• 🟡 General issues: 1 issue found
• 🟢 Security: all looks good
• 🟡 Testing: 1 issue found
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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package/tests/test_PartSegImage/test_image_reader.py (1)

42-42: LGTM! Consider adding a comment for clarity.

The new assertion correctly checks the color values returned by image.get_colors(), which aligns with the PR objective of reading channel colors from CZI metadata. This addition enhances the test coverage by verifying the color information associated with the image.

Consider adding a brief comment explaining the significance of these color values, e.g.:

# Verify that the correct channel colors are read from the CZI metadata
assert image.get_colors() == ["#FFFFFF", "#FF0000", "#00FF00", "#0000FF"]

This would provide context for future developers or reviewers about the purpose of this specific assertion.

package/PartSegImage/image_reader.py (2)

136-137: LGTM! Consider adding type hints for clarity.

The addition of self.colors and self.ranges attributes, along with the new _get_channel_info method, improves the handling of channel information. The use of zip_longest ensures that the method can handle cases where the lengths of channel_names, colors, and ranges might differ.

Consider adding type hints to the _get_channel_info method for improved clarity:

-    def _get_channel_info(self):
+    def _get_channel_info(self) -> List[ChannelInfo]:

Also, you might want to add type hints for the self.colors and self.ranges attributes in the __init__ method:

-        self.colors = None
-        self.ranges = None
+        self.colors: Optional[List[Tuple[int, int, int]]] = None
+        self.ranges: Optional[List[Tuple[float, float]]] = None

Also applies to: 143-149

---

381-387: LGTM! Consider adding error handling for metadata extraction.

The changes in the CziImageReader class improve the handling of channel metadata, supporting both single-channel and multi-channel cases. The use of _get_channel_info in the image object creation ensures consistency with the new implementation.

Consider adding error handling for cases where the expected metadata structure is not present:

         with suppress(KeyError):
             channel_meta = metadata["ImageDocument"]["Metadata"]["DisplaySetting"]["Channels"]["Channel"]
             if isinstance(channel_meta, dict):
                 # single channel saved in czifile
                 channel_meta = [channel_meta]
-            self.channel_names = [x["Name"] for x in channel_meta]
-            self.colors = [x["Color"] for x in channel_meta]
+            self.channel_names = [x.get("Name", f"Channel {i+1}") for i, x in enumerate(channel_meta)]
+            self.colors = [x.get("Color", (255, 255, 255)) for x in channel_meta]

This change ensures that default values are used if "Name" or "Color" keys are missing in the metadata.

Also applies to: 398-398

package/PartSegImage/image.py (1)

Line range hint 919-929: LGTM! Consider a minor improvement for clarity.

The changes to the get_colors method look good. The addition of the return type hint improves code readability and type checking. The implementation correctly handles different color representations (strings, 2D arrays, and 1D arrays).

For improved clarity, consider adding a brief docstring explaining the method's purpose and the format of the returned colors. For example:

def get_colors(self) -> list[str | list[int]]:
    """
    Get the colors for each channel in the image.
    
    Returns:
        A list where each element is either a color name (str) or 
        an RGB color represented as a list of integers.
    """
    # ... rest of the method implementation

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Review profile: CHILL

package/PartSegImage/image_reader.py (2)

32-34: Suggestion: Add a docstring to empty_list_if_none function

Adding a docstring to empty_list_if_none would improve code readability by explaining its purpose and usage.

---

143-150: Suggestion: Add a docstring to _get_channel_info method

Including a docstring for _get_channel_info would enhance maintainability by explaining how it constructs the list of ChannelInfo objects from the channel-related attributes.

Configuration used: CodeRabbit UI
Review profile: CHILL