missed staging for git

Author: dehann

ext/FluxFactorsExt.jl

@@ -1,18 +1,27 @@
+module FluxFactorsExt
 
-@info "IncrementalInference is adding Flux related functionality."
 
-# the factor definitions
-export FluxModelsDistribution
-export MixtureFluxModels
+@info "IncrementalInference is loading extension functionality related to Flux.jl"
 
 # Required packages
-using .Flux
+using Flux
 using DataStructures: OrderedDict
-using Random, Statistics
+using LinearAlgebra
+using Base64
+
+import Base: convert
 
 # import Base: convert
+using Random, Statistics
 import Random: rand
 
+using IncrementalInference
+import IncrementalInference: samplePoint, sampleTangent
+
+# the factor definitions
+# export FluxModelsDistribution
+export MixtureFluxModels
+
 const _IIFListTypes = Union{<:AbstractVector, <:Tuple, <:NTuple, <:NamedTuple}
 
 function Random.rand(nfb::FluxModelsDistribution, N::Integer = 1)
@@ -164,3 +173,8 @@ function MixtureFluxModels(::Type{F}, w...; kw...) where {F <: AbstractFactor}
 end
 
 #
+
+include("FluxModelsSerialization.jl")
+
+
+end # module

ext/FluxModelsSerialization.jl

@@ -2,9 +2,6 @@
 
 # @info "IncrementalInference is adding Flux/BSON serialization functionality."
 
-using Base64
-
-import Base: convert
 
 function _serializeFluxModelBase64(model::Flux.Chain)
   io = IOBuffer()

ext/HeatmapSampler.jl

@@ -1,5 +1,110 @@
 # heatmap sampler (experimental)
 
+
+(hmd::HeatmapGridDensity)(w...; kw...) = hmd.densityFnc(w...; kw...)
+
+function sampleTangent(M::AbstractManifold, hms::HeatmapGridDensity)
+  return sampleTangent(M, hms.densityFnc)
+end
+
+function Base.show(io::IO, x::HeatmapGridDensity{T, H, B}) where {T, H, B}
+  printstyled(io, "HeatmapGridDensity{"; bold = true, color = :blue)
+  println(io)
+  printstyled(io, "    T"; color = :magenta, bold = true)
+  println(io, "      = ", T)
+  printstyled(io, "    H"; color = :magenta, bold = true)
+  println(io, "`int  = ", H)
+  printstyled(io, "    B"; color = :magenta, bold = true)
+  println(io, "      = ", B)
+  printstyled(io, " }"; color = :blue, bold = true)
+  println(io, "(")
+  println(io, "  data:       ", size(x.data))
+  println(
+    io,
+    "    min/max:    ",
+    round(minimum(x.data); digits = 5),
+    " / ",
+    round(maximum(x.data); digits = 5),
+  )
+  println(io, "  domain:     ", size(x.domain[1]), ", ", size(x.domain[2]))
+  println(
+    io,
+    "    min/max:    ",
+    round(minimum(x.domain[1]); digits = 5),
+    " / ",
+    round(maximum(x.domain[1]); digits = 5),
+  )
+  println(
+    io,
+    "    min/max:    ",
+    round(minimum(x.domain[2]); digits = 5),
+    " / ",
+    round(maximum(x.domain[2]); digits = 5),
+  )
+  println(io, "  bw_factor:  ", x.bw_factor)
+  print(io, "  ")
+  show(io, x.densityFnc)
+  return nothing
+end
+
+Base.show(io::IO, ::MIME"text/plain", x::HeatmapGridDensity) = show(io, x)
+Base.show(io::IO, ::MIME"application/prs.juno.inline", x::HeatmapGridDensity) = show(io, x)
+
+"""
+    $SIGNATURES
+
+Internal function for updating HGD.  
+  
+Notes
+- Likely to be used for [unstashing packed factors](@ref section_stash_unstash) via [`preambleCache`](@ref).
+- Counterpart to `AMP._update!` function for stashing of either MKD or HGD.
+"""
+function _update!(
+  dst::HeatmapGridDensity{T, H, B},
+  src::HeatmapGridDensity{T, H, B},
+) where {T, H, B}
+  @assert size(dst.data) == size(src.data) "Updating HeatmapDensityGrid can only be done for data of the same size"
+  dst.data .= src.data
+  if !isapprox(dst.domain[1], src.domain[1])
+    dst.domain[1] .= src.domain[1]
+  end
+  if !isapprox(dst.domain[2], src.domain[2])
+    dst.domain[2] .= src.domain[2]
+  end
+  AMP._update!(dst.densityFnc, src.densityFnc)
+  return dst
+end
+
+
+##
+
+(lsg::LevelSetGridNormal)(w...; kw...) = lsg.densityFnc(w...; kw...)
+
+function sampleTangent(M::AbstractManifold, lsg::LevelSetGridNormal)
+  return sampleTangent(M, lsg.heatmap.densityFnc)
+end
+
+function Base.show(io::IO, x::LevelSetGridNormal{T, H}) where {T, H}
+  printstyled(io, "LevelSetGridNormal{"; bold = true, color = :blue)
+  println(io)
+  printstyled(io, "    T"; color = :magenta, bold = true)
+  println(io, "      = ", T)
+  printstyled(io, "    H"; color = :magenta, bold = true)
+  println(io, "`int  = ", H)
+  printstyled(io, " }"; color = :blue, bold = true)
+  println(io, "(")
+  println(io, "  level:      ", x.level)
+  println(io, "  sigma:      ", x.sigma)
+  println(io, "  sig.scale:  ", x.sigma_scale)
+  println(io, "  heatmap:    ")
+  show(io, x.heatmap)
+  return nothing
+end
+
+Base.show(io::IO, ::MIME"text/plain", x::LevelSetGridNormal) = show(io, x)
+Base.show(io::IO, ::MIME"application/prs.juno.inline", x::LevelSetGridNormal) = show(io, x)
+
+
 ##
 
