"""
Miscellaneous utility functions.
"""
from __future__ import division
__all__ = ["kbhit", "profile", "pushdir", "push_seed", "redirect_console"]
import sys
import os
import types
try: # CRUFT: python 2.x
from cStringIO import StringIO
except ImportError:
from io import StringIO
import numpy as np
from numpy import ascontiguousarray as _dense
# **DEPRECATED** we can import erf directly from scipy.special.erf
# so there is no longer a need for bumps.util.erf.
from scipy.special import erf
def parse_errfile(errfile):
"""
Parse dream statistics from a particular fit.
Returns overall chisq, list of chisq for individual models and
a parameter dictionary with attributes for number, name, mean, median,
p68 for 68% credible interval and p95 for 95% credible interval.
The parameter dictionary is keyed by parameter name.
Usually there is only one errfile in a directory, which can be
retrieved using::
import os.path
import glob
errfile = glob.glob(os.path.join(path, '*.err'))[0]
"""
from .dream.stats import parse_var
pars = []
chisq = []
overall = None
with open(errfile) as fid:
for line in fid:
if line.startswith("[overall"):
overall = float(line.split()[1][6:-1])
continue
if line.startswith("[chisq"):
chisq.append(float(line.split()[0][7:-1]))
continue
p = parse_var(line)
if p is not None:
pars.append(p)
if overall is None:
overall = chisq[0]
pardict = dict((p.name, p) for p in pars)
return overall, chisq, pardict
[docs]
def profile(fn, *args, **kw):
"""
Profile a function called with the given arguments.
"""
import cProfile
import pstats
result = [None]
def call():
result[0] = fn(*args, **kw)
datafile = 'profile.out'
cProfile.runctx('call()', dict(call=call), {}, datafile)
stats = pstats.Stats(datafile)
# order='calls'
order = 'cumulative'
# order='pcalls'
# order='time'
stats.sort_stats(order)
stats.print_stats()
os.unlink(datafile)
return result[0]
[docs]
def kbhit():
"""
Check whether a key has been pressed on the console.
"""
try: # Windows
import msvcrt
return msvcrt.kbhit()
except ImportError: # Unix
import select
i, _, _ = select.select([sys.stdin], [], [], 0.0001)
return sys.stdin in i
class DynamicModule(types.ModuleType):
def __init__(self, path, name):
self.__path__ = [path]
self.__name__ = name
# In the bowels of importlib the parent spec attribute is used to
# avoid circular imports, but only if spec is not None. This behaviour
# was observed on python 3.11, and perhaps earlier.
self.__spec__ = None
def relative_import(filename, module_name="relative_import"):
"""
Define an empty module allowing relative imports from a script.
By setting :code:`__package__ = relative_import(__file__)` at the top of
your script file you can even run your model as a python script. So long
as the script behaviour is isolated in :code:`if __name__ == "__main__":`
code block and :code:`problem = FitProblem(...)` is defined, the same model
can be used both within and outside of bumps.
"""
path = os.path.dirname(os.path.abspath(filename))
if (module_name in sys.modules
and not isinstance(sys.modules[module_name], DynamicModule)):
raise ImportError("relative import would override the existing module %s. Use another name"
% module_name)
sys.modules[module_name] = DynamicModule(path, module_name)
return module_name
[docs]
class redirect_console(object):
"""
Console output redirection context
The output can be redirected to a string, to an already opened file
(anything with a *write* attribute), or to a filename which will be
opened for the duration of the with context. Unless *stderr* is
specified, then both standard output and standard error are
redirected to the same file. The open file handle is returned on
enter, and (if it was not an already opened file) it is closed on exit.
If no file is specified, then output is redirected to a StringIO
object, which has a getvalue() method which can retrieve the string.
The StringIO object is deleted when the context ends, so be sure to
retrieve its value within the redirect_console context.
