,
0,
0.5682,
0.25,
0,
0.66,
0.5,
903,
0,
1,
0,
0,
0,
0,
9
],
[
8,
1,
0.4773,
0.0227,
1,
0.97,
... | [
"from ctypes import *",
"def setProcName(name):\n \"\"\"Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differin... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import multiprocessing as mp
import multiprocessing.synchronize # To make sure we have all the functionality.
import types
import marshal
import unittest
def repeat(x):
"""A generator that repeats the input forever - can be used with the mp_map function to give data to a function that is constant."""
while True: yield x
def run_code(code,args):
"""Internal use function that does the work in each process."""
code = marshal.loads(code)
func = types.FunctionType(code, globals(), '_')
return func(*args)
def mp_map(func, *iters, **keywords):
"""A multiprocess version of the map function. Note that func must limit itself to the data provided - if it accesses anything else (globals, locals to its definition.) it will fail. There is a repeat generator provided in this module to work around such issues. Note that, unlike map, this iterates the length of the shortest of inputs, rather than the longest - whilst this makes it not a perfect substitute it makes passing constant argumenmts easier as they can just repeat for infinity."""
if 'pool' in keywords: pool = keywords['pool']
else: pool = mp.Pool()
code = marshal.dumps(func.func_code)
jobs = []
for args in zip(*iters):
jobs.append(pool.apply_async(run_code,(code,args)))
for i in xrange(len(jobs)):
jobs[i] = jobs[i].get()
return jobs
class TestMpMap(unittest.TestCase):
def test_simple1(self):
data = ['a','b','c','d']
def noop(data):
return data
data_noop = mp_map(noop, data)
self.assertEqual(data, data_noop)
def test_simple2(self):
data = [x for x in xrange(1000)]
data_double = mp_map(lambda a: a*2, data)
self.assertEqual(map(lambda a: a*2,data), data_double)
def test_gen(self):
def gen():
for i in xrange(100): yield i
data_double = mp_map(lambda a: a*2, gen())
self.assertEqual(map(lambda a: a*2,gen()), data_double)
def test_repeat(self):
def mult(a,b):
return a*b
data = [x for x in xrange(50,5000,5)]
data_triple = mp_map(mult, data, repeat(3))
self.assertEqual(map(lambda a: a*3,data),data_triple)
def test_none(self):
data = []
data_sqr = mp_map(lambda x: x*x, data)
self.assertEqual([],data_sqr)
if __name__ == '__main__':
unittest.main()
| [
[
1,
0,
0.1456,
0.0097,
0,
0.66,
0,
901,
0,
1,
0,
0,
901,
0,
0
],
[
1,
0,
0.1553,
0.0097,
0,
0.66,
0.1111,
99,
0,
1,
0,
0,
99,
0,
0
],
[
1,
0,
0.1748,
0.0097,
0,
0.... | [
"import multiprocessing as mp",
"import multiprocessing.synchronize # To make sure we have all the functionality.",
"import types",
"import marshal",
"import unittest",
"def repeat(x):\n \"\"\"A generator that repeats the input forever - can be used with the mp_map function to give data to a function tha... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from utils.start_cpp import start_cpp
# Defines helper functions for accessing numpy arrays...
numpy_util_code = start_cpp() + """
#ifndef NUMPY_UTIL_CODE
#define NUMPY_UTIL_CODE
float & Float1D(PyArrayObject * arr, int index = 0)
{
return *(float*)(arr->data + index*arr->strides[0]);
}
float & Float2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
float & Float3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
unsigned char & Byte1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index*arr->strides[0]);
}
unsigned char & Byte2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
unsigned char & Byte3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
int & Int1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index*arr->strides[0]);
}
int & Int2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
int & Int3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
#endif
"""
| [
[
1,
0,
0.1923,
0.0128,
0,
0.66,
0,
972,
0,
1,
0,
0,
972,
0,
0
],
[
14,
0,
0.6282,
0.7564,
0,
0.66,
1,
799,
4,
0,
0,
0,
0,
0,
1
]
] | [
"from utils.start_cpp import start_cpp",
"numpy_util_code = start_cpp() + \"\"\"\n#ifndef NUMPY_UTIL_CODE\n#define NUMPY_UTIL_CODE\n\nfloat & Float1D(PyArrayObject * arr, int index = 0)\n{\n return *(float*)(arr->data + index*arr->strides[0]);\n}"
] |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import cvarray
import mp_map
import prog_bar
import numpy_help_cpp
import python_obj_cpp
import matrix_cpp
import gamma_cpp
import setProcName
import start_cpp
import make
import doc_gen
# Setup...
doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of miscellaneous stuff - most modules depend on this.')
doc.addFile('readme.txt', 'Overview')
# Variables...
doc.addVariable('numpy_help_cpp.numpy_util_code', 'Assorted utility functions for accessing numpy arrays within scipy.weave C++ code.')
doc.addVariable('python_obj_cpp.python_obj_code', 'Assorted utility functions for interfacing with python objects from scipy.weave C++ code.')
doc.addVariable('matrix_cpp.matrix_code', 'Matrix manipulation routines for use in scipy.weave C++')
doc.addVariable('gamma_cpp.gamma_code', 'Gamma and related functions for use in scipy.weave C++')
# Functions...
doc.addFunction(make.make_mod)
doc.addFunction(cvarray.cv2array)
doc.addFunction(cvarray.array2cv)
doc.addFunction(mp_map.repeat)
doc.addFunction(mp_map.mp_map)
doc.addFunction(setProcName.setProcName)
doc.addFunction(start_cpp.start_cpp)
doc.addFunction(make.make_mod)
# Classes...
doc.addClass(prog_bar.ProgBar)
doc.addClass(doc_gen.DocGen)
| [
[
1,
0,
0.2857,
0.0179,
0,
0.66,
0,
192,
0,
1,
0,
0,
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0,
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],
[
1,
0,
0.3036,
0.0179,
0,
0.66,
0.0385,
905,
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1,
0,
0,
905,
0,
0
],
[
1,
0,
0.3214,
0.0179,
0,
... | [
"import cvarray",
"import mp_map",
"import prog_bar",
"import numpy_help_cpp",
"import python_obj_cpp",
"import matrix_cpp",
"import gamma_cpp",
"import setProcName",
"import start_cpp",
"import make",
"import doc_gen",
"doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of misc... |
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import unittest
import random
import math
from scipy.special import gammaln, psi, polygamma
from scipy import weave
from utils.start_cpp import start_cpp
# Provides various gamma-related functions...
gamma_code = start_cpp() + """
#ifndef GAMMA_CODE
#define GAMMA_CODE
#include <cmath>
// Returns the natural logarithm of the Gamma function...
// (Uses Lanczos's approximation.)
double lnGamma(double z)
{
static const double coeff[9] = {0.99999999999980993, 676.5203681218851, -1259.1392167224028, 771.32342877765313, -176.61502916214059, 12.507343278686905, -0.13857109526572012, 9.9843695780195716e-6, 1.5056327351493116e-7};
if (z<0.5)
{
// Use reflection formula, as approximation doesn't work down here...
return log(M_PI) - log(sin(M_PI*z)) - lnGamma(1.0-z);
}
else
{
double x = coeff[0];
for (int i=1;i<9;i++) x += coeff[i]/(z+i-1);
double t = z + 6.5;
return log(sqrt(2.0*M_PI)) + (z-0.5)*log(t) - t + log(x);
}
}
// Calculates the Digamma function, i.e. the derivative of the log of the Gamma function - uses a partial expansion of an infinite series to 4 terms that is good for high values, and an identity to express lower values in terms of higher values...
double digamma(double z)
{
static const double highVal = 13.0; // A bit of fiddling shows that the last term with this is of the order 1e-10, so we can expect at least 9 digits of accuracy past the decimal point.
double ret = 0.0;
while (z<highVal)
{
ret -= 1.0/z;
z += 1.0;
}
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz4 = iz2*iz2;
double iz6 = iz4*iz2;
ret += log(z) - iz1/2.0 - iz2/12.0 + iz4/120.0 - iz6/252.0;
return ret;
}
// Calculates the trigamma function - uses a partial expansion of an infinite series that is accurate for large values, and then uses an identity to express lower values in terms of higher values - same approach as for the digamma function basically...
double trigamma(double z)
{
static const double highVal = 8.0;
double ret = 0.0;
while (z<highVal)
{
ret += 1.0/(z*z);
z += 1.0;
}
z -= 1.0;
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz3 = iz1*iz2;
double iz5 = iz3*iz2;
double iz7 = iz5*iz2;
double iz9 = iz7*iz2;
ret += iz1 - 0.5*iz2 + iz3/6.0 - iz5/30.0 + iz7/42.0 - iz9/30.0;
return ret;
}
#endif
"""
def lnGamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns the logorithm of the gamma function"""
code = start_cpp(gamma_code) + """
return_val = lnGamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def digamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the digamma function"""
code = start_cpp(gamma_code) + """
return_val = digamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def trigamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the trigamma function"""
code = start_cpp(gamma_code) + """
return_val = trigamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
class TestFuncs(unittest.TestCase):
"""Test code for the assorted gamma-related functions."""
def test_compile(self):
code = start_cpp(gamma_code) + """
"""
weave.inline(code, support_code=gamma_code)
def test_error_lngamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = lnGamma(z)
good = gammaln(z)
assert(math.fabs(own-good)<1e-12)
def test_error_digamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = digamma(z)
good = psi(z)
assert(math.fabs(own-good)<1e-9)
def test_error_trigamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = trigamma(z)
good = polygamma(1,z)
assert(math.fabs(own-good)<1e-9)
# If this file is run do the unit tests...
if __name__ == '__main__':
unittest.main()
| [
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0.... | [
"import unittest",
"import random",
"import math",
"from scipy.special import gammaln, psi, polygamma",
"from scipy import weave",
"from utils.start_cpp import start_cpp",
"gamma_code = start_cpp() + \"\"\"\n#ifndef GAMMA_CODE\n#define GAMMA_CODE\n\n#include <cmath>\n\n// Returns the natural logarithm o... |
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import inspect
import hashlib
def start_cpp(hash_str = None):
"""This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for working around the fact the scipy.weave only recompiles if the hash of the code changes, but ignores the support_code - passing the support_code into start_cpp avoids this problem by putting its hash into the code and forcing a recompile when that code changes. Usage is <code variable> = start_cpp([support_code variable]) + <3 quotations to start big comment with code in, typically going over many lines.>"""
frame = inspect.currentframe().f_back
info = inspect.getframeinfo(frame)
if hash_str==None:
return '#line %i "%s"\n'%(info[1],info[0])
else:
h = hashlib.md5()
h.update(hash_str)
hash_val = h.hexdigest()
return '#line %i "%s" // %s\n'%(info[1],info[0],hash_val)
| [
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1,
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[
2,
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... | [
"import inspect",
"import hashlib",
"def start_cpp(hash_str = None):\n \"\"\"This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for work... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import sys
import os.path
import tempfile
import shutil
from distutils.core import setup, Extension
import distutils.ccompiler
import distutils.dep_util
try:
__default_compiler = distutils.ccompiler.new_compiler()
except:
__default_compiler = None
def make_mod(name, base, source, openCL = False):
"""Uses distutils to compile a python module - really just a set of hacks to allow this to be done 'on demand', so it only compiles if the module does not exist or is older than the current source, and after compilation the program can continue on its merry way, and immediatly import the just compiled module. Note that on failure erros can be thrown - its your choice to catch them or not. name is the modules name, i.e. what you want to use with the import statement. base is the base directory for the module, which contains the source file - often you would want to set this to 'os.path.dirname(__file__)', assuming the .py file that imports the module is in the same directory as the code. It is this directory that the module is output to. source is the filename of the source code to compile, or alternativly a list of filenames. openCL indicates if OpenCL is used by the module, in which case it does all the necesary setup - done like this so these setting can be kept centralised, so when they need to be different for a new platform they only have to be changed in one place."""
if __default_compiler==None: raise Exception('No compiler!')
# Work out the various file names - check if we actually need to do anything...
if not isinstance(source, list): source = [source]
source_path = map(lambda s: os.path.join(base, s), source)
library_path = os.path.join(base, __default_compiler.shared_object_filename(name))
if reduce(lambda a,b: a or b, map(lambda s: distutils.dep_util.newer(s, library_path), source_path)):
try:
print 'b'
# Backup the argv variable and create a temporary directory to do all work in...
old_argv = sys.argv[:]
temp_dir = tempfile.mkdtemp()
# Prepare the extension...
sys.argv = ['','build_ext','--build-lib', base, '--build-temp', temp_dir]
comp_path = filter(lambda s: not s.endswith('.h'), source_path)
depends = filter(lambda s: s.endswith('.h'), source_path)
if openCL:
ext = Extension(name, comp_path, include_dirs=['/usr/local/cuda/include', '/opt/AMDAPP/include'], libraries = ['OpenCL'], library_dirs = ['/usr/lib64/nvidia', '/opt/AMDAPP/lib/x86_64'], depends=depends)
else:
ext = Extension(name, comp_path, depends=depends)
# Compile...
setup(name=name, version='1.0.0', ext_modules=[ext])
finally:
# Cleanup the argv variable and the temporary directory...
sys.argv = old_argv
shutil.rmtree(temp_dir, True)
| [
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[
1,
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79,
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[
1,
0,
0.2344,
0.0156,
0,
0.6... | [
"import sys",
"import os.path",
"import tempfile",
"import shutil",
"from distutils.core import setup, Extension",
"import distutils.ccompiler",
"import distutils.dep_util",
"try:\n __default_compiler = distutils.ccompiler.new_compiler()\nexcept:\n __default_compiler = None",
" __default_compiler... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import pydoc
import inspect
class DocGen:
"""A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code."""
def __init__(self, name, title = None, summary = None):
"""name is the module name - primarilly used for the file names. title is the title used as applicable - if not provide it just uses the name. summary is an optional line to go below the title."""
if title==None: title = name
if summary==None: summary = title
self.doc = pydoc.HTMLDoc()
self.html = open('%s.html'%name,'w')
self.html.write('<html>\n')
self.html.write('<head>\n')
self.html.write('<title>%s</title>\n'%title)
self.html.write('</head>\n')
self.html.write('<body>\n')
self.html_variables = ''
self.html_functions = ''
self.html_classes = ''
self.wiki = open('%s.wiki'%name,'w')
self.wiki.write('#summary %s\n\n'%summary)
self.wiki.write('= %s= \n\n'%title)
self.wiki_variables = ''
self.wiki_functions = ''
self.wiki_classes = ''
def __del__(self):
if self.html_variables!='':
self.html.write(self.doc.bigsection('Synonyms', '#ffffff', '#8d50ff', self.html_variables))
if self.html_functions!='':
self.html.write(self.doc.bigsection('Functions', '#ffffff', '#eeaa77', self.html_functions))
if self.html_classes!='':
self.html.write(self.doc.bigsection('Classes', '#ffffff', '#ee77aa', self.html_classes))
self.html.write('</body>\n')
self.html.write('</html>\n')
self.html.close()
if self.wiki_variables!='':
self.wiki.write('= Variables =\n\n')
self.wiki.write(self.wiki_variables)
self.wiki.write('\n')
if self.wiki_functions!='':
self.wiki.write('= Functions =\n\n')
self.wiki.write(self.wiki_functions)
self.wiki.write('\n')
if self.wiki_classes!='':
self.wiki.write('= Classes =\n\n')
self.wiki.write(self.wiki_classes)
self.wiki.write('\n')
self.wiki.close()
def addFile(self, fn, title, fls = True):
"""Given a filename and section title adds the contents of said file to the output. Various flags influence how this works."""
html = []
wiki = []
for i, line in enumerate(open(fn,'r').readlines()):
hl = line.replace('\n', '')
if i==0 and fls:
hl = '<strong>' + hl + '</strong>'
for ext in ['py','txt']:
if '.%s - '%ext in hl:
s = hl.split('.%s - '%ext, 1)
hl = '<i>' + s[0] + '.%s</i> - '%ext + s[1]
html.append(hl)
wl = line.strip()
if i==0 and fls:
wl = '*%s*'%wl
for ext in ['py','txt']:
if '.%s - '%ext in wl:
s = wl.split('.%s - '%ext, 1)
wl = '`' + s[0] + '.%s` - '%ext + s[1] + '\n'
wiki.append(wl)
self.html.write(self.doc.bigsection(title, '#ffffff', '#7799ee', '<br/>'.join(html)))
self.wiki.write('== %s ==\n'%title)
self.wiki.write('\n'.join(wiki))
self.wiki.write('----\n\n')
def addVariable(self, var, desc):
"""Adds a variable to the documentation. Given the nature of this you provide it as a pair of strings - one referencing the variable, the other some kind of description of its use etc.."""
self.html_variables += '<strong>%s</strong><br/>'%var
self.html_variables += '%s<br/><br/>\n'%desc
self.wiki_variables += '*`%s`*\n'%var
self.wiki_variables += ' %s\n\n'%desc
def addFunction(self, func):
"""Adds a function to the documentation. You provide the actual function instance."""
self.html_functions += self.doc.docroutine(func).replace(' ',' ')
self.html_functions += '\n'
name = func.__name__
args, varargs, keywords, defaults = inspect.getargspec(func)
doc = inspect.getdoc(func)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
self.wiki_functions += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_functions += ' %s\n\n'%doc
def addClass(self, cls):
"""Adds a class to the documentation. You provide the actual class object."""
self.html_classes += self.doc.docclass(cls).replace(' ',' ')
self.html_classes += '\n'
name = cls.__name__
parents = filter(lambda a: a!=cls, inspect.getmro(cls))
doc = inspect.getdoc(cls)
par_str = ''
if len(parents)!=0:
par_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda p: p.__name__, parents))
self.wiki_classes += '== %s(%s) ==\n'%(name, par_str)
self.wiki_classes += ' %s\n\n'%doc
methods = inspect.getmembers(cls, inspect.ismethod)
def method_key(pair):
if pair[0]=='__init__': return '___'
else: return pair[0]
methods.sort(key=method_key)
for name, method in methods:
if not name.startswith('_%s'%cls.__name__):
args, varargs, keywords, defaults = inspect.getargspec(method)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
def fetch_doc(cls, name):
try:
method = getattr(cls, name)
if method.__doc__!=None: return inspect.getdoc(method)
except: pass
for parent in filter(lambda a: a!=cls, inspect.getmro(cls)):
ret = fetch_doc(parent, name)
if ret!=None: return ret
return None
doc = fetch_doc(cls, name)
self.wiki_classes += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_classes += ' %s\n\n'%doc
variables = inspect.getmembers(cls, lambda x: isinstance(x, int) or isinstance(x, str) or isinstance(x, float))
for name, var in variables:
if not name.startswith('__'):
self.wiki_classes += '*`%s`* = %s\n\n'%(name, str(var))
| [
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0.0049,
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[
3,
0,
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"import pydoc",
"import inspect",
"class DocGen:\n \"\"\"A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code.\"\"\"\n def __init__(self, name, ... |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from ctypes import *
def setProcName(name):
"""Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differing amounts in differing cases."""
# Call the process control function...
libc = cdll.LoadLibrary('libc.so.6')
libc.prctl(15, c_char_p(name), 0, 0, 0)
# Update argv...
charPP = POINTER(POINTER(c_char))
argv = charPP.in_dll(libc,'_dl_argv')
size = libc.strlen(argv[0])
libc.strncpy(argv[0],c_char_p(name),size)
if __name__=='__main__':
# Quick test that it works...
import os
ps1 = 'ps'
ps2 = 'ps -f'
os.system(ps1)
os.system(ps2)
setProcName('wibble_wobble')
os.system(ps1)
os.system(ps2)
| [
[
1,
0,
0.3636,
0.0227,
0,
0.66,
0,
182,
0,
1,
0,
0,
182,
0,
0
],
[
2,
0,
0.5682,
0.25,
0,
0.66,
0.5,
903,
0,
1,
0,
0,
0,
0,
9
],
[
8,
1,
0.4773,
0.0227,
1,
0.5,
... | [
"from ctypes import *",
"def setProcName(name):\n \"\"\"Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differin... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import multiprocessing as mp
import multiprocessing.synchronize # To make sure we have all the functionality.
import types
import marshal
import unittest
def repeat(x):
"""A generator that repeats the input forever - can be used with the mp_map function to give data to a function that is constant."""
while True: yield x
def run_code(code,args):
"""Internal use function that does the work in each process."""
code = marshal.loads(code)
func = types.FunctionType(code, globals(), '_')
return func(*args)
def mp_map(func, *iters, **keywords):
"""A multiprocess version of the map function. Note that func must limit itself to the data provided - if it accesses anything else (globals, locals to its definition.) it will fail. There is a repeat generator provided in this module to work around such issues. Note that, unlike map, this iterates the length of the shortest of inputs, rather than the longest - whilst this makes it not a perfect substitute it makes passing constant argumenmts easier as they can just repeat for infinity."""
if 'pool' in keywords: pool = keywords['pool']
else: pool = mp.Pool()
code = marshal.dumps(func.func_code)
jobs = []
for args in zip(*iters):
jobs.append(pool.apply_async(run_code,(code,args)))
for i in xrange(len(jobs)):
jobs[i] = jobs[i].get()
return jobs
class TestMpMap(unittest.TestCase):
def test_simple1(self):
data = ['a','b','c','d']
def noop(data):
return data
data_noop = mp_map(noop, data)
self.assertEqual(data, data_noop)
def test_simple2(self):
data = [x for x in xrange(1000)]
data_double = mp_map(lambda a: a*2, data)
self.assertEqual(map(lambda a: a*2,data), data_double)
def test_gen(self):
def gen():
for i in xrange(100): yield i
data_double = mp_map(lambda a: a*2, gen())
self.assertEqual(map(lambda a: a*2,gen()), data_double)
def test_repeat(self):
def mult(a,b):
return a*b
data = [x for x in xrange(50,5000,5)]
data_triple = mp_map(mult, data, repeat(3))
self.assertEqual(map(lambda a: a*3,data),data_triple)
def test_none(self):
data = []
data_sqr = mp_map(lambda x: x*x, data)
self.assertEqual([],data_sqr)
if __name__ == '__main__':
unittest.main()
| [
[
1,
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0.0097,
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[
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[
1,
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0.... | [
"import multiprocessing as mp",
"import multiprocessing.synchronize # To make sure we have all the functionality.",
"import types",
"import marshal",
"import unittest",
"def repeat(x):\n \"\"\"A generator that repeats the input forever - can be used with the mp_map function to give data to a function tha... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from utils.start_cpp import start_cpp
# Defines helper functions for accessing numpy arrays...
numpy_util_code = start_cpp() + """
#ifndef NUMPY_UTIL_CODE
#define NUMPY_UTIL_CODE
float & Float1D(PyArrayObject * arr, int index = 0)
{
return *(float*)(arr->data + index*arr->strides[0]);
}
float & Float2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
float & Float3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
unsigned char & Byte1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index*arr->strides[0]);
}
unsigned char & Byte2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
unsigned char & Byte3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
int & Int1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index*arr->strides[0]);
}
int & Int2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
int & Int3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
#endif
"""
| [
[
1,
0,
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0.0128,
0,
0.66,
0,
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0,
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0,
0,
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],
[
14,
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0.7564,
0,
0.66,
1,
799,
4,
0,
0,
0,
0,
0,
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]
] | [
"from utils.start_cpp import start_cpp",
"numpy_util_code = start_cpp() + \"\"\"\n#ifndef NUMPY_UTIL_CODE\n#define NUMPY_UTIL_CODE\n\nfloat & Float1D(PyArrayObject * arr, int index = 0)\n{\n return *(float*)(arr->data + index*arr->strides[0]);\n}"
] |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import cvarray
import mp_map
import prog_bar
import numpy_help_cpp
import python_obj_cpp
import matrix_cpp
import gamma_cpp
import setProcName
import start_cpp
import make
import doc_gen
# Setup...
doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of miscellaneous stuff - most modules depend on this.')
doc.addFile('readme.txt', 'Overview')
# Variables...
doc.addVariable('numpy_help_cpp.numpy_util_code', 'Assorted utility functions for accessing numpy arrays within scipy.weave C++ code.')
doc.addVariable('python_obj_cpp.python_obj_code', 'Assorted utility functions for interfacing with python objects from scipy.weave C++ code.')
doc.addVariable('matrix_cpp.matrix_code', 'Matrix manipulation routines for use in scipy.weave C++')
doc.addVariable('gamma_cpp.gamma_code', 'Gamma and related functions for use in scipy.weave C++')
# Functions...
doc.addFunction(make.make_mod)
doc.addFunction(cvarray.cv2array)
doc.addFunction(cvarray.array2cv)
doc.addFunction(mp_map.repeat)
doc.addFunction(mp_map.mp_map)
doc.addFunction(setProcName.setProcName)
doc.addFunction(start_cpp.start_cpp)
doc.addFunction(make.make_mod)
# Classes...
doc.addClass(prog_bar.ProgBar)
doc.addClass(doc_gen.DocGen)
| [
[
1,
0,
0.2857,
0.0179,
0,
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0,
192,
0,
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0,
0,
192,
0,
0
],
[
1,
0,
0.3036,
0.0179,
0,
0.66,
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905,
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1,
0,
0,
905,
0,
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],
[
1,
0,
0.3214,
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0,
... | [
"import cvarray",
"import mp_map",
"import prog_bar",
"import numpy_help_cpp",
"import python_obj_cpp",
"import matrix_cpp",
"import gamma_cpp",
"import setProcName",
"import start_cpp",
"import make",
"import doc_gen",
"doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of misc... |
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import unittest
import random
import math
from scipy.special import gammaln, psi, polygamma
from scipy import weave
from utils.start_cpp import start_cpp
# Provides various gamma-related functions...
gamma_code = start_cpp() + """
#ifndef GAMMA_CODE
#define GAMMA_CODE
#include <cmath>
// Returns the natural logarithm of the Gamma function...
// (Uses Lanczos's approximation.)
double lnGamma(double z)
{
static const double coeff[9] = {0.99999999999980993, 676.5203681218851, -1259.1392167224028, 771.32342877765313, -176.61502916214059, 12.507343278686905, -0.13857109526572012, 9.9843695780195716e-6, 1.5056327351493116e-7};
if (z<0.5)
{
// Use reflection formula, as approximation doesn't work down here...
return log(M_PI) - log(sin(M_PI*z)) - lnGamma(1.0-z);
}
else
{
double x = coeff[0];
for (int i=1;i<9;i++) x += coeff[i]/(z+i-1);
double t = z + 6.5;
return log(sqrt(2.0*M_PI)) + (z-0.5)*log(t) - t + log(x);
}
}
// Calculates the Digamma function, i.e. the derivative of the log of the Gamma function - uses a partial expansion of an infinite series to 4 terms that is good for high values, and an identity to express lower values in terms of higher values...
double digamma(double z)
{
static const double highVal = 13.0; // A bit of fiddling shows that the last term with this is of the order 1e-10, so we can expect at least 9 digits of accuracy past the decimal point.
double ret = 0.0;
while (z<highVal)
{
ret -= 1.0/z;
z += 1.0;
}
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz4 = iz2*iz2;
double iz6 = iz4*iz2;
ret += log(z) - iz1/2.0 - iz2/12.0 + iz4/120.0 - iz6/252.0;
return ret;
}
// Calculates the trigamma function - uses a partial expansion of an infinite series that is accurate for large values, and then uses an identity to express lower values in terms of higher values - same approach as for the digamma function basically...
double trigamma(double z)
{
static const double highVal = 8.0;
double ret = 0.0;
while (z<highVal)
{
ret += 1.0/(z*z);
z += 1.0;
}
z -= 1.0;
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz3 = iz1*iz2;
double iz5 = iz3*iz2;
double iz7 = iz5*iz2;
double iz9 = iz7*iz2;
ret += iz1 - 0.5*iz2 + iz3/6.0 - iz5/30.0 + iz7/42.0 - iz9/30.0;
return ret;
}
#endif
"""
def lnGamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns the logorithm of the gamma function"""
code = start_cpp(gamma_code) + """
return_val = lnGamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def digamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the digamma function"""
code = start_cpp(gamma_code) + """
return_val = digamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def trigamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the trigamma function"""
code = start_cpp(gamma_code) + """
return_val = trigamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
class TestFuncs(unittest.TestCase):
"""Test code for the assorted gamma-related functions."""
def test_compile(self):
code = start_cpp(gamma_code) + """
"""
weave.inline(code, support_code=gamma_code)
def test_error_lngamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = lnGamma(z)
good = gammaln(z)
assert(math.fabs(own-good)<1e-12)
def test_error_digamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = digamma(z)
good = psi(z)
assert(math.fabs(own-good)<1e-9)
def test_error_trigamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = trigamma(z)
good = polygamma(1,z)
assert(math.fabs(own-good)<1e-9)
# If this file is run do the unit tests...
if __name__ == '__main__':
unittest.main()
| [
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[
1,
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0.... | [
"import unittest",
"import random",
"import math",
"from scipy.special import gammaln, psi, polygamma",
"from scipy import weave",
"from utils.start_cpp import start_cpp",
"gamma_code = start_cpp() + \"\"\"\n#ifndef GAMMA_CODE\n#define GAMMA_CODE\n\n#include <cmath>\n\n// Returns the natural logarithm o... |
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import inspect
import hashlib
def start_cpp(hash_str = None):
"""This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for working around the fact the scipy.weave only recompiles if the hash of the code changes, but ignores the support_code - passing the support_code into start_cpp avoids this problem by putting its hash into the code and forcing a recompile when that code changes. Usage is <code variable> = start_cpp([support_code variable]) + <3 quotations to start big comment with code in, typically going over many lines.>"""
frame = inspect.currentframe().f_back
info = inspect.getframeinfo(frame)
if hash_str==None:
return '#line %i "%s"\n'%(info[1],info[0])
else:
h = hashlib.md5()
h.update(hash_str)
hash_val = h.hexdigest()
return '#line %i "%s" // %s\n'%(info[1],info[0],hash_val)
| [
[
1,
0,
0.5,
0.0333,
0,
0.66,
0,
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0,
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[
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[
2,
0,
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0.3667,
0,
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... | [
"import inspect",
"import hashlib",
"def start_cpp(hash_str = None):\n \"\"\"This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for work... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import sys
import os.path
import tempfile
import shutil
from distutils.core import setup, Extension
import distutils.ccompiler
import distutils.dep_util
try:
__default_compiler = distutils.ccompiler.new_compiler()
except:
__default_compiler = None
def make_mod(name, base, source, openCL = False):
"""Uses distutils to compile a python module - really just a set of hacks to allow this to be done 'on demand', so it only compiles if the module does not exist or is older than the current source, and after compilation the program can continue on its merry way, and immediatly import the just compiled module. Note that on failure erros can be thrown - its your choice to catch them or not. name is the modules name, i.e. what you want to use with the import statement. base is the base directory for the module, which contains the source file - often you would want to set this to 'os.path.dirname(__file__)', assuming the .py file that imports the module is in the same directory as the code. It is this directory that the module is output to. source is the filename of the source code to compile, or alternativly a list of filenames. openCL indicates if OpenCL is used by the module, in which case it does all the necesary setup - done like this so these setting can be kept centralised, so when they need to be different for a new platform they only have to be changed in one place."""
if __default_compiler==None: raise Exception('No compiler!')
# Work out the various file names - check if we actually need to do anything...
if not isinstance(source, list): source = [source]
source_path = map(lambda s: os.path.join(base, s), source)
library_path = os.path.join(base, __default_compiler.shared_object_filename(name))
if reduce(lambda a,b: a or b, map(lambda s: distutils.dep_util.newer(s, library_path), source_path)):
try:
print 'b'
# Backup the argv variable and create a temporary directory to do all work in...
old_argv = sys.argv[:]
temp_dir = tempfile.mkdtemp()
# Prepare the extension...
sys.argv = ['','build_ext','--build-lib', base, '--build-temp', temp_dir]
comp_path = filter(lambda s: not s.endswith('.h'), source_path)
depends = filter(lambda s: s.endswith('.h'), source_path)
if openCL:
ext = Extension(name, comp_path, include_dirs=['/usr/local/cuda/include', '/opt/AMDAPP/include'], libraries = ['OpenCL'], library_dirs = ['/usr/lib64/nvidia', '/opt/AMDAPP/lib/x86_64'], depends=depends)
else:
ext = Extension(name, comp_path, depends=depends)
# Compile...
setup(name=name, version='1.0.0', ext_modules=[ext])
finally:
# Cleanup the argv variable and the temporary directory...
sys.argv = old_argv
shutil.rmtree(temp_dir, True)
| [
[
1,
0,
0.2031,
0.0156,
0,
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0,
509,
0,
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0,
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509,
0,
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],
[
1,
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0,
79,
0,
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],
[
1,
0,
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0.0156,
0,
0.6... | [
"import sys",
"import os.path",
"import tempfile",
"import shutil",
"from distutils.core import setup, Extension",
"import distutils.ccompiler",
"import distutils.dep_util",
"try:\n __default_compiler = distutils.ccompiler.new_compiler()\nexcept:\n __default_compiler = None",
" __default_compiler... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import pydoc
import inspect
class DocGen:
"""A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code."""
def __init__(self, name, title = None, summary = None):
"""name is the module name - primarilly used for the file names. title is the title used as applicable - if not provide it just uses the name. summary is an optional line to go below the title."""
if title==None: title = name
if summary==None: summary = title
self.doc = pydoc.HTMLDoc()
self.html = open('%s.html'%name,'w')
self.html.write('<html>\n')
self.html.write('<head>\n')
self.html.write('<title>%s</title>\n'%title)
self.html.write('</head>\n')
self.html.write('<body>\n')
self.html_variables = ''
self.html_functions = ''
self.html_classes = ''
self.wiki = open('%s.wiki'%name,'w')
self.wiki.write('#summary %s\n\n'%summary)
self.wiki.write('= %s= \n\n'%title)
self.wiki_variables = ''
self.wiki_functions = ''
self.wiki_classes = ''
def __del__(self):
if self.html_variables!='':
self.html.write(self.doc.bigsection('Synonyms', '#ffffff', '#8d50ff', self.html_variables))
if self.html_functions!='':
self.html.write(self.doc.bigsection('Functions', '#ffffff', '#eeaa77', self.html_functions))
if self.html_classes!='':
self.html.write(self.doc.bigsection('Classes', '#ffffff', '#ee77aa', self.html_classes))
self.html.write('</body>\n')
self.html.write('</html>\n')
self.html.close()
if self.wiki_variables!='':
self.wiki.write('= Variables =\n\n')
self.wiki.write(self.wiki_variables)
self.wiki.write('\n')
if self.wiki_functions!='':
self.wiki.write('= Functions =\n\n')
self.wiki.write(self.wiki_functions)
self.wiki.write('\n')
if self.wiki_classes!='':
self.wiki.write('= Classes =\n\n')
self.wiki.write(self.wiki_classes)
self.wiki.write('\n')
self.wiki.close()
def addFile(self, fn, title, fls = True):
"""Given a filename and section title adds the contents of said file to the output. Various flags influence how this works."""
html = []
wiki = []
for i, line in enumerate(open(fn,'r').readlines()):
hl = line.replace('\n', '')
if i==0 and fls:
hl = '<strong>' + hl + '</strong>'
for ext in ['py','txt']:
if '.%s - '%ext in hl:
s = hl.split('.%s - '%ext, 1)
hl = '<i>' + s[0] + '.%s</i> - '%ext + s[1]
html.append(hl)
wl = line.strip()
if i==0 and fls:
wl = '*%s*'%wl
for ext in ['py','txt']:
if '.%s - '%ext in wl:
s = wl.split('.%s - '%ext, 1)
wl = '`' + s[0] + '.%s` - '%ext + s[1] + '\n'
wiki.append(wl)
self.html.write(self.doc.bigsection(title, '#ffffff', '#7799ee', '<br/>'.join(html)))
self.wiki.write('== %s ==\n'%title)
self.wiki.write('\n'.join(wiki))
self.wiki.write('----\n\n')
def addVariable(self, var, desc):
"""Adds a variable to the documentation. Given the nature of this you provide it as a pair of strings - one referencing the variable, the other some kind of description of its use etc.."""
self.html_variables += '<strong>%s</strong><br/>'%var
self.html_variables += '%s<br/><br/>\n'%desc
self.wiki_variables += '*`%s`*\n'%var
self.wiki_variables += ' %s\n\n'%desc
def addFunction(self, func):
"""Adds a function to the documentation. You provide the actual function instance."""
self.html_functions += self.doc.docroutine(func).replace(' ',' ')
self.html_functions += '\n'
name = func.__name__
args, varargs, keywords, defaults = inspect.getargspec(func)
doc = inspect.getdoc(func)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
self.wiki_functions += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_functions += ' %s\n\n'%doc
def addClass(self, cls):
"""Adds a class to the documentation. You provide the actual class object."""
self.html_classes += self.doc.docclass(cls).replace(' ',' ')
self.html_classes += '\n'
name = cls.__name__
parents = filter(lambda a: a!=cls, inspect.getmro(cls))
doc = inspect.getdoc(cls)
par_str = ''
if len(parents)!=0:
par_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda p: p.__name__, parents))
self.wiki_classes += '== %s(%s) ==\n'%(name, par_str)
self.wiki_classes += ' %s\n\n'%doc
methods = inspect.getmembers(cls, inspect.ismethod)
def method_key(pair):
if pair[0]=='__init__': return '___'
else: return pair[0]
methods.sort(key=method_key)
for name, method in methods:
if not name.startswith('_%s'%cls.__name__):
args, varargs, keywords, defaults = inspect.getargspec(method)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
def fetch_doc(cls, name):
try:
method = getattr(cls, name)
if method.__doc__!=None: return inspect.getdoc(method)
except: pass
for parent in filter(lambda a: a!=cls, inspect.getmro(cls)):
ret = fetch_doc(parent, name)
if ret!=None: return ret
return None
doc = fetch_doc(cls, name)
self.wiki_classes += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_classes += ' %s\n\n'%doc
variables = inspect.getmembers(cls, lambda x: isinstance(x, int) or isinstance(x, str) or isinstance(x, float))
for name, var in variables:
if not name.startswith('__'):
self.wiki_classes += '*`%s`* = %s\n\n'%(name, str(var))
| [
[
1,
0,
0.0634,
0.0049,
0,
0.66,
0,
291,
0,
1,
0,
0,
291,
0,
0
],
[
1,
0,
0.0683,
0.0049,
0,
0.66,
0.5,
878,
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1,
0,
0,
878,
0,
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],
[
3,
0,
0.5439,
0.9171,
0,
0.6... | [
"import pydoc",
"import inspect",
"class DocGen:\n \"\"\"A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code.\"\"\"\n def __init__(self, name, ... |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from ctypes import *
def setProcName(name):
"""Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differing amounts in differing cases."""
# Call the process control function...
libc = cdll.LoadLibrary('libc.so.6')
libc.prctl(15, c_char_p(name), 0, 0, 0)
# Update argv...
charPP = POINTER(POINTER(c_char))
argv = charPP.in_dll(libc,'_dl_argv')
size = libc.strlen(argv[0])
libc.strncpy(argv[0],c_char_p(name),size)
if __name__=='__main__':
# Quick test that it works...
import os
ps1 = 'ps'
ps2 = 'ps -f'
os.system(ps1)
os.system(ps2)
setProcName('wibble_wobble')
os.system(ps1)
os.system(ps2)
| [
[
1,
0,
0.3636,
0.0227,
0,
0.66,
0,
182,
0,
1,
0,
0,
182,
0,
0
],
[
2,
0,
0.5682,
0.25,
0,
0.66,
0.5,
903,
0,
1,
0,
0,
0,
0,
9
],
[
8,
1,
0.4773,
0.0227,
1,
0.92,
... | [
"from ctypes import *",
"def setProcName(name):\n \"\"\"Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differin... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import multiprocessing as mp
import multiprocessing.synchronize # To make sure we have all the functionality.
import types
import marshal
import unittest
def repeat(x):
"""A generator that repeats the input forever - can be used with the mp_map function to give data to a function that is constant."""
while True: yield x
def run_code(code,args):
"""Internal use function that does the work in each process."""
code = marshal.loads(code)
func = types.FunctionType(code, globals(), '_')
return func(*args)
def mp_map(func, *iters, **keywords):
"""A multiprocess version of the map function. Note that func must limit itself to the data provided - if it accesses anything else (globals, locals to its definition.) it will fail. There is a repeat generator provided in this module to work around such issues. Note that, unlike map, this iterates the length of the shortest of inputs, rather than the longest - whilst this makes it not a perfect substitute it makes passing constant argumenmts easier as they can just repeat for infinity."""
if 'pool' in keywords: pool = keywords['pool']
else: pool = mp.Pool()
code = marshal.dumps(func.func_code)
jobs = []
for args in zip(*iters):
jobs.append(pool.apply_async(run_code,(code,args)))
for i in xrange(len(jobs)):
jobs[i] = jobs[i].get()
return jobs
class TestMpMap(unittest.TestCase):
def test_simple1(self):
data = ['a','b','c','d']
def noop(data):
return data
data_noop = mp_map(noop, data)
self.assertEqual(data, data_noop)
def test_simple2(self):
data = [x for x in xrange(1000)]
data_double = mp_map(lambda a: a*2, data)
self.assertEqual(map(lambda a: a*2,data), data_double)
def test_gen(self):
def gen():
for i in xrange(100): yield i
data_double = mp_map(lambda a: a*2, gen())
self.assertEqual(map(lambda a: a*2,gen()), data_double)
def test_repeat(self):
def mult(a,b):
return a*b
data = [x for x in xrange(50,5000,5)]
data_triple = mp_map(mult, data, repeat(3))
self.assertEqual(map(lambda a: a*3,data),data_triple)
def test_none(self):
data = []
data_sqr = mp_map(lambda x: x*x, data)
self.assertEqual([],data_sqr)
if __name__ == '__main__':
unittest.main()
| [
[
1,
0,
0.1456,
0.0097,
0,
0.66,
0,
901,
0,
1,
0,
0,
901,
0,
0
],
[
1,
0,
0.1553,
0.0097,
0,
0.66,
0.1111,
99,
0,
1,
0,
0,
99,
0,
0
],
[
1,
0,
0.1748,
0.0097,
0,
0.... | [
"import multiprocessing as mp",
"import multiprocessing.synchronize # To make sure we have all the functionality.",
"import types",
"import marshal",
"import unittest",
"def repeat(x):\n \"\"\"A generator that repeats the input forever - can be used with the mp_map function to give data to a function tha... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from utils.start_cpp import start_cpp
# Defines helper functions for accessing numpy arrays...
numpy_util_code = start_cpp() + """
#ifndef NUMPY_UTIL_CODE
#define NUMPY_UTIL_CODE
float & Float1D(PyArrayObject * arr, int index = 0)
{
return *(float*)(arr->data + index*arr->strides[0]);
}
float & Float2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
float & Float3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
unsigned char & Byte1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index*arr->strides[0]);
}
unsigned char & Byte2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
unsigned char & Byte3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
int & Int1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index*arr->strides[0]);
}
int & Int2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
int & Int3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
#endif
"""
| [
[
1,
0,
0.1923,
0.0128,
0,
0.66,
0,
972,
0,
1,
0,
0,
972,
0,
0
],
[
14,
0,
0.6282,
0.7564,
0,
0.66,
1,
799,
4,
0,
0,
0,
0,
0,
1
]
] | [
"from utils.start_cpp import start_cpp",
"numpy_util_code = start_cpp() + \"\"\"\n#ifndef NUMPY_UTIL_CODE\n#define NUMPY_UTIL_CODE\n\nfloat & Float1D(PyArrayObject * arr, int index = 0)\n{\n return *(float*)(arr->data + index*arr->strides[0]);\n}"
] |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import cvarray
import mp_map
import prog_bar
import numpy_help_cpp
import python_obj_cpp
import matrix_cpp
import gamma_cpp
import setProcName
import start_cpp
import make
import doc_gen
# Setup...
doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of miscellaneous stuff - most modules depend on this.')
doc.addFile('readme.txt', 'Overview')
# Variables...
doc.addVariable('numpy_help_cpp.numpy_util_code', 'Assorted utility functions for accessing numpy arrays within scipy.weave C++ code.')
doc.addVariable('python_obj_cpp.python_obj_code', 'Assorted utility functions for interfacing with python objects from scipy.weave C++ code.')
doc.addVariable('matrix_cpp.matrix_code', 'Matrix manipulation routines for use in scipy.weave C++')
doc.addVariable('gamma_cpp.gamma_code', 'Gamma and related functions for use in scipy.weave C++')
# Functions...
doc.addFunction(make.make_mod)
doc.addFunction(cvarray.cv2array)
doc.addFunction(cvarray.array2cv)
doc.addFunction(mp_map.repeat)
doc.addFunction(mp_map.mp_map)
doc.addFunction(setProcName.setProcName)
doc.addFunction(start_cpp.start_cpp)
doc.addFunction(make.make_mod)
# Classes...
doc.addClass(prog_bar.ProgBar)
doc.addClass(doc_gen.DocGen)
| [
[
1,
0,
0.2857,
0.0179,
0,
0.66,
0,
192,
0,
1,
0,
0,
192,
0,
0
],
[
1,
0,
0.3036,
0.0179,
0,
0.66,
0.0385,
905,
0,
1,
0,
0,
905,
0,
0
],
[
1,
0,
0.3214,
0.0179,
0,
... | [
"import cvarray",
"import mp_map",
"import prog_bar",
"import numpy_help_cpp",
"import python_obj_cpp",
"import matrix_cpp",
"import gamma_cpp",
"import setProcName",
"import start_cpp",
"import make",
"import doc_gen",
"doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of misc... |
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import unittest
import random
import math
from scipy.special import gammaln, psi, polygamma
from scipy import weave
from utils.start_cpp import start_cpp
# Provides various gamma-related functions...
gamma_code = start_cpp() + """
#ifndef GAMMA_CODE
#define GAMMA_CODE
#include <cmath>
// Returns the natural logarithm of the Gamma function...
// (Uses Lanczos's approximation.)
double lnGamma(double z)
{
static const double coeff[9] = {0.99999999999980993, 676.5203681218851, -1259.1392167224028, 771.32342877765313, -176.61502916214059, 12.507343278686905, -0.13857109526572012, 9.9843695780195716e-6, 1.5056327351493116e-7};
if (z<0.5)
{
// Use reflection formula, as approximation doesn't work down here...
return log(M_PI) - log(sin(M_PI*z)) - lnGamma(1.0-z);
}
else
{
double x = coeff[0];
for (int i=1;i<9;i++) x += coeff[i]/(z+i-1);
double t = z + 6.5;
return log(sqrt(2.0*M_PI)) + (z-0.5)*log(t) - t + log(x);
}
}
// Calculates the Digamma function, i.e. the derivative of the log of the Gamma function - uses a partial expansion of an infinite series to 4 terms that is good for high values, and an identity to express lower values in terms of higher values...
double digamma(double z)
{
static const double highVal = 13.0; // A bit of fiddling shows that the last term with this is of the order 1e-10, so we can expect at least 9 digits of accuracy past the decimal point.
double ret = 0.0;
while (z<highVal)
{
ret -= 1.0/z;
z += 1.0;
}
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz4 = iz2*iz2;
double iz6 = iz4*iz2;
ret += log(z) - iz1/2.0 - iz2/12.0 + iz4/120.0 - iz6/252.0;
return ret;
}
// Calculates the trigamma function - uses a partial expansion of an infinite series that is accurate for large values, and then uses an identity to express lower values in terms of higher values - same approach as for the digamma function basically...
double trigamma(double z)
{
static const double highVal = 8.0;
double ret = 0.0;
while (z<highVal)
{
ret += 1.0/(z*z);
z += 1.0;
}
z -= 1.0;
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz3 = iz1*iz2;
double iz5 = iz3*iz2;
double iz7 = iz5*iz2;
double iz9 = iz7*iz2;
ret += iz1 - 0.5*iz2 + iz3/6.0 - iz5/30.0 + iz7/42.0 - iz9/30.0;
return ret;
}
#endif
"""
def lnGamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns the logorithm of the gamma function"""
code = start_cpp(gamma_code) + """
return_val = lnGamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def digamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the digamma function"""
code = start_cpp(gamma_code) + """
return_val = digamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def trigamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the trigamma function"""
code = start_cpp(gamma_code) + """
return_val = trigamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
class TestFuncs(unittest.TestCase):
"""Test code for the assorted gamma-related functions."""
def test_compile(self):
code = start_cpp(gamma_code) + """
"""
weave.inline(code, support_code=gamma_code)
def test_error_lngamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = lnGamma(z)
good = gammaln(z)
assert(math.fabs(own-good)<1e-12)
def test_error_digamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = digamma(z)
good = psi(z)
assert(math.fabs(own-good)<1e-9)
def test_error_trigamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = trigamma(z)
good = polygamma(1,z)
assert(math.fabs(own-good)<1e-9)
# If this file is run do the unit tests...
if __name__ == '__main__':
unittest.main()
| [
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[
1,
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0.... | [
"import unittest",
"import random",
"import math",
"from scipy.special import gammaln, psi, polygamma",
"from scipy import weave",
"from utils.start_cpp import start_cpp",
"gamma_code = start_cpp() + \"\"\"\n#ifndef GAMMA_CODE\n#define GAMMA_CODE\n\n#include <cmath>\n\n// Returns the natural logarithm o... |
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import inspect
import hashlib
def start_cpp(hash_str = None):
"""This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for working around the fact the scipy.weave only recompiles if the hash of the code changes, but ignores the support_code - passing the support_code into start_cpp avoids this problem by putting its hash into the code and forcing a recompile when that code changes. Usage is <code variable> = start_cpp([support_code variable]) + <3 quotations to start big comment with code in, typically going over many lines.>"""
frame = inspect.currentframe().f_back
info = inspect.getframeinfo(frame)
if hash_str==None:
return '#line %i "%s"\n'%(info[1],info[0])
else:
h = hashlib.md5()
h.update(hash_str)
hash_val = h.hexdigest()
return '#line %i "%s" // %s\n'%(info[1],info[0],hash_val)
| [
[
1,
0,
0.5,
0.0333,
0,
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0,
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0,
1,
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[
1,
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[
2,
0,
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0,
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... | [
"import inspect",
"import hashlib",
"def start_cpp(hash_str = None):\n \"\"\"This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for work... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import sys
import os.path
import tempfile
import shutil
from distutils.core import setup, Extension
import distutils.ccompiler
import distutils.dep_util
try:
__default_compiler = distutils.ccompiler.new_compiler()
except:
__default_compiler = None
def make_mod(name, base, source, openCL = False):
"""Uses distutils to compile a python module - really just a set of hacks to allow this to be done 'on demand', so it only compiles if the module does not exist or is older than the current source, and after compilation the program can continue on its merry way, and immediatly import the just compiled module. Note that on failure erros can be thrown - its your choice to catch them or not. name is the modules name, i.e. what you want to use with the import statement. base is the base directory for the module, which contains the source file - often you would want to set this to 'os.path.dirname(__file__)', assuming the .py file that imports the module is in the same directory as the code. It is this directory that the module is output to. source is the filename of the source code to compile, or alternativly a list of filenames. openCL indicates if OpenCL is used by the module, in which case it does all the necesary setup - done like this so these setting can be kept centralised, so when they need to be different for a new platform they only have to be changed in one place."""
if __default_compiler==None: raise Exception('No compiler!')
# Work out the various file names - check if we actually need to do anything...
if not isinstance(source, list): source = [source]
source_path = map(lambda s: os.path.join(base, s), source)
library_path = os.path.join(base, __default_compiler.shared_object_filename(name))
if reduce(lambda a,b: a or b, map(lambda s: distutils.dep_util.newer(s, library_path), source_path)):
try:
print 'b'
# Backup the argv variable and create a temporary directory to do all work in...
old_argv = sys.argv[:]
temp_dir = tempfile.mkdtemp()
# Prepare the extension...
sys.argv = ['','build_ext','--build-lib', base, '--build-temp', temp_dir]
comp_path = filter(lambda s: not s.endswith('.h'), source_path)
depends = filter(lambda s: s.endswith('.h'), source_path)
if openCL:
ext = Extension(name, comp_path, include_dirs=['/usr/local/cuda/include', '/opt/AMDAPP/include'], libraries = ['OpenCL'], library_dirs = ['/usr/lib64/nvidia', '/opt/AMDAPP/lib/x86_64'], depends=depends)
else:
ext = Extension(name, comp_path, depends=depends)
# Compile...
setup(name=name, version='1.0.0', ext_modules=[ext])
finally:
# Cleanup the argv variable and the temporary directory...
sys.argv = old_argv
shutil.rmtree(temp_dir, True)
| [
[
1,
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[
1,
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[
1,
0,
0.2344,
0.0156,
0,
0.6... | [
"import sys",
"import os.path",
"import tempfile",
"import shutil",
"from distutils.core import setup, Extension",
"import distutils.ccompiler",
"import distutils.dep_util",
"try:\n __default_compiler = distutils.ccompiler.new_compiler()\nexcept:\n __default_compiler = None",
" __default_compiler... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import pydoc
import inspect
class DocGen:
"""A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code."""
def __init__(self, name, title = None, summary = None):
"""name is the module name - primarilly used for the file names. title is the title used as applicable - if not provide it just uses the name. summary is an optional line to go below the title."""
if title==None: title = name
if summary==None: summary = title
self.doc = pydoc.HTMLDoc()
self.html = open('%s.html'%name,'w')
self.html.write('<html>\n')
self.html.write('<head>\n')
self.html.write('<title>%s</title>\n'%title)
self.html.write('</head>\n')
self.html.write('<body>\n')
self.html_variables = ''
self.html_functions = ''
self.html_classes = ''
self.wiki = open('%s.wiki'%name,'w')
self.wiki.write('#summary %s\n\n'%summary)
self.wiki.write('= %s= \n\n'%title)
self.wiki_variables = ''
self.wiki_functions = ''
self.wiki_classes = ''
def __del__(self):
if self.html_variables!='':
self.html.write(self.doc.bigsection('Synonyms', '#ffffff', '#8d50ff', self.html_variables))
if self.html_functions!='':
self.html.write(self.doc.bigsection('Functions', '#ffffff', '#eeaa77', self.html_functions))
if self.html_classes!='':
self.html.write(self.doc.bigsection('Classes', '#ffffff', '#ee77aa', self.html_classes))
self.html.write('</body>\n')
self.html.write('</html>\n')
self.html.close()
if self.wiki_variables!='':
self.wiki.write('= Variables =\n\n')
self.wiki.write(self.wiki_variables)
self.wiki.write('\n')
if self.wiki_functions!='':
self.wiki.write('= Functions =\n\n')
self.wiki.write(self.wiki_functions)
self.wiki.write('\n')
if self.wiki_classes!='':
self.wiki.write('= Classes =\n\n')
self.wiki.write(self.wiki_classes)
self.wiki.write('\n')
self.wiki.close()
def addFile(self, fn, title, fls = True):
"""Given a filename and section title adds the contents of said file to the output. Various flags influence how this works."""
html = []
wiki = []
for i, line in enumerate(open(fn,'r').readlines()):
hl = line.replace('\n', '')
if i==0 and fls:
hl = '<strong>' + hl + '</strong>'
for ext in ['py','txt']:
if '.%s - '%ext in hl:
s = hl.split('.%s - '%ext, 1)
hl = '<i>' + s[0] + '.%s</i> - '%ext + s[1]
html.append(hl)
wl = line.strip()
if i==0 and fls:
wl = '*%s*'%wl
for ext in ['py','txt']:
if '.%s - '%ext in wl:
s = wl.split('.%s - '%ext, 1)
wl = '`' + s[0] + '.%s` - '%ext + s[1] + '\n'
wiki.append(wl)
self.html.write(self.doc.bigsection(title, '#ffffff', '#7799ee', '<br/>'.join(html)))
self.wiki.write('== %s ==\n'%title)
self.wiki.write('\n'.join(wiki))
self.wiki.write('----\n\n')
def addVariable(self, var, desc):
"""Adds a variable to the documentation. Given the nature of this you provide it as a pair of strings - one referencing the variable, the other some kind of description of its use etc.."""
self.html_variables += '<strong>%s</strong><br/>'%var
self.html_variables += '%s<br/><br/>\n'%desc
self.wiki_variables += '*`%s`*\n'%var
self.wiki_variables += ' %s\n\n'%desc
def addFunction(self, func):
"""Adds a function to the documentation. You provide the actual function instance."""
self.html_functions += self.doc.docroutine(func).replace(' ',' ')
self.html_functions += '\n'
name = func.__name__
args, varargs, keywords, defaults = inspect.getargspec(func)
doc = inspect.getdoc(func)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
self.wiki_functions += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_functions += ' %s\n\n'%doc
def addClass(self, cls):
"""Adds a class to the documentation. You provide the actual class object."""
self.html_classes += self.doc.docclass(cls).replace(' ',' ')
self.html_classes += '\n'
name = cls.__name__
parents = filter(lambda a: a!=cls, inspect.getmro(cls))
doc = inspect.getdoc(cls)
par_str = ''
if len(parents)!=0:
par_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda p: p.__name__, parents))
self.wiki_classes += '== %s(%s) ==\n'%(name, par_str)
self.wiki_classes += ' %s\n\n'%doc
methods = inspect.getmembers(cls, inspect.ismethod)
def method_key(pair):
if pair[0]=='__init__': return '___'
else: return pair[0]
methods.sort(key=method_key)
for name, method in methods:
if not name.startswith('_%s'%cls.__name__):
args, varargs, keywords, defaults = inspect.getargspec(method)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
def fetch_doc(cls, name):
try:
method = getattr(cls, name)
if method.__doc__!=None: return inspect.getdoc(method)
except: pass
for parent in filter(lambda a: a!=cls, inspect.getmro(cls)):
ret = fetch_doc(parent, name)
if ret!=None: return ret
return None
doc = fetch_doc(cls, name)
self.wiki_classes += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_classes += ' %s\n\n'%doc
variables = inspect.getmembers(cls, lambda x: isinstance(x, int) or isinstance(x, str) or isinstance(x, float))
for name, var in variables:
if not name.startswith('__'):
self.wiki_classes += '*`%s`* = %s\n\n'%(name, str(var))
| [
[
1,
0,
0.0634,
0.0049,
0,
0.66,
0,
291,
0,
1,
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291,
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],
[
1,
0,
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0.0049,
0,
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0,
1,
0,
0,
878,
0,
0
],
[
3,
0,
0.5439,
0.9171,
0,
0.6... | [
"import pydoc",
"import inspect",
"class DocGen:\n \"\"\"A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code.\"\"\"\n def __init__(self, name, ... |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from ctypes import *
def setProcName(name):
"""Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differing amounts in differing cases."""