 getManifold(hgd::HeatmapGridDensity) = getManifold(hgd.densityFnc)

ext/InterpolationsExt.jl

@@ -11,7 +11,8 @@ using ApproxManifoldProducts
 import ApproxManifoldProducts: sample
 const AMP = ApproxManifoldProducts
 
-import IncrementalInference: getManifold
+import Base: show
+import IncrementalInference: getManifold, sampleTangent
 import IncrementalInference: HeatmapGridDensity, PackedHeatmapGridDensity
 import IncrementalInference: LevelSetGridNormal, PackedLevelSetGridNormal
 

ext/WeakDepsPrototypes.jl

@@ -1,31 +1,4 @@
 
-"""
-    $TYPEDEF
-
-Build a full ODE solution into a relative factor to condense possible sensor data into a relative transformation,
-but keeping the parameter estimation process fluid.  Assumes first and second variable in order 
-are of same dimension and compatible manifolds, such that ODE runs from Xi to Xi+1 on all
-dimensions.  Internal state vector can be decoupled onto different domain as needed.
-
-Notes
-- Based on DifferentialEquations.jl
-- `getSample` step does the `solve(ODEProblem)` step.
-- `tspan` is taken from variables only once at object construction -- i.e. won't detect changed timestamps.
-- Regular factor evaluation is done as full dimension `AbstractRelativeRoots`, and is basic linear difference.
-
-DevNotes
-- FIXME see 1025, `multihypo=` will not yet work. 
-- FIXME Lots of consolidation and standardization to do, see RoME.jl #244 regarding Manifolds.jl.
-- TODO does not yet handle case where a factor spans across two timezones.
-"""
-struct DERelative{T <: InferenceVariable, P, D} <: AbstractRelativeMinimize
-  domain::Type{T}
-  forwardProblem::P
-  backwardProblem::P
-  # second element of this data tuple is additional variables that will be passed down as a parameter
-  data::D
-  specialSampler::Function
-end
 
 # InteractiveUtils.jl
 function getCurrentWorkspaceFactors end

src/ExportAPI.jl

@@ -310,7 +310,7 @@ export PackedUniform, PackedNormal
 export PackedZeroMeanDiagNormal,
   PackedZeroMeanFullNormal, PackedDiagNormal, PackedFullNormal
 export PackedManifoldKernelDensity
-export PackedAliasingScalarSampler, PackedHeatmapGridDensity, PackedLevelSetGridNormal
+export PackedAliasingScalarSampler
 export PackedRayleigh
 
 export Mixture, PackedMixture
@@ -358,13 +358,23 @@ export makeSolverData!
 
 export MetaPrior
 
+
+# weakdeps on Interpolations.jl
+export HeatmapGridDensity, LevelSetGridNormal
+export PackedHeatmapGridDensity, PackedLevelSetGridNormal
+
+# weakdeps on DifferentialEquations.jl
 export DERelative
 
