feat: Use image color when add layer to napari #1200
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Reviewer's Guide by SourceryThis pull request enhances the image color handling in the napari reader plugin. It introduces a new function to adjust color values and modifies existing functions to support both RGB and RGBA color formats. The changes primarily affect how colors are processed and applied to image layers in napari. Sequence DiagramsequenceDiagram
participant Client
participant _image_to_layers
participant adjust_color
participant Image
Client->>_image_to_layers: Create layers
_image_to_layers->>Image: get_colors()
Image-->>_image_to_layers: Return colors
_image_to_layers->>adjust_color: Adjust color
adjust_color-->>_image_to_layers: Return adjusted color
_image_to_layers->>Client: Return layers with adjusted colors
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Warning Rate limit exceeded@Czaki has exceeded the limit for the number of commits or files that can be reviewed per hour. Please wait 12 minutes and 5 seconds before requesting another review. ⌛ How to resolve this issue?After the wait time has elapsed, a review can be triggered using the We recommend that you space out your commits to avoid hitting the rate limit. 🚦 How do rate limits work?CodeRabbit enforces hourly rate limits for each developer per organization. Our paid plans have higher rate limits than the trial, open-source and free plans. In all cases, we re-allow further reviews after a brief timeout. Please see our FAQ for further information. WalkthroughThe changes introduce a new function Changes
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Hey @Czaki - I've reviewed your changes and they look great!
Here's what I looked at during the review
- 🟡 General issues: 2 issues found
- 🟢 Security: all looks good
- 🟢 Testing: all looks good
- 🟢 Complexity: all looks good
- 🟢 Documentation: all looks good
Help me be more useful! Please click 👍 or 👎 on each comment to tell me if it was helpful.
| from PartSegCore.mask.io_functions import MaskProjectTuple | ||
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| def adjust_color(color): |
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suggestion: Consider a more robust approach for color adjustment
The current implementation may lead to unexpected results by simply truncating the alpha channel. Consider handling alpha channels more explicitly or using a color library for more robust color manipulations.
def adjust_color(color: str) -> str:
from colorsys import rgb_to_hls, hls_to_rgb
def hex_to_rgb(hex_color):
return tuple(int(hex_color[i:i+2], 16) for i in (1, 3, 5))
def rgb_to_hex(rgb):
return f"#{''.join([f'{int(x):02x}' for x in rgb])}"
if color.startswith("#") and len(color) >= 7:
rgb = hex_to_rgb(color[:7])
| """ | ||
| hex_code = hex_code.lstrip("#") | ||
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| if len(hex_code) == 3: |
There was a problem hiding this comment.
suggestion: Improve handling of hex codes with alpha channels
While the function now accepts 4-digit and 8-digit hex codes, it still only returns RGB values, discarding any alpha information. Consider extending the function to handle and return alpha channel information when present.
def hex_to_rgb(hex_code):
"""Convert hex color code to RGB tuple."""
hex_code = hex_code.lstrip("#")
if len(hex_code) in {3, 4, 6, 8}:
if len(hex_code) < 5:
hex_code = "".join([c * 2 for c in hex_code])
rgb = tuple(int(hex_code[i:i+2], 16) for i in (0, 2, 4))
if len(hex_code) == 8:
return rgb + (int(hex_code[6:8], 16),)
return rgb
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (3)
package/PartSegCore/napari_plugins/loader.py (1)
Line range hint
1-124: Summary of changes and next stepsThe changes in this file successfully implement the PR objective of incorporating channel colors when adding layers to napari. The new
adjust_colorfunction and its integration into_image_to_layersachieve this goal.However, there are opportunities for improvement:
- Enhance the robustness and clarity of the
adjust_colorfunction as suggested earlier.- Verify the compatibility of the adjusted colors with napari's color handling.
- Consider adding unit tests for the new
adjust_colorfunction and the modified_image_to_layersfunction to ensure correct behavior and prevent regressions.To further improve the code:
- Consider moving the color adjustment logic to a separate module dedicated to color operations if it's likely to be used elsewhere in the project.
- If this color adjustment is specific to napari integration, consider adding a comment explaining its purpose and any napari-specific color format requirements.