:Example:
Show that output is captured in a file:
>>> from bumps.util import redirect_console
>>> print("hello")
hello
>>> with redirect_console("redirect_out.log"):
... print("captured")
>>> print("hello")
hello
>>> print(open("redirect_out.log").read()[:-1])
captured
>>> import os; os.unlink("redirect_out.log")
Output can also be captured to a string:
>>> with redirect_console() as fid:
... print("captured to string")
... captured_string = fid.getvalue()
>>> print(captured_string.strip())
captured to string
"""
def __init__(self, stdout=None, stderr=None):
self.open_files = []
self.sys_stdout = []
self.sys_stderr = []
if stdout is None:
self.open_files.append(StringIO())
self.stdout = self.open_files[-1]
elif hasattr(stdout, 'write'):
self.stdout = stdout
else:
self.open_files.append(open(stdout, 'w'))
self.stdout = self.open_files[-1]
if stderr is None:
self.stderr = self.stdout
elif hasattr(stderr, 'write'):
self.stderr = stderr
else:
self.open_files.append(open(stderr, 'w'))
self.stderr = self.open_files[-1]
def __del__(self):
for f in self.open_files:
f.close()
def __enter__(self):
self.sys_stdout.append(sys.stdout)
self.sys_stderr.append(sys.stderr)
sys.stdout = self.stdout
sys.stderr = self.stderr
return self.open_files[-1]
def __exit__(self, *args):
sys.stdout = self.sys_stdout[-1]
sys.stderr = self.sys_stderr[-1]
del self.sys_stdout[-1]
del self.sys_stderr[-1]
return False
class push_python_path(object):
"""
Change sys.path for the duration of a with statement.
:Example:
Show that the original directory is restored::
>>> import sys, os
>>> original_path = list(sys.path)
>>> with push_python_path('/tmp'):
... assert sys.path[-1] == '/tmp'
>>> restored_path = list(sys.path)
>>> assert original_path == restored_path
"""
def __init__(self, path):
self.path = path
def __enter__(self):
sys.path.append(self.path)
def __exit__(self, *args):
del sys.path[-1]
[docs]
class pushdir(object):
"""
Change directories for the duration of a with statement.
:Example:
Show that the original directory is restored::
>>> import sys, os
>>> original_wd = os.getcwd()
>>> with pushdir(sys.path[0]):
... pushed_wd = os.getcwd()
... first_site = os.path.abspath(sys.path[0])
... assert pushed_wd == first_site
>>> restored_wd = os.getcwd()
>>> assert original_wd == restored_wd
"""
def __init__(self, path):
self.path = os.path.abspath(path)
def __enter__(self):
self._cwd = os.getcwd()
os.chdir(self.path)
def __exit__(self, *args):
os.chdir(self._cwd)
[docs]
class push_seed(object):
"""
Set the seed value for the random number generator.
When used in a with statement, the random number generator state is
restored after the with statement is complete.
:Parameters:
*seed* : int or array_like, optional
Seed for RandomState
:Example:
Seed can be used directly to set the seed::
>>> from numpy.random import randint
>>> push_seed(24)
<...push_seed object at...>
>>> print(randint(0,1000000,3))
[242082 899 211136]
Seed can also be used in a with statement, which sets the random
number generator state for the enclosed computations and restores
it to the previous state on completion::
>>> with push_seed(24):
... print(randint(0,1000000,3))
[242082 899 211136]
Using nested contexts, we can demonstrate that state is indeed
restored after the block completes::
>>> with push_seed(24):
... print(randint(0,1000000))
... with push_seed(24):
... print(randint(0,1000000,3))
... print(randint(0,1000000))
242082
[242082 899 211136]
899
The restore step is protected against exceptions in the block::
>>> with push_seed(24):
... print(randint(0,1000000))
... try:
... with push_seed(24):
... print(randint(0,1000000,3))
... raise Exception()
... except Exception:
... print("Exception raised")
... print(randint(0,1000000))
242082
[242082 899 211136]
Exception raised
899
"""
def __init__(self, seed=None):
self._state = np.random.get_state()
np.random.seed(seed)
def __enter__(self):
return None
def __exit__(self, *args):
np.random.set_state(self._state)