fix: Fix error when image changed during segmentation #1218
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Reviewer's Guide by SourceryThis pull request addresses two issues (PARTSEG-WK and PARTSEG-WN) related to error handling during image segmentation and improves logging format across multiple files. The changes primarily focus on updating the logging format, adding a check for image changes during segmentation, and refactoring some code for better error handling and consistency. Sequence diagram for image segmentation error handlingsequenceDiagram
participant User
participant SegmentationThread
participant Logger
User->>SegmentationThread: Start segmentation
SegmentationThread->>Logger: Log error if no image
SegmentationThread->>SegmentationThread: Check if image changed
alt Image changed
SegmentationThread->>Logger: Log image change
SegmentationThread->>User: Return without segmentation
else Image not changed
SegmentationThread->>User: Emit execution_done
end
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WalkthroughThe pull request introduces several modifications across three files in the PartSeg package. Key changes include updates to logging formats for clarity, the addition of a new parameter in the 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: all looks good
- 🟢 Security: all looks good
- 🟢 Testing: all looks good
- 🟢 Complexity: all looks good
- 🟢 Documentation: all looks good
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
package/PartSeg/common_backend/segmentation_thread.py (1)
66-69: Improved handling of image changes during calculation.The addition of this check effectively addresses the PR objective by preventing the emission of potentially incorrect results when the image changes during segmentation. This enhances the thread's robustness and prevents race conditions.
Consider adding a log message or emitting a signal to indicate that the calculation was aborted due to an image change. This would improve debugging and provide better feedback to the calling code. For example:
if self._image is not None: logging.info("Image changed during calculation. Aborting.") self.info_signal.emit("Calculation aborted: Image changed") returnpackage/PartSeg/_roi_analysis/export_batch.py (1)
Line range hint
409-521: Improved flexibility with newzenodo_urlparameter inexport_to_zenodofunctionThe addition of the
zenodo_urlparameter enhances the function's flexibility by allowing users to specify different Zenodo API endpoints (e.g., production vs. sandbox) without modifying the code. This change is backwards-compatible and improves the function's reusability.The error message has been updated to use the dynamic
zenodo_url, which provides more accurate information to the user.Consider improving the error message formatting for better readability:
- f" You could create token at " - f"{zenodo_url.replace('api/deposit/depositions', 'account/settings/applications/')}" - f" {initial_request.status_code} {initial_request.json()['message']}" + f" You can create a token at " + f"{zenodo_url.replace('api/deposit/depositions', 'account/settings/applications/')}." + f" Status code: {initial_request.status_code}. Message: {initial_request.json()['message']}"
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📒 Files selected for processing (3)
- package/PartSeg/_roi_analysis/export_batch.py (1 hunks)
- package/PartSeg/common_backend/segmentation_thread.py (2 hunks)
- package/PartSeg/common_gui/advanced_tabs.py (1 hunks)
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🔇 Additional comments (6)
package/PartSeg/common_backend/segmentation_thread.py (2)
52-54: Improved logging format and added stack trace information.The changes to the logging statement are beneficial:
- Using positional placeholders (
%s) instead of named ones simplifies the logging format.- Adding
stack_info=Trueprovides valuable stack trace information for debugging.These improvements align with Python logging best practices and enhance error traceability.
Line range hint
1-180: Summary: Effective implementation addressing PR objectivesThe changes in this file successfully address the PR objective of fixing errors when the image changes during segmentation. The modifications improve error handling, logging, and thread robustness. The code quality is good, and the changes are well-implemented.
Key improvements:
- Enhanced logging with better formatting and additional stack trace information.
- Added a check to prevent emitting results when the image changes during calculation.
These changes contribute to a more stable and reliable segmentation process in the PartSeg application.
package/PartSeg/common_gui/advanced_tabs.py (2)
69-69: Improved logging format for better readability.The logging statements have been updated to use a simpler string formatting method. This change enhances code readability and maintainability while adhering to Python's recommended logging practices.
Also applies to: 71-71, 74-74, 77-77
84-86: Enhanced robustness with conditional check forreload_list.A conditional check has been added to ensure the
reload_listattribute exists before iterating over it. This defensive programming practice prevents potential AttributeErrors, improving the overall robustness of the code.package/PartSeg/_roi_analysis/export_batch.py (2)
395-395: Improved logging format insleep_with_ratefunctionThe change from
%(sleep_time)to%sin the logging statement simplifies the code and aligns it with Python's standard logging practices. This modification enhances readability without affecting functionality.
Line range hint
1-521: Summary of changes inexport_batch.pyThe modifications in this file focus on two main areas:
- Improving the logging format in the
sleep_with_ratefunction for better readability.- Enhancing the flexibility of the
export_to_zenodofunction by adding a configurable Zenodo API endpoint.These changes improve code quality and maintainability without introducing new risks or breaking existing functionality. While they don't directly address the PR's objective of fixing errors related to image changes during segmentation, they contribute to the overall improvement of the codebase.
To ensure these changes don't have unintended consequences, please run the existing test suite, particularly any tests related to Zenodo exports and rate limiting functionality.
Czaki
changed the title
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #1218 +/- ##
===========================================
- Coverage 93.15% 93.13% -0.03%
===========================================
Files 210 210
Lines 33169 33172 +3
===========================================
- Hits 30898 30894 -4
- Misses 2271 2278 +7 ☔ View full report in Codecov by Sentry. |
fix PARTSEG-WK
fix PARTSEG-WN
Summary by Sourcery
Fix error handling in the segmentation process by checking for image changes during execution and correct logging format strings across the codebase.
Bug Fixes:
Summary by CodeRabbit
New Features
Bug Fixes
Documentation
Refactor