Makie extension

Project.toml

@@ -17,9 +17,11 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [weakdeps]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 
 [extensions]
 DecapodesCUDAExt = "CUDA"
+DecapodesMakieExt = "Makie"
 
 [compat]
 ACSets = "0.2"
@@ -34,6 +36,7 @@ JSON = "0.21"
 Krylov = "0.9.6"
 LinearAlgebra = "1.9"
 MLStyle = "0.4.17"
+Makie = "0.21"
 Markdown = "1.9"
 OrdinaryDiffEq = "6.47"
 PreallocationTools = "0.4"

docs/src/ch/cahn-hilliard.md

@@ -75,7 +75,7 @@ constants = (D = 0.5, γ = 0.5);
 fig = Figure() # hide
 ax = CairoMakie.Axis(fig[1,1], aspect=1) # hide
 msh = CairoMakie.mesh!(ax, s, color=C, colormap=:jet, colorrange=extrema(C)) # hide
-Colorbar(fig[1,2], msh)
+Colorbar(fig[1,2], msh) # hide
 save("CahnHilliard_initial.png", fig) # hide
 nothing # hide
 ```
@@ -102,21 +102,18 @@ soln.retcode
 
 And we can see the result as a gif.
 
-```@setup DEC
-function create_gif(solution, file_name)
-  frames = 200
-  fig = Figure()
-  ax = CairoMakie.Axis(fig[1,1])
-  msh = CairoMakie.mesh!(ax, s, color=solution(0).C, colormap=:jet, colorrange=extrema(solution(0).C))
-  Colorbar(fig[1,2], msh)
-  CairoMakie.record(fig, file_name, range(0.0, tₑ; length=frames); framerate = 15) do t
-    msh.color = solution(t).C
-  end
-end
-create_gif(soln, "CahnHilliard_Rect.gif")
+```@example DEC
+dynam = t -> soln(t).C
+frames = 200
+
+mesh_args = (colormap = :jet, colorrange = extrema(dynam(0)))
+record_args = (framerate = 30,)
+
+record_dynamics(dynam, s, "CahnHilliard_Rect.webm", range(0.0, tₑ; length = frames); 
+    mesh_args = mesh_args, record_args = record_args)
 ```
 
