cmp.stages.common module

Definition of common parent classes for stages.

class cmp.stages.common.Stage

Bases: traits.has_traits.HasTraits

Parent class that extends HasTraits and represents a processing pipeline stage.

It is extended by the various pipeline stage subclasses.

bids_dir

BIDS dataset root directory

Type

traits.Str

output_dir

Output directory

Type

traits.Str

inspect_outputs

Dictionary of stage outputs with corresponding commands for visual inspection (Initialization: ‘Outputs not available’)

Type

traits.Dict

inspect_outputs_enum

Choice of output to be visually inspected (values=’inspect_outputs’)

Type

traits.Enum

enabled

Stage enabled in the pipeline (Default: True)

Type

traits.Bool

config

Instance of stage configuration

Type

Instance(HasTraits)

See also

cmp.stages.preprocessing.preprocessing.PreprocessingStage, cmp.stages.diffusion.diffusion.DiffusionStage, cmp.stages.registration.registration.RegistrationStage, cmp.stages.connectome.connectome.ConnectomeStage, cmp.stages.preprocessing.fmri_preprocessing.PreprocessingStage, cmp.stages.functional.functionalMRI.FunctionalMRIStage, cmp.stages.connectome.fmri_connectome.ConnectomeStage

enabled = True

inspect_outputs = ['Outputs not available']

is_running()

Return the number of unfinished files in the stage.

Returns

nb_of_unfinished_files – Number of unfinished files in the stage

Return type

int