cmp.bidsappmanager.gui.bidsapp module

Connectome Mapper BIDS App Interface Window.

class cmp.bidsappmanager.gui.bidsapp.BIDSAppInterfaceWindow(project_info=None, bids_root='', subjects=None, anat_config='', dmri_config='', fmri_config='')[source]

Bases: traits.has_traits.HasTraits

Class that defines the Window of the BIDS App Interface.

project_info

Instance of CMP_Project_Info that represents the processing project

Type: ProjectInfo

bids_root

BIDS root dataset directory

Type: traits.Directory

output_dir

Output directory

Type: traits.Directory

subjects

List of subjects (in the form sub-XX) present in the dataset

Type: traits.List

number_of_participants_processed_in_parallel

Number of participants / subjects to be processed in parallel that takes values in the [1, # of CPUs - 1] range

Type: traits.Range

number_threads_max

Maximal number of threads to be used by OpenMP programs (4 by default)

Type: traits.Int

number_of_threads

Number of threads to be used by OpenMP programs that takes values in the [1, number_threads_max] range

Type: traits.Range

fs_file

Path to Freesurfer license file

Type: traits.File

list_of_subjects_to_be_processed

Selection of subjects to be processed from the subjects list

Type: List(Str)

dmri_inputs_checked

True if dMRI data is available in the dataset

Type: traits.Bool

fmri_inputs_checked

rue if fMRI data is available in the dataset

Type: traits.Bool

anat_config

Configuration file for the anatomical MRI pipeline

Type: traits.File

dmri_config

Configuration file for the diffusion MRI pipeline

Type: traits.File

fmri_config

Configuration file for the functional MRI pipeline

Type: traits.File

run_anat_pipeline

If True, run the anatomical pipeline

Type: traits.Bool

run_dmri_pipeline

If True, run the diffusion pipeline

Type: traits.Bool

run_fmri_pipeline

If True, run the functional pipeline

Type: traits.Bool

bidsapp_tag

Selection of BIDS App version to use

Type: traits.Enum

data_provenance_tracking

If set and if datalad_is_available is True run the BIDS App using datalad (False by default)

Type: traits.Bool

datalad_update_environment

If True and data_provenance_tracking is True, tell to datalad to update the BIDS App container image if there was a previous execution (True by default)

Type: traits.Bool

datalad_is_available

Boolean used to store if datalad is available in the computing environment (False by default)

Type: traits.Bool

track_carbon_footprint

Track carbon footprint if True (True by default)

Type: traits.Bool

carbon_emission_msg

Carbon footprint reporting message

Type: traits.Str

check

Button to check if all parameters are properly set for execution of the BIDS App

Type: traits.ui.Button

start_bidsapp

Button to run the BIDS App

Type: traits.ui.Button

traits_view

TraitsUI QtView that describes the content of the window

Type: QtView

check_settings()[source]: Checks if all the parameters of the BIDS App run are properly set before execution.

classmethod manage_bidsapp_procs(proclist)[source]

Manage parallelized process at the participant level

Parameters: proclist (List of subprocess.Popen) – List of Popen processes

number_of_parallel_procs_updated(new)[source]: Callback function when number_of_parallel_procs is updated.

classmethod run(command, env=None, cwd='/home/docs/checkouts/readthedocs.org/user_builds/connectome-mapper-3/checkouts/v3.0.4/docs')[source]

Function to run datalad commands.

It runs the command specified as input via subprocess.run().

Parameters

command (string) – String containing the command to be executed (required)
env (os.environ) – Specify a custom os.environ
cwd (os.path) – Specify a custom current working directory

Examples

>>> cmd = 'datalad save -m my dataset change message'
>>> run(cmd) 

start_bids_app()[source]

Function executed when the Run BIDS App button is clicked.

It implements all steps in the creation and execution of the BIDS App with or without datalad.

start_bidsapp_participant_level_process(bidsapp_tag, participant_labels)[source]

Create and run the BIDS App command.

Parameters

bidsapp_tag (traits.Str) – Version tag of the CMP 3 BIDS App
participant_labels (traits.List) – List of participants labels in the form [“01”, “03”, “04”, …]

start_bidsapp_participant_level_process_with_datalad(bidsapp_tag, participant_labels)[source]

Create and run the BIDS App command with Datalad.

Parameters

bidsapp_tag (traits.Str) – Version tag of the CMP 3 BIDS App
participant_labels (traits.List) – List of participants labels in the form [“01”, “03”, “04”, …]

update_checksettings(new)[source]: Function that reset settings_checked attribute to False.

update_run_anat_pipeline(new)[source]: Callback function when run_anat_pipeline is updated.

update_run_dmri_pipeline(new)[source]: Callback function when run_dmri_pipeline is updated.

update_run_fmri_pipeline(new)[source]: Callback function when run_fmri_pipeline is updated.