Merge pull request #1693 from JuliaRobotics/23Q1/enh/dropjson12

drop JSON1 and 2

Project.toml

@@ -18,8 +18,6 @@ Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 FunctionalStateMachine = "3e9e306e-7e3c-11e9-12d2-8f8f67a2f951"
-JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
-JSON2 = "2535ab7d-5cd8-5a07-80ac-9b1792aadce3"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 KernelDensityEstimate = "2472808a-b354-52ea-a80e-1658a3c6056d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -52,13 +50,11 @@ ApproxManifoldProducts = "0.6.3"
 BSON = "0.2, 0.3"
 Combinatorics = "1.0"
 DataStructures = "0.16, 0.17, 0.18"
-DistributedFactorGraphs = "0.19.3, 0.20"
+DistributedFactorGraphs = "0.20"
 Distributions = "0.24, 0.25"
 DocStringExtensions = "0.8, 0.9"
 FileIO = "1"
 FunctionalStateMachine = "0.2.9"
-JSON = "0.21"
-JSON2 = "0.3"
 JSON3 = "1"
 KernelDensityEstimate = "0.5.6"
 Manifolds = "0.8.15"

src/Deprecated.jl

@@ -1,69 +1,34 @@
+## ================================================================================================
+## Manifolds.jl Consolidation
+## TODO: Still to be completed and tested.
+## ================================================================================================
+# struct ManifoldsVector <: Optim.Manifold
+#   manis::Vector{Manifold}
+# end
 
-##==============================================================================
-## LEGACY, towards Sidecar
-##==============================================================================
-
-"""
-Converter: Prior -> PackedPrior::Dict{String, Any}
-
-FIXME see DFG #590 for consolidation with Serialization and Marshaling
-"""
-function convert(::Type{Dict{String, Any}}, prior::IncrementalInference.Prior)
-  @error("Obsolete, use pack/unpack converters instead")
-  z = convert(Type{Dict{String, Any}}, prior.Z)
-  return Packed_Factor([z], "Prior")
-end
-
-"""
-Converter: PackedPrior::Dict{String, Any} -> Prior
-
-FIXME see DFG #590 for consolidation on Serialization and Marshaling
-"""
-function convert(::Type{<:Prior}, prior::Dict{String, Any})
-  @error("Obsolete, use pack/unpack converters instead")
-  # Genericize to any packed type next.
-  z = prior["measurement"][1]
-  z = convert(DFG.getTypeFromSerializationModule(z["distType"]), z)
-  return Prior(z)
-end
-
-# more legacy, dont delete yet
-function Base.getproperty(ccw::CommonConvWrapper, f::Symbol)
-  if f == :threadmodel
-    @warn "CommonConvWrapper.threadmodel is obsolete" maxlog=3
-    return SingleThreaded
-  elseif f == :params
-    @warn "CommonConvWrapper.params is deprecated, use .varValsAll instead" maxlog=3
-    return ccw.varValsAll
-  elseif f == :vartypes
-    @warn "CommonConvWrapper.vartypes is deprecated, use typeof.(getVariableType.(ccw.fullvariables) instead" maxlog=3
-    return typeof.(getVariableType.(ccw.fullvariables))
-  else
-    return getfield(ccw, f)
-  end
-end
-
-
-##==============================================================================
-## Deprecate code below before v0.33
-##==============================================================================
-
-# export setThreadModel!
-  # introduced for approximate convolution operations
-export SingleThreaded, MultiThreaded
-
-function setThreadModel!(fgl::AbstractDFG; model = IIF.SingleThreaded)
-  #
-  @error("Obsolete, ThreadModel types are no longer in use.")
-  # for (key, id) in fgl.fIDs
-  #   _getCCW(fgl, key).threadmodel = model
-  # end
-  return nothing
-end
+# Base.getindex(mv::ManifoldsVector, inds...) = getindex(mv.mani, inds...)
+# Base.setindex!(mv, X, inds...) =  setindex!(mv.mani, X, inds...)
 
