Service to run imod batchruntomo#258
Merged
Merged
Conversation
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #258 +/- ##
==========================================
- Coverage 83.11% 83.08% -0.03%
==========================================
Files 70 72 +2
Lines 9065 9265 +200
Branches 1245 1264 +19
==========================================
+ Hits 7534 7698 +164
- Misses 1048 1075 +27
- Partials 483 492 +9 🚀 New features to boost your workflow:
|
This was referenced Jun 18, 2026
tieneupin
reviewed
Jun 22, 2026
| ) | ||
| # Let this run, and check later if the output file exists | ||
| subprocess.run(["tif2mrc", str(tifftomo), stack_file]) | ||
| subprocess.run(["tif2mrc", str(tifftomo), stack_file], capture_output=True) |
Contributor
There was a problem hiding this comment.
You're capturing the output, but it doesn't look there are any logs in place to note the output.
tieneupin
reviewed
Jun 22, 2026
| adoc_file = Path(tomo_params.stack_file).with_suffix(".adoc") | ||
| with open(adoc_file, "w") as adoc: | ||
| # Commands for copytomocoms | ||
| adoc.write(f"setupset.datasetDirectory={adoc_file.parent}\n") |
Contributor
There was a problem hiding this comment.
This file writing logic could be implemented by running adoc.write(...) in a for loop over the lines, with if blocks to handle the optional sections. That way, you wouldn't have to write adoc.write(...) repeatedly for each line.
tieneupin
approved these changes
Jun 22, 2026
tieneupin
left a comment
tieneupin
left a comment
Contributor
There was a problem hiding this comment.
Looks fine overall, with some suggestions for optimisation.
stephen-riggs
added a commit
to DiamondLightSource/python-murfey
that referenced
this pull request
Jun 22, 2026
This moves the SXT processing into a rabbitmq message, and adds support for more recipes. Recipes in the machine config are detected and all of these are used to send processing if the collection type is SXT. This will allow for using imod and aretomo. Links to DiamondLightSource/cryoem-services#258
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
For SXT imod batchruntomo is desired as an alternative to aretomo. This makes a service which can run batchruntomo with a limited subset of options.
In particular, patch or bead and wbp or sirt, with two recipes to support this.
Some of the aretomo parts of this repo are renamed.
Tested through the dev setup and Imod runs successfully, but currently only with version 4.9.2
To do in future PR:
Links to DiamondLightSource/python-murfey#830 and #273