core

class trame_slicer.core.DisplayManager(view_manager: ViewManager, volume_rendering: VolumeRendering)

Bases: object

Helper class to display volume nodes in given view group

hide_volume(volume_node: vtkMRMLVolumeNode, view_group: int | None = None)

reset_views(view_group: int | None = None)

set_node_visible_in_group(node: vtkMRMLDisplayableNode, view_group: int | None = None)

show_volume(volume_node: vtkMRMLVolumeNode, view_group: int | None = None, vr_preset: str = '', do_reset_views: bool = False) → None

show_volume_in_slice_background(volume_node: vtkMRMLVolumeNode | None, view_group: int | None = None)

show_volume_in_slice_foreground(volume_node: vtkMRMLVolumeNode | None, view_group: int | None = None)

class trame_slicer.core.IOManager(scene: vtkMRMLScene, app_logic: vtkMRMLApplicationLogic, segmentation_editor: SegmentationEditor)

Bases: object

Class responsible for loading files in the scene.

load_model(model_file: str | Path, do_convert_to_slicer_coord: bool = True) → vtkMRMLModelNode | None

load_scene(scene_path) → bool

load_segmentation(segmentation_file: str | Path, do_convert_to_slicer_coord=True) → vtkMRMLSegmentationNode | None

load_volumes(volume_files: str | list[str]) → list[vtkMRMLVolumeNode]

save_scene(scene_path: str | Path) → bool

classmethod write_model(model_node, model_file: str | Path, do_convert_from_slicer_coord: bool = True) → None

classmethod write_node(node, node_file, storage_type: type, do_convert_from_slicer_coord: bool) → None

write_scene(scene_path: str | Path) → bool

write_segmentation(segmentation_node, segmentation_file: str | Path)

classmethod write_volume(volume_node, volume_file: str | Path) → None

class trame_slicer.core.LayoutManager(scene: vtkMRMLScene, view_manager: ViewManager, server: Server, *, virtual_node: VirtualNode | None = None, is_virtual_node_initialized: bool = False)

Bases: object

Class responsible for instantiating views depending on the layout node.

Creates a singleton layout node at initialization.
Observes layout node changes to notify observers of layout id changes.
Can register layouts with their associated descriptions
Notifies view manager of requested view on layout change

create_layout_views_if_needed(layout_id: str) → None

current_layout_changed

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

classmethod default_grid_configuration() → dict[str, Layout]

get_layout(layout_id: str, default_layout: Layout | None = None) → Layout

get_layout_ids() → list[str]

has_layout(layout_id: str) → bool

initialize_layout_grid(layout: AbstractLayout): Initialize the LayoutGrid placeholder in the layout at the call position.

property layout_id: str | None

register_layout(layout_id: str, layout: Layout, lazy_initialization: bool = False) → None: Registers the given layout id to the associated layout. Will overwrite any pre existing layout with this ID. If lazy_initialization is False, the views will not be instantiated unless the passed layout id matches the current selected layout id.

register_layout_dict(layout_dict: dict[str, Layout], lazy_initialization: bool = False) → None

Parameters:

layout_dict – Layout dictionary to register to the layout manager
lazy_initialization – If True, the layout views will not be created until explicitly requested by set_layout or create_layout_views_if_needed

registered_layouts_changed

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

set_layout(layout_id: str) → None

set_layout_from_node(node: vtkMRMLScriptedModuleNode) → None

class trame_slicer.core.SegmentationEditor(scene: vtkMRMLScene, logic: vtkSlicerSegmentationsModuleLogic, view_manager: ViewManager, *, builtin_effects: list[type[SegmentationEffect]] | None = None)

Bases: SignalContainer

Class responsible for editing the segmentation. Meant to be used by the application to activate / deactivate segmentation effects.

property active_effect: SegmentationEffect | None

property active_effect_name: str

active_effect_name_changed

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

property active_segment_id: str

active_segment_id_changed

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

property active_segment_modifier: SegmentModifier | None

property active_segmentation: Segmentation | None

property active_segmentation_display: SegmentationDisplay | None

property active_segmentation_node

property active_volume_node: vtkMRMLVolumeNode | None

add_empty_segment(*, segment_id='', segment_name='', segment_color: list[float] | None = None, segment_value: int | None = None) → str

