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

Missing type annotations for constructor params of `TransformLayer` Open

minor

DiamondLightSource/httomo#394 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Removed unused `self._block_start` and `self._chunk_start` private attributes of `DataSetBlock` Open

minor

DiamondLightSource/httomo#400 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Revise where `xp` should and shouldn't be used Open

minor refactor

DiamondLightSource/httomo#403 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Refactor data store reader + writer classes to extract utilities Open

framework refactor

DiamondLightSource/httomo#404 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Check valid slicing in `preview` in YAML checker if data is given Open

enhancement

DiamondLightSource/httomo#406 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Check use of `global_index` in image saver wrapper when given a padded block Open

framework

DiamondLightSource/httomo#407 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Fix small typo/misleading var name in wrapper output dims calculator test Open

minor

DiamondLightSource/httomo#410 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Direct memory estimators data type change Open

DiamondLightSource/httomo#436 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Task checker github action not passing even though all checkboxes are completed? Open

ci

DiamondLightSource/httomo#439 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Data type conversion, support for uint16 processing Open

DiamondLightSource/httomo#440 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
`RotationWrapper` unnecessarily calculates core of block instead of using `DataSetBlock.data_unpadded` Open

minor

DiamondLightSource/httomo#447 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
FFT plan in both paganin filter methods sometimes has a negligible size Open

memory-estimation question

DiamondLightSource/httomo#456 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Use `click.IntRange` type to catch integer values < 1 instead of manually checking `max_cpu_slices` Open

minor

DiamondLightSource/httomo#459 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Watermarks are difficult to read/pixelated in result of sweep for images of small dimension Open

minor

DiamondLightSource/httomo#462 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Outdated CLI `run` command flags Open

documentation

DiamondLightSource/httomo#465 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Incorrect type-hint in UI layer's `check_valid_ref_id()` function Open

minor refactor

DiamondLightSource/httomo#474 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Methods without a `side_outputs` field may be unnecessarily included in `method_id_map` Open

question refactor

DiamondLightSource/httomo#475 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Unnecessary list of one element per iteration in loop in YAML checker? Open

question refactor

DiamondLightSource/httomo#477 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Combining `|` and `xp.ndarray` in a type causes warning in sphinx API docs build Open

bug documentation

DiamondLightSource/httomo#492 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Unnecessary `nvtx` dependency Open

minor

DiamondLightSource/httomo#493 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Sphinx docs build in CI produces warning due to import error when importing `httomo.cli` module Open

ci documentation

DiamondLightSource/httomo#495 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
`cufft.py` module excluded from API docs Open

documentation memory-estimation

DiamondLightSource/httomo#498 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Inconsistent docstring format across codebase Open

documentation

DiamondLightSource/httomo#499 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Sort out inconsistencies and oddities with the loader's YAML template and how a loader is referenced in a pipeline file Open

loader refactor

DiamondLightSource/httomo#501 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
Revaluate whether `StandardLoaderWrapper` is needed or not Open

loader refactor

DiamondLightSource/httomo#504 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Potentially confusing print by YAML checker when checking a loader is first in the pipeline Open

DiamondLightSource/httomo#515 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
fixing versions for dependencies Open

question

DiamondLightSource/httomo#518 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
YAML with a colon but no space is valid YAML, but produces a string instead of a map Open

question

DiamondLightSource/httomo#524 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Old preview syntax in testing pipeline Open

minor

DiamondLightSource/httomo#525 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Loader factory function doesn't use `MethodRepository` or `module_path` params Open

loader

DiamondLightSource/httomo#533 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Unnecessary setting of `parameters["in_file"]` in `UiLayer._setup_loader()` Open

minor

DiamondLightSource/httomo#546 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Document method wrappers which transform the `auto` value for a parameter Open

documentation

DiamondLightSource/httomo#547 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
preview is smaller than the padded data Open

bug

DiamondLightSource/httomo#548 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Pyright error if `import httomo` used instead of `import httomo.globals` Open

minor

DiamondLightSource/httomo#561 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Unnecessary `typing_extensions` dev dependency Open

packaging

DiamondLightSource/httomo#563 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Some framework tests require tomopy Open

testing

DiamondLightSource/httomo#565 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Consider removing unused plumbum dependency Open

DiamondLightSource/httomo#568 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Code block not rendered in docs Open

documentation

DiamondLightSource/httomo#576 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Inconsistent creation of blocks by test loader compared to real loader Open

testing

DiamondLightSource/httomo#579 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Out of date mention of python pipelines in `UiLayer` docstring Open

documentation

DiamondLightSource/httomo#582 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
UI layer test name lacks information on what it's testing Open

testing

DiamondLightSource/httomo#584 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Document pipeline transformations applied by `UiLayer` Open

documentation

DiamondLightSource/httomo#585 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Pascal case instance attribute in `UiLayer` Open

minor

DiamondLightSource/httomo#589 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Failing conda env creation command in installation docs Open

bug documentation

DiamondLightSource/httomo#591 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Some UI layer tests take longer than expected to run Open

testing

DiamondLightSource/httomo#593 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Validate fields given in `preview` loader parameter Open

DiamondLightSource/httomo#597 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Include MPI process rank in exception log messages Open

logging minor

DiamondLightSource/httomo#601 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Handle numpy `_ArrayMemoryError` in reslice `np.concatenate()` call to avoid deadlock in multi-process runs Open

bug

DiamondLightSource/httomo#602 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add ignoring a specific subset of darks and/or flats feature to `StandardTomoLoader` Open

enhancement loader

DiamondLightSource/httomo#603 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Inappropriate tuple-like type for `RawAngles` Open

DiamondLightSource/httomo#606 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026

DiamondLightSource/httomo

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