segmentation

class trame_slicer.segmentation.AbstractSegmentationEffectBrush(mode: ModificationMode)

Bases: SegmentationEffect, ABC

Abstract class for segmentation effect implementing a brush behavior in views

decrease_brush_size(decrease_ratio: float | None = None)

get_brush_diameter() → float

get_brush_diameter_mode() → BrushDiameterMode

increase_brush_size(increase_ratio: float | None = None)

is_sphere_brush() → bool

abstractmethod paint_glyph_at_world_coordinates(polydata: vtkPolyData, paint_coordinates_world: vtkPoints)

set_active(is_active)

set_brush_diameter(diameter: float, diameter_mode: BrushDiameterMode | None = None)

set_use_sphere_brush(use_sphere_brush)

class trame_slicer.segmentation.AutoThresholdMethod(*values)

Bases: Enum

HUANG = 1

INTERMODES = 2

ISO_DATA = 3

KITTLER_ILLINGWORTH = 4

LI = 5

MAXIMUM_ENTROPY = 6

MOMENTS = 7

OTSU = 8

RENYI_ENTROPY = 9

SHANBHAG = 10

TRIANGLE = 11

YEN = 12

class trame_slicer.segmentation.AutoThresholdMode(*values)

Bases: IntFlag

UPPER = 1

LOWER = 2

MIN = 4

MAX = 8

MIN_UPPER = 5

LOWER_MAX = 10

class trame_slicer.segmentation.BrushDiameterMode(*values)

Bases: Enum

Absolute = 1

ScreenRelative = 2

class trame_slicer.segmentation.BrushInteractionMode(*values)

Bases: Enum

CONTINUOUS = 1

POINT_BY_POINT = 2

class trame_slicer.segmentation.BrushShape(*values)

Bases: Enum

Sphere = 0

Cylinder = 1

class trame_slicer.segmentation.BrushSource(shape: BrushShape, diameter: float = 16.0, cylinder_height: float = 1.0)

Bases: object

property brush_to_world_origin_transform: vtkTransform

get_diameter()

get_transformed_polydata_output_port() → vtkAlgorithmOutput: Return the output port of transformed brush model

get_untransformed_output_port() → vtkAlgorithmOutput: Return the output port of untransformed brush model Useful for feedback actors

set_brush_rotation(slice_to_ras: vtkMatrix4x4)

set_brush_to_world_position(world_pos)

set_cylinder_height(cylinder_height: float)

set_diameter(diameter: float)

set_shape(shape: BrushShape) → None

property world_origin_to_world_transform: vtkTransform

class trame_slicer.segmentation.ModificationMode(*values)

Bases: IntEnum

Set = 1

Add = 2

Remove = 3

RemoveAll = 4

class trame_slicer.segmentation.ScissorsEffectFillMode(*values)

Bases: Enum

ERASE_INSIDE = 1

ERASE_OUTSIDE = 2

FILL_INSIDE = 3

FILL_OUTSIDE = 4

class trame_slicer.segmentation.ScissorsEffectRangeMode(*values)

Bases: Enum

UNLIMITED = 1

POSITIVE = 2

NEGATIVE = 3

SYMMETRIC = 4

class trame_slicer.segmentation.ScissorsPolygonBrush

Bases: object

Display the scissors as 2D lines

add_point(x: int, y: int) → None

get_props() → list[vtkProp]

property points: vtkPoints

preview_point(x: int, y: int) → None

remove_last_point() → None

reset() → None

set_visible(visible: bool)

class trame_slicer.segmentation.SegmentModifier(segmentation: Segmentation)

Bases: object

Helper class to apply modifications to a given segment in the segmentation of a segmentation node. Should be used by segmentation widgets.

property active_segment_id

apply_glyph(poly: vtkPolyData, world_locations: vtkPoints) → None

Parameters:

poly – in world origin coordinates (no transform but world-coords sized)
world_locations – each location where glyph will be rendered at (world-coords)

apply_labelmap(modifier_labelmap: vtkOrientedImageData, *, segment_id: str | None = None, modification_mode: ModificationMode | None = None, modifier_extent=None, is_per_segment: bool = True, do_bypass_masking: bool = False): Modify active segment using input modifier labelmap in source IJK coordinates. When applying, pushes the modifications to the current undo stack if any is defined.

apply_polydata_world(poly_world: vtkPolyData)

Parameters:: poly_world – Poly in world coordinates

create_modifier_labelmap() → vtkOrientedImageData | None

get_segment_labelmap(segment_id, *, as_numpy_array=False) → ndarray[tuple[Any, ...], dtype[_ScalarT]] | vtkImageData

get_source_image_data() → vtkOrientedImageData | None

get_source_volume_intensity_mask_range() → tuple[float, float] | None

group_undo_commands(text: str = '') → AbstractContextManager[None]

is_source_volume_intensity_mask_enabled() → bool

property logic: vtkSlicerSegmentEditorLogic

property modification_mode: ModificationMode

on_segmentation_modified()

paint_glyph_in_labelmap(polydata: vtkPolyData, world_locations: vtkPoints, labelmap: vtkOrientedImageData) → list[float]

property segment_editor_node: vtkMRMLSegmentEditorNode | None

property segmentation: Segmentation

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_segment_labelmap(segment_id, label_map: vtkImageData | ndarray[tuple[Any, ...], dtype[_ScalarT]])

set_source_volume_intensity_mask_enabled(is_enabled: bool) → None

set_source_volume_intensity_mask_range(min_value: float, max_value: float) → None

trigger_active_segment_modified()

property volume_node

class trame_slicer.segmentation.SegmentProperties(color: 'list[float]', name: 'str', label_value: 'int', terminology_tag: 'str' = '')

Bases: object

property color_hex: str

classmethod from_segment(segment: vtkSegment) → SegmentProperties | None

terminology_tag: str = ''

to_dict()

to_segment(segment: vtkSegment)

color: list[float]

name: str

label_value: int

class trame_slicer.segmentation.Segmentation(segmentation_node: vtkMRMLSegmentationNode, volume_node, *, editor_logic: vtkSlicerSegmentEditorLogic = None, undo_stack: UndoStack = None)

Bases: object

Wrapper around vtkMRMLSegmentationNode for segmentation access.

