simind-python-connector

Contents:

  • Introduction
    • Disclaimer
  • Installation
    • Prerequisites
    • Install the Python Package
    • Development Install
    • SIMIND Requirement (External Dependency)
      • Disclaimer
      • Repo/Docker Layout
      • Local Runtime Environment
      • Docker Behavior
    • Quick Verification
  • Usage Guide
    • Quick Start
    • Adaptor Workflows
      • STIR adaptor
      • SIRF adaptor
      • PyTomography adaptor
    • Density Conversion
  • Backend and Adaptor Dependencies
    • Dependency Matrix
    • Backend Abstraction Module
  • Geometry Considerations
    • At-a-Glance Axis Conventions
    • Practical Implication
    • Units
    • Example Configuration Guardrails
    • Debug Checklist
  • Examples
    • Running Examples
    • Output Files
  • API Documentation
    • Top-Level Package
    • Core
      • SimulationConfig
        • SimulationConfig.filepath
        • SimulationConfig.index_dict
        • SimulationConfig.flag_dict
        • SimulationConfig.data_file_dict
        • SimulationConfig.data
        • SimulationConfig.flags
        • SimulationConfig.text_variables
        • SimulationConfig.data_files
        • SimulationConfig.comment
        • SimulationConfig.__init__()
        • SimulationConfig.import_smc()
        • SimulationConfig.to_yaml_dict()
        • SimulationConfig.export_yaml()
        • SimulationConfig.import_yaml()
        • SimulationConfig.validate_parameters()
        • SimulationConfig.get_simind_version_info()
        • SimulationConfig.print_config()
        • SimulationConfig.get_value()
        • SimulationConfig.set_value()
        • SimulationConfig.get_flag()
        • SimulationConfig.set_flag()
        • SimulationConfig.set_data_file()
        • SimulationConfig.get_data_file()
        • SimulationConfig.get_comment()
        • SimulationConfig.set_comment()
        • SimulationConfig.save_file()
      • RuntimeSwitches
        • RuntimeSwitches.__init__()
        • RuntimeSwitches.combined_switch_dict
        • RuntimeSwitches.set_switch()
        • RuntimeSwitches.print_switches()
        • RuntimeSwitches.print_available_switches()
      • SimindExecutor
        • SimindExecutor.__init__()
        • SimindExecutor.run_simulation()
    • Connectors and Adaptors
      • BaseConnector
        • BaseConnector.add_config_value()
        • BaseConnector.add_runtime_switch()
        • BaseConnector.set_runtime_switches()
        • BaseConnector.run()
        • BaseConnector.get_outputs()
        • BaseConnector.get_config()
      • NumpyConnector
      • PyTomographySimindAdaptor
        • PyTomographySimindAdaptor.__init__()
        • PyTomographySimindAdaptor.set_source()
        • PyTomographySimindAdaptor.set_mu_map()
        • PyTomographySimindAdaptor.set_energy_windows()
        • PyTomographySimindAdaptor.add_config_value()
        • PyTomographySimindAdaptor.add_runtime_switch()
        • PyTomographySimindAdaptor.run()
        • PyTomographySimindAdaptor.get_outputs()
        • PyTomographySimindAdaptor.get_output_metadata()
        • PyTomographySimindAdaptor.get_output_header_path()
        • PyTomographySimindAdaptor.get_total_output()
        • PyTomographySimindAdaptor.get_scatter_output()
        • PyTomographySimindAdaptor.get_primary_output()
        • PyTomographySimindAdaptor.get_air_output()
        • PyTomographySimindAdaptor.get_config()
        • PyTomographySimindAdaptor.from_simind_image_axes()
        • PyTomographySimindAdaptor.to_simind_image_axes()
      • ProjectionResult
        • ProjectionResult.projection
        • ProjectionResult.header_path
        • ProjectionResult.data_path
        • ProjectionResult.metadata
        • ProjectionResult.__init__()
      • RuntimeOperator
        • RuntimeOperator.switches
        • RuntimeOperator.orbit_file
        • RuntimeOperator.__init__()
      • SirfSimindAdaptor
        • SirfSimindAdaptor.__init__()
        • SirfSimindAdaptor.set_source()
        • SirfSimindAdaptor.set_mu_map()
        • SirfSimindAdaptor.set_energy_windows()
        • SirfSimindAdaptor.add_config_value()
        • SirfSimindAdaptor.add_runtime_switch()
        • SirfSimindAdaptor.run()
        • SirfSimindAdaptor.get_outputs()
        • SirfSimindAdaptor.get_total_output()
        • SirfSimindAdaptor.get_scatter_output()
        • SirfSimindAdaptor.get_primary_output()
        • SirfSimindAdaptor.get_air_output()
        • SirfSimindAdaptor.get_penetrate_output()
        • SirfSimindAdaptor.list_available_outputs()
        • SirfSimindAdaptor.get_scoring_routine()
        • SirfSimindAdaptor.get_config()
      • SimindPythonConnector
        • SimindPythonConnector.__init__()
        • SimindPythonConnector.add_runtime_switch()
        • SimindPythonConnector.add_config_value()
        • SimindPythonConnector.configure_voxel_phantom()
