refactor: merge all channel-specific attributes of the Image class (#…

…1191)

Also make all except `data` arguments keyword only

<!-- Generated by sourcery-ai[bot]: start summary -->

## Summary by Sourcery

Refactor the Image class to consolidate channel-specific attributes into
a unified channel_info attribute, enforce keyword-only arguments, and
update tests accordingly.

Enhancements:
- Refactor the Image class to merge all channel-specific attributes into
a single channel_info attribute, improving the organization and
management of channel metadata.
- Introduce decorators to handle deprecated arguments and enforce
keyword-only arguments for the Image class, enhancing code clarity and
future-proofing.
- Add utility functions for color conversion from hex and named colors
to RGB, supporting more flexible color specifications.

Tests:
- Update tests to accommodate the refactored Image class, ensuring
compatibility with the new channel_info attribute and keyword-only
arguments.

<!-- Generated by sourcery-ai[bot]: end summary -->

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

## Release Notes

- **New Features**
- Introduced `ChannelInfo` and `ChannelInfoFull` classes for enhanced
channel metadata management.
- Updated image processing to use `spacing` instead of `image_spacing`,
improving parameter clarity.

- **Bug Fixes**
- Corrected parameter names across various tests and functionalities to
align with the updated `Image` class interface.

- **Tests**
- Updated numerous test cases to reflect changes in parameter names and
structures, ensuring consistency throughout the test suite.
- Added a new test for saving color images with specific channel
information.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

package/PartSeg/plugins/napari_widgets/simple_measurement_widget.py

@@ -84,7 +84,7 @@ def _calculate(self, event=None):
             )
             return
         data_scale = data_layer.scale[-3:] / UNIT_SCALE[self.scale_units_select.get_value().value]
-        image = Image(data_layer.data, data_scale, axes_order="TZYX"[-data_ndim:])
+        image = Image(data_layer.data, spacing=data_scale, axes_order="TZYX"[-data_ndim:])
         worker = _prepare_data(profile, image, self.labels_choice.value.data)
         worker.returned.connect(self._calculate_next)
         worker.errored.connect(self._finished)

package/PartSeg/plugins/napari_widgets/utils.py

@@ -12,7 +12,7 @@
 from PartSeg.common_gui.custom_save_dialog import FormDialog
 from PartSegCore import UNIT_SCALE, Units
 from PartSegCore.algorithm_describe_base import AlgorithmProperty
-from PartSegImage import Channel, Image
+from PartSegImage import Channel, ChannelInfo, Image
 
 
 class QtNapariAlgorithmProperty(QtAlgorithmProperty):
@@ -69,9 +69,9 @@ def generate_image(viewer: Viewer, *layer_names):
         image_list.append(
             Image(
                 image_layer.data,
-                data_scale,
+                spacing=data_scale,
                 axes_order=axis_order[-image_layer.data.ndim :],
-                channel_names=[image_layer.name],
+                channel_info=[ChannelInfo(name=name.value)],
             )
         )
     res_image = image_list[0]

package/PartSegCore/analysis/measurement_calculation.py

@@ -208,7 +208,7 @@ def get_global_parameters(self):
             res = [name]
             iterator = iter(self._data_dict.keys())
             with suppress(StopIteration):
-                next(iterator)  # skipcq: PTC-W0063`
+                next(iterator)  # skipcq: PTC-W0063
         else:
             res = []
             iterator = iter(self._data_dict.keys())
@@ -233,7 +233,7 @@ def _prepare_res_iterator(self, counts):
             res = [[name] for _ in range(counts)]
             iterator = iter(self._data_dict.keys())
             with suppress(StopIteration):
-                next(iterator)  # skipcq: PTC-W0063`
+                next(iterator)  # skipcq: PTC-W0063
         else:
             res = [[] for _ in range(counts)]
             iterator = iter(self._data_dict.keys())

package/PartSegCore/image_transforming/image_projection.py

@@ -58,8 +58,8 @@ def transform(
         return (
             image.__class__(
                 data=new_channels,
-                image_spacing=tuple(spacing),
-                channel_names=image.channel_names,
+                spacing=tuple(spacing),
+                channel_info=image.channel_info,
                 mask=new_mask,
                 axes_order=image.axis_order,
             ),

package/PartSegCore/mask/io_functions.py

@@ -132,7 +132,7 @@ def _save_mask_roi(project: MaskProjectTuple, tar_file: tarfile.TarFile, paramet
         spacing = project.image.spacing
     else:
         spacing = parameters.spacing
-    segmentation_image = Image(project.roi_info.roi, spacing, axes_order=Image.axis_order.replace("C", ""))
+    segmentation_image = Image(project.roi_info.roi, spacing=spacing, axes_order=Image.axis_order.replace("C", ""))
     try:
         ImageWriter.save(segmentation_image, segmentation_buff, compression=None)
     except ValueError:

package/PartSegCore/napari_plugins/save_tiff_layer.py

@@ -4,7 +4,7 @@
 import numpy as np
 from napari.types import FullLayerData
 
-from PartSegImage import Image, ImageWriter
+from PartSegImage import ChannelInfo, Image, ImageWriter
 from PartSegImage.image import DEFAULT_SCALE_FACTOR
 
 
@@ -15,9 +15,9 @@ def napari_write_labels(path: str, data: Any, meta: dict) -> Optional[str]:
     scale_shift = min(data.ndim, 3)
     image = Image(
         data,
-        np.divide(meta["scale"], DEFAULT_SCALE_FACTOR)[-scale_shift:],
+        spacing=np.divide(meta["scale"], DEFAULT_SCALE_FACTOR)[-scale_shift:],
         axes_order="TZYX"[-data.ndim :],
-        channel_names=[meta["name"]],
+        channel_info=[ChannelInfo(name=meta["name"])],
         shift=np.divide(meta["translate"], DEFAULT_SCALE_FACTOR)[-scale_shift:],
         name="ROI",
     )
@@ -50,9 +50,9 @@ def napari_write_images(path: str, layer_data: List[FullLayerData]) -> List[str]
         scale_shift -= 1
     image = Image(
         data,
-        np.divide(meta["scale"], DEFAULT_SCALE_FACTOR)[-scale_shift:],
+        spacing=np.divide(meta["scale"], DEFAULT_SCALE_FACTOR)[-scale_shift:],
         axes_order=axes,
-        channel_names=channel_names,
+        channel_info=[ChannelInfo(name=x) for x in channel_names],
         shift=np.divide(meta["translate"], DEFAULT_SCALE_FACTOR)[-scale_shift:],
         name="Image",
     )

package/PartSegImage/__init__.py

@@ -3,7 +3,7 @@
 
 from PartSegImage import tifffile_fixes  # noqa: F401
 from PartSegImage.channel_class import Channel
-from PartSegImage.image import Image
+from PartSegImage.image import ChannelInfo, ChannelInfoFull, Image
 from PartSegImage.image_reader import (
     CziImageReader,
     GenericImageReader,
@@ -17,6 +17,8 @@
 __all__ = (
     "BaseImageWriter",
     "Channel",
+    "ChannelInfo",
+    "ChannelInfoFull",
     "Image",
     "TiffImageReader",
     "IMAGEJImageWriter",