# Call the process control function...
libc = cdll.LoadLibrary('libc.so.6')
libc.prctl(15, c_char_p(name), 0, 0, 0)
# Update argv...
charPP = POINTER(POINTER(c_char))
argv = charPP.in_dll(libc,'_dl_argv')
size = libc.strlen(argv[0])
libc.strncpy(argv[0],c_char_p(name),size)
if __name__=='__main__':
# Quick test that it works...
import os
ps1 = 'ps'
ps2 = 'ps -f'
os.system(ps1)
os.system(ps2)
setProcName('wibble_wobble')
os.system(ps1)
os.system(ps2)
| [
[
1,
0,
0.3636,
0.0227,
0,
0.66,
0,
182,
0,
1,
0,
0,
182,
0,
0
],
[
2,
0,
0.5682,
0.25,
0,
0.66,
0.5,
903,
0,
1,
0,
0,
0,
0,
9
],
[
8,
1,
0.4773,
0.0227,
1,
0.65,
... | [
"from ctypes import *",
"def setProcName(name):\n \"\"\"Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differin... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import multiprocessing as mp
import multiprocessing.synchronize # To make sure we have all the functionality.
import types
import marshal
import unittest
def repeat(x):
"""A generator that repeats the input forever - can be used with the mp_map function to give data to a function that is constant."""
while True: yield x
def run_code(code,args):
"""Internal use function that does the work in each process."""
code = marshal.loads(code)
func = types.FunctionType(code, globals(), '_')
return func(*args)
def mp_map(func, *iters, **keywords):
"""A multiprocess version of the map function. Note that func must limit itself to the data provided - if it accesses anything else (globals, locals to its definition.) it will fail. There is a repeat generator provided in this module to work around such issues. Note that, unlike map, this iterates the length of the shortest of inputs, rather than the longest - whilst this makes it not a perfect substitute it makes passing constant argumenmts easier as they can just repeat for infinity."""
if 'pool' in keywords: pool = keywords['pool']
else: pool = mp.Pool()
code = marshal.dumps(func.func_code)
jobs = []
for args in zip(*iters):
jobs.append(pool.apply_async(run_code,(code,args)))
for i in xrange(len(jobs)):
jobs[i] = jobs[i].get()
return jobs
class TestMpMap(unittest.TestCase):
def test_simple1(self):
data = ['a','b','c','d']
def noop(data):
return data
data_noop = mp_map(noop, data)
self.assertEqual(data, data_noop)
def test_simple2(self):
data = [x for x in xrange(1000)]
data_double = mp_map(lambda a: a*2, data)
self.assertEqual(map(lambda a: a*2,data), data_double)
def test_gen(self):
def gen():
for i in xrange(100): yield i
data_double = mp_map(lambda a: a*2, gen())
self.assertEqual(map(lambda a: a*2,gen()), data_double)
def test_repeat(self):
def mult(a,b):
return a*b
data = [x for x in xrange(50,5000,5)]
data_triple = mp_map(mult, data, repeat(3))
self.assertEqual(map(lambda a: a*3,data),data_triple)
def test_none(self):
data = []
data_sqr = mp_map(lambda x: x*x, data)
self.assertEqual([],data_sqr)
if __name__ == '__main__':
unittest.main()
| [
[
1,
0,
0.1456,
0.0097,
0,
0.66,
0,
901,
0,
1,
0,
0,
901,
0,
0
],
[
1,
0,
0.1553,
0.0097,
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99,
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1,
0,
0,
99,
0,
0
],
[
1,
0,
0.1748,
0.0097,
0,
0.... | [
"import multiprocessing as mp",
"import multiprocessing.synchronize # To make sure we have all the functionality.",
"import types",
"import marshal",
"import unittest",
"def repeat(x):\n \"\"\"A generator that repeats the input forever - can be used with the mp_map function to give data to a function tha... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from utils.start_cpp import start_cpp
# Defines helper functions for accessing numpy arrays...
numpy_util_code = start_cpp() + """
#ifndef NUMPY_UTIL_CODE
#define NUMPY_UTIL_CODE
float & Float1D(PyArrayObject * arr, int index = 0)
{
return *(float*)(arr->data + index*arr->strides[0]);
}
float & Float2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
float & Float3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
unsigned char & Byte1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index*arr->strides[0]);
}
unsigned char & Byte2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
unsigned char & Byte3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
int & Int1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index*arr->strides[0]);
}
int & Int2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
int & Int3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
#endif
"""
| [
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] | [
"from utils.start_cpp import start_cpp",
"numpy_util_code = start_cpp() + \"\"\"\n#ifndef NUMPY_UTIL_CODE\n#define NUMPY_UTIL_CODE\n\nfloat & Float1D(PyArrayObject * arr, int index = 0)\n{\n return *(float*)(arr->data + index*arr->strides[0]);\n}"
] |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import cvarray
import mp_map
import prog_bar
import numpy_help_cpp
import python_obj_cpp
import matrix_cpp
import gamma_cpp
import setProcName
import start_cpp
import make
import doc_gen
# Setup...
doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of miscellaneous stuff - most modules depend on this.')
doc.addFile('readme.txt', 'Overview')
# Variables...
doc.addVariable('numpy_help_cpp.numpy_util_code', 'Assorted utility functions for accessing numpy arrays within scipy.weave C++ code.')
doc.addVariable('python_obj_cpp.python_obj_code', 'Assorted utility functions for interfacing with python objects from scipy.weave C++ code.')
doc.addVariable('matrix_cpp.matrix_code', 'Matrix manipulation routines for use in scipy.weave C++')
doc.addVariable('gamma_cpp.gamma_code', 'Gamma and related functions for use in scipy.weave C++')
# Functions...
doc.addFunction(make.make_mod)
doc.addFunction(cvarray.cv2array)
doc.addFunction(cvarray.array2cv)
doc.addFunction(mp_map.repeat)
doc.addFunction(mp_map.mp_map)
doc.addFunction(setProcName.setProcName)
doc.addFunction(start_cpp.start_cpp)
doc.addFunction(make.make_mod)
# Classes...
doc.addClass(prog_bar.ProgBar)
doc.addClass(doc_gen.DocGen)
| [
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1,
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[
1,
0,
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[
1,
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0,
... | [
"import cvarray",
"import mp_map",
"import prog_bar",
"import numpy_help_cpp",
"import python_obj_cpp",
"import matrix_cpp",
"import gamma_cpp",
"import setProcName",
"import start_cpp",
"import make",
"import doc_gen",
"doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of misc... |
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import unittest
import random
import math
from scipy.special import gammaln, psi, polygamma
from scipy import weave
from utils.start_cpp import start_cpp
# Provides various gamma-related functions...
gamma_code = start_cpp() + """
#ifndef GAMMA_CODE
#define GAMMA_CODE
#include <cmath>
// Returns the natural logarithm of the Gamma function...
// (Uses Lanczos's approximation.)
double lnGamma(double z)
{
static const double coeff[9] = {0.99999999999980993, 676.5203681218851, -1259.1392167224028, 771.32342877765313, -176.61502916214059, 12.507343278686905, -0.13857109526572012, 9.9843695780195716e-6, 1.5056327351493116e-7};
if (z<0.5)
{
// Use reflection formula, as approximation doesn't work down here...
return log(M_PI) - log(sin(M_PI*z)) - lnGamma(1.0-z);
}
else
{
double x = coeff[0];
for (int i=1;i<9;i++) x += coeff[i]/(z+i-1);
double t = z + 6.5;
return log(sqrt(2.0*M_PI)) + (z-0.5)*log(t) - t + log(x);
}
}
// Calculates the Digamma function, i.e. the derivative of the log of the Gamma function - uses a partial expansion of an infinite series to 4 terms that is good for high values, and an identity to express lower values in terms of higher values...
double digamma(double z)
{
static const double highVal = 13.0; // A bit of fiddling shows that the last term with this is of the order 1e-10, so we can expect at least 9 digits of accuracy past the decimal point.
double ret = 0.0;
while (z<highVal)
{
ret -= 1.0/z;
z += 1.0;
}
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz4 = iz2*iz2;
double iz6 = iz4*iz2;
ret += log(z) - iz1/2.0 - iz2/12.0 + iz4/120.0 - iz6/252.0;
return ret;
}
// Calculates the trigamma function - uses a partial expansion of an infinite series that is accurate for large values, and then uses an identity to express lower values in terms of higher values - same approach as for the digamma function basically...
double trigamma(double z)
{
static const double highVal = 8.0;
double ret = 0.0;
while (z<highVal)
{
ret += 1.0/(z*z);
z += 1.0;
}
z -= 1.0;
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz3 = iz1*iz2;
double iz5 = iz3*iz2;
double iz7 = iz5*iz2;
double iz9 = iz7*iz2;
ret += iz1 - 0.5*iz2 + iz3/6.0 - iz5/30.0 + iz7/42.0 - iz9/30.0;
return ret;
}
#endif
"""
def lnGamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns the logorithm of the gamma function"""
code = start_cpp(gamma_code) + """
return_val = lnGamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def digamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the digamma function"""
code = start_cpp(gamma_code) + """
return_val = digamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def trigamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the trigamma function"""
code = start_cpp(gamma_code) + """
return_val = trigamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
class TestFuncs(unittest.TestCase):
"""Test code for the assorted gamma-related functions."""
def test_compile(self):
code = start_cpp(gamma_code) + """
"""
weave.inline(code, support_code=gamma_code)
def test_error_lngamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = lnGamma(z)
good = gammaln(z)
assert(math.fabs(own-good)<1e-12)
def test_error_digamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = digamma(z)
good = psi(z)
assert(math.fabs(own-good)<1e-9)
def test_error_trigamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = trigamma(z)
good = polygamma(1,z)
assert(math.fabs(own-good)<1e-9)
# If this file is run do the unit tests...
if __name__ == '__main__':
unittest.main()
| [
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715,
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[
1,
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0.0063,
0,
0.... | [
"import unittest",
"import random",
"import math",
"from scipy.special import gammaln, psi, polygamma",
"from scipy import weave",
"from utils.start_cpp import start_cpp",
"gamma_code = start_cpp() + \"\"\"\n#ifndef GAMMA_CODE\n#define GAMMA_CODE\n\n#include <cmath>\n\n// Returns the natural logarithm o... |
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import inspect
import hashlib
def start_cpp(hash_str = None):
"""This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for working around the fact the scipy.weave only recompiles if the hash of the code changes, but ignores the support_code - passing the support_code into start_cpp avoids this problem by putting its hash into the code and forcing a recompile when that code changes. Usage is <code variable> = start_cpp([support_code variable]) + <3 quotations to start big comment with code in, typically going over many lines.>"""
frame = inspect.currentframe().f_back
info = inspect.getframeinfo(frame)
if hash_str==None:
return '#line %i "%s"\n'%(info[1],info[0])
else:
h = hashlib.md5()
h.update(hash_str)
hash_val = h.hexdigest()
return '#line %i "%s" // %s\n'%(info[1],info[0],hash_val)
| [
[
1,
0,
0.5,
0.0333,
0,
0.66,
0,
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0,
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[
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[
2,
0,
0.8333,
0.3667,
0,
0.66,
... | [
"import inspect",
"import hashlib",
"def start_cpp(hash_str = None):\n \"\"\"This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for work... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import sys
import os.path
import tempfile
import shutil
from distutils.core import setup, Extension
import distutils.ccompiler
import distutils.dep_util
try:
__default_compiler = distutils.ccompiler.new_compiler()
except:
__default_compiler = None
def make_mod(name, base, source, openCL = False):
"""Uses distutils to compile a python module - really just a set of hacks to allow this to be done 'on demand', so it only compiles if the module does not exist or is older than the current source, and after compilation the program can continue on its merry way, and immediatly import the just compiled module. Note that on failure erros can be thrown - its your choice to catch them or not. name is the modules name, i.e. what you want to use with the import statement. base is the base directory for the module, which contains the source file - often you would want to set this to 'os.path.dirname(__file__)', assuming the .py file that imports the module is in the same directory as the code. It is this directory that the module is output to. source is the filename of the source code to compile, or alternativly a list of filenames. openCL indicates if OpenCL is used by the module, in which case it does all the necesary setup - done like this so these setting can be kept centralised, so when they need to be different for a new platform they only have to be changed in one place."""
if __default_compiler==None: raise Exception('No compiler!')
# Work out the various file names - check if we actually need to do anything...
if not isinstance(source, list): source = [source]
source_path = map(lambda s: os.path.join(base, s), source)
library_path = os.path.join(base, __default_compiler.shared_object_filename(name))
if reduce(lambda a,b: a or b, map(lambda s: distutils.dep_util.newer(s, library_path), source_path)):
try:
print 'b'
# Backup the argv variable and create a temporary directory to do all work in...
old_argv = sys.argv[:]
temp_dir = tempfile.mkdtemp()
# Prepare the extension...
sys.argv = ['','build_ext','--build-lib', base, '--build-temp', temp_dir]
comp_path = filter(lambda s: not s.endswith('.h'), source_path)
depends = filter(lambda s: s.endswith('.h'), source_path)
if openCL:
ext = Extension(name, comp_path, include_dirs=['/usr/local/cuda/include', '/opt/AMDAPP/include'], libraries = ['OpenCL'], library_dirs = ['/usr/lib64/nvidia', '/opt/AMDAPP/lib/x86_64'], depends=depends)
else:
ext = Extension(name, comp_path, depends=depends)
# Compile...
setup(name=name, version='1.0.0', ext_modules=[ext])
finally:
# Cleanup the argv variable and the temporary directory...
sys.argv = old_argv
shutil.rmtree(temp_dir, True)
| [
[
1,
0,
0.2031,
0.0156,
0,
0.66,
0,
509,
0,
1,
0,
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509,
0,
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],
[
1,
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0.2188,
0.0156,
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0,
0,
79,
0,
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],
[
1,
0,
0.2344,
0.0156,
0,
0.6... | [
"import sys",
"import os.path",
"import tempfile",
"import shutil",
"from distutils.core import setup, Extension",
"import distutils.ccompiler",
"import distutils.dep_util",
"try:\n __default_compiler = distutils.ccompiler.new_compiler()\nexcept:\n __default_compiler = None",
" __default_compiler... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import pydoc
import inspect
class DocGen:
"""A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code."""
def __init__(self, name, title = None, summary = None):
"""name is the module name - primarilly used for the file names. title is the title used as applicable - if not provide it just uses the name. summary is an optional line to go below the title."""
if title==None: title = name
if summary==None: summary = title
self.doc = pydoc.HTMLDoc()
self.html = open('%s.html'%name,'w')
self.html.write('<html>\n')
self.html.write('<head>\n')
self.html.write('<title>%s</title>\n'%title)
self.html.write('</head>\n')
self.html.write('<body>\n')
self.html_variables = ''
self.html_functions = ''
self.html_classes = ''
self.wiki = open('%s.wiki'%name,'w')
self.wiki.write('#summary %s\n\n'%summary)
self.wiki.write('= %s= \n\n'%title)
self.wiki_variables = ''
self.wiki_functions = ''
self.wiki_classes = ''
def __del__(self):
if self.html_variables!='':
self.html.write(self.doc.bigsection('Synonyms', '#ffffff', '#8d50ff', self.html_variables))
if self.html_functions!='':
self.html.write(self.doc.bigsection('Functions', '#ffffff', '#eeaa77', self.html_functions))
if self.html_classes!='':
self.html.write(self.doc.bigsection('Classes', '#ffffff', '#ee77aa', self.html_classes))
self.html.write('</body>\n')
self.html.write('</html>\n')
self.html.close()
if self.wiki_variables!='':
self.wiki.write('= Variables =\n\n')
self.wiki.write(self.wiki_variables)
self.wiki.write('\n')
if self.wiki_functions!='':
self.wiki.write('= Functions =\n\n')
self.wiki.write(self.wiki_functions)
self.wiki.write('\n')
if self.wiki_classes!='':
self.wiki.write('= Classes =\n\n')
self.wiki.write(self.wiki_classes)
self.wiki.write('\n')
self.wiki.close()
def addFile(self, fn, title, fls = True):
"""Given a filename and section title adds the contents of said file to the output. Various flags influence how this works."""
html = []
wiki = []
for i, line in enumerate(open(fn,'r').readlines()):
hl = line.replace('\n', '')
if i==0 and fls:
hl = '<strong>' + hl + '</strong>'
for ext in ['py','txt']:
if '.%s - '%ext in hl:
s = hl.split('.%s - '%ext, 1)
hl = '<i>' + s[0] + '.%s</i> - '%ext + s[1]
html.append(hl)
wl = line.strip()
if i==0 and fls:
wl = '*%s*'%wl
for ext in ['py','txt']:
if '.%s - '%ext in wl:
s = wl.split('.%s - '%ext, 1)
wl = '`' + s[0] + '.%s` - '%ext + s[1] + '\n'
wiki.append(wl)
self.html.write(self.doc.bigsection(title, '#ffffff', '#7799ee', '<br/>'.join(html)))
self.wiki.write('== %s ==\n'%title)
self.wiki.write('\n'.join(wiki))
self.wiki.write('----\n\n')
def addVariable(self, var, desc):
"""Adds a variable to the documentation. Given the nature of this you provide it as a pair of strings - one referencing the variable, the other some kind of description of its use etc.."""
self.html_variables += '<strong>%s</strong><br/>'%var
self.html_variables += '%s<br/><br/>\n'%desc
self.wiki_variables += '*`%s`*\n'%var
self.wiki_variables += ' %s\n\n'%desc
def addFunction(self, func):
"""Adds a function to the documentation. You provide the actual function instance."""
self.html_functions += self.doc.docroutine(func).replace(' ',' ')
self.html_functions += '\n'
name = func.__name__
args, varargs, keywords, defaults = inspect.getargspec(func)
doc = inspect.getdoc(func)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
self.wiki_functions += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_functions += ' %s\n\n'%doc
def addClass(self, cls):
"""Adds a class to the documentation. You provide the actual class object."""
self.html_classes += self.doc.docclass(cls).replace(' ',' ')
self.html_classes += '\n'
name = cls.__name__
parents = filter(lambda a: a!=cls, inspect.getmro(cls))
doc = inspect.getdoc(cls)
par_str = ''
if len(parents)!=0:
par_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda p: p.__name__, parents))
self.wiki_classes += '== %s(%s) ==\n'%(name, par_str)
self.wiki_classes += ' %s\n\n'%doc
methods = inspect.getmembers(cls, inspect.ismethod)
def method_key(pair):
if pair[0]=='__init__': return '___'
else: return pair[0]
methods.sort(key=method_key)
for name, method in methods:
if not name.startswith('_%s'%cls.__name__):
args, varargs, keywords, defaults = inspect.getargspec(method)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
def fetch_doc(cls, name):
try:
method = getattr(cls, name)
if method.__doc__!=None: return inspect.getdoc(method)
except: pass
for parent in filter(lambda a: a!=cls, inspect.getmro(cls)):
ret = fetch_doc(parent, name)
if ret!=None: return ret
return None
doc = fetch_doc(cls, name)
self.wiki_classes += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_classes += ' %s\n\n'%doc
variables = inspect.getmembers(cls, lambda x: isinstance(x, int) or isinstance(x, str) or isinstance(x, float))
for name, var in variables:
if not name.startswith('__'):
self.wiki_classes += '*`%s`* = %s\n\n'%(name, str(var))
| [
[
1,
0,
0.0634,
0.0049,
0,
0.66,
0,
291,
0,
1,
0,
0,
291,
0,
0
],
[
1,
0,
0.0683,
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0,
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878,
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],
[
3,
0,
0.5439,
0.9171,
0,
0.6... | [
"import pydoc",
"import inspect",
"class DocGen:\n \"\"\"A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code.\"\"\"\n def __init__(self, name, ... |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from ctypes import *
def setProcName(name):
"""Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differing amounts in differing cases."""
# Call the process control function...
libc = cdll.LoadLibrary('libc.so.6')
libc.prctl(15, c_char_p(name), 0, 0, 0)
# Update argv...
charPP = POINTER(POINTER(c_char))
argv = charPP.in_dll(libc,'_dl_argv')
size = libc.strlen(argv[0])
libc.strncpy(argv[0],c_char_p(name),size)
if __name__=='__main__':
# Quick test that it works...
import os
ps1 = 'ps'
ps2 = 'ps -f'
os.system(ps1)
os.system(ps2)
setProcName('wibble_wobble')
os.system(ps1)
os.system(ps2)
| [
[
1,
0,
0.3636,
0.0227,
0,
0.66,
0,
182,
0,
1,
0,
0,
182,
0,
0
],
[
2,
0,
0.5682,
0.25,
0,
0.66,
0.5,
903,
0,
1,
0,
0,
0,
0,
9
],
[
8,
1,
0.4773,
0.0227,
1,
0.13,
... | [
"from ctypes import *",
"def setProcName(name):\n \"\"\"Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differin... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import multiprocessing as mp
import multiprocessing.synchronize # To make sure we have all the functionality.
import types
import marshal
import unittest
def repeat(x):
"""A generator that repeats the input forever - can be used with the mp_map function to give data to a function that is constant."""
while True: yield x
def run_code(code,args):
"""Internal use function that does the work in each process."""
code = marshal.loads(code)
func = types.FunctionType(code, globals(), '_')
return func(*args)
def mp_map(func, *iters, **keywords):
"""A multiprocess version of the map function. Note that func must limit itself to the data provided - if it accesses anything else (globals, locals to its definition.) it will fail. There is a repeat generator provided in this module to work around such issues. Note that, unlike map, this iterates the length of the shortest of inputs, rather than the longest - whilst this makes it not a perfect substitute it makes passing constant argumenmts easier as they can just repeat for infinity."""
if 'pool' in keywords: pool = keywords['pool']
else: pool = mp.Pool()
code = marshal.dumps(func.func_code)
jobs = []
for args in zip(*iters):
jobs.append(pool.apply_async(run_code,(code,args)))
for i in xrange(len(jobs)):
jobs[i] = jobs[i].get()
return jobs
class TestMpMap(unittest.TestCase):
def test_simple1(self):
data = ['a','b','c','d']
def noop(data):
return data
data_noop = mp_map(noop, data)
self.assertEqual(data, data_noop)
def test_simple2(self):
data = [x for x in xrange(1000)]
data_double = mp_map(lambda a: a*2, data)
self.assertEqual(map(lambda a: a*2,data), data_double)
def test_gen(self):
def gen():
for i in xrange(100): yield i
data_double = mp_map(lambda a: a*2, gen())
self.assertEqual(map(lambda a: a*2,gen()), data_double)
def test_repeat(self):
def mult(a,b):
return a*b
data = [x for x in xrange(50,5000,5)]
data_triple = mp_map(mult, data, repeat(3))
self.assertEqual(map(lambda a: a*3,data),data_triple)
def test_none(self):
data = []
data_sqr = mp_map(lambda x: x*x, data)
self.assertEqual([],data_sqr)
if __name__ == '__main__':
unittest.main()
| [
[
1,
0,
0.1456,
0.0097,
0,
0.66,
0,
901,
0,
1,
0,
0,
901,
0,
0
],
[
1,
0,
0.1553,
0.0097,
0,
0.66,
0.1111,
99,
0,
1,
0,
0,
99,
0,
0
],
[
1,
0,
0.1748,
0.0097,
0,
0.... | [
"import multiprocessing as mp",
"import multiprocessing.synchronize # To make sure we have all the functionality.",
"import types",
"import marshal",
"import unittest",
"def repeat(x):\n \"\"\"A generator that repeats the input forever - can be used with the mp_map function to give data to a function tha... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from utils.start_cpp import start_cpp
# Defines helper functions for accessing numpy arrays...
numpy_util_code = start_cpp() + """
#ifndef NUMPY_UTIL_CODE
#define NUMPY_UTIL_CODE
float & Float1D(PyArrayObject * arr, int index = 0)
{
return *(float*)(arr->data + index*arr->strides[0]);
}
float & Float2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
float & Float3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
unsigned char & Byte1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index*arr->strides[0]);
}
unsigned char & Byte2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
unsigned char & Byte3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
int & Int1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index*arr->strides[0]);
}
int & Int2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
int & Int3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
#endif
"""
| [
[
1,
0,
0.1923,
0.0128,
0,
0.66,
0,
972,
0,
1,
0,
0,
972,
0,
0
],
[
14,
0,
0.6282,
0.7564,
0,
0.66,
1,
799,
4,
0,
0,
0,
0,
0,
1
]
] | [
"from utils.start_cpp import start_cpp",
"numpy_util_code = start_cpp() + \"\"\"\n#ifndef NUMPY_UTIL_CODE\n#define NUMPY_UTIL_CODE\n\nfloat & Float1D(PyArrayObject * arr, int index = 0)\n{\n return *(float*)(arr->data + index*arr->strides[0]);\n}"
] |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import cvarray
import mp_map
import prog_bar
import numpy_help_cpp
import python_obj_cpp
import matrix_cpp
import gamma_cpp
import setProcName
import start_cpp
import make
import doc_gen
# Setup...
doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of miscellaneous stuff - most modules depend on this.')
doc.addFile('readme.txt', 'Overview')
# Variables...
doc.addVariable('numpy_help_cpp.numpy_util_code', 'Assorted utility functions for accessing numpy arrays within scipy.weave C++ code.')
doc.addVariable('python_obj_cpp.python_obj_code', 'Assorted utility functions for interfacing with python objects from scipy.weave C++ code.')
doc.addVariable('matrix_cpp.matrix_code', 'Matrix manipulation routines for use in scipy.weave C++')
doc.addVariable('gamma_cpp.gamma_code', 'Gamma and related functions for use in scipy.weave C++')
# Functions...
doc.addFunction(make.make_mod)
doc.addFunction(cvarray.cv2array)
doc.addFunction(cvarray.array2cv)
doc.addFunction(mp_map.repeat)
doc.addFunction(mp_map.mp_map)
doc.addFunction(setProcName.setProcName)
doc.addFunction(start_cpp.start_cpp)
doc.addFunction(make.make_mod)
# Classes...
doc.addClass(prog_bar.ProgBar)
doc.addClass(doc_gen.DocGen)
| [
[
1,
0,
0.2857,
0.0179,
0,
0.66,
0,
192,
0,
1,
0,
0,
192,
0,
0
],
[
1,
0,
0.3036,
0.0179,
0,
0.66,
0.0385,
905,
0,
1,
0,
0,
905,
0,
0
],
[
1,
0,
0.3214,
0.0179,
0,
... | [
"import cvarray",
"import mp_map",
"import prog_bar",
"import numpy_help_cpp",
"import python_obj_cpp",
"import matrix_cpp",
"import gamma_cpp",
"import setProcName",
"import start_cpp",
"import make",
"import doc_gen",
"doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of misc... |
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import unittest
import random
import math
from scipy.special import gammaln, psi, polygamma
from scipy import weave
from utils.start_cpp import start_cpp
# Provides various gamma-related functions...
gamma_code = start_cpp() + """
#ifndef GAMMA_CODE
#define GAMMA_CODE
#include <cmath>
// Returns the natural logarithm of the Gamma function...
