nipype.utils.misc module¶
Miscellaneous utility functions
- nipype.utils.misc.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 – Container elements joined into a string.
- Return type:
string
- nipype.utils.misc.dict_diff(dold, dnew, indent=0)¶
Helper to log what actually changed from old to new values of dictionaries.
typical use – log difference for hashed_inputs
- nipype.utils.misc.find_indices(condition)¶
Return the indices where ravel(condition) is true
- nipype.utils.misc.flatten(S)¶
- nipype.utils.misc.human_order_sorted(l)¶
Sorts string in human order (i.e. ‘stat10’ will go after ‘stat2’)
- nipype.utils.misc.is_container(item)¶
Checks if item is a container (list, tuple, dict, set)
- Parameters:
item (object) – object to check for .__iter__
- Returns:
output – True if container False if not (eg string)
- Return type:
Boolean
- nipype.utils.misc.normalize_mc_params(params, source)¶
Normalize a single row of motion parameters to the SPM format.
- SPM saves motion parameters as:
x Right-Left (mm) y Anterior-Posterior (mm) z Superior-Inferior (mm) rx Pitch (rad) ry Roll (rad) rz Yaw (rad)
- nipype.utils.misc.package_check(pkg_name, version=None, app=None, checker=<class 'looseversion.LooseVersion'>, exc_failed_import=<class 'ImportError'>, exc_failed_check=<class '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 nipype.external.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(‘scipy’, ‘0.7’, ‘tutorial1’)
- nipype.utils.misc.rgetcwd(error=True)¶
Robust replacement for getcwd when folders get removed If error==True, this is just an alias for os.getcwd()
- nipype.utils.misc.str2bool(v)¶
Convert strings (and bytearrays) to boolean values
>>> all([str2bool(v) for v in (True, "yes", "true", ... "y", "t", "Yes", "True", "1", "on", "On")]) True >>> all([str2bool(v.encode('utf-8')) ... for v in ("yes", "true", "y", "t", "1", "Yes", "on", "On")]) True >>> any([str2bool(v) for v in (False, "no", "false", "n", "f", ... "False", "0", "off", "Off")]) False >>> any([str2bool(v.encode('utf-8')) ... for v in ("no", "false", "n", "f", "0", "off", "Off")]) False >>> str2bool(None) Traceback (most recent call last): ... ValueError: ... >>> str2bool('/some/path') Traceback (most recent call last): ... ValueError: ... >>> str2bool('Agg') Traceback (most recent call last): ... ValueError: ... >>> str2bool('INFO') Traceback (most recent call last): ... ValueError: ... >>> str2bool('/some/bytes/path'.encode('utf-8')) Traceback (most recent call last): ... ValueError: ...
- nipype.utils.misc.trim(docstring, marker=None)¶
- nipype.utils.misc.unflatten(in_list, prev_structure)¶