chore: refactor and simplify menu bar creation, add workaround for ma…

…cOS numpy problem (#1124)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **Refactor**
- Improved code readability and maintainability by moving menu bar setup
logic to a dedicated method in the main window classes of the `ROI
Analysis` and `ROI Mask` modules.

- **Bug Fixes**
- Added conditional logic to manage thread usage based on the numpy
version and macOS arm64 architecture in the napari image view.

- **Chores**
- Simplified dependencies in `pyproject.toml` by combining them into a
single string `"PartSeg[accelerate,pyqt5]"`.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

package/PartSeg/_roi_analysis/main_window.py

@@ -577,35 +577,11 @@ def __init__(  # noqa: PLR0915
         elif initial_image is not False:
             self.settings.image = initial_image
 
+        self._setup_menu_bar()
+
         icon = QIcon(os.path.join(PartSegData.icons_dir, "icon.png"))
         self.setWindowIcon(icon)
 
-        menu_bar = self.menuBar()
-        file_menu = menu_bar.addMenu("File")
-        file_menu.addAction("&Open").triggered.connect(self.main_menu.load_data)
-        file_menu.addMenu(self.recent_file_menu)
-        file_menu.addAction("&Save").triggered.connect(self.main_menu.save_file)
-        file_menu.addAction("Batch processing").triggered.connect(self.main_menu.batch_window)
-        view_menu = menu_bar.addMenu("View")
-        view_menu.addAction("Settings and Measurement").triggered.connect(self.main_menu.advanced_window_show)
-        view_menu.addAction("Additional output").triggered.connect(self.additional_layers_show)
-        view_menu.addAction("Additional output with data").triggered.connect(lambda: self.additional_layers_show(True))
-        view_menu.addAction("Napari viewer").triggered.connect(self.napari_viewer_show)
-        view_menu.addAction("Toggle Multiple Files").triggered.connect(self.toggle_multiple_files)
-        view_menu.addAction("Toggle left panel").triggered.connect(self.toggle_left_panel)
-        view_menu.addAction("Toggle console").triggered.connect(self._toggle_console)
-        view_menu.addAction("Toggle scale bar").triggered.connect(self._toggle_scale_bar)
-        action = view_menu.addAction("Screenshot right panel")
-        action.triggered.connect(self.screenshot(self.result_image))
-        action.setShortcut(QKeySequence.Print)
-        view_menu.addAction("Screenshot left panel").triggered.connect(self.screenshot(self.raw_image))
-        image_menu = menu_bar.addMenu("Image operations")
-        image_menu.addAction("Image adjustment").triggered.connect(self.image_adjust_exec)
-        image_menu.addAction("Mask manager").triggered.connect(self.main_menu.mask_manager)
-        help_menu = menu_bar.addMenu("Help")
-        help_menu.addAction("State directory").triggered.connect(self.show_settings_directory)
-        help_menu.addAction("About").triggered.connect(self.show_about_dialog)
-
         layout = QGridLayout()
         layout.setSpacing(0)
         info_layout = QHBoxLayout()
@@ -632,6 +608,33 @@ def __init__(  # noqa: PLR0915
             geometry = self.settings.get_from_profile("main_window_geometry")
             self.restoreGeometry(QByteArray.fromHex(bytes(geometry, "ascii")))
 
