Index

A

angle_step (ewokstomo.tasks.buildgallery.ProjectionsGalleryInputModel attribute) apply_correction() (ewokstomo.tasks.online.preprocessing.FlatFieldCorrection method) apply_flat_field_correction() (ewokstomo.tasks.buildgallery.BuildProjectionsGallery method)

apply_phase_retrieval() (in module ewokstomo.tasks.online.preprocessing) ApplyAttenuators (class in ewokstomo.tasks.energycalculation) assert_icat_accepts_metadata_keys() (in module ewokstomo.tests.test_dataportalupload)

B

bliss_hdf5_path (ewokstomo.tasks.nxtomomill.FluoToNxInputModel attribute) (ewokstomo.tasks.nxtomomill.H5ToNxInputModel attribute) bounds (ewokstomo.tasks.buildgallery.ProjectionsGalleryInputModel attribute) (ewokstomo.tasks.buildgallery.SlicesGalleryInputModel attribute) (ewokstomo.tasks.buildgallery.VolumeGalleryInputModel attribute) build_nxtomo_from_inputs() (in module ewokstomo.tasks.nxtomo_utils)

BuildDataPortalMetadata (class in ewokstomo.tasks.dataportalupload) BuildDataPortalMetadataInputModel (class in ewokstomo.tasks.dataportalupload) BuildDataPortalMetadataOutputModel (class in ewokstomo.tasks.dataportalupload) BuildProjectionsGallery (class in ewokstomo.tasks.buildgallery) BuildSlicesGallery (class in ewokstomo.tasks.buildgallery) BuildVolumeGallery (class in ewokstomo.tasks.buildgallery)

C

clean_angle_key() (in module ewokstomo.tasks.buildgallery) ComputeBMSpectrum (class in ewokstomo.tasks.energycalculation) ComputeWigglerSpectrum (class in ewokstomo.tasks.energycalculation) config_dict (ewokstomo.tasks.reconstruct_slice.ReconstructSliceInputModel attribute) (ewokstomo.tasks.reconstruct_volume.ReconstructVolumeInputsModel attribute)

converted_volume_path (ewokstomo.tasks.convert_volume.ConvertVolumeTo16BitOutputsModel attribute) ConvertVolumeTo16Bit (class in ewokstomo.tasks.convert_volume) ConvertVolumeTo16BitInputsModel (class in ewokstomo.tasks.convert_volume) ConvertVolumeTo16BitOutputsModel (class in ewokstomo.tasks.convert_volume) cursor() (ewokstomo.tests.online.mock.FakeImageStream method) (ewokstomo.tests.online.mock.FakeStream method)

D

dark_reduction_method (ewokstomo.tasks.reducedarkflat.ReduceDarkFlatInputModel attribute) dataportal_metadata (ewokstomo.tasks.dataportalupload.BuildDataPortalMetadataOutputModel attribute) DataPortalUpload (class in ewokstomo.tasks.dataportalupload)

DataPortalUploadInputModel (class in ewokstomo.tasks.dataportalupload) dataset (ewokstomo.tasks.dataportalupload.DataPortalUploadInputModel attribute) dry_run (ewokstomo.tasks.dataportalupload.DataPortalUploadInputModel attribute)

E

ewokstomo module ewokstomo.tasks module ewokstomo.tasks.buildgallery module ewokstomo.tasks.convert_volume module ewokstomo.tasks.dataportalupload module ewokstomo.tasks.energycalculation module ewokstomo.tasks.linkresults module ewokstomo.tasks.nxtomo_utils module ewokstomo.tasks.nxtomomill module ewokstomo.tasks.online module ewokstomo.tasks.online.preprocessing module ewokstomo.tasks.online.reconstruct_slice module ewokstomo.tasks.online.reducedarkflat module ewokstomo.tasks.reconstruct_slice module ewokstomo.tasks.reconstruct_volume module ewokstomo.tasks.reducedarkflat module ewokstomo.tasks.tomobasictonxtomo module ewokstomo.tasks.utils module

