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 1 commit into from
Sep 19, 2024
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fix: Fix reading channel names from single channel czi files #1194

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8 changes: 5 additions & 3 deletions package/PartSegImage/image_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -358,9 +358,11 @@
scale_info.get("Y", self.default_spacing[1]),
scale_info.get("X", self.default_spacing[2]),
)
self.channel_names = [
x["Name"] for x in metadata["ImageDocument"]["Metadata"]["DisplaySetting"]["Channels"]["Channel"]
]
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 = []

self.channel_names = [x["Name"] for x in channel_meta]
# TODO add mask reading
if isinstance(image_path, BytesIO):
image_path = ""
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