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

create_modifier_labelmap() → vtkOrientedImageData | None

disable_surface_representation() → None

property editor_logic: vtkSlicerSegmentEditorLogic | None

enable_surface_representation() → None

property first_segment_id: str

get_display() → SegmentationDisplay | None

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

get_nth_segment(i_segment: int) → vtkSegment | None

get_nth_segment_id(i_segment: int) → str

get_segment(segment_id: str) → vtkSegment | None

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

get_segment_ids() → list[str]

get_segment_labelmap(segment_id: str, *, as_numpy_array: bool = False) → ndarray[tuple[Any, ...], dtype[_ScalarT]] | vtkOrientedImageData: Returns the labelmap corresponding to the input segment ID. Labelmap is guaranteed to have the same dimensions as the reference volume.

get_segment_names() → list[str]

get_segment_properties(segment_id) → SegmentProperties | None

get_segment_value(segment_id) → int

get_segment_values()

get_visible_segment_ids() → list[str]

group_undo_commands(text: str = '') → Generator[None, Any, None]

is_surface_representation_enabled() → bool

property n_segments: int

push_undo(cmd)

remove_segment(segment_id) → None

property segmentation: vtkSegmentation | None

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.

property segmentation_node: vtkMRMLSegmentationNode | None

set_active()

set_segment_editor_logic(logic: vtkSlicerSegmentEditorLogic)

set_segment_properties(segment_id, segment_properties: SegmentProperties)

set_segment_value(segment_id, segment_value: int | None)

set_surface_representation_enabled(is_enabled: bool) → None

set_undo_stack(undo_stack)

trigger_modified()

property undo_stack: UndoStack | None

property volume_node: vtkMRMLVolumeNode | None

class trame_slicer.segmentation.SegmentationDisplay(slicer_obj: T | None = None)

Bases: SlicerWrapper[vtkMRMLSegmentationDisplayNode]

Wrapper around the segmentation display node.

get_border_thickness() → int | None

get_opacity_2d() → float | None

get_opacity_mode() → SegmentationOpacityEnum | None

set_border_thickness(thickness: float) → None

set_opacity_2d(opacity: float) → None

set_opacity_mode(opacity_mode: SegmentationOpacityEnum) → None

class trame_slicer.segmentation.SegmentationEditableAreaMode(*values)

Bases: Enum

EVERYWHERE = 0

INSIDE_SINGLE_SEGMENT = 5

INSIDE_ALL_SEGMENTS = 1

INSIDE_ALL_VISIBLE_SEGMENTS = 2

OUTSIDE_ALL_SEGMENTS = 3

OUTSIDE_ALL_VISIBLE_SEGMENTS = 4

class trame_slicer.segmentation.SegmentationEffect

Bases: ABC

activate() → None

create_pipeline(view_node: vtkMRMLAbstractViewNode, parameter: vtkMRMLNode) → SegmentationEffectPipeline | None

deactivate() → None

property editor: SegmentationEditor | None

property editor_node: vtkMRMLSegmentEditorNode | None

classmethod get_effect_name()

get_parameter_node()

property is_active: bool

is_effect_parameter(parameter: vtkMRMLNode) → bool

property modifier: SegmentModifier | None

parameters_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 pipelines: list[ref[SegmentationEffectPipeline]]

set_active(is_active)

set_editor(editor: SegmentationEditor) → None

set_mode(mode: ModificationMode)

set_scene(scene: vtkMRMLScene)

trigger_pipeline_parameter_change(*_)

class trame_slicer.segmentation.SegmentationEffectDraw: Bases: SegmentationEffectScissors

class trame_slicer.segmentation.SegmentationEffectErase: Bases: SegmentationEffectPaintErase

class trame_slicer.segmentation.SegmentationEffectIslands

Bases: SegmentationEffect

add_island_at_position(world_pos: tuple[float, float, float])

apply(island_mode: SegmentationIslandsMode | None = None) → None

get_island_labelmap(*, min_voxel_size: int = 0, segment_id: str | None = None) → vtkOrientedImageData

get_island_mode() → SegmentationIslandsMode

get_minimum_island_size() → int

is_in_interactive_mode() → bool

keep_island_at_position(world_pos: tuple[float, float, float])

keep_largest_island() → None

keep_n_largest_islands(number_of_islands: int) → None

remove_island_at_position(world_pos: tuple[float, float, float])

remove_small_islands(min_voxel_size: int | None = None) → None

select_island_at_position(world_pos: tuple[float, float, float], island_mode: SegmentationIslandsMode | None = None) → None

set_island_mode(island_mode: SegmentationIslandsMode) → None

set_minimum_island_size(minimum_island_size: int) → None

split_islands_to_segments() → None

class trame_slicer.segmentation.SegmentationEffectLogicalOperators

Bases: SegmentationEffect

add(segment_id: str | None) → None

clear() → None

copy(segment_id: str | None) → None

fill() → None

intersect(segment_id: str | None) → None

invert() → None

subtract(segment_id: str | None) → None

class trame_slicer.segmentation.SegmentationEffectNoTool

Bases: SegmentationEffect

Empty implementation when no segmentation effect is selected.

class trame_slicer.segmentation.SegmentationEffectPaint: Bases: SegmentationEffectPaintErase

class trame_slicer.segmentation.SegmentationEffectPaintErase(mode: ModificationMode)

Bases: AbstractSegmentationEffectBrush

paint_glyph_at_world_coordinates(polydata: vtkPolyData, paint_coordinates_world: vtkPoints)

class trame_slicer.segmentation.SegmentationEffectPipeline

Bases: vtkMRMLLayerDMScriptedPipeline, Generic[T]

GetEffectParameterNode() → vtkMRMLScriptedModuleNode | None

GetModifier() → SegmentModifier | None

GetSegmentation() → Segmentation | None

IsActive() → bool

OnEffectParameterUpdate()

OnUpdate(obj: vtkObject, _eventId: int, _callData: Any | None) → None

Observer update callback. Triggered when any object & events observed using UpdateObserver is triggered.