        • SimindPythonConnector.set_energy_windows()
        • SimindPythonConnector.run()
        • SimindPythonConnector.get_outputs()
        • SimindPythonConnector.get_config()
      • StirSimindAdaptor
        • StirSimindAdaptor.__init__()
        • StirSimindAdaptor.set_source()
        • StirSimindAdaptor.set_mu_map()
        • StirSimindAdaptor.set_energy_windows()
        • StirSimindAdaptor.add_config_value()
        • StirSimindAdaptor.add_runtime_switch()
        • StirSimindAdaptor.run()
        • StirSimindAdaptor.get_outputs()
        • StirSimindAdaptor.get_total_output()
        • StirSimindAdaptor.get_scatter_output()
        • StirSimindAdaptor.get_primary_output()
        • StirSimindAdaptor.get_air_output()
        • StirSimindAdaptor.get_penetrate_output()
        • StirSimindAdaptor.list_available_outputs()
        • StirSimindAdaptor.get_scoring_routine()
        • StirSimindAdaptor.get_config()
      • NumpyConnector
      • ProjectionResult
        • ProjectionResult.projection
        • ProjectionResult.header_path
        • ProjectionResult.data_path
        • ProjectionResult.metadata
        • ProjectionResult.__init__()
      • RuntimeOperator
        • RuntimeOperator.switches
        • RuntimeOperator.orbit_file
        • RuntimeOperator.__init__()
      • SimindPythonConnector
        • SimindPythonConnector.__init__()
        • SimindPythonConnector.add_runtime_switch()
        • SimindPythonConnector.add_config_value()
        • SimindPythonConnector.configure_voxel_phantom()
        • SimindPythonConnector.set_energy_windows()
        • SimindPythonConnector.run()
        • SimindPythonConnector.get_outputs()
        • SimindPythonConnector.get_config()
      • StirSimindAdaptor
        • StirSimindAdaptor.__init__()
        • StirSimindAdaptor.set_source()
        • StirSimindAdaptor.set_mu_map()
        • StirSimindAdaptor.set_energy_windows()
        • StirSimindAdaptor.add_config_value()
        • StirSimindAdaptor.add_runtime_switch()
        • StirSimindAdaptor.run()
        • StirSimindAdaptor.get_outputs()
        • StirSimindAdaptor.get_total_output()
        • StirSimindAdaptor.get_scatter_output()
        • StirSimindAdaptor.get_primary_output()
        • StirSimindAdaptor.get_air_output()
        • StirSimindAdaptor.get_penetrate_output()
        • StirSimindAdaptor.list_available_outputs()
        • StirSimindAdaptor.get_scoring_routine()
        • StirSimindAdaptor.get_config()
      • SirfSimindAdaptor
        • SirfSimindAdaptor.__init__()
        • SirfSimindAdaptor.set_source()
        • SirfSimindAdaptor.set_mu_map()
        • SirfSimindAdaptor.set_energy_windows()
        • SirfSimindAdaptor.add_config_value()
        • SirfSimindAdaptor.add_runtime_switch()
        • SirfSimindAdaptor.run()
        • SirfSimindAdaptor.get_outputs()
        • SirfSimindAdaptor.get_total_output()
        • SirfSimindAdaptor.get_scatter_output()
        • SirfSimindAdaptor.get_primary_output()
        • SirfSimindAdaptor.get_air_output()
        • SirfSimindAdaptor.get_penetrate_output()
        • SirfSimindAdaptor.list_available_outputs()
        • SirfSimindAdaptor.get_scoring_routine()
        • SirfSimindAdaptor.get_config()
      • PyTomographySimindAdaptor
        • PyTomographySimindAdaptor.__init__()
        • PyTomographySimindAdaptor.set_source()
        • PyTomographySimindAdaptor.set_mu_map()
        • PyTomographySimindAdaptor.set_energy_windows()
        • PyTomographySimindAdaptor.add_config_value()
        • PyTomographySimindAdaptor.add_runtime_switch()
        • PyTomographySimindAdaptor.run()
        • PyTomographySimindAdaptor.get_outputs()
        • PyTomographySimindAdaptor.get_output_metadata()
        • PyTomographySimindAdaptor.get_output_header_path()
        • PyTomographySimindAdaptor.get_total_output()
        • PyTomographySimindAdaptor.get_scatter_output()
        • PyTomographySimindAdaptor.get_primary_output()
        • PyTomographySimindAdaptor.get_air_output()
        • PyTomographySimindAdaptor.get_config()
        • PyTomographySimindAdaptor.from_simind_image_axes()
        • PyTomographySimindAdaptor.to_simind_image_axes()
      • RuntimeOperator
        • RuntimeOperator.switches
        • RuntimeOperator.orbit_file
        • RuntimeOperator.__init__()
    • Converters
      • get_package_data_path()
      • interpolate_attenuation_coefficient()
      • get_attenuation_coefficient()
      • hu_to_attenuation()
      • hu_to_density()
      • attenuation_to_density()
      • load_schneider_data()
      • hu_to_density_schneider_piecewise()
      • hu_to_density_schneider()
      • get_schneider_tissue_info()
      • compare_density_methods()
      • ConversionConfig
        • ConversionConfig.radius_scale_factor
        • ConversionConfig.angle_offset
        • ConversionConfig.default_number_format
