Index

A

after_sweep (httomo.sweep_runner.stages.Stages attribute) AggregateMonitoring (class in httomo.monitors.aggregate) all (httomo.utils.Pattern attribute) alltoall() (in module httomo.data.mpiutil) angles (httomo.base_block.BaseBlock property) (httomo.block_interfaces.BlockData property) (httomo.preview.PreviewConfig attribute) (httomo.transform_loader_params.PreviewParam attribute) angles_dtype (httomo.runner.auxiliary_data.AuxiliaryData property) angles_length (httomo.runner.auxiliary_data.AuxiliaryData property) angles_radians (httomo.base_block.BaseBlock property) (httomo.block_interfaces.BlockData property) angles_total (httomo.loaders.standard_tomo_loader.StandardLoaderWrapper property) (httomo.loaders.types.UserDefinedAngles attribute) (httomo.runner.loader.LoaderInterface property) (httomo.transform_loader_params.UserDefinedAnglesParamInner attribute)

append() (httomo.sweep_runner.side_output_manager.SideOutputManager method) append_config_params() (httomo.method_wrappers.generic.GenericMethodWrapper method) (httomo.runner.method_wrapper.MethodWrapper method) append_side_outputs() (httomo.runner.task_runner.TaskRunner method) aux_data (httomo.base_block.BaseBlock property) (httomo.block_interfaces.BlockData property) (httomo.data.dataset_store.DataSetStoreReader property) (httomo.data.dataset_store.DataSetStoreWriter property) (httomo.data.param_sweep_store.ParamSweepReader property) (httomo.data.param_sweep_store.ParamSweepWriter property) (httomo.loaders.standard_tomo_loader.StandardTomoLoader property) (httomo.runner.dataset_store_interfaces.DataSetSource property) (httomo.sweep_runner.param_sweep_store_interfaces.ParamSweepSource property) AuxiliaryData (class in httomo.runner.auxiliary_data)

B

BACKG_RED (httomo.yaml_checker.Colour attribute) BaseBlock (class in httomo.base_block) before_sweep (httomo.sweep_runner.stages.Stages attribute) BenchmarkMonitoring (class in httomo.monitors.benchmark) Block (class in httomo.block_interfaces) block (httomo.sweep_runner.param_sweep_runner.ParamSweepRunner property)

BlockData (class in httomo.block_interfaces) BlockIndexing (class in httomo.block_interfaces) BlockSplitter (class in httomo.runner.block_split) BlockTransfer (class in httomo.block_interfaces) BLUE (httomo.yaml_checker.Colour attribute) build_pipeline() (httomo.ui_layer.UiLayer method) BVIOLET (httomo.yaml_checker.Colour attribute)

C

calculate_max_slices() (httomo.method_wrappers.generic.GenericMethodWrapper method) (httomo.runner.method_wrapper.MethodWrapper method) calculate_memory_bytes() (httomo.runner.methods_repository_interface.MethodQuery method) calculate_output_dims() (httomo.method_wrappers.generic.GenericMethodWrapper method) (httomo.runner.method_wrapper.MethodWrapper method) (httomo.runner.methods_repository_interface.MethodQuery method) calculate_padding() (httomo.method_wrappers.generic.GenericMethodWrapper method) (httomo.runner.method_wrapper.MethodWrapper method) (httomo.runner.methods_repository_interface.MethodQuery method) calculate_section_chunk_bytes() (in module httomo.runner.dataset_store_backing) calculate_section_chunk_shape() (in module httomo.runner.dataset_store_backing) calculate_stats() (in module httomo.methods) catch_gputime (class in httomo.utils) catchtime (class in httomo.utils) check_first_method_is_loader() (in module httomo.yaml_checker) check_hdf5_paths_against_loader() (in module httomo.yaml_checker) check_id_has_side_out() (in module httomo.yaml_checker) check_keys() (in module httomo.yaml_checker) check_methods_exist_in_templates() (in module httomo.yaml_checker) check_no_duplicated_keys() (in module httomo.yaml_checker) check_no_imagesaver_after_sweep_method() (in module httomo.yaml_checker) check_no_required_parameter_values() (in module httomo.yaml_checker) check_parameter_names_are_known() (in module httomo.yaml_checker) check_parameter_names_are_str() (in module httomo.yaml_checker) check_ref_id_valid() (in module httomo.yaml_checker) check_side_out_matches_ref_arg() (in module httomo.yaml_checker) check_valid_ref_id() (in module httomo.ui_layer) chunk_index (httomo.block_interfaces.BlockIndexing property) (httomo.runner.dataset.DataSetBlock property) (httomo.sweep_runner.param_sweep_block.ParamSweepBlock property)

