cmp.bidsappmanager.project module

Connectome Mapper Controler for handling GUI and non GUI general events.

class cmp.bidsappmanager.project.ProjectInfoUI[source]

Bases: cmp.project.ProjectInfo

Class that extends the ProjectInfo with graphical components.

It supports graphically the setting of all processing properties / attributes of an ProjectInfo instance.

creation_mode

Mode for loading the dataset. Valid values are ‘Load BIDS dataset’, ‘Install Datalad BIDS dataset’

Type

traits.Enum

install_datalad_dataset_via_ssh

If set to True install the datalad dataset from a remote server via ssh.(True by default)

Type

traits.Bool

ssh_user

Remote server username. (Required if install_datalad_dataset_via_ssh is True)

Type

traits.Str

ssh_pwd <traits.Password>

Remote server password. (Required if install_datalad_dataset_via_ssh is True)

ssh_remote

Remote server IP or URL. (Required if install_datalad_dataset_via_ssh is True)

Type

traits.Str

datalad_dataset_path

Path to the datalad dataset on the remote server. (Required if install_datalad_dataset_via_ssh is True)

Type

traits.Directory

summary_view_button

Button that shows the pipeline processing summary table

Type

traits.ui.Button

pipeline_processing_summary_view

TraitsUI VGroup that contains Item('pipeline_processing_summary')

Type

traits.ui.VGroup

dataset_view

TraitsUI View that shows a summary of project settings and modality available for a given subject

Type

traits.ui.View

traits_view

TraitsUI QtView that includes the View ‘dataset_view’

Type

QtView

create_view

Dialog view to create a BIDS Dataset

Type

traits.ui.View

subject_view

Dialog view to select of subject

Type

traits.ui.View

subject_session_view

Dialog view to select the subject session

Type

traits.ui.View

dmri_bids_acq_view

Dialog view to select the diffusion acquisition model

Type

traits.ui.View

anat_warning_view

View that displays a warning message regarding the anatomical T1w data

Type

traits.ui.View

anat_config_error_view

Error view that displays an error message regarding the configuration of the anatomical pipeline

Type

traits.ui.View

dmri_warning_view

View that displays a warning message regarding the diffusion MRI data

Type

traits.ui.View

dmri_config_error_view

View that displays an error message regarding the configuration of the diffusion pipeline

Type

traits.ui.View

fmri_warning_view

View that displays a warning message regarding the functional MRI data

Type

traits.ui.View

fmri_config_error_view

View that displays an error message regarding the configuration of the fMRI pipeline

Type

traits.ui.View

open_view

Dialog view to load a BIDS Dataset

Type

traits.ui.View

anat_select_config_to_load

Dialog view to load the configuration file of the anatomical pipeline

Type

traits.ui.View

diffusion_imaging_model_select_view

Dialog view to select the diffusion acquisition model

Type

traits.ui.View

dmri_select_config_to_load

Dialog view to load the configuration file of the diffusion MRI pipeline

Type

traits.ui.View

fmri_select_config_to_load

Dialog view to load the configuration file of the fMRI pipeline

Type

traits.ui.View

cmp.bidsappmanager.project.clean_cache(bids_root)[source]

Clean cache stored in /tmp.

Target issue related to that a dataset directory is mounted into /tmp and used for caching by java/matlab/matplotlib/xvfb-run in the container image.

Parameters

bids_root (string) – BIDS root dataset directory

cmp.bidsappmanager.project.init_anat_project(project_info, is_new_project)[source]

Create and initialize a AnatomicalPipelineUI instance

Parameters
  • project_info (ProjectInfoUI) – Instance of ProjectInfoUI class

  • is_new_project (bool) – If True, this is a new project which has been never processed

cmp.bidsappmanager.project.init_dmri_project(project_info, bids_layout, is_new_project, gui=True)[source]

Create and initialize a DiffusionPipelineUI instance

Parameters
  • project_info (ProjectInfoUI) – Instance of ProjectInfoUI class

  • bids_layout (bids.BIDSLayout) – PyBIDS BIDS Layout object describing the BIDS dataset

  • is_new_project (bool) – If True, this is a new project which has been never processed

  • gui (bool) – If True, display messages in GUI

cmp.bidsappmanager.project.init_fmri_project(project_info, bids_layout, is_new_project, gui=True)[source]

Create and initialize a fMRIPipelineUI instance

Parameters
  • project_info (ProjectInfoUI) – Instance of ProjectInfoUI class

  • bids_layout (bids.BIDSLayout) – PyBIDS BIDS Layout object describing the BIDS dataset

  • is_new_project (bool) – If True, this is a new project which has been never processed

  • gui (bool) – If True, display messgae in GUI

cmp.bidsappmanager.project.is_tool(name)[source]

Check whether name is on PATH.

cmp.bidsappmanager.project.refresh_folder(derivatives_directory, subject, input_folders, session=None)[source]

Creates (if needed) the folder hierarchy.

Parameters
  • derivatives_directory (string) –

  • subject (string) – Subject label (sub-XX) for which we create the output folder hierarchy

  • session (string) – Subject session label (ses-YY)

  • input_folders (list of string) – List of folders to create in derivative_directory/sub-XX/(ses-YY)/ folder for the given subject

cmp.bidsappmanager.project.update_anat_last_processed(project_info, pipeline)[source]

Update anatomical pipeline processing information

Parameters
cmp.bidsappmanager.project.update_dmri_last_processed(project_info, pipeline)[source]

Update diffusion pipeline processing information

Parameters
cmp.bidsappmanager.project.update_fmri_last_processed(project_info, pipeline)[source]

Update functional MRI pipeline processing information

Parameters