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Introduction

  • About HTTomo
  • How HTTomo runs a pipeline
  • Core concepts
    • Pipelines and templates
    • Chunks and blocks
    • Sections
    • Re-slicing

Getting started

  • Installation
    • Windows
    • macOS (Apple Silicon)
  • 10-minute quickstart
  • Run your first pipeline
  • Running HTTomo at Diamond

User guide

  • Loading data
    • Standard tomography loader
    • Darks and flats
    • Rotation angles
    • Previewing
    • Continuous-scan subsets
    • Creating an NXtomo file
  • Pipeline features
    • Configure a pipeline
    • Optimise pipeline performance
    • Memory and performance
    • Side outputs
    • Centre of Rotation
    • Parameter Sweeping
    • Save intermediate datasets
    • Padding
  • Tutorials
    • Real data processing
      • Sandstone data
      • Stripe-removal data
      • Lorentz data
    • Generate synthetic data
  • Troubleshooting
  • Frequently asked questions

Pipelines and methods

  • Ready-to-use pipelines
  • Versioned downloads
  • Choose a pipeline
  • Available methods
  • Processing libraries
  • Reconstruction ecosystem

Reference

  • Command-line interface
  • Pipeline file reference
  • Run output, logs and monitoring
  • Version compatibility
  • Glossary

