nipype.utils.misc module¶
Miscellaneous utility functions
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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
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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
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nipype.utils.misc.
find_indices
(condition)¶ Return the indices where ravel(condition) is true
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nipype.utils.misc.
flatten
(S)¶
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nipype.utils.misc.
human_order_sorted
(l)¶ Sorts string in human order (i.e. ‘stat10’ will go after ‘stat2’)
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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
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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)
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nipype.utils.misc.
package_check
(pkg_name, version=None, app=None, checker=<class 'distutils.version.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 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(‘scipy’, ‘0.7’, ‘tutorial1’)
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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()
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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: ...
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nipype.utils.misc.
trim
(docstring, marker=None)¶
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nipype.utils.misc.
unflatten
(in_list, prev_structure)¶