cmp.bidsappmanager.pipelines.anatomical.anatomical module

Anatomical pipeline UI Class definition.

class cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI(project_info)[source]

Bases: cmp.pipelines.anatomical.anatomical.AnatomicalPipeline

Class that extends the AnatomicalPipeline with graphical components.

segmentation

Button to open the window for configuration or quality inspection of the segmentation stage depending on the view_mode

Type

traits.ui.Button

parcellation

Button to open the window for configuration or quality inspection of the segmentation stage depending on the view_mode

Type

traits.ui.Button

view_mode

Variable used to control the display of either (1) the configuration or (2) the quality inspection of stage of the pipeline

Type

[‘config_view’, ‘inspect_outputs_view’]

pipeline_group

Panel defining the layout of the buttons of the stages with corresponding images

Type

traitsUI panel

traits_view

QtView that includes the pipeline_group panel

Type

QtView

See also

cmp.pipelines.anatomical.anatomical.AnatomicalPipeline

check_input(layout, gui=True)[source]

Method that checks if inputs of the anatomical pipeline are available in the datasets.

Parameters

  • layout (bids.BIDSLayout) – BIDSLayout object used to query

  • gui (Boolean) – If True display messages and errors in graphical window

Returns

valid_inputs – True in all inputs of the anatomical pipeline are available

Return type

bool

check_output()[source]

Method that checks if outputs of the anatomical pipeline are available.

Returns

  • valid_output (bool) – True is all outputs are found

  • error_message (string) – Message in case there is an error

class cmp.bidsappmanager.pipelines.anatomical.anatomical.Check_Input_NotificationUI[source]

Bases: cmp.pipelines.anatomical.anatomical.Check_Input_Notification