Parameters:

obj – vtkObject instance which triggered the callback
eventId – Event id which triggered the callback
callData – Optional observer call data. Use self.CastCallData(callData, vtkType) to convert to Python

SetActive(isActive: bool)

SetDisplayNode(displayNode: vtkMRMLNode) → None

Set the display node for the pipeline has changed (initialization). default behavior: Stored and display node is observed for vtkCommand::ModifiedEvent. See also: self.UpdateObserver(prevObj, newObj, eventIds) See also: self.OnUpdate(obj, eventId, callData)

Parameters:: displayNode – The new instance of display node for the pipeline

SetSegmentationEffect(effect: T)

SetView(view: AbstractViewChild)

class trame_slicer.segmentation.SegmentationEffectScissors

Bases: SegmentationEffect

apply_points_display_coordinates(points_display: vtkPoints, view: AbstractView) → None: Apply scissors points as defined in display coordinates in the input view.

property brush_interaction_mode: BrushInteractionMode

set_brush_interaction_mode(mode: BrushInteractionMode)

set_fill_mode(fill_mode: ScissorsEffectFillMode)

set_range_mode(range_mode: ScissorsEffectRangeMode)

set_symmetric_distance(symmetric_distance: float)

class trame_slicer.segmentation.SegmentationEffectSmoothing

Bases: AbstractSegmentationEffectBrush

apply_closing(kernel_size: float, segment_id: str, mask_labelmap: vtkOrientedImageData | None = None)

apply_gaussian_smoothing(std: float, segment_id: str, mask_labelmap: vtkOrientedImageData | None = None)

apply_joint_smoothing(smoothing_factor: float, mask_labelmap: vtkOrientedImageData | None = None)

apply_median_smoothing(kernel_size: float, segment_id: str, mask_labelmap: vtkOrientedImageData | None = None)

apply_opening(kernel_size: float, segment_id: str, mask_labelmap: vtkOrientedImageData | None = None)

apply_smoothing(mask_labelmap: vtkOrientedImageData | None = None, smoothing_mode: SmoothingEffectMode | None = None)

paint_glyph_at_world_coordinates(polydata: vtkPolyData, paint_coordinates_world: vtkPoints)

set_joint_smoothing_factor(joint_smoothing_factor: float)

set_kernel_size(kernel_size: float)

set_smoothing_mode(mode: SmoothingEffectMode)

set_standard_deviation(standard_deviation: float)

class trame_slicer.segmentation.SegmentationEffectThreshold

Bases: SegmentationEffect

apply()

auto_threshold(auto_method: ~trame_slicer.segmentation.segmentation_effect_threshold.AutoThresholdMethod = AutoThresholdMethod.OTSU, mode: ~trame_slicer.segmentation.segmentation_effect_threshold.AutoThresholdMode = <AutoThresholdMode.LOWER_MAX: 10>): Use auto threshold to set the threshold min / max values. Does nothing if the segmentation effect is not currently active.

get_param_proxy() → ThresholdParameters

get_threshold_min_max_values() → tuple[float, float]

set_active(is_active: bool)

set_editor(editor: SegmentationEditor) → None

set_threshold_min_max_values(value: tuple[float, float])

use_for_volume_intensity_masking() → None

class trame_slicer.segmentation.SegmentationEffectVolumeIntensityMask

Bases: SegmentationEffect

get_mask_range() → tuple[float, float]

get_param_proxy() → ThresholdParameters

is_mask_enabled() → bool

property is_visible: bool

set_editor(editor: SegmentationEditor) → None

set_mask_enabled(is_enabled: bool) → None

set_mask_range(min_value: float, max_value: float) → None

set_mask_visible(is_visible: bool) → None

class trame_slicer.segmentation.SegmentationIslandsMode(*values)

Bases: Enum

classmethod get_interactive_modes() → list[SegmentationIslandsMode]

is_interactive() → bool

KEEP_LARGEST_ISLAND = 1

REMOVE_SMALL_ISLANDS = 2

SPLIT_TO_SEGMENTS = 3

KEEP_SELECTED = 4

REMOVE_SELECTED = 5

ADD_SELECTED = 6

class trame_slicer.segmentation.SegmentationIslandsPipeline

Bases: SegmentationEffectPipeline[SegmentationEffectIslands]

CanProcessInteractionEvent(eventData: vtkMRMLInteractionEventData) → tuple[bool, float]: Should return true + distance2 to interaction if the pipeline can process the input event data. :param eventData: The MRML event needing to be processed :return: (bool, distance2) default = False, float_max

IsSupportedEvent(event_data: vtkMRMLInteractionEventData)

ProcessInteractionEvent(event_data: vtkMRMLInteractionEventData) → bool

Triggered when the pipeline can process the interaction and is at the top of the priority list. default behavior: does nothing and returns false.

Parameters:: eventData – The MRML event needing to be processed
Returns:: True if event was processed. False otherwise (default = false)

class trame_slicer.segmentation.SegmentationOpacityEnum(*values)

Bases: Flag

FILL = 1

OUTLINE = 2

BOTH = 3

class trame_slicer.segmentation.SegmentationOverwriteMode(*values)

Bases: Enum

OVERWRITE_ALL = 0

OVERWRITE_ALL_VISIBLE_SEGMENTS = 1

ALLOW_OVERLAP = 2

class trame_slicer.segmentation.SegmentationPaintPipeline2D

Bases: SegmentationPaintPipeline

CreateWidget()

IsSupportedEvent(event_data: vtkMRMLInteractionEventData)

class trame_slicer.segmentation.SegmentationPaintPipeline3D

Bases: SegmentationPaintPipeline

CreateWidget()

HasLastPickPosition()

IsSupportedEvent(event_data: vtkMRMLInteractionEventData)

Pick(event_data)

class trame_slicer.segmentation.SegmentationPaintWidget(view: T)

Bases: Generic[T], ABC

clear()

get_brush_polydata_port() → vtkAlgorithmOutput

get_feedback_polydata_port()

get_paint_glyph() → vtkPolyData

is_painting() → bool

paint_interaction_stopped

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.

start_painting() → None

stop_painting() → None

update_paint_parameters(params: PaintEffectParameters)

update_widget_position(position)

class trame_slicer.segmentation.SegmentationPaintWidget2D(view: T): Bases: SegmentationPaintWidget[SliceView]

class trame_slicer.segmentation.SegmentationPaintWidget3D(view: T): Bases: SegmentationPaintWidget[ThreeDView]

class trame_slicer.segmentation.SegmentationScissorsPipeline

Bases: SegmentationEffectPipeline[SegmentationEffectScissors]

CanProcessInteractionEvent(eventData: vtkMRMLInteractionEventData) → tuple[bool, float]: Should return true + distance2 to interaction if the pipeline can process the input event data. :param eventData: The MRML event needing to be processed :return: (bool, distance2) default = False, float_max

IsSupportedEvent(event_data: vtkMRMLInteractionEventData)

OnRendererAdded(renderer: vtkRenderer | None) → None

Triggered when the pipeline is displayed on a new renderer. default behavior: does nothing. See also: self.GetRenderer() See also: self.ResetDisplay() See also: self.RequestRender()

Parameters:: renderer – Optional instance or renderer on which the pipeline is added

OnRendererRemoved(_renderer: vtkRenderer) → None

Triggered when the pipeline is removed from its previous renderer. default behavior: does nothing. See also: self.GetRenderer()

Parameters:: renderer – Optional instance or renderer from which the pipeline was removed
Returns:

ProcessInteractionEvent(event_data: vtkMRMLInteractionEventData) → bool

Triggered when the pipeline can process the interaction and is at the top of the priority list. default behavior: does nothing and returns false.

