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Jo-ByrThibault-Pelletier
Jo-Byr
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Thibault-Pelletier
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feat(segmentation): add logical operators effect
Add logical operators segmentation effect logic and example
1 parent a6a6de3 commit dcdbea0

16 files changed

Lines changed: 427 additions & 14 deletions

‎examples/viewer_lib/logic/__init__.py‎

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@@ -5,6 +5,7 @@
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from .segmentation import (
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EraseEffectLogic,
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IslandsEffectLogic,
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LogicalOperatorsEffectLogic,
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PaintEffectLogic,
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PaintEraseEffectLogic,
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ScissorsEffectLogic,
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"EraseEffectLogic",
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"IslandsEffectLogic",
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"LoadVolumeLogic",
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"LogicalOperatorsEffectLogic",
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"MarkupsButtonLogic",
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"MedicalViewerLogic",
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"PaintEffectLogic",

‎examples/viewer_lib/logic/segmentation/__init__.py‎

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from .base_segmentation_logic import BaseEffectLogic, BaseSegmentationLogic
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from .brush_effect_logic import BrushEffectLogic
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from .islands_effect_logic import IslandsEffectLogic
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from .logical_operators_effect_logic import LogicalOperatorsEffectLogic
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from .paint_erase_effect_logic import (
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EraseEffectLogic,
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PaintEffectLogic,
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"BrushEffectLogic",
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"EraseEffectLogic",
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"IslandsEffectLogic",
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"LogicalOperatorsEffectLogic",
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"PaintEffectLogic",
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"PaintEraseEffectLogic",
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"ScissorsEffectLogic",

‎examples/viewer_lib/logic/segmentation/logical_operators_effect_logic.py‎

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from trame_server import Server
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from trame_slicer.core import SlicerApp
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from trame_slicer.segmentation import SegmentationEffectLogicalOperators
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from ...ui import (
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LogicalOperatorsEffectUI,
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LogicalOperatorsSegmentationMode,
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LogicalOperatorsState,
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SegmentEditorUI,
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SegmentState,
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)
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from .base_segmentation_logic import BaseEffectLogic
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class LogicalOperatorsEffectLogic(BaseEffectLogic[LogicalOperatorsState, SegmentationEffectLogicalOperators]):
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def __init__(self, server: Server, slicer_app: SlicerApp):
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super().__init__(server, slicer_app, LogicalOperatorsState, SegmentationEffectLogicalOperators)
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self.segmentation_editor.active_segment_id_changed.connect(self._update_available_segments)
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def set_ui(self, ui: SegmentEditorUI):
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self.set_effect_ui(ui.get_effect_ui(SegmentationEffectLogicalOperators))
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def set_effect_ui(self, logical_operators_ui: LogicalOperatorsEffectUI):
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logical_operators_ui.apply_clicked.connect(self._on_apply_clicked)
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def _update_available_segments(self, *_args, **_kwargs):
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self.data.available_segments = [
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SegmentState(
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name=segment_properties.name,
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color=segment_properties.color_hex,
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segment_id=segment_id,
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is_visible=self.segmentation_editor.get_segment_visibility(segment_id),
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)
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for segment_id, segment_properties in self.segmentation_editor.get_all_segment_properties().items()
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]
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if self.data.reference_segment_id not in [segment.segment_id for segment in self.data.available_segments]:
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self.data.reference_segment_id = None
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def _on_apply_clicked(self):
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if not self.is_active():
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return
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match self.data.logical_operator:
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case LogicalOperatorsSegmentationMode.ADD:
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self.effect.add(self.data.reference_segment_id)
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case LogicalOperatorsSegmentationMode.COPY:
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self.effect.copy(self.data.reference_segment_id)
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case LogicalOperatorsSegmentationMode.SUBTRACT:
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self.effect.subtract(self.data.reference_segment_id)
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case LogicalOperatorsSegmentationMode.INTERSECT:
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self.effect.intersect(self.data.reference_segment_id)
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case LogicalOperatorsSegmentationMode.INVERT:
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self.effect.invert()
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case LogicalOperatorsSegmentationMode.CLEAR:
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self.effect.clear()
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case LogicalOperatorsSegmentationMode.FILL:
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self.effect.fill()

‎examples/viewer_lib/logic/segmentation/segment_editor_logic.py‎

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)
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from .base_segmentation_logic import BaseEffectLogic, BaseSegmentationLogic
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from .islands_effect_logic import IslandsEffectLogic
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from .logical_operators_effect_logic import LogicalOperatorsEffectLogic
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from .paint_erase_effect_logic import EraseEffectLogic, PaintEffectLogic
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from .scissors_effect_logic import ScissorsEffectLogic
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from .segment_edit_logic import SegmentEditLogic
@@ -30,6 +31,7 @@ def __init__(self, server: Server, slicer_app: SlicerApp):
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effect_logic = [
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IslandsEffectLogic,
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LogicalOperatorsEffectLogic,
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ThresholdEffectLogic,
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PaintEffectLogic,
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EraseEffectLogic,

‎examples/viewer_lib/ui/__init__.py‎

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@@ -10,6 +10,9 @@
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BrushParametersUI,
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IslandsEffectUI,
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IslandsState,
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LogicalOperatorsEffectUI,
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LogicalOperatorsSegmentationMode,
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LogicalOperatorsState,
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PaintEffectState,
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PaintEffectUI,
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ScissorsEffectState,
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"LayoutButtonState",
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"LoadVolumeState",
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"LoadVolumeUI",
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"LogicalOperatorsEffectUI",
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"LogicalOperatorsSegmentationMode",
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"LogicalOperatorsState",
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"MarkupsButton",
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"MedicalViewerUI",
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"MprInteractionButton",