-# should have been deleted in v0.31 but no harm in keeping this one a bit longer
-@deprecate initManual!(w...; kw...) initVariable!(w...; kw...)
+# function ManifoldsVector(fg::AbstractDFG, varIds::Vector{Symbol})
+#   manis = Bool[]
+#   for k = varIds
+#     push!(manis, getVariableType(fg, k) |> getManifold)
+#   end
+#   ManifoldsVector(manis)
+# end
 
+# function Optim.retract!(manis::ManifoldsVector, x)
+#   for (i,M) = enumerate(manis)
+#     x[i] = project(M, x[i])
+#   end
+#   return x 
+# end
+# function Optim.project_tangent!(manis::ManifoldsVector, G, x)
+#   for (i, M) = enumerate(manis)
+#     G[i] = project(M, x[i], G)
+#   end
+#   return G
+# end
 
 
 ##==============================================================================
@@ -146,34 +111,102 @@ function solveGraphParametric2(
   return d, result, flatvar.idx, Σ
 end
 
-## ================================================================================================
-## Manifolds.jl Consolidation
-## TODO: Still to be completed and tested.
-## ================================================================================================
-# struct ManifoldsVector <: Optim.Manifold
-#   manis::Vector{Manifold}
-# end
 
-# Base.getindex(mv::ManifoldsVector, inds...) = getindex(mv.mani, inds...)
-# Base.setindex!(mv, X, inds...) =  setindex!(mv.mani, X, inds...)
+##==============================================================================
+## Deprecate code below before v0.34
+##==============================================================================
 
-# function ManifoldsVector(fg::AbstractDFG, varIds::Vector{Symbol})
-#   manis = Bool[]
-#   for k = varIds
-#     push!(manis, getVariableType(fg, k) |> getManifold)
-#   end
-#   ManifoldsVector(manis)
+# function CommonConvWrapper(
+#   usrfnc::T,
+#   fullvariables, #::Tuple ::Vector{<:DFGVariable};
+#   varValsAll::Tuple,
+#   X::AbstractVector{P}; #TODO remove X completely
+#   # xDim::Int = size(X, 1),
+#   userCache::CT = nothing,
+#   manifold = getManifold(usrfnc),
+#   partialDims::AbstractVector{<:Integer} = 1:length(X),
+#   partial::Bool = false,
+#   nullhypo::Real = 0,
+#   inflation::Real = 3.0,
+#   hypotheses::H = nothing,
+#   certainhypo = nothing,
+#   activehypo = collect(1:length(varValsAll)),
+#   measurement::AbstractVector = Vector(Vector{Float64}()),
+#   varidx::Int = 1,
+#   particleidx::Int = 1,
+#   res::AbstractVector{<:Real} = zeros(manifold_dimension(manifold)), # zDim
+#   gradients = nothing,
+# ) where {T <: AbstractFactor, P, H, CT}
+#   #
+#   return CommonConvWrapper(
+#     usrfnc,
+#     tuple(fullvariables...),
+#     varValsAll,
+#     userCache,
+#     manifold,
+#     partialDims,
+#     partial,
+#     # xDim,
+#     float(nullhypo),
+#     float(inflation),
+#     hypotheses,
+#     certainhypo,
+#     activehypo,
+#     measurement,
+#     Ref(varidx),
+#     Ref(particleidx),
+#     res,
+#     gradients,
+#   )
 # end
 