Parameters:: eventData – The MRML event needing to be processed
Returns:: True if event was processed. False otherwise (default = false)

SetActive(isActive: bool)

SetDisplayNode(displayNode: vtkMRMLNode) → None

Set the display node for the pipeline has changed (initialization). default behavior: Stored and display node is observed for vtkCommand::ModifiedEvent. See also: self.UpdateObserver(prevObj, newObj, eventIds) See also: self.OnUpdate(obj, eventId, callData)

Parameters:: displayNode – The new instance of display node for the pipeline

SetViewNode(viewNode: vtkMRMLAbstractViewNode) → None: Set the pipeline view node (initialization). default behavior: Stored and view node is observed for vtkCommand::ModifiedEvent. :param viewNode: The instance of viewNode the pipeline is attached to

property brush_interaction_mode: BrushInteractionMode

class trame_slicer.segmentation.SegmentationScissorsWidget

Bases: object

On slice view project 2D points on slice (world pos) On 3D view project 2D points on focal plane (world pos)

add_point(x: int, y: int) → None

cancel_painting() → None

disable_brush() → None

enable_brush() → None

interaction_stopped

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.

is_brush_enabled() → bool

is_painting() → bool

preview_point(x: int, y: int) → None

remove_last_point() → None

set_active(is_active: bool) → None

set_modifier(modifier: SegmentModifier)

set_renderer(renderer)

set_view_node(view_node)

start_painting(x: int, y: int) → None

stop_painting() → None

class trame_slicer.segmentation.SegmentationThresholdPipeline2D

Bases: SegmentationEffectPipeline

OnEffectParameterUpdate()

OnRendererAdded(renderer: vtkRenderer | None) → None

Triggered when the pipeline is displayed on a new renderer. default behavior: does nothing. See also: self.GetRenderer() See also: self.ResetDisplay() See also: self.RequestRender()

Parameters:: renderer – Optional instance or renderer on which the pipeline is added

OnRendererRemoved(renderer: vtkRenderer) → None

Triggered when the pipeline is removed from its previous renderer. default behavior: does nothing. See also: self.GetRenderer()

Parameters:: renderer – Optional instance or renderer from which the pipeline was removed
Returns:

OnViewModified(*_)

SetView(view: SliceView)

class trame_slicer.segmentation.ThresholdOpacityBlinker

Bases: object

opacity_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_active(is_active: bool) → None

set_opacity_range(low: float, high: float)

start()

stop()

class trame_slicer.segmentation.ThresholdParameters(min_value: 'float' = 0, max_value: 'float' = 0, preview_opacity: 'float' = 0.5, is_visible: 'bool' = False, is_hatched: 'bool' = False)

Bases: object

is_hatched: bool = False

is_visible: bool = False

max_value: float = 0

min_value: float = 0

preview_opacity: float = 0.5

trame_slicer.segmentation.abstract_segmentation_effect_brush module

class trame_slicer.segmentation.abstract_segmentation_effect_brush.AbstractSegmentationEffectBrush(mode: ModificationMode)

Bases: SegmentationEffect, ABC

Abstract class for segmentation effect implementing a brush behavior in views

set_active(is_active)

set_use_sphere_brush(use_sphere_brush)

set_brush_diameter(diameter: float, diameter_mode: BrushDiameterMode | None = None)

increase_brush_size(increase_ratio: float | None = None)

decrease_brush_size(decrease_ratio: float | None = None)

is_sphere_brush() → bool

get_brush_diameter() → float

get_brush_diameter_mode() → BrushDiameterMode

abstractmethod paint_glyph_at_world_coordinates(polydata: vtkPolyData, paint_coordinates_world: vtkPoints)

trame_slicer.segmentation.brush_source module

class trame_slicer.segmentation.brush_source.BrushSource(shape: BrushShape, diameter: float = 16.0, cylinder_height: float = 1.0)

Bases: object

property brush_to_world_origin_transform: vtkTransform

property world_origin_to_world_transform: vtkTransform

set_shape(shape: BrushShape) → None

get_diameter()

set_diameter(diameter: float)

set_cylinder_height(cylinder_height: float)

get_transformed_polydata_output_port() → vtkAlgorithmOutput: Return the output port of transformed brush model

get_untransformed_output_port() → vtkAlgorithmOutput: Return the output port of untransformed brush model Useful for feedback actors

set_brush_rotation(slice_to_ras: vtkMatrix4x4)

set_brush_to_world_position(world_pos)

trame_slicer.segmentation.paint_effect_parameters module

class trame_slicer.segmentation.paint_effect_parameters.BrushShape(*values)

Bases: Enum

Sphere = 0

Cylinder = 1

class trame_slicer.segmentation.paint_effect_parameters.BrushDiameterMode(*values)

Bases: Enum

Absolute = 1

ScreenRelative = 2

class trame_slicer.segmentation.paint_effect_parameters.PaintEffectParameters(brush_diameter: 'float' = 6.0, brush_diameter_mode: 'BrushDiameterMode' = <BrushDiameterMode.ScreenRelative: 2>, use_sphere_brush: 'bool' = False, brush_model_node: 'vtkMRMLModelNode | None' = None, paint_feedback_model_node: 'vtkMRMLModelNode | None' = None)

Bases: object

brush_diameter: float = 6.0

brush_diameter_mode: BrushDiameterMode = 2

use_sphere_brush: bool = False

brush_model_node: vtkMRMLModelNode | None = None

paint_feedback_model_node: vtkMRMLModelNode | None = None

trame_slicer.segmentation.scissors_effect_parameters module

class trame_slicer.segmentation.scissors_effect_parameters.BrushInteractionMode(*values)

Bases: Enum

CONTINUOUS = 1

POINT_BY_POINT = 2

class trame_slicer.segmentation.scissors_effect_parameters.ScissorsEffectFillMode(*values)

Bases: Enum

ERASE_INSIDE = 1

ERASE_OUTSIDE = 2

FILL_INSIDE = 3

FILL_OUTSIDE = 4

class trame_slicer.segmentation.scissors_effect_parameters.ScissorsEffectRangeMode(*values)

Bases: Enum

UNLIMITED = 1

POSITIVE = 2

NEGATIVE = 3

SYMMETRIC = 4

trame_slicer.segmentation.segment_modifier module

class trame_slicer.segmentation.segment_modifier.ModificationMode(*values)

Bases: IntEnum

Set = 1

Add = 2

Remove = 3

RemoveAll = 4

class trame_slicer.segmentation.segment_modifier.SegmentModifier(segmentation: Segmentation)

Bases: object

Helper class to apply modifications to a given segment in the segmentation of a segmentation node. Should be used by segmentation widgets.

