feat: Use QScrollArea for components selection (#1328)

## Summary by Sourcery

Make component selection scrollable and update ROI handling hooks to
keep chosen components in sync with ROI changes.

New Features:
- Allow scrolling through the list of selectable components using a
scrollable container.

Enhancements:
- Ensure selected components are automatically brought into view when
toggled or changed.
- Separate initialization of component checkboxes from updating their
checked state via a dedicated setter.
- Adjust the main ROI mask layout to use a splitter between algorithm
selection and component selection panels.
- Introduce a post-ROI-set hook for subclasses to perform additional
updates after ROI changes.
- Tighten type annotations for napari layer addition utility.

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

* **New Features**
* Component list now scrolls vertically and auto-scrolls toggled items
into view
  * Component and algorithm selectors placed in a resizable split layout
* Settings run a post-ROI sync so component choices stay in sync after
ROI changes

* **Refactor**
* Component-selection API reorganized to support typed calls and a
lighter update method that updates checks without full rebuild

* **Bug Fixes**
* Batch select/unselect updates checkboxes while emitting a single
consolidated change signal
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Author: Czaki

package/PartSeg/_roi_mask/main_window.py

@@ -1,6 +1,8 @@
 import os
+from collections.abc import Sequence
 from contextlib import suppress
 from functools import partial
+from typing import Union
 
 import numpy as np
 from qtpy.QtCore import QByteArray, Qt, Signal, Slot
@@ -16,8 +18,10 @@
     QMessageBox,
     QProgressBar,
     QPushButton,
+    QScrollArea,
     QSizePolicy,
     QSpinBox,
+    QSplitter,
     QTabWidget,
     QTextEdit,
     QVBoxLayout,
@@ -393,7 +397,7 @@ def leaveEvent(self, _event):
         self.mouse_leave.emit(self.number)
 
 
-class ChosenComponents(QWidget):
+class ChosenComponents(QScrollArea):
     """
     :type check_box: dict[int, ComponentCheckBox]
     """
@@ -404,6 +408,7 @@ class ChosenComponents(QWidget):
 
     def __init__(self):
         super().__init__()
+        self.setWidget(QWidget(self))
         self.check_box = {}
         self.check_all_btn = QPushButton("Select all")
         self.check_all_btn.clicked.connect(self.check_all)
@@ -416,19 +421,33 @@ def __init__(self):
         self.check_layout = FlowLayout()
         main_layout.addLayout(btn_layout)
         main_layout.addLayout(self.check_layout)
-        self.setLayout(main_layout)
+        self.widget().setLayout(main_layout)
+        self.setWidgetResizable(True)
+        self.setHorizontalScrollBarPolicy(Qt.ScrollBarPolicy.ScrollBarAlwaysOff)
+        self.setVerticalScrollBarPolicy(Qt.ScrollBarPolicy.ScrollBarAsNeeded)
 
     def other_component_choose(self, num):
         check = self.check_box[num]
         check.setChecked(not check.isChecked())
+        self.ensureWidgetVisible(check)
 
     def check_all(self):
-        for el in self.check_box.values():
-            el.setChecked(True)
+        prev = self.blockSignals(True)
+        try:
+            for el in self.check_box.values():
+                el.setChecked(True)
+        finally:
+            self.blockSignals(prev)
+        self.check_change_signal.emit()
 
     def un_check_all(self):
-        for el in self.check_box.values():
-            el.setChecked(False)
+        prev = self.blockSignals(True)
+        try:
+            for el in self.check_box.values():
+                el.setChecked(False)
+        finally:
+            self.blockSignals(prev)
+        self.check_change_signal.emit()
 
     def remove_components(self):
         self.check_layout.clear()
@@ -439,31 +458,46 @@ def remove_components(self):
             el.mouse_enter.disconnect()
         self.check_box.clear()
 
-    def new_choose(self, num, chosen_components):
-        self.set_chose(range(1, num + 1), chosen_components)
+    def new_choose(self, num: int, chosen_components: Sequence[int]) -> None:
+        self.set_components(range(1, num + 1), chosen_components)
 
