mypy, lint, refactor

src/allencell_ml_segmenter/_tests/fakes/fake_viewer.py

@@ -106,7 +106,20 @@ def _on_layers_change(self):
             fn(FakeNapariEvent())
 
     def get_seg_layers(self, layer_list: list[Layer]) -> list[Layer]:
-        return [layer for layer in self._image_layers.values() if layer.name.startswith("[seg]")]
-
-    def insert_segmentation(self, layer_name: str, img: np.ndarray, seg_layers: bool = False) -> None:
+        return [
+            layer
+            for layer in self._image_layers.values()
+            if layer.name.startswith("[seg]")
+        ]
+
+    def insert_segmentation(
+        self, layer_name: str, img: np.ndarray, seg_layers: bool = False
+    ) -> None:
         self.segmentation_inserted[f"[threshold] {layer_name}"] = img
+
+    def get_layers_nonthreshold(self) -> list[Layer]:
+        return [
+            layer
+            for layer in self._image_layers.values()
+            if not layer.name.startswith("[threshold]")
+        ]

src/allencell_ml_segmenter/_tests/thresholding/test_thresholding_model.py

@@ -2,7 +2,9 @@
 
 from allencell_ml_segmenter._tests.fakes.fake_subscriber import FakeSubscriber
 from allencell_ml_segmenter.core.event import Event
-from allencell_ml_segmenter.thresholding.thresholding_model import ThresholdingModel
+from allencell_ml_segmenter.thresholding.thresholding_model import (
+    ThresholdingModel,
+)
 
 
 @pytest.fixture
@@ -16,7 +18,7 @@ def test_set_thresholding_value_dispatches_event(thresholding_model):
     thresholding_model.subscribe(
         Event.ACTION_THRESHOLDING_VALUE_CHANGED,
         fake_subscriber,
-        fake_subscriber.handle
+        fake_subscriber.handle,
     )
 
     thresholding_model.set_thresholding_value(2)
@@ -29,19 +31,22 @@ def test_set_autothresholding_enabled_dispatches_event(thresholding_model):
     thresholding_model.subscribe(
         Event.ACTION_THRESHOLDING_AUTOTHRESHOLDING_SELECTED,
         fake_subscriber,
-        fake_subscriber.handle
+        fake_subscriber.handle,
     )
 
     thresholding_model.set_autothresholding_enabled(True)
 
-    assert fake_subscriber.was_handled(Event.ACTION_THRESHOLDING_AUTOTHRESHOLDING_SELECTED)
+    assert fake_subscriber.was_handled(
+        Event.ACTION_THRESHOLDING_AUTOTHRESHOLDING_SELECTED
+    )
+
 
 def test_dispatch_save_thresholded_images(thresholding_model):
     fake_subscriber: FakeSubscriber = FakeSubscriber()
     thresholding_model.subscribe(
         Event.ACTION_SAVE_THRESHOLDING_IMAGES,
         fake_subscriber,
-        fake_subscriber.handle
+        fake_subscriber.handle,
     )
 
     thresholding_model.dispatch_save_thresholded_images()

src/allencell_ml_segmenter/_tests/thresholding/test_thresholding_service.py

@@ -2,10 +2,16 @@
 import numpy as np
 
 from allencell_ml_segmenter.core.file_input_model import FileInputModel
-from allencell_ml_segmenter._tests.fakes.fake_experiments_model import FakeExperimentsModel
+from allencell_ml_segmenter._tests.fakes.fake_experiments_model import (
+    FakeExperimentsModel,
+)
 from allencell_ml_segmenter.main.main_model import MainModel
-from allencell_ml_segmenter.thresholding.thresholding_model import ThresholdingModel
-from allencell_ml_segmenter.thresholding.thresholding_service import ThresholdingService
+from allencell_ml_segmenter.thresholding.thresholding_model import (
+    ThresholdingModel,
+)
+from allencell_ml_segmenter.thresholding.thresholding_service import (
+    ThresholdingService,
+)
 from allencell_ml_segmenter.core.task_executor import SynchroTaskExecutor
 from allencell_ml_segmenter._tests.fakes.fake_viewer import FakeViewer
 
@@ -15,12 +21,18 @@ def test_image():
     """Create a small test image for thresholding."""
     return np.array([[10, 20, 30], [40, 50, 60], [70, 80, 90]])
 
+
 def test_on_threshold_changed_non_prediction(test_image):
     thresholding_model: ThresholdingModel = ThresholdingModel()
     viewer: FakeViewer = FakeViewer()
-    thresholding_service: ThresholdingService = ThresholdingService(thresholding_model, FakeExperimentsModel(),
-                                                                    FileInputModel(), MainModel(), viewer,
-                                                                    task_executor=SynchroTaskExecutor.global_instance())
+    thresholding_service: ThresholdingService = ThresholdingService(
+        thresholding_model,
+        FakeExperimentsModel(),
+        FileInputModel(),
+        MainModel(),
+        viewer,
+        task_executor=SynchroTaskExecutor.global_instance(),
+    )
     viewer.add_image(test_image, name="test_layer")
 
     # ACT set a threshold to trigger
@@ -37,14 +49,20 @@ def test_on_threshold_changed_non_prediction(test_image):
     seg_data = viewer.segmentation_inserted["[threshold] test_layer"]
     assert np.array_equal(seg_data, (test_image > 100).astype(int))
 
+
 def test_on_threshold_changed_non_prediction(test_image):
     thresholding_model: ThresholdingModel = ThresholdingModel()
     viewer: FakeViewer = FakeViewer()
     main_model: MainModel = MainModel()
     main_model.set_predictions_in_viewer(True)
-    thresholding_service: ThresholdingService = ThresholdingService(thresholding_model, FakeExperimentsModel(),
-                                                                    FileInputModel(), main_model, viewer,
-                                                                    task_executor=SynchroTaskExecutor.global_instance())
+    thresholding_service: ThresholdingService = ThresholdingService(
+        thresholding_model,
+        FakeExperimentsModel(),
+        FileInputModel(),
+        main_model,
+        viewer,
+        task_executor=SynchroTaskExecutor.global_instance(),
+    )
     viewer.add_image(test_image, name="[raw] test_layer 1")
     viewer.add_image(test_image, name="[seg] test_layer 1")
     viewer.add_image(test_image, name="[raw] test_layer 2")