// (Uses Lanczos's approximation.)
double lnGamma(double z)
{
static const double coeff[9] = {0.99999999999980993, 676.5203681218851, -1259.1392167224028, 771.32342877765313, -176.61502916214059, 12.507343278686905, -0.13857109526572012, 9.9843695780195716e-6, 1.5056327351493116e-7};
if (z<0.5)
{
// Use reflection formula, as approximation doesn't work down here...
return log(M_PI) - log(sin(M_PI*z)) - lnGamma(1.0-z);
}
else
{
double x = coeff[0];
for (int i=1;i<9;i++) x += coeff[i]/(z+i-1);
double t = z + 6.5;
return log(sqrt(2.0*M_PI)) + (z-0.5)*log(t) - t + log(x);
}
}
// Calculates the Digamma function, i.e. the derivative of the log of the Gamma function - uses a partial expansion of an infinite series to 4 terms that is good for high values, and an identity to express lower values in terms of higher values...
double digamma(double z)
{
static const double highVal = 13.0; // A bit of fiddling shows that the last term with this is of the order 1e-10, so we can expect at least 9 digits of accuracy past the decimal point.
double ret = 0.0;
while (z<highVal)
{
ret -= 1.0/z;
z += 1.0;
}
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz4 = iz2*iz2;
double iz6 = iz4*iz2;
ret += log(z) - iz1/2.0 - iz2/12.0 + iz4/120.0 - iz6/252.0;
return ret;
}
// Calculates the trigamma function - uses a partial expansion of an infinite series that is accurate for large values, and then uses an identity to express lower values in terms of higher values - same approach as for the digamma function basically...
double trigamma(double z)
{
static const double highVal = 8.0;
double ret = 0.0;
while (z<highVal)
{
ret += 1.0/(z*z);
z += 1.0;
}
z -= 1.0;
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz3 = iz1*iz2;
double iz5 = iz3*iz2;
double iz7 = iz5*iz2;
double iz9 = iz7*iz2;
ret += iz1 - 0.5*iz2 + iz3/6.0 - iz5/30.0 + iz7/42.0 - iz9/30.0;
return ret;
}
#endif
"""
def lnGamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns the logorithm of the gamma function"""
code = start_cpp(gamma_code) + """
return_val = lnGamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def digamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the digamma function"""
code = start_cpp(gamma_code) + """
return_val = digamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def trigamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the trigamma function"""
code = start_cpp(gamma_code) + """
return_val = trigamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
class TestFuncs(unittest.TestCase):
"""Test code for the assorted gamma-related functions."""
def test_compile(self):
code = start_cpp(gamma_code) + """
"""
weave.inline(code, support_code=gamma_code)
def test_error_lngamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = lnGamma(z)
good = gammaln(z)
assert(math.fabs(own-good)<1e-12)
def test_error_digamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = digamma(z)
good = psi(z)
assert(math.fabs(own-good)<1e-9)
def test_error_trigamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = trigamma(z)
good = polygamma(1,z)
assert(math.fabs(own-good)<1e-9)
# If this file is run do the unit tests...
if __name__ == '__main__':
unittest.main()
| [
[
1,
0,
0.0818,
0.0063,
0,
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0,
88,
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0,
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0,
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],
[
1,
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0.0063,
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0,
715,
0,
0
],
[
1,
0,
0.0943,
0.0063,
0,
0.... | [
"import unittest",
"import random",
"import math",
"from scipy.special import gammaln, psi, polygamma",
"from scipy import weave",
"from utils.start_cpp import start_cpp",
"gamma_code = start_cpp() + \"\"\"\n#ifndef GAMMA_CODE\n#define GAMMA_CODE\n\n#include <cmath>\n\n// Returns the natural logarithm o... |
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import inspect
import hashlib
def start_cpp(hash_str = None):
"""This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for working around the fact the scipy.weave only recompiles if the hash of the code changes, but ignores the support_code - passing the support_code into start_cpp avoids this problem by putting its hash into the code and forcing a recompile when that code changes. Usage is <code variable> = start_cpp([support_code variable]) + <3 quotations to start big comment with code in, typically going over many lines.>"""
frame = inspect.currentframe().f_back
info = inspect.getframeinfo(frame)
if hash_str==None:
return '#line %i "%s"\n'%(info[1],info[0])
else:
h = hashlib.md5()
h.update(hash_str)
hash_val = h.hexdigest()
return '#line %i "%s" // %s\n'%(info[1],info[0],hash_val)
| [
[
1,
0,
0.5,
0.0333,
0,
0.66,
0,
878,
0,
1,
0,
0,
878,
0,
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],
[
1,
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0,
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],
[
2,
0,
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0.3667,
0,
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... | [
"import inspect",
"import hashlib",
"def start_cpp(hash_str = None):\n \"\"\"This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for work... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import sys
import os.path
import tempfile
import shutil
from distutils.core import setup, Extension
import distutils.ccompiler
import distutils.dep_util
try:
__default_compiler = distutils.ccompiler.new_compiler()
except:
__default_compiler = None
def make_mod(name, base, source, openCL = False):
"""Uses distutils to compile a python module - really just a set of hacks to allow this to be done 'on demand', so it only compiles if the module does not exist or is older than the current source, and after compilation the program can continue on its merry way, and immediatly import the just compiled module. Note that on failure erros can be thrown - its your choice to catch them or not. name is the modules name, i.e. what you want to use with the import statement. base is the base directory for the module, which contains the source file - often you would want to set this to 'os.path.dirname(__file__)', assuming the .py file that imports the module is in the same directory as the code. It is this directory that the module is output to. source is the filename of the source code to compile, or alternativly a list of filenames. openCL indicates if OpenCL is used by the module, in which case it does all the necesary setup - done like this so these setting can be kept centralised, so when they need to be different for a new platform they only have to be changed in one place."""
if __default_compiler==None: raise Exception('No compiler!')
# Work out the various file names - check if we actually need to do anything...
if not isinstance(source, list): source = [source]
source_path = map(lambda s: os.path.join(base, s), source)
library_path = os.path.join(base, __default_compiler.shared_object_filename(name))
if reduce(lambda a,b: a or b, map(lambda s: distutils.dep_util.newer(s, library_path), source_path)):
try:
print 'b'
# Backup the argv variable and create a temporary directory to do all work in...
old_argv = sys.argv[:]
temp_dir = tempfile.mkdtemp()
# Prepare the extension...
sys.argv = ['','build_ext','--build-lib', base, '--build-temp', temp_dir]
comp_path = filter(lambda s: not s.endswith('.h'), source_path)
depends = filter(lambda s: s.endswith('.h'), source_path)
if openCL:
ext = Extension(name, comp_path, include_dirs=['/usr/local/cuda/include', '/opt/AMDAPP/include'], libraries = ['OpenCL'], library_dirs = ['/usr/lib64/nvidia', '/opt/AMDAPP/lib/x86_64'], depends=depends)
else:
ext = Extension(name, comp_path, depends=depends)
# Compile...
setup(name=name, version='1.0.0', ext_modules=[ext])
finally:
# Cleanup the argv variable and the temporary directory...
sys.argv = old_argv
shutil.rmtree(temp_dir, True)
| [
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[
1,
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0.6... | [
"import sys",
"import os.path",
"import tempfile",
"import shutil",
"from distutils.core import setup, Extension",
"import distutils.ccompiler",
"import distutils.dep_util",
"try:\n __default_compiler = distutils.ccompiler.new_compiler()\nexcept:\n __default_compiler = None",
" __default_compiler... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import pydoc
import inspect
class DocGen:
"""A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code."""
def __init__(self, name, title = None, summary = None):
"""name is the module name - primarilly used for the file names. title is the title used as applicable - if not provide it just uses the name. summary is an optional line to go below the title."""
if title==None: title = name
if summary==None: summary = title
self.doc = pydoc.HTMLDoc()
self.html = open('%s.html'%name,'w')
self.html.write('<html>\n')
self.html.write('<head>\n')
self.html.write('<title>%s</title>\n'%title)
self.html.write('</head>\n')
self.html.write('<body>\n')
self.html_variables = ''
self.html_functions = ''
self.html_classes = ''
self.wiki = open('%s.wiki'%name,'w')
self.wiki.write('#summary %s\n\n'%summary)
self.wiki.write('= %s= \n\n'%title)
self.wiki_variables = ''
self.wiki_functions = ''
self.wiki_classes = ''
def __del__(self):
if self.html_variables!='':
self.html.write(self.doc.bigsection('Synonyms', '#ffffff', '#8d50ff', self.html_variables))
if self.html_functions!='':
self.html.write(self.doc.bigsection('Functions', '#ffffff', '#eeaa77', self.html_functions))
if self.html_classes!='':
self.html.write(self.doc.bigsection('Classes', '#ffffff', '#ee77aa', self.html_classes))
self.html.write('</body>\n')
self.html.write('</html>\n')
self.html.close()
if self.wiki_variables!='':
self.wiki.write('= Variables =\n\n')
self.wiki.write(self.wiki_variables)
self.wiki.write('\n')
if self.wiki_functions!='':
self.wiki.write('= Functions =\n\n')
self.wiki.write(self.wiki_functions)
self.wiki.write('\n')
if self.wiki_classes!='':
self.wiki.write('= Classes =\n\n')
self.wiki.write(self.wiki_classes)
self.wiki.write('\n')
self.wiki.close()
def addFile(self, fn, title, fls = True):
"""Given a filename and section title adds the contents of said file to the output. Various flags influence how this works."""
html = []
wiki = []
for i, line in enumerate(open(fn,'r').readlines()):
hl = line.replace('\n', '')
if i==0 and fls:
hl = '<strong>' + hl + '</strong>'
for ext in ['py','txt']:
if '.%s - '%ext in hl:
s = hl.split('.%s - '%ext, 1)
hl = '<i>' + s[0] + '.%s</i> - '%ext + s[1]
html.append(hl)
wl = line.strip()
if i==0 and fls:
wl = '*%s*'%wl
for ext in ['py','txt']:
if '.%s - '%ext in wl:
s = wl.split('.%s - '%ext, 1)
wl = '`' + s[0] + '.%s` - '%ext + s[1] + '\n'
wiki.append(wl)
self.html.write(self.doc.bigsection(title, '#ffffff', '#7799ee', '<br/>'.join(html)))
self.wiki.write('== %s ==\n'%title)
self.wiki.write('\n'.join(wiki))
self.wiki.write('----\n\n')
def addVariable(self, var, desc):
"""Adds a variable to the documentation. Given the nature of this you provide it as a pair of strings - one referencing the variable, the other some kind of description of its use etc.."""
self.html_variables += '<strong>%s</strong><br/>'%var
self.html_variables += '%s<br/><br/>\n'%desc
self.wiki_variables += '*`%s`*\n'%var
self.wiki_variables += ' %s\n\n'%desc
def addFunction(self, func):
"""Adds a function to the documentation. You provide the actual function instance."""
self.html_functions += self.doc.docroutine(func).replace(' ',' ')
self.html_functions += '\n'
name = func.__name__
args, varargs, keywords, defaults = inspect.getargspec(func)
doc = inspect.getdoc(func)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
self.wiki_functions += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_functions += ' %s\n\n'%doc
def addClass(self, cls):
"""Adds a class to the documentation. You provide the actual class object."""
self.html_classes += self.doc.docclass(cls).replace(' ',' ')
self.html_classes += '\n'
name = cls.__name__
parents = filter(lambda a: a!=cls, inspect.getmro(cls))
doc = inspect.getdoc(cls)
par_str = ''
if len(parents)!=0:
par_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda p: p.__name__, parents))
self.wiki_classes += '== %s(%s) ==\n'%(name, par_str)
self.wiki_classes += ' %s\n\n'%doc
methods = inspect.getmembers(cls, inspect.ismethod)
def method_key(pair):
if pair[0]=='__init__': return '___'
else: return pair[0]
methods.sort(key=method_key)
for name, method in methods:
if not name.startswith('_%s'%cls.__name__):
args, varargs, keywords, defaults = inspect.getargspec(method)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
def fetch_doc(cls, name):
try:
method = getattr(cls, name)
if method.__doc__!=None: return inspect.getdoc(method)
except: pass
for parent in filter(lambda a: a!=cls, inspect.getmro(cls)):
ret = fetch_doc(parent, name)
if ret!=None: return ret
return None
doc = fetch_doc(cls, name)
self.wiki_classes += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_classes += ' %s\n\n'%doc
variables = inspect.getmembers(cls, lambda x: isinstance(x, int) or isinstance(x, str) or isinstance(x, float))
for name, var in variables:
if not name.startswith('__'):
self.wiki_classes += '*`%s`* = %s\n\n'%(name, str(var))
| [
[
1,
0,
0.0634,
0.0049,
0,
0.66,
0,
291,
0,
1,
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291,
0,
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],
[
1,
0,
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0.0049,
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878,
0,
1,
0,
0,
878,
0,
0
],
[
3,
0,
0.5439,
0.9171,
0,
0.6... | [
"import pydoc",
"import inspect",
"class DocGen:\n \"\"\"A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code.\"\"\"\n def __init__(self, name, ... |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from ctypes import *
def setProcName(name):
"""Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differing amounts in differing cases."""
# Call the process control function...
libc = cdll.LoadLibrary('libc.so.6')
libc.prctl(15, c_char_p(name), 0, 0, 0)
# Update argv...
charPP = POINTER(POINTER(c_char))
argv = charPP.in_dll(libc,'_dl_argv')
size = libc.strlen(argv[0])
libc.strncpy(argv[0],c_char_p(name),size)
if __name__=='__main__':
# Quick test that it works...
import os
ps1 = 'ps'
ps2 = 'ps -f'
os.system(ps1)
os.system(ps2)
setProcName('wibble_wobble')
os.system(ps1)
os.system(ps2)
| [
[
1,
0,
0.3636,
0.0227,
0,
0.66,
0,
182,
0,
1,
0,
0,
182,
0,
0
],
[
2,
0,
0.5682,
0.25,
0,
0.66,
0.5,
903,
0,
1,
0,
0,
0,
0,
9
],
[
8,
1,
0.4773,
0.0227,
1,
0.92,
... | [
"from ctypes import *",
"def setProcName(name):\n \"\"\"Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differin... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import multiprocessing as mp
import multiprocessing.synchronize # To make sure we have all the functionality.
import types
import marshal
import unittest
def repeat(x):
"""A generator that repeats the input forever - can be used with the mp_map function to give data to a function that is constant."""
while True: yield x
def run_code(code,args):
"""Internal use function that does the work in each process."""
code = marshal.loads(code)
func = types.FunctionType(code, globals(), '_')
return func(*args)
def mp_map(func, *iters, **keywords):
"""A multiprocess version of the map function. Note that func must limit itself to the data provided - if it accesses anything else (globals, locals to its definition.) it will fail. There is a repeat generator provided in this module to work around such issues. Note that, unlike map, this iterates the length of the shortest of inputs, rather than the longest - whilst this makes it not a perfect substitute it makes passing constant argumenmts easier as they can just repeat for infinity."""
if 'pool' in keywords: pool = keywords['pool']
else: pool = mp.Pool()
code = marshal.dumps(func.func_code)
jobs = []
for args in zip(*iters):
jobs.append(pool.apply_async(run_code,(code,args)))
for i in xrange(len(jobs)):
jobs[i] = jobs[i].get()
return jobs
class TestMpMap(unittest.TestCase):
def test_simple1(self):
data = ['a','b','c','d']
def noop(data):
return data
data_noop = mp_map(noop, data)
self.assertEqual(data, data_noop)
def test_simple2(self):
data = [x for x in xrange(1000)]
data_double = mp_map(lambda a: a*2, data)
self.assertEqual(map(lambda a: a*2,data), data_double)
def test_gen(self):
def gen():
for i in xrange(100): yield i
data_double = mp_map(lambda a: a*2, gen())
self.assertEqual(map(lambda a: a*2,gen()), data_double)
def test_repeat(self):
def mult(a,b):
return a*b
data = [x for x in xrange(50,5000,5)]
data_triple = mp_map(mult, data, repeat(3))
self.assertEqual(map(lambda a: a*3,data),data_triple)
def test_none(self):
data = []
data_sqr = mp_map(lambda x: x*x, data)
self.assertEqual([],data_sqr)
if __name__ == '__main__':
unittest.main()
| [
[
1,
0,
0.1456,
0.0097,
0,
0.66,
0,
901,
0,
1,
0,
0,
901,
0,
0
],
[
1,
0,
0.1553,
0.0097,
0,
0.66,
0.1111,
99,
0,
1,
0,
0,
99,
0,
0
],
[
1,
0,
0.1748,
0.0097,
0,
0.... | [
"import multiprocessing as mp",
"import multiprocessing.synchronize # To make sure we have all the functionality.",
"import types",
"import marshal",
"import unittest",
"def repeat(x):\n \"\"\"A generator that repeats the input forever - can be used with the mp_map function to give data to a function tha... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from utils.start_cpp import start_cpp
# Defines helper functions for accessing numpy arrays...
numpy_util_code = start_cpp() + """
#ifndef NUMPY_UTIL_CODE
#define NUMPY_UTIL_CODE
float & Float1D(PyArrayObject * arr, int index = 0)
{
return *(float*)(arr->data + index*arr->strides[0]);
}
float & Float2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
float & Float3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
unsigned char & Byte1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index*arr->strides[0]);
}
unsigned char & Byte2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
unsigned char & Byte3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
int & Int1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index*arr->strides[0]);
}
int & Int2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
int & Int3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
#endif
"""
| [
[
1,
0,
0.1923,
0.0128,
0,
0.66,
0,
972,
0,
1,
0,
0,
972,
0,
0
],
[
14,
0,
0.6282,
0.7564,
0,
0.66,
1,
799,
4,
0,
0,
0,
0,
0,
1
]
] | [
"from utils.start_cpp import start_cpp",
"numpy_util_code = start_cpp() + \"\"\"\n#ifndef NUMPY_UTIL_CODE\n#define NUMPY_UTIL_CODE\n\nfloat & Float1D(PyArrayObject * arr, int index = 0)\n{\n return *(float*)(arr->data + index*arr->strides[0]);\n}"
] |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import cvarray
import mp_map
import prog_bar
import numpy_help_cpp
import python_obj_cpp
import matrix_cpp
import gamma_cpp
import setProcName
import start_cpp
import make
import doc_gen
# Setup...
doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of miscellaneous stuff - most modules depend on this.')
doc.addFile('readme.txt', 'Overview')
# Variables...
doc.addVariable('numpy_help_cpp.numpy_util_code', 'Assorted utility functions for accessing numpy arrays within scipy.weave C++ code.')
doc.addVariable('python_obj_cpp.python_obj_code', 'Assorted utility functions for interfacing with python objects from scipy.weave C++ code.')
doc.addVariable('matrix_cpp.matrix_code', 'Matrix manipulation routines for use in scipy.weave C++')
doc.addVariable('gamma_cpp.gamma_code', 'Gamma and related functions for use in scipy.weave C++')
# Functions...
doc.addFunction(make.make_mod)
doc.addFunction(cvarray.cv2array)
doc.addFunction(cvarray.array2cv)
doc.addFunction(mp_map.repeat)
doc.addFunction(mp_map.mp_map)
doc.addFunction(setProcName.setProcName)
doc.addFunction(start_cpp.start_cpp)
doc.addFunction(make.make_mod)
# Classes...
doc.addClass(prog_bar.ProgBar)
doc.addClass(doc_gen.DocGen)
| [
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1,
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[
1,
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... | [
"import cvarray",
"import mp_map",
"import prog_bar",
"import numpy_help_cpp",
"import python_obj_cpp",
"import matrix_cpp",
"import gamma_cpp",
"import setProcName",
"import start_cpp",
"import make",
"import doc_gen",
"doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of misc... |
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import unittest
import random
import math
from scipy.special import gammaln, psi, polygamma
from scipy import weave
from utils.start_cpp import start_cpp
# Provides various gamma-related functions...
gamma_code = start_cpp() + """
#ifndef GAMMA_CODE
#define GAMMA_CODE
#include <cmath>
// Returns the natural logarithm of the Gamma function...
// (Uses Lanczos's approximation.)
double lnGamma(double z)
{
static const double coeff[9] = {0.99999999999980993, 676.5203681218851, -1259.1392167224028, 771.32342877765313, -176.61502916214059, 12.507343278686905, -0.13857109526572012, 9.9843695780195716e-6, 1.5056327351493116e-7};
if (z<0.5)
{
// Use reflection formula, as approximation doesn't work down here...
return log(M_PI) - log(sin(M_PI*z)) - lnGamma(1.0-z);
}
else
{
double x = coeff[0];
for (int i=1;i<9;i++) x += coeff[i]/(z+i-1);
double t = z + 6.5;
return log(sqrt(2.0*M_PI)) + (z-0.5)*log(t) - t + log(x);
}
}
// Calculates the Digamma function, i.e. the derivative of the log of the Gamma function - uses a partial expansion of an infinite series to 4 terms that is good for high values, and an identity to express lower values in terms of higher values...
double digamma(double z)
{
static const double highVal = 13.0; // A bit of fiddling shows that the last term with this is of the order 1e-10, so we can expect at least 9 digits of accuracy past the decimal point.
double ret = 0.0;
while (z<highVal)
{
ret -= 1.0/z;
z += 1.0;
}
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz4 = iz2*iz2;
double iz6 = iz4*iz2;
ret += log(z) - iz1/2.0 - iz2/12.0 + iz4/120.0 - iz6/252.0;
return ret;
}
// Calculates the trigamma function - uses a partial expansion of an infinite series that is accurate for large values, and then uses an identity to express lower values in terms of higher values - same approach as for the digamma function basically...
double trigamma(double z)
{
static const double highVal = 8.0;
double ret = 0.0;
while (z<highVal)
{
ret += 1.0/(z*z);
z += 1.0;
}
z -= 1.0;
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz3 = iz1*iz2;
double iz5 = iz3*iz2;
double iz7 = iz5*iz2;
double iz9 = iz7*iz2;
ret += iz1 - 0.5*iz2 + iz3/6.0 - iz5/30.0 + iz7/42.0 - iz9/30.0;
return ret;
}
#endif
"""
def lnGamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns the logorithm of the gamma function"""
code = start_cpp(gamma_code) + """
return_val = lnGamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def digamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the digamma function"""
code = start_cpp(gamma_code) + """
return_val = digamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def trigamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the trigamma function"""
code = start_cpp(gamma_code) + """
return_val = trigamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
class TestFuncs(unittest.TestCase):
"""Test code for the assorted gamma-related functions."""
def test_compile(self):
code = start_cpp(gamma_code) + """
"""
weave.inline(code, support_code=gamma_code)
def test_error_lngamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = lnGamma(z)
good = gammaln(z)
assert(math.fabs(own-good)<1e-12)
def test_error_digamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = digamma(z)
good = psi(z)
assert(math.fabs(own-good)<1e-9)
def test_error_trigamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = trigamma(z)
good = polygamma(1,z)
assert(math.fabs(own-good)<1e-9)
# If this file is run do the unit tests...
if __name__ == '__main__':
unittest.main()
| [
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0.... | [
"import unittest",
"import random",
"import math",
"from scipy.special import gammaln, psi, polygamma",
"from scipy import weave",
"from utils.start_cpp import start_cpp",
"gamma_code = start_cpp() + \"\"\"\n#ifndef GAMMA_CODE\n#define GAMMA_CODE\n\n#include <cmath>\n\n// Returns the natural logarithm o... |
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import inspect
import hashlib
def start_cpp(hash_str = None):
"""This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for working around the fact the scipy.weave only recompiles if the hash of the code changes, but ignores the support_code - passing the support_code into start_cpp avoids this problem by putting its hash into the code and forcing a recompile when that code changes. Usage is <code variable> = start_cpp([support_code variable]) + <3 quotations to start big comment with code in, typically going over many lines.>"""
frame = inspect.currentframe().f_back
info = inspect.getframeinfo(frame)
if hash_str==None:
return '#line %i "%s"\n'%(info[1],info[0])
else:
h = hashlib.md5()
h.update(hash_str)
hash_val = h.hexdigest()
return '#line %i "%s" // %s\n'%(info[1],info[0],hash_val)
| [
[
1,
0,
0.5,
0.0333,
0,
0.66,
0,
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0,
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[
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0,
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],
[
2,
0,
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0.3667,
0,
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... | [
"import inspect",
"import hashlib",
"def start_cpp(hash_str = None):\n \"\"\"This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for work... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import sys
import os.path
import tempfile
import shutil
from distutils.core import setup, Extension
import distutils.ccompiler
import distutils.dep_util
try:
__default_compiler = distutils.ccompiler.new_compiler()
except:
__default_compiler = None
def make_mod(name, base, source, openCL = False):
"""Uses distutils to compile a python module - really just a set of hacks to allow this to be done 'on demand', so it only compiles if the module does not exist or is older than the current source, and after compilation the program can continue on its merry way, and immediatly import the just compiled module. Note that on failure erros can be thrown - its your choice to catch them or not. name is the modules name, i.e. what you want to use with the import statement. base is the base directory for the module, which contains the source file - often you would want to set this to 'os.path.dirname(__file__)', assuming the .py file that imports the module is in the same directory as the code. It is this directory that the module is output to. source is the filename of the source code to compile, or alternativly a list of filenames. openCL indicates if OpenCL is used by the module, in which case it does all the necesary setup - done like this so these setting can be kept centralised, so when they need to be different for a new platform they only have to be changed in one place."""
if __default_compiler==None: raise Exception('No compiler!')
# Work out the various file names - check if we actually need to do anything...
if not isinstance(source, list): source = [source]
source_path = map(lambda s: os.path.join(base, s), source)
library_path = os.path.join(base, __default_compiler.shared_object_filename(name))
if reduce(lambda a,b: a or b, map(lambda s: distutils.dep_util.newer(s, library_path), source_path)):
try:
print 'b'
# Backup the argv variable and create a temporary directory to do all work in...
old_argv = sys.argv[:]
temp_dir = tempfile.mkdtemp()
# Prepare the extension...
sys.argv = ['','build_ext','--build-lib', base, '--build-temp', temp_dir]
comp_path = filter(lambda s: not s.endswith('.h'), source_path)
depends = filter(lambda s: s.endswith('.h'), source_path)
if openCL:
ext = Extension(name, comp_path, include_dirs=['/usr/local/cuda/include', '/opt/AMDAPP/include'], libraries = ['OpenCL'], library_dirs = ['/usr/lib64/nvidia', '/opt/AMDAPP/lib/x86_64'], depends=depends)
else:
ext = Extension(name, comp_path, depends=depends)
# Compile...
setup(name=name, version='1.0.0', ext_modules=[ext])
finally:
# Cleanup the argv variable and the temporary directory...
sys.argv = old_argv
shutil.rmtree(temp_dir, True)
| [
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[
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[
1,
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0.0156,
0,
0.6... | [
"import sys",
"import os.path",
"import tempfile",
"import shutil",
"from distutils.core import setup, Extension",
"import distutils.ccompiler",
"import distutils.dep_util",
"try:\n __default_compiler = distutils.ccompiler.new_compiler()\nexcept:\n __default_compiler = None",
" __default_compiler... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import pydoc
import inspect
class DocGen:
"""A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code."""
def __init__(self, name, title = None, summary = None):
"""name is the module name - primarilly used for the file names. title is the title used as applicable - if not provide it just uses the name. summary is an optional line to go below the title."""
if title==None: title = name
if summary==None: summary = title
self.doc = pydoc.HTMLDoc()
self.html = open('%s.html'%name,'w')
self.html.write('<html>\n')
self.html.write('<head>\n')
self.html.write('<title>%s</title>\n'%title)
self.html.write('</head>\n')
self.html.write('<body>\n')
self.html_variables = ''
self.html_functions = ''
self.html_classes = ''
self.wiki = open('%s.wiki'%name,'w')
self.wiki.write('#summary %s\n\n'%summary)
self.wiki.write('= %s= \n\n'%title)
self.wiki_variables = ''
self.wiki_functions = ''
self.wiki_classes = ''
def __del__(self):
if self.html_variables!='':
self.html.write(self.doc.bigsection('Synonyms', '#ffffff', '#8d50ff', self.html_variables))
if self.html_functions!='':
self.html.write(self.doc.bigsection('Functions', '#ffffff', '#eeaa77', self.html_functions))
if self.html_classes!='':
self.html.write(self.doc.bigsection('Classes', '#ffffff', '#ee77aa', self.html_classes))
self.html.write('</body>\n')
self.html.write('</html>\n')
self.html.close()
if self.wiki_variables!='':
self.wiki.write('= Variables =\n\n')
self.wiki.write(self.wiki_variables)
self.wiki.write('\n')
if self.wiki_functions!='':
self.wiki.write('= Functions =\n\n')
self.wiki.write(self.wiki_functions)
self.wiki.write('\n')
if self.wiki_classes!='':
self.wiki.write('= Classes =\n\n')
self.wiki.write(self.wiki_classes)
self.wiki.write('\n')
self.wiki.close()
def addFile(self, fn, title, fls = True):
"""Given a filename and section title adds the contents of said file to the output. Various flags influence how this works."""
html = []
wiki = []
for i, line in enumerate(open(fn,'r').readlines()):
hl = line.replace('\n', '')
if i==0 and fls:
hl = '<strong>' + hl + '</strong>'
for ext in ['py','txt']:
if '.%s - '%ext in hl:
s = hl.split('.%s - '%ext, 1)
hl = '<i>' + s[0] + '.%s</i> - '%ext + s[1]
html.append(hl)
wl = line.strip()
if i==0 and fls:
wl = '*%s*'%wl
for ext in ['py','txt']:
if '.%s - '%ext in wl:
s = wl.split('.%s - '%ext, 1)
wl = '`' + s[0] + '.%s` - '%ext + s[1] + '\n'
wiki.append(wl)
self.html.write(self.doc.bigsection(title, '#ffffff', '#7799ee', '<br/>'.join(html)))
self.wiki.write('== %s ==\n'%title)
self.wiki.write('\n'.join(wiki))
self.wiki.write('----\n\n')
def addVariable(self, var, desc):
"""Adds a variable to the documentation. Given the nature of this you provide it as a pair of strings - one referencing the variable, the other some kind of description of its use etc.."""
self.html_variables += '<strong>%s</strong><br/>'%var
self.html_variables += '%s<br/><br/>\n'%desc
self.wiki_variables += '*`%s`*\n'%var
self.wiki_variables += ' %s\n\n'%desc
def addFunction(self, func):
"""Adds a function to the documentation. You provide the actual function instance."""
self.html_functions += self.doc.docroutine(func).replace(' ',' ')
self.html_functions += '\n'
name = func.__name__
args, varargs, keywords, defaults = inspect.getargspec(func)
doc = inspect.getdoc(func)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
self.wiki_functions += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_functions += ' %s\n\n'%doc
def addClass(self, cls):
"""Adds a class to the documentation. You provide the actual class object."""
self.html_classes += self.doc.docclass(cls).replace(' ',' ')
self.html_classes += '\n'
name = cls.__name__
parents = filter(lambda a: a!=cls, inspect.getmro(cls))
doc = inspect.getdoc(cls)
par_str = ''
if len(parents)!=0:
par_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda p: p.__name__, parents))
self.wiki_classes += '== %s(%s) ==\n'%(name, par_str)
self.wiki_classes += ' %s\n\n'%doc
methods = inspect.getmembers(cls, inspect.ismethod)
def method_key(pair):
if pair[0]=='__init__': return '___'
else: return pair[0]
methods.sort(key=method_key)
for name, method in methods:
if not name.startswith('_%s'%cls.__name__):
args, varargs, keywords, defaults = inspect.getargspec(method)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
def fetch_doc(cls, name):
try:
method = getattr(cls, name)
if method.__doc__!=None: return inspect.getdoc(method)
except: pass
for parent in filter(lambda a: a!=cls, inspect.getmro(cls)):
ret = fetch_doc(parent, name)
if ret!=None: return ret
return None
doc = fetch_doc(cls, name)
self.wiki_classes += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_classes += ' %s\n\n'%doc
variables = inspect.getmembers(cls, lambda x: isinstance(x, int) or isinstance(x, str) or isinstance(x, float))
for name, var in variables:
if not name.startswith('__'):
self.wiki_classes += '*`%s`* = %s\n\n'%(name, str(var))
| [
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[
3,
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0.6... | [
"import pydoc",
"import inspect",
"class DocGen:\n \"\"\"A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code.\"\"\"\n def __init__(self, name, ... |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from ctypes import *
def setProcName(name):
"""Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differing amounts in differing cases."""
