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Convert xrm images to tiffs#837

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stephen-riggs merged 11 commits into
mainfrom
sxt-metadata
Jul 3, 2026
Merged

Convert xrm images to tiffs#837
stephen-riggs merged 11 commits into
mainfrom
sxt-metadata

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@stephen-riggs

@stephen-riggs stephen-riggs commented Jul 3, 2026

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This adds functionality to read xrm images and request these are converted to tiffs.

Currently this identifies atlas and roi images by finding out if they are montages, and splits them based on pixel size. Better methods may be possible but this should work for now.

Rather than doing the xrm to tiff conversion here it puts a message onto rabbitmq. See DiamondLightSource/cryoem-services#278

Also contains a stub for registering rois in the database.

@stephen-riggs stephen-riggs requested a review from tieneupin July 3, 2026 10:43
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codecov Bot commented Jul 3, 2026

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Codecov Report

❌ Patch coverage is 80.68182% with 17 lines in your changes missing coverage. Please review.
✅ Project coverage is 53.23%. Comparing base (8aa4d35) to head (c12f36f).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #837      +/-   ##
==========================================
+ Coverage   53.10%   53.23%   +0.12%     
==========================================
  Files         100      101       +1     
  Lines       10855    11106     +251     
  Branches     1439     1489      +50     
==========================================
+ Hits         5765     5912     +147     
- Misses       4783     4873      +90     
- Partials      307      321      +14     
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  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

Comment thread src/murfey/client/contexts/sxt.py
Comment thread src/murfey/client/contexts/sxt.py
Comment thread src/murfey/client/contexts/sxt.py

@tieneupin tieneupin left a comment

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Some comments and suggestions, but the code looks good otherwise!

Comment thread src/murfey/client/contexts/sxt.py Outdated
stephen-riggs added a commit to DiamondLightSource/cryoem-services that referenced this pull request Jul 3, 2026
Add an images plugin which runs txrm2tiff conversion of xrms to annotated tiffs, then makes a jpg thumbnail for display

Links to DiamondLightSource/python-murfey#837
@stephen-riggs stephen-riggs merged commit 975c2f3 into main Jul 3, 2026
17 checks passed
@stephen-riggs stephen-riggs deleted the sxt-metadata branch July 3, 2026 16:26
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2 participants