apply_labelmap(labelmap) → None

apply_polydata_world(poly_world) → None

builtin_effects: ClassVar[list[type[SegmentationEffect]]] = [<class 'trame_slicer.segmentation.segmentation_effect_draw.SegmentationEffectDraw'>, <class 'trame_slicer.segmentation.segmentation_effect_paint_erase.SegmentationEffectErase'>, <class 'trame_slicer.segmentation.segmentation_effect_islands.SegmentationEffectIslands'>, <class 'trame_slicer.segmentation.segmentation_effect_logical_operators.SegmentationEffectLogicalOperators'>, <class 'trame_slicer.segmentation.segmentation_effect_no_tool.SegmentationEffectNoTool'>, <class 'trame_slicer.segmentation.segmentation_effect_paint_erase.SegmentationEffectPaint'>, <class 'trame_slicer.segmentation.segmentation_effect_scissors.SegmentationEffectScissors'>, <class 'trame_slicer.segmentation.segmentation_effect_smoothing.SegmentationEffectSmoothing'>, <class 'trame_slicer.segmentation.segmentation_effect_threshold.SegmentationEffectThreshold'>, <class 'trame_slicer.segmentation.segmentation_effect_volume_intensity_mask.SegmentationEffectVolumeIntensityMask'>]

clear()

create_empty_segmentation_node() → vtkMRMLSegmentationNode

create_modifier_labelmap() → vtkImageData | None

create_segmentation_node_from_labelmap(labelmap_node: vtkMRMLLabelMapVolumeNode) → vtkMRMLSegmentationNode

create_segmentation_node_from_model_node(model_node: vtkMRMLModelNode) → vtkMRMLSegmentationNode

deactivate_effect()

property editor_logic: vtkSlicerSegmentEditorLogic

property editor_node: vtkMRMLSegmentEditorNode

editor_node_modified

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

export_segmentation_to_file(segmentation_node: vtkMRMLSegmentationNode, file_path: str) → None

export_segmentation_to_labelmap(segmentation_node: vtkMRMLSegmentationNode, labelmap: vtkMRMLLabelMapVolumeNode = None) → vtkMRMLLabelMapVolumeNode

export_segmentation_to_models(segmentation_node: vtkMRMLSegmentationNode, folder_item_id: int) → None

export_segmentation_to_stl(segmentation_node: vtkMRMLSegmentationNode, out_folder: str, segment_ids: list[str] | None = None) → None

get_active_effect_name() → str

get_active_segment_id() → str

get_all_segment_properties() → dict[str, SegmentProperties]

get_editable_area() → SegmentationEditableAreaMode

get_effect(effect_type: type[TEffect]) → TEffect | None

get_effect_parameter_node(effect: SegmentationEffect | type[SegmentationEffect]) → vtkMRMLScriptedModuleNode: returns segmentation effect parameter node as used by this segment editor. When passing effect types as inputs, this method will ensure the effect has been registered. If the parameter node doesn’t exist in the current scene, the parameter node will be added automatically.

get_mask_segment_id() → str

get_nth_segment(i_segment: int) → vtkSegment | None

get_nth_segment_id(i_segment: int) → str

get_overwrite_mode() → SegmentationOverwriteMode

get_segment(segment_id: str) → vtkSegment | None

get_segment_ids() → list[str]

get_segment_labelmap(segment_id: str, *, as_numpy_array: bool = False) → vtkImageData | ndarray[tuple[Any, ...], dtype[_ScalarT]] | None

get_segment_names() → list[str]

get_segment_properties(segment_id)

get_segment_visibility(segment_id) → bool | None

is_3d_shown()

is_effect_type_registered(effect_type: type[SegmentationEffect]) → bool

is_surface_representation_enabled() → bool

load_segmentation_from_file(segmentation_file: str) → vtkMRMLSegmentationNode | None

property n_segments: int

parameter_changed

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

register_effect_type(effect_type: type[SegmentationEffect]) → None: Registers the input segment editor effect type for the segmentation editor.

remove_segment(segment_id)

segmentation_display_modified

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

segmentation_modified

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

set_active_effect(effect: SegmentationEffect | None) → SegmentationEffect | None

set_active_effect_name(effect_id: str) → SegmentationEffect | None

set_active_effect_type(effect_type: type[SegmentationEffect]) → SegmentationEffect | None

set_active_segment_id(segment_id)

set_active_segmentation(segmentation_node: vtkMRMLSegmentationNode, volume_node: vtkMRMLVolumeNode) → Segmentation

set_editable_area(editable_area: SegmentationEditableAreaMode) → None

set_mask_segment_id(segment_id: str)

set_overwrite_mode(overwrite_mode: SegmentationOverwriteMode) → None

set_segment_properties(segment_id, segment_properties: SegmentProperties)

set_segment_visibility(segment_id, visibility: bool) → None

set_surface_representation_enabled(is_enabled: bool) → None

set_undo_stack(undo_stack: UndoStack)

show_3d(show_3d: bool)

show_3d_changed

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

trigger_all_signals()

property undo_stack: UndoStack | None

class trame_slicer.core.SlicerApp(share_directory: str | None = None)

Bases: object

Container for the core components of a Slicer application. Instantiates the scene, application logic and layout manager. Configures the default nodes present in the scene.

register_module_logic(logic: vtkSlicerModuleLogic, *, logic_name: str = '', share_sub_folder: str = '')

Configure the input module logic with the application scene, logic and share directory. Registers the logic to the application logic with the given input logic name if any, module name otherwise.