ewokstomo.tests module ewokstomo.tests.online module ewokstomo.tests.online.mock module ewokstomo.tests.online.test_preprocessing module ewokstomo.tests.online.test_reconstruction module ewokstomo.tests.online.test_reducedarkflat module ewokstomo.tests.test_convertvolume module ewokstomo.tests.test_dataportalupload module ewokstomo.tests.test_energycalculation module ewokstomo.tests.test_gallery module ewokstomo.tests.test_linkresults module ewokstomo.tests.test_nxtomomill module ewokstomo.tests.test_reconstructslice module ewokstomo.tests.test_reconstructvolume module ewokstomo.tests.test_reducedarkflat module ewokstomo.tests.test_tomobasictonxtomo module ewokstomo.tests.test_utils module ewokstomo.workflows module

F

fake_hdf5_volume() (in module ewokstomo.tests.test_convertvolume) fake_hdf5_volume_no_32bit() (in module ewokstomo.tests.test_convertvolume) fake_tiff_volume() (in module ewokstomo.tests.test_convertvolume) fake_tiff_volume_no_32bit() (in module ewokstomo.tests.test_convertvolume) FakeCursor (class in ewokstomo.tests.online.mock) FakeImageStream (class in ewokstomo.tests.online.mock) FakeMotorStream (class in ewokstomo.tests.online.mock) FakeScan (class in ewokstomo.tests.online.mock)

FakeScanWithMotor (class in ewokstomo.tests.online.mock) FakeStream (class in ewokstomo.tests.online.mock) fbp_reconstruction_slice() (in module ewokstomo.tasks.online.reconstruct_slice) flat_reduction_method (ewokstomo.tasks.reducedarkflat.ReduceDarkFlatInputModel attribute) FlatFieldCorrection (class in ewokstomo.tasks.online.preprocessing) FluoToNx (class in ewokstomo.tasks.nxtomomill) FluoToNxInputModel (class in ewokstomo.tasks.nxtomomill) FluoToNxOutputModel (class in ewokstomo.tasks.nxtomomill)

G

gallery_image_path (ewokstomo.tasks.buildgallery.SlicesGalleryOutputModel attribute) gallery_image_paths (ewokstomo.tasks.buildgallery.VolumeGalleryOutputModel attribute) gallery_path (ewokstomo.tasks.buildgallery.ProjectionsGalleryOutputModel attribute) (ewokstomo.tasks.buildgallery.SlicesGalleryOutputModel attribute) (ewokstomo.tasks.buildgallery.VolumeGalleryOutputModel attribute) get_beam_intensities() (ewokstomo.tasks.buildgallery.BuildProjectionsGallery method) get_darks_from_h5() (ewokstomo.tasks.buildgallery.BuildProjectionsGallery method) get_data_dir() (in module ewokstomo.tests.test_gallery) (in module ewokstomo.tests.test_reconstructslice) (in module ewokstomo.tests.test_reconstructvolume) (in module ewokstomo.tests.test_reducedarkflat) get_data_file() (in module ewokstomo.tests.test_nxtomomill) (in module ewokstomo.tests.test_reconstructslice) (in module ewokstomo.tests.test_reconstructvolume)

get_flats_from_h5() (ewokstomo.tasks.buildgallery.BuildProjectionsGallery method) get_gallery_dir() (ewokstomo.tasks.buildgallery.BuildProjectionsGallery method) (ewokstomo.tasks.buildgallery.BuildSlicesGallery method) get_gallery_file_path() (ewokstomo.tasks.buildgallery.BuildProjectionsGallery method) (ewokstomo.tasks.buildgallery.BuildSlicesGallery method) get_image_stream_name() (ewokstomo.tasks.online.reducedarkflat.OnlineReduceDarkFlat method) get_json_file() (in module ewokstomo.tests.test_nxtomomill) (in module ewokstomo.tests.test_reconstructslice) (in module ewokstomo.tests.test_reconstructvolume) (in module ewokstomo.tests.test_reducedarkflat) get_proj_from_data_url() (ewokstomo.tasks.buildgallery.BuildProjectionsGallery method) get_projections_by_angle_step() (ewokstomo.tasks.buildgallery.BuildProjectionsGallery method) get_raw_data_dir() (in module ewokstomo.tests.test_reducedarkflat) get_reduction_function() (ewokstomo.tasks.online.reducedarkflat.OnlineReduceDarkFlat method) get_slice_index() (in module ewokstomo.tasks.online.reconstruct_slice)

