DiamondLightSource/httomo

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High-throughput tomography pipeline

Stars: 10
Forks: 5
Open beginner issues: 0
Indexed issues: 116
Avg merge: 5d 17h
Merged PRs (30d): 1

Dominant language: Python
License: No license data
Last GitHub push: Aug 27, 2026
Latest indexed: Sep 15, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

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116 open issues indexed

Use DAGs ("directed acyclic graphs") to inform the re-running of a pipeline Open

enhancement

DiamondLightSource/httomo#11 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Verify the number of MPI processes to use for a run before launching a cluster job Open

enhancement

DiamondLightSource/httomo#52 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
Document performance of in-memory reslice operation on real data Open

documentation

DiamondLightSource/httomo#85 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
`sino_360_to_180` method changing data shape breaks GPU loop Open

bug

DiamondLightSource/httomo#160 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Improve CPU memory efficiency Open

enhancement framework

DiamondLightSource/httomo#170 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Move index calculations out of `StandardTomoLoader` Open

enhancement loader

DiamondLightSource/httomo#208 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Enable `StandardTomoLoader` to load sinogram blocks Open

enhancement loader

DiamondLightSource/httomo#211 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add ignoring specific projections feature to `StandardTomoLoader` Open

enhancement loader

DiamondLightSource/httomo#221 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Update `MonitoringInterface.write_results()` to use an IO protocol rather than `typing.TextIO` Open

enhancement

DiamondLightSource/httomo#226 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Replace angles length consistency check appropriately Open

enhancement

DiamondLightSource/httomo#236 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Replace any remaining references to `dataset` with `block` Open

enhancement

DiamondLightSource/httomo#237 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Check for missing method parameters in pipeline config with YAML checker Open

enhancement

DiamondLightSource/httomo#241 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Performance benchmarks Open

DiamondLightSource/httomo#247 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add tests for YAML generator Open

testing

DiamondLightSource/httomo#255 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Remove unused `_get_discard_data_out()` function from YAML template generator Open

enhancement minor

DiamondLightSource/httomo#258 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Don't rely on `output_folder` global variable in YAML generator Open

minor

DiamondLightSource/httomo#259 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Fix `StandardTomoLoader` not being garbage collected until program termination Open

bug enhancement loader

DiamondLightSource/httomo#266 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add checks for obvious incorrect data values in optional debug run Open

enhancement

DiamondLightSource/httomo#267 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Question about github mechanisms for checking PR readiness before merge Open

question

DiamondLightSource/httomo#273 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Segfault in `Alltoallv()` operation in reslice Open

bug enhancement

DiamondLightSource/httomo#274 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Remove unused imports in various python files Open

minor

DiamondLightSource/httomo#293 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add loader for loading images Open

enhancement loader

DiamondLightSource/httomo#295 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Type-hint the data type of numpy/cupy arrays with `np.typing.NDArray` and `cp.typing.NDArray` Open

enhancement minor

DiamondLightSource/httomo#297 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Based on first method's pattern, infer whether loader should load blocks as projections or sinograms Open

enhancement loader

DiamondLightSource/httomo#298 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Investigate other means of reporting block processing progress Open

enhancement

DiamondLightSource/httomo#303 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Debug log message if try/except cupy import fails in `cli.py` Open

logging minor

DiamondLightSource/httomo#310 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Fix small typo in `_get_middle_slice_indices()` docstring Open

minor

DiamondLightSource/httomo#312 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Move pipeline file extension check to YAML checker -> question regarding a generic pipeline checker Open

question

DiamondLightSource/httomo#313 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Choose a more descriptive parameter name in place of `i` in `UiLayer._append_methods_list()` Open

minor

DiamondLightSource/httomo#314 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Remove redundant loader check in UI layer Open

minor

DiamondLightSource/httomo#315 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Choose a more descriptive parameter name in place of `v` in `check_valid_ref_id()` Open

minor

DiamondLightSource/httomo#316 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Remove any duplication of side output checking between UI layer and YAML checker? Open

minor question

DiamondLightSource/httomo#317 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
"Refactor nested if" comment, probably referring to `DataSetStoreReader._reslice()` Open

refactor

DiamondLightSource/httomo#318 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Don't assume cwd is root dir in relative paths in `conftest.py` Open

minor testing

DiamondLightSource/httomo#320 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Nonexistent method in pipeline YAML causes YAML checker to fail unexpectedly Open

bug

DiamondLightSource/httomo#331 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Log absolute path of input data in loader Open

logging

DiamondLightSource/httomo#337 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Remove unnecessary globbing pattern in package data section of `pyproject.toml` Open

minor packaging

DiamondLightSource/httomo#342 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Replace redundant globbing in package data section in `pyproject.toml` Open

minor packaging

DiamondLightSource/httomo#343 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Generate YAML template for `standard_tomo` from new block loader Open

enhancement loader

DiamondLightSource/httomo#349 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Remove unnecessary dependency of `mpi4py` in `standard_tomo.py` Open

loader

DiamondLightSource/httomo#350 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Remove `mpi4py` dependency from conda package build config Open

enhancement packaging

DiamondLightSource/httomo#351 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Templates testing Open

DiamondLightSource/httomo#370 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Remove unnecessary `pass` in `elif` block `_build_kwargs()` generic wrapper(?) Open

minor

DiamondLightSource/httomo#374 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Do something with undocumented `pass` in `GenericMethodWrapper._build_kwargs()` Open

minor

DiamondLightSource/httomo#375 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
YAML checker fails to detect incorrect angles path in loader config Open

bug

DiamondLightSource/httomo#378 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Sinogram centering method for multiple vertical slices Open

enhancement

DiamondLightSource/httomo#379 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add pipeline files with invalid syntax to UI layer tests Open

testing

DiamondLightSource/httomo#381 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Restructure methods database to avoid redundant information in path Open

minor

DiamondLightSource/httomo#382 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
OpenMPI setting for saving compressed hdf5 chunks Open

documentation

DiamondLightSource/httomo#389 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 15, 2026
Unnecessary `workflow_dispatch` in docs github action workflow? Open

ci question

DiamondLightSource/httomo#391 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026

DiamondLightSource/httomo

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