feat: Show filename when importing with PartSeg in napari (#1226)

Hi,

Thank you for developing this fantastic tool! It has been incredibly
valuable for our research.

While working with PartSeg in Napari, we noticed that the filename does
not appear in the layer names, making distinguishing between multiple
imported files challenging. To address this, I’ve updated the code in
this pull request to add the filename as a prefix to the layer names.

I’m open to feedback on this approach and would love your thoughts or
suggestions for further improvement!

Best,
David

## Summary by Sourcery

New Features:
- Add filename as a prefix to layer names when importing with PartSeg in
Napari.

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

- **New Features**
- Introduced a new method for adjusting color values, enhancing color
processing capabilities.
- Added conditional functionality for adding color based on the version
of the application.
- Improved layer naming conventions by incorporating file name prefixes
for better clarity.
	- Added a new property for selecting layer naming formats in settings.
- Introduced a new enumeration for layer naming formats with multiple
options.
	- Added new test cases to validate layer naming format functionality.

- **Bug Fixes**
- Enhanced handling of alpha channels in color strings to ensure
accurate color representation.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Grzegorz Bokota <[email protected]>

package/PartSeg/plugins/napari_io/loader.py

@@ -1,3 +1,4 @@
+import os
 import typing
 from importlib.metadata import version
 
@@ -9,6 +10,7 @@
 from PartSegCore.analysis import ProjectTuple
 from PartSegCore.io_utils import LoadBase, WrongFileTypeException
 from PartSegCore.mask.io_functions import MaskProjectTuple
+from PartSegCore.universal_const import format_layer_name
 from PartSegImage import Image
 
 
@@ -54,12 +56,20 @@ def add_color(image: Image, idx: int) -> dict:  # noqa: ARG001
 
 
 def _image_to_layers(project_info, scale, translate):
+    settings = get_settings()
+    filename = os.path.basename(project_info.file_path)
     res_layers = []
     if project_info.image.name == "ROI" and project_info.image.channels == 1:
         res_layers.append(
             (
                 project_info.image.get_channel(0),
-                {"scale": scale, "name": project_info.image.channel_names[0], "translate": translate},
+                {
+                    "scale": scale,
+                    "name": format_layer_name(
+                        settings.layer_naming_format, filename, project_info.image.channel_names[0]
+                    ),
+                    "translate": translate,
+                },
                 "labels",
             )
         )
@@ -69,7 +79,9 @@ def _image_to_layers(project_info, scale, translate):
                 project_info.image.get_channel(i),
                 {
                     "scale": scale,
-                    "name": project_info.image.channel_names[i],
+                    "name": format_layer_name(
+                        settings.layer_naming_format, filename, project_info.image.channel_names[i]
+                    ),
                     "blending": "additive",
                     "translate": translate,
                     "metadata": project_info.image.metadata,

package/PartSeg/plugins/napari_widgets/_settings.py

@@ -7,6 +7,7 @@
 from PartSeg.common_backend import napari_get_settings
 from PartSegCore import Units
 from PartSegCore.json_hooks import PartSegEncoder
+from PartSegCore.universal_const import LayerNamingFormat
 
 _SETTINGS = None
 
@@ -29,6 +30,14 @@ def io_units(self) -> Units:
     def io_units(self, value: Units):
         self.set("io_units", value)
 
+    @property
+    def layer_naming_format(self) -> LayerNamingFormat:
+        return self.get("layer_naming_format", LayerNamingFormat.channel_only)
+
+    @layer_naming_format.setter
+    def layer_naming_format(self, value: LayerNamingFormat):
+        self.set("layer_naming_format", value)
+
 
 def get_settings() -> PartSegNapariSettings:
     global _SETTINGS  # noqa: PLW0603  # pylint: disable=global-statement
@@ -51,10 +60,23 @@ def __init__(self):
         self.units_select.changed.connect(self.units_selection_changed)
         self.settings.connect_("io_units", self.units_changed)
         self.append(self.units_select)
+        self.layer_naming_select = create_widget(
+            self.settings.layer_naming_format, annotation=LayerNamingFormat, label="Format for Layer Name"
+        )
+        self.layer_naming_select.changed.connect(self.layer_naming_format_selection_changed)
+        self.settings.connect_("layer_naming_format", self.layer_naming_format_changed)
+        self.append(self.layer_naming_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
+
+    def layer_naming_format_selection_changed(self, value):
+        self.settings.layer_naming_format = value
+        self.settings.dump()
+
+    def layer_naming_format_changed(self):
+        self.layer_naming_select.value = self.settings.layer_naming_format

package/PartSegCore/universal_const.py

@@ -17,3 +17,26 @@ def __str__(self):
 
