cmp.bidsappmanager.gui module¶
Connectome Mapper GUI.
-
class
cmp.bidsappmanager.gui.
CMP_BIDSAppWindow
(project_info=None, bids_root='', subjects=None, list_of_subjects_to_be_processed=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
-
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
-
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/v3.0.0-rc3_a/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”, …]
-
-
class
cmp.bidsappmanager.gui.
CMP_ConfiguratorWindow
(project_info=None, anat_pipeline=None, dmri_pipeline=None, fmri_pipeline=None, anat_inputs_checked=False, dmri_inputs_checked=False, fmri_inputs_checked=False)[source]¶ Bases:
traits.has_traits.HasTraits
Class that defines the Configurator Window.
-
project_info
¶ Instance of
CMP_Project_Info
that represents the processing project- Type
-
anat_pipeline
¶ Instance of anatomical MRI pipeline UI
- Type
Instance(HasTraits)
-
dmri_pipeline
¶ Instance of diffusion MRI pipeline UI
- Type
Instance(HasTraits)
-
fmri_pipeline
¶ Instance of functional MRI pipeline UI
- Type
Instance(HasTraits)
-
anat_inputs_checked
¶ Boolean that indicates if anatomical pipeline inputs are available (Default: False)
- dmri_inputs_checked =traits.Bool
Boolean that indicates if diffusion pipeline inputs are available (Default: False)
- fmri_inputs_checkedtraits.Bool
Boolean that indicates if functional pipeline inputs are available (Default: False)
- Type
traits.Bool
-
anat_save_config
¶ TraitsUI Action to save the anatomical pipeline configuration
- Type
traits.ui.Action
-
dmri_save_config
¶ TraitsUI Action to save the diffusion pipeline configuration
- Type
traits.ui.Action
-
fmri_save_config
¶ TraitsUI Action to save the functional pipeline configuration
- Type
traits.ui.Action
-
save_all_config
¶ Button to save all configuration files at once
- Type
traits.ui.Button
-
traits_view
¶ TraitsUI QtView that describes the content of the window
- Type
QtView
-
-
class
cmp.bidsappmanager.gui.
CMP_InspectorWindow
(project_info=None, anat_inputs_checked=False, dmri_inputs_checked=False, fmri_inputs_checked=False)[source]¶ Bases:
traits.has_traits.HasTraits
Class that defines the Configurator Window.
-
project_info
¶ Instance of
CMP_Project_Info
that represents the processing project- Type
-
anat_pipeline
¶ Instance of anatomical MRI pipeline
- Type
Instance(HasTraits)
-
dmri_pipeline
¶ Instance of diffusion MRI pipeline
- Type
Instance(HasTraits)
-
fmri_pipeline
¶ Instance of functional MRI pipeline
- Type
Instance(HasTraits)
-
anat_inputs_checked
¶ Indicates if inputs of anatomical pipeline are available (Default: False)
- Type
traits.Bool
-
dmri_inputs_checked
¶ Indicates if inputs of diffusion pipeline are available (Default: False)
- Type
traits.Bool
-
fmri_inputs_checked
¶ Indicates if inputs of functional pipeline are available (Default: False)
- Type
traits.Bool
-
output_anat_available
¶ Indicates if outputs of anatomical pipeline are available (Default: False)
- Type
traits.Bool
-
output_dmri_available
¶ Indicates if outputs of diffusion pipeline are available (Default: False)
- Type
traits.Bool
-
output_fmri_available
¶ Indicates if outputs of functional pipeline are available (Default: False)
- Type
traits.Bool
-
traits_view
¶ TraitsUI QtView that describes the content of the window
- Type
QtView
-
-
class
cmp.bidsappmanager.gui.
CMP_MainWindow
[source]¶ Bases:
traits.has_traits.HasTraits
Class that defines the Main window of the Connectome Mapper 3 GUI.
-
project_info
¶ Instance of
CMP_Project_InfoUI
that represents the processing project- Type
-
anat_pipeline
¶ Instance of anatomical MRI pipeline UI
- Type
Instance(HasTraits)
-
dmri_pipeline
¶ Instance of diffusion MRI pipeline UI
- Type
Instance(HasTraits)
-
fmri_pipeline
¶ Instance of functional MRI pipeline UI
- Type
Instance(HasTraits)
-
bidsapp_ui
¶ Instance of
CMP_BIDSAppWindow
- Type
-
load_dataset
¶ TraitsUI Action to load a BIDS dataset
- Type
traits.ui.Action
-
bidsapp
¶ Button that displays the BIDS App Interface window
- Type
traits.ui.Button
-
configurator
¶ Button thats displays the pipeline Configurator window
- Type
traits.ui.Button
-
quality_control
¶ Button that displays the pipeline Quality Control / Inspector window
- Type
traits.ui.Button
-
manager_group
¶ TraitsUI View that describes the content of the main window
- Type
traits.ui.View
-
traits_view
¶ TraitsUI QtView that includes
manager_group
and parameterize the window with menu- Type
QtView
-
show_bidsapp_interface
()[source]¶ Callback of the “BIDS App” button. This displays the BIDS App Interface Window.
-
view_mode
= 1¶
-
-
class
cmp.bidsappmanager.gui.
CMP_Project_InfoUI
[source]¶ Bases:
cmp.project.CMP_Project_Info
Class that extends the
CMP_Project_Info
with graphical components.It supports graphically the setting of all processing properties / attributes of an
CMP_Project_Info
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
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
-