Once these improvements are made, the changes will be more robust and maintainable.
package/tests/test_PartSegImage/test_image.py (1)
703-706: LGTM! Good additions to test cases.The new test cases for hex color codes with alpha channels (#ff0000ff and #b00f) are valuable additions. They improve the coverage of the
_hex_to_rgbfunction by testing its ability to handle 8-digit hex codes and 4-digit shorthand codes with alpha.The modification of the ValueError test case is also correct, as "#b0000" is indeed an invalid hex code, while the previous "#b000" was actually valid.
Consider adding a test case for a 4-digit hex code without alpha, such as "#0f0f", to ensure complete coverage of all valid hex code formats.
Also applies to: 709-709
package/PartSegImage/image.py (1)
976-978: LGTM! Consider adding support for alpha channel.The changes to the
_hex_to_rgbfunction improve its flexibility by accepting hex codes with 3, 4, 6, or 8 characters. The logic for handling short-form hex codes is correct, and the error handling for invalid hex code lengths is appropriate.Consider extending the function to support the alpha channel for 4 and 8 character hex codes. This could be done by returning a tuple of 4 values (R, G, B, A) when an alpha channel is present. Here's a suggested implementation:
def _hex_to_rgb(hex_code: str) -> tuple[int, int, int]: - """ - Convert a hex color code to an RGB tuple. + """ + Convert a hex color code to an RGB or RGBA tuple. - :param str hex_code: The hex color code, either short form (#RGB) or long form (#RRGGBB) - :return: A tuple containing the RGB values (R, G, B) + :param str hex_code: The hex color code, either short form (#RGB or #RGBA) or long form (#RRGGBB or #RRGGBBAA) + :return: A tuple containing the RGB or RGBA values (R, G, B) or (R, G, B, A) """ hex_code = hex_code.lstrip("#") if len(hex_code) in {3, 4}: hex_code = "".join([c * 2 for c in hex_code]) elif len(hex_code) not in {6, 8}: raise ValueError(f"Invalid hex code format: {hex_code}") - return int(hex_code[:2], 16), int(hex_code[2:4], 16), int(hex_code[4:6], 16) + rgb = tuple(int(hex_code[i:i+2], 16) for i in (0, 2, 4)) + if len(hex_code) == 8: + return rgb + (int(hex_code[6:8], 16),) + return rgbThis change would make the function more versatile while maintaining backwards compatibility.
📜 Review details
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Review profile: CHILL
📒 Files selected for processing (3)
- package/PartSegCore/napari_plugins/loader.py (2 hunks)
- package/PartSegImage/image.py (1 hunks)
- package/tests/test_PartSegImage/test_image.py (1 hunks)
🔇 Additional comments (2)
package/PartSegCore/napari_plugins/loader.py (1)
39-39: Verify color compatibility with napariThe integration of the
adjust_colorfunction in the_image_to_layersfunction aligns well with the PR objective of incorporating the channel color when adding a layer to napari.To ensure compatibility, please verify that:
- The adjusted colors are always in a format that napari can interpret correctly.
- This change doesn't negatively impact existing color handling in napari.
You can run the following script to check the usage and impact of this change:
This will help identify any potential conflicts or areas that might need additional testing.
✅ Verification successful
Color Integration Verified
The addition of the
adjust_colorfunction in the_image_to_layersmethod has been successfully verified. The function is correctly integrated, and existing color handling within napari remains unaffected. Comprehensive tests related to color management are present, ensuring that the changes are well-supported.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check the usage of adjust_color and potential impacts # Search for other usages of adjust_color echo "Searching for other usages of adjust_color:" rg "adjust_color\(" --type python # Search for napari color handling to check for potential conflicts echo "\nSearching for napari color handling:" rg "colormap" --type python # Search for tests related to color handling echo "\nSearching for color-related tests:" rg "test.*color" --type pythonLength of output: 456
Script:
#!/bin/bash # Description: Re-attempt searching with explicit Python file patterns # Search for other usages of adjust_color in Python files echo "Searching for other usages of adjust_color in Python files:" fd --extension py --type file | xargs rg "adjust_color\(" # Search for napari color handling to check for potential conflicts in Python files echo "\nSearching for napari color handling in Python files:" fd --extension py --type file | xargs rg "colormap" # Search for tests related to color handling in Python files echo "\nSearching for color-related tests in Python files:" fd --extension py --type file | xargs rg "test.*color"Length of output: 48516
package/PartSegImage/image.py (1)
976-978: Verify the impact of _hex_to_rgb changes on existing code.The changes to the
_hex_to_rgbfunction improve its flexibility, but we should ensure that this doesn't unintentionally affect other parts of the codebase that may be using this function.Let's run a quick check to find all occurrences of
_hex_to_rgbin the codebase:Please review the results of this search to ensure that all usages of
_hex_to_rgbare compatible with the new implementation.✅ Verification successful
Impact of
_hex_to_rgbChanges Verified Successfully.All usages of the
_hex_to_rgbfunction have been reviewed, and existing functionality remains intact without introducing any issues.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Find all occurrences of _hex_to_rgb in the codebase # Expected result: A list of files and line numbers where _hex_to_rgb is used rg --type python '_hex_to_rgb'Length of output: 61
Script:
#!/bin/bash # Description: Find all occurrences of _hex_to_rgb in Python files using the correct type alias # Expected result: A list of files and line numbers where _hex_to_rgb is used rg --type py '_hex_to_rgb'Length of output: 1098
| def adjust_color(color): | ||
| if color.startswith("#"): | ||
| if len(color) == 9: | ||
| return color[:7] | ||
| if len(color) == 5: | ||
| return color[:4] | ||
| return color |
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🛠️ Refactor suggestion
Improve robustness and clarity of the adjust_color function
The new adjust_color function has a few areas for improvement:
- The function doesn't validate the input color format, which could lead to unexpected behavior with invalid inputs.