Parameters:

logic – instance of logic to register
logic_name – name of the logic in the application logic
share_sub_folder – sub folder of the share directory (if no sub folder, common share directory is used)

Returns:

instance of logic

class trame_slicer.core.ViewManager(scene: vtkMRMLScene, application_logic: vtkMRMLApplicationLogic)

Bases: object

Class responsible for creating views given view descriptions and factories. Create views with the first factory available which can create view spec. Provides access to created views but doesn’t hold strong ownership of the views.

create_view(view: ViewLayoutDefinition) → AbstractViewChild | None: Uses the best registered factory to create the view with given id / type. Overwrites view stored if it exists. Returns created view.

filter_visible_views(views: list[AbstractViewChild]) → list[AbstractViewChild]: Filter input view list by ones currently displayed in the layout.

get_current_view_ids() → list[str]

get_slice_views(view_group: int | None = None) → list[SliceView]

get_threed_views(view_group: int | None = None) → list[ThreeDView]

get_view(view_id: str | vtkMRMLAbstractViewNode) → AbstractViewChild | None: Get view associated with input view ID.

get_views(view_group: int | None = None) → list[AbstractView]: Return all Slicer views matching view group in the view manager.

is_view_created(view_id: str) → bool: Returns true if view id is created, false otherwise.

register_factory(view_factory: IViewFactory) → None: Allows to register a factory for given view type.

remove_view(view_id: str) → bool

set_current_view_ids(view_ids: list[str]) → None: Set which views are currently displayed in the application. To be used by layout manager or equivalent classes.

class trame_slicer.core.VolumeRendering(slicer_app: SlicerApp)

Bases: SlicerWrapper[vtkSlicerVolumeRenderingLogic]

Simple facade for volume rendering logic.

apply_preset(display: vtkMRMLVolumeRenderingDisplayNode | None, preset_name: str)

static apply_vr_node_property(display: vtkMRMLVolumeRenderingDisplayNode, property_node: vtkMRMLVolumePropertyNode)

create_display_node(volume_node: vtkMRMLVolumeNode, preset_name: str = '') → vtkMRMLVolumeRenderingDisplayNode

property crop_logic: vtkSlicerCropVolumeLogic

get_cropping_roi_node(volume_node: vtkMRMLVolumeNode | None) → vtkMRMLMarkupsROINode | None: Returns the ROI node instance attached to the input volume node’s VR display node if any.

get_cropping_roi_visiblity(volume_node: vtkMRMLVolumeNode | None) → bool: Returns the input volume node’s VR crop ROI node’s visibility. If the input volume node doesn’t have a ROI node, returns False.

get_preset_node(preset_name: str) → vtkMRMLVolumePropertyNode | None

get_preset_property(preset_name) → VolumeProperty

get_preset_vr_shift_range(preset_name: str) → tuple[float, float]

get_volume_node_property(volume_node: vtkMRMLVolumeNode) → VolumeProperty

get_vr_display_node(volume_node: vtkMRMLVolumeNode) → vtkMRMLVolumeRenderingDisplayNode | None

get_vr_shift_range(volume_node: vtkMRMLVolumeNode) → tuple[float, float]

has_vr_display_node(volume_node: vtkMRMLVolumeNode) → bool

preset_names() → list[str]

set_absolute_vr_shift_from_preset(volume_node: ~slicer_core.MRMLCore.vtkMRMLVolumeNode, preset_name: str | None, shift: float, shift_mode: ~trame_slicer.core.volume_property.VRShiftMode = <VRShiftMode.BOTH: 3>) → None

Shift the volume rendering opacity and colors by a given value. The shift is a scalar value representing how much the preset should be moved compared to a preset default.

Which

See also:

ref:: set_relative_vr_shift

set_cropping_enabled(volume_node: vtkMRMLVolumeNode, roi_node: vtkMRMLMarkupsROINode | None, is_enabled: bool) → vtkMRMLMarkupsROINode | None

Enable or disable the VR cropping for the input volume node. If the volume node doesn’t have a cropping ROI node and is_enabled is True, a new ROI node will be initialized and encompass the full volume node.

The ROI Node attached to the display node will be returned.

set_cropping_roi_node_visibile(volume_node: vtkMRMLVolumeNode | None, is_visible: bool) → bool

Sets the inputs volume node’s VR cropping ROI visible. If the input volume node doesn’t have a cropping node, does nothgin.