# Call the process control function...
libc = cdll.LoadLibrary('libc.so.6')
libc.prctl(15, c_char_p(name), 0, 0, 0)
# Update argv...
charPP = POINTER(POINTER(c_char))
argv = charPP.in_dll(libc,'_dl_argv')
size = libc.strlen(argv[0])
libc.strncpy(argv[0],c_char_p(name),size)
if __name__=='__main__':
# Quick test that it works...
import os
ps1 = 'ps'
ps2 = 'ps -f'
os.system(ps1)
os.system(ps2)
setProcName('wibble_wobble')
os.system(ps1)
os.system(ps2)
| [
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1,
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0.3636,
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0,
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[
8,
1,
0.4773,
0.0227,
1,
0.31,
... | [
"from ctypes import *",
"def setProcName(name):\n \"\"\"Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differin... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import multiprocessing as mp
import multiprocessing.synchronize # To make sure we have all the functionality.
import types
import marshal
import unittest
def repeat(x):
"""A generator that repeats the input forever - can be used with the mp_map function to give data to a function that is constant."""
while True: yield x
def run_code(code,args):
"""Internal use function that does the work in each process."""
code = marshal.loads(code)
func = types.FunctionType(code, globals(), '_')
return func(*args)
def mp_map(func, *iters, **keywords):
"""A multiprocess version of the map function. Note that func must limit itself to the data provided - if it accesses anything else (globals, locals to its definition.) it will fail. There is a repeat generator provided in this module to work around such issues. Note that, unlike map, this iterates the length of the shortest of inputs, rather than the longest - whilst this makes it not a perfect substitute it makes passing constant argumenmts easier as they can just repeat for infinity."""
if 'pool' in keywords: pool = keywords['pool']
else: pool = mp.Pool()
code = marshal.dumps(func.func_code)
jobs = []
for args in zip(*iters):
jobs.append(pool.apply_async(run_code,(code,args)))
for i in xrange(len(jobs)):
jobs[i] = jobs[i].get()
return jobs
class TestMpMap(unittest.TestCase):
def test_simple1(self):
data = ['a','b','c','d']
def noop(data):
return data
data_noop = mp_map(noop, data)
self.assertEqual(data, data_noop)
def test_simple2(self):
data = [x for x in xrange(1000)]
data_double = mp_map(lambda a: a*2, data)
self.assertEqual(map(lambda a: a*2,data), data_double)
def test_gen(self):
def gen():
for i in xrange(100): yield i
data_double = mp_map(lambda a: a*2, gen())
self.assertEqual(map(lambda a: a*2,gen()), data_double)
def test_repeat(self):
def mult(a,b):
return a*b
data = [x for x in xrange(50,5000,5)]
data_triple = mp_map(mult, data, repeat(3))
self.assertEqual(map(lambda a: a*3,data),data_triple)
def test_none(self):
data = []
data_sqr = mp_map(lambda x: x*x, data)
self.assertEqual([],data_sqr)
if __name__ == '__main__':
unittest.main()
| [
[
1,
0,
0.1456,
0.0097,
0,
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0,
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],
[
1,
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0,
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[
1,
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0,
0.... | [
"import multiprocessing as mp",
"import multiprocessing.synchronize # To make sure we have all the functionality.",
"import types",
"import marshal",
"import unittest",
"def repeat(x):\n \"\"\"A generator that repeats the input forever - can be used with the mp_map function to give data to a function tha... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from utils.start_cpp import start_cpp
# Defines helper functions for accessing numpy arrays...
numpy_util_code = start_cpp() + """
#ifndef NUMPY_UTIL_CODE
#define NUMPY_UTIL_CODE
float & Float1D(PyArrayObject * arr, int index = 0)
{
return *(float*)(arr->data + index*arr->strides[0]);
}
float & Float2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
float & Float3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
unsigned char & Byte1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index*arr->strides[0]);
}
unsigned char & Byte2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
unsigned char & Byte3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
int & Int1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index*arr->strides[0]);
}
int & Int2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
int & Int3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
#endif
"""
| [
[
1,
0,
0.1923,
0.0128,
0,
0.66,
0,
972,
0,
1,
0,
0,
972,
0,
0
],
[
14,
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0.7564,
0,
0.66,
1,
799,
4,
0,
0,
0,
0,
0,
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]
] | [
"from utils.start_cpp import start_cpp",
"numpy_util_code = start_cpp() + \"\"\"\n#ifndef NUMPY_UTIL_CODE\n#define NUMPY_UTIL_CODE\n\nfloat & Float1D(PyArrayObject * arr, int index = 0)\n{\n return *(float*)(arr->data + index*arr->strides[0]);\n}"
] |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import cvarray
import mp_map
import prog_bar
import numpy_help_cpp
import python_obj_cpp
import matrix_cpp
import gamma_cpp
import setProcName
import start_cpp
import make
import doc_gen
# Setup...
doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of miscellaneous stuff - most modules depend on this.')
doc.addFile('readme.txt', 'Overview')
# Variables...
doc.addVariable('numpy_help_cpp.numpy_util_code', 'Assorted utility functions for accessing numpy arrays within scipy.weave C++ code.')
doc.addVariable('python_obj_cpp.python_obj_code', 'Assorted utility functions for interfacing with python objects from scipy.weave C++ code.')
doc.addVariable('matrix_cpp.matrix_code', 'Matrix manipulation routines for use in scipy.weave C++')
doc.addVariable('gamma_cpp.gamma_code', 'Gamma and related functions for use in scipy.weave C++')
# Functions...
doc.addFunction(make.make_mod)
doc.addFunction(cvarray.cv2array)
doc.addFunction(cvarray.array2cv)
doc.addFunction(mp_map.repeat)
doc.addFunction(mp_map.mp_map)
doc.addFunction(setProcName.setProcName)
doc.addFunction(start_cpp.start_cpp)
doc.addFunction(make.make_mod)
# Classes...
doc.addClass(prog_bar.ProgBar)
doc.addClass(doc_gen.DocGen)
| [
[
1,
0,
0.2857,
0.0179,
0,
0.66,
0,
192,
0,
1,
0,
0,
192,
0,
0
],
[
1,
0,
0.3036,
0.0179,
0,
0.66,
0.0385,
905,
0,
1,
0,
0,
905,
0,
0
],
[
1,
0,
0.3214,
0.0179,
0,
... | [
"import cvarray",
"import mp_map",
"import prog_bar",
"import numpy_help_cpp",
"import python_obj_cpp",
"import matrix_cpp",
"import gamma_cpp",
"import setProcName",
"import start_cpp",
"import make",
"import doc_gen",
"doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of misc... |
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import unittest
import random
import math
from scipy.special import gammaln, psi, polygamma
from scipy import weave
from utils.start_cpp import start_cpp
# Provides various gamma-related functions...
gamma_code = start_cpp() + """
#ifndef GAMMA_CODE
#define GAMMA_CODE
#include <cmath>
// Returns the natural logarithm of the Gamma function...
// (Uses Lanczos's approximation.)
double lnGamma(double z)
{
static const double coeff[9] = {0.99999999999980993, 676.5203681218851, -1259.1392167224028, 771.32342877765313, -176.61502916214059, 12.507343278686905, -0.13857109526572012, 9.9843695780195716e-6, 1.5056327351493116e-7};
if (z<0.5)
{
// Use reflection formula, as approximation doesn't work down here...
return log(M_PI) - log(sin(M_PI*z)) - lnGamma(1.0-z);
}
else
{
double x = coeff[0];
for (int i=1;i<9;i++) x += coeff[i]/(z+i-1);
double t = z + 6.5;
return log(sqrt(2.0*M_PI)) + (z-0.5)*log(t) - t + log(x);
}
}
// Calculates the Digamma function, i.e. the derivative of the log of the Gamma function - uses a partial expansion of an infinite series to 4 terms that is good for high values, and an identity to express lower values in terms of higher values...
double digamma(double z)
{
static const double highVal = 13.0; // A bit of fiddling shows that the last term with this is of the order 1e-10, so we can expect at least 9 digits of accuracy past the decimal point.
double ret = 0.0;
while (z<highVal)
{
ret -= 1.0/z;
z += 1.0;
}
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz4 = iz2*iz2;
double iz6 = iz4*iz2;
ret += log(z) - iz1/2.0 - iz2/12.0 + iz4/120.0 - iz6/252.0;
return ret;
}
// Calculates the trigamma function - uses a partial expansion of an infinite series that is accurate for large values, and then uses an identity to express lower values in terms of higher values - same approach as for the digamma function basically...
double trigamma(double z)
{
static const double highVal = 8.0;
double ret = 0.0;
while (z<highVal)
{
ret += 1.0/(z*z);
z += 1.0;
}
z -= 1.0;
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz3 = iz1*iz2;
double iz5 = iz3*iz2;
double iz7 = iz5*iz2;
double iz9 = iz7*iz2;
ret += iz1 - 0.5*iz2 + iz3/6.0 - iz5/30.0 + iz7/42.0 - iz9/30.0;
return ret;
}
#endif
"""
def lnGamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns the logorithm of the gamma function"""
code = start_cpp(gamma_code) + """
return_val = lnGamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def digamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the digamma function"""
code = start_cpp(gamma_code) + """
return_val = digamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def trigamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the trigamma function"""
code = start_cpp(gamma_code) + """
return_val = trigamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
class TestFuncs(unittest.TestCase):
"""Test code for the assorted gamma-related functions."""
def test_compile(self):
code = start_cpp(gamma_code) + """
"""
weave.inline(code, support_code=gamma_code)
def test_error_lngamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = lnGamma(z)
good = gammaln(z)
assert(math.fabs(own-good)<1e-12)
def test_error_digamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = digamma(z)
good = psi(z)
assert(math.fabs(own-good)<1e-9)
def test_error_trigamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = trigamma(z)
good = polygamma(1,z)
assert(math.fabs(own-good)<1e-9)
# If this file is run do the unit tests...
if __name__ == '__main__':
unittest.main()
| [
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[
1,
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0.... | [
"import unittest",
"import random",
"import math",
"from scipy.special import gammaln, psi, polygamma",
"from scipy import weave",
"from utils.start_cpp import start_cpp",
"gamma_code = start_cpp() + \"\"\"\n#ifndef GAMMA_CODE\n#define GAMMA_CODE\n\n#include <cmath>\n\n// Returns the natural logarithm o... |
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import inspect
import hashlib
def start_cpp(hash_str = None):
"""This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for working around the fact the scipy.weave only recompiles if the hash of the code changes, but ignores the support_code - passing the support_code into start_cpp avoids this problem by putting its hash into the code and forcing a recompile when that code changes. Usage is <code variable> = start_cpp([support_code variable]) + <3 quotations to start big comment with code in, typically going over many lines.>"""
frame = inspect.currentframe().f_back
info = inspect.getframeinfo(frame)
if hash_str==None:
return '#line %i "%s"\n'%(info[1],info[0])
else:
h = hashlib.md5()
h.update(hash_str)
hash_val = h.hexdigest()
return '#line %i "%s" // %s\n'%(info[1],info[0],hash_val)
| [
[
1,
0,
0.5,
0.0333,
0,
0.66,
0,
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0,
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[
1,
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[
2,
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... | [
"import inspect",
"import hashlib",
"def start_cpp(hash_str = None):\n \"\"\"This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for work... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import sys
import os.path
import tempfile
import shutil
from distutils.core import setup, Extension
import distutils.ccompiler
import distutils.dep_util
try:
__default_compiler = distutils.ccompiler.new_compiler()
except:
__default_compiler = None
def make_mod(name, base, source, openCL = False):
"""Uses distutils to compile a python module - really just a set of hacks to allow this to be done 'on demand', so it only compiles if the module does not exist or is older than the current source, and after compilation the program can continue on its merry way, and immediatly import the just compiled module. Note that on failure erros can be thrown - its your choice to catch them or not. name is the modules name, i.e. what you want to use with the import statement. base is the base directory for the module, which contains the source file - often you would want to set this to 'os.path.dirname(__file__)', assuming the .py file that imports the module is in the same directory as the code. It is this directory that the module is output to. source is the filename of the source code to compile, or alternativly a list of filenames. openCL indicates if OpenCL is used by the module, in which case it does all the necesary setup - done like this so these setting can be kept centralised, so when they need to be different for a new platform they only have to be changed in one place."""
if __default_compiler==None: raise Exception('No compiler!')
# Work out the various file names - check if we actually need to do anything...
if not isinstance(source, list): source = [source]
source_path = map(lambda s: os.path.join(base, s), source)
library_path = os.path.join(base, __default_compiler.shared_object_filename(name))
if reduce(lambda a,b: a or b, map(lambda s: distutils.dep_util.newer(s, library_path), source_path)):
try:
print 'b'
# Backup the argv variable and create a temporary directory to do all work in...
old_argv = sys.argv[:]
temp_dir = tempfile.mkdtemp()
# Prepare the extension...
sys.argv = ['','build_ext','--build-lib', base, '--build-temp', temp_dir]
comp_path = filter(lambda s: not s.endswith('.h'), source_path)
depends = filter(lambda s: s.endswith('.h'), source_path)
if openCL:
ext = Extension(name, comp_path, include_dirs=['/usr/local/cuda/include', '/opt/AMDAPP/include'], libraries = ['OpenCL'], library_dirs = ['/usr/lib64/nvidia', '/opt/AMDAPP/lib/x86_64'], depends=depends)
else:
ext = Extension(name, comp_path, depends=depends)
# Compile...
setup(name=name, version='1.0.0', ext_modules=[ext])
finally:
# Cleanup the argv variable and the temporary directory...
sys.argv = old_argv
shutil.rmtree(temp_dir, True)
| [
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1,
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[
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0,
0.6... | [
"import sys",
"import os.path",
"import tempfile",
"import shutil",
"from distutils.core import setup, Extension",
"import distutils.ccompiler",
"import distutils.dep_util",
"try:\n __default_compiler = distutils.ccompiler.new_compiler()\nexcept:\n __default_compiler = None",
" __default_compiler... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import pydoc
import inspect
class DocGen:
"""A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code."""
def __init__(self, name, title = None, summary = None):
"""name is the module name - primarilly used for the file names. title is the title used as applicable - if not provide it just uses the name. summary is an optional line to go below the title."""
if title==None: title = name
if summary==None: summary = title
self.doc = pydoc.HTMLDoc()
self.html = open('%s.html'%name,'w')
self.html.write('<html>\n')
self.html.write('<head>\n')
self.html.write('<title>%s</title>\n'%title)
self.html.write('</head>\n')
self.html.write('<body>\n')
self.html_variables = ''
self.html_functions = ''
self.html_classes = ''
self.wiki = open('%s.wiki'%name,'w')
self.wiki.write('#summary %s\n\n'%summary)
self.wiki.write('= %s= \n\n'%title)
self.wiki_variables = ''
self.wiki_functions = ''
self.wiki_classes = ''
def __del__(self):
if self.html_variables!='':
self.html.write(self.doc.bigsection('Synonyms', '#ffffff', '#8d50ff', self.html_variables))
if self.html_functions!='':
self.html.write(self.doc.bigsection('Functions', '#ffffff', '#eeaa77', self.html_functions))
if self.html_classes!='':
self.html.write(self.doc.bigsection('Classes', '#ffffff', '#ee77aa', self.html_classes))
self.html.write('</body>\n')
self.html.write('</html>\n')
self.html.close()
if self.wiki_variables!='':
self.wiki.write('= Variables =\n\n')
self.wiki.write(self.wiki_variables)
self.wiki.write('\n')
if self.wiki_functions!='':
self.wiki.write('= Functions =\n\n')
self.wiki.write(self.wiki_functions)
self.wiki.write('\n')
if self.wiki_classes!='':
self.wiki.write('= Classes =\n\n')
self.wiki.write(self.wiki_classes)
self.wiki.write('\n')
self.wiki.close()
def addFile(self, fn, title, fls = True):
"""Given a filename and section title adds the contents of said file to the output. Various flags influence how this works."""
html = []
wiki = []
for i, line in enumerate(open(fn,'r').readlines()):
hl = line.replace('\n', '')
if i==0 and fls:
hl = '<strong>' + hl + '</strong>'
for ext in ['py','txt']:
if '.%s - '%ext in hl:
s = hl.split('.%s - '%ext, 1)
hl = '<i>' + s[0] + '.%s</i> - '%ext + s[1]
html.append(hl)
wl = line.strip()
if i==0 and fls:
wl = '*%s*'%wl
for ext in ['py','txt']:
if '.%s - '%ext in wl:
s = wl.split('.%s - '%ext, 1)
wl = '`' + s[0] + '.%s` - '%ext + s[1] + '\n'
wiki.append(wl)
self.html.write(self.doc.bigsection(title, '#ffffff', '#7799ee', '<br/>'.join(html)))
self.wiki.write('== %s ==\n'%title)
self.wiki.write('\n'.join(wiki))
self.wiki.write('----\n\n')
def addVariable(self, var, desc):
"""Adds a variable to the documentation. Given the nature of this you provide it as a pair of strings - one referencing the variable, the other some kind of description of its use etc.."""
self.html_variables += '<strong>%s</strong><br/>'%var
self.html_variables += '%s<br/><br/>\n'%desc
self.wiki_variables += '*`%s`*\n'%var
self.wiki_variables += ' %s\n\n'%desc
def addFunction(self, func):
"""Adds a function to the documentation. You provide the actual function instance."""
self.html_functions += self.doc.docroutine(func).replace(' ',' ')
self.html_functions += '\n'
name = func.__name__
args, varargs, keywords, defaults = inspect.getargspec(func)
doc = inspect.getdoc(func)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
self.wiki_functions += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_functions += ' %s\n\n'%doc
def addClass(self, cls):
"""Adds a class to the documentation. You provide the actual class object."""
self.html_classes += self.doc.docclass(cls).replace(' ',' ')
self.html_classes += '\n'
name = cls.__name__
parents = filter(lambda a: a!=cls, inspect.getmro(cls))
doc = inspect.getdoc(cls)
par_str = ''
if len(parents)!=0:
par_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda p: p.__name__, parents))
self.wiki_classes += '== %s(%s) ==\n'%(name, par_str)
self.wiki_classes += ' %s\n\n'%doc
methods = inspect.getmembers(cls, inspect.ismethod)
def method_key(pair):
if pair[0]=='__init__': return '___'
else: return pair[0]
methods.sort(key=method_key)
for name, method in methods:
if not name.startswith('_%s'%cls.__name__):
args, varargs, keywords, defaults = inspect.getargspec(method)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
def fetch_doc(cls, name):
try:
method = getattr(cls, name)
if method.__doc__!=None: return inspect.getdoc(method)
except: pass
for parent in filter(lambda a: a!=cls, inspect.getmro(cls)):
ret = fetch_doc(parent, name)
if ret!=None: return ret
return None
doc = fetch_doc(cls, name)
self.wiki_classes += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_classes += ' %s\n\n'%doc
variables = inspect.getmembers(cls, lambda x: isinstance(x, int) or isinstance(x, str) or isinstance(x, float))
for name, var in variables:
if not name.startswith('__'):
self.wiki_classes += '*`%s`* = %s\n\n'%(name, str(var))
| [
[
1,
0,
0.0634,
0.0049,
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0,
291,
0,
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],
[
1,
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[
3,
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0.5439,
0.9171,
0,
0.6... | [
"import pydoc",
"import inspect",
"class DocGen:\n \"\"\"A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code.\"\"\"\n def __init__(self, name, ... |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from ctypes import *
def setProcName(name):
"""Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differing amounts in differing cases."""
# Call the process control function...
libc = cdll.LoadLibrary('libc.so.6')
libc.prctl(15, c_char_p(name), 0, 0, 0)
# Update argv...
charPP = POINTER(POINTER(c_char))
argv = charPP.in_dll(libc,'_dl_argv')
size = libc.strlen(argv[0])
libc.strncpy(argv[0],c_char_p(name),size)
if __name__=='__main__':
# Quick test that it works...
import os
ps1 = 'ps'
ps2 = 'ps -f'
os.system(ps1)
os.system(ps2)
setProcName('wibble_wobble')
os.system(ps1)
os.system(ps2)
| [
[
1,
0,
0.3636,
0.0227,
0,
0.66,
0,
182,
0,
1,
0,
0,
182,
0,
0
],
[
2,
0,
0.5682,
0.25,
0,
0.66,
0.5,
903,
0,
1,
0,
0,
0,
0,
9
],
[
8,
1,
0.4773,
0.0227,
1,
0.95,
... | [
"from ctypes import *",
"def setProcName(name):\n \"\"\"Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differin... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import multiprocessing as mp
import multiprocessing.synchronize # To make sure we have all the functionality.
import types
import marshal
import unittest
def repeat(x):
"""A generator that repeats the input forever - can be used with the mp_map function to give data to a function that is constant."""
while True: yield x
def run_code(code,args):
"""Internal use function that does the work in each process."""
code = marshal.loads(code)
func = types.FunctionType(code, globals(), '_')
return func(*args)
def mp_map(func, *iters, **keywords):
"""A multiprocess version of the map function. Note that func must limit itself to the data provided - if it accesses anything else (globals, locals to its definition.) it will fail. There is a repeat generator provided in this module to work around such issues. Note that, unlike map, this iterates the length of the shortest of inputs, rather than the longest - whilst this makes it not a perfect substitute it makes passing constant argumenmts easier as they can just repeat for infinity."""
if 'pool' in keywords: pool = keywords['pool']
else: pool = mp.Pool()
code = marshal.dumps(func.func_code)
jobs = []
for args in zip(*iters):
jobs.append(pool.apply_async(run_code,(code,args)))
for i in xrange(len(jobs)):
jobs[i] = jobs[i].get()
return jobs
class TestMpMap(unittest.TestCase):
def test_simple1(self):
data = ['a','b','c','d']
def noop(data):
return data
data_noop = mp_map(noop, data)
self.assertEqual(data, data_noop)
def test_simple2(self):
data = [x for x in xrange(1000)]
data_double = mp_map(lambda a: a*2, data)
self.assertEqual(map(lambda a: a*2,data), data_double)
def test_gen(self):
def gen():
for i in xrange(100): yield i
data_double = mp_map(lambda a: a*2, gen())
self.assertEqual(map(lambda a: a*2,gen()), data_double)
def test_repeat(self):
def mult(a,b):
return a*b
data = [x for x in xrange(50,5000,5)]
data_triple = mp_map(mult, data, repeat(3))
self.assertEqual(map(lambda a: a*3,data),data_triple)
def test_none(self):
data = []
data_sqr = mp_map(lambda x: x*x, data)
self.assertEqual([],data_sqr)
if __name__ == '__main__':
unittest.main()
| [
[
1,
0,
0.1456,
0.0097,
0,
0.66,
0,
901,
0,
1,
0,
0,
901,
0,
0
],
[
1,
0,
0.1553,
0.0097,
0,
0.66,
0.1111,
99,
0,
1,
0,
0,
99,
0,
0
],
[
1,
0,
0.1748,
0.0097,
0,
0.... | [
"import multiprocessing as mp",
"import multiprocessing.synchronize # To make sure we have all the functionality.",
"import types",
"import marshal",
"import unittest",
"def repeat(x):\n \"\"\"A generator that repeats the input forever - can be used with the mp_map function to give data to a function tha... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from utils.start_cpp import start_cpp
# Defines helper functions for accessing numpy arrays...
numpy_util_code = start_cpp() + """
#ifndef NUMPY_UTIL_CODE
#define NUMPY_UTIL_CODE
float & Float1D(PyArrayObject * arr, int index = 0)
{
return *(float*)(arr->data + index*arr->strides[0]);
}
float & Float2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
float & Float3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
unsigned char & Byte1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index*arr->strides[0]);
}
unsigned char & Byte2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
unsigned char & Byte3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
int & Int1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index*arr->strides[0]);
}
int & Int2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
int & Int3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
#endif
"""
| [
[
1,
0,
0.1923,
0.0128,
0,
0.66,
0,
972,
0,
1,
0,
0,
972,
0,
0
],
[
14,
0,
0.6282,
0.7564,
0,
0.66,
1,
799,
4,
0,
0,
0,
0,
0,
1
]
] | [
"from utils.start_cpp import start_cpp",
"numpy_util_code = start_cpp() + \"\"\"\n#ifndef NUMPY_UTIL_CODE\n#define NUMPY_UTIL_CODE\n\nfloat & Float1D(PyArrayObject * arr, int index = 0)\n{\n return *(float*)(arr->data + index*arr->strides[0]);\n}"
] |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import cvarray
import mp_map
import prog_bar
import numpy_help_cpp
import python_obj_cpp
import matrix_cpp
import gamma_cpp
import setProcName
import start_cpp
import make
import doc_gen
# Setup...
doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of miscellaneous stuff - most modules depend on this.')
doc.addFile('readme.txt', 'Overview')
# Variables...
doc.addVariable('numpy_help_cpp.numpy_util_code', 'Assorted utility functions for accessing numpy arrays within scipy.weave C++ code.')
doc.addVariable('python_obj_cpp.python_obj_code', 'Assorted utility functions for interfacing with python objects from scipy.weave C++ code.')
doc.addVariable('matrix_cpp.matrix_code', 'Matrix manipulation routines for use in scipy.weave C++')
doc.addVariable('gamma_cpp.gamma_code', 'Gamma and related functions for use in scipy.weave C++')
# Functions...
doc.addFunction(make.make_mod)
doc.addFunction(cvarray.cv2array)
doc.addFunction(cvarray.array2cv)
doc.addFunction(mp_map.repeat)
doc.addFunction(mp_map.mp_map)
doc.addFunction(setProcName.setProcName)
doc.addFunction(start_cpp.start_cpp)
doc.addFunction(make.make_mod)
# Classes...
doc.addClass(prog_bar.ProgBar)
doc.addClass(doc_gen.DocGen)
| [
[
1,
0,
0.2857,
0.0179,
0,
0.66,
0,
192,
0,
1,
0,
0,
192,
0,
0
],
[
1,
0,
0.3036,
0.0179,
0,
0.66,
0.0385,
905,
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1,
0,
0,
905,
0,
0
],
[
1,
0,
0.3214,
0.0179,
0,
... | [
"import cvarray",
"import mp_map",
"import prog_bar",
"import numpy_help_cpp",
"import python_obj_cpp",
"import matrix_cpp",
"import gamma_cpp",
"import setProcName",
"import start_cpp",
"import make",
"import doc_gen",
"doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of misc... |
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import unittest
import random
import math
from scipy.special import gammaln, psi, polygamma
from scipy import weave
from utils.start_cpp import start_cpp
# Provides various gamma-related functions...
gamma_code = start_cpp() + """
#ifndef GAMMA_CODE
#define GAMMA_CODE
#include <cmath>
// Returns the natural logarithm of the Gamma function...