+    def _setup_menu_bar(self):
+        menu_bar = self.menuBar()
+        file_menu = menu_bar.addMenu("File")
+        file_menu.addAction("&Open").triggered.connect(self.main_menu.load_data)
+        file_menu.addMenu(self.recent_file_menu)
+        file_menu.addAction("&Save").triggered.connect(self.main_menu.save_file)
+        file_menu.addAction("Batch processing").triggered.connect(self.main_menu.batch_window)
+        view_menu = menu_bar.addMenu("View")
+        view_menu.addAction("Settings and Measurement").triggered.connect(self.main_menu.advanced_window_show)
+        view_menu.addAction("Additional output").triggered.connect(self.additional_layers_show)
+        view_menu.addAction("Additional output with data").triggered.connect(lambda: self.additional_layers_show(True))
+        view_menu.addAction("Napari viewer").triggered.connect(self.napari_viewer_show)
+        view_menu.addAction("Toggle Multiple Files").triggered.connect(self.toggle_multiple_files)
+        view_menu.addAction("Toggle left panel").triggered.connect(self.toggle_left_panel)
+        view_menu.addAction("Toggle console").triggered.connect(self._toggle_console)
+        view_menu.addAction("Toggle scale bar").triggered.connect(self._toggle_scale_bar)
+        action = view_menu.addAction("Screenshot right panel")
+        action.triggered.connect(self.screenshot(self.result_image))
+        action.setShortcut(QKeySequence.Print)
+        view_menu.addAction("Screenshot left panel").triggered.connect(self.screenshot(self.raw_image))
+        image_menu = menu_bar.addMenu("Image operations")
+        image_menu.addAction("Image adjustment").triggered.connect(self.image_adjust_exec)
+        image_menu.addAction("Mask manager").triggered.connect(self.main_menu.mask_manager)
+        help_menu = menu_bar.addMenu("Help")
+        help_menu.addAction("State directory").triggered.connect(self.show_settings_directory)
+        help_menu.addAction("About").triggered.connect(self.show_about_dialog)
+
     def _toggle_scale_bar(self):
         self.raw_image.toggle_scale_bar()
         self.result_image.toggle_scale_bar()

package/PartSeg/_roi_mask/main_window.py

@@ -891,7 +891,7 @@ def get_setting_class(cls) -> Type[StackSettings]:
 
     initial_image_path = PartSegData.segmentation_mask_default_image
 
-    def __init__(  # noqa: PLR0915
+    def __init__(
         self, config_folder=CONFIG_FOLDER, title="PartSeg", settings=None, signal_fun=None, initial_image=None
     ):
         super().__init__(config_folder, title, settings, io_functions.load_dict, signal_fun)
@@ -916,28 +916,7 @@ def __init__(  # noqa: PLR0915
         icon = QIcon(os.path.join(PartSegData.icons_dir, "icon_stack.png"))
         self.setWindowIcon(icon)
 
-        menu_bar = self.menuBar()
-        file_menu = menu_bar.addMenu("File")
-        file_menu.addAction("&Open").triggered.connect(self.main_menu.load_image)
-        file_menu.addMenu(self.recent_file_menu)
-        file_menu.addAction("&Save segmentation").triggered.connect(self.main_menu.save_segmentation)
-        file_menu.addAction("&Save components").triggered.connect(self.main_menu.save_result)
-        view_menu = menu_bar.addMenu("View")
-        view_menu.addAction("Settings and Measurement").triggered.connect(self.main_menu.show_advanced_window)
-        view_menu.addAction("Additional output").triggered.connect(self.additional_layers_show)
-        view_menu.addAction("Additional output with data").triggered.connect(lambda: self.additional_layers_show(True))
-        view_menu.addAction("Napari viewer").triggered.connect(self.napari_viewer_show)
-        view_menu.addAction("Toggle Multiple Files").triggered.connect(self.toggle_multiple_files)
-        view_menu.addAction("Toggle console").triggered.connect(self._toggle_console)
-        view_menu.addAction("Toggle scale bar").triggered.connect(self._toggle_scale_bar)
-        action = view_menu.addAction("Screenshot")
-        action.triggered.connect(self.screenshot(self.image_view))
-        action.setShortcut(QKeySequence.StandardKey.Print)
-        image_menu = menu_bar.addMenu("Image operations")
-        image_menu.addAction("Image adjustment").triggered.connect(self.image_adjust_exec)
-        help_menu = menu_bar.addMenu("Help")
-        help_menu.addAction("State directory").triggered.connect(self.show_settings_directory)
-        help_menu.addAction("About").triggered.connect(self.show_about_dialog)
+        self._setup_menu_bar()
 
         layout = QVBoxLayout()
         layout.addWidget(self.main_menu)
@@ -968,6 +947,30 @@ def __init__(  # noqa: PLR0915
             geometry = self.settings.get_from_profile("main_window_geometry")
             self.restoreGeometry(QByteArray.fromHex(bytes(geometry, "ascii")))
 