- The purpose of truncating a 5-character color to 4 characters is unclear and may not be the intended behavior.
- The function name doesn't clearly indicate that it's potentially truncating the color.
Consider the following improvements:
- Add input validation to ensure the color is in a valid format.
- Clarify or reconsider the handling of 5-character colors.
- Rename the function to better reflect its purpose, e.g.,
truncate_color_alpha.
Here's a suggested implementation:
def truncate_color_alpha(color: str) -> str:
"""
Truncate the alpha channel from hex color strings.
:param color: A string representing a color in hex format.
:return: The color string with the alpha channel removed, if present.
:raises ValueError: If the input is not a valid hex color string.
"""
if not isinstance(color, str):
raise ValueError("Color must be a string")
if color.startswith("#"):
if len(color) == 9: # #RRGGBBAA
return color[:7] # Return #RRGGBB
elif len(color) == 7: # #RRGGBB
return color
elif len(color) == 5: # #RGBA
return f"#{color[1]}{color[1]}{color[2]}{color[2]}{color[3]}{color[3]}" # Expand to #RRGGBB
elif len(color) == 4: # #RGB
return color
# If it's not a hex color or doesn't need truncation, return as is
return colorThis implementation adds input validation, handles 5-character colors by expanding them to 6 characters (which is more common for hex shorthand notation), and includes a docstring for clarity.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #1200 +/- ##
========================================
Coverage 93.12% 93.13%
========================================
Files 210 210
Lines 33121 33149 +28
========================================
+ Hits 30845 30873 +28
Misses 2276 2276 ☔ View full report in Codecov by Sentry. |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
package/tests/conftest.py (1)
85-97: LGTM: Enhancedstack_imagefixture with channel-specific metadata.The
stack_imagefixture has been successfully updated to include channel-specific metadata, which aligns with the PR objective of incorporating channel colors when adding layers to napari. The changes improve the image representation and support better testing of color-related functionality.A minor suggestion for consistency:
Consider using the same format for both color map hex codes. Currently, you're using an 8-character hex code for the first channel and a 4-character hex code for the second channel. For consistency, you might want to use 8-character hex codes for both:
channel_info=[ - ChannelInfo(name="channel 1", color_map="#00FF00FF"), - ChannelInfo(name="channel 2", color_map="#00FF"), + ChannelInfo(name="channel 1", color_map="#00FF00FF"), + ChannelInfo(name="channel 2", color_map="#0000FFFF"), ],This change would ensure that both color maps are represented in the same format, potentially preventing any issues with color interpretation in different parts of the codebase.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (3)
- package/PartSegCore/napari_plugins/loader.py (2 hunks)
- package/tests/conftest.py (3 hunks)
- package/tests/test_PartSegCore/test_napari_plugins.py (1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- package/PartSegCore/napari_plugins/loader.py
🔇 Additional comments (7)
package/tests/test_PartSegCore/test_napari_plugins.py (5)
34-34: Colormap assertion added for the first layerThe new assertion checks that the colormap name of the first layer (l1) is "green". This aligns with the PR objective of incorporating channel colors when adding layers to napari.
