Allow selecy to which units the layers should be loaded

package/PartSeg/napari.yaml

@@ -77,6 +77,9 @@ contributions:
   - id: PartSeg.Metadata
     title: View Layer Metadata
     python_name: PartSeg.plugins.napari_widgets:LayerMetadata
+  - id: PartSeg.Settings
+    title: PartSeg Settings
+    python_name: PartSeg.plugins.napari_widgets:SettingsEditor
   readers:
   - command: PartSeg.load_roi_project
     filename_patterns:
@@ -162,3 +165,5 @@ contributions:
     display_name: Watershed
   - command: PartSeg.Metadata
     display_name: Layer Metadata
+  - command: PartSeg.Settings
+    display_name: Settings Editor

package/PartSeg/plugins/napari_io/loader.py

@@ -4,6 +4,8 @@
 import numpy as np
 from packaging.version import parse as parse_version
 
+from PartSeg.plugins.napari_widgets._settings import get_settings
+from PartSegCore import UNIT_SCALE
 from PartSegCore.analysis import ProjectTuple
 from PartSegCore.io_utils import LoadBase, WrongFileTypeException
 from PartSegCore.mask.io_functions import MaskProjectTuple
@@ -84,7 +86,8 @@ def _image_to_layers(project_info, scale, translate):
 def project_to_layers(project_info: typing.Union[ProjectTuple, MaskProjectTuple]):
     res_layers = []
     if project_info.image is not None and not isinstance(project_info.image, str):
-        scale = project_info.image.normalized_scaling()
+        settings = get_settings()
+        scale = project_info.image.normalized_scaling(UNIT_SCALE[settings.io_units.value])
         translate = project_info.image.shift
         translate = (0,) * (len(project_info.image.axis_order.replace("C", "")) - len(translate)) + translate
         res_layers.extend(_image_to_layers(project_info, scale, translate))

package/PartSeg/plugins/napari_widgets/__init__.py

@@ -1,4 +1,5 @@
 from PartSeg._launcher.main_window import PartSegGUILauncher
+from PartSeg.plugins.napari_widgets._settings import SettingsEditor
 from PartSeg.plugins.napari_widgets.algorithm_widgets import (
     BorderSmooth,
     ConnectedComponents,
@@ -33,4 +34,5 @@
     "ROIAnalysisExtraction",
     "ROIMaskExtraction",
     "SearchLabel",
+    "SettingsEditor",
 )

package/PartSeg/plugins/napari_widgets/_settings.py

@@ -1,9 +1,11 @@
 import os
 
+from magicgui.widgets import Container, create_widget
 from napari.layers import Layer
 
 from PartSeg._roi_analysis.partseg_settings import PartSettings
 from PartSeg.common_backend import napari_get_settings
+from PartSegCore import Units
 from PartSegCore.json_hooks import PartSegEncoder
 
 _SETTINGS = None
@@ -19,8 +21,16 @@ def default(self, o):
 class PartSegNapariSettings(PartSettings):
     json_encoder_class = PartSegNapariEncoder
 
+    @property
+    def io_units(self) -> Units:
+        return self.get("io_units", Units.nm)
 
-def get_settings() -> PartSettings:
+    @io_units.setter
+    def io_units(self, value: Units):
+        self.set("io_units", value)
+
+
+def get_settings() -> PartSegNapariSettings:
     global _SETTINGS  # noqa: PLW0603  # pylint: disable=global-statement
     if _SETTINGS is None:
         napari_settings = napari_get_settings()
@@ -31,3 +41,16 @@ def get_settings() -> PartSettings:
         _SETTINGS = PartSegNapariSettings(os.path.join(save_path, "PartSeg_napari_plugins"))
         _SETTINGS.load()
     return _SETTINGS
+
+
+class SettingsEditor(Container):
+    def __init__(self):
+        super().__init__()
+        self.settings = get_settings()
+        self.units_select = create_widget(self.settings.io_units, annotation=Units, label="Units for io")
+        self.units_select.changed.connect(self.units_changed)
+        self.append(self.units_select)
+
+    def units_changed(self, value):
+        self.settings.io_units = value
+        self.settings.dump()