‎examples/viewer_lib/ui/segmentation/__init__.py‎

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from .brush_parameters_ui import BrushParametersState, BrushParametersUI
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from .islands_effect_ui import IslandsEffectUI, IslandsState
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from .logical_operators_effect_ui import (
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LogicalOperatorsEffectUI,
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LogicalOperatorsSegmentationMode,
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LogicalOperatorsState,
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)
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from .paint_effect_ui import PaintEffectState, PaintEffectUI
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from .scissors_effect_ui import ScissorsEffectState, ScissorsEffectUI
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from .segment_display_ui import SegmentDisplayState, SegmentDisplayUI
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"BrushParametersUI",
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"IslandsEffectUI",
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"IslandsState",
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"LogicalOperatorsEffectUI",
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"LogicalOperatorsSegmentationMode",
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"LogicalOperatorsState",
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"PaintEffectState",
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"PaintEffectUI",
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"ScissorsEffectState",

‎examples/viewer_lib/ui/segmentation/logical_operators_effect_ui.py‎

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from dataclasses import dataclass, field
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from enum import Enum, auto
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from trame_server.utils.typed_state import TypedState
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from trame_vuetify.widgets.vuetify3 import VBtn, VSelect
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from undo_stack import Signal
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from ..flex_container import FlexContainer
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from .segment_state import SegmentState
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class LogicalOperatorsSegmentationMode(Enum):
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COPY = auto()
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ADD = auto()
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SUBTRACT = auto()
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INTERSECT = auto()
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INVERT = auto()
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CLEAR = auto()
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FILL = auto()
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@dataclass
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class LogicalOperatorsState:
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logical_operator: LogicalOperatorsSegmentationMode = LogicalOperatorsSegmentationMode.COPY
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reference_segment_id: str | None = None
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available_segments: list[SegmentState] = field(default_factory=list)
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class LogicalOperatorsEffectUI(FlexContainer):
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apply_clicked = Signal()
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def __init__(self, **kwargs):
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super().__init__(**kwargs)
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self._typed_state = TypedState(self.state, LogicalOperatorsState)
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modes_with_reference = [
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LogicalOperatorsSegmentationMode.COPY,
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LogicalOperatorsSegmentationMode.ADD,
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LogicalOperatorsSegmentationMode.SUBTRACT,
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LogicalOperatorsSegmentationMode.INTERSECT,
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]
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with self:
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VSelect(
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v_model=self._typed_state.name.logical_operator,
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label="Logical Operator",
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density="comfortable",
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hide_details=True,
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item_title="title",
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item_value="value",
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items=(
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[
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{"title": mode.name.capitalize(), "value": self._typed_state.encode(mode)}
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for mode in LogicalOperatorsSegmentationMode
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],
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),
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)
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is_mode_with_reference_state_str = f"{[self._typed_state.encode(mode) for mode in modes_with_reference]}.includes({self._typed_state.name.logical_operator})"
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VSelect(
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v_model=self._typed_state.name.reference_segment_id,
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label="Reference segment",
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density="comfortable",
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hide_details=True,
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item_title="title",
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item_value="value",
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items=(
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f"{self._typed_state.name.available_segments}.map((segment) => ({{ 'title': segment.name, 'value': segment.segment_id }}))",
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),
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v_if=(is_mode_with_reference_state_str,),
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)
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available_segment_ids = f"{self._typed_state.name.available_segments}.map((segment) => segment.segment_id)"
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VBtn(
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"Apply",
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click=self.apply_clicked,
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disabled=(
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f"{is_mode_with_reference_state_str} && ({self._typed_state.name.reference_segment_id} === null || !{available_segment_ids}.includes({self._typed_state.name.reference_segment_id}))",
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),
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)

‎examples/viewer_lib/ui/segmentation/segment_editor_ui.py‎

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SegmentationEffectDraw,
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SegmentationEffectErase,
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SegmentationEffectIslands,
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SegmentationEffectLogicalOperators,
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SegmentationEffectNoTool,
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SegmentationEffectPaint,
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SegmentationEffectScissors,
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from ..flex_container import FlexContainer
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from ..viewer_layout import ViewerLayoutState
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from .islands_effect_ui import IslandsEffectUI
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from .logical_operators_effect_ui import LogicalOperatorsEffectUI
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from .paint_effect_ui import PaintEffectUI
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from .scissors_effect_ui import ScissorsEffectUI
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from .segment_display_ui import SegmentDisplayState, SegmentDisplayUI
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with VCardText(classes="align-center", style="flex: 1; min-height: 0; overflow-y: auto;"):
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self._register_effect_ui(SegmentationEffectPaint, PaintEffectUI)
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self._register_effect_ui(SegmentationEffectErase, PaintEffectUI)
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self._register_effect_ui(SegmentationEffectLogicalOperators, LogicalOperatorsEffectUI)
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self._register_effect_ui(SegmentationEffectThreshold, ThresholdEffectUI)
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self._register_effect_ui(SegmentationEffectIslands, IslandsEffectUI)
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self._register_effect_ui(SegmentationEffectScissors, ScissorsEffectUI)
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**kwargs,
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)
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if all:
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self._create_effect_button(
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"Logical Operators",
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"mdi-vector-intersection",
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SegmentationEffectLogicalOperators,
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)
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self._create_effect_button(
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"Threshold",
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"mdi-auto-fix",

‎tests/conftest.py‎

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return a_data_folder.joinpath("segmentation.nii.gz")
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@pytest.fixture
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def a_segmentation_overlap_file_path(a_data_folder) -> Path:
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return a_data_folder.joinpath("segmentation_overlap.nrrd")
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@pytest.fixture
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def a_model_node(a_slicer_app, a_model_file_path):
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return load_model_node(

‎tests/data‎

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