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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
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httomo.globals
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