:return visibility state of the ROI node

set_relative_vr_shift(volume_node: ~slicer_core.MRMLCore.vtkMRMLVolumeNode, shift: float, shift_mode: ~trame_slicer.core.volume_property.VRShiftMode = <VRShiftMode.BOTH: 3>) → None

Shift the volume rendering opacity and colors by a given value for the current scalar/opacity values.

See also:

ref:: set_absolute_vr_shift_from_preset

set_volume_node_property(volume_node: vtkMRMLVolumeNode, property_node: vtkMRMLVolumePropertyNode)

set_vr_opacity(volume_node: vtkMRMLVolumeNode, opacity: float, gradient_threshold_hu: float = 0)

Update volume node gradient opacity function applied on RBG value. Copied from: https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#show-volume-rendering-making-soft-tissues-transparent

Updates the Volume property node gradient opacity with 0 opacity below a given HU value and the updated slider position opacity value above.

By default, the gradient threshold is set to around water HU value https://www.sciencedirect.com/topics/medicine-and-dentistry/hounsfield-scale

Parameters:

volume_node – volume node on which the VR opacity will be applied
opacity – Opacity value between [0, 1]. 1 = fully opaque, 0 = fully transparent.
gradient_threshold_hu – Cut off for opacity gradient.

toggle_cropping_visibility(volume_node: vtkMRMLVolumeNode | None) → bool

Toggle input volume node cropping visibility. Toggling the visibility will activate and initialize the cropping ROI Node if needed.

Returns:: New visibility state of the Cropping ROI Node

class trame_slicer.core.VolumeWindowLevel

Bases: object

Collection of helper functions to update a volume’s window / level

classmethod get_volume_auto_min_max_range(volume_node: vtkMRMLVolumeNode) → tuple[float, float]

classmethod get_volume_display_node(volume_node: vtkMRMLVolumeNode) → vtkMRMLVolumeDisplayNode

classmethod get_volume_display_range(volume_node: vtkMRMLVolumeNode) → tuple[float, float]

classmethod get_volume_scalar_range(volume_node: vtkMRMLVolumeNode) → tuple[float, float]

classmethod min_max_to_window_level(min_value: float, max_value: float) → tuple[float, float]

classmethod set_volume_node_display_min_max_range(volume_node: vtkMRMLVolumeNode, min_value: float, max_value: float) → None

classmethod set_volume_node_window_level(volume_node: vtkMRMLVolumeNode, window: float, level: float) → None

classmethod window_level_to_min_max(window: float, level: float) → tuple[float, float]

class trame_slicer.core.VolumesReader

Bases: object

Adapted from Modules/Scripted/DICOMPlugins/DICOMScalarVolumePlugin.py

classmethod contains_dcm_volume(volume_files: list[str]) → bool

dcm_read_lru_cache_size = 5000

classmethod is_dcm_file(file_name: str) → bool

classmethod load_dcm_volumes(scene: vtkMRMLScene, volume_files: list[vtkMRMLVolumeNode | None])

classmethod load_single_dcm_volume(scene: vtkMRMLScene, volume_files: list[str]) → vtkMRMLVolumeNode | None

classmethod load_single_file_volume(scene: vtkMRMLScene, app_logic: vtkMRMLApplicationLogic, volume_file: str) → vtkMRMLVolumeNode | None

classmethod load_volumes(scene: vtkMRMLScene, app_logic: vtkMRMLApplicationLogic, volume_files: list[str] | str) → list[vtkMRMLVolumeNode]

classmethod split_volumes(volume_files: list[str]) → list[list[str]]

classmethod tag_value_to_vector(value)

trame_slicer.core.display_manager module

class trame_slicer.core.display_manager.DisplayManager(view_manager: ViewManager, volume_rendering: VolumeRendering)

Bases: object

Helper class to display volume nodes in given view group

show_volume(volume_node: vtkMRMLVolumeNode, view_group: int | None = None, vr_preset: str = '', do_reset_views: bool = False) → None

hide_volume(volume_node: vtkMRMLVolumeNode, view_group: int | None = None)

reset_views(view_group: int | None = None)

show_volume_in_slice_background(volume_node: vtkMRMLVolumeNode | None, view_group: int | None = None)

show_volume_in_slice_foreground(volume_node: vtkMRMLVolumeNode | None, view_group: int | None = None)

set_node_visible_in_group(node: vtkMRMLDisplayableNode, view_group: int | None = None)

trame_slicer.core.io_manager module

class trame_slicer.core.io_manager.IOManager(scene: vtkMRMLScene, app_logic: vtkMRMLApplicationLogic, segmentation_editor: SegmentationEditor)

Bases: object

Class responsible for loading files in the scene.