36-39: Updated creation and assertions for the second layerThe second layer (l2) is now created from
res[1]instead ofres[2], and new assertions have been added to check its type, name, and colormap. This change reflects a reordering of the layers returned byproject_to_layersand adds color information checking.
40-42: Updated creation and assertions for the third layerThe third layer (l3) is now created from
res[2]and is asserted to be a Labels type with the name "ROI". This change is consistent with the reordering of layers in theproject_to_layersoutput.
44-48: New layer added with assertionsA fourth layer (l4) has been added, created from
res[3]. It's asserted to be a Labels type with the name "test" and is set to not be visible. This addition expands the test coverage to include all layers returned byproject_to_layers.
34-48: Summary of changes in test_project_to_layers_analysis functionThe modifications to this test function reflect significant changes in the
project_to_layersfunction's output:
- Layer ordering has been updated.
- Color information (colormap) is now being checked for image layers.
- A new layer (l4) has been added to the test, expanding coverage.
These changes align well with the PR objective of incorporating channel colors when adding layers to napari. The test now provides more comprehensive coverage of the
project_to_layersfunction's output.package/tests/conftest.py (2)
28-28: LGTM: Import statement updated correctly.The import statement has been updated to include
ChannelInfoalong withImage. This change is consistent with the modifications in thestack_imagefixture and supports the enhanced functionality for channel-specific metadata.
Line range hint
1-97: Summary: Changes align with PR objectives and enhance testing capabilities.The modifications to
package/tests/conftest.pysuccessfully implement the PR objective of incorporating channel colors when adding layers to napari. The changes are focused and improve the testing capabilities for color-related functionality. The updatedstack_imagefixture now includes channel-specific metadata, which will allow for more comprehensive testing of color handling in napari layers.No major issues were found during the review. The only suggestion was a minor improvement for consistency in color map representation. Overall, these changes contribute positively to the project's testing framework and support the enhanced functionality described in the PR objectives.
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
package/PartSeg/common_gui/advanced_tabs.py (1)
278-282: LGTM! Consider a minor readability improvement.The changes effectively implement the PR objective by including color information for each channel. This enhancement provides more detailed and useful information to the user.
For improved readability, consider using an f-string with line breaks:
text = ", ".join( f"{name}: {color}" for name, color in zip(self.settings.image.channel_names, self.settings.image.get_colors()) ) self.channel_info.setText(f"Channels with colors:\n{text}")This change would display the channel information on a new line, potentially making it easier to read, especially when there are many channels.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- package/PartSeg/common_gui/advanced_tabs.py (1 hunks)
- package/PartSegCore/napari_plugins/loader.py (2 hunks)
🔇 Additional comments (3)
package/PartSegCore/napari_plugins/loader.py (3)
2-2: LGTM: New imports are appropriate for the changes.The new imports for version parsing and the
Imagetype are relevant to the implemented changes. They support version-based conditional logic and improve type annotations.Also applies to: 5-5, 10-10
69-69: LGTM: Proper integration of color handling in_image_to_layers.The addition of
**add_color(project_info.image, i)to the layer properties is a good way to incorporate the new color handling functionality. It ensures that color information is added when supported without affecting older versions.
Line range hint
1-150: LGTM: Overall structure and consistency maintained.The file maintains a logical structure with the new additions. The use of type hints is consistent, and the changes are well-integrated without disrupting existing functionality. The focus on color handling and version compatibility is clear and appropriate.
| @typing.overload | ||
| def adjust_color(color: str) -> str: ... | ||
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| @typing.overload | ||
| def adjust_color(color: typing.List[int]) -> typing.List[int]: ... | ||
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| def adjust_color(color: typing.Union[str, typing.List[int]]) -> typing.Union[str, typing.List[int]]: | ||
| # as napari ignore alpha channel in color, and adding it to | ||
| # color cause that napari fails to detect that such colormap is already present | ||
| # in this function I remove alpha channel if it is present | ||
| if isinstance(color, str) and color.startswith("#"): | ||
| if len(color) == 9: | ||
| # case when color is in format #RRGGBBAA | ||
| return color[:7] | ||
| if len(color) == 5: | ||
| # case when color is in format #RGBA | ||
| return color[:4] | ||
| return color |
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🛠️ Refactor suggestion
Enhance adjust_color function for clarity and robustness.
The adjust_color function is a good addition, but consider the following improvements:
- Rename the function to better reflect its purpose, e.g.,
truncate_color_alpha. - Add input validation for the list input type to ensure it contains valid color values.
