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Introduction
HTTomo concept
Detailed concepts
Sections
Re-slicing
Method Wrappers
Memory Estimators
Chunks
Blocks
What is a template?
What is a process list?
Frequently Asked Questions
How To's
Installation Guide
How to run HTTomo
Inside Diamond
Outside Diamond
Process Lists Guide
HTTomo-specific parameters
Side outputs
Saving intermediate files
Configure efficient pipelines
HTTomo Features
Previewing
Centre of Rotation (CoR)
Parameter Sweeping
Padding
Interpret Log File
Reference guides
What is YAML?
HTTomo Loaders
Data processing
Supported libraries
Methods YAML Templates
Ready-to-use pipelines
Full YAML pipelines
Utilities
YAML Checker - Why use it?
Developers
How to contribute
GPU memory calculations
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.execute_high_throughput_run
httomo.cli.execute_sweep_run
httomo.cli.generate_pipeline
httomo.cli.initialise_output_directory
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.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.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_chunk_bytes
httomo.runner.dataset_store_backing.calculate_section_chunk_shape
httomo.runner.dataset_store_backing.determine_store_backing
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.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.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
.pdf
httomo.globals
httomo.globals
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