-    def set_chose(self, components_index, chosen_components):
+    def set_components(self, components_index, chosen_components: Union[Sequence[int], None] = None):
+        if chosen_components is None:
+            chosen_components = []
         chosen_components = set(chosen_components)
-        self.blockSignals(True)
-        self.remove_components()
-        for el in components_index:
-            check = ComponentCheckBox(el)
-            if el in chosen_components:
-                check.setChecked(True)
-            check.stateChanged.connect(self.check_change)
-            check.mouse_enter.connect(self.mouse_enter.emit)
-            check.mouse_leave.connect(self.mouse_leave.emit)
-            self.check_box[el] = check
-            self.check_layout.addWidget(check)
-        self.blockSignals(False)
+        prev = self.blockSignals(True)
+        try:
+            self.remove_components()
+            for el in components_index:
+                check = ComponentCheckBox(el)
+                if el in chosen_components:
+                    check.setChecked(True)
+                check.stateChanged.connect(self.check_change)
+                check.mouse_enter.connect(self.mouse_enter.emit)
+                check.mouse_leave.connect(self.mouse_leave.emit)
+                self.check_box[el] = check
+                self.check_layout.addWidget(check)
+        finally:
+            self.blockSignals(prev)
         self.update()
         self.check_change_signal.emit()
 
+    def set_chosen(self, chosen_components: Sequence[int]):
+        prev = self.blockSignals(True)
+        chosen_components = set(chosen_components)
+        try:
+            for num, check in self.check_box.items():
+                check.setChecked(num in chosen_components)
+        finally:
+            self.blockSignals(prev)
+        self.check_change_signal.emit()
+
     def check_change(self):
         self.check_change_signal.emit()
 
     def change_state(self, num, val):
         self.check_box[num].setChecked(val)
+        self.ensureWidgetVisible(self.check_box[num])
 
     def get_state(self, num: int) -> bool:
         # TODO Check what situation create report of id ID: af9b57f074264169b4353aa1e61d8bc2
@@ -527,6 +561,7 @@ def __init__(self, settings: StackSettings, image_view: StackImageView):  # noqa
         self.choose_components.check_change_signal.connect(image_view.refresh_selected)
         self.choose_components.mouse_leave.connect(image_view.component_unmark)
         self.choose_components.mouse_enter.connect(image_view.component_mark)
+
         self.chosen_list = []
         self.progress_bar2 = QProgressBar()
         self.progress_bar2.setHidden(True)
@@ -566,8 +601,10 @@ def __init__(self, settings: StackSettings, image_view: StackImageView):  # noqa
         main_layout.addWidget(self.progress_bar2)
         main_layout.addWidget(self.progress_bar)
         main_layout.addWidget(self.progress_info_lab)
-        main_layout.addWidget(self.algorithm_choose_widget, 1)
-        main_layout.addWidget(self.choose_components)
+        split = QSplitter(Qt.Orientation.Vertical)
+        split.addWidget(self.algorithm_choose_widget)
+        split.addWidget(self.choose_components)
+        main_layout.addWidget(split, 1)
         down_layout = QHBoxLayout()
         down_layout.addWidget(self.keep_chosen_components_chk)
         down_layout.addWidget(self.show_parameters)
@@ -659,7 +696,7 @@ def segmentation(self, val):
 
     def _image_changed(self):
         self.settings.roi = None
-        self.choose_components.set_chose([], [])
+        self.choose_components.set_components([], [])
 
     def _execute_in_background_init(self):
         if self.batch_process.isRunning():

package/PartSeg/_roi_mask/stack_settings.py

@@ -170,17 +170,15 @@ def set_project_info(self, data: typing.Union[MaskProjectTuple, PointsInfo]):
                 data.selected_components,
                 self.keep_chosen_components,
             )
-            self.chosen_components_widget.set_chose(
-                sorted(state2.roi_extraction_parameters.keys()), state2.selected_components
-            )
             self.roi = state2.roi_info
+            self.chosen_components_widget.set_chosen(state2.selected_components)
+
             self.components_parameters_dict = state2.roi_extraction_parameters
         else:
             self.set_history(data.history)
-            self.chosen_components_widget.set_chose(
-                sorted(data.roi_extraction_parameters.keys()), data.selected_components
-            )
             self.roi = data.roi_info
+            self.chosen_components_widget.set_chosen(data.selected_components)
+
             self.components_parameters_dict = data.roi_extraction_parameters
 