- Consider handling 8-character hex codes (#RRGGBBAA) in addition to 9-character ones.
- Add a docstring to explain the function's purpose and behavior.
Here's a suggested implementation:
@typing.overload
def truncate_color_alpha(color: str) -> str: ...
@typing.overload
def truncate_color_alpha(color: typing.List[int]) -> typing.List[int]: ...
def truncate_color_alpha(color: typing.Union[str, typing.List[int]]) -> typing.Union[str, typing.List[int]]:
"""
Truncate the alpha channel from color representations.
For hex strings, removes the alpha channel if present.
For integer lists, ensures the list has 3 elements (RGB).
:param color: A string (hex color) or list of integers (RGB/RGBA values).
:return: The color with the alpha channel removed, if present.
:raises ValueError: If the input is invalid.
"""
if isinstance(color, str):
if color.startswith("#"):
if len(color) in (9, 8): # #RRGGBBAA or #RRGGBB
return color[:7]
if len(color) == 5: # #RGBA
return color[:4]
if len(color) in (7, 4): # #RRGGBB or #RGB
return color
raise ValueError(f"Invalid hex color format: {color}")
elif isinstance(color, list):
if len(color) == 4:
return color[:3]
if len(color) == 3:
return color
raise ValueError(f"Invalid color list length: {len(color)}")
raise TypeError(f"Unsupported color type: {type(color)}")This implementation adds input validation, handles various hex color formats, and includes a docstring for clarity.
| if parse_version(version("napari")) >= parse_version("0.4.19a1"): | ||
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| def add_color(image: Image, idx: int) -> dict: | ||
| return { | ||
| "colormap": adjust_color(image.get_colors()[idx]), | ||
| } | ||
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| else: | ||
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| def add_color(image: Image, idx: int) -> dict: # noqa: ARG001 | ||
| # Do nothing, as napari is not able to pass hex color to image | ||
| return {} |
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🛠️ Refactor suggestion
Improve version-based add_color implementation.
The conditional definition of add_color is a good approach for maintaining compatibility. However, consider the following improvements:
- Add a comment explaining why older versions return an empty dict.
- Consider raising a warning for older versions to inform users about the lack of color support.
- Use a constant for the version number to improve maintainability.
Here's a suggested implementation:
NAPARI_COLOR_SUPPORT_VERSION = "0.4.19a1"
if parse_version(version("napari")) >= parse_version(NAPARI_COLOR_SUPPORT_VERSION):
def add_color(image: Image, idx: int) -> dict:
return {
"colormap": truncate_color_alpha(image.get_colors()[idx]),
}
else:
import warnings
def add_color(image: Image, idx: int) -> dict:
warnings.warn(
f"Napari version < {NAPARI_COLOR_SUPPORT_VERSION} does not support custom colormaps. "
"Upgrade napari for full color support.",
UserWarning
)
return {}This implementation adds a warning for older versions and uses a constant for the version number.
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In this case, I do not want to emit warning, just not support.
There was a problem hiding this comment.
@Czaki, understood. I'll remember that you prefer not to emit warnings in such cases and just not support the feature.
(_/)
(._.)
('')('')
✏️ Learnings added
Learnt from: Czaki
PR: 4DNucleome/PartSeg#1200
File: package/PartSegCore/napari_plugins/loader.py:35-46
Timestamp: 2024-09-27T10:16:22.220Z
Learning: When handling version compatibility, prefer to avoid emitting warnings for unsupported features in older versions and simply not support the feature without warnings.
Note: Learnings are effective only in the context of similar code segments. To apply general coding guidelines, please configure review instructions. You can manage existing learnings in the app.
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Use color associated with the channel in napari reader plugin.
Summary by Sourcery
Add functionality to use channel-associated colors in napari layers by adjusting hex color codes. Enhance the
_hex_to_rgbfunction to support additional hex code formats and update tests accordingly.New Features:
Enhancements:
_hex_to_rgbfunction to handle 4 and 8 character hex codes, ensuring proper conversion and validation.Tests:
_hex_to_rgbfunction to include cases for 4 and 8 character hex codes, ensuring correct functionality and error handling.Summary by CodeRabbit
New Features
adjust_colorfunction to modify color strings based on length, enhancing color handling._hex_to_rgbfunction to support additional hexadecimal color formats.Bug Fixes
Tests
_hex_to_rgbto validate behavior with hex codes including alpha channels.