chunk_index_unpadded (httomo.block_interfaces.BlockIndexing property) (httomo.runner.dataset.DataSetBlock property) (httomo.sweep_runner.param_sweep_block.ParamSweepBlock property) chunk_shape (httomo.block_interfaces.BlockIndexing property) (httomo.data.dataset_store.DataSetStoreReader property) (httomo.data.dataset_store.DataSetStoreWriter property) (httomo.loaders.standard_tomo_loader.StandardTomoLoader property) (httomo.runner.dataset.DataSetBlock property) (httomo.runner.dataset_store_interfaces.DataSetSink property) (httomo.runner.dataset_store_interfaces.DataSetSource property) (httomo.runner.dataset_store_interfaces.DummySink property) (httomo.sweep_runner.param_sweep_block.ParamSweepBlock property) chunk_shape_unpadded (httomo.block_interfaces.BlockIndexing property) (httomo.runner.dataset.DataSetBlock property) (httomo.sweep_runner.param_sweep_block.ParamSweepBlock property) Colour (class in httomo.yaml_checker) comm (httomo.data.dataset_store.DataSetStoreWriter property) (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.method_wrapper.MethodWrapper property) concat_dim (httomo.data.param_sweep_store.ParamSweepWriter property) (httomo.sweep_runner.param_sweep_store_interfaces.ParamSweepSink property) config_params (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.method_wrapper.MethodWrapper property) construct_mapping() (httomo.yaml_checker.UniqueKeyLoader method) cupyrun (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.method_wrapper.MethodWrapper property) CYAN (httomo.yaml_checker.Colour attribute)

D

dark (httomo.base_block.BaseBlock property) (httomo.block_interfaces.BlockData property) darks (httomo.base_block.BaseBlock property) (httomo.block_interfaces.BlockData property) (httomo.loaders.standard_tomo_loader.StandardTomoLoader property) darks_dtype (httomo.runner.auxiliary_data.AuxiliaryData property) darks_shape (httomo.runner.auxiliary_data.AuxiliaryData property) DarksFlatsFileConfig (class in httomo.darks_flats) data (httomo.base_block.BaseBlock property) (httomo.block_interfaces.BlockData property) (httomo.runner.dataset.DataSetBlock property) data_indices (httomo.preview.Preview property) data_path (httomo.darks_flats.DarksFlatsFileConfig attribute) (httomo.loaders.types.RawAngles attribute) (httomo.transform_loader_params.RawAnglesParam attribute) data_unpadded (httomo.block_interfaces.BlockIndexing property) (httomo.runner.dataset.DataSetBlock property) (httomo.sweep_runner.param_sweep_block.ParamSweepBlock property) DatareducerWrapper (class in httomo.method_wrappers.datareducer) DataSetBlock (class in httomo.runner.dataset) DataSetSink (class in httomo.runner.dataset_store_interfaces) DataSetSource (class in httomo.runner.dataset_store_interfaces)

DataSetStoreBacking (class in httomo.runner.dataset_store_backing) DataSetStoreReader (class in httomo.data.dataset_store) DataSetStoreWriter (class in httomo.data.dataset_store) detector_x (httomo.loaders.standard_tomo_loader.StandardLoaderWrapper property) (httomo.preview.PreviewConfig attribute) (httomo.runner.loader.LoaderInterface property) (httomo.transform_loader_params.PreviewParam attribute) detector_y (httomo.loaders.standard_tomo_loader.StandardLoaderWrapper property) (httomo.preview.PreviewConfig attribute) (httomo.runner.loader.LoaderInterface property) (httomo.transform_loader_params.PreviewParam attribute) determine_max_slices() (httomo.runner.task_runner.TaskRunner method) determine_section_padding() (in module httomo.runner.section) determine_stages() (httomo.sweep_runner.param_sweep_runner.ParamSweepRunner method) determine_store_backing() (in module httomo.runner.dataset_store_backing) device2host (httomo.runner.method_wrapper.GpuTimeInfo attribute) DezingingWrapper (class in httomo.method_wrappers.dezinging) DistortionCorrectionWrapper (class in httomo.method_wrappers.distortion_correction) drop_darks_flats() (httomo.runner.auxiliary_data.AuxiliaryData method) dtype (httomo.data.dataset_store.DataSetStoreReader property) (httomo.loaders.standard_tomo_loader.StandardTomoLoader property) (httomo.runner.dataset_store_interfaces.DataSetSource property) DummySink (class in httomo.runner.dataset_store_interfaces)

