Command line spectral doc

[cyrilmory]

Adds Simon Rit's python spectral examples from PR#635, and uses the data it generates (tweaked a bit and uploaded to Girder) to document the spectral tools' command line applications.

Confidence Score: 5/5

The PR appears safe to merge; no new actionable issues were established.

Summary

Adds Python examples and command-line guides for spectral CT simulation and reconstruction.

• Spectral command guides show how to run each reconstruction stage.
• A Python example builds spectral data and runs one-step reconstruction.
• A Python example decomposes spectral measurements and reconstructs each material.
• Python test installs include the tools used by spectral examples.

Diagram

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  A[Phantom and scan geometry] --> B[Material projections]
  C[Spectrum and detector response] --> D[Simulated photon counts]
  B --> D
  D --> E[One-step reconstruction]
  D --> F[Material decomposition]
  F --> G[Two-step reconstruction]

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_{Reviews (10) · Last reviewed commit: "ENH: Add Python examples and associated ..." · Reviewed by Greptile}

[greptile-apps]

Required test packages are missing

Both new examples import spekpy and xraylib, but neither package is installed by the wheel-test workflows or listed in the test dependencies. Once the directory argument is fixed, both new tests fail at import spekpy. Add both packages to the test setup used by the CPU and CUDA workflows.

[SimonRit]

They are now listed in pyproject.toml in the test group so the tests will execute fine. The user will have to install those dependencies manually if they want to run the examples which is not unreasonable.

[greptile-apps]

Thanks — adding spekpy and xraylib to the test dependency group covers installations that explicitly run pip install --group test, and it’s reasonable for users running the examples to install those separately.

However, the wheel-test jobs do not install that group: they install the wheel followed by only pytest matplotlib. Since test_SpectralOneStep and test_SpectralTwoStep import those modules, those CI jobs will still fail with ModuleNotFoundError. The workflow setup needs to install the test group or add spekpy xraylib to its existing install command.