load_volumes(volume_files: str | list[str]) → list[vtkMRMLVolumeNode]

classmethod write_volume(volume_node, volume_file: str | Path) → None

load_model(model_file: str | Path, do_convert_to_slicer_coord: bool = True) → vtkMRMLModelNode | None

classmethod write_model(model_node, model_file: str | Path, do_convert_from_slicer_coord: bool = True) → None

load_segmentation(segmentation_file: str | Path, do_convert_to_slicer_coord=True) → vtkMRMLSegmentationNode | None

write_segmentation(segmentation_node, segmentation_file: str | Path)

classmethod write_node(node, node_file, storage_type: type, do_convert_from_slicer_coord: bool) → None

load_scene(scene_path) → bool

write_scene(scene_path: str | Path) → bool

save_scene(scene_path: str | Path) → bool

trame_slicer.core.layout_manager module

class trame_slicer.core.layout_manager.LayoutManager(scene: vtkMRMLScene, view_manager: ViewManager, server: Server, *, virtual_node: VirtualNode | None = None, is_virtual_node_initialized: bool = False)

Bases: object

Class responsible for instantiating views depending on the layout node.

Creates a singleton layout node at initialization.
Observes layout node changes to notify observers of layout id changes.
Can register layouts with their associated descriptions
Notifies view manager of requested view on layout change

registered_layouts_changed

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

current_layout_changed

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

property layout_id: str | None

get_layout_ids() → list[str]

register_layout(layout_id: str, layout: Layout, lazy_initialization: bool = False) → None: Registers the given layout id to the associated layout. Will overwrite any pre existing layout with this ID. If lazy_initialization is False, the views will not be instantiated unless the passed layout id matches the current selected layout id.

set_layout(layout_id: str) → None

create_layout_views_if_needed(layout_id: str) → None

set_layout_from_node(node: vtkMRMLScriptedModuleNode) → None

has_layout(layout_id: str) → bool

get_layout(layout_id: str, default_layout: Layout | None = None) → Layout

register_layout_dict(layout_dict: dict[str, Layout], lazy_initialization: bool = False) → None

Parameters:

layout_dict – Layout dictionary to register to the layout manager
lazy_initialization – If True, the layout views will not be created until explicitly requested by set_layout or create_layout_views_if_needed

classmethod default_grid_configuration() → dict[str, Layout]

initialize_layout_grid(layout: AbstractLayout): Initialize the LayoutGrid placeholder in the layout at the call position.

trame_slicer.core.markups_logic module

class trame_slicer.core.markups_logic.MarkupsLogic(slicer_app: SlicerApp)

Bases: SlicerWrapper[vtkSlicerMarkupsLogic]

Thin wrapper around vtkSlicerMarkupsLogic

property interaction_node: vtkMRMLInteractionNode | None

place_node(node: vtkMRMLMarkupsNode, persistent: bool = False)

disable_place_mode()

trame_slicer.core.segmentation_editor module

class trame_slicer.core.segmentation_editor.SegmentationEditor(scene: vtkMRMLScene, logic: vtkSlicerSegmentationsModuleLogic, view_manager: ViewManager, *, builtin_effects: list[type[SegmentationEffect]] | None = None)

Bases: SignalContainer

Class responsible for editing the segmentation. Meant to be used by the application to activate / deactivate segmentation effects.

builtin_effects: ClassVar[list[type[SegmentationEffect]]] = [<class 'trame_slicer.segmentation.segmentation_effect_draw.SegmentationEffectDraw'>, <class 'trame_slicer.segmentation.segmentation_effect_paint_erase.SegmentationEffectErase'>, <class 'trame_slicer.segmentation.segmentation_effect_islands.SegmentationEffectIslands'>, <class 'trame_slicer.segmentation.segmentation_effect_logical_operators.SegmentationEffectLogicalOperators'>, <class 'trame_slicer.segmentation.segmentation_effect_no_tool.SegmentationEffectNoTool'>, <class 'trame_slicer.segmentation.segmentation_effect_paint_erase.SegmentationEffectPaint'>, <class 'trame_slicer.segmentation.segmentation_effect_scissors.SegmentationEffectScissors'>, <class 'trame_slicer.segmentation.segmentation_effect_smoothing.SegmentationEffectSmoothing'>, <class 'trame_slicer.segmentation.segmentation_effect_threshold.SegmentationEffectThreshold'>, <class 'trame_slicer.segmentation.segmentation_effect_volume_intensity_mask.SegmentationEffectVolumeIntensityMask'>]

segmentation_modified

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

segmentation_display_modified

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

active_segment_id_changed

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

active_effect_name_changed

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

show_3d_changed

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

parameter_changed

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

editor_node_modified

Signal implementation. Can be connected to one or more callables. When called, will call associated callables with the provided args and kwargs.