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.

property logic: vtkSlicerSegmentEditorLogic

property segment_editor_node: vtkMRMLSegmentEditorNode | None

property active_segment_id

property modification_mode: ModificationMode

property segmentation: Segmentation

property volume_node

paint_glyph_in_labelmap(polydata: vtkPolyData, world_locations: vtkPoints, labelmap: vtkOrientedImageData) → list[float]

apply_glyph(poly: vtkPolyData, world_locations: vtkPoints) → None

Parameters:

poly – in world origin coordinates (no transform but world-coords sized)
world_locations – each location where glyph will be rendered at (world-coords)

apply_polydata_world(poly_world: vtkPolyData)

Parameters:: poly_world – Poly in world coordinates

apply_labelmap(modifier_labelmap: vtkOrientedImageData, *, segment_id: str | None = None, modification_mode: ModificationMode | None = None, modifier_extent=None, is_per_segment: bool = True, do_bypass_masking: bool = False): Modify active segment using input modifier labelmap in source IJK coordinates. When applying, pushes the modifications to the current undo stack if any is defined.

get_segment_labelmap(segment_id, *, as_numpy_array=False) → ndarray[tuple[Any, ...], dtype[_ScalarT]] | vtkImageData

set_segment_labelmap(segment_id, label_map: vtkImageData | ndarray[tuple[Any, ...], dtype[_ScalarT]])

trigger_active_segment_modified()

on_segmentation_modified()

get_source_image_data() → vtkOrientedImageData | None

create_modifier_labelmap() → vtkOrientedImageData | None

set_source_volume_intensity_mask_range(min_value: float, max_value: float) → None

get_source_volume_intensity_mask_range() → tuple[float, float] | None

set_source_volume_intensity_mask_enabled(is_enabled: bool) → None

is_source_volume_intensity_mask_enabled() → bool

group_undo_commands(text: str = '') → AbstractContextManager[None]

trame_slicer.segmentation.segment_properties module

class trame_slicer.segmentation.segment_properties.SegmentProperties(color: 'list[float]', name: 'str', label_value: 'int', terminology_tag: 'str' = '')

Bases: object

color: list[float]

name: str

label_value: int

terminology_tag: str = ''

classmethod from_segment(segment: vtkSegment) → SegmentProperties | None

to_segment(segment: vtkSegment)

property color_hex: str

to_dict()

trame_slicer.segmentation.segmentation module

class trame_slicer.segmentation.segmentation.Segmentation(segmentation_node: vtkMRMLSegmentationNode, volume_node, *, editor_logic: vtkSlicerSegmentEditorLogic = None, undo_stack: UndoStack = None)

Bases: object

Wrapper around vtkMRMLSegmentationNode for segmentation access.

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.

property editor_logic: vtkSlicerSegmentEditorLogic | None

set_active()

set_undo_stack(undo_stack)

set_segment_editor_logic(logic: vtkSlicerSegmentEditorLogic)

property undo_stack: UndoStack | None

property segmentation: vtkSegmentation | None

property volume_node: vtkMRMLVolumeNode | None

property segmentation_node: vtkMRMLSegmentationNode | None

get_segment_ids() → list[str]

get_segment_names() → list[str]

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

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) → None

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

get_segment_values()

get_segment_labelmap(segment_id: str, *, as_numpy_array: bool = False) → ndarray[tuple[Any, ...], dtype[_ScalarT]] | vtkOrientedImageData: Returns the labelmap corresponding to the input segment ID. Labelmap is guaranteed to have the same dimensions as the reference volume.

set_surface_representation_enabled(is_enabled: bool) → None

is_surface_representation_enabled() → bool

enable_surface_representation() → None

disable_surface_representation() → None

get_visible_segment_ids() → list[str]

get_segment_value(segment_id) → int

set_segment_value(segment_id, segment_value: int | None)

property first_segment_id: str

create_modifier_labelmap() → vtkOrientedImageData | None

trigger_modified()

get_segment_properties(segment_id) → SegmentProperties | None

set_segment_properties(segment_id, segment_properties: SegmentProperties)

push_undo(cmd)

get_display() → SegmentationDisplay | None

group_undo_commands(text: str = '') → Generator[None, Any, None]

trame_slicer.segmentation.segmentation_display module

class trame_slicer.segmentation.segmentation_display.SegmentationOpacityEnum(*values)

Bases: Flag

FILL = 1

OUTLINE = 2

BOTH = 3

class trame_slicer.segmentation.segmentation_display.SegmentationDisplay(slicer_obj: T | None = None)

Bases: SlicerWrapper[vtkMRMLSegmentationDisplayNode]

Wrapper around the segmentation display node.

get_border_thickness() → int | None

set_border_thickness(thickness: float) → None

get_opacity_2d() → float | None

set_opacity_2d(opacity: float) → None

get_opacity_mode() → SegmentationOpacityEnum | None

set_opacity_mode(opacity_mode: SegmentationOpacityEnum) → None

trame_slicer.segmentation.segmentation_editable_area_mode module

class trame_slicer.segmentation.segmentation_editable_area_mode.SegmentationEditableAreaMode(*values)

Bases: Enum

EVERYWHERE = 0

INSIDE_SINGLE_SEGMENT = 5

INSIDE_ALL_SEGMENTS = 1

INSIDE_ALL_VISIBLE_SEGMENTS = 2

OUTSIDE_ALL_SEGMENTS = 3

OUTSIDE_ALL_VISIBLE_SEGMENTS = 4

trame_slicer.segmentation.segmentation_effect module

class trame_slicer.segmentation.segmentation_effect.SegmentationEffect

Bases: ABC

parameters_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 editor: SegmentationEditor | None

set_editor(editor: SegmentationEditor) → None

property editor_node: vtkMRMLSegmentEditorNode | None

property modifier: SegmentModifier | None

property pipelines: list[ref[SegmentationEffectPipeline]]

property is_active: bool

set_scene(scene: vtkMRMLScene)

set_mode(mode: ModificationMode)

classmethod get_effect_name()

get_parameter_node()

is_effect_parameter(parameter: vtkMRMLNode) → bool

activate() → None

deactivate() → None

set_active(is_active)

create_pipeline(view_node: vtkMRMLAbstractViewNode, parameter: vtkMRMLNode) → SegmentationEffectPipeline | None

trigger_pipeline_parameter_change(*_)

trame_slicer.segmentation.segmentation_effect_draw module

class trame_slicer.segmentation.segmentation_effect_draw.SegmentationEffectDraw: Bases: SegmentationEffectScissors

trame_slicer.segmentation.segmentation_effect_islands module

class trame_slicer.segmentation.segmentation_effect_islands.SegmentationIslandsMode(*values)

