API

This reference is generated from HTTomo’s Python modules. Most of these modules support the framework’s internal execution machinery rather than the scientific methods used in a YAML pipeline. Backend method developers should normally begin with Adding a processing method and Integrating methods with httomo-backends; use this API when extending HTTomo itself or integrating with its runner interfaces.

Module overview

Module	Responsibility
httomo.base_block	Provides BaseBlock, the default implementation of block data access and CPU/GPU transfer behaviour, including access to angles, darks and flats.
httomo.block_interfaces	Defines the protocols that a processable block must satisfy: data and auxiliary-data access, global indexing, and transfer between CPU and GPU memory.
httomo.cli	Implements the check, memory-check and run commands, converts command-line options, prepares the output directory and starts the appropriate runner.
httomo.cli_utils	Contains command-line support functions, principally detection of parameter sweeps in YAML files, JSON strings and parsed configurations.
httomo.darks_flats	Describes where dark-field and flat-field images are stored and loads or selects those calibration images for a loader.
httomo.data	Contains RAM- and HDF5-backed dataset stores, MPI redistribution helpers, padding operations and the stores used during parameter sweeps.
httomo.globals	Holds process-wide runtime settings populated by the CLI, such as the output directory, selected GPU, chunking, compression and reconstruction filename options.
httomo.loaders	Creates loader implementations from pipeline configuration. The standard tomography loader reads projections, angles, darks and flats from HDF5/NeXus input.
httomo.logger	Configures concise terminal and user.log output, detailed debug.log output and optional GELF syslog reporting.
httomo.methods	Provides framework-owned pipeline operations, including global statistics calculation and block-wise writing of intermediate HDF5 datasets.
httomo.method_wrappers	Selects and constructs the adapter that invokes each backend function. Specialised wrappers handle reconstruction, rotation, image output, statistics and other non-generic method behaviour.
httomo.monitors	Constructs summary and benchmark monitors and combines multiple monitors into one reporting interface.
httomo.preview	Represents input cropping selections, checks their bounds and calculates the selected indices and resulting global data shape.
httomo.runner	Contains the main execution engine and its contracts: pipelines, sections, block splitting, dataset blocks and stores, loaders, method wrappers, monitoring, side-output references and GPU utilities.
httomo.sweep_runner	Parses and executes single-parameter sweeps, divides sweep values among MPI ranks, manages sweep stages and side outputs, and stores sweep results.
httomo.transform_layer	Rewrites an executable pipeline before it runs by inserting framework operations such as data reduction, data checking, intermediate saving and sweep image output.
httomo.transform_loader_params	Converts loader values parsed from YAML or JSON into validated internal configurations for previews, angles, calibration images and continuous scan subsets.
httomo.types	Defines shared type aliases, notably the generic array type used for either NumPy CPU arrays or CuPy GPU arrays.
httomo.ui_layer	Converts a user-facing YAML or JSON pipeline into the internal immutable Pipeline, constructing its loader and method wrappers and resolving output references.
httomo.utils	Supplies shared array, timing, logging, error-handling, snapshot and block-size helpers, as well as NumPy/CuPy backend selection.
httomo.yaml_checker	Validates pipeline YAML structure, loader position, methods, parameters, side-output references and, when input data is supplied, referenced HDF5 paths.

Generated reference

httomo.base_block
httomo.block_interfaces
httomo.cli
httomo.cli_utils
httomo.darks_flats	Dark-field/flat-field storage location configuration type and reading function, used by loaders.
httomo.data
httomo.globals
httomo.loaders
httomo.logger
httomo.methods
httomo.method_wrappers
httomo.monitors
httomo.preview	Slicing configuration types used by loaders to crop the input data.
httomo.runner
httomo.sweep_runner
httomo.transform_layer
httomo.transform_loader_params	Types that represent python dicts for angles, preview, and darks/flats configuration, which are generated from parsing a pipeline file into python, and functions to transform these python dicts to internal types that loaders can use.
httomo.types
httomo.ui_layer
httomo.utils
httomo.yaml_checker	Module for checking the validity of yaml files.