Provides utility methods and contextmanager to control signal execution. Can be used both as class property and instance.

Parameters:: type_info – Types of arguments expected by the signal.

property editor_logic: vtkSlicerSegmentEditorLogic

property editor_node: vtkMRMLSegmentEditorNode

is_effect_type_registered(effect_type: type[SegmentationEffect]) → bool

register_effect_type(effect_type: type[SegmentationEffect]) → None: Registers the input segment editor effect type for the segmentation editor.

set_undo_stack(undo_stack: UndoStack)

property undo_stack: UndoStack | None

property active_segmentation: Segmentation | None

property active_segmentation_display: SegmentationDisplay | None

property active_segmentation_node

property active_volume_node: vtkMRMLVolumeNode | None

property active_segment_modifier: SegmentModifier | None

property active_effect: SegmentationEffect | None

set_active_segmentation(segmentation_node: vtkMRMLSegmentationNode, volume_node: vtkMRMLVolumeNode) → Segmentation

create_segmentation_node_from_model_node(model_node: vtkMRMLModelNode) → vtkMRMLSegmentationNode

create_segmentation_node_from_labelmap(labelmap_node: vtkMRMLLabelMapVolumeNode) → vtkMRMLSegmentationNode

create_empty_segmentation_node() → vtkMRMLSegmentationNode

set_active_effect_type(effect_type: type[SegmentationEffect]) → SegmentationEffect | None

set_active_effect_name(effect_id: str) → SegmentationEffect | None

set_active_effect(effect: SegmentationEffect | None) → SegmentationEffect | None

property active_effect_name: str

get_active_effect_name() → str

deactivate_effect()

get_segment_ids() → list[str]

get_segment_names() → list[str]

get_all_segment_properties() → dict[str, SegmentProperties]

get_segment_properties(segment_id)

set_segment_properties(segment_id, segment_properties: SegmentProperties)

property n_segments: int

get_nth_segment(i_segment: int) → vtkSegment | None

get_nth_segment_id(i_segment: int) → str

get_segment(segment_id: str) → vtkSegment | None

add_empty_segment(*, segment_id='', segment_name='', segment_color: list[float] | None = None, segment_value: int | None = None) → str

remove_segment(segment_id)

get_active_segment_id() → str

set_active_segment_id(segment_id)

property active_segment_id: str

get_segment_labelmap(segment_id: str, *, as_numpy_array: bool = False) → vtkImageData | ndarray[tuple[Any, ...], dtype[_ScalarT]] | None

export_segmentation_to_labelmap(segmentation_node: vtkMRMLSegmentationNode, labelmap: vtkMRMLLabelMapVolumeNode = None) → vtkMRMLLabelMapVolumeNode

export_segmentation_to_file(segmentation_node: vtkMRMLSegmentationNode, file_path: str) → None

export_segmentation_to_models(segmentation_node: vtkMRMLSegmentationNode, folder_item_id: int) → None

export_segmentation_to_stl(segmentation_node: vtkMRMLSegmentationNode, out_folder: str, segment_ids: list[str] | None = None) → None

load_segmentation_from_file(segmentation_file: str) → vtkMRMLSegmentationNode | None

set_surface_representation_enabled(is_enabled: bool) → None

is_surface_representation_enabled() → bool

show_3d(show_3d: bool)

is_3d_shown()

create_modifier_labelmap() → vtkImageData | None

apply_labelmap(labelmap) → None

apply_polydata_world(poly_world) → None

trigger_all_signals()

set_segment_visibility(segment_id, visibility: bool) → None

get_segment_visibility(segment_id) → bool | None

set_editable_area(editable_area: SegmentationEditableAreaMode) → None

get_editable_area() → SegmentationEditableAreaMode

set_mask_segment_id(segment_id: str)

get_mask_segment_id() → str

set_overwrite_mode(overwrite_mode: SegmentationOverwriteMode) → None

get_overwrite_mode() → SegmentationOverwriteMode

get_effect_parameter_node(effect: SegmentationEffect | type[SegmentationEffect]) → vtkMRMLScriptedModuleNode: returns segmentation effect parameter node as used by this segment editor. When passing effect types as inputs, this method will ensure the effect has been registered. If the parameter node doesn’t exist in the current scene, the parameter node will be added automatically.

get_effect(effect_type: type[TEffect]) → TEffect | None

clear()

trame_slicer.core.slicer_app module

class trame_slicer.core.slicer_app.SlicerApp(share_directory: str | None = None)

Bases: object

Container for the core components of a Slicer application. Instantiates the scene, application logic and layout manager. Configures the default nodes present in the scene.

register_module_logic(logic: vtkSlicerModuleLogic, *, logic_name: str = '', share_sub_folder: str = '')

Configure the input module logic with the application scene, logic and share directory. Registers the logic to the application logic with the given input logic name if any, module name otherwise.

