# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """Miscellaneous utility functions """ from cPickle import dumps, loads import inspect from distutils.version import LooseVersion import numpy as np from textwrap import dedent import sys import re def human_order_sorted(l): """Sorts string in human order (i.e. 'stat10' will go after 'stat2')""" def atoi(text): return int(text) if text.isdigit() else text def natural_keys(text): return [ atoi(c) for c in re.split('(\d+)', text) ] return sorted(l, key=natural_keys) def trim(docstring, marker=None): if not docstring: return '' # Convert tabs to spaces (following the normal Python rules) # and split into a list of lines: lines = docstring.expandtabs().splitlines() # Determine minimum indentation (first line doesn't count): indent = sys.maxint for line in lines[1:]: stripped = line.lstrip() if stripped: indent = min(indent, len(line) - len(stripped)) # Remove indentation (first line is special): trimmed = [lines[0].strip()] if indent < sys.maxint: for line in lines[1:]: # replace existing REST marker with doc level marker stripped = line.lstrip().strip().rstrip() if marker is not None and stripped and \ all([s==stripped[0] for s in stripped]) and \ stripped[0] not in [':']: line = line.replace(stripped[0], marker) trimmed.append(line[indent:].rstrip()) # Strip off trailing and leading blank lines: while trimmed and not trimmed[-1]: trimmed.pop() while trimmed and not trimmed[0]: trimmed.pop(0) # Return a single string: return '\n'.join(trimmed) def getsource(function): """Returns the source code of a function""" src = dumps(dedent(inspect.getsource(function))) return src def create_function_from_source(function_source, imports=None): """Return a function object from a function source Parameters ---------- function_source : pickled string string in pickled form defining a function imports : list of strings list of import statements in string form that allow the function to be executed in an otherwise empty namespace """ ns = {} import_keys = [] try: if imports is not None: for statement in imports: exec statement in ns import_keys = ns.keys() exec loads(function_source) in ns except Exception, msg: msg = str(msg) + '\nError executing function:\n %s\n'%function_source msg += '\n'.join(["Functions in connection strings have to be standalone.", "They cannot be declared either interactively or inside", "another function or inline in the connect string. Any", "imports should be done inside the function" ]) raise RuntimeError(msg) ns_funcs = list(set(ns) - set(import_keys + ['__builtins__'])) assert len(ns_funcs) == 1, "Function or inputs are ill-defined" funcname = ns_funcs[0] func = ns[funcname] return func def find_indices(condition): "Return the indices where ravel(condition) is true" res, = np.nonzero(np.ravel(condition)) return res def is_container(item): """Checks if item is a container (list, tuple, dict, set) Parameters ---------- item : object object to check for .__iter__ Returns ------- output : Boolean True if container False if not (eg string) """ if hasattr(item, '__iter__'): return True else: return False def container_to_string(cont): """Convert a container to a command line string. Elements of the container are joined with a space between them, suitable for a command line parameter. If the container `cont` is only a sequence, like a string and not a container, it is returned unmodified. Parameters ---------- cont : container A container object like a list, tuple, dict, or a set. Returns ------- cont_str : string Container elements joined into a string. """ if hasattr(cont, '__iter__'): return ' '.join(cont) else: return str(cont) # Dependency checks. Copied this from Nipy, with some modificiations # (added app as a parameter). def package_check(pkg_name, version=None, app=None, checker=LooseVersion, exc_failed_import=ImportError, exc_failed_check=RuntimeError): """Check that the minimal version of the required package is installed. Parameters ---------- pkg_name : string Name of the required package. version : string, optional Minimal version number for required package. app : string, optional Application that is performing the check. For instance, the name of the tutorial being executed that depends on specific packages. Default is *Nipype*. checker : object, optional The class that will perform the version checking. Default is distutils.version.LooseVersion. exc_failed_import : Exception, optional Class of the exception to be thrown if import failed. exc_failed_check : Exception, optional Class of the exception to be thrown if version check failed. Examples -------- package_check('numpy', '1.3') package_check('networkx', '1.0', 'tutorial1') """ if app: msg = '%s requires %s' % (app, pkg_name) else: msg = 'Nipype requires %s' % pkg_name if version: msg += ' with version >= %s' % (version,) try: mod = __import__(pkg_name) except ImportError: raise exc_failed_import(msg) if not version: return try: have_version = mod.__version__ except AttributeError: raise exc_failed_check('Cannot find version for %s' % pkg_name) if checker(have_version) < checker(version): raise exc_failed_check(msg) def str2bool(v): if isinstance(v, bool): return v lower = v.lower() if lower in ("yes", "true", "t", "1"): return True elif lower in ("no", "false", "n", "f", "0"): return False else: raise ValueError("%s cannot be converted to bool"%v)