pymkm

pyMKM: Microdosimetric modeling toolkit for ion beam radiotherapy.

pyMKM provides tools to compute microdosimetric and radiobiological quantities based on ion-specific LET data and linear-quadratic (LQ) survival models. It supports:

• Radial dose modeling using Scholz-Kraft and Kiefer-Chatterjee formalisms

• Specific energy and saturation-corrected z̄ calculations

• Microdosimetric Kinetic Model (MKM), Stochastic MKM (SMK), and OSMK 2021/2023

• Pre-bundled stopping power datasets (MSTAR, Geant4, FLUKA)

• Survival fraction table generation and visualization

• Full support for oxygen-effect modeling

Main subpackages

• pymkm.io: Data loading and parsing of stopping power tables.

• pymkm.data: Bundled LET datasets and element metadata.

• pymkm.physics: Core models for track structure and specific energy.

• pymkm.mktable: LET-to-z̄ computation for MKM/SMK/OSMK tables.

• pymkm.sftable: LQ model application and survival fraction calculations.

• pymkm.biology: Oxygen-effect models and radiobiological corrections.

• pymkm.utils: Utilities for interpolation, geometry, and parallelism.

pyMKM is intended for researchers and clinicians working in particle therapy, microdosimetry, and radiobiology modeling.

Subpackages

• pymkm.biology
  • Modules
  • Submodules
    • pymkm.biology.oxygen_effect
      • apply_oxygen_correction_alpha()
      • apply_oxygen_correction_beta()
      • compute_osmk_radioresistance()
      • compute_relative_radioresistance()
      • compute_scaling_factors()
• pymkm.data
  • Contents
  • Subpackages
    • pymkm.data.defaults
      • Subpackages
• pymkm.io
  • Modules
  • StoppingPowerTable
    • StoppingPowerTable.DEFAULT_TARGET
    • StoppingPowerTable.REQUIRED_DICT_KEYS
    • StoppingPowerTable.REQUIRED_HEADER_KEYS
    • StoppingPowerTable.energy_grid
    • StoppingPowerTable.from_dict()
    • StoppingPowerTable.from_txt()
    • StoppingPowerTable.get_lookup_table()
    • StoppingPowerTable.interpolate()
    • StoppingPowerTable.ion_name
    • StoppingPowerTable.plot()
    • StoppingPowerTable.resample()
    • StoppingPowerTable.stopping_power
    • StoppingPowerTable.to_dict()
  • StoppingPowerTableSet
    • StoppingPowerTableSet.add()
    • StoppingPowerTableSet.filter_by_ions()
    • StoppingPowerTableSet.from_default_source()
    • StoppingPowerTableSet.from_dict()
    • StoppingPowerTableSet.from_directory()
    • StoppingPowerTableSet.from_json()
    • StoppingPowerTableSet.get()
    • StoppingPowerTableSet.get_available_ions()
    • StoppingPowerTableSet.get_common_energy_range()
    • StoppingPowerTableSet.get_energy_grid()
    • StoppingPowerTableSet.get_stopping_power()
    • StoppingPowerTableSet.interpolate_all()
    • StoppingPowerTableSet.items()
    • StoppingPowerTableSet.keys()
    • StoppingPowerTableSet.load()
    • StoppingPowerTableSet.plot()
    • StoppingPowerTableSet.remove()
    • StoppingPowerTableSet.resample_all()
    • StoppingPowerTableSet.save()
    • StoppingPowerTableSet.to_dict()
    • StoppingPowerTableSet.to_json()
    • StoppingPowerTableSet.values()
  • Submodules
    • pymkm.io.data_registry
      • get_available_sources()
      • get_default_txt_path()
      • list_available_defaults()
      • load_lookup_table()
    • pymkm.io.stopping_power
      • Main features
      • StoppingPowerTable
    • pymkm.io.table_set
      • Main features
      • StoppingPowerTableSet
• pymkm.mktable
  • Modules
  • Usage
  • MKTable
    • MKTable.compute()
    • MKTable.display()
    • MKTable.get_table()
    • MKTable.load()
    • MKTable.model_version
    • MKTable.plot()
    • MKTable.save()
    • MKTable.summary()
    • MKTable.write_txt()
  • MKTableParameters
    • MKTableParameters.K
    • MKTableParameters.Rmax
    • MKTableParameters.apply_oxygen_effect
    • MKTableParameters.base_points_b
    • MKTableParameters.base_points_r
    • MKTableParameters.beta0
    • MKTableParameters.core_radius_type
    • MKTableParameters.domain_radius
    • MKTableParameters.f_rd_max
    • MKTableParameters.f_z0_max
    • MKTableParameters.from_dict()
    • MKTableParameters.model_name
    • MKTableParameters.nucleus_radius
    • MKTableParameters.pO2
    • MKTableParameters.use_stochastic_model
    • MKTableParameters.z0
  • Submodules
    • pymkm.mktable.compute
      • compute()
    • pymkm.mktable.core
    • pymkm.mktable.plot
      • plot()
• pymkm.physics
  • Modules
  • ParticleTrack
    • ParticleTrack.initial_local_dose()
  • SpecificEnergy
    • SpecificEnergy.compute_saturation_parameter()
    • SpecificEnergy.dose_averaged_specific_energy()
    • SpecificEnergy.saturation_corrected_single_event_specific_energy()
    • SpecificEnergy.single_event_specific_energy()
  • Submodules
    • pymkm.physics.particle_track
      • ParticleTrack
    • pymkm.physics.specific_energy
      • SpecificEnergy
• pymkm.sftable
  • Models supported
  • Modules
  • Usage
  • SFTable
    • SFTable.compute()
    • SFTable.display()
    • SFTable.plot()
    • SFTable.summary()
  • SFTableParameters
    • SFTableParameters.K
    • SFTableParameters.Rm
    • SFTableParameters.Rmax
    • SFTableParameters.alpha0
    • SFTableParameters.alphaL
    • SFTableParameters.alphaS
    • SFTableParameters.beta0
    • SFTableParameters.dose_grid
    • SFTableParameters.f_rd_max
    • SFTableParameters.f_z0_max
    • SFTableParameters.from_dict()
    • SFTableParameters.gamma
    • SFTableParameters.mktable
    • SFTableParameters.pO2
    • SFTableParameters.zR
  • Submodules
    • pymkm.sftable.compute
      • compute()
    • pymkm.sftable.core
      • SFTable
      • SFTableParameters
    • pymkm.sftable.plot
      • plot()
• pymkm.utils
  • Modules
  • Submodules
    • pymkm.utils.geometry_tools
      • GeometryTools
    • pymkm.utils.interpolation
      • Interpolator
    • pymkm.utils.parallel
      • optimal_worker_count()