// (Uses Lanczos's approximation.)
double lnGamma(double z)
{
static const double coeff[9] = {0.99999999999980993, 676.5203681218851, -1259.1392167224028, 771.32342877765313, -176.61502916214059, 12.507343278686905, -0.13857109526572012, 9.9843695780195716e-6, 1.5056327351493116e-7};
if (z<0.5)
{
// Use reflection formula, as approximation doesn't work down here...
return log(M_PI) - log(sin(M_PI*z)) - lnGamma(1.0-z);
}
else
{
double x = coeff[0];
for (int i=1;i<9;i++) x += coeff[i]/(z+i-1);
double t = z + 6.5;
return log(sqrt(2.0*M_PI)) + (z-0.5)*log(t) - t + log(x);
}
}
// Calculates the Digamma function, i.e. the derivative of the log of the Gamma function - uses a partial expansion of an infinite series to 4 terms that is good for high values, and an identity to express lower values in terms of higher values...
double digamma(double z)
{
static const double highVal = 13.0; // A bit of fiddling shows that the last term with this is of the order 1e-10, so we can expect at least 9 digits of accuracy past the decimal point.
double ret = 0.0;
while (z<highVal)
{
ret -= 1.0/z;
z += 1.0;
}
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz4 = iz2*iz2;
double iz6 = iz4*iz2;
ret += log(z) - iz1/2.0 - iz2/12.0 + iz4/120.0 - iz6/252.0;
return ret;
}
// Calculates the trigamma function - uses a partial expansion of an infinite series that is accurate for large values, and then uses an identity to express lower values in terms of higher values - same approach as for the digamma function basically...
double trigamma(double z)
{
static const double highVal = 8.0;
double ret = 0.0;
while (z<highVal)
{
ret += 1.0/(z*z);
z += 1.0;
}
z -= 1.0;
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz3 = iz1*iz2;
double iz5 = iz3*iz2;
double iz7 = iz5*iz2;
double iz9 = iz7*iz2;
ret += iz1 - 0.5*iz2 + iz3/6.0 - iz5/30.0 + iz7/42.0 - iz9/30.0;
return ret;
}
#endif
"""
def lnGamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns the logorithm of the gamma function"""
code = start_cpp(gamma_code) + """
return_val = lnGamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def digamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the digamma function"""
code = start_cpp(gamma_code) + """
return_val = digamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def trigamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the trigamma function"""
code = start_cpp(gamma_code) + """
return_val = trigamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
class TestFuncs(unittest.TestCase):
"""Test code for the assorted gamma-related functions."""
def test_compile(self):
code = start_cpp(gamma_code) + """
"""
weave.inline(code, support_code=gamma_code)
def test_error_lngamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = lnGamma(z)
good = gammaln(z)
assert(math.fabs(own-good)<1e-12)
def test_error_digamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = digamma(z)
good = psi(z)
assert(math.fabs(own-good)<1e-9)
def test_error_trigamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = trigamma(z)
good = polygamma(1,z)
assert(math.fabs(own-good)<1e-9)
# If this file is run do the unit tests...
if __name__ == '__main__':
unittest.main()
| [
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[
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[
1,
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0.... | [
"import unittest",
"import random",
"import math",
"from scipy.special import gammaln, psi, polygamma",
"from scipy import weave",
"from utils.start_cpp import start_cpp",
"gamma_code = start_cpp() + \"\"\"\n#ifndef GAMMA_CODE\n#define GAMMA_CODE\n\n#include <cmath>\n\n// Returns the natural logarithm o... |
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import inspect
import hashlib
def start_cpp(hash_str = None):
"""This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for working around the fact the scipy.weave only recompiles if the hash of the code changes, but ignores the support_code - passing the support_code into start_cpp avoids this problem by putting its hash into the code and forcing a recompile when that code changes. Usage is <code variable> = start_cpp([support_code variable]) + <3 quotations to start big comment with code in, typically going over many lines.>"""
frame = inspect.currentframe().f_back
info = inspect.getframeinfo(frame)
if hash_str==None:
return '#line %i "%s"\n'%(info[1],info[0])
else:
h = hashlib.md5()
h.update(hash_str)
hash_val = h.hexdigest()
return '#line %i "%s" // %s\n'%(info[1],info[0],hash_val)
| [
[
1,
0,
0.5,
0.0333,
0,
0.66,
0,
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0,
1,
0,
0,
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0,
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],
[
1,
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0,
0,
154,
0,
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],
[
2,
0,
0.8333,
0.3667,
0,
0.66,
... | [
"import inspect",
"import hashlib",
"def start_cpp(hash_str = None):\n \"\"\"This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for work... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import sys
import os.path
import tempfile
import shutil
from distutils.core import setup, Extension
import distutils.ccompiler
import distutils.dep_util
try:
__default_compiler = distutils.ccompiler.new_compiler()
except:
__default_compiler = None
def make_mod(name, base, source, openCL = False):
"""Uses distutils to compile a python module - really just a set of hacks to allow this to be done 'on demand', so it only compiles if the module does not exist or is older than the current source, and after compilation the program can continue on its merry way, and immediatly import the just compiled module. Note that on failure erros can be thrown - its your choice to catch them or not. name is the modules name, i.e. what you want to use with the import statement. base is the base directory for the module, which contains the source file - often you would want to set this to 'os.path.dirname(__file__)', assuming the .py file that imports the module is in the same directory as the code. It is this directory that the module is output to. source is the filename of the source code to compile, or alternativly a list of filenames. openCL indicates if OpenCL is used by the module, in which case it does all the necesary setup - done like this so these setting can be kept centralised, so when they need to be different for a new platform they only have to be changed in one place."""
if __default_compiler==None: raise Exception('No compiler!')
# Work out the various file names - check if we actually need to do anything...
if not isinstance(source, list): source = [source]
source_path = map(lambda s: os.path.join(base, s), source)
library_path = os.path.join(base, __default_compiler.shared_object_filename(name))
if reduce(lambda a,b: a or b, map(lambda s: distutils.dep_util.newer(s, library_path), source_path)):
try:
print 'b'
# Backup the argv variable and create a temporary directory to do all work in...
old_argv = sys.argv[:]
temp_dir = tempfile.mkdtemp()
# Prepare the extension...
sys.argv = ['','build_ext','--build-lib', base, '--build-temp', temp_dir]
comp_path = filter(lambda s: not s.endswith('.h'), source_path)
depends = filter(lambda s: s.endswith('.h'), source_path)
if openCL:
ext = Extension(name, comp_path, include_dirs=['/usr/local/cuda/include', '/opt/AMDAPP/include'], libraries = ['OpenCL'], library_dirs = ['/usr/lib64/nvidia', '/opt/AMDAPP/lib/x86_64'], depends=depends)
else:
ext = Extension(name, comp_path, depends=depends)
# Compile...
setup(name=name, version='1.0.0', ext_modules=[ext])
finally:
# Cleanup the argv variable and the temporary directory...
sys.argv = old_argv
shutil.rmtree(temp_dir, True)
| [
[
1,
0,
0.2031,
0.0156,
0,
0.66,
0,
509,
0,
1,
0,
0,
509,
0,
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],
[
1,
0,
0.2188,
0.0156,
0,
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0.125,
79,
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1,
0,
0,
79,
0,
0
],
[
1,
0,
0.2344,
0.0156,
0,
0.6... | [
"import sys",
"import os.path",
"import tempfile",
"import shutil",
"from distutils.core import setup, Extension",
"import distutils.ccompiler",
"import distutils.dep_util",
"try:\n __default_compiler = distutils.ccompiler.new_compiler()\nexcept:\n __default_compiler = None",
" __default_compiler... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import pydoc
import inspect
class DocGen:
"""A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code."""
def __init__(self, name, title = None, summary = None):
"""name is the module name - primarilly used for the file names. title is the title used as applicable - if not provide it just uses the name. summary is an optional line to go below the title."""
if title==None: title = name
if summary==None: summary = title
self.doc = pydoc.HTMLDoc()
self.html = open('%s.html'%name,'w')
self.html.write('<html>\n')
self.html.write('<head>\n')
self.html.write('<title>%s</title>\n'%title)
self.html.write('</head>\n')
self.html.write('<body>\n')
self.html_variables = ''
self.html_functions = ''
self.html_classes = ''
self.wiki = open('%s.wiki'%name,'w')
self.wiki.write('#summary %s\n\n'%summary)
self.wiki.write('= %s= \n\n'%title)
self.wiki_variables = ''
self.wiki_functions = ''
self.wiki_classes = ''
def __del__(self):
if self.html_variables!='':
self.html.write(self.doc.bigsection('Synonyms', '#ffffff', '#8d50ff', self.html_variables))
if self.html_functions!='':
self.html.write(self.doc.bigsection('Functions', '#ffffff', '#eeaa77', self.html_functions))
if self.html_classes!='':
self.html.write(self.doc.bigsection('Classes', '#ffffff', '#ee77aa', self.html_classes))
self.html.write('</body>\n')
self.html.write('</html>\n')
self.html.close()
if self.wiki_variables!='':
self.wiki.write('= Variables =\n\n')
self.wiki.write(self.wiki_variables)
self.wiki.write('\n')
if self.wiki_functions!='':
self.wiki.write('= Functions =\n\n')
self.wiki.write(self.wiki_functions)
self.wiki.write('\n')
if self.wiki_classes!='':
self.wiki.write('= Classes =\n\n')
self.wiki.write(self.wiki_classes)
self.wiki.write('\n')
self.wiki.close()
def addFile(self, fn, title, fls = True):
"""Given a filename and section title adds the contents of said file to the output. Various flags influence how this works."""
html = []
wiki = []
for i, line in enumerate(open(fn,'r').readlines()):
hl = line.replace('\n', '')
if i==0 and fls:
hl = '<strong>' + hl + '</strong>'
for ext in ['py','txt']:
if '.%s - '%ext in hl:
s = hl.split('.%s - '%ext, 1)
hl = '<i>' + s[0] + '.%s</i> - '%ext + s[1]
html.append(hl)
wl = line.strip()
if i==0 and fls:
wl = '*%s*'%wl
for ext in ['py','txt']:
if '.%s - '%ext in wl:
s = wl.split('.%s - '%ext, 1)
wl = '`' + s[0] + '.%s` - '%ext + s[1] + '\n'
wiki.append(wl)
self.html.write(self.doc.bigsection(title, '#ffffff', '#7799ee', '<br/>'.join(html)))
self.wiki.write('== %s ==\n'%title)
self.wiki.write('\n'.join(wiki))
self.wiki.write('----\n\n')
def addVariable(self, var, desc):
"""Adds a variable to the documentation. Given the nature of this you provide it as a pair of strings - one referencing the variable, the other some kind of description of its use etc.."""
self.html_variables += '<strong>%s</strong><br/>'%var
self.html_variables += '%s<br/><br/>\n'%desc
self.wiki_variables += '*`%s`*\n'%var
self.wiki_variables += ' %s\n\n'%desc
def addFunction(self, func):
"""Adds a function to the documentation. You provide the actual function instance."""
self.html_functions += self.doc.docroutine(func).replace(' ',' ')
self.html_functions += '\n'
name = func.__name__
args, varargs, keywords, defaults = inspect.getargspec(func)
doc = inspect.getdoc(func)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
self.wiki_functions += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_functions += ' %s\n\n'%doc
def addClass(self, cls):
"""Adds a class to the documentation. You provide the actual class object."""
self.html_classes += self.doc.docclass(cls).replace(' ',' ')
self.html_classes += '\n'
name = cls.__name__
parents = filter(lambda a: a!=cls, inspect.getmro(cls))
doc = inspect.getdoc(cls)
par_str = ''
if len(parents)!=0:
par_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda p: p.__name__, parents))
self.wiki_classes += '== %s(%s) ==\n'%(name, par_str)
self.wiki_classes += ' %s\n\n'%doc
methods = inspect.getmembers(cls, inspect.ismethod)
def method_key(pair):
if pair[0]=='__init__': return '___'
else: return pair[0]
methods.sort(key=method_key)
for name, method in methods:
if not name.startswith('_%s'%cls.__name__):
args, varargs, keywords, defaults = inspect.getargspec(method)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
def fetch_doc(cls, name):
try:
method = getattr(cls, name)
if method.__doc__!=None: return inspect.getdoc(method)
except: pass
for parent in filter(lambda a: a!=cls, inspect.getmro(cls)):
ret = fetch_doc(parent, name)
if ret!=None: return ret
return None
doc = fetch_doc(cls, name)
self.wiki_classes += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_classes += ' %s\n\n'%doc
variables = inspect.getmembers(cls, lambda x: isinstance(x, int) or isinstance(x, str) or isinstance(x, float))
for name, var in variables:
if not name.startswith('__'):
self.wiki_classes += '*`%s`* = %s\n\n'%(name, str(var))
| [
[
1,
0,
0.0634,
0.0049,
0,
0.66,
0,
291,
0,
1,
0,
0,
291,
0,
0
],
[
1,
0,
0.0683,
0.0049,
0,
0.66,
0.5,
878,
0,
1,
0,
0,
878,
0,
0
],
[
3,
0,
0.5439,
0.9171,
0,
0.6... | [
"import pydoc",
"import inspect",
"class DocGen:\n \"\"\"A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code.\"\"\"\n def __init__(self, name, ... |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from ctypes import *
def setProcName(name):
"""Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differing amounts in differing cases."""
# Call the process control function...
libc = cdll.LoadLibrary('libc.so.6')
libc.prctl(15, c_char_p(name), 0, 0, 0)
# Update argv...
charPP = POINTER(POINTER(c_char))
argv = charPP.in_dll(libc,'_dl_argv')
size = libc.strlen(argv[0])
libc.strncpy(argv[0],c_char_p(name),size)
if __name__=='__main__':
# Quick test that it works...
import os
ps1 = 'ps'
ps2 = 'ps -f'
os.system(ps1)
os.system(ps2)
setProcName('wibble_wobble')
os.system(ps1)
os.system(ps2)
| [
[
1,
0,
0.3636,
0.0227,
0,
0.66,
0,
182,
0,
1,
0,
0,
182,
0,
0
],
[
2,
0,
0.5682,
0.25,
0,
0.66,
0.5,
903,
0,
1,
0,
0,
0,
0,
9
],
[
8,
1,
0.4773,
0.0227,
1,
0.61,
... | [
"from ctypes import *",
"def setProcName(name):\n \"\"\"Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differin... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import multiprocessing as mp
import multiprocessing.synchronize # To make sure we have all the functionality.
import types
import marshal
import unittest
def repeat(x):
"""A generator that repeats the input forever - can be used with the mp_map function to give data to a function that is constant."""
while True: yield x
def run_code(code,args):
"""Internal use function that does the work in each process."""
code = marshal.loads(code)
func = types.FunctionType(code, globals(), '_')
return func(*args)
def mp_map(func, *iters, **keywords):
"""A multiprocess version of the map function. Note that func must limit itself to the data provided - if it accesses anything else (globals, locals to its definition.) it will fail. There is a repeat generator provided in this module to work around such issues. Note that, unlike map, this iterates the length of the shortest of inputs, rather than the longest - whilst this makes it not a perfect substitute it makes passing constant argumenmts easier as they can just repeat for infinity."""
if 'pool' in keywords: pool = keywords['pool']
else: pool = mp.Pool()
code = marshal.dumps(func.func_code)
jobs = []
for args in zip(*iters):
jobs.append(pool.apply_async(run_code,(code,args)))
for i in xrange(len(jobs)):
jobs[i] = jobs[i].get()
return jobs
class TestMpMap(unittest.TestCase):
def test_simple1(self):
data = ['a','b','c','d']
def noop(data):
return data
data_noop = mp_map(noop, data)
self.assertEqual(data, data_noop)
def test_simple2(self):
data = [x for x in xrange(1000)]
data_double = mp_map(lambda a: a*2, data)
self.assertEqual(map(lambda a: a*2,data), data_double)
def test_gen(self):
def gen():
for i in xrange(100): yield i
data_double = mp_map(lambda a: a*2, gen())
self.assertEqual(map(lambda a: a*2,gen()), data_double)
def test_repeat(self):
def mult(a,b):
return a*b
data = [x for x in xrange(50,5000,5)]
data_triple = mp_map(mult, data, repeat(3))
self.assertEqual(map(lambda a: a*3,data),data_triple)
def test_none(self):
data = []
data_sqr = mp_map(lambda x: x*x, data)
self.assertEqual([],data_sqr)
if __name__ == '__main__':
unittest.main()
| [
[
1,
0,
0.1456,
0.0097,
0,
0.66,
0,
901,
0,
1,
0,
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901,
0,
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[
1,
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0.0097,
0,
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99,
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1,
0,
0,
99,
0,
0
],
[
1,
0,
0.1748,
0.0097,
0,
0.... | [
"import multiprocessing as mp",
"import multiprocessing.synchronize # To make sure we have all the functionality.",
"import types",
"import marshal",
"import unittest",
"def repeat(x):\n \"\"\"A generator that repeats the input forever - can be used with the mp_map function to give data to a function tha... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from utils.start_cpp import start_cpp
# Defines helper functions for accessing numpy arrays...
numpy_util_code = start_cpp() + """
#ifndef NUMPY_UTIL_CODE
#define NUMPY_UTIL_CODE
float & Float1D(PyArrayObject * arr, int index = 0)
{
return *(float*)(arr->data + index*arr->strides[0]);
}
float & Float2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
float & Float3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
unsigned char & Byte1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index*arr->strides[0]);
}
unsigned char & Byte2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
unsigned char & Byte3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
int & Int1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index*arr->strides[0]);
}
int & Int2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
int & Int3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
#endif
"""
| [
[
1,
0,
0.1923,
0.0128,
0,
0.66,
0,
972,
0,
1,
0,
0,
972,
0,
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],
[
14,
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0.7564,
0,
0.66,
1,
799,
4,
0,
0,
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0,
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]
] | [
"from utils.start_cpp import start_cpp",
"numpy_util_code = start_cpp() + \"\"\"\n#ifndef NUMPY_UTIL_CODE\n#define NUMPY_UTIL_CODE\n\nfloat & Float1D(PyArrayObject * arr, int index = 0)\n{\n return *(float*)(arr->data + index*arr->strides[0]);\n}"
] |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import cvarray
import mp_map
import prog_bar
import numpy_help_cpp
import python_obj_cpp
import matrix_cpp
import gamma_cpp
import setProcName
import start_cpp
import make
import doc_gen
# Setup...
doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of miscellaneous stuff - most modules depend on this.')
doc.addFile('readme.txt', 'Overview')
# Variables...
doc.addVariable('numpy_help_cpp.numpy_util_code', 'Assorted utility functions for accessing numpy arrays within scipy.weave C++ code.')
doc.addVariable('python_obj_cpp.python_obj_code', 'Assorted utility functions for interfacing with python objects from scipy.weave C++ code.')
doc.addVariable('matrix_cpp.matrix_code', 'Matrix manipulation routines for use in scipy.weave C++')
doc.addVariable('gamma_cpp.gamma_code', 'Gamma and related functions for use in scipy.weave C++')
# Functions...
doc.addFunction(make.make_mod)
doc.addFunction(cvarray.cv2array)
doc.addFunction(cvarray.array2cv)
doc.addFunction(mp_map.repeat)
doc.addFunction(mp_map.mp_map)
doc.addFunction(setProcName.setProcName)
doc.addFunction(start_cpp.start_cpp)
doc.addFunction(make.make_mod)
# Classes...
doc.addClass(prog_bar.ProgBar)
doc.addClass(doc_gen.DocGen)
| [
[
1,
0,
0.2857,
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0,
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],
[
1,
0,
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0,
905,
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[
1,
0,
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0,
... | [
"import cvarray",
"import mp_map",
"import prog_bar",
"import numpy_help_cpp",
"import python_obj_cpp",
"import matrix_cpp",
"import gamma_cpp",
"import setProcName",
"import start_cpp",
"import make",
"import doc_gen",
"doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of misc... |
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import unittest
import random
import math
from scipy.special import gammaln, psi, polygamma
from scipy import weave
from utils.start_cpp import start_cpp
# Provides various gamma-related functions...
gamma_code = start_cpp() + """
#ifndef GAMMA_CODE
#define GAMMA_CODE
#include <cmath>
// Returns the natural logarithm of the Gamma function...
// (Uses Lanczos's approximation.)
double lnGamma(double z)
{
static const double coeff[9] = {0.99999999999980993, 676.5203681218851, -1259.1392167224028, 771.32342877765313, -176.61502916214059, 12.507343278686905, -0.13857109526572012, 9.9843695780195716e-6, 1.5056327351493116e-7};
if (z<0.5)
{
// Use reflection formula, as approximation doesn't work down here...
return log(M_PI) - log(sin(M_PI*z)) - lnGamma(1.0-z);
}
else
{
double x = coeff[0];
for (int i=1;i<9;i++) x += coeff[i]/(z+i-1);
double t = z + 6.5;
return log(sqrt(2.0*M_PI)) + (z-0.5)*log(t) - t + log(x);
}
}
// Calculates the Digamma function, i.e. the derivative of the log of the Gamma function - uses a partial expansion of an infinite series to 4 terms that is good for high values, and an identity to express lower values in terms of higher values...
double digamma(double z)
{
static const double highVal = 13.0; // A bit of fiddling shows that the last term with this is of the order 1e-10, so we can expect at least 9 digits of accuracy past the decimal point.
double ret = 0.0;
while (z<highVal)
{
ret -= 1.0/z;
z += 1.0;
}
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz4 = iz2*iz2;
double iz6 = iz4*iz2;
ret += log(z) - iz1/2.0 - iz2/12.0 + iz4/120.0 - iz6/252.0;
return ret;
}
// Calculates the trigamma function - uses a partial expansion of an infinite series that is accurate for large values, and then uses an identity to express lower values in terms of higher values - same approach as for the digamma function basically...
double trigamma(double z)
{
static const double highVal = 8.0;
double ret = 0.0;
while (z<highVal)
{
ret += 1.0/(z*z);
z += 1.0;
}
z -= 1.0;
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz3 = iz1*iz2;
double iz5 = iz3*iz2;
double iz7 = iz5*iz2;
double iz9 = iz7*iz2;
ret += iz1 - 0.5*iz2 + iz3/6.0 - iz5/30.0 + iz7/42.0 - iz9/30.0;
return ret;
}
#endif
"""
def lnGamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns the logorithm of the gamma function"""
code = start_cpp(gamma_code) + """
return_val = lnGamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def digamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the digamma function"""
code = start_cpp(gamma_code) + """
return_val = digamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def trigamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the trigamma function"""
code = start_cpp(gamma_code) + """
return_val = trigamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
class TestFuncs(unittest.TestCase):
"""Test code for the assorted gamma-related functions."""
def test_compile(self):
code = start_cpp(gamma_code) + """
"""
weave.inline(code, support_code=gamma_code)
def test_error_lngamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = lnGamma(z)
good = gammaln(z)
assert(math.fabs(own-good)<1e-12)
def test_error_digamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = digamma(z)
good = psi(z)
assert(math.fabs(own-good)<1e-9)
def test_error_trigamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = trigamma(z)
good = polygamma(1,z)
assert(math.fabs(own-good)<1e-9)
# If this file is run do the unit tests...
if __name__ == '__main__':
unittest.main()
| [
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0,
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],
[
1,
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0.0063,
0,
0.... | [
"import unittest",
"import random",
"import math",
"from scipy.special import gammaln, psi, polygamma",
"from scipy import weave",
"from utils.start_cpp import start_cpp",
"gamma_code = start_cpp() + \"\"\"\n#ifndef GAMMA_CODE\n#define GAMMA_CODE\n\n#include <cmath>\n\n// Returns the natural logarithm o... |
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import inspect
import hashlib
def start_cpp(hash_str = None):
"""This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for working around the fact the scipy.weave only recompiles if the hash of the code changes, but ignores the support_code - passing the support_code into start_cpp avoids this problem by putting its hash into the code and forcing a recompile when that code changes. Usage is <code variable> = start_cpp([support_code variable]) + <3 quotations to start big comment with code in, typically going over many lines.>"""
frame = inspect.currentframe().f_back
info = inspect.getframeinfo(frame)
if hash_str==None:
return '#line %i "%s"\n'%(info[1],info[0])
else:
h = hashlib.md5()
h.update(hash_str)
hash_val = h.hexdigest()
return '#line %i "%s" // %s\n'%(info[1],info[0],hash_val)
| [
[
1,
0,
0.5,
0.0333,
0,
0.66,
0,
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0,
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[
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0,
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],
[
2,
0,
0.8333,
0.3667,
0,
0.66,
... | [
"import inspect",
"import hashlib",
"def start_cpp(hash_str = None):\n \"\"\"This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for work... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import sys
import os.path
import tempfile
import shutil
from distutils.core import setup, Extension
import distutils.ccompiler
import distutils.dep_util
try:
__default_compiler = distutils.ccompiler.new_compiler()
except:
__default_compiler = None
def make_mod(name, base, source, openCL = False):
"""Uses distutils to compile a python module - really just a set of hacks to allow this to be done 'on demand', so it only compiles if the module does not exist or is older than the current source, and after compilation the program can continue on its merry way, and immediatly import the just compiled module. Note that on failure erros can be thrown - its your choice to catch them or not. name is the modules name, i.e. what you want to use with the import statement. base is the base directory for the module, which contains the source file - often you would want to set this to 'os.path.dirname(__file__)', assuming the .py file that imports the module is in the same directory as the code. It is this directory that the module is output to. source is the filename of the source code to compile, or alternativly a list of filenames. openCL indicates if OpenCL is used by the module, in which case it does all the necesary setup - done like this so these setting can be kept centralised, so when they need to be different for a new platform they only have to be changed in one place."""
if __default_compiler==None: raise Exception('No compiler!')
# Work out the various file names - check if we actually need to do anything...
if not isinstance(source, list): source = [source]
source_path = map(lambda s: os.path.join(base, s), source)
library_path = os.path.join(base, __default_compiler.shared_object_filename(name))
if reduce(lambda a,b: a or b, map(lambda s: distutils.dep_util.newer(s, library_path), source_path)):
try:
print 'b'
# Backup the argv variable and create a temporary directory to do all work in...
old_argv = sys.argv[:]
temp_dir = tempfile.mkdtemp()
# Prepare the extension...
sys.argv = ['','build_ext','--build-lib', base, '--build-temp', temp_dir]
comp_path = filter(lambda s: not s.endswith('.h'), source_path)
depends = filter(lambda s: s.endswith('.h'), source_path)
if openCL:
ext = Extension(name, comp_path, include_dirs=['/usr/local/cuda/include', '/opt/AMDAPP/include'], libraries = ['OpenCL'], library_dirs = ['/usr/lib64/nvidia', '/opt/AMDAPP/lib/x86_64'], depends=depends)
else:
ext = Extension(name, comp_path, depends=depends)
# Compile...
setup(name=name, version='1.0.0', ext_modules=[ext])
finally:
# Cleanup the argv variable and the temporary directory...
sys.argv = old_argv
shutil.rmtree(temp_dir, True)
| [
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1,
0,
0.2031,
0.0156,
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],
[
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[
1,
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0,
0.6... | [
"import sys",
"import os.path",
"import tempfile",
"import shutil",
"from distutils.core import setup, Extension",
"import distutils.ccompiler",
"import distutils.dep_util",
"try:\n __default_compiler = distutils.ccompiler.new_compiler()\nexcept:\n __default_compiler = None",
" __default_compiler... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import pydoc
import inspect
class DocGen:
"""A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code."""
def __init__(self, name, title = None, summary = None):
"""name is the module name - primarilly used for the file names. title is the title used as applicable - if not provide it just uses the name. summary is an optional line to go below the title."""
if title==None: title = name
if summary==None: summary = title
self.doc = pydoc.HTMLDoc()
self.html = open('%s.html'%name,'w')
self.html.write('<html>\n')
self.html.write('<head>\n')
self.html.write('<title>%s</title>\n'%title)
self.html.write('</head>\n')
self.html.write('<body>\n')
self.html_variables = ''
self.html_functions = ''
self.html_classes = ''
self.wiki = open('%s.wiki'%name,'w')
self.wiki.write('#summary %s\n\n'%summary)
self.wiki.write('= %s= \n\n'%title)
self.wiki_variables = ''
self.wiki_functions = ''
self.wiki_classes = ''
def __del__(self):
if self.html_variables!='':
self.html.write(self.doc.bigsection('Synonyms', '#ffffff', '#8d50ff', self.html_variables))
if self.html_functions!='':
self.html.write(self.doc.bigsection('Functions', '#ffffff', '#eeaa77', self.html_functions))
if self.html_classes!='':
self.html.write(self.doc.bigsection('Classes', '#ffffff', '#ee77aa', self.html_classes))
self.html.write('</body>\n')
self.html.write('</html>\n')
self.html.close()
if self.wiki_variables!='':
self.wiki.write('= Variables =\n\n')
self.wiki.write(self.wiki_variables)
self.wiki.write('\n')
if self.wiki_functions!='':
self.wiki.write('= Functions =\n\n')
self.wiki.write(self.wiki_functions)
self.wiki.write('\n')
if self.wiki_classes!='':
self.wiki.write('= Classes =\n\n')
self.wiki.write(self.wiki_classes)
self.wiki.write('\n')
self.wiki.close()
def addFile(self, fn, title, fls = True):
"""Given a filename and section title adds the contents of said file to the output. Various flags influence how this works."""
html = []
wiki = []
for i, line in enumerate(open(fn,'r').readlines()):
hl = line.replace('\n', '')
if i==0 and fls:
hl = '<strong>' + hl + '</strong>'
for ext in ['py','txt']:
if '.%s - '%ext in hl:
s = hl.split('.%s - '%ext, 1)
hl = '<i>' + s[0] + '.%s</i> - '%ext + s[1]
html.append(hl)
wl = line.strip()
if i==0 and fls:
wl = '*%s*'%wl
for ext in ['py','txt']:
if '.%s - '%ext in wl:
s = wl.split('.%s - '%ext, 1)
wl = '`' + s[0] + '.%s` - '%ext + s[1] + '\n'
wiki.append(wl)
self.html.write(self.doc.bigsection(title, '#ffffff', '#7799ee', '<br/>'.join(html)))
self.wiki.write('== %s ==\n'%title)
self.wiki.write('\n'.join(wiki))
self.wiki.write('----\n\n')
def addVariable(self, var, desc):
"""Adds a variable to the documentation. Given the nature of this you provide it as a pair of strings - one referencing the variable, the other some kind of description of its use etc.."""
self.html_variables += '<strong>%s</strong><br/>'%var
self.html_variables += '%s<br/><br/>\n'%desc
self.wiki_variables += '*`%s`*\n'%var
self.wiki_variables += ' %s\n\n'%desc
def addFunction(self, func):
"""Adds a function to the documentation. You provide the actual function instance."""
self.html_functions += self.doc.docroutine(func).replace(' ',' ')
self.html_functions += '\n'
name = func.__name__
args, varargs, keywords, defaults = inspect.getargspec(func)
doc = inspect.getdoc(func)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
self.wiki_functions += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_functions += ' %s\n\n'%doc
def addClass(self, cls):
"""Adds a class to the documentation. You provide the actual class object."""
self.html_classes += self.doc.docclass(cls).replace(' ',' ')
self.html_classes += '\n'
name = cls.__name__
parents = filter(lambda a: a!=cls, inspect.getmro(cls))
doc = inspect.getdoc(cls)
par_str = ''
if len(parents)!=0:
par_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda p: p.__name__, parents))
self.wiki_classes += '== %s(%s) ==\n'%(name, par_str)
self.wiki_classes += ' %s\n\n'%doc
methods = inspect.getmembers(cls, inspect.ismethod)
def method_key(pair):
if pair[0]=='__init__': return '___'
else: return pair[0]
methods.sort(key=method_key)
for name, method in methods:
if not name.startswith('_%s'%cls.__name__):
args, varargs, keywords, defaults = inspect.getargspec(method)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
def fetch_doc(cls, name):
try:
method = getattr(cls, name)
if method.__doc__!=None: return inspect.getdoc(method)
except: pass
for parent in filter(lambda a: a!=cls, inspect.getmro(cls)):
ret = fetch_doc(parent, name)
if ret!=None: return ret
return None
doc = fetch_doc(cls, name)
self.wiki_classes += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_classes += ' %s\n\n'%doc
variables = inspect.getmembers(cls, lambda x: isinstance(x, int) or isinstance(x, str) or isinstance(x, float))
for name, var in variables:
if not name.startswith('__'):
self.wiki_classes += '*`%s`* = %s\n\n'%(name, str(var))
| [
[
1,
0,
0.0634,
0.0049,
0,
0.66,
0,
291,
0,
1,
0,
0,
291,
0,
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],
[
1,
0,
0.0683,
0.0049,
0,
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0.5,
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0,
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878,
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[
3,
0,
0.5439,
0.9171,
0,
0.6... | [
"import pydoc",
"import inspect",
"class DocGen:\n \"\"\"A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code.\"\"\"\n def __init__(self, name, ... |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from ctypes import *
def setProcName(name):
"""Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differing amounts in differing cases."""