Parameters:

logic – instance of logic to register
logic_name – name of the logic in the application logic
share_sub_folder – sub folder of the share directory (if no sub folder, common share directory is used)

Returns:

instance of logic

trame_slicer.core.view_manager module

class trame_slicer.core.view_manager.ViewManager(scene: vtkMRMLScene, application_logic: vtkMRMLApplicationLogic)

Bases: object

Class responsible for creating views given view descriptions and factories. Create views with the first factory available which can create view spec. Provides access to created views but doesn’t hold strong ownership of the views.

set_current_view_ids(view_ids: list[str]) → None: Set which views are currently displayed in the application. To be used by layout manager or equivalent classes.

get_current_view_ids() → list[str]

register_factory(view_factory: IViewFactory) → None: Allows to register a factory for given view type.

get_view(view_id: str | vtkMRMLAbstractViewNode) → AbstractViewChild | None: Get view associated with input view ID.

remove_view(view_id: str) → bool

create_view(view: ViewLayoutDefinition) → AbstractViewChild | None: Uses the best registered factory to create the view with given id / type. Overwrites view stored if it exists. Returns created view.

is_view_created(view_id: str) → bool: Returns true if view id is created, false otherwise.

get_views(view_group: int | None = None) → list[AbstractView]: Return all Slicer views matching view group in the view manager.

get_slice_views(view_group: int | None = None) → list[SliceView]

get_threed_views(view_group: int | None = None) → list[ThreeDView]

filter_visible_views(views: list[AbstractViewChild]) → list[AbstractViewChild]: Filter input view list by ones currently displayed in the layout.

trame_slicer.core.volume_property module

class trame_slicer.core.volume_property.VRShiftMode(*values)

Bases: Flag

OPACITY = 1

COLOR = 2

BOTH = 3

class trame_slicer.core.volume_property.VolumeProperty(volume_property_node: vtkMRMLVolumePropertyNode | None)

Bases: SlicerWrapper[vtkMRMLVolumePropertyNode]

Thin facade for volume property node. Allows more pythonic access to the scalar / opacity properties of a volume rendering display node.

property volume_property: vtkVolumeProperty

property property_node: vtkMRMLVolumePropertyNode

property opacity_map: vtkPiecewiseFunction

property color_map: vtkColorTransferFunction

get_color_map_values() → list[list[float]]

get_opacity_map_values() → list[list[float]]

set_color_map_values(values: list[list[float]])

set_opacity_values(values: list[list[float]])

shift_color_map(shift: float) → None

shift_opacity_map(shift: float) → None

get_effective_range() → tuple[float, float]

static shift_values(values, shift)

set_vr_shift(shift: float, shift_mode: VRShiftMode, ref_prop: VolumeProperty | None = None)

trame_slicer.core.volume_rendering module

class trame_slicer.core.volume_rendering.VolumeRendering(slicer_app: SlicerApp)

Bases: SlicerWrapper[vtkSlicerVolumeRenderingLogic]

Simple facade for volume rendering logic.

property crop_logic: vtkSlicerCropVolumeLogic

create_display_node(volume_node: vtkMRMLVolumeNode, preset_name: str = '') → vtkMRMLVolumeRenderingDisplayNode

apply_preset(display: vtkMRMLVolumeRenderingDisplayNode | None, preset_name: str)

set_volume_node_property(volume_node: vtkMRMLVolumeNode, property_node: vtkMRMLVolumePropertyNode)

static apply_vr_node_property(display: vtkMRMLVolumeRenderingDisplayNode, property_node: vtkMRMLVolumePropertyNode)

get_preset_property(preset_name) → VolumeProperty

get_vr_display_node(volume_node: vtkMRMLVolumeNode) → vtkMRMLVolumeRenderingDisplayNode | None

has_vr_display_node(volume_node: vtkMRMLVolumeNode) → bool

preset_names() → list[str]

get_preset_node(preset_name: str) → vtkMRMLVolumePropertyNode | None

set_absolute_vr_shift_from_preset(volume_node: ~slicer_core.MRMLCore.vtkMRMLVolumeNode, preset_name: str | None, shift: float, shift_mode: ~trame_slicer.core.volume_property.VRShiftMode = <VRShiftMode.BOTH: 3>) → None

Shift the volume rendering opacity and colors by a given value. The shift is a scalar value representing how much the preset should be moved compared to a preset default.

Which

See also:

ref:: set_relative_vr_shift

set_relative_vr_shift(volume_node: ~slicer_core.MRMLCore.vtkMRMLVolumeNode, shift: float, shift_mode: ~trame_slicer.core.volume_property.VRShiftMode = <VRShiftMode.BOTH: 3>) → None

Shift the volume rendering opacity and colors by a given value for the current scalar/opacity values.

