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Improved documentation
Restructure documentation to keep the main page short and with the most important information. Move other documentation to its oen pages and cross reference.
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‎docs/make.jl‎

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@@ -15,8 +15,11 @@ makedocs(sitename = "JetReconstruction.jl",
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"Examples" => "examples.md",
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"EDM4hep" => "EDM4hep.md",
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"Visualisation" => "visualisation.md",
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"Reference" => Any["Public API" => "lib/public.md",
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"Internal API" => "lib/internal.md"]
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"Particle Inputs" => "particles.md",
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"Reconstruction Strategies" => "strategy.md",
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"Reference Docs" => Any["Public API" => "lib/public.md",
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"Internal API" => "lib/internal.md"],
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"Extras" => Any["Serialisation" => "extras/serialisation.md"]
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])
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deploydocs(repo = "github.com/JuliaHEP/JetReconstruction.jl.git",

‎docs/src/EDM4hep.md‎

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# EDM4hep
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# EDM4hep Inputs
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Extension functionality to read EDM4hep ReconstructedParticles
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Extension functionality to read EDM4hep ReconstructedParticles, using the
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[EDM4hep.jl](https://github.com/peremato/EDM4hep.jl) package.
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## Index
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## Examples
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EDM4hep `ReconstructedParticles` can be used as direct input into jet
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reconstruction.
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A number of working examples are maintained in the [EDM4hep examples
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directory](https://github.com/JuliaHEP/JetReconstruction.jl/tree/main/examples/EDM4hep)
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of the package's `examples`.
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Here is a snippet that shows the main steps:
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```julia
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using EDM4hep
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using EDM4hep.RootIO
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using JetReconstruction
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# Change this to something that works on your system
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input_file = joinpath("directory", "EDM4hep.root")
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reader = RootIO.Reader(input_file)
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events = RootIO.get(reader, "events")
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evt = events[1]
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recps = RootIO.get(reader, evt, "ReconstructedParticles")
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cs = jet_reconstruct(recps; algorithm = JetAlgorithm.Durham)
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```
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## Function Index
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```@index
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Pages = ["EDM4hep.md"]

‎docs/src/examples.md‎

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# Jet Reconstruction Examples
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The Jet Reconstruction package has a number of example files that show how to
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usage.
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usage. These are in the `examples` subdirectory of the package and can be
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browsed directly on
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[GitHub](https://github.com/JuliaHEP/JetReconstruction.jl/tree/main/examples).
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*Note:* because of extra dependencies in these scripts, one must use the
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`Project.toml` file in the `examples` directory.
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The `examples/EDM4hep` folder contains examples of using EDM4hep reconstructed
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particles as input to jet reconstruction. See the specific `README.md` file in
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that directory.
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that directory as well as [EDM4hep Inputs](@ref).

‎docs/src/extras/serialisation.md‎

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# Jet Serialisation
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The package provides methods such as `loadjets`, `loadjets!`, and `savejets`
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that one can use to save and load objects on/from disk easily in a very flexible
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format. See documentation for more.

