Fix legacy mpp factor + multiple dcm files #270
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Claude finished @blanca-pablos's task —— View job Code Review: PR #270 - Fix legacy mpp factor + multiple dcm filesSummaryThis PR addresses two important issues in WSI (Whole Slide Image) processing:
Overall, this is a solid medical imaging fix addressing real-world compatibility issues. However, there are 5 linting issues that must be fixed and missing test coverage for the new functionality. 🔴 BLOCKING ISSUES (Must Fix)1. Linting Failures (5 errors)The following linting issues were found: File: Fix: # Current (line 351):
for file_path, r, c in files_with_dims:
# Should be:
for file_path, _r, _c in files_with_dims:File: Fix for line 67: # Change from instance method to static method:
@staticmethod
def _get_mpp_correction_factor(props: dict[str, Any]) -> float:Fix for line 77: # Change:
_LEGACY_MPP_FACTOR = 1 / 10
# To (define at module level as constant):
LEGACY_MPP_FACTOR = 1 / 10
# Or inline it:
legacy_mpp_factor = 1 / 10Verify fixes: uv run ruff check --fix src/aignostics/application/_service.py src/aignostics/wsi/_openslide_handler.py
make lint2. Missing Test Coverage (CRITICAL for Medical Device Software)The new functionality has zero test coverage:
Required test cases:
Test example: @pytest.mark.unit
def test_filter_dicom_series_files_single_file(tmp_path):
"""Test that single DICOM files are not filtered."""
# Create test DICOM file
ds = pydicom.Dataset()
ds.SeriesInstanceUID = "1.2.3.4.5"
ds.Rows = 1024
ds.Columns = 1024
dcm_file = tmp_path / "test.dcm"
ds.save_as(dcm_file)
excluded = Service._filter_dicom_series_files(tmp_path)
assert len(excluded) == 0
@pytest.mark.unit
def test_mpp_correction_factor_legacy_libvips():
"""Test MPP correction for legacy libvips <8.8.3."""
props = {
"tiff.ImageDescription": """<vips libVips-version="8.7.0" />"""
}
handler = OpenSlideHandler(test_file_path)
factor = handler._get_mpp_correction_factor(props)
assert factor == 0.1 # Legacy correctionWhy this is critical:
🟡 SUGGESTIONS (Non-Blocking)3. Commit Message ConventionCurrent commits: Issue: First commit doesn't follow conventional commits format. Should be: Why it matters: Conventional commits enable automatic changelog generation. 4. PR Description MissingIssue: No PR description provided. For a medical device SDK, this is concerning. Should include:
Example: ## Problem
1. TIFF files exported with libvips <8.8.3 have incorrect MPP values (10x off)
2. Multi-file DICOM series cause duplicate processing of the same image data
## Solution
1. Detect libvips version from TIFF metadata and apply 0.1 correction factor for buggy versions
2. Filter DICOM files by SeriesInstanceUID, keeping only highest resolution file per series
## Testing
- Manual testing with legacy TIFF files from libvips 8.7.0
- Manual testing with multi-file DICOM series
## References
- libvips bug: https://github.com/libvips/libvips/issues/14215. Documentation Updates NeededFile: Should document:
File: Should document:
6. Error Handling in
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❌ 1 Tests Failed:
View the full list of 1 ❄️ flaky test(s)
To view more test analytics, go to the Test Analytics Dashboard |
* Add mpp correction factor for tiffs written using older versions of vips containing a bug that wrote resolution as px / mm instead of cm. * Select only highest resolution file from DICOM series in multiple files.
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Claude finished @blanca-pablos's task —— View job PR Review: Fix legacy mpp factor + multiple dcm filesComprehensive review of PR #270 for medical device SDK completed. Todo List:
SummaryThis PR addresses two important medical imaging compatibility issues:
Overall Assessment: Good fix for real-world issues, but has 1 CRITICAL bug causing test failure, missing test coverage (regulatory requirement), and several smaller issues. 🔴 BLOCKING ISSUES (Must Fix Before Merge)1. CRITICAL BUG: MPP Correction Applied to DICOM Files ❌Location: Issue: The MPP correction factor is being incorrectly applied to DICOM files, breaking the test and producing wrong MPP values (10x error in medical measurements!). Root Cause: Inconsistent logic between line 164 and line 212.
