fix: Workaround for lack of zsd support in czifile #1142
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WalkthroughRecent updates to the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant CziImageReader
participant image_file
User->>CziImageReader: read(image_path, mask_path, ext)
CziImageReader->>CziImageReader: Determine max_workers
CziImageReader->>image_file: asarray(max_workers)
image_file->>CziImageReader: Return image data
CziImageReader->>User: Return Image
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Actionable comments posted: 2
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Files selected for processing (1)
- package/PartSegImage/image_reader.py (3 hunks)
Additional comments not posted (6)
package/PartSegImage/image_reader.py (6)
6-6: LGTM! New imports are appropriate.The new imports are necessary for the new functionalities introduced related to ZSTD decoding and version checking.
Also applies to: 11-11, 17-17
28-37: LGTM! ClassZSTD1Headeris well-defined.The class represents the header structure for ZSTD1 compression and references an external source for clarity.
39-57: LGTM! Functionparse_zstd1_headeris correctly implemented.The function parses the header for ZSTD1 compression using data and size parameters and references an external source for accuracy.
60-61: Potential maintenance issue with_get_dtype.The function relies on specific assumptions about the calling context, which could lead to maintenance challenges. Ensure that the context in which this function is used is well-documented and consistent.
81-83: LGTM! Dictionary modifications are appropriate.The
DECOMPRESSdictionary is correctly updated to handle ZSTD0 and ZSTD1 decoding.
335-335: LGTM! Addition ofmax_workersparameter is beneficial.The
max_workersparameter potentially improves performance by enabling parallel processing.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #1142 +/- ##
===========================================
+ Coverage 93.01% 93.02% +0.01%
===========================================
Files 207 207
Lines 32658 32700 +42
===========================================
+ Hits 30376 30420 +44
+ Misses 2282 2280 -2 ☔ View full report in Codecov by Sentry. |
Czaki
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Actionable comments posted: 1
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Files selected for processing (2)
- package/PartSegImage/image_reader.py (3 hunks)
- package/tests/test_PartSegImage/test_image_reader.py (1 hunks)
Additional comments not posted (7)
package/tests/test_PartSegImage/test_image_reader.py (1)
38-45: LGTM!The test function
test_czi_file_read_compressedis well-written and effectively tests the decompression functionality of CZI files.package/PartSegImage/image_reader.py (6)
1-17: LGTM!The new imports are necessary and correctly imported.
28-37: LGTM!The class
ZSTD1Headeris well-defined and includes appropriate attributes with a clear docstring.
39-57: LGTM!The function
parse_zstd1_headeris well-written and includes a clear docstring. The logic for parsing the header is correct.
60-61: LGTM!The function
_get_dtypecorrectly determines the data type usinginspect.
343-343: LGTM!The addition of the
max_workersparameter in theimage_file.asarray()call potentially improves performance by leveraging parallel processing.
81-86: Replacenp.fromstringwithnp.frombuffer.The function decodes ZSTD0 data correctly, but
np.fromstringis deprecated.- return np.fromstring(imagecodecs.zstd_decode(data), dtype) + return np.frombuffer(imagecodecs.zstd_decode(data), dtype)Likely invalid or redundant comment.
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Files selected for processing (2)
- package/PartSegImage/image_reader.py (4 hunks)
- package/tests/test_PartSegImage/test_image_reader.py (2 hunks)
Files skipped from review as they are similar to previous changes (1)
- package/PartSegImage/image_reader.py
Additional comments not posted (1)
package/tests/test_PartSegImage/test_image_reader.py (1)
6-6: Review of New Imports, Fixtures, and Test Functions
New Imports:
- The imports on lines 6 and 12 (
versionfromimportlib.metadataandparse_versionfrompackaging.version) are correctly added and relevant to the new features being tested, particularly the version checking forczifile.New Fixture
_set_max_workers_czi:
- This fixture correctly sets the
CZI_MAX_WORKERSto 1 usingmonkeypatch. This is a good practice to ensure that the tests are not affected by parallel execution environments which might introduce non-determinism.New Test
test_czi_file_read_compressed:
- The test uses version checking to skip tests for versions of
czifilebelow2019.7.2, which is a good practice to ensure backward compatibility.- The use of
pytest.mark.parametrizeto test multiple file types (test_czi_zstd0.czi,test_czi_zstd1.czi,test_czi_zstd1_hilo.czi) is excellent for ensuring that all relevant cases are covered.- Assertions in the test are comprehensive, checking for non-zero channel data, correct number of channels and layers, file path correctness, and spatial dimensions.
Assertions:
- The assertions on lines 39 and 67 are crucial for verifying the integrity and correctness of the image data loaded from different types of CZI files.
These changes are well-implemented and follow good testing practices. No further action is required unless additional test scenarios are considered necessary.
Also applies to: 12-12, 18-22, 39-39, 47-61, 67-67
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Files selected for processing (1)
- package/PartSegImage/image_reader.py (4 hunks)
Files skipped from review as they are similar to previous changes (1)
- package/PartSegImage/image_reader.py
Workaround for bug reported cgohlke/czifile#10
Summary by CodeRabbit
New Features
max_workersparameter for improved image processing performance.Tests
fix PARTSEG-V0