H

H5ToNx (class in ewokstomo.tasks.nxtomomill)

H5ToNxInputModel (class in ewokstomo.tasks.nxtomomill) H5ToNxOutputModel (class in ewokstomo.tasks.nxtomomill)

I

icat_client_factory() (ewokstomo.tasks.dataportalupload.DataPortalUpload static method) image_size (ewokstomo.tasks.buildgallery.ProjectionsGalleryInputModel attribute) (ewokstomo.tasks.buildgallery.SlicesGalleryInputModel attribute) (ewokstomo.tasks.buildgallery.VolumeGalleryInputModel attribute)

L

LinkSlices (class in ewokstomo.tasks.linkresults) LinkSlicesInputModel (class in ewokstomo.tasks.linkresults) LinkSlicesOutputModel (class in ewokstomo.tasks.linkresults)

LinkVolumes (class in ewokstomo.tasks.linkresults) LinkVolumesInputModel (class in ewokstomo.tasks.linkresults) LinkVolumesOutputModel (class in ewokstomo.tasks.linkresults) load_reduced_data_from_file() (ewokstomo.tasks.online.preprocessing.FlatFieldCorrection method)

M

make_task() (in module ewokstomo.tests.test_dataportalupload) metadata (ewokstomo.tasks.dataportalupload.DataPortalUploadInputModel attribute) model_config (ewokstomo.tasks.buildgallery.ProjectionsGalleryInputModel attribute) (ewokstomo.tasks.buildgallery.ProjectionsGalleryOutputModel attribute) (ewokstomo.tasks.buildgallery.SlicesGalleryInputModel attribute) (ewokstomo.tasks.buildgallery.SlicesGalleryOutputModel attribute) (ewokstomo.tasks.buildgallery.VolumeGalleryInputModel attribute) (ewokstomo.tasks.buildgallery.VolumeGalleryOutputModel attribute) (ewokstomo.tasks.convert_volume.ConvertVolumeTo16BitInputsModel attribute) (ewokstomo.tasks.convert_volume.ConvertVolumeTo16BitOutputsModel attribute) (ewokstomo.tasks.dataportalupload.BuildDataPortalMetadataInputModel attribute) (ewokstomo.tasks.dataportalupload.BuildDataPortalMetadataOutputModel attribute) (ewokstomo.tasks.dataportalupload.DataPortalUploadInputModel attribute) (ewokstomo.tasks.linkresults.LinkSlicesInputModel attribute) (ewokstomo.tasks.linkresults.LinkSlicesOutputModel attribute) (ewokstomo.tasks.linkresults.LinkVolumesInputModel attribute) (ewokstomo.tasks.linkresults.LinkVolumesOutputModel attribute) (ewokstomo.tasks.nxtomomill.FluoToNxInputModel attribute) (ewokstomo.tasks.nxtomomill.FluoToNxOutputModel attribute) (ewokstomo.tasks.nxtomomill.H5ToNxInputModel attribute) (ewokstomo.tasks.nxtomomill.H5ToNxOutputModel attribute) (ewokstomo.tasks.reconstruct_slice.ReconstructSliceInputModel attribute) (ewokstomo.tasks.reconstruct_slice.ReconstructSliceOutputModel attribute) (ewokstomo.tasks.reconstruct_volume.ReconstructVolumeInputsModel attribute) (ewokstomo.tasks.reconstruct_volume.ReconstructVolumeOutputsModel attribute) (ewokstomo.tasks.reducedarkflat.ReduceDarkFlatInputModel attribute) (ewokstomo.tasks.reducedarkflat.ReduceDarkFlatOutputModel attribute) module ewokstomo ewokstomo.tasks ewokstomo.tasks.buildgallery ewokstomo.tasks.convert_volume ewokstomo.tasks.dataportalupload ewokstomo.tasks.energycalculation ewokstomo.tasks.linkresults ewokstomo.tasks.nxtomo_utils ewokstomo.tasks.nxtomomill ewokstomo.tasks.online ewokstomo.tasks.online.preprocessing ewokstomo.tasks.online.reconstruct_slice ewokstomo.tasks.online.reducedarkflat ewokstomo.tasks.reconstruct_slice ewokstomo.tasks.reconstruct_volume ewokstomo.tasks.reducedarkflat ewokstomo.tasks.tomobasictonxtomo ewokstomo.tasks.utils ewokstomo.tests ewokstomo.tests.online ewokstomo.tests.online.mock ewokstomo.tests.online.test_preprocessing ewokstomo.tests.online.test_reconstruction ewokstomo.tests.online.test_reducedarkflat ewokstomo.tests.test_convertvolume ewokstomo.tests.test_dataportalupload ewokstomo.tests.test_energycalculation ewokstomo.tests.test_gallery ewokstomo.tests.test_linkresults ewokstomo.tests.test_nxtomomill ewokstomo.tests.test_reconstructslice ewokstomo.tests.test_reconstructvolume ewokstomo.tests.test_reducedarkflat ewokstomo.tests.test_tomobasictonxtomo ewokstomo.tests.test_utils ewokstomo.workflows