+# weakdeps on Flux.jl
+export FluxModelsDistribution, PackedFluxModelsDistribution
+
 # weakdeps on InteractiveUtils.jl
 export getCurrentWorkspaceFactors, getCurrentWorkspaceVariables
 export listTypeTree
 
 # weakdeps on Gadfly.jl
 export exportimg, spyCliqMat
 
-#
+
+#

src/IncrementalInference.jl

@@ -130,7 +130,7 @@ include("entities/FactorOperationalMemory.jl")
 include("Factors/GenericMarginal.jl")
 # Special belief types for sampling as a distribution
 include("entities/AliasScalarSampling.jl")
-include("entities/OptionalDensities.jl")
+include("entities/OptionalDensities.jl") # used in BeliefTypes.jl::SamplableBeliefs
 include("entities/BeliefTypes.jl")
 
 include("services/HypoRecipe.jl")
@@ -234,6 +234,10 @@ include("services/SolverAPI.jl")
 # Symbolic tree analysis files.
 include("services/AnalysisTools.jl")
 
+# optional densities on weakdeps
+include("Serialization/entities/SerializingOptionalDensities.jl")
+include("Serialization/services/SerializingOptionalDensities.jl")
+
 include("../ext/WeakDepsPrototypes.jl")
 
 # deprecation legacy support
@@ -253,12 +257,11 @@ function __init__()
   #   "services/HeatmapSampler.jl",
   # )
 
-  # combining neural networks natively into the non-Gaussian  factor graph object
-  @require Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" begin
-    include("Flux/FluxModelsDistribution.jl")
-    include("Serialization/entities/FluxModelsSerialization.jl")
-    include("Serialization/services/FluxModelsSerialization.jl") # uses BSON
-  end
+  # # combining neural networks natively into the non-Gaussian  factor graph object
+  # @require Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" begin
+  #   # include("Flux/FluxModelsDistribution.jl")
+  #   include("Serialization/services/FluxModelsSerialization.jl") # uses BSON
+  # end
 end
 
 @compile_workload begin

src/Serialization/entities/AdditionalDensities.jl

@@ -13,22 +13,3 @@ Base.@kwdef struct PackedAliasingScalarSampler <: PackedSamplableBelief
   domain::Vector{Float64} = [0; 1.0]
   weights::Vector{Float64} = [0.5; 0.5]
 end
-
-Base.@kwdef mutable struct PackedHeatmapGridDensity <: PackedSamplableBelief
-  _type::String = "IncrementalInference.PackedHeatmapGridDensity"
-  data::Vector{Vector{Float64}}
-  domain::Tuple{Vector{Float64}, Vector{Float64}}
-  hint_callback::String
-  bw_factor::Float64
-  N::Int
-  # _densityFnc::String = "" # only use if storing parched belief data entry label/id
-end
-
-Base.@kwdef mutable struct PackedLevelSetGridNormal <: PackedSamplableBelief
-  _type::String = "IncrementalInference.PackedLevelSetGridNormal"
-  level::Float64
-  sigma::Float64
-  sigma_scale::Float64
-  # make sure the JSON nested packing works with the serialization overlords
-  heatmap::PackedHeatmapGridDensity
-end

src/Serialization/entities/SerializingOptionalDensities.jl

@@ -1,5 +1,26 @@
 
-export PackedFluxModelsDistribution
+
+
+Base.@kwdef mutable struct PackedHeatmapGridDensity <: PackedSamplableBelief
+  _type::String = "IncrementalInference.PackedHeatmapGridDensity"
+  data::Vector{Vector{Float64}}
+  domain::Tuple{Vector{Float64}, Vector{Float64}}
+  hint_callback::String
+  bw_factor::Float64
+  N::Int
+  # _densityFnc::String = "" # only use if storing parched belief data entry label/id
+end
+
+
+Base.@kwdef mutable struct PackedLevelSetGridNormal <: PackedSamplableBelief
+  _type::String = "IncrementalInference.PackedLevelSetGridNormal"
+  level::Float64
+  sigma::Float64
+  sigma_scale::Float64
+  # make sure the JSON nested packing works with the serialization overlords
+  heatmap::PackedHeatmapGridDensity
+end
+
 
 Base.@kwdef mutable struct PackedFluxModelsDistribution <: PackedSamplableBelief
   # standardized _type field