-# function Optim.retract!(manis::ManifoldsVector, x)
-#   for (i,M) = enumerate(manis)
-#     x[i] = project(M, x[i])
-#   end
-#   return x 
+# function approxConvOnElements!(
+#   ccwl::Union{CommonConvWrapper{F}, CommonConvWrapper{Mixture{N_, F, S, T}}},
+#   elements::Union{Vector{Int}, UnitRange{Int}},
+#   ::Type{<:MultiThreaded},
+#   _slack = nothing,
+# ) where {N_, F <: AbstractRelative, S, T}
+#   #
+#   return error(
+#     "MultiThreaded `approxConvOnElements!` is deprecated and will soon be replaced",
+#   )
+#   # Threads.@threads for n in elements
+#   #   # ccwl.thrid_ = Threads.threadid()
+#   #   ccwl.cpt[Threads.threadid()].particleidx = n
+
+#   #   # ccall(:jl_, Nothing, (Any,), "starting loop, thrid_=$(Threads.threadid()), partidx=$(ccwl.cpt[Threads.threadid()].particleidx)")
+#   #   _solveCCWNumeric!( ccwl, _slack=_slack)
+#   # end
+#   # nothing
 # end
-# function Optim.project_tangent!(manis::ManifoldsVector, G, x)
-#   for (i, M) = enumerate(manis)
-#     G[i] = project(M, x[i], G)
-#   end
-#   return G
+
+# function approxConvOnElements!(
+#   ccwl::Union{CommonConvWrapper{F}, CommonConvWrapper{Mixture{N_, F, S, T}}},
+#   elements::Union{Vector{Int}, UnitRange{Int}},
+#   _slack = nothing,
+# ) where {N_, F <: AbstractRelative, S, T}
+#   #
+#   return approxConvOnElements!(ccwl, elements, ccwl.threadmodel, _slack)
 # end
+
+# more legacy, dont delete yet
+function Base.getproperty(ccw::CommonConvWrapper, f::Symbol)
+  if f == :threadmodel
+    error("CommonConvWrapper.threadmodel is obsolete")
+    # return SingleThreaded
+  elseif f == :params
+    error("CommonConvWrapper.params is deprecated, use .varValsAll instead")
+    return ccw.varValsAll
+  elseif f == :vartypes
+    @warn "CommonConvWrapper.vartypes is deprecated, use typeof.(getVariableType.(ccw.fullvariables) instead" maxlog=3
+    return typeof.(getVariableType.(ccw.fullvariables))
+  else
+    return getfield(ccw, f)
+  end
+end
+
+##==============================================================================
+## Deprecate code below before v0.35
+##==============================================================================
+
+##

src/IncrementalInference.jl

@@ -41,7 +41,6 @@ using Dates,
   ProgressMeter,
   DocStringExtensions,
   FunctionalStateMachine,
-  JSON2,  
   JSON3,
   Combinatorics,
   UUIDs,

src/Serialization/services/DispatchPackedConversions.jl

@@ -50,6 +50,7 @@ function reconstFactorData(
     certainhypo = packed.certainhypo,
     inflation = packed.inflation,
     userCache,
+    attemptGradients = getSolverParams(dfg).attemptGradients,
     # Block recursion if NoSolverParams or if set to not attempt gradients.
     _blockRecursion=
       getSolverParams(dfg) isa NoSolverParams || 

src/Serialization/services/SerializationMKD.jl

@@ -75,7 +75,7 @@ end
 function Base.convert(::Type{String}, mkd::ManifoldKernelDensity)
   #
   packedMKD = packDistribution(mkd)
-  return JSON2.write(packedMKD)
+  return JSON3.write(packedMKD)
 end
 
 # Use general dispatch
@@ -86,7 +86,7 @@ end
 #  https://discourse.julialang.org/t/converting-string-to-datatype-with-meta-parse/33024/2
 #  https://discourse.julialang.org/t/is-there-a-way-to-import-modules-with-a-string/15723/6
 function Base.convert(::Type{<:ManifoldKernelDensity}, str::AbstractString)
-  dtr = JSON2.read(str, PackedManifoldKernelDensity)
+  dtr = JSON3.read(str, PackedManifoldKernelDensity)
   return unpackDistribution(dtr)
 end
 

src/Serialization/services/SerializingDistributions.jl

@@ -170,18 +170,18 @@ end
 # FIXME ON FIRE, must deprecate nested JSON written fields in all serialization
 # TODO is string necessary, because unpacking templated e.g. PackedType{T} has problems, see DFG #668
 function convert(::Type{String}, dtr::StringThemSamplableBeliefs)
-  return JSON2.write(packDistribution(dtr))
+  return JSON3.write(packDistribution(dtr))
 end
 