        • ConversionConfig.ignored_patterns
        • ConversionConfig.__init__()
      • ConversionRule
        • ConversionRule.matches()
        • ConversionRule.convert()
      • RadiusConversionRule
        • RadiusConversionRule.__init__()
        • RadiusConversionRule.matches()
        • RadiusConversionRule.convert()
      • OrbitFileRule
        • OrbitFileRule.__init__()
        • OrbitFileRule.matches()
        • OrbitFileRule.convert()
      • StartAngleConversionRule
        • StartAngleConversionRule.__init__()
        • StartAngleConversionRule.matches()
        • StartAngleConversionRule.convert()
      • RotationDirectionRule
        • RotationDirectionRule.matches()
        • RotationDirectionRule.convert()
      • NumberFormatRule
        • NumberFormatRule.matches()
        • NumberFormatRule.convert()
      • OrbitConversionRule
        • OrbitConversionRule.matches()
        • OrbitConversionRule.convert()
      • ImageDurationRule
        • ImageDurationRule.matches()
        • ImageDurationRule.convert()
      • EnergyWindowRule
        • EnergyWindowRule.__init__()
        • EnergyWindowRule.matches()
        • EnergyWindowRule.convert()
      • DataFileNameRule
        • DataFileNameRule.__init__()
        • DataFileNameRule.matches()
        • DataFileNameRule.convert()
      • IgnorePatternRule
        • IgnorePatternRule.__init__()
        • IgnorePatternRule.matches()
        • IgnorePatternRule.convert()
      • SimindToStirConverter
        • SimindToStirConverter.__init__()
        • SimindToStirConverter.convert_line()
        • SimindToStirConverter.convert_file()
        • SimindToStirConverter.create_penetrate_headers_from_template()
        • SimindToStirConverter.find_penetrate_h00_file()
        • SimindToStirConverter.read_parameter()
        • SimindToStirConverter.edit_parameter()
        • SimindToStirConverter.add_parameter()
        • SimindToStirConverter.validate_and_fix_scaling_factors()
        • SimindToStirConverter.add_custom_rule()
        • SimindToStirConverter.validate_and_correct_radius()
    • Utilities
      • parse_sinogram()
      • parse_interfile()
      • get_sirf_attenuation_from_simind()
      • convert_value()
      • harmonize_stir_attributes()
      • extract_attributes_from_stir()
      • extract_attributes_from_stir_headerfile()
      • create_stir_image()
      • create_stir_acqdata()
      • create_simple_phantom()
      • create_attenuation_map()
      • SimindError
      • SimindNotFoundError
      • create_window_file()
      • temporary_directory()
      • InterfileArray
        • InterfileArray.array
        • InterfileArray.header_path
        • InterfileArray.data_path
        • InterfileArray.metadata
        • InterfileArray.__init__()
      • load_interfile_array()
  • Testing
    • Test Organization
      • Test Markers
      • Automatic Dependency Detection
    • Running Tests
      • Local Development (All Tests)
      • CI Environment (GitHub Actions)
      • Docker Backend Isolation
      • Alternative CI Configuration
    • Test Categories
      • CI-Friendly Test Suites
      • Backend-Dependent Suites
      • SIMIND and Container Diagnostics
      • Integration Test
    • Configuration Files
      • pytest.ini (Local Development)
      • pytest-ci.ini (CI Environment)
      • tests/conftest.py
    • Adding New Tests
    • Continuous Integration
  • Changelog
    • 1.0.1 - 2026-04-16
      • Fixed
    • 1.0.0 - 2026-04-16
      • Breaking Changes
      • Added
      • Changed
      • Fixed
    • [0.4.0] - 2026-02-26
      • Breaking Changes
      • Added
      • Changed
      • Fixed
    • [0.3.0] - 2025-01-23
      • Breaking Changes
      • Changed
      • Fixed
      • Added
      • Changed
    • Version 0.2.1
      • New Features
      • Improvements
      • Fixed
    • Version 0.2.0
      • Breaking Changes
      • New Features
      • Improvements
    • Version 0.1.1
    • Version 0.1.0
  • Contributing
    • Development Setup
    • Testing Your Changes
    • Documentation Updates
simind-python-connector
  • Overview: module code

All modules for which code is available

  • simind_python_connector.connectors.base
  • simind_python_connector.connectors.python_connector
  • simind_python_connector.connectors.pytomography_adaptor
  • simind_python_connector.connectors.sirf_adaptor
  • simind_python_connector.connectors.stir_adaptor
  • simind_python_connector.converters.attenuation
  • simind_python_connector.converters.simind_to_stir
  • simind_python_connector.core.config
  • simind_python_connector.core.executor
  • simind_python_connector.utils.interfile_numpy
  • simind_python_connector.utils.io_utils
  • simind_python_connector.utils.simind_utils
  • simind_python_connector.utils.stir_utils

© Copyright 2026, Sam Porter, Efstathios Varzakis.

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