Merge branch 'develop' into pre-commit-ci-update-config

.github/project_dict.pws

@@ -1,4 +1,4 @@
-personal_ws-1.1 en 12
+personal_ws-1.1 en 14
 napari
 autoupdate
 aspell
@@ -12,3 +12,4 @@ pre
 bool
 changelog
 czi
+PartSeg

launcher.spec

@@ -90,7 +90,7 @@ hiddenimports = (
         "psygnal._weak_callback",
         "imagecodecs._imagecodecs",
         "PartSeg.plugins.napari_widgets",
-        "PartSegCore.napari_plugins",
+        "PartSegCore.napari_io",
     ]
     + [x.module_name for x in imageio_known_plugins.values()]
     + [x for x in collect_submodules("skimage") if "tests" not in x]

package/PartSeg/common_backend/__init__.py

@@ -2,6 +2,7 @@
 This module contains non gui Qt based components
 """
 
+import contextlib
 import os.path
 from typing import TYPE_CHECKING
 
@@ -14,11 +15,10 @@ def napari_get_settings(path=None) -> "NapariSettings":
 
     if path is not None:
         path = os.path.join(path, "settings.yaml")
-
-    try:
-        return _napari_get_settings(path)
-    except Exception:  # pylint: disable=broad-except
-        return _napari_get_settings()
+    if path is not None:
+        with contextlib.suppress(Exception):
+            return _napari_get_settings(path)
+    return _napari_get_settings()
 
 
 __all__ = ("napari_get_settings",)

package/PartSeg/launcher_main.py

@@ -26,14 +26,13 @@ def _test_imports():  # pragma: no cover
     from PartSeg._roi_mask.main_window import MainWindow as MaskMain
     from PartSeg.common_backend.base_argparser import _setup_sentry
     from PartSeg.common_gui.label_create import LabelChoose
-    from PartSeg.plugins import napari_widgets
-    from PartSegCore import napari_plugins
+    from PartSeg.plugins import napari_io, napari_widgets
 
     if "BorderSmooth" not in dir(napari_widgets):
         raise ImportError("napari_widgets not loaded")
 
-    if "load_image" not in dir(napari_plugins):
-        raise ImportError("napari_plugins not loaded")
+    if "load_image" not in dir(napari_io):
+        raise ImportError("napari_io not loaded")
 
     with suppress(ImportError):
         from napari.qt import get_app

package/PartSeg/napari.yaml

@@ -4,25 +4,25 @@ contributions:
   commands:
   - id: PartSeg.load_roi_project
     title: Get PartSeg ROI project Reader
-    python_name: PartSegCore.napari_plugins.load_roi_project:napari_get_reader
+    python_name: PartSeg.plugins.napari_io.load_roi_project:napari_get_reader
   - id: PartSeg.load_image
     title: Get Image Reader
-    python_name: PartSegCore.napari_plugins.load_image:napari_get_reader
+    python_name: PartSeg.plugins.napari_io.load_image:napari_get_reader
   - id: PartSeg.write_tiff_image
     title: Write tiff Image
-    python_name: PartSegCore.napari_plugins.save_tiff_layer:napari_write_images
+    python_name: PartSeg.plugins.napari_io.save_tiff_layer:napari_write_images
   - id: PartSeg.write_tiff_labels
     title: Write tiff Labels
-    python_name: PartSegCore.napari_plugins.save_tiff_layer:napari_write_labels
+    python_name: PartSeg.plugins.napari_io.save_tiff_layer:napari_write_labels
   - id: PartSeg.load_mask_project
     title: Get PartSeg mask project Reader
-    python_name: PartSegCore.napari_plugins.load_mask_project:napari_get_reader
+    python_name: PartSeg.plugins.napari_io.load_mask_project:napari_get_reader
   - id: PartSeg.save_mask_roi
     title: Write Labels as mask project
-    python_name: PartSegCore.napari_plugins.save_mask_roi:napari_write_labels
+    python_name: PartSeg.plugins.napari_io.save_mask_roi:napari_write_labels
   - id: PartSeg.load_masked_image
     title: Get Reader for image with mask
-    python_name: PartSegCore.napari_plugins.load_masked_image:napari_get_reader
+    python_name: PartSeg.plugins.napari_io.load_masked_image:napari_get_reader
   - id: PartSeg.SimpleMeasurement
     title: Create Simple Measurement
     python_name: PartSeg.plugins.napari_widgets.simple_measurement_widget:SimpleMeasurement
@@ -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/PartSegCore/napari_plugins/__init__.py → package/PartSeg/plugins/napari_io/__init__.py

@@ -1,4 +1,4 @@
-from PartSegCore.napari_plugins import (
+from PartSeg.plugins.napari_io import (
     load_image,
     load_mask_project,
     load_masked_image,

package/PartSegCore/napari_plugins/load_image.py → package/PartSeg/plugins/napari_io/load_image.py

@@ -1,7 +1,7 @@
 import functools
 
+from PartSeg.plugins.napari_io.loader import partseg_loader
 from PartSegCore.analysis.load_functions import LoadStackImage
-from PartSegCore.napari_plugins.loader import partseg_loader
 
 
 def napari_get_reader(path: str):

package/PartSegCore/napari_plugins/load_mask_project.py → package/PartSeg/plugins/napari_io/load_mask_project.py

@@ -1,7 +1,7 @@
 import functools
 
+from PartSeg.plugins.napari_io.loader import partseg_loader
 from PartSegCore.mask.io_functions import LoadROI
-from PartSegCore.napari_plugins.loader import partseg_loader
 
 
 def napari_get_reader(path: str):

package/PartSegCore/napari_plugins/load_masked_image.py → package/PartSeg/plugins/napari_io/load_masked_image.py