N

nabu_dict (ewokstomo.tasks.convert_volume.ConvertVolumeTo16BitInputsModel attribute) (ewokstomo.tasks.reconstruct_slice.ReconstructSliceOutputModel attribute) (ewokstomo.tasks.reconstruct_volume.ReconstructVolumeOutputsModel attribute) nx_path (ewokstomo.tasks.buildgallery.ProjectionsGalleryInputModel attribute) (ewokstomo.tasks.nxtomomill.FluoToNxInputModel attribute) (ewokstomo.tasks.nxtomomill.FluoToNxOutputModel attribute) (ewokstomo.tasks.nxtomomill.H5ToNxInputModel attribute) (ewokstomo.tasks.nxtomomill.H5ToNxOutputModel attribute) (ewokstomo.tasks.reconstruct_slice.ReconstructSliceInputModel attribute) (ewokstomo.tasks.reconstruct_volume.ReconstructVolumeInputsModel attribute) (ewokstomo.tasks.reducedarkflat.ReduceDarkFlatInputModel attribute)

O

OnlineReconstructSlice (class in ewokstomo.tasks.online.reconstruct_slice) OnlineReduceDarkFlat (class in ewokstomo.tasks.online.reducedarkflat) output_dtype (ewokstomo.tasks.reducedarkflat.ReduceDarkFlatInputModel attribute) output_format (ewokstomo.tasks.buildgallery.ProjectionsGalleryInputModel attribute) (ewokstomo.tasks.buildgallery.SlicesGalleryInputModel attribute) (ewokstomo.tasks.buildgallery.VolumeGalleryInputModel attribute) (ewokstomo.tasks.convert_volume.ConvertVolumeTo16BitInputsModel attribute)

overwrite (ewokstomo.tasks.buildgallery.ProjectionsGalleryInputModel attribute) (ewokstomo.tasks.buildgallery.SlicesGalleryInputModel attribute) (ewokstomo.tasks.buildgallery.VolumeGalleryInputModel attribute) (ewokstomo.tasks.linkresults.LinkSlicesInputModel attribute) (ewokstomo.tasks.linkresults.LinkVolumesInputModel attribute) (ewokstomo.tasks.reducedarkflat.ReduceDarkFlatInputModel attribute)

