feat: Allow set units that will be used for load/save data using Part…

…Seg as napari plugin (#1228)

This PR add "Settings Editor" widget to allow edit PartSeg specific
settings.

This PR add option to set to which units, the scale should be set when
loading to the viewer.

This PR also contains refactor that is mentioned here:
#1226 (comment)

## Summary by Sourcery

Add a 'Settings Editor' widget to the PartSeg napari plugin to enable
editing of specific settings, including setting units for data scaling.
Refactor the plugin structure by relocating files to a new 'napari_io'
directory for improved organization.

New Features:
- Introduce a 'Settings Editor' widget to allow users to edit PartSeg
specific settings within the napari plugin.
- Add functionality to set the units for scaling when loading data into
the viewer.

Enhancements:
- Refactor the PartSeg napari plugin structure by moving files from
'napari_plugins' to 'napari_io' for better organization.

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

- **New Features**
- Introduced a new `SettingsEditor` for managing unit settings within
the PartSeg interface.
- Enhanced plugin handling based on the version of the `napari` library.
- **Bug Fixes**
	- Improved clarity of error messages related to plugin loading.
- **Documentation**
- Updated command signatures in the configuration to reflect new module
structure.
- **Chores**
- Restructured import paths across various modules to enhance
organization and maintainability.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

.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 @@
     "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 +41,20 @@ 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