Bases: Enum

KEEP_LARGEST_ISLAND = 1

REMOVE_SMALL_ISLANDS = 2

SPLIT_TO_SEGMENTS = 3

KEEP_SELECTED = 4

REMOVE_SELECTED = 5

ADD_SELECTED = 6

classmethod get_interactive_modes() → list[SegmentationIslandsMode]

is_interactive() → bool

class trame_slicer.segmentation.segmentation_effect_islands.SegmentationEffectIslands

Bases: SegmentationEffect

is_in_interactive_mode() → bool

set_island_mode(island_mode: SegmentationIslandsMode) → None

get_island_mode() → SegmentationIslandsMode

set_minimum_island_size(minimum_island_size: int) → None

get_minimum_island_size() → int

apply(island_mode: SegmentationIslandsMode | None = None) → None

select_island_at_position(world_pos: tuple[float, float, float], island_mode: SegmentationIslandsMode | None = None) → None

remove_island_at_position(world_pos: tuple[float, float, float])

keep_island_at_position(world_pos: tuple[float, float, float])

add_island_at_position(world_pos: tuple[float, float, float])

remove_small_islands(min_voxel_size: int | None = None) → None

keep_n_largest_islands(number_of_islands: int) → None

keep_largest_island() → None

split_islands_to_segments() → None

get_island_labelmap(*, min_voxel_size: int = 0, segment_id: str | None = None) → vtkOrientedImageData

trame_slicer.segmentation.segmentation_effect_logical_operators module

class trame_slicer.segmentation.segmentation_effect_logical_operators.SegmentationEffectLogicalOperators

Bases: SegmentationEffect

add(segment_id: str | None) → None

subtract(segment_id: str | None) → None

copy(segment_id: str | None) → None

intersect(segment_id: str | None) → None

invert() → None

clear() → None

fill() → None

trame_slicer.segmentation.segmentation_effect_no_tool module

class trame_slicer.segmentation.segmentation_effect_no_tool.SegmentationEffectNoTool

Bases: SegmentationEffect

Empty implementation when no segmentation effect is selected.

trame_slicer.segmentation.segmentation_effect_paint_erase module

class trame_slicer.segmentation.segmentation_effect_paint_erase.SegmentationEffectPaintErase(mode: ModificationMode)

Bases: AbstractSegmentationEffectBrush

paint_glyph_at_world_coordinates(polydata: vtkPolyData, paint_coordinates_world: vtkPoints)

class trame_slicer.segmentation.segmentation_effect_paint_erase.SegmentationEffectPaint: Bases: SegmentationEffectPaintErase

class trame_slicer.segmentation.segmentation_effect_paint_erase.SegmentationEffectErase: Bases: SegmentationEffectPaintErase

trame_slicer.segmentation.segmentation_effect_pipeline module

class trame_slicer.segmentation.segmentation_effect_pipeline.SegmentationEffectPipeline

Bases: vtkMRMLLayerDMScriptedPipeline, Generic[T]

GetModifier() → SegmentModifier | None

GetSegmentation() → Segmentation | None

IsActive() → bool

SetSegmentationEffect(effect: T)

SetDisplayNode(displayNode: vtkMRMLNode) → None

Set the display node for the pipeline has changed (initialization). default behavior: Stored and display node is observed for vtkCommand::ModifiedEvent. See also: self.UpdateObserver(prevObj, newObj, eventIds) See also: self.OnUpdate(obj, eventId, callData)

Parameters:: displayNode – The new instance of display node for the pipeline

SetView(view: AbstractViewChild)

SetActive(isActive: bool)

OnUpdate(obj: vtkObject, _eventId: int, _callData: Any | None) → None

Observer update callback. Triggered when any object & events observed using UpdateObserver is triggered.

Parameters:

obj – vtkObject instance which triggered the callback
eventId – Event id which triggered the callback
callData – Optional observer call data. Use self.CastCallData(callData, vtkType) to convert to Python

OnEffectParameterUpdate()

GetEffectParameterNode() → vtkMRMLScriptedModuleNode | None

trame_slicer.segmentation.segmentation_effect_scissors module

class trame_slicer.segmentation.segmentation_effect_scissors.SegmentationEffectScissors

Bases: SegmentationEffect

property brush_interaction_mode: BrushInteractionMode

set_brush_interaction_mode(mode: BrushInteractionMode)

set_symmetric_distance(symmetric_distance: float)

set_fill_mode(fill_mode: ScissorsEffectFillMode)

set_range_mode(range_mode: ScissorsEffectRangeMode)

apply_points_display_coordinates(points_display: vtkPoints, view: AbstractView) → None: Apply scissors points as defined in display coordinates in the input view.

trame_slicer.segmentation.segmentation_effect_scissors_widget module

class trame_slicer.segmentation.segmentation_effect_scissors_widget.ScissorsPolygonBrush

Bases: object

Display the scissors as 2D lines

set_visible(visible: bool)

preview_point(x: int, y: int) → None

add_point(x: int, y: int) → None

remove_last_point() → None

reset() → None

property points: vtkPoints

get_props() → list[vtkProp]

class trame_slicer.segmentation.segmentation_effect_scissors_widget.SegmentationScissorsWidget

Bases: object

On slice view project 2D points on slice (world pos) On 3D view project 2D points on focal plane (world pos)

interaction_stopped

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_view_node(view_node)

set_modifier(modifier: SegmentModifier)

set_renderer(renderer)

preview_point(x: int, y: int) → None

add_point(x: int, y: int) → None

set_active(is_active: bool) → None

enable_brush() → None

disable_brush() → None

is_brush_enabled() → bool

start_painting(x: int, y: int) → None

stop_painting() → None

cancel_painting() → None

remove_last_point() → None

is_painting() → bool

class trame_slicer.segmentation.segmentation_effect_scissors_widget.SegmentationScissorsPipeline

Bases: SegmentationEffectPipeline[SegmentationEffectScissors]

property brush_interaction_mode: BrushInteractionMode

SetActive(isActive: bool)