E

elapsed (httomo.utils.catch_gputime property) END (httomo.yaml_checker.Colour attribute) execute() (httomo.method_wrappers.datareducer.DatareducerWrapper method) (httomo.method_wrappers.dezinging.DezingingWrapper method) (httomo.method_wrappers.generic.GenericMethodWrapper method) (httomo.method_wrappers.images.ImagesWrapper method) (httomo.method_wrappers.save_intermediate.SaveIntermediateFilesWrapper method) (httomo.runner.method_wrapper.MethodWrapper method) (httomo.runner.task_runner.TaskRunner method) (httomo.sweep_runner.param_sweep_runner.ParamSweepRunner method)

execute_after_sweep() (httomo.sweep_runner.param_sweep_runner.ParamSweepRunner method) execute_before_sweep() (httomo.sweep_runner.param_sweep_runner.ParamSweepRunner method) execute_sweep() (httomo.sweep_runner.param_sweep_runner.ParamSweepRunner method) extract_dim (httomo.data.param_sweep_store.ParamSweepReader property) (httomo.sweep_runner.param_sweep_store_interfaces.ParamSweepSource property) extrapolate_after() (in module httomo.data.padding) extrapolate_before() (in module httomo.data.padding)

F

file (httomo.darks_flats.DarksFlatsFileConfig attribute) File (httomo.runner.dataset_store_backing.DataSetStoreBacking attribute) filename (httomo.data.dataset_store.DataSetStoreReader property) (httomo.data.dataset_store.DataSetStoreWriter property) finalize() (httomo.data.dataset_store.DataSetStoreReader method) (httomo.data.dataset_store.DataSetStoreWriter method) (httomo.loaders.standard_tomo_loader.StandardTomoLoader method) (httomo.runner.dataset_store_interfaces.DataSetSink method) (httomo.runner.dataset_store_interfaces.DataSetSource method) (httomo.runner.dataset_store_interfaces.DummySink method) (httomo.sweep_runner.param_sweep_store_interfaces.ParamSweepSink method)

flat (httomo.base_block.BaseBlock property) (httomo.block_interfaces.BlockData property) flats (httomo.base_block.BaseBlock property) (httomo.block_interfaces.BlockData property) (httomo.loaders.standard_tomo_loader.StandardTomoLoader property) flats_dtype (httomo.runner.auxiliary_data.AuxiliaryData property) flats_shape (httomo.runner.auxiliary_data.AuxiliaryData property)

G

GenericMethodWrapper (class in httomo.method_wrappers.generic) get() (httomo.sweep_runner.side_output_manager.SideOutputManager method) get_angles() (httomo.runner.auxiliary_data.AuxiliaryData method) get_available_gpu_memory() (in module httomo.runner.gpu_utils) get_darks() (httomo.runner.auxiliary_data.AuxiliaryData method) get_darks_flats() (in module httomo.darks_flats) get_data_in_data_out() (in module httomo.utils) get_flats() (httomo.runner.auxiliary_data.AuxiliaryData method) get_gpu_id() (in module httomo.runner.gpu_utils) get_implementation() (httomo.runner.methods_repository_interface.MethodQuery method) get_memory_gpu_params() (httomo.runner.methods_repository_interface.MethodQuery method) get_output_dims_change() (httomo.runner.methods_repository_interface.MethodQuery method) get_param_sweep_yaml_loader() (in module httomo.sweep_runner.param_sweep_yaml_loader) get_pattern() (httomo.runner.methods_repository_interface.MethodQuery method) get_ref_split() (in module httomo.ui_layer) get_regex_pattern() (in module httomo.ui_layer) get_side_output() (httomo.method_wrappers.generic.GenericMethodWrapper method) (httomo.runner.method_wrapper.MethodWrapper method) get_valid_ref_str() (in module httomo.ui_layer) global_index (httomo.block_interfaces.BlockIndexing property) (httomo.data.dataset_store.DataSetStoreReader property) (httomo.data.dataset_store.DataSetStoreWriter property) (httomo.loaders.standard_tomo_loader.StandardTomoLoader property) (httomo.runner.dataset.DataSetBlock property) (httomo.runner.dataset_store_interfaces.DataSetSink property) (httomo.runner.dataset_store_interfaces.DataSetSource property) (httomo.runner.dataset_store_interfaces.DummySink property) (httomo.sweep_runner.param_sweep_block.ParamSweepBlock property)