-!["CahnHilliardRes"](CahnHilliard_Rect.gif)
+!["CahnHilliardRes"](CahnHilliard_Rect.webm)
 
 ```@example INFO
 DocInfo.get_report(info) # hide

ext/DecapodesMakieExt.jl

@@ -0,0 +1,55 @@
+module DecapodesMakieExt
+
+using CombinatorialSpaces
+using Makie
+import Decapodes: record_dynamics
+
+"""
+    record_dynamics(dynamics, mesh::HasDeltaSet, path::AbstractString, iter; use_colorbar=true, figure_args=NamedTuple(), axis_args=NamedTuple(), mesh_args=NamedTuple(), colorbar_args=NamedTuple(), record_args=NamedTuple())
+
+The Decapodes implementation of Makie's `record` function. This function is meant serve as a helper function
+to quickly generate animations based on the resulting dynamics of a Decapodes.
+
+**Arguments:**
+
+`dynamics`: A function that accepts a time and returns the value of a particular state variable at that time.
+
+`mesh`: A CombinatorialSpaces mesh upon which the Decapode was run.
+
+`path`: The path of the created file recording.
+
+`iter`: The range of times where `dynamics` will be sampled.
+
+**Keyword arguments:**
+
+`use_colorbar = true`: Determines whether display a colorbar alongside the recording.
+
+`figure_args`: Keyword arguments passed into Makie's `Figure` funcion.
+
+`axis_args`: Keyword arguments passed into Makie's `Axis` funcion.
+
+`mesh_args`: Keyword argumentsp assed into Makie's `mesh!` function. Note that `color` is already used to take the value of dynamics at time `t`.
+
+`colorbar_args`: Keyword arguments passed into Makie's `Colorbar` funcion. Note that if `use_colorbar = false` these will have no effect.
+
+`record_args`: Keyword arguments passed into Makie's `record` funcion.
+
+"""
+function record_dynamics(dynamics, mesh::HasDeltaSet, path::AbstractString, iter; use_colorbar=true, figure_args=NamedTuple(), axis_args=NamedTuple(), mesh_args=NamedTuple(), colorbar_args=NamedTuple(), record_args=NamedTuple())
+
+  time = Observable(0.0)
+  lift_dynam = @lift(dynamics($time))
+
+  figure = Makie.Figure(;figure_args...)
+  ax = Makie.Axis(figure[1,1]; axis_args...)
+
+  makie_msh = Makie.mesh!(ax, mesh; color=lift_dynam, mesh_args...)
+
+  use_colorbar ? Makie.Colorbar(figure[1,2], makie_msh; colorbar_args...) : nothing
+
+  Makie.record(figure, path, iter; record_args...) do t
+    time[] = t
+  end
+end
+
+end

src/Decapodes.jl

@@ -7,7 +7,12 @@ using MLStyle
 
 export
 gensim, evalsim, compile, compile_env, default_dec_matrix_generate, default_dec_cu_matrix_generate, default_dec_generate,
-CPUBackend, CUDABackend, CPUTarget, CUDATarget
+CPUBackend, CUDABackend, CPUTarget, CUDATarget,
+record_dynamics
+
+function record_dynamics()
+  error("Please load Makie.jl to use this function")
+end;
 
 include("operators.jl")
 include("simulation.jl")

src/operators.jl

@@ -5,7 +5,9 @@ using Krylov
 using LinearAlgebra
 using SparseArrays
 
-function default_dec_cu_matrix_generate() end;
+function default_dec_cu_matrix_generate()
+  error("Please load CUDA.jl to use this function")
+end;
 
 function default_dec_matrix_generate(sd::HasDeltaSet, my_symbol::Symbol, hodge::DiscreteHodge)
   op = @match my_symbol begin

src/simulation.jl

@@ -375,7 +375,7 @@ Function that compiles the computation body. `d` is the input Decapode, `inputs`
 `alloc_vec` should be empty when passed in, `optimizable_dec_operators` is a collection of all DEC operator symbols that can use special
 in-place methods, `dimension` is the dimension of the problem (usually 1 or 2), `stateeltype` is the type of the state elements
 (usually Float32 or Float64), `code_target` determines what architecture the code is compiled for (either CPU or CUDA), and `preallocate`
-which is set to `true` by default and determines if intermediate results can be preallocated..
+which is set to `true` by default and determines if intermediate results can be preallocated.
 """
 function compile(d::SummationDecapode, inputs::Vector{Symbol}, alloc_vectors::Vector{AllocVecCall}, optimizable_dec_operators::Set{Symbol}, dimension::Int, stateeltype::DataType, code_target::AbstractGenerationTarget, preallocate::Bool)
   # Get the Vars of the inputs (probably state Vars).
@@ -679,14 +679,14 @@ Base.showerror(io::IO, e::UnsupportedStateeltypeException) = print(io, "Decapode
 """
     gensim(user_d::SummationDecapode, input_vars::Vector{Symbol}; dimension::Int=2, stateeltype::DataType = Float64, code_target::AbstractGenerationTarget = CPUTarget(), preallocate::Bool = true)
 
-Generates the entire code body for the simulation function. The returned simulation function can then be combined with a mesh, provided by `CombinatorialSpaces`, and a function describing symbol 
+Generates the entire code body for the simulation function. The returned simulation function can then be combined with a mesh, provided by `CombinatorialSpaces`, and a function describing symbol
 to operator mappings to return a simulator that can be used to solve the represented equations given initial conditions.
-  
+
 **Arguments:**
-
-`user_d`: The user passed Decapode for which simulation code will be generated. (This is not modified) 
 
-`input_vars` is the collection of variables whose values are known at the beginning of the simulation. (Defaults to all state variables and literals in the Decapode)
+`user_d`: The user passed Decapode for which simulation code will be generated. (This is not modified)
+
+`input_vars`: is the collection of variables whose values are known at the beginning of the simulation. (Defaults to all state variables and literals in the Decapode)
 
 **Keyword arguments:**