 _UNITS_LIST = ["mm", "µm", "nm", "pm"]
 UNIT_SCALE = [10**3, 10**6, 10**9, 10**12]
+
+
+@register_class()
+class LayerNamingFormat(Enum):
+    channel_only = 0
+    filename_only = 1
+    filename_channel = 2
+    channel_filename = 3
+
+    def __str__(self):
+        return self.name.replace("_", " ")
+
+
+def format_layer_name(layer_format: LayerNamingFormat, file_name: str, channel_name: str) -> str:
+    if layer_format == LayerNamingFormat.channel_only:
+        return channel_name
+    if layer_format == LayerNamingFormat.filename_only:
+        return file_name
+    if layer_format == LayerNamingFormat.filename_channel:
+        return f"{file_name} | {channel_name}"
+    if layer_format == LayerNamingFormat.channel_filename:
+        return f"{channel_name} | {file_name}"
+    raise ValueError("Unknown format")  # pragma: no cover

package/tests/test_PartSeg/test_napari_widgets.py

@@ -57,6 +57,7 @@
 from PartSegCore.segmentation.noise_filtering import NoiseFilterSelection
 from PartSegCore.segmentation.threshold import DoubleThresholdSelection, ThresholdSelection
 from PartSegCore.segmentation.watershed import WatershedSelection
+from PartSegCore.universal_const import LayerNamingFormat
 
 NAPARI_GE_5_0 = parse_version(version("napari")) >= parse_version("0.5.0a1")
 NAPARI_GE_4_19 = parse_version(version("napari")) >= parse_version("0.4.19a1")
@@ -655,3 +656,13 @@ def test_change_units(self, qtbot):
         assert s.io_units == Units.nm
         s.io_units = Units.mm
         assert w.units_select.value == Units.mm
+
+    def test_change_layer_name_format(self, qtbot):
+        s = _settings.get_settings()
+        s.layer_naming_format = LayerNamingFormat.channel_only
+        w = _settings.SettingsEditor()
+        qtbot.addWidget(w.native)
+        w.layer_naming_select.value = LayerNamingFormat.channel_filename
+        assert s.layer_naming_format == LayerNamingFormat.channel_filename
+        s.layer_naming_format = LayerNamingFormat.channel_only
+        assert w.layer_naming_select.value == LayerNamingFormat.channel_only

package/tests/test_PartSegCore/test_io.py

@@ -62,6 +62,7 @@
 from PartSegCore.segmentation.noise_filtering import DimensionType
 from PartSegCore.segmentation.segmentation_algorithm import ThresholdAlgorithm
 from PartSegCore.segmentation.threshold import RangeThresholdSelection
+from PartSegCore.universal_const import LayerNamingFormat, format_layer_name
 from PartSegCore.utils import ProfileDict, check_loaded_dict
 from PartSegImage import Image
 
@@ -911,6 +912,19 @@ def test_load(self, tmp_path):
         assert res.roi_info.roi.shape == (1, 1, 100, 100)
 
 
+@pytest.mark.parametrize(
+    ("value", "expected"),
+    [
+        (LayerNamingFormat.channel_only, "b"),
+        (LayerNamingFormat.filename_only, "a"),
+        (LayerNamingFormat.filename_channel, "a | b"),
+        (LayerNamingFormat.channel_filename, "b | a"),
+    ],
+)
+def test_format_layer_name(value, expected):
+    assert format_layer_name(value, "a", "b") == expected
+
+
 UPDATE_NAME_JSON = """
 {"problematic set": {
       "__MeasurementProfile__": true,