OnRendererAdded(renderer: vtkRenderer | None) → None

Triggered when the pipeline is displayed on a new renderer. default behavior: does nothing. See also: self.GetRenderer() See also: self.ResetDisplay() See also: self.RequestRender()

Parameters:: renderer – Optional instance or renderer on which the pipeline is added

OnRendererRemoved(_renderer: vtkRenderer) → None

Triggered when the pipeline is removed from its previous renderer. default behavior: does nothing. See also: self.GetRenderer()

Parameters:: renderer – Optional instance or renderer from which the pipeline was removed
Returns:

SetViewNode(viewNode: vtkMRMLAbstractViewNode) → None: Set the pipeline view node (initialization). default behavior: Stored and view node is observed for vtkCommand::ModifiedEvent. :param viewNode: The instance of viewNode the pipeline is attached to

SetDisplayNode(displayNode: vtkMRMLNode) → None

Set the display node for the pipeline has changed (initialization). default behavior: Stored and display node is observed for vtkCommand::ModifiedEvent. See also: self.UpdateObserver(prevObj, newObj, eventIds) See also: self.OnUpdate(obj, eventId, callData)

Parameters:: displayNode – The new instance of display node for the pipeline

CanProcessInteractionEvent(eventData: vtkMRMLInteractionEventData) → tuple[bool, float]: Should return true + distance2 to interaction if the pipeline can process the input event data. :param eventData: The MRML event needing to be processed :return: (bool, distance2) default = False, float_max

ProcessInteractionEvent(event_data: vtkMRMLInteractionEventData) → bool

Triggered when the pipeline can process the interaction and is at the top of the priority list. default behavior: does nothing and returns false.

Parameters:: eventData – The MRML event needing to be processed
Returns:: True if event was processed. False otherwise (default = false)

IsSupportedEvent(event_data: vtkMRMLInteractionEventData)

trame_slicer.segmentation.segmentation_effect_smoothing module

class trame_slicer.segmentation.segmentation_effect_smoothing.SmoothingEffectMode(*values)

Bases: Enum

MEDIAN = 1

OPENING = 2

CLOSING = 3

GAUSSIAN = 4

JOINT = 5

class trame_slicer.segmentation.segmentation_effect_smoothing.SegmentationEffectSmoothing

Bases: AbstractSegmentationEffectBrush

set_smoothing_mode(mode: SmoothingEffectMode)

set_kernel_size(kernel_size: float)

set_standard_deviation(standard_deviation: float)

set_joint_smoothing_factor(joint_smoothing_factor: float)

apply_median_smoothing(kernel_size: float, segment_id: str, mask_labelmap: vtkOrientedImageData | None = None)

apply_opening(kernel_size: float, segment_id: str, mask_labelmap: vtkOrientedImageData | None = None)

apply_closing(kernel_size: float, segment_id: str, mask_labelmap: vtkOrientedImageData | None = None)

apply_gaussian_smoothing(std: float, segment_id: str, mask_labelmap: vtkOrientedImageData | None = None)

apply_joint_smoothing(smoothing_factor: float, mask_labelmap: vtkOrientedImageData | None = None)

apply_smoothing(mask_labelmap: vtkOrientedImageData | None = None, smoothing_mode: SmoothingEffectMode | None = None)

paint_glyph_at_world_coordinates(polydata: vtkPolyData, paint_coordinates_world: vtkPoints)

trame_slicer.segmentation.segmentation_effect_threshold module

class trame_slicer.segmentation.segmentation_effect_threshold.AutoThresholdMethod(*values)

Bases: Enum

HUANG = 1

INTERMODES = 2

ISO_DATA = 3

KITTLER_ILLINGWORTH = 4

LI = 5

MAXIMUM_ENTROPY = 6

MOMENTS = 7

OTSU = 8

RENYI_ENTROPY = 9

SHANBHAG = 10

TRIANGLE = 11

YEN = 12

class trame_slicer.segmentation.segmentation_effect_threshold.AutoThresholdMode(*values)

Bases: IntFlag

UPPER = 1

LOWER = 2

MIN = 4

MAX = 8

MIN_UPPER = 5

LOWER_MAX = 10

class trame_slicer.segmentation.segmentation_effect_threshold.SegmentationEffectThreshold

Bases: SegmentationEffect

set_editor(editor: SegmentationEditor) → None

set_active(is_active: bool)

apply()

auto_threshold(auto_method: ~trame_slicer.segmentation.segmentation_effect_threshold.AutoThresholdMethod = AutoThresholdMethod.OTSU, mode: ~trame_slicer.segmentation.segmentation_effect_threshold.AutoThresholdMode = <AutoThresholdMode.LOWER_MAX: 10>): Use auto threshold to set the threshold min / max values. Does nothing if the segmentation effect is not currently active.

get_param_proxy() → ThresholdParameters

get_threshold_min_max_values() → tuple[float, float]

set_threshold_min_max_values(value: tuple[float, float])

use_for_volume_intensity_masking() → None

trame_slicer.segmentation.segmentation_effect_volume_intensity_mask module

class trame_slicer.segmentation.segmentation_effect_volume_intensity_mask.SegmentationEffectVolumeIntensityMask

Bases: SegmentationEffect

set_editor(editor: SegmentationEditor) → None

set_mask_visible(is_visible: bool) → None

set_mask_enabled(is_enabled: bool) → None

set_mask_range(min_value: float, max_value: float) → None

get_mask_range() → tuple[float, float]

is_mask_enabled() → bool

get_param_proxy() → ThresholdParameters

property is_visible: bool

trame_slicer.segmentation.segmentation_islands_pipeline module

class trame_slicer.segmentation.segmentation_islands_pipeline.SegmentationIslandsPipeline

Bases: SegmentationEffectPipeline[SegmentationEffectIslands]

IsSupportedEvent(event_data: vtkMRMLInteractionEventData)

ProcessInteractionEvent(event_data: vtkMRMLInteractionEventData) → bool

Triggered when the pipeline can process the interaction and is at the top of the priority list. default behavior: does nothing and returns false.

