cmp.bidsappmanager.pipelines.anatomical.anatomical module

Anatomical pipeline UI Class definition.

class cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI(project_info)

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)

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

Parameters

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

Returns

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

Return type

bool

check_output()

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