neuroworkflow 0.1.2b0

A well orgnized way and tool to write a mri data analysis workflow

install

pip install neuroworkfow

overview

provide a way to format code for processing neural data, get researches rid of file finding, name jointing and other dirty works when writing data process workflow.

Offer tools for quick inspecting pipline such as:

• generate a pseudo dataset to simplify how to arrange a dataset to run a pipline or how a data set looks like after running
• generate a subpipline from a existing pipline, this is useful when only partially result is needed or using some intermediate result.

usage

to write a data processing pipline using neuroworkflow, one need use three basic object: component, work and workflow. when run a processing pipline, one need additionally provide metadata which provide prossesed information such as subject, session and other setting.

Component

component is the representation of a file.

initial

when writing pipline, one need add propertis of a component to define a component. like

example_component = Component(suffix = 'bold', datatype = 'func', extension = 'nii')

some of the available properties are

property	function	example
desc	describe	smooth6mm
datatype	data type	func
suffix	suffix	bold
extension	extension	nii.gz
task	task	eyesopen
space	space	MNI152
echo	echo	2
data_place	folder to place	echo_2
use_extension	force using extension	true

when running, component will generate a file's name and directory according to its property, metadata and it's position in the whole pipline.

init_from

to simplify the initialization of a component, one can use init from to initialize a component

example_epi_json = Component.init_from(origin_epi_list, extension = 'json')

this will init a

init_multi

Work

a work is the representation of a processing step.

initial

when writing pipline, one need add components to a work's input_components and output_components indicate what to process and what will be generated, add action as the processs.

copy_epis = Work(f'copy_epi',
                  [origin_epi_list],
                  [copied_origin_epi_list],
                  action = copy_file
                  )

and the copy_file is

def copy_file(input_file, output_file):
    shutil.copyfile(input_file[0], output_file[0])

a action should accept two (input_file, output_file) or three (input_file, output_file, run_meta_data) parameters.

CommandWork