‎docs/src/index.md‎

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or with some of the optional arguments,
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```julia
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jet_reconstruct(particles; algorithm = JetAlgorithm.GenKt, R = 0.4, p = 0.5, recombine = +, strategy = RecoStrategy.Best)
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jet_reconstruct(particles; algorithm = JetAlgorithm.GenKt, R = 0.4,
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p = 0.5, recombine = +, strategy = RecoStrategy.Best)
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```
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Where `particles` is a collection of 4-vector objects to reconstruct and the
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algorithm is either given explicitly or implied by the power value. For the case
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of generalised ``k_T`` (for ``pp`` and ``e^+e^-``) both the algorithm
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(`JetAlgorithm.GenKt`) and `p` are needed. For the case of the Durham algorithm
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the `R` value is ignored.
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Where `particles` is a collection of 4-vector objects (see [Input Particle
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Types](@ref)) to reconstruct and the algorithm is either given explicitly or
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implied by the power value.
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The object returned is a [`ClusterSequence`](@ref), which internally tracks all
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merge steps.
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### Input Particle Types
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For the `particles` input to the reconstruction any one dimensional
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`AbstractArray{T, 1}` can be used, where the type `T` has to implement methods
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to extract the 4-vector components, viz, the following are required:
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- `JetReconstuction.px(particle::T)`
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- `JetReconstuction.py(particle::T)`
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- `JetReconstuction.pz(particle::T)`
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- `JetReconstuction.energy(particle::T)`
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Currently built-in supported types are
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[`LorentzVectorHEP`](https://github.com/JuliaHEP/LorentzVectorHEP.jl), the
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`PseudoJet` and `EEjet`s from this package, and `ReconstructedParticles` from
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[EDM4hep](https://github.com/peremato/EDM4hep.jl).
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For the case of generalised ``k_T`` (for ``pp`` and ``e^+e^-``) both the
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algorithm (`GenKt`, `EEKt`) and `p` are needed.
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If you require support for a different input collection type then ensure you
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define the `px()`, etc. methods *for your specific type* and *in the
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`JetReconstruction` package*. This use of what might be considered type piracy
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is blessed as long as you are en *end user* of the jet reconstruction package.
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The `R` value determines the cone size; in the case of the Durham algorithm the
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`R` value is ignored.
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If your type is used in several places or by different users, please consider
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writing a package extension that will support your type, following the model for
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EDM4hep in `ext/EDM4hepJets.jl`.
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The object returned is a [`ClusterSequence`](@ref), which internally tracks all
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merge steps and is used for [Inclusive and Exclusive Selections](@ref).
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### Algorithm Types
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| ``e^+e-`` ``k_\text{T}`` / Durham | `JetAlgorithm.Durham` | `R` value ignored and can be omitted |
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| generalised ``e^+e-`` ``k_\text{T}`` | `JetAlgorithm.EEKt` | For ``e^+e^-``, value of `p` must also be specified |
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### ``pp`` Algorithms
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#### ``pp`` Algorithms
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For the three ``pp`` algorithms with fixed `p` values, the `p` value can be
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given instead of the algorithm name. However, this should be considered
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*deprecated* and will be removed in a future release.
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## Strategy
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For the ``pp`` algorithms three strategies are available for the different
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algorithms, which can be specified by passing the named argument `strategy=...`.
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| Strategy Name | Notes | Interface |
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|---|---|---|
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| `RecoStrategy.Best` | Dynamically switch strategy based on input particle density | `jet_reconstruct` |
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| `RecoStrategy.N2Plain` | Global matching of particles at each interation (works well for low $N$) | `plain_jet_reconstruct` |
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| `RecoStrategy.N2Tiled` | Use tiles of radius $R$ to limit search space (works well for higher $N$) | `tiled_jet_reconstruct` |
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Generally one can use the `jet_reconstruct` interface, shown above, as the
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*Best* strategy safely as the overhead is extremely low. That interface supports
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a `strategy` option to switch to a different option.
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### Strategy
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For ``e^+e^-`` algorithms particle densities are low, so the only implementation
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is of the same type as `N2Plain`.
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Generally one does not need to manually specify a strategy, but [Algorithm
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Strategy](@ref) describes how to do this, if desired.
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## Inclusive and Exclusive Selections
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To obtain final jets both inclusive (``p_T`` cut) and exclusive (``n_{jets}`` or
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``d_{ij}`` cut) selections are supported:
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- [inclusive_jets(clusterseq::ClusterSequence, ptmin = 0.0)](@ref)
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- [exclusive_jets(clusterseq::ClusterSequence; dcut = nothing, njets = nothing)](@ref)
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- [`inclusive_jets(clusterseq::ClusterSequence, ptmin = 0.0)`](@ref)
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- [`exclusive_jets(clusterseq::ClusterSequence; dcut = nothing, njets = nothing)`](@ref)
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(For `exclusive_jets` either `dcut` or `njets` is needed, but not both.)
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### Sorting
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by=JetReconstruction.energy, rev=true)
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```
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## Plotting and Animation
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![illustration](assets/jetvis.png)
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To visualise the clustered jets as a 3d bar plot (see illustration above) we now
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use `Makie.jl`. See the `jetsplot` function in `ext/JetVisualisation.jl` and its
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documentation for more. There are two worked examples in the `examples`
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directory.
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The plotting code is a package extension and will load if the one of the `Makie`
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modules is loaded in the environment.
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The [`animatereco`](@ref) function will animate the reconstruction sequence, given a
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`ClusterSequence` object. See the function documentation for the many options
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that can be customised.
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## Serialisation
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The package also provides methods such as `loadjets`, `loadjets!`, and
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`savejets` that one can use to save and load objects on/from disk easily in a
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very flexible format. See documentation for more.
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## Reference
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## References
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Although it has been developed further since the CHEP2023 conference, the CHEP
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conference proceedings,