global_index_unpadded (httomo.block_interfaces.BlockIndexing property) (httomo.runner.dataset.DataSetBlock property) (httomo.sweep_runner.param_sweep_block.ParamSweepBlock property) global_shape (httomo.block_interfaces.BlockIndexing property) (httomo.data.dataset_store.DataSetStoreReader property) (httomo.data.dataset_store.DataSetStoreWriter property) (httomo.loaders.standard_tomo_loader.StandardTomoLoader property) (httomo.preview.Preview property) (httomo.runner.dataset.DataSetBlock property) (httomo.runner.dataset_store_interfaces.DataSetSink property) (httomo.runner.dataset_store_interfaces.DataSetSource property) (httomo.runner.dataset_store_interfaces.DummySink property) (httomo.sweep_runner.param_sweep_block.ParamSweepBlock property) gpu_time (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.method_wrapper.MethodWrapper property) gpumem_cleanup() (in module httomo.runner.gpu_utils) GpuMemoryRequirement (class in httomo.runner.methods_repository_interface) GpuTimeInfo (class in httomo.runner.method_wrapper) GREEN (httomo.yaml_checker.Colour attribute)

H

host2device (httomo.runner.method_wrapper.GpuTimeInfo attribute) httomo.base_block module httomo.block_interfaces module httomo.cli_utils module httomo.darks_flats module httomo.data module httomo.data.dataset_store module httomo.data.hdf module httomo.data.mpiutil module httomo.data.padding module httomo.data.param_sweep_store module httomo.globals module httomo.loaders module httomo.loaders.standard_tomo_loader module httomo.loaders.types module httomo.logger module httomo.method_wrappers module httomo.method_wrappers.datareducer module httomo.method_wrappers.dezinging module httomo.method_wrappers.distortion_correction module httomo.method_wrappers.generic module httomo.method_wrappers.images module httomo.method_wrappers.reconstruction module httomo.method_wrappers.rotation module httomo.method_wrappers.save_intermediate module httomo.method_wrappers.stats_calc module httomo.methods module httomo.monitors module httomo.monitors.aggregate module httomo.monitors.benchmark module

httomo.monitors.summary module httomo.preview module httomo.runner module httomo.runner.auxiliary_data module httomo.runner.block_split module httomo.runner.dataset module httomo.runner.dataset_store_backing module httomo.runner.dataset_store_interfaces module httomo.runner.gpu_utils module httomo.runner.loader module httomo.runner.method_wrapper module httomo.runner.methods_repository_interface module httomo.runner.monitoring_interface module httomo.runner.output_ref module httomo.runner.pipeline module httomo.runner.section module httomo.runner.task_runner module httomo.sweep_runner module httomo.sweep_runner.param_sweep_block module httomo.sweep_runner.param_sweep_runner module httomo.sweep_runner.param_sweep_store_interfaces module httomo.sweep_runner.param_sweep_yaml_loader module httomo.sweep_runner.side_output_manager module httomo.sweep_runner.stages module httomo.transform_layer module httomo.transform_loader_params module httomo.types module httomo.ui_layer module httomo.utils module httomo.yaml_checker module