See also:

ref:: set_absolute_vr_shift_from_preset

get_vr_shift_range(volume_node: vtkMRMLVolumeNode) → tuple[float, float]

get_preset_vr_shift_range(preset_name: str) → tuple[float, float]

get_volume_node_property(volume_node: vtkMRMLVolumeNode) → VolumeProperty

set_cropping_enabled(volume_node: vtkMRMLVolumeNode, roi_node: vtkMRMLMarkupsROINode | None, is_enabled: bool) → vtkMRMLMarkupsROINode | None

Enable or disable the VR cropping for the input volume node. If the volume node doesn’t have a cropping ROI node and is_enabled is True, a new ROI node will be initialized and encompass the full volume node.

The ROI Node attached to the display node will be returned.

get_cropping_roi_node(volume_node: vtkMRMLVolumeNode | None) → vtkMRMLMarkupsROINode | None: Returns the ROI node instance attached to the input volume node’s VR display node if any.

get_cropping_roi_visiblity(volume_node: vtkMRMLVolumeNode | None) → bool: Returns the input volume node’s VR crop ROI node’s visibility. If the input volume node doesn’t have a ROI node, returns False.

set_cropping_roi_node_visibile(volume_node: vtkMRMLVolumeNode | None, is_visible: bool) → bool

Sets the inputs volume node’s VR cropping ROI visible. If the input volume node doesn’t have a cropping node, does nothgin.

:return visibility state of the ROI node

toggle_cropping_visibility(volume_node: vtkMRMLVolumeNode | None) → bool

Toggle input volume node cropping visibility. Toggling the visibility will activate and initialize the cropping ROI Node if needed.

Returns:: New visibility state of the Cropping ROI Node

set_vr_opacity(volume_node: vtkMRMLVolumeNode, opacity: float, gradient_threshold_hu: float = 0)

Update volume node gradient opacity function applied on RBG value. Copied from: https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#show-volume-rendering-making-soft-tissues-transparent

Updates the Volume property node gradient opacity with 0 opacity below a given HU value and the updated slider position opacity value above.

By default, the gradient threshold is set to around water HU value https://www.sciencedirect.com/topics/medicine-and-dentistry/hounsfield-scale

Parameters:

volume_node – volume node on which the VR opacity will be applied
opacity – Opacity value between [0, 1]. 1 = fully opaque, 0 = fully transparent.
gradient_threshold_hu – Cut off for opacity gradient.

trame_slicer.core.volume_window_level module

class trame_slicer.core.volume_window_level.VolumeWindowLevel

Bases: object

Collection of helper functions to update a volume’s window / level

classmethod get_volume_auto_min_max_range(volume_node: vtkMRMLVolumeNode) → tuple[float, float]

classmethod get_volume_scalar_range(volume_node: vtkMRMLVolumeNode) → tuple[float, float]

classmethod set_volume_node_window_level(volume_node: vtkMRMLVolumeNode, window: float, level: float) → None

classmethod set_volume_node_display_min_max_range(volume_node: vtkMRMLVolumeNode, min_value: float, max_value: float) → None

classmethod get_volume_display_range(volume_node: vtkMRMLVolumeNode) → tuple[float, float]

classmethod window_level_to_min_max(window: float, level: float) → tuple[float, float]

classmethod min_max_to_window_level(min_value: float, max_value: float) → tuple[float, float]

classmethod get_volume_display_node(volume_node: vtkMRMLVolumeNode) → vtkMRMLVolumeDisplayNode

trame_slicer.core.volumes_reader module

class trame_slicer.core.volumes_reader.VolumesReader

Bases: object

Adapted from Modules/Scripted/DICOMPlugins/DICOMScalarVolumePlugin.py

dcm_read_lru_cache_size = 5000

classmethod load_volumes(scene: vtkMRMLScene, app_logic: vtkMRMLApplicationLogic, volume_files: list[str] | str) → list[vtkMRMLVolumeNode]

classmethod load_single_file_volume(scene: vtkMRMLScene, app_logic: vtkMRMLApplicationLogic, volume_file: str) → vtkMRMLVolumeNode | None

classmethod contains_dcm_volume(volume_files: list[str]) → bool

classmethod is_dcm_file(file_name: str) → bool

classmethod load_dcm_volumes(scene: vtkMRMLScene, volume_files: list[vtkMRMLVolumeNode | None])

classmethod split_volumes(volume_files: list[str]) → list[list[str]]

classmethod tag_value_to_vector(value)

classmethod load_single_dcm_volume(scene: vtkMRMLScene, volume_files: list[str]) → vtkMRMLVolumeNode | None