‎docs/src/particles.md‎

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# Input Particle Types
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For the `particles` input to the reconstruction any one dimensional
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`AbstractArray{T, 1}` can be used, where the type `T` has to implement methods
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to extract the 4-vector components, viz, the following are required:
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- `JetReconstuction.px(particle::T)`
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- `JetReconstuction.py(particle::T)`
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- `JetReconstuction.pz(particle::T)`
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- `JetReconstuction.energy(particle::T)`
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Currently built-in supported types are
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[`LorentzVectorHEP`](https://github.com/JuliaHEP/LorentzVectorHEP.jl), the
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`PseudoJet` and `EEjet`s from this package, and `ReconstructedParticles` from
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[EDM4hep Inputs](@ref).
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If you require support for a different input collection type then ensure you
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define the `px()`, etc. methods *for your specific type* and *in the
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`JetReconstruction` package*. This use of what might be considered type piracy
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is blessed as long as you are en *end user* of the jet reconstruction package.
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If your type is used in several places or by different users, please consider
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writing a package extension that will support your type, following the model for
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EDM4hep in `ext/EDM4hepJets.jl`.

‎docs/src/strategy.md‎

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# Algorithm Strategy
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For the ``pp`` algorithms three strategies are available for the different
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algorithms, which can be specified by passing the named argument `strategy=...`
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to the reconstruction.
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| Strategy Name | Notes | Interface |
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|---|---|---|
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| `RecoStrategy.Best` | Dynamically switch strategy based on input particle density | `jet_reconstruct` |
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| `RecoStrategy.N2Plain` | Global matching of particles at each interation (works well for low $N$) | `plain_jet_reconstruct` |
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| `RecoStrategy.N2Tiled` | Use tiles of radius $R$ to limit search space (works well for higher $N$) | `tiled_jet_reconstruct` |
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Generally one can use the `jet_reconstruct` interface, shown above, as the
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*Best* strategy safely as the overhead is extremely low. That interface supports
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a `strategy` option to switch to a different option.
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For ``e^+e^-`` algorithms particle densities are low, so the only implementation
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is of the same type as `N2Plain`.

‎docs/src/visualisation.md‎

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Documentation for visualisation interfaces extension module.
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## Index
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## Plotting and Animation
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![illustration](assets/jetvis.png)
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To visualise the clustered jets as a 3d bar plot (see illustration above)
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`Makie.jl` is used. See the `jetsplot` function in `ext/JetVisualisation.jl` and
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its documentation for more. There are two worked examples in the `examples`
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directory of this package.
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The plotting code is a package extension and will load if the one of the `Makie`
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modules is loaded in the environment.
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The [`animatereco`](@ref) function will animate the reconstruction sequence,
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given a `ClusterSequence` object. See the function documentation below for the
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many options that can be customised.
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## Function Index
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```@index
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Pages = ["visualisation.md"]

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