I

image_key_path (httomo.darks_flats.DarksFlatsFileConfig attribute) ImagesWrapper (class in httomo.method_wrappers.images) implementation (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.method_wrapper.MethodWrapper property) increment_no_of_sweeps_written() (httomo.data.param_sweep_store.ParamSweepWriter method) insert_data_reducer() (httomo.transform_layer.TransformLayer method) insert_save_images_after_sweep() (httomo.transform_layer.TransformLayer method) insert_save_methods() (httomo.transform_layer.TransformLayer method) is_cpu (httomo.base_block.BaseBlock property) (httomo.block_interfaces.BlockTransfer property) (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.method_wrapper.MethodWrapper property)

is_file_based (httomo.data.dataset_store.DataSetStoreReader property) (httomo.data.dataset_store.DataSetStoreWriter property) is_gpu (httomo.base_block.BaseBlock property) (httomo.block_interfaces.BlockTransfer property) (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.method_wrapper.MethodWrapper property) is_last_in_chunk (httomo.block_interfaces.BlockIndexing property) (httomo.runner.dataset.DataSetBlock property) (httomo.sweep_runner.param_sweep_block.ParamSweepBlock property) is_padded (httomo.block_interfaces.BlockIndexing property) (httomo.runner.dataset.DataSetBlock property) (httomo.sweep_runner.param_sweep_block.ParamSweepBlock property) is_sweep_pipeline() (in module httomo.cli_utils)

K

kernel (httomo.runner.method_wrapper.GpuTimeInfo attribute)

L

labels (httomo.sweep_runner.side_output_manager.SideOutputManager property) LIGHT_BLUE (httomo.yaml_checker.Colour attribute) LIGHT_BLUE_BCKGR (httomo.yaml_checker.Colour attribute) loader (httomo.runner.pipeline.Pipeline property) loader_pattern (httomo.runner.pipeline.Pipeline property)

LoaderInterface (class in httomo.runner.loader) log_exception() (in module httomo.utils) log_once() (in module httomo.utils) log_rank() (in module httomo.utils) LYELLOW (httomo.yaml_checker.Colour attribute)

M

MAGENTA (httomo.yaml_checker.Colour attribute) make_3d_shape_from_array() (in module httomo.utils) make_3d_shape_from_shape() (in module httomo.utils) make_data_source() (httomo.loaders.standard_tomo_loader.StandardLoaderWrapper method) (httomo.runner.loader.LoaderInterface method) make_loader() (in module httomo.loaders) make_method_wrapper() (in module httomo.method_wrappers) make_monitors() (in module httomo.monitors) make_reader() (httomo.data.dataset_store.DataSetStoreWriter method) (httomo.data.param_sweep_store.ParamSweepWriter method) (httomo.runner.dataset_store_interfaces.ReadableDataSetSink method) (httomo.sweep_runner.param_sweep_store_interfaces.ParamSweepSink method) memory_gpu (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.method_wrapper.MethodWrapper property) method (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.method_wrapper.MethodWrapper property) (httomo.runner.methods_repository_interface.GpuMemoryRequirement attribute) (httomo.sweep_runner.stages.SweepStage attribute) method_name (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.loader.LoaderInterface attribute) (httomo.runner.method_wrapper.MethodWrapper property) MethodQuery (class in httomo.runner.methods_repository_interface) MethodRepository (class in httomo.runner.methods_repository_interface) methods (httomo.sweep_runner.stages.NonSweepStage attribute) MethodWrapper (class in httomo.runner.method_wrapper) module httomo.base_block httomo.block_interfaces httomo.cli_utils httomo.darks_flats httomo.data httomo.data.dataset_store httomo.data.hdf httomo.data.mpiutil httomo.data.padding httomo.data.param_sweep_store httomo.globals httomo.loaders httomo.loaders.standard_tomo_loader httomo.loaders.types httomo.logger httomo.method_wrappers httomo.method_wrappers.datareducer httomo.method_wrappers.dezinging httomo.method_wrappers.distortion_correction httomo.method_wrappers.generic httomo.method_wrappers.images httomo.method_wrappers.reconstruction httomo.method_wrappers.rotation httomo.method_wrappers.save_intermediate httomo.method_wrappers.stats_calc httomo.methods httomo.monitors httomo.monitors.aggregate httomo.monitors.benchmark httomo.monitors.summary httomo.preview httomo.runner httomo.runner.auxiliary_data httomo.runner.block_split httomo.runner.dataset httomo.runner.dataset_store_backing httomo.runner.dataset_store_interfaces httomo.runner.gpu_utils httomo.runner.loader httomo.runner.method_wrapper httomo.runner.methods_repository_interface httomo.runner.monitoring_interface httomo.runner.output_ref httomo.runner.pipeline httomo.runner.section httomo.runner.task_runner httomo.sweep_runner httomo.sweep_runner.param_sweep_block httomo.sweep_runner.param_sweep_runner httomo.sweep_runner.param_sweep_store_interfaces httomo.sweep_runner.param_sweep_yaml_loader httomo.sweep_runner.side_output_manager httomo.sweep_runner.stages httomo.transform_layer httomo.transform_loader_params httomo.types httomo.ui_layer httomo.utils httomo.yaml_checker