P

process_folder_path (ewokstomo.tasks.dataportalupload.DataPortalUploadInputModel attribute) processed_data_dir (ewokstomo.tasks.buildgallery.ProjectionsGalleryOutputModel attribute) (ewokstomo.tasks.buildgallery.SlicesGalleryOutputModel attribute) (ewokstomo.tasks.buildgallery.VolumeGalleryOutputModel attribute)

processing_options (ewokstomo.tasks.dataportalupload.BuildDataPortalMetadataInputModel attribute) (ewokstomo.tasks.reconstruct_slice.ReconstructSliceOutputModel attribute) (ewokstomo.tasks.reconstruct_volume.ReconstructVolumeOutputsModel attribute) ProjectionsGalleryInputModel (class in ewokstomo.tasks.buildgallery) ProjectionsGalleryOutputModel (class in ewokstomo.tasks.buildgallery)

R

read() (ewokstomo.tests.online.mock.FakeCursor method) read_stream() (ewokstomo.tasks.online.reducedarkflat.OnlineReduceDarkFlat method) reconstruct_batch() (ewokstomo.tasks.online.reconstruct_slice.OnlineReconstructSlice method) reconstructed_slice_path (ewokstomo.tasks.buildgallery.SlicesGalleryInputModel attribute) (ewokstomo.tasks.linkresults.LinkSlicesInputModel attribute) (ewokstomo.tasks.linkresults.LinkSlicesOutputModel attribute) (ewokstomo.tasks.reconstruct_slice.ReconstructSliceOutputModel attribute) reconstructed_volume_path (ewokstomo.tasks.buildgallery.VolumeGalleryInputModel attribute) (ewokstomo.tasks.convert_volume.ConvertVolumeTo16BitInputsModel attribute) (ewokstomo.tasks.linkresults.LinkVolumesInputModel attribute) (ewokstomo.tasks.linkresults.LinkVolumesOutputModel attribute) (ewokstomo.tasks.reconstruct_volume.ReconstructVolumeOutputsModel attribute) ReconstructSlice (class in ewokstomo.tasks.reconstruct_slice) ReconstructSliceInputModel (class in ewokstomo.tasks.reconstruct_slice) ReconstructSliceOutputModel (class in ewokstomo.tasks.reconstruct_slice) ReconstructVolume (class in ewokstomo.tasks.reconstruct_volume) ReconstructVolumeInputsModel (class in ewokstomo.tasks.reconstruct_volume) ReconstructVolumeOutputsModel (class in ewokstomo.tasks.reconstruct_volume) reduced_darks_path (ewokstomo.tasks.buildgallery.ProjectionsGalleryInputModel attribute) (ewokstomo.tasks.reducedarkflat.ReduceDarkFlatOutputModel attribute) reduced_flats_path (ewokstomo.tasks.buildgallery.ProjectionsGalleryInputModel attribute) (ewokstomo.tasks.reducedarkflat.ReduceDarkFlatOutputModel attribute) ReduceDarkFlat (class in ewokstomo.tasks.reducedarkflat)

ReduceDarkFlatInputModel (class in ewokstomo.tasks.reducedarkflat) ReduceDarkFlatOutputModel (class in ewokstomo.tasks.reducedarkflat) reference_dir_to_soft_link (ewokstomo.tasks.reducedarkflat.ReduceDarkFlatInputModel attribute) return_info (ewokstomo.tasks.reducedarkflat.ReduceDarkFlatInputModel attribute) run() (ewokstomo.tasks.buildgallery.BuildProjectionsGallery method) (ewokstomo.tasks.buildgallery.BuildSlicesGallery method) (ewokstomo.tasks.buildgallery.BuildVolumeGallery method) (ewokstomo.tasks.convert_volume.ConvertVolumeTo16Bit method) (ewokstomo.tasks.dataportalupload.BuildDataPortalMetadata method) (ewokstomo.tasks.dataportalupload.DataPortalUpload method) (ewokstomo.tasks.energycalculation.ApplyAttenuators method) (ewokstomo.tasks.energycalculation.ComputeBMSpectrum method) (ewokstomo.tasks.energycalculation.ComputeWigglerSpectrum method) (ewokstomo.tasks.energycalculation.SpectrumStats method) (ewokstomo.tasks.linkresults.LinkSlices method) (ewokstomo.tasks.linkresults.LinkVolumes method) (ewokstomo.tasks.nxtomomill.FluoToNx method) (ewokstomo.tasks.nxtomomill.H5ToNx method) (ewokstomo.tasks.online.reconstruct_slice.OnlineReconstructSlice method) (ewokstomo.tasks.online.reducedarkflat.OnlineReduceDarkFlat method) (ewokstomo.tasks.reconstruct_slice.ReconstructSlice method) (ewokstomo.tasks.reconstruct_volume.ReconstructVolume method) (ewokstomo.tasks.reducedarkflat.ReduceDarkFlat method) (ewokstomo.tasks.tomobasictonxtomo.TomoBasicToNXtomo method)