     @staticmethod
@@ -304,18 +302,22 @@ def _set_roi_info(
             raise ValueError("ROI do not fit to image") from e
         if save_chosen:
             state2 = self.transform_state(state, new_roi_info, segmentation_parameters, list_of_components, save_chosen)
-            self.chosen_components_widget.set_chose(
-                sorted(state2.roi_extraction_parameters.keys()), state2.selected_components
-            )
             self.roi = state2.roi_info
+            self.chosen_components_widget.set_chosen(state2.selected_components)
             self.components_parameters_dict = state2.roi_extraction_parameters
         else:
-            selected_parameters = {i: segmentation_parameters[i] for i in new_roi_info.bound_info}
-
-            self.chosen_components_widget.set_chose(sorted(selected_parameters.keys()), list_of_components)
             self.roi = new_roi_info
+            self.chosen_components_widget.set_chosen(list_of_components)
             self.components_parameters_dict = segmentation_parameters
 
+    def post_roi_set(self):
+        if self.chosen_components_widget is not None:
+            prev = self.chosen_components_widget.blockSignals(True)
+            try:
+                self.chosen_components_widget.set_components(self.roi_info.bound_info.keys(), [])
+            finally:
+                self.chosen_components_widget.blockSignals(prev)
+
 
 def get_mask(
     segmentation: typing.Optional[np.ndarray], mask: typing.Optional[np.ndarray], selected: list[int]

package/PartSeg/common_backend/base_settings.py

@@ -126,11 +126,6 @@ def segmentation(self) -> np.ndarray:  # pragma: no cover
         warnings.warn("segmentation parameter is renamed to roi", DeprecationWarning, stacklevel=2)
         return self.roi
 
-    @property
-    def roi(self) -> np.ndarray:
-        """current roi"""
-        return self._roi_info.roi
-
     @property
     def segmentation_info(self) -> ROIInfo:  # pragma: no cover
         warnings.warn("segmentation info parameter is renamed to roi", DeprecationWarning, stacklevel=2)
@@ -140,11 +135,17 @@ def segmentation_info(self) -> ROIInfo:  # pragma: no cover
     def roi_info(self) -> ROIInfo:
         return self._roi_info
 
+    @property
+    def roi(self) -> np.ndarray:
+        """current roi"""
+        return self._roi_info.roi
+
     @roi.setter
     def roi(self, val: Union[np.ndarray, ROIInfo]):
         if val is None:
             self._roi_info = ROIInfo(val)
             self._additional_layers = {}
+            self.post_roi_set()
             self.roi_clean.emit()
             return
         try:
@@ -155,8 +156,12 @@ def roi(self, val: Union[np.ndarray, ROIInfo]):
         except ValueError as e:
             raise ValueError(ROI_NOT_FIT) from e
         self._additional_layers = {}
+        self.post_roi_set()
         self.roi_changed.emit(self._roi_info)
 
+    def post_roi_set(self) -> None:
+        """called after roi is set, for subclasses to override"""
+
     @property
     def sizes(self):
         return self._roi_info.sizes
@@ -524,14 +529,9 @@ def set_segmentation_result(self, result: ROIExtractionResult):
         self.last_executed_algorithm = result.parameters.algorithm
         self.set_algorithm(f"algorithms.{result.parameters.algorithm}", result.parameters.values)
         # Fixme not use EventedDict here
-        try:
-            roi_info = result.roi_info.fit_to_image(self.image)
-        except ValueError as e:  # pragma: no cover
-            raise ValueError(ROI_NOT_FIT) from e
+        self.roi = result.roi_info
         if result.points is not None:
             self.points = result.points
-        self._roi_info = roi_info
-        self.roi_changed.emit(self._roi_info)
 
     def _load_files_call(self, files_list: list[str]):
         self.request_load_files.emit(files_list)

package/PartSeg/common_gui/napari_image_view.py

@@ -584,7 +584,7 @@ def _remove_worker(self, sender=None):
         else:
             logging.debug("[_remove_worker] %s", sender)
 
-    def _add_layer_util(self, index, layer, filters):
+    def _add_layer_util(self, index: int, layer: _NapariImage, filters: list[tuple[NoiseFilterType, float]]) -> None:
         if layer not in self.viewer.layers:
             self.viewer.add_layer(layer)