IMPERANDI

User guide

  • Installation
    • Optional features
    • Build these docs
    • Jupyter quality-control viewer
  • Quickstart
    • 1. Inspect the plan
    • 2. Ingest DICOM metadata
    • 3. Convert volumes to NIfTI
    • 4. Segment images
    • 5. Extract phase and radiomics
    • 6. Check failures before analysis
  • Workflow
    • Parse
    • Clean
    • Convert
    • Segment, phase, and radiomics
    • Checkpoints and resume
    • Example Slurm batch script
    • Operational recommendations
  • CLI Commands
    • parse
    • clean
    • ingest
    • convert
    • segment
    • phase
    • radiomics
    • Shared long-running options
  • Outputs
    • Identity and traceability
    • Image and mask paths
    • Error tables
  • Configuration
    • How configuration works
    • Manifest structure
    • Customize a manifest file
      • Identity and cohort metadata
      • Segmentation
      • Segmentation Mask Postprocessing
      • Radiomics
    • Hooks
      • id_standardization hooks
      • derived_columns hooks
      • Writing a custom hook
    • Precedence
    • Validation advice
  • Troubleshooting
    • The segment or phase command reports missing dependencies
    • Radiomics cannot import PyRadiomics
    • No DICOM files are found
    • IDs are empty or unexpected
    • Cleaning removes too many volumes
    • Conversion fails for archive-backed series
    • A resumed run uses stale results
    • Multiprocessing hangs or exhausts memory
    • The documentation build fails during API imports

Python API

  • Top-level package
    • main()
    • Command-line dispatcher
      • build_parser()
      • main()
  • Ingestion API
    • Parsing
      • add_parse_arguments()
      • build_effective_tags()
      • build_global_readers()
      • build_parser()
      • choose_ids()
      • default_output_dir()
      • detect_archive_mode_by_subsample()
      • ensure_directory_exists()
      • extract_dicom_tags_recursive()
      • get_dicom_path_entries()
      • get_dicom_paths()
      • main()
      • normalize_parse_args()
      • parse_arguments()
      • process_with_checkpoint()
      • read_dicom_header()
      • read_dicom_header_archive_aware()
      • read_dicom_header_selected()
      • read_dicom_header_selected_archive_aware()
      • read_dicom_header_selected_standard()
      • read_dicom_header_standard()
      • read_dicom_header_with_force()
      • resolve_root_paths()
      • write_dicom_tags_snapshot()
    • Cleaning
      • add_clean_arguments()
      • add_date()
      • add_time()
      • build_parser()
      • calculate_volume_length()
      • clean_and_save_data()
      • clean_pixel_spacing()
      • clean_scan_size()
      • compute_acquisition_order()
      • compute_visit_order()
      • correct_volume_ids()
      • drop_irrelevant_dicom_tags()
      • filter_by_acquisition_plane()
      • filter_ct_modality()
      • filter_image_type()
      • filter_volumes_by_size()
      • generate_volume_id()
      • group_volumes()
      • load_data()
      • map_series_description()
      • normalize_clean_args()
      • parse_arguments()
      • read_csv_with_valid_columns()
      • remove_mpr()
      • remove_other_organs_description()
      • remove_pet_ct()
      • remove_scouts_localizers()
      • reorder_columns()
      • reorder_rows()
      • uniform_string()
    • Manifest hooks
      • apply_derived_columns()
      • apply_id_standardization()
  • Processing API
    • DICOM conversion
      • add_convert_arguments()
      • build_parser()
      • convert_dicom_to_nifti_parallel()
      • convert_list_str_to_list()
      • main()
      • materialize_archive_dicom_paths()
      • normalize_convert_args()
      • parse_arguments()
      • process_single_volume()
    • Segmentation
      • segment.py
      • TotalSegmentatorBackend
      • add_segment_arguments()
      • build_output_column_map()
      • build_output_fetch_map()
      • build_parser()
      • clean_and_merge_masks()
      • compute_struct_elem()
      • infer_task_fetch_outputs()
      • infer_task_outputs()
      • load_nifti()
      • load_segmentation_config()
      • main()
      • normalize_segment_args()
      • prefetch_totalsegmentator_models()
      • process_single_volume()
      • resolve_merge_outputs()
      • save_nifti()
      • segment_volume()
  • Extraction API
    • Contrast phase
      • add_phase_arguments()
      • build_parser()
      • main()
      • normalize_phase_args()
      • parse_arguments()
      • process_single_volume()
    • Radiomics
      • add_radiomics_arguments()
      • build_parser()
      • extract_radiomics_organ_minus_tumor()
      • extract_radiomics_safe()
      • main()
      • mask_has_voxels()
      • normalize_radiomics_args()
      • parse_arguments()
  • Quality-control Dashboards
    • Interactive viewer in Jupyter Notebook
      • CTScanViewer
      • clip_hu_values()
      • load_nifti()
    • Viewer resampling helpers
      • load_nifti_isotropic()
      • load_oriented_nifti()
      • resample_to_isotropic()
      • validate_isotropic_resolution()
IMPERANDI
  • Python Module Index

Python Module Index

i
 
i
- imperandi
    imperandi.cli
    imperandi.extract.phase
    imperandi.extract.radiomics
    imperandi.ingest.apply_hook_manifests
    imperandi.ingest.clean
    imperandi.ingest.parse
    imperandi.process.convert
    imperandi.process.segment
    imperandi.qc.viewer
    imperandi.qc.viewer_resample

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