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Add guard against negative z-slice in signal analysis program #426

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merged 1 commit into from
Feb 19, 2025
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Add guard against negative z-slice in signal analysis program #426

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ and this project will adhere to [Semantic Versioning](https://semver.org/spec/v2

### Fixed
* Field of view name matching for cross-channel signal analysis. See [Issue 424](https://github.com/gerlichlab/looptrace/issues/424).
* Safety against negative z-slice in cross-channel signal analysis

## [v0.12.0] - 2025-02-18

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27 changes: 15 additions & 12 deletions bin/cli/run_signal_analysis.py
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Expand Up @@ -200,18 +200,21 @@ def workflow(
except ValueError as e:
logging.error(f"Can't compute shifted center for original center {pt0}: {e}")
else:
# TODO: need to be robust to bounding box with negative coordinate(s)
# TODO: https://github.com/gerlichlab/gertils/issues/34
for stats in compute_pixel_statistics(
img=img,
pt=dc_pt,
channels=spec.channels,
diameter=spec.roi_diameter,
channel_column=SIGNAL_CHANNEL_COLUMN,
):
ch: int = stats[SIGNAL_CHANNEL_COLUMN]
# Add the original record and signal stats to the growing collection for this channel.
by_raw_channel[ch].append({**r.to_dict(), **stats})
if dc_pt.z < 0:
logging.error(f"Can't extract signal for negative z-coordinate: {dc_pt.z}")
else:
# TODO: need to be robust to bounding box with negative coordinate(s)
# TODO: https://github.com/gerlichlab/gertils/issues/34
for stats in compute_pixel_statistics(
img=img,
pt=dc_pt,
channels=spec.channels,
diameter=spec.roi_diameter,
channel_column=SIGNAL_CHANNEL_COLUMN,
):
ch: int = stats[SIGNAL_CHANNEL_COLUMN]
# Add the original record and signal stats to the growing collection for this channel.
by_raw_channel[ch].append({**r.to_dict(), **stats})

# Write the output file for this ROI type, across all FOVs.
for raw_channel, records in sorted(by_raw_channel.items(), key=itemgetter(0)):
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