 function convert(::Type{<:SamplableBelief}, str_obj::AbstractString)
   #
 
   # go from stringified to generic packed (no type info)
-  _pck = JSON2.read(str_obj)
+  _pck = JSON3.read(str_obj)
   # NOTE, get the packed type from strong assumption that field `_type` exists in the 
-  T = DFG.getTypeFromSerializationModule(_pck[:_type])
+  T = DFG.getTypeFromSerializationModule(_pck._type)
   # unpack again to described packedType
-  pckT = JSON2.read(str_obj, T)
+  pckT = JSON3.read(str_obj, T)
 
   # unpack to regular <:SamplableBelief
   return unpackDistribution(pckT)

src/entities/FactorOperationalMemory.jl

@@ -80,7 +80,7 @@ Related
 
 [`CalcFactor`](@ref), [`CalcFactorMahalanobis`](@ref)
 """
-struct CommonConvWrapper{
+Base.@kwdef struct CommonConvWrapper{
   T <: AbstractFactor, 
   VT <: Tuple,
   NTP <: Tuple, 
@@ -101,39 +101,39 @@ struct CommonConvWrapper{
       to each hypothesis evaluation event on user function via CalcFactor, #1321 """
   varValsAll::NTP
   """ dummy cache value to be deep copied later for each of the CalcFactor instances """
-  dummyCache::CT
+  dummyCache::CT = nothing
   # derived config parameters for this factor
   """ Factor manifold definition for frequent use (not the variables manifolds) """
-  manifold::AM
+  manifold::AM = getManifold(usrfnc!)
   """ Which dimensions does this factor influence.  Sensitive (mutable) to both which 'solvefor index' variable and whether the factor is partial dimension """
-  partialDims::Vector{<:Integer}
+  partialDims::Vector{<:Integer} = collect(1:manifold_dimension(manifold))
   """ is this a partial constraint as defined by the existance of factor field `.partial::Tuple` """
-  partial::Bool
+  partial::Bool = false
   """ probability that this factor is wholly incorrect and should be ignored during solving """
-  nullhypo::Float64
+  nullhypo::Float64 = 0.0
   """ inflationSpread particular to this factor (by how much to dispurse the belief initial values before numerical optimization is run).  Analogous to stochastic search """
-  inflation::Float64
+  inflation::Float64 = 3.0
   # multihypo specific field containers for recipe of hypotheses to compute
   """ multi hypothesis settings #NOTE no need for a parameter as type is known from `parseusermultihypo` """
-  hypotheses::HP
+  hypotheses::HP = nothing
   """ categorical to select which hypothesis is being considered during convolution operation """
-  certainhypo::CH
+  certainhypo::CH = nothing
   """ subsection indices to select which params should be used for this hypothesis evaluation """
-  activehypo::Vector{Int}
+  activehypo::Vector{Int} = collect(1:length(varValsAll))
   # buffers and indices to point numerical computations to specific memory locations
   """ user defined measurement values for each approxConv operation
       FIXME make type stable, JT should now be type stable if rest works.
       SUPER IMPORTANT, if prior=>point or relative=>tangent, see #1661 
       can be a Vector{<:Tuple} or more direct Vector{<: pointortangenttype} """
-  measurement::Vector{MT}
+  measurement::Vector{MT} = Vector(Vector{Float64}())
   """ which index is being solved for in params? """
-  varidx::Base.RefValue{Int}
+  varidx::Base.RefValue{Int} = Ref(1)
   """ Consolidation from CPT, the actual particle being solved at this moment """
-  particleidx::Base.RefValue{Int}
+  particleidx::Base.RefValue{Int} = Ref(1)
   """ working memory to store residual for optimization routines """
-  res::Vector{Float64}
+  res::Vector{Float64} = zeros(manifold_dimension(manifold))
   """ experimental feature to embed gradient calcs with ccw """
-  _gradients::G
+  _gradients::G = nothing
 end