S

save_reconstructed_slice() (ewokstomo.tasks.online.reconstruct_slice.OnlineReconstructSlice method) simple_image() (in module ewokstomo.tests.test_gallery) slice_index (ewokstomo.tasks.reconstruct_slice.ReconstructSliceInputModel attribute) (ewokstomo.tasks.reconstruct_slice.ReconstructSliceOutputModel attribute) slice_index_range (ewokstomo.tasks.reconstruct_volume.ReconstructVolumeInputsModel attribute)

slices_link_collection_file (ewokstomo.tasks.linkresults.LinkSlicesOutputModel attribute) slices_link_root_file (ewokstomo.tasks.linkresults.LinkSlicesOutputModel attribute) SlicesGalleryInputModel (class in ewokstomo.tasks.buildgallery) SlicesGalleryOutputModel (class in ewokstomo.tasks.buildgallery) SpectrumStats (class in ewokstomo.tasks.energycalculation)

T

test_apply_attenuators_missing_flux_sentinel() (in module ewokstomo.tests.test_energycalculation) test_apply_attenuators_respects_order_duplicates() (in module ewokstomo.tests.test_energycalculation) test_apply_attenuators_without_flux() (in module ewokstomo.tests.test_energycalculation) test_apply_flat_field_correction_calls_normalize() (in module ewokstomo.tests.online.test_preprocessing) test_apply_phase_retrieval_basic_flow() (in module ewokstomo.tests.online.test_preprocessing) test_auto_bounds_handles_negative_values() (in module ewokstomo.tests.test_gallery) test_build_dataportal_metadata_accepts_string_and_sequence_voxel_size() (in module ewokstomo.tests.test_dataportalupload) test_build_dataportal_metadata_prefers_processing_options_for_recon() (in module ewokstomo.tests.test_dataportalupload) test_build_dataportal_metadata_skips_invalid_voxel_size() (in module ewokstomo.tests.test_dataportalupload) test_build_dataportal_metadata_task_handles_missing_and_invalid() (in module ewokstomo.tests.test_dataportalupload) test_build_dataportal_metadata_transforms_and_filters() (in module ewokstomo.tests.test_dataportalupload) test_build_dataportal_metadata_with_string_none_method_skips_dataset_metadata() (in module ewokstomo.tests.test_dataportalupload) test_build_from_inputs_coerces_integer_translation_inputs_to_float64() (in module ewokstomo.tests.test_tomobasictonxtomo) test_build_from_inputs_detector_data_axes_no_flip() (in module ewokstomo.tests.test_tomobasictonxtomo) test_build_from_inputs_matches_reference() (in module ewokstomo.tests.test_tomobasictonxtomo) test_build_from_inputs_rejects_h5_url_entries() (in module ewokstomo.tests.test_tomobasictonxtomo) test_build_from_inputs_sets_energy_without_deprecation_warning() (in module ewokstomo.tests.test_tomobasictonxtomo) test_build_from_inputs_succeeds_on_missing_source_dataset() (in module ewokstomo.tests.test_tomobasictonxtomo) test_build_from_inputs_supports_detector_data_axes() (in