module_path (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.method_wrapper.MethodWrapper property) MonitoringInterface (class in httomo.runner.monitoring_interface) multiplier (httomo.runner.methods_repository_interface.GpuMemoryRequirement attribute)

N

no_of_sweeps (httomo.data.param_sweep_store.ParamSweepReader property) (httomo.data.param_sweep_store.ParamSweepWriter property) (httomo.sweep_runner.param_sweep_store_interfaces.ParamSweepSink property) (httomo.sweep_runner.param_sweep_store_interfaces.ParamSweepSource property)

no_of_sweeps_written (httomo.data.param_sweep_store.ParamSweepWriter property) NonSweepStage (class in httomo.sweep_runner.stages) normalize_sino() (httomo.method_wrappers.rotation.RotationWrapper method)

O

output_dims_change (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.method_wrapper.MethodWrapper property)

OutputRef (class in httomo.runner.output_ref)

P

package_name (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.loader.LoaderInterface attribute) (httomo.runner.method_wrapper.MethodWrapper property) padding (httomo.block_interfaces.BlockIndexing property) (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.dataset.DataSetBlock property) (httomo.runner.method_wrapper.MethodWrapper property) (httomo.sweep_runner.param_sweep_block.ParamSweepBlock property) padding() (httomo.runner.methods_repository_interface.MethodQuery method) param_name (httomo.sweep_runner.stages.SweepStage attribute) parameters (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.method_wrapper.MethodWrapper property) ParamSweepBlock (class in httomo.sweep_runner.param_sweep_block) ParamSweepReader (class in httomo.data.param_sweep_store) ParamSweepRunner (class in httomo.sweep_runner.param_sweep_runner)

ParamSweepSink (class in httomo.sweep_runner.param_sweep_store_interfaces) ParamSweepSource (class in httomo.sweep_runner.param_sweep_store_interfaces) ParamSweepWriter (class in httomo.data.param_sweep_store) ParamSweepYamlLoader (class in httomo.sweep_runner.param_sweep_yaml_loader) parse_angles() (in module httomo.transform_loader_params) parse_preview() (in module httomo.transform_loader_params) Pattern (class in httomo.utils) pattern (httomo.runner.loader.LoaderInterface attribute) (httomo.runner.method_wrapper.MethodWrapper attribute) Pipeline (class in httomo.runner.pipeline) prepare() (httomo.sweep_runner.param_sweep_runner.ParamSweepRunner method) Preview (class in httomo.preview) PreviewConfig (class in httomo.preview) PreviewDimConfig (class in httomo.preview) PreviewParam (class in httomo.transform_loader_params) projection (httomo.utils.Pattern attribute)

Q

query() (httomo.runner.methods_repository_interface.MethodRepository method)