# Call the process control function...
libc = cdll.LoadLibrary('libc.so.6')
libc.prctl(15, c_char_p(name), 0, 0, 0)
# Update argv...
charPP = POINTER(POINTER(c_char))
argv = charPP.in_dll(libc,'_dl_argv')
size = libc.strlen(argv[0])
libc.strncpy(argv[0],c_char_p(name),size)
if __name__=='__main__':
# Quick test that it works...
import os
ps1 = 'ps'
ps2 = 'ps -f'
os.system(ps1)
os.system(ps2)
setProcName('wibble_wobble')
os.system(ps1)
os.system(ps2)
| [
[
1,
0,
0.3636,
0.0227,
0,
0.66,
0,
182,
0,
1,
0,
0,
182,
0,
0
],
[
2,
0,
0.5682,
0.25,
0,
0.66,
0.5,
903,
0,
1,
0,
0,
0,
0,
9
],
[
8,
1,
0.4773,
0.0227,
1,
0.57,
... | [
"from ctypes import *",
"def setProcName(name):\n \"\"\"Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differin... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import multiprocessing as mp
import multiprocessing.synchronize # To make sure we have all the functionality.
import types
import marshal
import unittest
def repeat(x):
"""A generator that repeats the input forever - can be used with the mp_map function to give data to a function that is constant."""
while True: yield x
def run_code(code,args):
"""Internal use function that does the work in each process."""
code = marshal.loads(code)
func = types.FunctionType(code, globals(), '_')
return func(*args)
def mp_map(func, *iters, **keywords):
"""A multiprocess version of the map function. Note that func must limit itself to the data provided - if it accesses anything else (globals, locals to its definition.) it will fail. There is a repeat generator provided in this module to work around such issues. Note that, unlike map, this iterates the length of the shortest of inputs, rather than the longest - whilst this makes it not a perfect substitute it makes passing constant argumenmts easier as they can just repeat for infinity."""
if 'pool' in keywords: pool = keywords['pool']
else: pool = mp.Pool()
code = marshal.dumps(func.func_code)
jobs = []
for args in zip(*iters):
jobs.append(pool.apply_async(run_code,(code,args)))
for i in xrange(len(jobs)):
jobs[i] = jobs[i].get()
return jobs
class TestMpMap(unittest.TestCase):
def test_simple1(self):
data = ['a','b','c','d']
def noop(data):
return data
data_noop = mp_map(noop, data)
self.assertEqual(data, data_noop)
def test_simple2(self):
data = [x for x in xrange(1000)]
data_double = mp_map(lambda a: a*2, data)
self.assertEqual(map(lambda a: a*2,data), data_double)
def test_gen(self):
def gen():
for i in xrange(100): yield i
data_double = mp_map(lambda a: a*2, gen())
self.assertEqual(map(lambda a: a*2,gen()), data_double)
def test_repeat(self):
def mult(a,b):
return a*b
data = [x for x in xrange(50,5000,5)]
data_triple = mp_map(mult, data, repeat(3))
self.assertEqual(map(lambda a: a*3,data),data_triple)
def test_none(self):
data = []
data_sqr = mp_map(lambda x: x*x, data)
self.assertEqual([],data_sqr)
if __name__ == '__main__':
unittest.main()
| [
[
1,
0,
0.1456,
0.0097,
0,
0.66,
0,
901,
0,
1,
0,
0,
901,
0,
0
],
[
1,
0,
0.1553,
0.0097,
0,
0.66,
0.1111,
99,
0,
1,
0,
0,
99,
0,
0
],
[
1,
0,
0.1748,
0.0097,
0,
0.... | [
"import multiprocessing as mp",
"import multiprocessing.synchronize # To make sure we have all the functionality.",
"import types",
"import marshal",
"import unittest",
"def repeat(x):\n \"\"\"A generator that repeats the input forever - can be used with the mp_map function to give data to a function tha... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from utils.start_cpp import start_cpp
# Defines helper functions for accessing numpy arrays...
numpy_util_code = start_cpp() + """
#ifndef NUMPY_UTIL_CODE
#define NUMPY_UTIL_CODE
float & Float1D(PyArrayObject * arr, int index = 0)
{
return *(float*)(arr->data + index*arr->strides[0]);
}
float & Float2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
float & Float3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
unsigned char & Byte1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index*arr->strides[0]);
}
unsigned char & Byte2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
unsigned char & Byte3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
int & Int1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index*arr->strides[0]);
}
int & Int2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
int & Int3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
#endif
"""
| [
[
1,
0,
0.1923,
0.0128,
0,
0.66,
0,
972,
0,
1,
0,
0,
972,
0,
0
],
[
14,
0,
0.6282,
0.7564,
0,
0.66,
1,
799,
4,
0,
0,
0,
0,
0,
1
]
] | [
"from utils.start_cpp import start_cpp",
"numpy_util_code = start_cpp() + \"\"\"\n#ifndef NUMPY_UTIL_CODE\n#define NUMPY_UTIL_CODE\n\nfloat & Float1D(PyArrayObject * arr, int index = 0)\n{\n return *(float*)(arr->data + index*arr->strides[0]);\n}"
] |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import cvarray
import mp_map
import prog_bar
import numpy_help_cpp
import python_obj_cpp
import matrix_cpp
import gamma_cpp
import setProcName
import start_cpp
import make
import doc_gen
# Setup...
doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of miscellaneous stuff - most modules depend on this.')
doc.addFile('readme.txt', 'Overview')
# Variables...
doc.addVariable('numpy_help_cpp.numpy_util_code', 'Assorted utility functions for accessing numpy arrays within scipy.weave C++ code.')
doc.addVariable('python_obj_cpp.python_obj_code', 'Assorted utility functions for interfacing with python objects from scipy.weave C++ code.')
doc.addVariable('matrix_cpp.matrix_code', 'Matrix manipulation routines for use in scipy.weave C++')
doc.addVariable('gamma_cpp.gamma_code', 'Gamma and related functions for use in scipy.weave C++')
# Functions...
doc.addFunction(make.make_mod)
doc.addFunction(cvarray.cv2array)
doc.addFunction(cvarray.array2cv)
doc.addFunction(mp_map.repeat)
doc.addFunction(mp_map.mp_map)
doc.addFunction(setProcName.setProcName)
doc.addFunction(start_cpp.start_cpp)
doc.addFunction(make.make_mod)
# Classes...
doc.addClass(prog_bar.ProgBar)
doc.addClass(doc_gen.DocGen)
| [
[
1,
0,
0.2857,
0.0179,
0,
0.66,
0,
192,
0,
1,
0,
0,
192,
0,
0
],
[
1,
0,
0.3036,
0.0179,
0,
0.66,
0.0385,
905,
0,
1,
0,
0,
905,
0,
0
],
[
1,
0,
0.3214,
0.0179,
0,
... | [
"import cvarray",
"import mp_map",
"import prog_bar",
"import numpy_help_cpp",
"import python_obj_cpp",
"import matrix_cpp",
"import gamma_cpp",
"import setProcName",
"import start_cpp",
"import make",
"import doc_gen",
"doc = doc_gen.DocGen('utils', 'Utilities/Miscellaneous', 'Library of misc... |
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import unittest
import random
import math
from scipy.special import gammaln, psi, polygamma
from scipy import weave
from utils.start_cpp import start_cpp
# Provides various gamma-related functions...
gamma_code = start_cpp() + """
#ifndef GAMMA_CODE
#define GAMMA_CODE
#include <cmath>
// Returns the natural logarithm of the Gamma function...
// (Uses Lanczos's approximation.)
double lnGamma(double z)
{
static const double coeff[9] = {0.99999999999980993, 676.5203681218851, -1259.1392167224028, 771.32342877765313, -176.61502916214059, 12.507343278686905, -0.13857109526572012, 9.9843695780195716e-6, 1.5056327351493116e-7};
if (z<0.5)
{
// Use reflection formula, as approximation doesn't work down here...
return log(M_PI) - log(sin(M_PI*z)) - lnGamma(1.0-z);
}
else
{
double x = coeff[0];
for (int i=1;i<9;i++) x += coeff[i]/(z+i-1);
double t = z + 6.5;
return log(sqrt(2.0*M_PI)) + (z-0.5)*log(t) - t + log(x);
}
}
// Calculates the Digamma function, i.e. the derivative of the log of the Gamma function - uses a partial expansion of an infinite series to 4 terms that is good for high values, and an identity to express lower values in terms of higher values...
double digamma(double z)
{
static const double highVal = 13.0; // A bit of fiddling shows that the last term with this is of the order 1e-10, so we can expect at least 9 digits of accuracy past the decimal point.
double ret = 0.0;
while (z<highVal)
{
ret -= 1.0/z;
z += 1.0;
}
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz4 = iz2*iz2;
double iz6 = iz4*iz2;
ret += log(z) - iz1/2.0 - iz2/12.0 + iz4/120.0 - iz6/252.0;
return ret;
}
// Calculates the trigamma function - uses a partial expansion of an infinite series that is accurate for large values, and then uses an identity to express lower values in terms of higher values - same approach as for the digamma function basically...
double trigamma(double z)
{
static const double highVal = 8.0;
double ret = 0.0;
while (z<highVal)
{
ret += 1.0/(z*z);
z += 1.0;
}
z -= 1.0;
double iz1 = 1.0/z;
double iz2 = iz1*iz1;
double iz3 = iz1*iz2;
double iz5 = iz3*iz2;
double iz7 = iz5*iz2;
double iz9 = iz7*iz2;
ret += iz1 - 0.5*iz2 + iz3/6.0 - iz5/30.0 + iz7/42.0 - iz9/30.0;
return ret;
}
#endif
"""
def lnGamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns the logorithm of the gamma function"""
code = start_cpp(gamma_code) + """
return_val = lnGamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def digamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the digamma function"""
code = start_cpp(gamma_code) + """
return_val = digamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
def trigamma(z):
"""Pointless as scipy, a library this is dependent on, defines this, but useful for testing. Returns an evaluation of the trigamma function"""
code = start_cpp(gamma_code) + """
return_val = trigamma(z);
"""
return weave.inline(code, ['z'], support_code=gamma_code)
class TestFuncs(unittest.TestCase):
"""Test code for the assorted gamma-related functions."""
def test_compile(self):
code = start_cpp(gamma_code) + """
"""
weave.inline(code, support_code=gamma_code)
def test_error_lngamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = lnGamma(z)
good = gammaln(z)
assert(math.fabs(own-good)<1e-12)
def test_error_digamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = digamma(z)
good = psi(z)
assert(math.fabs(own-good)<1e-9)
def test_error_trigamma(self):
for _ in xrange(1000):
z = random.uniform(0.01, 100.0)
own = trigamma(z)
good = polygamma(1,z)
assert(math.fabs(own-good)<1e-9)
# If this file is run do the unit tests...
if __name__ == '__main__':
unittest.main()
| [
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1,
0,
0.0818,
0.0063,
0,
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0,
88,
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1,
0,
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0,
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],
[
1,
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0,
715,
0,
0
],
[
1,
0,
0.0943,
0.0063,
0,
0.... | [
"import unittest",
"import random",
"import math",
"from scipy.special import gammaln, psi, polygamma",
"from scipy import weave",
"from utils.start_cpp import start_cpp",
"gamma_code = start_cpp() + \"\"\"\n#ifndef GAMMA_CODE\n#define GAMMA_CODE\n\n#include <cmath>\n\n// Returns the natural logarithm o... |
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import inspect
import hashlib
def start_cpp(hash_str = None):
"""This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for working around the fact the scipy.weave only recompiles if the hash of the code changes, but ignores the support_code - passing the support_code into start_cpp avoids this problem by putting its hash into the code and forcing a recompile when that code changes. Usage is <code variable> = start_cpp([support_code variable]) + <3 quotations to start big comment with code in, typically going over many lines.>"""
frame = inspect.currentframe().f_back
info = inspect.getframeinfo(frame)
if hash_str==None:
return '#line %i "%s"\n'%(info[1],info[0])
else:
h = hashlib.md5()
h.update(hash_str)
hash_val = h.hexdigest()
return '#line %i "%s" // %s\n'%(info[1],info[0],hash_val)
| [
[
1,
0,
0.5,
0.0333,
0,
0.66,
0,
878,
0,
1,
0,
0,
878,
0,
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],
[
1,
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0.0333,
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0,
0,
154,
0,
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],
[
2,
0,
0.8333,
0.3667,
0,
0.66,
... | [
"import inspect",
"import hashlib",
"def start_cpp(hash_str = None):\n \"\"\"This method does two things - firstly it adds the correct line numbers to scipy.weave code (Good for debugging) and secondly it can optionaly inserts a hash code of some other code into the code. This latter feature is useful for work... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import sys
import os.path
import tempfile
import shutil
from distutils.core import setup, Extension
import distutils.ccompiler
import distutils.dep_util
try:
__default_compiler = distutils.ccompiler.new_compiler()
except:
__default_compiler = None
def make_mod(name, base, source, openCL = False):
"""Uses distutils to compile a python module - really just a set of hacks to allow this to be done 'on demand', so it only compiles if the module does not exist or is older than the current source, and after compilation the program can continue on its merry way, and immediatly import the just compiled module. Note that on failure erros can be thrown - its your choice to catch them or not. name is the modules name, i.e. what you want to use with the import statement. base is the base directory for the module, which contains the source file - often you would want to set this to 'os.path.dirname(__file__)', assuming the .py file that imports the module is in the same directory as the code. It is this directory that the module is output to. source is the filename of the source code to compile, or alternativly a list of filenames. openCL indicates if OpenCL is used by the module, in which case it does all the necesary setup - done like this so these setting can be kept centralised, so when they need to be different for a new platform they only have to be changed in one place."""
if __default_compiler==None: raise Exception('No compiler!')
# Work out the various file names - check if we actually need to do anything...
if not isinstance(source, list): source = [source]
source_path = map(lambda s: os.path.join(base, s), source)
library_path = os.path.join(base, __default_compiler.shared_object_filename(name))
if reduce(lambda a,b: a or b, map(lambda s: distutils.dep_util.newer(s, library_path), source_path)):
try:
print 'b'
# Backup the argv variable and create a temporary directory to do all work in...
old_argv = sys.argv[:]
temp_dir = tempfile.mkdtemp()
# Prepare the extension...
sys.argv = ['','build_ext','--build-lib', base, '--build-temp', temp_dir]
comp_path = filter(lambda s: not s.endswith('.h'), source_path)
depends = filter(lambda s: s.endswith('.h'), source_path)
if openCL:
ext = Extension(name, comp_path, include_dirs=['/usr/local/cuda/include', '/opt/AMDAPP/include'], libraries = ['OpenCL'], library_dirs = ['/usr/lib64/nvidia', '/opt/AMDAPP/lib/x86_64'], depends=depends)
else:
ext = Extension(name, comp_path, depends=depends)
# Compile...
setup(name=name, version='1.0.0', ext_modules=[ext])
finally:
# Cleanup the argv variable and the temporary directory...
sys.argv = old_argv
shutil.rmtree(temp_dir, True)
| [
[
1,
0,
0.2031,
0.0156,
0,
0.66,
0,
509,
0,
1,
0,
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],
[
1,
0,
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79,
0,
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],
[
1,
0,
0.2344,
0.0156,
0,
0.6... | [
"import sys",
"import os.path",
"import tempfile",
"import shutil",
"from distutils.core import setup, Extension",
"import distutils.ccompiler",
"import distutils.dep_util",
"try:\n __default_compiler = distutils.ccompiler.new_compiler()\nexcept:\n __default_compiler = None",
" __default_compiler... |
# Copyright (c) 2012, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import pydoc
import inspect
class DocGen:
"""A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code."""
def __init__(self, name, title = None, summary = None):
"""name is the module name - primarilly used for the file names. title is the title used as applicable - if not provide it just uses the name. summary is an optional line to go below the title."""
if title==None: title = name
if summary==None: summary = title
self.doc = pydoc.HTMLDoc()
self.html = open('%s.html'%name,'w')
self.html.write('<html>\n')
self.html.write('<head>\n')
self.html.write('<title>%s</title>\n'%title)
self.html.write('</head>\n')
self.html.write('<body>\n')
self.html_variables = ''
self.html_functions = ''
self.html_classes = ''
self.wiki = open('%s.wiki'%name,'w')
self.wiki.write('#summary %s\n\n'%summary)
self.wiki.write('= %s= \n\n'%title)
self.wiki_variables = ''
self.wiki_functions = ''
self.wiki_classes = ''
def __del__(self):
if self.html_variables!='':
self.html.write(self.doc.bigsection('Synonyms', '#ffffff', '#8d50ff', self.html_variables))
if self.html_functions!='':
self.html.write(self.doc.bigsection('Functions', '#ffffff', '#eeaa77', self.html_functions))
if self.html_classes!='':
self.html.write(self.doc.bigsection('Classes', '#ffffff', '#ee77aa', self.html_classes))
self.html.write('</body>\n')
self.html.write('</html>\n')
self.html.close()
if self.wiki_variables!='':
self.wiki.write('= Variables =\n\n')
self.wiki.write(self.wiki_variables)
self.wiki.write('\n')
if self.wiki_functions!='':
self.wiki.write('= Functions =\n\n')
self.wiki.write(self.wiki_functions)
self.wiki.write('\n')
if self.wiki_classes!='':
self.wiki.write('= Classes =\n\n')
self.wiki.write(self.wiki_classes)
self.wiki.write('\n')
self.wiki.close()
def addFile(self, fn, title, fls = True):
"""Given a filename and section title adds the contents of said file to the output. Various flags influence how this works."""
html = []
wiki = []
for i, line in enumerate(open(fn,'r').readlines()):
hl = line.replace('\n', '')
if i==0 and fls:
hl = '<strong>' + hl + '</strong>'
for ext in ['py','txt']:
if '.%s - '%ext in hl:
s = hl.split('.%s - '%ext, 1)
hl = '<i>' + s[0] + '.%s</i> - '%ext + s[1]
html.append(hl)
wl = line.strip()
if i==0 and fls:
wl = '*%s*'%wl
for ext in ['py','txt']:
if '.%s - '%ext in wl:
s = wl.split('.%s - '%ext, 1)
wl = '`' + s[0] + '.%s` - '%ext + s[1] + '\n'
wiki.append(wl)
self.html.write(self.doc.bigsection(title, '#ffffff', '#7799ee', '<br/>'.join(html)))
self.wiki.write('== %s ==\n'%title)
self.wiki.write('\n'.join(wiki))
self.wiki.write('----\n\n')
def addVariable(self, var, desc):
"""Adds a variable to the documentation. Given the nature of this you provide it as a pair of strings - one referencing the variable, the other some kind of description of its use etc.."""
self.html_variables += '<strong>%s</strong><br/>'%var
self.html_variables += '%s<br/><br/>\n'%desc
self.wiki_variables += '*`%s`*\n'%var
self.wiki_variables += ' %s\n\n'%desc
def addFunction(self, func):
"""Adds a function to the documentation. You provide the actual function instance."""
self.html_functions += self.doc.docroutine(func).replace(' ',' ')
self.html_functions += '\n'
name = func.__name__
args, varargs, keywords, defaults = inspect.getargspec(func)
doc = inspect.getdoc(func)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
self.wiki_functions += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_functions += ' %s\n\n'%doc
def addClass(self, cls):
"""Adds a class to the documentation. You provide the actual class object."""
self.html_classes += self.doc.docclass(cls).replace(' ',' ')
self.html_classes += '\n'
name = cls.__name__
parents = filter(lambda a: a!=cls, inspect.getmro(cls))
doc = inspect.getdoc(cls)
par_str = ''
if len(parents)!=0:
par_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda p: p.__name__, parents))
self.wiki_classes += '== %s(%s) ==\n'%(name, par_str)
self.wiki_classes += ' %s\n\n'%doc
methods = inspect.getmembers(cls, inspect.ismethod)
def method_key(pair):
if pair[0]=='__init__': return '___'
else: return pair[0]
methods.sort(key=method_key)
for name, method in methods:
if not name.startswith('_%s'%cls.__name__):
args, varargs, keywords, defaults = inspect.getargspec(method)
if defaults==None: defaults = list()
defaults = (len(args)-len(defaults)) * [None] + list(defaults)
arg_str = ''
if len(args)!=0:
arg_str += reduce(lambda a, b: '%s, %s'%(a,b), map(lambda arg, d: arg if d==None else '%s = %s'%(arg,d), args, defaults))
if varargs!=None:
arg_str += ', *%s'%varargs if arg_str!='' else '*%s'%varargs
if keywords!=None:
arg_str += ', **%s'%keywords if arg_str!='' else '**%s'%keywords
def fetch_doc(cls, name):
try:
method = getattr(cls, name)
if method.__doc__!=None: return inspect.getdoc(method)
except: pass
for parent in filter(lambda a: a!=cls, inspect.getmro(cls)):
ret = fetch_doc(parent, name)
if ret!=None: return ret
return None
doc = fetch_doc(cls, name)
self.wiki_classes += '*`%s(%s)`*\n'%(name, arg_str)
self.wiki_classes += ' %s\n\n'%doc
variables = inspect.getmembers(cls, lambda x: isinstance(x, int) or isinstance(x, str) or isinstance(x, float))
for name, var in variables:
if not name.startswith('__'):
self.wiki_classes += '*`%s`* = %s\n\n'%(name, str(var))
| [
[
1,
0,
0.0634,
0.0049,
0,
0.66,
0,
291,
0,
1,
0,
0,
291,
0,
0
],
[
1,
0,
0.0683,
0.0049,
0,
0.66,
0.5,
878,
0,
1,
0,
0,
878,
0,
0
],
[
3,
0,
0.5439,
0.9171,
0,
0.6... | [
"import pydoc",
"import inspect",
"class DocGen:\n \"\"\"A helper class that is used to generate documentation for the system. Outputs multiple formats simultaneously, specifically html for local reading with a webbrowser and the markup used by the wiki system on Google code.\"\"\"\n def __init__(self, name, ... |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from ctypes import *
def setProcName(name):
"""Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differing amounts in differing cases."""
# Call the process control function...
libc = cdll.LoadLibrary('libc.so.6')
libc.prctl(15, c_char_p(name), 0, 0, 0)
# Update argv...
charPP = POINTER(POINTER(c_char))
argv = charPP.in_dll(libc,'_dl_argv')
size = libc.strlen(argv[0])
libc.strncpy(argv[0],c_char_p(name),size)
if __name__=='__main__':
# Quick test that it works...
import os
ps1 = 'ps'
ps2 = 'ps -f'
os.system(ps1)
os.system(ps2)
setProcName('wibble_wobble')
os.system(ps1)
os.system(ps2)
| [
[
1,
0,
0.3636,
0.0227,
0,
0.66,
0,
182,
0,
1,
0,
0,
182,
0,
0
],
[
2,
0,
0.5682,
0.25,
0,
0.66,
0.5,
903,
0,
1,
0,
0,
0,
0,
9
],
[
8,
1,
0.4773,
0.0227,
1,
0.44,
... | [
"from ctypes import *",
"def setProcName(name):\n \"\"\"Sets the process name, linux only - useful for those programs where you might want to do a killall, but don't want to slaughter all the other python processes. Note that there are multiple mechanisms, and that the given new name can be shortened by differin... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import multiprocessing as mp
import multiprocessing.synchronize # To make sure we have all the functionality.
import types
import marshal
import unittest
def repeat(x):
"""A generator that repeats the input forever - can be used with the mp_map function to give data to a function that is constant."""
while True: yield x
def run_code(code,args):
"""Internal use function that does the work in each process."""
code = marshal.loads(code)
func = types.FunctionType(code, globals(), '_')
return func(*args)
def mp_map(func, *iters, **keywords):
"""A multiprocess version of the map function. Note that func must limit itself to the data provided - if it accesses anything else (globals, locals to its definition.) it will fail. There is a repeat generator provided in this module to work around such issues. Note that, unlike map, this iterates the length of the shortest of inputs, rather than the longest - whilst this makes it not a perfect substitute it makes passing constant argumenmts easier as they can just repeat for infinity."""
if 'pool' in keywords: pool = keywords['pool']
else: pool = mp.Pool()
code = marshal.dumps(func.func_code)
jobs = []
for args in zip(*iters):
jobs.append(pool.apply_async(run_code,(code,args)))
for i in xrange(len(jobs)):
jobs[i] = jobs[i].get()
return jobs
class TestMpMap(unittest.TestCase):
def test_simple1(self):
data = ['a','b','c','d']
def noop(data):
return data
data_noop = mp_map(noop, data)
self.assertEqual(data, data_noop)
def test_simple2(self):
data = [x for x in xrange(1000)]
data_double = mp_map(lambda a: a*2, data)
self.assertEqual(map(lambda a: a*2,data), data_double)
def test_gen(self):
def gen():
for i in xrange(100): yield i
data_double = mp_map(lambda a: a*2, gen())
self.assertEqual(map(lambda a: a*2,gen()), data_double)
def test_repeat(self):
def mult(a,b):
return a*b
data = [x for x in xrange(50,5000,5)]
data_triple = mp_map(mult, data, repeat(3))
self.assertEqual(map(lambda a: a*3,data),data_triple)
def test_none(self):
data = []
data_sqr = mp_map(lambda x: x*x, data)
self.assertEqual([],data_sqr)
if __name__ == '__main__':
unittest.main()
| [
[
1,
0,
0.1456,
0.0097,
0,
0.66,
0,
901,
0,
1,
0,
0,
901,
0,
0
],
[
1,
0,
0.1553,
0.0097,
0,
0.66,
0.1111,
99,
0,
1,
0,
0,
99,
0,
0
],
[
1,
0,
0.1748,
0.0097,
0,
0.... | [
"import multiprocessing as mp",
"import multiprocessing.synchronize # To make sure we have all the functionality.",
"import types",
"import marshal",
"import unittest",
"def repeat(x):\n \"\"\"A generator that repeats the input forever - can be used with the mp_map function to give data to a function tha... |
# -*- coding: utf-8 -*-
# Copyright (c) 2011, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from utils.start_cpp import start_cpp
# Defines helper functions for accessing numpy arrays...
numpy_util_code = start_cpp() + """
#ifndef NUMPY_UTIL_CODE
#define NUMPY_UTIL_CODE
float & Float1D(PyArrayObject * arr, int index = 0)
{
return *(float*)(arr->data + index*arr->strides[0]);
}
float & Float2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
float & Float3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
return *(float*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
unsigned char & Byte1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index*arr->strides[0]);
}
unsigned char & Byte2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
unsigned char & Byte3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(unsigned char));
return *(unsigned char*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
int & Int1D(PyArrayObject * arr, int index = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index*arr->strides[0]);
}
int & Int2D(PyArrayObject * arr, int index1 = 0, int index2 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1]);
}
int & Int3D(PyArrayObject * arr, int index1 = 0, int index2 = 0, int index3 = 0)
{
//assert(arr->strides[0]==sizeof(int));
return *(int*)(arr->data + index1*arr->strides[0] + index2*arr->strides[1] + index3*arr->strides[2]);
}
#endif
"""
| [
[
1,
0,
0.1923,
0.0128,
0,
0.66,
0,
972,
0,
1,
0,
0,
972,
0,
0
],
[
14,
0,
0.6282,
0.7564,
0,
0.66,
1,
799,
4,
0,
0,
0,
0,
0,
1
]
] | [
"from utils.start_cpp import start_cpp",
"numpy_util_code = start_cpp() + \"\"\"\n#ifndef NUMPY_UTIL_CODE\n#define NUMPY_UTIL_CODE\n\nfloat & Float1D(PyArrayObject * arr, int index = 0)\n{\n return *(float*)(arr->data + index*arr->strides[0]);\n}"
] |
# -*- coding: utf-8 -*-
# Copyright 2011 Tom SF Haines
# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
import math
import numpy
import numpy.linalg
import numpy.random
from wishart import Wishart
from gaussian import Gaussian
from student_t import StudentT
class GaussianPrior:
"""The conjugate prior for the multivariate Gaussian distribution. Maintains the 4 values and supports various operations of interest - initialisation of prior, Bayesian update, drawing a Gaussian and calculating the probability of a data point comming from a Gaussian drawn from the distribution. Not a particularly efficient implimentation, and it has no numerical protection against extremelly large data sets. Interface is not entirly orthogonal, due to the demands of real world usage."""
