SQUASHME: fix PR

Author: Jo-Byr

examples/viewer_lib/ui/segmentation/islands_effect_ui.py

@@ -1,15 +1,15 @@
-import enum
 from dataclasses import dataclass
+from enum import Enum, auto
 
 from trame_server.utils.typed_state import TypedState
 from trame_vuetify.widgets.vuetify3 import VBtn, VContainer, VNumberInput, VSelect
 from undo_stack import Signal
 
 
-class IslandsSegmentationMode(enum.Enum):
-    KEEP_LARGEST_ISLAND = enum.auto()
-    REMOVE_SMALL_ISLANDS = enum.auto()
-    SPLIT_TO_SEGMENTS = enum.auto()
+class IslandsSegmentationMode(Enum):
+    KEEP_LARGEST_ISLAND = auto()
+    REMOVE_SMALL_ISLANDS = auto()
+    SPLIT_TO_SEGMENTS = auto()
 
 
 @dataclass

examples/viewer_lib/ui/segmentation/segment_editor_ui.py

@@ -107,7 +107,7 @@ def __init__(self, **kwargs):
                 self._create_effect_button("Erase", "mdi-eraser", SegmentationEffectErase)
                 self._create_effect_button("Scissors", "mdi-content-cut", SegmentationEffectScissors)
                 self._create_effect_button("Threshold", "mdi-auto-fix", SegmentationEffectThreshold)
-                self._create_effect_button("Islands", "mdi-chart-scatter-plot", SegmentationEffectIslands)
+                self._create_effect_button("Islands", "mdi-scatter-plot", SegmentationEffectIslands)
                 VDivider()
 
             with VRow():

tests/test_segmentation_islands_effect.py

@@ -4,7 +4,6 @@
 import pytest
 from undo_stack import UndoStack
 
-from trame_slicer.core import IOManager
 from trame_slicer.segmentation import SegmentationEffectIslands
 
 
@@ -15,23 +14,13 @@ def undo_stack(a_segmentation_editor):
     return undo_stack
 
 
-@pytest.fixture
-def an_io_manager(a_slicer_app):
-    return IOManager(
-        a_slicer_app.scene,
-        a_slicer_app.app_logic,
-        a_slicer_app.segmentation_editor,
-    )
-
-
 @pytest.fixture
 def a_segmentation_spheres_file_path(a_data_folder) -> Path:
     return a_data_folder.joinpath("segmentation_spheres.nii.gz")
 
 
 def test_paint_effect_adds_segmentation_to_selected_segment(
     a_slicer_app,
-    an_io_manager,
     a_segmentation_editor,
     a_volume_node,
     a_slice_view,
@@ -42,7 +31,7 @@ def test_paint_effect_adds_segmentation_to_selected_segment(
     a_slicer_app.display_manager.show_volume(a_volume_node, vr_preset="MR-Default")
 
     undo_stack.clear()
-    segmentation_node = an_io_manager.load_segmentation(a_segmentation_spheres_file_path)
+    segmentation_node = a_slicer_app.io_manager.load_segmentation(a_segmentation_spheres_file_path)
     a_segmentation_editor.set_active_segmentation(segmentation_node, a_volume_node)
     segment_id = a_segmentation_editor.get_nth_segment_id(0)
 

trame_slicer/segmentation/segmentation_effect_islands.py

@@ -7,14 +7,21 @@
 from vtkmodules.vtkCommonCore import vtkIntArray
 from vtkmodules.vtkCommonMath import vtkMatrix4x4
 from vtkmodules.vtkImagingCore import vtkImageCast, vtkImageThreshold
-from vtkmodules.vtkITK import vtkITKIslandMath
 
-from trame_slicer.segmentation import ModificationMode
+try:
+    from vtkmodules.vtkITK import vtkITKIslandMath
+except ImportError:
+    from vtkITK import vtkITKIslandMath
 
+from . import ModificationMode
 from .segmentation_effect import SegmentationEffect
 
 
 class SegmentationEffectIslands(SegmentationEffect):
+    def __init__(self) -> None:
+        super().__init__()
+        self.set_mode(ModificationMode.Set)
+
     def _create_pipeline(self, _view_node: vtkMRMLAbstractViewNode, _parameter: vtkMRMLNode) -> None:
         # Islands effect does not require a pipeline
         return None
@@ -26,8 +33,6 @@ def apply(
             return
 
         island_image = self.get_island_labelmap(segment_id, minimum_size)
-        modification_mode = self.modifier.modification_mode
-        self.modifier.modification_mode = ModificationMode.Set
 
         label_values = vtkIntArray()
         vtkSlicerSegmentationsModuleLogic.GetAllLabelValues(label_values, island_image)
@@ -71,7 +76,6 @@ def apply(
                     self.modifier.segmentation.segmentation_node,
                     self.modifier.segmentation.get_segment(segment_id).GetName(),
                 )
-            self.modifier.modification_mode = modification_mode
             self.modifier.segmentation.segmentation_modified.emit()
 
     def get_island_labelmap(self, segment_id: str, minimum_size: int = 0) -> vtkOrientedImageData: