cmp.bidsappmanager.project module
Connectome Mapper Controler for handling GUI and non GUI general events.
- class cmp.bidsappmanager.project.CMP_BIDSAppWindowHandler[source]
Bases:
traitsui.handler.Handler
Event handler of the BIDS App Interface window.
- docker_process
Instance of
subprocess.Popen
where BIDS App docker image is run- Type
- check_settings(ui_info)[source]
Function that checks if all parameters are properly set before execution of the BIDS App.
- Parameters
ui_info (QtView) – TraitsUI QtView associated with
self
- classmethod manage_bidsapp_procs(proclist)[source]
Function that managed the parallelized BIDS App Popen process.
- Parameters
proclist – List of
Popen
processes running the BIDS App on a single subject
- start_bids_app(ui_info)[source]
Main function that runs the BIDS App on a set or sub-set of participants.
- Parameters
ui_info (QtView) – TraitsUI QtView associated with this handler
- class cmp.bidsappmanager.project.CMP_ConfigQualityWindowHandler[source]
Bases:
traitsui.handler.Handler
Event handler of the Configurator and Inspector (Quality Control) windows.
- project_loaded
Indicate if project has been successfully loaded (Default: False)
- Type
traits.Bool
- anat_pipeline
Instance of
AnatomicalPipelineUI
class- Type
Instance(HasTraits)
- anat_inputs_checked
Indicate if anatomical pipeline inputs are available (Default: False)
- Type
traits.Bool
- anat_outputs_checked
Indicate if anatomical pipeline outputs are available (Default: False)
- Type
traits.Bool
- anatomical_processed
Indicate if anatomical pipeline was run (Default: False)
- Type
traits.Bool
- dmri_pipeline
Instance of
DiffusionPipelineUI
class- Type
Instance(HasTraits)
- dmri_inputs_checked
Indicate if diffusion pipeline inputs are available (Default: False)
- Type
traits.Bool
- dmri_processed
Indicate if diffusion pipeline was run (Default: False)
- Type
traits.Bool
- fmri_pipeline
Instance of
fMRIPipelineUI
class- Type
Instance(HasTraits)
- fmri_inputs_checked
Indicate if fMRI pipeline inputs are available (Default: False)
- Type
traits.Bool
- fmri_processed
Indicate if fMRI pipeline was run (Default: False)
- Type
traits.Bool
- load_anat_config_file(ui_info)[source]
Function that loads the anatomical pipeline configuration file.
- Parameters
ui_info (QtView) – TraitsUI QtView associated with
self
- load_dmri_config_file(ui_info)[source]
Function that loads the diffusion pipeline configuration file.
- Parameters
ui_info (QtView) – TraitsUI QtView associated with
self
- load_fmri_config_file(ui_info)[source]
Function that loads the fMRI pipeline configuration file.
- Parameters
ui_info (QtView) – TraitsUI QtView associated with
self
- load_project(ui_info)[source]
Function that creates a new
CMP_Project_InfoUI
instance from an existing project.- Parameters
ui_info (QtView) – TraitsUI QtView associated with
self
- new_project(ui_info)[source]
Function that creates a new
CMP_Project_InfoUI
instance.- Parameters
ui_info (QtView) – TraitsUI QtView associated with
self
- classmethod save_anat_config_file(ui_info)[source]
Function that saves the anatomical pipeline configuration file.
- Parameters
ui_info (QtView) – TraitsUI QtView associated with
self
- classmethod save_dmri_config_file(ui_info)[source]
Function that saves the diffusion pipeline configuration file.
- Parameters
ui_info (QtView) – TraitsUI QtView associated with
self
- classmethod save_fmri_config_file(ui_info)[source]
Function that saves the fMRI pipeline configuration file.
- Parameters
ui_info (QtView) – TraitsUI QtView associated with
self
- classmethod show_bidsapp_window()[source]
Function that shows the BIDS App Interface Window.
- Parameters
ui_info (QtView) – TraitsUI QtView associated with this handler
- update_subject_anat_pipeline(ui_info)[source]
Function that updates attributes of the
AnatomicalPipelineUI
instance.- Parameters
ui_info (QtView) – TraitsUI QtView associated with
self
- class cmp.bidsappmanager.project.CMP_MainWindowHandler[source]
Bases:
traitsui.handler.Handler
Event handler of the Configurator and Inspector (Quality Control) windows.
- project_loaded
Indicate if project has been successfully loaded (Default: False)
- Type
traits.Bool
- anat_pipeline
Instance of
AnatomicalPipelineUI
class- Type
Instance(HasTraits)
- anat_inputs_checked
Indicate if anatomical pipeline inputs are available (Default: False)
- Type
traits.Bool
- anat_outputs_checked
Indicate if anatomical pipeline outputs are available (Default: False)
- Type
traits.Bool
- anatomical_processed
Indicate if anatomical pipeline was run (Default: False)
- Type
traits.Bool
- dmri_pipeline
Instance of
DiffusionPipelineUI
class- Type
Instance(HasTraits)
- dmri_inputs_checked
Indicate if diffusion pipeline inputs are available (Default: False)
- Type
traits.Bool
- dmri_processed
Indicate if diffusion pipeline was run (Default: False)
- Type
traits.Bool
- fmri_pipeline
Instance of
fMRIPipelineUI
class- Type
Instance(HasTraits)
- fmri_inputs_checked
Indicate if fMRI pipeline inputs are available (Default: False)
- Type
traits.Bool
- fmri_processed
Indicate if fMRI pipeline was run (Default: False)
- Type
traits.Bool
- 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 (CMP_Project_InfoUI) – Instance of
CMP_Project_InfoUI
classis_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
- cmp.bidsappmanager.project.init_fmri_project(project_info, bids_layout, is_new_project, gui=True)[source]
Create and initialize a
fMRIPipelineUI
instance- Parameters
- 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 hierarchysession (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 givensubject
- cmp.bidsappmanager.project.update_anat_last_processed(project_info, pipeline)[source]
Update anatomical pipeline processing information
- Parameters
project_info (CMP_Project_InfoUI) – Instance of
CMP_Project_InfoUI
classpipeline (AnatomicalPipelineUI) – Instance of
AnatomicalPipelineUI
- cmp.bidsappmanager.project.update_dmri_last_processed(project_info, pipeline)[source]
Update diffusion pipeline processing information
- Parameters
project_info (CMP_Project_InfoUI) – Instance of
CMP_Project_InfoUI
classpipeline (DiffusionPipelineUI) – Instance of
DiffusionPipelineUI
- cmp.bidsappmanager.project.update_fmri_last_processed(project_info, pipeline)[source]
Update functional MRI pipeline processing information
- Parameters
project_info (CMP_Project_InfoUI) – Instance of
CMP_Project_InfoUI
classpipeline (fMRIPipelineUI) – Instance of
fMRIPipelineUI