Developers

  • Architecture and internals
    • Method wrappers
    • GPU memory estimation
  • Development setup and testing
  • How to contribute
  • Adding a processing method
  • Integrating methods with httomo-backends
  • Memory estimation and block sizing
  • Profiling and tracing
  • API
    • httomo.base_block
      • httomo.base_block.BaseBlock
    • httomo.block_interfaces
      • httomo.block_interfaces.Block
      • httomo.block_interfaces.BlockData
      • httomo.block_interfaces.BlockIndexing
      • httomo.block_interfaces.BlockTransfer
    • httomo.cli
      • httomo.cli.PipelineFilePathOrString
      • httomo.cli.estimate_cpu_memory
      • httomo.cli.execute_high_throughput_run
      • httomo.cli.execute_sweep_run
      • httomo.cli.generate_pipeline
      • httomo.cli.initialise_output_dir_copy_files_inject_defaults
      • httomo.cli.set_global_constants
      • httomo.cli.transform_limit_str_to_bytes
    • httomo.cli_utils
      • httomo.cli_utils.is_sweep_pipeline
    • httomo.darks_flats
      • httomo.darks_flats.DarksFlatsFileConfig
      • httomo.darks_flats.ImageType
      • httomo.darks_flats.get_darks_flats
    • httomo.data
      • httomo.data.dataset_store
        • httomo.data.dataset_store.DataSetStoreReader
        • httomo.data.dataset_store.DataSetStoreWriter
      • httomo.data.hdf
      • httomo.data.mpiutil
        • httomo.data.mpiutil.alltoall
        • httomo.data.mpiutil.alltoall_ring
      • httomo.data.padding
        • httomo.data.padding.extrapolate_after
        • httomo.data.padding.extrapolate_before
      • httomo.data.param_sweep_store
        • httomo.data.param_sweep_store.ParamSweepReader
        • httomo.data.param_sweep_store.ParamSweepWriter
    • httomo.globals
    • httomo.loaders
      • httomo.loaders.standard_tomo_loader
        • httomo.loaders.standard_tomo_loader.StandardLoaderWrapper
        • httomo.loaders.standard_tomo_loader.StandardTomoLoader
      • httomo.loaders.types
        • httomo.loaders.types.DataConfig
        • httomo.loaders.types.RawAngles
        • httomo.loaders.types.UserDefinedAngles
      • httomo.loaders.make_loader
    • httomo.logger
      • httomo.logger.setup_logger
    • httomo.methods
      • httomo.methods.calculate_stats
      • httomo.methods.save_intermediate_data
      • httomo.methods.setup_dataset
    • httomo.method_wrappers
      • httomo.method_wrappers.average_frames
        • httomo.method_wrappers.average_frames.AverageFramesWrapper
      • httomo.method_wrappers.datareducer
        • httomo.method_wrappers.datareducer.DatareducerWrapper
      • httomo.method_wrappers.dezinging
        • httomo.method_wrappers.dezinging.DezingingWrapper
      • httomo.method_wrappers.distortion_correction
        • httomo.method_wrappers.distortion_correction.DistortionCorrectionWrapper
      • httomo.method_wrappers.generic
        • httomo.method_wrappers.generic.GenericMethodWrapper
      • httomo.method_wrappers.images
        • httomo.method_wrappers.images.ImagesWrapper
      • httomo.method_wrappers.reconstruction
        • httomo.method_wrappers.reconstruction.ReconstructionWrapper
      • httomo.method_wrappers.rotation
        • httomo.method_wrappers.rotation.RotationWrapper
      • httomo.method_wrappers.save_intermediate
        • httomo.method_wrappers.save_intermediate.SaveIntermediateFilesWrapper
      • httomo.method_wrappers.seam_blender
        • httomo.method_wrappers.seam_blender.SeamBlenderWrapper
      • httomo.method_wrappers.sino360_to_180
        • httomo.method_wrappers.sino360_to_180.Sino360to180Wrapper
      • httomo.method_wrappers.stats_calc
        • httomo.method_wrappers.stats_calc.StatsCalcWrapper
      • httomo.method_wrappers.make_method_wrapper
    • httomo.monitors
      • httomo.monitors.aggregate
        • httomo.monitors.aggregate.AggregateMonitoring
      • httomo.monitors.benchmark
        • httomo.monitors.benchmark.BenchmarkMonitoring
      • httomo.monitors.summary
        • httomo.monitors.summary.SummaryMonitor
      • httomo.monitors.make_monitors
    • httomo.preview
      • httomo.preview.Preview
      • httomo.preview.PreviewConfig
      • httomo.preview.PreviewDimConfig
    • httomo.runner
      • httomo.runner.auxiliary_data
        • httomo.runner.auxiliary_data.AuxiliaryData
      • httomo.runner.block_split
        • httomo.runner.block_split.BlockSplitter
      • httomo.runner.dataset
        • httomo.runner.dataset.DataSetBlock
      • httomo.runner.dataset_store_backing
        • httomo.runner.dataset_store_backing.DataSetStoreBacking
        • httomo.runner.dataset_store_backing.calculate_section_input_chunk_shape
        • httomo.runner.dataset_store_backing.calculate_section_output_chunk_shape
        • httomo.runner.dataset_store_backing.determine_store_backing
        • httomo.runner.dataset_store_backing.estimate_section_memory
      • httomo.runner.dataset_store_interfaces
        • httomo.runner.dataset_store_interfaces.DataSetSink
        • httomo.runner.dataset_store_interfaces.DataSetSource
        • httomo.runner.dataset_store_interfaces.DummySink
        • httomo.runner.dataset_store_interfaces.ReadableDataSetSink
      • httomo.runner.gpu_utils
        • httomo.runner.gpu_utils.get_available_gpu_memory
