Script

Import in python using from mcutils.pipe import Script

Documentation

class mcutils.pipe.Script(pipeline: mcutils.pipe.Pipeline, func, in_files, out_files, in_vars=None, possible_values=None, iter_vars=None, allow_missing=False, **submit_params)[source]
__init__(pipeline: mcutils.pipe.Pipeline, func, in_files, out_files, in_vars=None, possible_values=None, iter_vars=None, allow_missing=False, **submit_params)[source]

Creates a new script.

Typically not called directly, but by using Pipeline object as a decorator

Parameters

  • pipeline – Pipeline object of which this script is a part

  • func – function to run when calling script

  • in_files – sequence of input short names of templates in FileTree

  • out_files – sequence of output short names of templates in FileTree

  • in_vars – sequence of variables names, whose values are required to run the script

  • possible_values – Dictionary listing for a variable which values it can take (optional)

  • iter_vars – Iterate over specific variables when producing input/output filenames

  • allow_missing – allow input filenames to be missing (None will be provided to the function)

  • submit_params – Any parameters used to submit the job to fsl_sub

Methods

iter_vars_array()

Return dictionary with the variables in N-dimensional arrays

Attributes

all_files

All the input and output template names

all_values

Dictionary defining which values each variable can take

all_variables

All the required and optional variable names

axes

Sorted list of along which variables the script can be run in parallel

tree

FileTree object from the pipeline