Evidence:
Fix: # Line 212 should be:
mpp_correction_factor = self._get_mpp_correction_factor(props) if "tiff.XResolution" in props else 1.0Why Critical: In computational pathology, incorrect MPP can lead to:
Verify Fix: uv run pytest tests/aignostics/wsi/cli_test.py::test_inspect_openslide_dicom -v2. Missing Test Coverage (Regulatory Requirement) ❌No tests exist for the new functionality: A.
B.
Required Test Cases: For DICOM filtering ( @pytest.mark.unit
def test_filter_dicom_series_single_file(tmp_path):
"""Single DICOM file should not be filtered."""
@pytest.mark.unit
def test_filter_dicom_series_multiple_files_same_series(tmp_path):
"""Keep highest resolution file from multi-file series."""
@pytest.mark.unit
def test_filter_dicom_series_multiple_series(tmp_path):
"""Filter each series independently."""
@pytest.mark.unit
def test_filter_dicom_series_invalid_files(tmp_path):
"""Files that fail to read should not be excluded."""For MPP correction ( @pytest.mark.unit
def test_mpp_correction_legacy_libvips():
"""libvips <8.8.3 should apply 0.1 correction."""
props = {"tiff.ImageDescription": '<vips libVips-version="8.7.0" />'}
# Assert correction = 0.1
@pytest.mark.unit
def test_mpp_correction_modern_libvips():
"""libvips ≥8.8.3 should apply 1.0 correction."""
props = {"tiff.ImageDescription": '<vips libVips-version="8.8.3" />'}
# Assert correction = 1.0
@pytest.mark.unit
def test_mpp_correction_no_version():
"""Missing version should default to 0.1 (legacy)."""
props = {"tiff.ImageDescription": '<vips />'}
# Assert correction = 0.1
@pytest.mark.unit
def test_mpp_correction_no_tiff_metadata():
"""Non-TIFF files should use 1.0 correction."""
props = {} # No tiff.ImageDescription
# Assert correction = 1.0Why Critical:
Action Required: Add comprehensive unit tests before merge. 3. Quality Gate Failures ❌SonarQube Report:
Action: Address SonarQube findings and add tests to meet 80% coverage threshold. 🟡 IMPORTANT ISSUES (Should Fix)4. Commit Message Convention ViolationCurrent commits: Issues:
Should be: Why it matters: Conventional commits enable automatic changelog generation per Reference: See root 5. Missing PR DescriptionIssue: No PR description provided. For medical device software, this is concerning. Should include:
Example: ## Problem
1. TIFF files exported with libvips <8.8.3 have incorrect MPP values (10x off)
2. Multi-file DICOM series cause duplicate processing of same image data
## Solution
1. Detect libvips version from TIFF metadata, apply 0.1 correction for buggy versions
2. Filter DICOM files by SeriesInstanceUID, keeping highest resolution per series
## Testing
- ✅ Linting passes
- ❌ Need unit tests for new functionality (see review)
- ✅ Manual testing with legacy TIFF files
- ✅ Manual testing with multi-file DICOM series
## References
- libvips bug: https://github.com/libvips/libvips/issues/1421
- DICOM SeriesInstanceUID: DICOM PS3.3 Section C.7.3.16. Documentation Updates NeededFiles to update: A.
B.
Why: The root 🟢 POSITIVE ASPECTS
🏥 MEDICAL DEVICE CONSIDERATIONSSeverity of IssuesMPP accuracy is critical in computational pathology:
The bug at line 212 would cause:
Regulatory ContextPer repository guidelines (
📋 ACTION ITEMSMust Fix Before Merge:
Should Fix (Recommended):
🔍 ARCHITECTURAL REVIEW✅ Modulith principles: Changes within appropriate module boundaries 🎯 VERIFICATION COMMANDSAfter fixing the bug and adding tests: # Fix linting if needed
make lint
# Run specific failing test
uv run pytest tests/aignostics/wsi/cli_test.py::test_inspect_openslide_dicom -v
# Run all WSI tests
uv run pytest tests/aignostics/wsi/ -v
# Run all application tests
uv run pytest tests/aignostics/application/ -v
# Check coverage
uv run pytest --cov=aignostics.application --cov=aignostics.wsi \
--cov-report=term-missing tests/aignostics/application tests/aignostics/wsi
# Full test suite
make test📊 REVIEW SUMMARY
🏁 FINAL VERDICTCannot merge until:
This is excellent work addressing real-world medical imaging issues, but medical device software requires comprehensive testing. The line 212 bug is critical and would cause 10x measurement errors in DICOM files. Recommendation: Fix the bug first, then add tests, then we can discuss documentation improvements in a follow-up. |
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