R

RAM (httomo.runner.dataset_store_backing.DataSetStoreBacking attribute) RawAngles (class in httomo.loaders.types) RawAnglesParam (class in httomo.transform_loader_params) read_block() (httomo.data.dataset_store.DataSetStoreReader method) (httomo.loaders.standard_tomo_loader.StandardTomoLoader method) (httomo.runner.dataset_store_interfaces.DataSetSource method) read_sweep_results() (httomo.data.param_sweep_store.ParamSweepReader method) (httomo.sweep_runner.param_sweep_store_interfaces.ParamSweepSource method) ReadableDataSetSink (class in httomo.runner.dataset_store_interfaces) recon_algorithm (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.method_wrappers.reconstruction.ReconstructionWrapper property) (httomo.runner.method_wrapper.MethodWrapper property) ReconstructionWrapper (class in httomo.method_wrappers.reconstruction) RED (httomo.yaml_checker.Colour attribute) report_method_block() (httomo.monitors.aggregate.AggregateMonitoring method) (httomo.monitors.benchmark.BenchmarkMonitoring method) (httomo.monitors.summary.SummaryMonitor method) (httomo.runner.monitoring_interface.MonitoringInterface method)

report_sink_block() (httomo.monitors.aggregate.AggregateMonitoring method) (httomo.monitors.benchmark.BenchmarkMonitoring method) (httomo.monitors.summary.SummaryMonitor method) (httomo.runner.monitoring_interface.MonitoringInterface method) report_source_block() (httomo.monitors.aggregate.AggregateMonitoring method) (httomo.monitors.benchmark.BenchmarkMonitoring method) (httomo.monitors.summary.SummaryMonitor method) (httomo.runner.monitoring_interface.MonitoringInterface method) report_total_time() (httomo.monitors.aggregate.AggregateMonitoring method) (httomo.monitors.benchmark.BenchmarkMonitoring method) (httomo.monitors.summary.SummaryMonitor method) (httomo.runner.monitoring_interface.MonitoringInterface method) requires_preview() (httomo.method_wrappers.distortion_correction.DistortionCorrectionWrapper class method) (httomo.method_wrappers.generic.GenericMethodWrapper class method) RotationWrapper (class in httomo.method_wrappers.rotation)

S

sanity_check() (in module httomo.yaml_checker) save_intermediate_data() (in module httomo.methods) save_result (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.method_wrapper.MethodWrapper property) save_result_default() (httomo.runner.methods_repository_interface.MethodQuery method) SaveIntermediateFilesWrapper (class in httomo.method_wrappers.save_intermediate) Section (class in httomo.runner.section) sectionize() (in module httomo.runner.section) set_angles() (httomo.runner.auxiliary_data.AuxiliaryData method) set_darks() (httomo.runner.auxiliary_data.AuxiliaryData method) set_flats() (httomo.runner.auxiliary_data.AuxiliaryData method) set_side_inputs() (httomo.runner.task_runner.TaskRunner method) setup_dataset() (in module httomo.methods) setup_logger() (in module httomo.logger) shape (httomo.base_block.BaseBlock property) (httomo.block_interfaces.BlockData property) shape_unpadded (httomo.block_interfaces.BlockData property) (httomo.runner.dataset.DataSetBlock property) (httomo.sweep_runner.param_sweep_block.ParamSweepBlock property) should_select_this_class() (httomo.method_wrappers.datareducer.DatareducerWrapper class method) (httomo.method_wrappers.dezinging.DezingingWrapper class method) (httomo.method_wrappers.distortion_correction.DistortionCorrectionWrapper class method) (httomo.method_wrappers.generic.GenericMethodWrapper class method) (httomo.method_wrappers.images.ImagesWrapper class method) (httomo.method_wrappers.reconstruction.ReconstructionWrapper class method) (httomo.method_wrappers.rotation.RotationWrapper class method) (httomo.method_wrappers.save_intermediate.SaveIntermediateFilesWrapper class method) (httomo.method_wrappers.stats_calc.StatsCalcWrapper class method) SideOutputManager (class in httomo.sweep_runner.side_output_manager) single_shape (httomo.data.param_sweep_store.ParamSweepReader property) (httomo.data.param_sweep_store.ParamSweepWriter property) (httomo.sweep_runner.param_sweep_store_interfaces.ParamSweepSink property) (httomo.sweep_runner.param_sweep_store_interfaces.ParamSweepSource property)