        • httomo.runner.gpu_utils.get_gpu_id
        • httomo.runner.gpu_utils.gpumem_cleanup
      • httomo.runner.loader
        • httomo.runner.loader.LoaderInterface
      • httomo.runner.method_wrapper
        • httomo.runner.method_wrapper.GpuTimeInfo
        • httomo.runner.method_wrapper.MethodWrapper
      • httomo.runner.methods_repository_interface
        • httomo.runner.methods_repository_interface.MethodQuery
        • httomo.runner.methods_repository_interface.MethodRepository
      • httomo.runner.monitoring_interface
        • httomo.runner.monitoring_interface.MonitoringInterface
      • httomo.runner.output_ref
        • httomo.runner.output_ref.OutputRef
      • httomo.runner.pipeline
        • httomo.runner.pipeline.Pipeline
      • httomo.runner.section
        • httomo.runner.section.Section
        • httomo.runner.section.determine_minimum_block_length
        • httomo.runner.section.determine_section_padding
        • httomo.runner.section.sectionize
      • httomo.runner.task_runner
        • httomo.runner.task_runner.TaskRunner
    • httomo.sweep_runner
      • httomo.sweep_runner.param_sweep_block
        • httomo.sweep_runner.param_sweep_block.ParamSweepBlock
      • httomo.sweep_runner.param_sweep_json_loader
        • httomo.sweep_runner.param_sweep_json_loader.ParamSweepJsonLoader
      • httomo.sweep_runner.param_sweep_runner
        • httomo.sweep_runner.param_sweep_runner.ParamSweepRunner
      • httomo.sweep_runner.param_sweep_store_interfaces
        • httomo.sweep_runner.param_sweep_store_interfaces.ParamSweepSink
        • httomo.sweep_runner.param_sweep_store_interfaces.ParamSweepSource
      • httomo.sweep_runner.param_sweep_yaml_loader
        • httomo.sweep_runner.param_sweep_yaml_loader.ParamSweepYamlLoader
        • httomo.sweep_runner.param_sweep_yaml_loader.get_param_sweep_yaml_loader
      • httomo.sweep_runner.side_output_manager
        • httomo.sweep_runner.side_output_manager.SideOutputManager
      • httomo.sweep_runner.stages
        • httomo.sweep_runner.stages.NonSweepStage
        • httomo.sweep_runner.stages.Stages
        • httomo.sweep_runner.stages.SweepStage
    • httomo.transform_layer
      • httomo.transform_layer.TransformLayer
    • httomo.transform_loader_params
      • httomo.transform_loader_params.ContinuousScanSubsetParam
      • httomo.transform_loader_params.DarksFlatsParam
      • httomo.transform_loader_params.PartialDarksFlatsParam
      • httomo.transform_loader_params.PreviewParam
      • httomo.transform_loader_params.RawAnglesParam
      • httomo.transform_loader_params.StartStopEntry
      • httomo.transform_loader_params.UserDefinedAnglesParam
      • httomo.transform_loader_params.UserDefinedAnglesParamInner
      • httomo.transform_loader_params.find_tomo_entry
      • httomo.transform_loader_params.parse_angles
      • httomo.transform_loader_params.parse_config
      • httomo.transform_loader_params.parse_darks_flats
      • httomo.transform_loader_params.parse_data
      • httomo.transform_loader_params.parse_preview
      • httomo.transform_loader_params.select_continuous_scan_subset
    • httomo.types
    • httomo.ui_layer
      • httomo.ui_layer.PipelineFormat
      • httomo.ui_layer.UiLayer
      • httomo.ui_layer.check_valid_ref_id
      • httomo.ui_layer.get_ref_split
      • httomo.ui_layer.get_regex_pattern
      • httomo.ui_layer.get_valid_ref_str
      • httomo.ui_layer.update_side_output_references
      • httomo.ui_layer.yaml_loader
    • httomo.utils
      • httomo.utils.catch_gputime
      • httomo.utils.catchtime
      • httomo.utils.clp2
      • httomo.utils.get_data_in_data_out
      • httomo.utils.log_exception
      • httomo.utils.log_once
      • httomo.utils.log_rank
      • httomo.utils.make_3d_shape_from_array
      • httomo.utils.make_3d_shape_from_shape
      • httomo.utils.make_pinned_host_array
      • httomo.utils.mpi_abort_excepthook
      • httomo.utils.save_2d_snapshot
      • httomo.utils.search_max_slices_iterative
    • httomo.yaml_checker
      • httomo.yaml_checker.Colour
      • httomo.yaml_checker.UniqueKeyLoader
      • httomo.yaml_checker.check_first_method_is_loader
      • httomo.yaml_checker.check_hdf5_paths_against_loader
      • httomo.yaml_checker.check_id_has_side_out
      • httomo.yaml_checker.check_keys
      • httomo.yaml_checker.check_methods_exist_in_templates
      • httomo.yaml_checker.check_no_duplicated_keys
      • httomo.yaml_checker.check_no_imagesaver_after_sweep_method
      • httomo.yaml_checker.check_no_required_parameter_values
      • httomo.yaml_checker.check_omitted_parameters_are_not_required
      • httomo.yaml_checker.check_parameter_names_are_known
      • httomo.yaml_checker.check_parameter_names_are_str
      • httomo.yaml_checker.check_ref_id_valid
      • httomo.yaml_checker.check_side_out_matches_ref_arg
      • httomo.yaml_checker.sanity_check
      • httomo.yaml_checker.validate_yaml_config
  • .rst

httomo.data

httomo.data#

Modules

httomo.data.dataset_store

httomo.data.hdf

httomo.data.mpiutil

httomo.data.padding

httomo.data.param_sweep_store

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By the Imaging Team

© Copyright 2026, Diamond Light Source.

Last updated on Oct 08, 2026.