Charged Particle Radiography: Detector Stacks

[pheuer]

Charged particle radiography detectors are usually comprised of multiple layers of active medium, each of which detects different energies of particles based on their Bragg peak. This PR adds a couple objects that represent these detector stacks and calculates the energies deposited in each layer using stopping power data from NIST.

This is Step 1 of adding support for detector stacks. Step 2, in a future PR, will create a new synthetic_radiograph function that takes a film stack object and produces a synthetic radiograph in each layer.

This PR depends on #1486 and should be merged after that PR Done

[pheuer]

@namurphy Something appears to not quite be working with the substitution for Layer?

Maybe it can't go in that parameters section?

[pheuer]

I think I fixed the issue with the substitution by moving it earlier before the parameters block.

Here are the remaining doc errors, broadly in two categories

A number of this first set relate to things like nenergies being marked like markdown but not corresponding to any actual variable?

/home/runner/work/PlasmaPy/PlasmaPy/plasmapy/diagnostics/charged_particle_radiography/detector_stacks.py:docstring of plasmapy.diagnostics.charged_particle_radiography.detector_stacks.Stack.deposition_curves:2: WARNING: py:obj reference target not found: nenergies
/home/runner/work/PlasmaPy/PlasmaPy/plasmapy/diagnostics/charged_particle_radiography/detector_stacks.py:docstring of plasmapy.diagnostics.charged_particle_radiography.detector_stacks.Stack.deposition_curves:17: WARNING: py:obj reference target not found: nlayers
/home/runner/work/PlasmaPy/PlasmaPy/plasmapy/diagnostics/charged_particle_radiography/detector_stacks.py:docstring of plasmapy.diagnostics.charged_particle_radiography.detector_stacks.Stack.deposition_curves:17: WARNING: py:obj reference target not found: nenergies
/home/runner/work/PlasmaPy/PlasmaPy/plasmapy/diagnostics/charged_particle_radiography/detector_stacks.py:docstring of plasmapy.diagnostics.charged_particle_radiography.detector_stacks.Stack.energy_bands:17: WARNING: py:obj reference target not found: nlayers

The rest are related to broken links in the What's New sections. I would suggest just removing this folder from the space that CI checks? Otherwise links will of course break every time we refactor anything.

/home/runner/work/PlasmaPy/PlasmaPy/docs/whatsnew/0.7.0.rst:42: WARNING: py:func reference target not found: plasmapy.diagnostics.charged_particle_radiography.synthetic_radiograph
/home/runner/work/PlasmaPy/PlasmaPy/docs/whatsnew/0.7.0.rst:42: WARNING: py:obj reference target not found: plasmapy.diagnostics.charged_particle_radiography.Tracker
/home/runner/work/PlasmaPy/PlasmaPy/docs/whatsnew/0.7.0.rst:42: WARNING: py:obj reference target not found: plasmapy.diagnostics.charged_particle_radiography.Tracker.results_dict
/home/runner/work/PlasmaPy/PlasmaPy/docs/whatsnew/0.7.0.rst:49: WARNING: py:obj reference target not found: plasmapy.diagnostics.charged_particle_radiography.Tracker
/home/runner/work/PlasmaPy/PlasmaPy/docs/whatsnew/0.7.0.rst:53: WARNING: py:obj reference target not found: plasmapy.diagnostics.charged_particle_radiography.Tracker
/home/runner/work/PlasmaPy/PlasmaPy/docs/whatsnew/0.7.0.rst:53: WARNING: py:obj reference target not found: plasmapy.diagnostics.charged_particle_radiography.Tracker
/home/runner/work/PlasmaPy/PlasmaPy/docs/whatsnew/0.7.0.rst:116: WARNING: py:meth reference target not found: plasmapy.diagnostics.charged_particle_radiography.Tracker.save_results
/home/runner/work/PlasmaPy/PlasmaPy/docs/whatsnew/0.7.0.rst:116: WARNING: py:obj reference target not found: plasmapy.diagnostics.charged_particle_radiography.Tracker
/home/runner/work/PlasmaPy/PlasmaPy/docs/whatsnew/0.7.0.rst:153: WARNING: py:obj reference target not found: plasmapy.diagnostics.charged_particle_radiography.synthetic_radiograph
/home/runner/work/PlasmaPy/PlasmaPy/docs/whatsnew/0.7.0.rst:[28](https://github.com/PlasmaPy/PlasmaPy/actions/runs/3682075943/jobs/6229365410#step:6:29)9: WARNING: py:obj reference target not found: plasmapy.diagnostics.charged_particle_radiography.synthetic_radiograph

[StanczakDominik]

Wow, pretty obvious in retrospect! The thing is, this is the actual sphinx build we're checking for the warnings. Obviously it's not enough anymore. I guess instead of running sphinx-build -W we could do sphinx-build -w output.log, then grep (well, regex) for PlasmaPy/docs/whatsnew/.*\.rst:.* WARNING: py:obj reference target not found .* and raise (or rather sys.exit(1) if any other warnings are found. Can't be that hard. Will do.

On the nenergies stuff... @namurphy, @rocco8773?

[pheuer]

On the nenergies stuff... @namurphy, @rocco8773?

These lines look like this:

energies : (`nenergies`,) `~astropy.units.Quantity` array
            Energies axis over which to calculate the deposition. Units
            convertible to J.

There is no variable nenergies. I could just remove the `` which would be the easiest solution?

[StanczakDominik]

Let's try it!

[StanczakDominik]

Actually, wisdom by @namurphy: do ``nenergies``, and it should work!

[namurphy]

Still getting a doc build error, seemingly due to a reST formatting problem.

WARNING: :40: (WARNING/2) Bullet list ends without a blank line; unexpected unindent.
WARNING: :47: (WARNING/2) Definition list ends without a blank line; unexpected unindent.

It would have been helpful if it had said the file that the issue is occurring in...sigh!

[pheuer]

It would have been helpful if it had said the file that the issue is occurring in...sigh!

Indeed...let's see if this works!

[pheuer]

@namurphy that worked! Merging before the linters change their mind :)

[namurphy]

@namurphy that worked! Merging before the linters change their mind :)

Congratulations on getting it merged! 🎈🎂🎆

It's strange that my suggestion actually worked. 👀🤔