[WIP] No Dose3D patient creation enabled, better CT export

[jhajduga]

Completed: Generic 3MF-based phantom and CT generation workflow

Implemented support for importing arbitrary 3MF/DB-based phantom geometries without constructing a patient object.

The new workflow allows geometry-only simulations to be run directly from imported 3MF models and supports generating synthetic CT data in both CSV and DICOM formats.

Completed changes:

• added GenericPhantom as an IPhysicalVolume-based geometry module,
• added the GenericPhantom_3mf envelope/build mode,
• allowed PatientGeometry to operate with m_patient == nullptr,
• added TOML-based configuration of DB/3MF geometry placement,
• made scoring-data merging safe when no patient object is defined,
• improved logging for CSV CT and DICOM CT export,
• made the Python DICOM exporter robust against unknown material names,
• extended the HU dictionary with materials available through MaterialsSvc,
• documented the complete 3MF-based CT generation workflow in README.md.

The documentation now includes:

• required input files,
• an example TOML configuration,
• build and execution commands,
• expected output directories,
• CSV CT export instructions,
• DICOM CT generation instructions.

This provides a complete geometry-only workflow for importing a 3MF model and generating synthetic CT output without requiring a conventional patient definition or sensitive detector configuration.

TODO: Generalized 3MF geometry and scoring configuration

The next step is to remove the remaining hard-coded assumptions from the geometry construction and scoring workflow.

Planned work:

• add basic aliases for biological tissues and commonly used material names, (in material service)

• add TOML-configurable sensitive-volume selection for geometries imported from 3MF/DB,

• allow sensitive volumes to be selected using a list of element names, database keys, logical-volume names, or other stable identifiers,

• extend the geometry-building loop so imported elements and their roles can be defined entirely in TOML,

• distinguish explicitly between:

  • geometry-only mode for CT generation,
  • geometry with scoring enabled,
  • conventional patient-based simulation,

• remove the current workarounds required to run simulations without a patient definition or sensitive volume,

• make geometry-only CT export a first-class execution mode rather than a special case of the standard simulation workflow,

• consider adding a dedicated executable or alternative main.cpp focused exclusively on geometry import and synthetic CT generation.

A possible target configuration could allow each imported element to define:

• its 3MF/DB identifier,
• placement and transformation,
• material override,
• whether it should be scored,
• the scoring type or sensitive-detector assignment,
• whether it should be included in CT export.

The final goal is to make arbitrary imported geometries fully configurable from TOML, without requiring source-code changes for each new phantom.