module ewokstomo.tests.test_tomobasictonxtomo) test_build_from_inputs_virtual_sources_without_opening_sources() (in module ewokstomo.tests.test_tomobasictonxtomo) test_build_payload_adds_workflow_type() (in module ewokstomo.tests.test_dataportalupload) test_build_payload_does_not_infer_workflow_type_from_folder_path() (in module ewokstomo.tests.test_dataportalupload) test_build_payload_overrides_workflow_type_to_match_dataset() (in module ewokstomo.tests.test_dataportalupload) test_buildgallery_angles() (in module ewokstomo.tests.test_gallery) test_buildgallery_task() (in module ewokstomo.tests.test_gallery) test_buildslicesgallery_bounds_and_resize() (in module ewokstomo.tests.test_gallery) test_buildslicesgallery_creates_one_image() (in module ewokstomo.tests.test_gallery) test_buildslicesgallery_drops_dataset_name_from_absorption_preview() (in module ewokstomo.tests.test_gallery) test_buildslicesgallery_overwrite_guard() (in module ewokstomo.tests.test_gallery) test_buildvolumegallery_creates_nine_images() (in module ewokstomo.tests.test_gallery) test_buildvolumegallery_overwrite_guard() (in module ewokstomo.tests.test_gallery) test_canonical_compound_name_strips_and_lowercases() (in module ewokstomo.tests.test_energycalculation) test_compute_bm_spectrum_sorts_outputs() (in module ewokstomo.tests.test_energycalculation) test_compute_bm_spectrum_validates_inputs() (in module ewokstomo.tests.test_energycalculation) test_compute_wiggler_spectrum_sorts_and_uses_defaults() (in module ewokstomo.tests.test_energycalculation) test_convert_volume_hdf5() (in module ewokstomo.tests.test_convertvolume) test_convert_volume_hdf5_no_32bit_warns() (in module ewokstomo.tests.test_convertvolume) test_convert_volume_tiff() (in module ewokstomo.tests.test_convertvolume) test_convert_volume_tiff_no_32bit_warns() (in module ewokstomo.tests.test_convertvolume) test_data() (in module ewokstomo.tests.online.test_reconstruction) test_dry_run_adds_missing_sample_key_is_mentioned() (in module ewokstomo.tests.test_dataportalupload) test_dry_run_filters_icat_metadata_compatibility_issues() (in module ewokstomo.tests.test_dataportalupload) test_dry_run_happy_case_logs_basic_fields() (in module ewokstomo.tests.test_dataportalupload) test_dry_run_infers_sample_name_is_mentioned() (in module ewokstomo.tests.test_dataportalupload) test_full_workflow_online_reconstruction() (in module ewokstomo.tests.online.test_reconstruction) test_get_image_stream_name_no_image_stream() (in module ewokstomo.tests.online.test_reconstruction) test_get_motor_stream_name_no_motor() (in module ewokstomo.tests.online.test_reconstruction) test_get_projections_stream_timeout() (in module ewokstomo.tests.online.test_reconstruction)