+    def _setup_menu_bar(self):
+        menu_bar = self.menuBar()
+        file_menu = menu_bar.addMenu("File")
+        file_menu.addAction("&Open").triggered.connect(self.main_menu.load_image)
+        file_menu.addMenu(self.recent_file_menu)
+        file_menu.addAction("&Save segmentation").triggered.connect(self.main_menu.save_segmentation)
+        file_menu.addAction("&Save components").triggered.connect(self.main_menu.save_result)
+        view_menu = menu_bar.addMenu("View")
+        view_menu.addAction("Settings and Measurement").triggered.connect(self.main_menu.show_advanced_window)
+        view_menu.addAction("Additional output").triggered.connect(self.additional_layers_show)
+        view_menu.addAction("Additional output with data").triggered.connect(lambda: self.additional_layers_show(True))
+        view_menu.addAction("Napari viewer").triggered.connect(self.napari_viewer_show)
+        view_menu.addAction("Toggle Multiple Files").triggered.connect(self.toggle_multiple_files)
+        view_menu.addAction("Toggle console").triggered.connect(self._toggle_console)
+        view_menu.addAction("Toggle scale bar").triggered.connect(self._toggle_scale_bar)
+        action = view_menu.addAction("Screenshot")
+        action.triggered.connect(self.screenshot(self.image_view))
+        action.setShortcut(QKeySequence.StandardKey.Print)
+        image_menu = menu_bar.addMenu("Image operations")
+        image_menu.addAction("Image adjustment").triggered.connect(self.image_adjust_exec)
+        help_menu = menu_bar.addMenu("Help")
+        help_menu.addAction("State directory").triggered.connect(self.show_settings_directory)
+        help_menu.addAction("About").triggered.connect(self.show_about_dialog)
+
     def _toggle_scale_bar(self):
         self.image_view.toggle_scale_bar()
         super()._toggle_scale_bar()

package/PartSeg/common_gui/napari_image_view.py

@@ -1,5 +1,6 @@
 import itertools
 import logging
+import platform
 from contextlib import suppress
 from dataclasses import dataclass, field
 from enum import Enum
@@ -44,6 +45,20 @@
 _napari_ge_4_17 = parse_version(napari.__version__) >= parse_version("0.4.17a1")
 _napari_ge_5 = parse_version(napari.__version__) >= parse_version("0.5.0a1")
 
+# if run with numpy<2 on macOS arm64 architecture compiled from pypi wheels
+# then it will crash with bus error if numpy is used in different thread
+if (
+    parse_version(np.__version__) < parse_version("2")
+    and platform.system() == "Darwin"
+    and platform.machine() == "arm64"
+):  # pragma: no cover
+    try:
+        USE_THREADS = "cibw-run" not in np.show_config("dicts")["Python Information"]["path"]
+    except (KeyError, TypeError):
+        USE_THREADS = True
+else:
+    USE_THREADS = True
+
 
 def get_highlight_colormap():
     cmap_dict = {0: (0, 0, 0, 0), 1: "white", None: (0, 0, 0, 0)}
@@ -717,12 +732,19 @@ def add_image(self, image: Optional[Image], replace=False):
 
         return image
 
-    def _prepare_layers(self, image, parameters, replace):
-        worker = prepare_layers(image, parameters, replace)
-        worker.returned.connect(self._add_image)
-        worker.finished.connect(self._remove_worker)
-        self.worker_list.append(worker)
-        worker.start()
+    if USE_THREADS:  # pragma: no cover
+
+        def _prepare_layers(self, image, parameters, replace):
+            worker = prepare_layers(image, parameters, replace)
+            worker.returned.connect(self._add_image)
+            worker.finished.connect(self._remove_worker)
+            self.worker_list.append(worker)
+            worker.start()
+
+    else:  # pragma: no cover
+
+        def _prepare_layers(self, image, parameters, replace):
+            self._add_image(_prepare_layers(image, parameters, replace))
 
     def images_bounds(self) -> Tuple[List[int], List[int]]:
         ranges = []

pyproject.toml

@@ -102,8 +102,7 @@ accelerate = [
     "PyOpenGL-accelerate>=3.1.5 ; platform_machine != 'arm64'",
 ]
 all = [
-    "PyOpenGL-accelerate>=3.1.5",
-    "PyQt5!=5.15.0,>=5.12.3",
+    "PartSeg[accelerate,pyqt5]"
 ]
 docs = [
     "autodoc-pydantic",