# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Scientific Package. This package holds all simulators, and
# analysers necessary to run brain-simulations. You can use it stand alone or
# in conjunction with TheVirtualBrain-Framework Package. See content of the
# documentation-folder for more details. See also http://www.thevirtualbrain.org
#
# (c) 2012-2023, Baycrest Centre for Geriatric Care ("Baycrest") and others
#
# 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/>.
#
#
# CITATION:
# When using The Virtual Brain for scientific publications, please cite it as explained here:
# https://www.thevirtualbrain.org/tvb/zwei/neuroscience-publications
#
#
"""
A module of classes and functions of common use.
.. moduleauthor:: Marmaduke Woodman <marmaduke.woodman@univ-amu.fr>
.. moduleauthor:: Stuart A. Knock <Stuart@tvb.invalid>
.. moduleauthor:: Paula Sanz Leon <Paula@tvb.invalid>
"""
import numpy
import os
import re
import six
import logging
from tvb.basic.logger.builder import GLOBAL_LOGGER_BUILDER, get_logger
from .backend.ref import ReferenceBackend
from deprecated import deprecated
[docs]@deprecated(reason="Use builder.set_logger_level instead")
def log_debug(debug=False, timestamp=False, prefix=''):
level_name = 'DEBUG' if debug else 'INFO'
level = getattr(logging, level_name)
GLOBAL_LOGGER_BUILDER.set_loggers_level(level)
LOG = get_logger(__name__)
for handler in LOG.root.handlers:
handler.setLevel(level)
# reset formatter more friendly for console work
if isinstance(handler, logging.StreamHandler) and not timestamp:
if prefix:
prefix += ' '
handler.setFormatter(logging.Formatter(prefix + '%(levelname)07s %(message)s'))
LOG.info('log level set to %s' % (level_name,))
[docs]def astr(ary):
"""Make short str repr of numerical value."""
if isinstance(ary, numpy.ndarray):
if ary.size == 1:
val = ary[0]
else:
val = 'ndarray(%s, %s)' % (ary.shape, ary.dtype)
elif isinstance(ary, bool):
val = str(ary)
elif isinstance(ary, float) or isinstance(ary, six.integer_types):
val = ary
else:
val = str(ary)
if isinstance(val, str):
return val
else:
is_py_int = isinstance(val, six.integer_types)
is_np_int = hasattr(val, 'dtype') and numpy.issubdtype(ary.dtype, numpy.integer)
if is_py_int or is_np_int:
return '%d' % (val,)
else:
return '%g' % (val,)
[docs]def map_astr(self, names):
"""Helper for generating a sequence of astr representation of attributes on self"""
strs = []
for name in names.split():
strs.append(astr(getattr(self, name)))
return tuple(strs)
[docs]def simple_gen_astr(self, names):
"""Helper for generating str for object with only numerical attributes."""
strs = []
for name, str_ in zip(names.split(), map_astr(self, names)):
strs.append('%s=%s' % (name, str_))
clsname = self.__class__.__name__
return '%s(%s)' % (clsname, ', '.join(strs))
numpy_add_at = ReferenceBackend.add_at
# loose couple psutil so it's an optional dependency
try:
import psutil
except ImportError:
msg = """psutil module not available: no warnings will be issued when a
simulation may require more memory than available"""
LOG = get_logger(__name__)
LOG.warning(msg)
psutil = None
[docs]class Struct(dict):
"""
the Struct class is a dictionary with matlab/C struct-like access
to its fields:
>>> parameters = Struct(x=23.4345, alpha=1.522e-4)
>>> parameters.x + 1
24.4345
>>> parameters.x_init = 6
>>> parameters.x_init + 1
7
>>> print(parameters.y)
None
note that this class returns None if the field does not exist!
"""
def __getattr__(self, attr):
return self.get(attr, None)
__setattr__ = dict.__setitem__
__delattr__ = dict.__delitem__
linear_interp1d = ReferenceBackend.linear_interp1d
heaviside = ReferenceBackend.heaviside
iround = ReferenceBackend.iround
[docs]def zip_directory(path, zip_file):
"""
Zip a given directory...
Didn't know where to put this.
I need to pack zips from the scripting interface.
To avoid duplicating code I leave this small function here.
:param path -- where to store the zip
:param zip_file
"""
for dirname, subdirs, files in os.walk(path):
zip_file.write(dirname)
for filename in files:
zip_file.write(os.path.join(dirname, filename))
zip_file.close()
[docs]def total_ms(duration="", hours=0, minutes=0, seconds=0):
re_times = re.compile(r'\s*(\d+\.?\d*)\s*(sec|ms|hr|min|s|m|h)\s*$')
re_decimals = re.compile(r'^[0-9]+([,.][0-9]+)?$')
total_milliseconds = 0
if duration == "":
if not hours == 0:
total_milliseconds = hours * 3600000
elif not minutes == 0:
total_milliseconds = minutes * 60000
elif not seconds == 0:
total_milliseconds = seconds * 1000
elif re_decimals.search(duration):
total_milliseconds = float(duration)
else:
match = re_times.match(duration)
if not match:
raise ValueError("unable to parse duration %r" % duration)
s_time, s_unit = match.group(1, 2)
s_time = float(s_time)
if s_unit in ('s', 'sec'):
total_milliseconds = s_time * 1000
elif s_unit in ('m', 'min'):
total_milliseconds = s_time * 60000
elif s_unit in ('hr', 'h'):
total_milliseconds = s_time * 3600000
elif s_unit in ('ms'):
total_milliseconds = s_time
return total_milliseconds