@@ -1,8 +1,8 @@
 import functools
 import os.path
 
+from PartSeg.plugins.napari_io.loader import partseg_loader
 from PartSegCore.mask.io_functions import LoadStackImageWithMask
-from PartSegCore.napari_plugins.loader import partseg_loader
 
 
 def napari_get_reader(path: str):

package/PartSegCore/napari_plugins/load_roi_project.py → package/PartSeg/plugins/napari_io/load_roi_project.py

@@ -1,8 +1,8 @@
 import functools
 import os.path
 
+from PartSeg.plugins.napari_io.loader import partseg_loader
 from PartSegCore.analysis.load_functions import LoadProject
-from PartSegCore.napari_plugins.loader import partseg_loader
 
 
 def napari_get_reader(path: str):

package/PartSegCore/napari_plugins/loader.py → 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 @@
     "SplitCoreObjects",
     "Threshold",
     "Watershed",
+    "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 +41,20 @@ 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_selection_changed)
+        self.settings.connect_("io_units", self.units_changed)
+        self.append(self.units_select)
+
+    def units_selection_changed(self, value):
+        self.settings.io_units = value
+        self.settings.dump()
+
+    def units_changed(self):
+        self.units_select.value = self.settings.io_units

package/tests/test_PartSegCore/test_napari_plugins.py → package/tests/test_PartSeg/test_napari_io.py

@@ -8,20 +8,20 @@
 from napari.layers import Image, Labels, Layer
 from packaging.version import parse as parse_version
 
-from PartSegCore.analysis import ProjectTuple
-from PartSegCore.mask.io_functions import LoadROIFromTIFF
-from PartSegCore.napari_plugins.load_image import napari_get_reader as napari_get_reader_image
-from PartSegCore.napari_plugins.load_mask_project import napari_get_reader as napari_get_reader_mask
-from PartSegCore.napari_plugins.load_masked_image import napari_get_reader as napari_get_reader_mask_image
-from PartSegCore.napari_plugins.load_roi_project import napari_get_reader as napari_get_reader_roi
-from PartSegCore.napari_plugins.loader import project_to_layers
-from PartSegCore.napari_plugins.save_mask_roi import napari_write_labels
-from PartSegCore.napari_plugins.save_tiff_layer import (
+from PartSeg.plugins.napari_io.load_image import napari_get_reader as napari_get_reader_image
+from PartSeg.plugins.napari_io.load_mask_project import napari_get_reader as napari_get_reader_mask
+from PartSeg.plugins.napari_io.load_masked_image import napari_get_reader as napari_get_reader_mask_image
+from PartSeg.plugins.napari_io.load_roi_project import napari_get_reader as napari_get_reader_roi
+from PartSeg.plugins.napari_io.loader import project_to_layers
+from PartSeg.plugins.napari_io.save_mask_roi import napari_write_labels
+from PartSeg.plugins.napari_io.save_tiff_layer import (
     napari_write_images,
 )
-from PartSegCore.napari_plugins.save_tiff_layer import (
+from PartSeg.plugins.napari_io.save_tiff_layer import (
     napari_write_labels as napari_write_labels_tiff,
 )
+from PartSegCore.analysis import ProjectTuple
+from PartSegCore.mask.io_functions import LoadROIFromTIFF
 from PartSegImage import GenericImageReader
 from PartSegImage import Image as PImage
 

package/tests/test_PartSeg/test_napari_widgets.py

@@ -14,7 +14,6 @@
 from packaging.version import parse as parse_version
 from qtpy.QtCore import QObject, QTimer, Signal
 
-from PartSeg._roi_analysis.partseg_settings import PartSettings
 from PartSeg._roi_analysis.profile_export import ExportDialog, ImportDialog
 from PartSeg.common_gui.custom_load_dialog import CustomLoadDialog
 from PartSeg.common_gui.custom_save_dialog import CustomSaveDialog
@@ -46,6 +45,7 @@
 from PartSeg.plugins.napari_widgets.measurement_widget import update_properties
 from PartSeg.plugins.napari_widgets.roi_extraction_algorithms import ProfilePreviewDialog, QInputDialog
 from PartSeg.plugins.napari_widgets.search_label_widget import HIGHLIGHT_LABEL_NAME
+from PartSegCore import Units
 from PartSegCore.algorithm_describe_base import ROIExtractionProfile
 from PartSegCore.analysis.algorithm_description import AnalysisAlgorithmSelection
 from PartSegCore.analysis.load_functions import LoadProfileFromJSON
@@ -85,7 +85,7 @@ def check_direct_mode(layer):
 @pytest.fixture(autouse=True)
 def _clean_settings(tmp_path):
     old_settings = _settings._SETTINGS
-    _settings._SETTINGS = PartSettings(tmp_path)
+    _settings._SETTINGS = _settings.PartSegNapariSettings(tmp_path)
     yield
     _settings._SETTINGS = old_settings
 
@@ -639,3 +639,19 @@ def test_add_layer_post_init(self, make_napari_viewer, qtbot):
 def test_enum():
     assert " " in str(CompareType.lower_threshold)
     assert " " in str(FlowType.dark_center)
+
+
+class TestSettingsWidget:
+    def test_create(self, qtbot):
+        w = _settings.SettingsEditor()
+        qtbot.addWidget(w.native)
+
+    def test_change_units(self, qtbot):
+        s = _settings.get_settings()
+        s.io_units = Units.µm
+        w = _settings.SettingsEditor()
+        qtbot.addWidget(w.native)
+        w.units_select.value = Units.nm
+        assert s.io_units == Units.nm
+        s.io_units = Units.mm
+        assert w.units_select.value == Units.mm