test_get_slice_index() (in module ewokstomo.tests.online.test_reconstruction) test_is_missing_data_detects_runtime_free_sentinel() (in module ewokstomo.tests.test_energycalculation) test_linkslices_creates_collection_and_root_symlinks() (in module ewokstomo.tests.test_linkresults) test_linkslices_is_noop_for_non_esrf_path() (in module ewokstomo.tests.test_linkresults) test_linkslices_overwrite_guard() (in module ewokstomo.tests.test_linkresults) test_linkvolumes_creates_collection_and_root_symlinks() (in module ewokstomo.tests.test_linkresults) test_linkvolumes_is_noop_for_non_esrf_path() (in module ewokstomo.tests.test_linkresults) test_linkvolumes_overwrite_guard() (in module ewokstomo.tests.test_linkresults) test_load_reduced_data_from_hdf5() (in module ewokstomo.tests.online.test_preprocessing) test_normalize_projections_by_beam_intensity() (in module ewokstomo.tests.test_gallery) test_nxtomomill_fluo2nx() (in module ewokstomo.tests.test_nxtomomill) test_nxtomomill_task_outputs() (in module ewokstomo.tests.test_nxtomomill) test_nxtomomill_workflow_fluo2nx() (in module ewokstomo.tests.test_nxtomomill) test_nxtomomill_workflow_outputs() (in module ewokstomo.tests.test_nxtomomill) test_projection_index_from_data_url() (in module ewokstomo.tests.test_gallery) test_reconstruct_batch_fbp_failure() (in module ewokstomo.tests.online.test_reconstruction) test_reconstruct_batch_phase_retrieval_failure() (in module ewokstomo.tests.online.test_reconstruction) test_reconstructslice_task_outputs() (in module ewokstomo.tests.test_reconstructslice) test_reconstructslice_workflow_outputs() (in module ewokstomo.tests.test_reconstructslice) test_reconstructvolume_and_convert_workflow_outputs() (in module ewokstomo.tests.test_reconstructvolume) test_reconstructvolume_task_outputs() (in module ewokstomo.tests.test_reconstructvolume) test_reducedarkflat_offline() (in module ewokstomo.tests.online.test_reducedarkflat) test_reducedarkflat_online() (in module ewokstomo.tests.online.test_reducedarkflat) test_reducedarkflat_task_outputs() (in module ewokstomo.tests.test_reducedarkflat) test_reducedarkflat_workflow_outputs() (in module ewokstomo.tests.test_reducedarkflat) test_resolve_mu_density_compound_parser_defaults_to_unit_density() (in module ewokstomo.tests.test_energycalculation) test_resolve_mu_density_compound_uses_alias() (in module ewokstomo.tests.test_energycalculation) test_resolve_mu_density_element_auto_density() (in module ewokstomo.tests.test_energycalculation) test_resolve_mu_density_unknown_material_raises() (in module ewokstomo.tests.test_energycalculation) test_run_stops_on_reconstruct_batch_runtime_error() (in module ewokstomo.tests.online.test_reconstruction) test_save_to_gallery_bounds() (in module ewokstomo.tests.test_gallery) test_spectrum_stats_mean_and_peak() (in module ewokstomo.tests.test_energycalculation) test_spectrum_stats_no_valid_entries() (in module ewokstomo.tests.test_energycalculation) test_spectrum_stats_requires_matching_shapes() (in module ewokstomo.tests.test_energycalculation) test_tomobasictonxtomo_matches_nxtomomill_ground_truth() (in module ewokstomo.tests.test_tomobasictonxtomo) test_transmission_handles_zero_thickness() (in module ewokstomo.tests.test_energycalculation) test_validation_errors_log_warning_and_no_dryrun() (in module ewokstomo.tests.test_dataportalupload) test_wait_for_scan_state_higher_state() (in module ewokstomo.tests.test_utils) test_wait_for_scan_state_reaches_desired_state() (in module ewokstomo.tests.test_utils) TestEwoksTomo_0010_dataset() (in module ewokstomo.tests.online.test_reconstruction) (in module ewokstomo.tests.online.test_reducedarkflat) tmp_dataset_path() (in module ewokstomo.tests.online.test_reconstruction) (in module ewokstomo.tests.test_gallery) (in module ewokstomo.tests.test_reconstructslice) (in module ewokstomo.tests.test_reconstructvolume) (in module ewokstomo.tests.test_reducedarkflat) TomoBasicToNXtomo (class in ewokstomo.tasks.tomobasictonxtomo) TomoPath (class in ewokstomo.tasks.buildgallery) (class in ewokstomo.tasks.linkresults)

V

VolumeGalleryInputModel (class in ewokstomo.tasks.buildgallery) VolumeGalleryOutputModel (class in ewokstomo.tasks.buildgallery)

volumes_link_collection_file (ewokstomo.tasks.linkresults.LinkVolumesOutputModel attribute) volumes_link_root_file (ewokstomo.tasks.linkresults.LinkVolumesOutputModel attribute)

W

wait_for_scan_state() (in module ewokstomo.tasks.utils)