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
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
project_info (ProjectInfoUI) – Instance of
ProjectInfoUI
classbids_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
classbids_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.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 (ProjectInfoUI) – Instance of
ProjectInfoUI
classpipeline (AnatomicalPipelineUI) – Instance of
AnatomicalPipelineUI
- cmp.bidsappmanager.project.update_dmri_last_processed(project_info, pipeline)[source]
Update diffusion pipeline processing information
- Parameters
project_info (ProjectInfoUI) – Instance of
ProjectInfoUI
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 (ProjectInfoUI) – Instance of
ProjectInfoUI
classpipeline (fMRIPipelineUI) – Instance of
fMRIPipelineUI