Parameters:: eventData – The MRML event needing to be processed
Returns:: True if event was processed. False otherwise (default = false)

CanProcessInteractionEvent(eventData: vtkMRMLInteractionEventData) → tuple[bool, float]: Should return true + distance2 to interaction if the pipeline can process the input event data. :param eventData: The MRML event needing to be processed :return: (bool, distance2) default = False, float_max

trame_slicer.segmentation.segmentation_overwrite_mode module

class trame_slicer.segmentation.segmentation_overwrite_mode.SegmentationOverwriteMode(*values)

Bases: Enum

OVERWRITE_ALL = 0

OVERWRITE_ALL_VISIBLE_SEGMENTS = 1

ALLOW_OVERLAP = 2

trame_slicer.segmentation.segmentation_paint_pipeline module

class trame_slicer.segmentation.segmentation_paint_pipeline.SegmentationPaintPipeline

Bases: SegmentationEffectPipeline

OnEffectParameterUpdate()

CreateWidget()

SetActive(isActive: bool)

OnPaintInteractionStopped()

IsSupportedEvent(event_data: vtkMRMLInteractionEventData)

ProcessInteractionEvent(event_data: vtkMRMLInteractionEventData) → bool

Triggered when the pipeline can process the interaction and is at the top of the priority list. default behavior: does nothing and returns false.

Parameters:: eventData – The MRML event needing to be processed
Returns:: True if event was processed. False otherwise (default = false)

CanProcessInteractionEvent(eventData: vtkMRMLInteractionEventData) → tuple[bool, float]: Should return true + distance2 to interaction if the pipeline can process the input event data. :param eventData: The MRML event needing to be processed :return: (bool, distance2) default = False, float_max

LoseFocus(eventData: vtkMRMLInteractionEventData | None) → None: Triggered when the pipeline had focus (processed an interaction) and loses the focus (other pipeline handled the new interaction or window leave event). default behavior: does nothing. :param eventData: Optional event data which triggered the lose focus

GetWidgetState() → int: Current widget state of the pipeline. :return: default = WidgetStateIdle

class trame_slicer.segmentation.segmentation_paint_pipeline.SegmentationPaintPipeline2D

Bases: SegmentationPaintPipeline

IsSupportedEvent(event_data: vtkMRMLInteractionEventData)

CreateWidget()

class trame_slicer.segmentation.segmentation_paint_pipeline.SegmentationPaintPipeline3D

Bases: SegmentationPaintPipeline

Pick(event_data)

HasLastPickPosition()

IsSupportedEvent(event_data: vtkMRMLInteractionEventData)

CreateWidget()

trame_slicer.segmentation.segmentation_paint_widget module

class trame_slicer.segmentation.segmentation_paint_widget.SegmentationPaintWidget(view: T)

Bases: Generic[T], ABC

paint_interaction_stopped

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.

clear()

get_brush_polydata_port() → vtkAlgorithmOutput

get_feedback_polydata_port()

start_painting() → None

stop_painting() → None

is_painting() → bool

update_widget_position(position)

get_paint_glyph() → vtkPolyData

update_paint_parameters(params: PaintEffectParameters)

class trame_slicer.segmentation.segmentation_paint_widget.SegmentationPaintWidget2D(view: T): Bases: SegmentationPaintWidget[SliceView]

class trame_slicer.segmentation.segmentation_paint_widget.SegmentationPaintWidget3D(view: T): Bases: SegmentationPaintWidget[ThreeDView]

trame_slicer.segmentation.segmentation_state_stack module

class trame_slicer.segmentation.segmentation_state_stack.SegmentationStateStack(segmentation: vtkSegmentation, max_size: int)

Bases: object

Simple segmentation stack. Deep copies input segmentation when saving state. Not optimized by any means.

save_state() → None

clear() → None

has_next()

has_previous()

restore_next(): Restore next saved state if stack has following states.

restore_previous(): Restore previous state if stack has previous states.

remove_next_states() → None: Pops all next states.

set_max_size(max_size: int) → None

get_max_size() → int

trame_slicer.segmentation.segmentation_threshold_pipeline module

class trame_slicer.segmentation.segmentation_threshold_pipeline.ThresholdParameters(min_value: 'float' = 0, max_value: 'float' = 0, preview_opacity: 'float' = 0.5, is_visible: 'bool' = False, is_hatched: 'bool' = False)

Bases: object

min_value: float = 0

max_value: float = 0

preview_opacity: float = 0.5

is_visible: bool = False

is_hatched: bool = False

class trame_slicer.segmentation.segmentation_threshold_pipeline.SegmentationThresholdPipeline2D

Bases: SegmentationEffectPipeline

OnRendererAdded(renderer: vtkRenderer | None) → None

Triggered when the pipeline is displayed on a new renderer. default behavior: does nothing. See also: self.GetRenderer() See also: self.ResetDisplay() See also: self.RequestRender()

Parameters:: renderer – Optional instance or renderer on which the pipeline is added

OnRendererRemoved(renderer: vtkRenderer) → None

Triggered when the pipeline is removed from its previous renderer. default behavior: does nothing. See also: self.GetRenderer()

Parameters:: renderer – Optional instance or renderer from which the pipeline was removed
Returns:

OnEffectParameterUpdate()

SetView(view: SliceView)

OnViewModified(*_)

trame_slicer.segmentation.segmentation_undo_command module

class trame_slicer.segmentation.segmentation_undo_command.SegmentationRemoveUndoCommand(segmentation: Segmentation, segment_id)

Bases: UndoCommand

undo() → None

redo() → None

class trame_slicer.segmentation.segmentation_undo_command.SegmentationAddUndoCommand(segmentation: Segmentation, segment_id, segment_name, segment_color, segment_value)

Bases: UndoCommand

undo() → None

redo() → None

merge_with(command: UndoCommand) → bool: Try to merge current command with provided input command. If merge is successful, only one undo action will be kept in the stack.

do_try_merge(command: UndoCommand) → bool

class trame_slicer.segmentation.segmentation_undo_command.SegmentPropertyChangeUndoCommand(segmentation: Segmentation, segment_id: str, segment_properties: SegmentProperties)

Bases: UndoCommand

Undo / Redo command for segment property changes. Property changes can be compressed if they apply to the same segment.

is_obsolete() → bool

undo() → None

redo() → None

merge_with(command: UndoCommand) → bool: Try to merge current command with provided input command. If merge is successful, only one undo action will be kept in the stack.

class trame_slicer.segmentation.segmentation_undo_command.SegmentationLabelMapUndoCommand(segmentation_stack: SegmentationStateStack, segmentation: Segmentation)

Bases: UndoCommand

undo() → None

redo() → None

classmethod push_state_change(segmentation: Segmentation)

trame_slicer.segmentation.threshold_opacity_blinker module

class trame_slicer.segmentation.threshold_opacity_blinker.ThresholdOpacityBlinker

Bases: object

opacity_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_active(is_active: bool) → None

set_opacity_range(low: float, high: float)

start()

stop()