8000 fix: Fix reading channel names from single channel czi files by Czaki · Pull Request #1194 · 4DNucleome/PartSeg · GitHub
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fix: Fix reading channel names from single channel czi files #1194

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Merged
merged 1 commit into from
Sep 19, 2024
Merged

fix: Fix reading channel names from single channel czi files #1194

merged 1 commit into from
Sep 19, 2024

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Czaki
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@Czaki Czaki commented Sep 19, 2024 •
edited by coderabbitai bot
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Summary by Sourcery

Fix the issue with reading channel names from single channel CZI files by ensuring the channel metadata is correctly processed when it is a dictionary.

Bug Fixes:

  • Fix reading channel names from single channel CZI files by handling the case where channel metadata is a dictionary instead of a list.

Summary by CodeRabbit

  • New Features

    • Improved handling of channel metadata when reading image files, ensuring consistent population of channel names for both single and multiple channels.

  • Bug Fixes

    • Resolved issues related to channel metadata processing that could occur with single-channel images.

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sourcery-ai bot commented Sep 19, 2024 •
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Reviewer's Guide by Sourcery

This pull request fixes an issue with reading channel names from single-channel CZI files. The main change is in the handling of metadata for channel information, ensuring that both single-channel and multi-channel CZI files are processed correctly.

File-Level Changes

Change Details Files
Modify channel metadata handling to support both single and multi-channel CZI files
  • Extract channel metadata from the CZI file metadata structure
  • Check if the channel metadata is a dictionary (single channel) or a list (multiple channels)
  • Convert single-channel metadata to a list format for consistent processing
  • Update channel names extraction to work with the new metadata format
 package/PartSegImage/image_reader.py
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coderabbitai bot commented Sep 19, 2024 •
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Walkthrough

The changes made to the read method in the PartSegImage/image_reader.py file improve how channel metadata is handled when reading image files. The previous implementation assumed that channel metadata was always a list, which could cause problems for single-channel images. The new logic checks if the channel_meta is a dictionary, converting it into a list if necessary. This ensures consistent population of the self.channel_names attribute, regardless of the number of channels in the image.

Changes

File Path Change Summary
package/PartSegImage/image_reader.py Enhanced channel metadata handling in the read method to support both single and multiple channels.

Poem

In the meadow where images play,
A rabbit hops with joy today.
Channels now dance in a list,
No more single ones to miss!
With metadata bright and clear,
Reading images brings us cheer! 🐇✨

Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 0b0b0f9 and 3d626ef.

Files selected for processing (1)
  • package/PartSegImage/image_reader.py (1 hunks)
Additional comments not posted (1)
package/PartSegImage/image_reader.py (1)

361-365: LGTM!

The changes improve the robustness of channel metadata handling for single channel CZI files. By consistently ensuring channel_meta is a list, it allows self.channel_names to be populated correctly regardless of the number of channels present.

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Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

sourcery-ai[bot]
sourcery-ai bot reviewed Sep 19, 2024
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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: 1 issue found
  • 🟢 Security: all looks good
  • 🟢 Testing: all looks good
  • 🟢 Complexity: all looks good
  • 🟢 Documentation: all looks good
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package/PartSegImage/image_reader.py
Comment on lines +361 to +364
channel_meta = metadata["ImageDocument"]["Metadata"]["DisplaySetting"]["Channels"]["Channel"]
if isinstance(channel_meta, dict):
# single channel saved in czifile
channel_meta = [channel_meta]
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suggestion: Consider adding error handling for unexpected metadata structure

The current implementation assumes the presence and structure of the 'Channel' key. Consider wrapping this block in a try-except to handle potential KeyError or TypeError exceptions, ensuring robustness against unexpected metadata formats.

try:
    channel_meta = metadata["ImageDocument"]["Metadata"]["DisplaySetting"]["Channels"]["Channel"]
    if isinstance(channel_meta, dict):
        channel_meta = [channel_meta]
except (KeyError, TypeError):
    channel_meta = []

@Czaki Czaki added the skip check PR title skip spellcheking PR title label Sep 19, 2024
@Czaki Czaki added this to the 0.15.4 milestone Sep 19, 2024
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codecov bot commented Sep 19, 2024 •
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Codecov Report

Attention: Patch coverage is 75.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 93.05%. Comparing base (0b0b0f9) to head (3d626ef).
Report is 36 commits behind head on develop.

Files with missing lines Patch % Lines
package/PartSegImage/image_reader.py 75.00% 1 Missing ⚠️
Additional details and impacted files 
@@             Coverage Diff             @@
##           develop    #1194      +/-   ##
===========================================
- Coverage    93.06%   93.05%   -0.01%     
===========================================
  Files          209      209              
  Lines        32906    32909       +3     
===========================================
+ Hits         30623    30625       +2     
- Misses        2283     2284       +1

☔ View full report in Codecov by Sentry.
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@Czaki Czaki merged commit a7ab81f into develop Sep 19, 2024
56 of 60 checks passed
@Czaki Czaki deleted the fix_czi_channel branch September 19, 2024 13:47
@coderabbitai coderabbitai bot mentioned this pull request Sep 23, 2024
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