def __init__(self, dims):
"""Initialises with everything zeroed out, such that a prior must added before anything interesting is done. Supports cloning."""
if isinstance(dims, GaussianPrior):
self.invShape = dims.invShape.copy()
self.shape = dims.shape.copy() if dims.shape!=None else None
self.mu = dims.mu.copy()
self.n = dims.n
self.k = dims.k
else:
self.invShape = numpy.zeros((dims,dims), dtype=numpy.float32) # The inverse of lambda in the equations.
self.shape = None # Cached value - inverse is considered primary.
self.mu = numpy.zeros(dims, dtype=numpy.float32)
self.n = 0.0
self.k = 0.0
def reset(self):
"""Resets as though there is no data, other than the dimensions of course."""
self.invShape[:] = 0.0
self.shape = None
self.mu[:] = 0.0
self.n = 0.0
self.k = 0.0
def addPrior(self, mean, covariance, weight = None):
"""Adds a prior to the structure, as an estimate of the mean and covariance matrix, with a weight which can be interpreted as how many samples that estimate is worth. Note the use of 'add' - you can call this after adding actual samples, or repeatedly. If weight is omitted it defaults to the number of dimensions, as the total weight in the system must match or excede this value before draws etc can be done."""
if weight==None: weight = float(self.mu.shape[0])
delta = mean - self.mu
self.invShape += weight * covariance # *weight converts to a scatter matrix.
self.invShape += ((self.k*weight)/(self.k+weight)) * numpy.outer(delta,delta)
self.shape = None
self.mu += (weight/(self.k+weight)) * delta
self.n += weight
self.k += weight
def addSample(self, sample, weight=1.0):
"""Updates the prior given a single sample drawn from the Gaussian being estimated. Can have a weight provided, in which case it will be equivalent to repetition of that data point, where the repetition count can be fractional."""
sample = numpy.asarray(sample, dtype=numpy.float32)
if len(sample.shape)==0: sample.shape = (1,)
delta = sample - self.mu
self.invShape += (weight*self.k/(self.k+weight)) * numpy.outer(delta,delta)
self.shape = None
self.mu += delta * (weight / (self.k+weight))
self.n += weight
self.k += weight
def remSample(self, sample):
"""Does the inverse of addSample, to in effect remove a previously added sample. Note that the issues of floating point (in-)accuracy mean its not perfect, and removing all samples is bad if there is no prior. Does not support weighting - effectvily removes a sample of weight 1."""
sample = numpy.asarray(sample, dtype=numpy.float32)
if len(sample.shape)==0: sample.shape = (1,)
delta = sample - self.mu
self.k -= 1.0
self.n -= 1.0
self.mu -= delta / self.k
self.invShape -= ((self.k+1.0)/self.k) * numpy.outer(delta,delta)
self.shape = None
def addSamples(self, samples, weight = None):
"""Updates the prior given multiple samples drawn from the Gaussian being estimated. Expects a data matrix ([sample, position in sample]), or an object that numpy.asarray will interpret as such. Note that if you have only a few samples it might be faster to repeatedly call addSample, as this is designed to be efficient for hundreds+ of samples. You can optionally weight the samples, by providing an array to the weight parameter."""
samples = numpy.asarray(samples, dtype=numpy.float32)
# Calculate the mean and scatter matrices...
if weight==None:
# Unweighted samples...
# Calculate the mean and scatter matrix...
d = self.mu.shape[0]
num = samples.shape[0]
mean = numpy.average(samples, axis=0)
scatter = numpy.tensordot(delta, delta, ([0],[0]))
else:
# Weighted samples...
# Calculate the mean and scatter matrix...
d = self.mu.shape[0]
num = weight.sum()
mean = numpy.average(samples, axis=0, weights=weight)
delta = samples - mean.reshape((1,-1))
scatter = numpy.tensordot(weight.reshape((-1,1))*delta, delta, ([0],[0]))
# Update parameters...
delta = mean-self.mu
self.invShape += scatter
self.invShape += ((self.k*num)/(self.k+num)) * numpy.outer(delta,delta)
self.shape = None
self.mu += (num/(self.k+num)) * delta
self.n += num
self.k += num
def addGP(self, gp):
"""Adds another Gaussian prior, combining the two."""
delta = gp.mu - self.mu
self.invShape += gp.invShape
self.invShape += ((gp.k*self.k)/(gp.k+self.k)) * numpy.outer(delta,delta)
self.shape = None
self.mu += (gp.k/(self.k+gp.k)) * delta
self.n += gp.n
self.k += gp.k
def make_safe(self):
"""Checks for a singular inverse shape matrix - if singular replaces it with the identity. Also makes sure n and k are not less than the number of dimensions, clamping them if need be. obviously the result of this is quite arbitary, but its better than getting a crash from bad data."""
dims = self.mu.shape[0]
det = math.fabs(numpy.linalg.det(self.invShape))
if det<1e-3:
self.invShape = numpy.identity(dims, dtype=numpy.float32)
if self.n<dims: self.n = dims
if self.k<1e-3: self.k = 1e-3
def reweight(self, newN = None, newK = None):
"""A slightly cheaky method that reweights the gp such that it has the new values of n and k, effectivly adjusting the relevant weightings of the samples - can be useful for generating a prior for some GPs using the data stored in those GPs. If a new k is not provided it is set to n; if a new n is not provided it is set to the number of dimensions."""
if newN==None: newN = float(self.mu.shape[0])
if newK==None: newK = newN
self.invShape *= newN / self.n
self.shape = None
self.n = newN
self.k = newK
def getN(self):
"""Returns n."""
return self.n
def getK(self):
"""Returns k."""
return self.k
def getMu(self):
"""Returns mu."""
return self.mu
def getLambda(self):
"""Returns lambda."""
if self.shape==None:
self.shape = numpy.linalg.inv(self.invShape)
return self.shape
def getInverseLambda(self):
"""Returns the inverse of lambda."""
return self.invShape
def safe(self):
"""Returns true if it is possible to sample the prior, work out the probability of samples or work out the probability of samples being drawn from a collapsed sample - basically a test that there is enough information."""
return self.n>=self.mu.shape[0] and self.k>0.0
def prob(self, gauss):
"""Returns the probability of drawing the provided Gaussian from this prior."""
d = self.mu.shape[0]
wishart = Wishart(d)
gaussian = Gaussian(d)
wishart.setDof(self.n)
wishart.setScale(self.getLambda())
gaussian.setMean(self.mu)
gaussian.setPrecision(self.k*gauss.getPrecision())
return wishart.prob(gauss.getPrecision()) * gaussian.prob(gauss.getMean())
def intProb(self):
"""Returns a multivariate student-t distribution object that gives the probability of drawing a sample from a Gaussian drawn from this prior, with the Gaussian integrated out. You may then call the prob method of this object on each sample obtained."""
d = self.mu.shape[0]
st = StudentT(d)
dof = self.n-d+1.0
st.setDOF(dof)
st.setLoc(self.mu)
mult = self.k*dof / (self.k+1.0)
st.setInvScale(mult * self.getLambda())
return st
def sample(self):
"""Returns a Gaussian, drawn from this prior."""
d = self.mu.shape[0]
wishart = Wishart(d)
gaussian = Gaussian(d)
ret = Gaussian(d)
wishart.setDof(self.n)
wishart.setScale(self.getLambda())
ret.setPrecision(wishart.sample())
gaussian.setPrecision(self.k*ret.getPrecision())
gaussian.setMean(self.mu)
ret.setMean(gaussian.sample())
return ret
def __str__(self):
return '{n:%f, k:%f, mu:%s, lambda:%s}'%(self.n, self.k, str(self.mu), str(self.getLambda()))
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"import math",
"import numpy",
"import numpy.linalg",
"import numpy.random",
"from wishart import Wishart",
"from gaussian import Gaussian",
"from student_t import StudentT",
"class GaussianPrior:\n \"\"\"The conjugate prior for the multivariate Gaussian distribution. Maintains the 4 values and suppo... |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2011 Tom SF Haines
# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
import gcp
from utils import doc_gen
# Setup...
doc = doc_gen.DocGen('gcp', 'Gaussian Conjugate Prior', 'Library of distributions focused on the Gaussian and its conjugate prior')
doc.addFile('readme.txt', 'Overview')
# Classes...
doc.addClass(gcp.Gaussian)
doc.addClass(gcp.GaussianInc)
doc.addClass(gcp.Wishart)
doc.addClass(gcp.StudentT)
doc.addClass(gcp.GaussianPrior)
| [
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"import gcp",
"from utils import doc_gen",
"doc = doc_gen.DocGen('gcp', 'Gaussian Conjugate Prior', 'Library of distributions focused on the Gaussian and its conjugate prior')",
"doc.addFile('readme.txt', 'Overview')",
"doc.addClass(gcp.Gaussian)",
"doc.addClass(gcp.GaussianInc)",
"doc.addClass(gcp.Wish... |
# -*- coding: utf-8 -*-
# Copyright 2011 Tom SF Haines
# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
from gaussian import Gaussian
from gaussian_inc import GaussianInc
from wishart import Wishart
from student_t import StudentT
from gaussian_prior import GaussianPrior
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"from gaussian import Gaussian",
"from gaussian_inc import GaussianInc",
"from wishart import Wishart",
"from student_t import StudentT",
"from gaussian_prior import GaussianPrior"
] |
# -*- coding: utf-8 -*-
# Copyright 2011 Tom SF Haines
# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
import math
import numpy
import numpy.linalg
import numpy.random
class Gaussian:
"""A basic multivariate Gaussian class. Has caching to avoid duplicate calculation."""
def __init__(self, dims):
"""dims is the number of dimensions. Initialises with mu at the origin and the identity matrix for the precision/covariance. dims can also be another Gaussian object, in which case it acts as a copy constructor."""
if isinstance(dims, Gaussian):
self.mean = dims.mean.copy()
self.precision = dims.precision.copy() if dims.precision!=None else None
self.covariance = dims.covariance.copy() if dims.covariance!=None else None
self.norm = dims.norm
self.cholesky = dims.cholesky.copy() if dims.cholesky!=None else None
else:
self.mean = numpy.zeros(dims, dtype=numpy.float32)
self.precision = numpy.identity(dims, dtype=numpy.float32)
self.covariance = None
self.norm = None
self.cholesky = None
def setMean(self, mean):
"""Sets the mean - you can use anything numpy will interprete as a 1D array of the correct length."""
nm = numpy.array(mean, dtype=numpy.float32)
assert(nm.shape==self.mean.shape)
self.mean = nm
def setPrecision(self, precision):
"""Sets the precision matrix. Alternativly you can use the setCovariance method."""
np = numpy.array(precision, dtype=numpy.float32)
assert(np.shape==(self.mean.shape[0],self.mean.shape[0]))
self.precision = np
self.covariance = None
self.norm = None
self.cholesky = None
def setCovariance(self, covariance):
"""Sets the covariance matrix. Alternativly you can use the setPrecision method."""
nc = numpy.array(covariance, dtype=numpy.float32)
assert(nc.shape==(self.mean.shape[0],self.mean.shape[0]))
self.covariance = nc
self.precision = None
self.norm = None
self.cholesky = None
def getMean(self):
"""Returns the mean."""
return self.mean
def getPrecision(self):
"""Returns the precision matrix."""
if self.precision==None:
self.precision = numpy.linalg.inv(self.covariance)
return self.precision
def getCovariance(self):
"""Returns the covariance matrix."""
if self.covariance==None:
self.covariance = numpy.linalg.inv(self.precision)
return self.covariance
def getNorm(self):
"""Returns the normalising constant of the distribution. Typically for internal use only."""
if self.norm==None:
self.norm = math.pow(2.0*math.pi,-0.5*self.mean.shape[0]) * math.sqrt(numpy.linalg.det(self.getPrecision()))
return self.norm
def prob(self, x):
"""Given a vector x evaluates the probability density function at that point."""
x = numpy.asarray(x)
offset = x - self.mean
val = numpy.dot(offset,numpy.dot(self.getPrecision(),offset))
return self.getNorm() * math.exp(-0.5 * val)
def sample(self):
"""Draws and returns a sample from the distribution."""
if self.cholesky==None:
self.cholesky = numpy.linalg.cholesky(self.getCovariance())
z = numpy.random.normal(size=self.mean.shape)
return self.mean + numpy.dot(self.cholesky,z)
def __str__(self):
return '{mean:%s, covar:%s}'%(str(self.mean), str(self.getCovariance()))
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"import numpy.random",
"class Gaussian:\n \"\"\"A basic multivariate Gaussian class. Has caching to avoid duplicate calculation.\"\"\"\n def __init__(self, dims):\n \"\"\"dims is the number of dimensions. Initialises with mu at the origin and the id... |
#! /usr/bin/env python
# Copyright 2011 Tom SF Haines
# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
import dpgmm
from utils import doc_gen
# Setup...
doc = doc_gen.DocGen('dpgmm', 'Dirichlet Process Gaussian Mixture Model', 'Dynamically resizing Gaussian mixture model')
doc.addFile('readme.txt', 'Overview')
# Classes...
doc.addClass(dpgmm.DPGMM)
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"doc = doc_gen.DocGen('dpgmm', 'Dirichlet Process Gaussian Mixture Model', 'Dynamically resizing Gaussian mixture model')",
"doc.addFile('readme.txt', 'Overview')",
"doc.addClass(dpgmm.DPGMM)"
] |
# -*- coding: utf-8 -*-
# Copyright 2010 Tom SF Haines
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from params import Params
from document import Document
from corpus import Corpus
# Load in a suitable solver - autodetect the most powerful supported...
try:
from solve_weave_mp import fit, fitDoc
__fitter = 'multiprocess weave'
except:
try:
from solve_weave import fit, fitDoc
__fitter = 'weave'
except:
raise Exception('All of the rLDA solvers failed to load.')
def getAlgorithm():
"""Returns a text string indicating which implimentation of the fitting algorithm is being used."""
global __fitter
return __fitter | [
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" from solve_weave_mp import fit, fitD... |
# -*- coding: utf-8 -*-
# Copyright 2010 Tom SF Haines
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import heapq
import numpy
import corpus
class State:
"""The state required by the solvers - stored as a few large numpy arrays for conveniance and speed. It is generated from a Corpus, but once generated is stand alone. It includes the ability to split out the final answer into the Corpus, as this is not seen as time critical (Must be the exact same and unedited Corpus.). To support parallel sampling you can duplicate this object, run the solvers on each duplicate, then merge them together, before extracting the final answer back into the Corpus."""
def __init__(self, obj):
"""Prepares the state object given a corpus, or alternativly another State, which it will then clone."""
if isinstance(obj,State):
self.alpha = obj.alpha
self.beta = obj.beta
self.gamma = obj.gamma
self.state = obj.state.copy()
self.sIndex = obj.sIndex.copy()
self.ir = obj.ir.copy()
self.wrt = obj.wrt.copy()
self.mt = obj.mt.copy()
self.mr = obj.mr.copy()
self.dt = obj.dt.copy()
else:
# Assume obj is a Corpus, or has the Corpus interface, and work from there.
# Counts of the assorted things avaliable...
sCount = obj.getSampleCount()
dCount = len(obj.documentList())
tCount = obj.getTopicCount()
rCount = obj.getRegionCount()
iCount = obj.getMaxIdentNum() + 1
wCount = obj.getMaxWordNum() + 1
# Extract the parameters needed from the corpus...
self.alpha = obj.getAlpha()
self.beta = obj.getBeta()
self.gamma = obj.getGamma()
# Create the samples array, this being an array with 4 columns - [document, topic, identifier, word]. It is sorted by identifier, and an index exists to grab the ranges for each identifier. During runtime only the topic column changes, during the t phase...
# Make array, plus indexing array...
self.state = numpy.empty((sCount,4), dtype=numpy.uint)
self.sIndex = numpy.zeros(iCount+1, dtype=numpy.uint)
# Fill array...
index = 0
for doc in obj.documentList():
dNum = doc.getNum()
words = doc.getWords()
for j in xrange(words.shape[0]):
for _ in xrange(words[j,2]): # Iterate the count of the number of words.
self.state[index,0] = dNum
self.state[index,1] = 1000000 # Dummy value.
self.state[index,2] = words[j,0]
self.state[index,3] = words[j,1]
self.sIndex[words[j,0]+1] += 1
index += 1
assert(index==sCount)
# Sort array by identifier...
self.state = self.state[self.state[:,2].argsort(),:]
# Create index from the data currently in the index...
for i in xrange(iCount):
self.sIndex[i+1] += self.sIndex[i]
assert(self.sIndex[-1]==sCount)
# Create the remaining state - the mapping from identifier to region - a simple vector indexed by identifier. Randomise it...
self.ir = numpy.random.randint(0, rCount, iCount)
# Create the region/topic/word count, of how many times each combo exists, [word,region,topic]. Initialise it zeroed out ready to be grown...
self.wrt = numpy.zeros((wCount,rCount,tCount), dtype=numpy.uint)
# Marginalised version of the wrt matrix - the first is marginalised over w and r, the second over w and t...
self.mt = numpy.zeros(tCount, dtype=numpy.uint)
self.mr = numpy.zeros(rCount, dtype=numpy.uint)
# Create the topic/document count, of how many instances of each topic exist in each document, [document,topic]. Zeroed out again...
self.dt = numpy.zeros((dCount,tCount), dtype=numpy.uint)
# Create the data structure to store sampled states in - just a list of tuples, (ir,wrt,dt)...
self.samples = []
def absorbClone(self,clone):
"""Absorbs a clone of this object by copying its sampled states into this objects sampled states list."""
if len(self.samples)==0:
self.samples += clone.samples
else:
# Need to merge the two samples lists - unfortunatly both regions and topics can end up at different indices, so we have to match them up (Which is of course assuming they can be matched up, which is not technically true. Works reasonably well however.)...
# First, regions...
# For each region calculate a multinomial from region to identifier...
# (Also adds one to every bin, to simulate a Dirichlet prior with a single parameter of 1, i.e. a flat prior.)
rCount = self.wrt.shape[1]
# self...
sMult = numpy.ones((rCount,self.ir.shape[0]), dtype=numpy.float_)
for sample in self.samples:
sMult[sample[0],numpy.arange(len(sample[0]))] += 1.0
sMult = (sMult.T / sMult.sum(axis=1)).T
# clone...
cMult = numpy.ones((rCount,self.ir.shape[0]), dtype=numpy.float_)
for sample in clone.samples:
cMult[sample[0],numpy.arange(len(sample[0]))] += 1.0
cMult = (cMult.T / cMult.sum(axis=1)).T
# Calculate Kullback-Leiber divergance between them all...
regionHeap = [] # List of tuples (symmetric kl, self r, clone r)
for sr in xrange(rCount):
for cr in xrange(rCount):
cost = 0.5 * (sMult[sr,:]*numpy.log(sMult[sr,:]/cMult[cr,:]) + cMult[cr,:]*numpy.log(cMult[cr,:]/sMult[sr,:])).sum()
regionHeap.append((cost,sr,cr))
# Use a heap to match them up, using a greedy algorithm...
heapq.heapify(regionHeap)
sUsed = numpy.zeros(rCount,dtype=numpy.int_)
cUsed = numpy.zeros(rCount,dtype=numpy.int_)
remain = rCount
regionC2S = numpy.zeros(rCount,dtype=numpy.int_)
regionS2C = numpy.zeros(rCount,dtype=numpy.int_)
while remain!=0:
match = heapq.heappop(regionHeap)
if (sUsed[match[1]]==0) and (cUsed[match[2]]==0):
sUsed[match[1]] = 1
cUsed[match[2]] = 1
remain -= 1
regionS2C[match[1]] = match[2]
regionC2S[match[2]] = match[1]
# Second, topics - same idea as above basically...
tCount = self.wrt.shape[2]
# self...
sMult = numpy.zeros(self.wrt.shape,dtype=numpy.float_)
for i, sample in enumerate(self.samples):
sMult += ((sample[1].astype(numpy.float_) + self.beta) - sMult) / float(i+1)
for t in xrange(tCount):
sMult[:,:,t] /= sMult[:,:,t].sum()
# clone...
cMult = numpy.zeros(self.wrt.shape,dtype=numpy.float_)
for i, sample in enumerate(clone.samples):
cMult += ((sample[1][:,regionS2C,:].astype(numpy.float_) + self.beta) - cMult) / float(i+1)
for t in xrange(tCount):
cMult[:,:,t] /= cMult[:,:,t].sum()
# Calculate Kullback-Leiber divergance between them all...
topicHeap = [] # List of tuples (symmetric kl, self t, clone t)
for st in xrange(tCount):
for ct in xrange(tCount):
cost = 0.5 * (sMult[:,:,st]*numpy.log(sMult[:,:,st]/cMult[:,:,ct]) + cMult[:,:,ct]*numpy.log(cMult[:,:,ct]/sMult[:,:,st])).sum()
topicHeap.append((cost,st,ct))
# Use a heap to match them up, using a greedy algorithm...
heapq.heapify(topicHeap)
sUsed = numpy.zeros(tCount,dtype=numpy.int_)
cUsed = numpy.zeros(tCount,dtype=numpy.int_)
remain = tCount
topicS2C = numpy.zeros(tCount,dtype=numpy.int_)
while remain!=0:
match = heapq.heappop(topicHeap)
if (sUsed[match[1]]==0) and (cUsed[match[2]]==0):
sUsed[match[1]] = 1
cUsed[match[2]] = 1
remain -= 1
topicS2C[match[1]] = match[2]
# Thirdly, merge in the data, making the relevant transform...
for sample in clone.samples:
nIR = regionC2S[sample[0]]
nWRT = sample[1][:,regionS2C,:][:,:,topicS2C]
nDT = sample[2][:,topicS2C]
self.samples.append((nIR,nWRT,nDT))
def extractModel(self,corpus):
"""Extracts the calculated model into the given corpus, to be called once the sampling is done."""
assert(len(self.samples)>0)
ir = numpy.zeros((self.ir.shape[0],self.wrt.shape[1]),dtype=numpy.float_)
wrt = numpy.zeros(self.wrt.shape,dtype=numpy.float_)
dt = numpy.zeros(self.dt.shape,dtype=numpy.float_)
for i in xrange(len(self.samples)):
sIR, sWRT, sDT = self.samples[i]
ir[numpy.arange(len(sIR)),sIR] += 1.0 # I ignore gamma - I'ld rather keep the distributions hard and I abused it for something else already.
wrt += ((sWRT.astype(numpy.float_) + self.beta) - wrt) / float(i+1)
dt += ((sDT.astype(numpy.float_) + self.alpha) - dt) / float(i+1)
corpus.setModel(wrt,ir)
for doc in corpus.documentList():
doc.setModel(dt[doc.getNum(),:])
def sample(self):
"""Samples the current state, storing it so it can be later used to determine the model."""
ss = (self.ir.copy(),self.wrt.copy(),self.dt.copy())
self.samples.append(ss)
| [
[
1,
0,
0.0885,
0.0044,
0,
0.66,
0,
251,
0,
1,
0,
0,
251,
0,
0
],
[
1,
0,
0.0929,
0.0044,
0,
0.66,
0.3333,
954,
0,
1,
0,
0,
954,
0,
0
],
[
1,
0,
0.0973,
0.0044,
0,
... | [
"import heapq",
"import numpy",
"import corpus",
"class State:\n \"\"\"The state required by the solvers - stored as a few large numpy arrays for conveniance and speed. It is generated from a Corpus, but once generated is stand alone. It includes the ability to split out the final answer into the Corpus, as ... |
# -*- coding: utf-8 -*-
# Copyright 2010 Tom SF Haines
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
class Params:
"""Parameters for running the fitter that are universal to all fitters."""
def __init__(self):
self.runs = 8
self.samples = 10
self.burnIn = 1000
self.lag = 100
self.iterT = 1
self.iterR = 1
def setRuns(self, runs):
"""Sets the number of runs, i.e. how many seperate chains are run."""
self.runs = runs
def setSamples(self, samples):
"""Number of samples to extract from each chain - total number of samples going into the final estimate will then be sampels*runs."""
self.samples = samples
def setBurnIn(self, burnIn):
"""Number of Gibbs iterations to do for burn in before sampling starts."""
self.burnIn = burnIn
def setLag(self, lag):
"""Number of Gibbs iterations to do between samples."""
self.lag = lag
def setIterT(self, iterT):
"""Number of iterations of updating t to do for each inner loop."""
self.iterT = iterT
def setIterR(self, iterR):
"""Number of iterations of updating r to do for each inner loop."""
self.iterR = iterR
def getRuns(self):
"""Returns the number of runs."""
return self.runs
def getSamples(self):
"""Returns the number of samples."""
return self.samples
def getBurnIn(self):
"""Returns the burn in length."""
return self.burnIn
def getLag(self):
"""Returns the lag length."""
return self.lag
def getIterT(self):
"""Return the number of t iterations."""
return self.iterT
def getIterR(self):
"""Return the number of r iterations."""
return self.iterR
def fromArgs(self, args, prefix = ''):
"""Extracts from an arg string, typically sys.argv[1:], the parameters, leaving them untouched if not given. Uses --runs, --samples, --burnIn, --lag, --iterT and --iterR. Can optionally provide a prefix which is inserted after the '--'"""
def getParam(args, prefix, name, default):
try:
ind = args[:-1].index('--'+prefix+name)
return int(args[ind+1])
except:
return default
self.runs = getParam(args,prefix,'runs' ,self.runs)
self.samples = getParam(args,prefix,'samples',self.samples)
self.burnIn = getParam(args,prefix,'burnIn' ,self.burnIn)
self.lag = getParam(args,prefix,'lag' ,self.lag)
self.iterT = getParam(args,prefix,'iterT' ,self.iterT)
self.iterR = getParam(args,prefix,'iterr' ,self.iterR)
| [
[
3,
0,
0.6031,
0.8041,
0,
0.66,
0,
219,
0,
15,
0,
0,
0,
0,
8
],
[
8,
1,
0.2165,
0.0103,
1,
0.15,
0,
0,
1,
0,
0,
0,
0,
0,
0
],
[
2,
1,
0.2629,
0.0825,
1,
0.15,
... | [
"class Params:\n \"\"\"Parameters for running the fitter that are universal to all fitters.\"\"\"\n def __init__(self):\n self.runs = 8\n self.samples = 10\n self.burnIn = 1000\n self.lag = 100",
" \"\"\"Parameters for running the fitter that are universal to all fitters.\"\"\"",
" def __init__(... |
# -*- coding: utf-8 -*-
# Copyright (c) 2010, Tom SF Haines
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import sys
import time
class ProgBar:
"""Simple console progress bar class. Note that object creation and destruction matter, as they indicate when processing starts and when it stops."""
def __init__(self, width = 60, onCallback = None):
self.start = time.time()
self.fill = 0
self.width = width
self.onCallback = onCallback
sys.stdout.write(('_'*self.width)+'\n')
sys.stdout.flush()
def __del__(self):
self.end = time.time()
self.__show(self.width)
sys.stdout.write('\nDone - '+str(self.end-self.start)+' seconds\n\n')
sys.stdout.flush()
def callback(self, nDone, nToDo):
"""Hand this into the callback of methods to get a progress bar - it works by users repeatedly calling it to indicate how many units of work they have done (nDone) out of the total number of units required (nToDo)."""
if self.onCallback:
self.onCallback()
n = int(float(self.width)*float(nDone)/float(nToDo))
n = min((n,self.width))
if n>self.fill:
self.__show(n)
def __show(self,n):
sys.stdout.write('|'*(n-self.fill))
sys.stdout.flush()
self.fill = n
| [
[
1,
0,
0.2941,
0.0196,
0,
0.66,
0,
509,
0,
1,
0,
0,
509,
0,
0
],
[
1,
0,
0.3137,
0.0196,
0,
0.66,
0.5,
654,
0,
1,
0,
0,
654,
0,
0
],
[
3,
0,
0.6863,
0.6078,
0,
0.6... | [
"import sys",
"import time",
"class ProgBar:\n \"\"\"Simple console progress bar class. Note that object creation and destruction matter, as they indicate when processing starts and when it stops.\"\"\"\n def __init__(self, width = 60, onCallback = None):\n self.start = time.time()\n self.fill = 0\n ... |
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