sinogram (httomo.utils.Pattern attribute) slices_per_block (httomo.runner.block_split.BlockSplitter property) slices_per_sweep (httomo.data.param_sweep_store.ParamSweepWriter property) slicing_dim (httomo.block_interfaces.BlockIndexing property) (httomo.data.dataset_store.DataSetStoreReader property) (httomo.data.dataset_store.DataSetStoreWriter property) (httomo.loaders.standard_tomo_loader.StandardTomoLoader property) (httomo.runner.dataset.DataSetBlock property) (httomo.runner.dataset_store_interfaces.DataSetSink property) (httomo.runner.dataset_store_interfaces.DataSetSource property) (httomo.runner.dataset_store_interfaces.DummySink property) (httomo.sweep_runner.param_sweep_block.ParamSweepBlock property) Stages (class in httomo.sweep_runner.stages) StandardLoaderWrapper (class in httomo.loaders.standard_tomo_loader) StandardTomoLoader (class in httomo.loaders.standard_tomo_loader) start (httomo.preview.PreviewDimConfig attribute) (httomo.transform_loader_params.StartStopEntry attribute) start_angle (httomo.loaders.types.UserDefinedAngles attribute) (httomo.transform_loader_params.UserDefinedAnglesParamInner attribute) StartStopEntry (class in httomo.transform_loader_params) StatsCalcWrapper (class in httomo.method_wrappers.stats_calc) stop (httomo.preview.PreviewDimConfig attribute) (httomo.transform_loader_params.StartStopEntry attribute) stop_angle (httomo.loaders.types.UserDefinedAngles attribute) (httomo.transform_loader_params.UserDefinedAnglesParamInner attribute) SummaryMonitor (class in httomo.monitors.summary) swap_dims_on_output() (httomo.runner.methods_repository_interface.MethodQuery method) sweep (httomo.method_wrappers.generic.GenericMethodWrapper property) (httomo.runner.method_wrapper.MethodWrapper property) (httomo.sweep_runner.stages.Stages attribute) sweep_manual() (httomo.sweep_runner.param_sweep_yaml_loader.ParamSweepYamlLoader method) sweep_range() (httomo.sweep_runner.param_sweep_yaml_loader.ParamSweepYamlLoader method) SweepStage (class in httomo.sweep_runner.stages)

T

task_id (httomo.runner.method_wrapper.MethodWrapper attribute) TaskRunner (class in httomo.runner.task_runner) to_cpu() (httomo.base_block.BaseBlock method) (httomo.block_interfaces.BlockTransfer method) to_gpu() (httomo.base_block.BaseBlock method) (httomo.block_interfaces.BlockTransfer method)

total_shape (httomo.data.param_sweep_store.ParamSweepReader property) (httomo.data.param_sweep_store.ParamSweepWriter property) (httomo.sweep_runner.param_sweep_store_interfaces.ParamSweepSink property) (httomo.sweep_runner.param_sweep_store_interfaces.ParamSweepSource property) transform() (httomo.transform_layer.TransformLayer method) TransformLayer (class in httomo.transform_layer)

U

UiLayer (class in httomo.ui_layer) UniqueKeyLoader (class in httomo.yaml_checker) update_params() (httomo.sweep_runner.side_output_manager.SideOutputManager method) update_side_output_references() (in module httomo.ui_layer)

user_defined (httomo.transform_loader_params.UserDefinedAnglesParam attribute) UserDefinedAngles (class in httomo.loaders.types) UserDefinedAnglesParam (class in httomo.transform_loader_params) UserDefinedAnglesParamInner (class in httomo.transform_loader_params)

V

validate_yaml_config() (in module httomo.yaml_checker)

value (httomo.runner.output_ref.OutputRef property) values (httomo.sweep_runner.stages.SweepStage attribute)

W

write_block() (httomo.data.dataset_store.DataSetStoreWriter method) (httomo.runner.dataset_store_interfaces.DataSetSink method) (httomo.runner.dataset_store_interfaces.DummySink method) write_results() (httomo.monitors.aggregate.AggregateMonitoring method) (httomo.monitors.benchmark.BenchmarkMonitoring method) (httomo.monitors.summary.SummaryMonitor method) (httomo.runner.monitoring_interface.MonitoringInterface method)

write_sweep_result() (httomo.data.param_sweep_store.ParamSweepWriter method) (httomo.sweep_runner.param_sweep_store_interfaces.ParamSweepSink method)

Y

yaml_loader() (in module httomo.ui_layer)

YELLOW (httomo.yaml_checker.Colour attribute)