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docs: add PositroniumSource user documentation#4

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docs: add PositroniumSource user documentation#4
MateuszBala wants to merge 2 commits into
cis-imaging:positronium_source_rebasedfrom
MateuszBala:docs/positronium-source

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Summary

This PR adds user documentation for the positronium source workflow and related Hits-tree metadata.

Documentation Changes

  • Added a dedicated PositroniumSource section to docs/source_and_particle_management.rst.
  • Documented how to create and configure PositroniumSource, including:
    • source creation,
    • required and optional commands,
    • event timing and generated vertices,
    • a minimal usage example.
  • Documented the dedicated Hits-tree branches relevant to positronium studies:
    • gammaType,
    • sourceType,
    • decayType,
    • decayIndex.
  • Added descriptions of the branch values for PositroniumSource and clarified how they should be interpreted.
  • Clarified that ExtendedVSource does not populate decayIndex, so this branch remains at the default value -1 there.
  • Updated docs/data_output_management.rst to include decayIndex in the documented Hits-tree branch list.

Validation

make -C docs html

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@wkrzemien wkrzemien left a comment

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Very small remarks

Comment thread docs/source_and_particle_management.rst Outdated

As for other sources, the activity and the spatial or temporal distributions are configured with the standard source commands, for example::

/gate/source/NAME/setActivity 1000 becquerel
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Is this correct unit here?

Lifetime of each component. The last token is a Geant4 time unit such as ``ns``.

``/gate/source/NAME/setPromptPhotonProbabilites p1 p2 ... pn``
Probability of prompt-gamma emission for each component. Values are clamped to the ``[0, 1]`` range by the messenger.
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I don't know the word clamp, maybe restricted or projected?

^^^^^^^^^^^^^^^^^

``/gate/source/NAME/setElectronCaptureProbabilities p1 p2 ... pn``
Probability that the positron is lost by electron capture and no annihilation vertex is produced for a given component. If this command is omitted, all probabilities default to ``0``. Values are clamped to the ``[0, 1]`` range.
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again clamped to restricted?

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