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Fix GetStepRanges
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@RafaelArutjunjan
RafaelArutjunjan committed Nov 20, 2024
1 parent 8baccd0 commit d8d1edd
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Showing 4 changed files with 36 additions and 7 deletions.
2 changes: 1 addition & 1 deletion Project.toml
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@@ -1,7 +1,7 @@
name = "InformationGeometry"
uuid = "ee9d1287-bbdf-432c-9920-c447cf97a828"
authors = ["Rafael Arutjunjan"]
version = "1.15.2"
version = "1.16.0"

[deps]
BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
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4 changes: 2 additions & 2 deletions src/CustomIO.jl
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Expand Up @@ -53,7 +53,7 @@ end
Base.summary(P::ParameterProfiles) = string(TYPE_COLOR, "ParameterProfiles", NO_COLOR, " with pdim="* string(pdim(P)), !HasTrajectories(P) ? string(", ", ORANGE_COLOR, "no trajectories", NO_COLOR) : "")
Base.summary(PV::ParameterProfilesView) = string(TYPE_COLOR, "ParameterProfile", NO_COLOR, " for index "* string(PV.i) *"/"* string(pdim(PV)), !HasTrajectories(PV) ? string(", ", ORANGE_COLOR, "no trajectories", NO_COLOR) : "")

Base.summary(R::MultistartResults) = string(TYPE_COLOR, "MultistartResults", NO_COLOR, " with "* string(findlast(isfinite, R.FinalObjectives)) *"/"* string(length(R)) *" successful starts")
Base.summary(R::MultistartResults) = string(TYPE_COLOR, "MultistartResults", NO_COLOR, " with "* string(FindLastIndSafe(R)) *"/"* string(length(R)) *" successful starts")


# http://docs.junolab.org/stable/man/info_developer/#
Expand Down Expand Up @@ -199,7 +199,7 @@ Base.show(io::IO, P::Union{ParameterProfiles,ParameterProfilesView}) = print(io,

# Multi-line display when used on its own in REPL
function Base.show(io::IO, ::MIME"text/plain", R::MultistartResults)
LastFinite = findlast(isfinite, R.FinalObjectives)
LastFinite = FindLastIndSafe(R)
FirstStepInd = GetFirstStepInd(R, LastFinite)
println(io, Base.summary(R))
println(io, "Median number of iterations: "*string(Int(round(median(@view R.Iterations[1:LastFinite])))))
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1 change: 1 addition & 0 deletions src/InformationGeometry.jl
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Expand Up @@ -244,6 +244,7 @@ export PlotRelativeParameterTrajectories

include("NumericalTools/Multistart.jl")
export MultistartFit, LocalMultistartFit, MultistartResults, WaterfallPlot, ParameterPlot
export DistanceMatrixWithinStep, DistanceMatrixBetweenSteps


include("Divergences.jl")
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36 changes: 32 additions & 4 deletions src/NumericalTools/Multistart.jl
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Expand Up @@ -180,10 +180,13 @@ catch E;
(E isa ErrorException ? throw("StatsPlots.jl needs to be loaded before using ParameterPlot.") : rethrow(E))
end

# Implement findlast in safe manner so "nothing" is never returned
GetStepInds(R::MultistartResults, ymaxind::Int=findlast(isfinite,R.FinalObjectives); StepTol::Real=0.01) = ((@assert 1 ≤ ymaxind ≤ length(R) && StepTol > 0); F=-R.FinalObjectives; [i for i in 1:ymaxind-1 if isfinite(F[i+1]) && abs(F[i+1]-F[i]) > StepTol])
FindLastIndSafe(R::MultistartResults) = (LastFinite=findlast(isfinite, R.FinalObjectives); isnothing(LastFinite) ? 0 : LastFinite)

function GetFirstStepInd(R::MultistartResults, ymaxind::Int=findlast(isfinite,R.FinalObjectives); StepTol::Real=0.01)
# GetStepInds always includes last point of lower step
GetStepInds(R::MultistartResults, ymaxind::Int=FindLastIndSafe(R); StepTol::Real=0.01) = ((@assert 1 ≤ ymaxind ≤ length(R) && StepTol > 0); F=-R.FinalObjectives; [i for i in 1:ymaxind-1 if isfinite(F[i+1]) && abs(F[i+1]-F[i]) > StepTol])
GetStepRanges(R::MultistartResults, ymaxind::Int=FindLastIndSafe(R), StepInds::AbstractVector{<:Int}=GetStepInds(R,ymaxind)) = vcat([1:StepInds[1]], [StepInds[i]+1:StepInds[i+1] for i in 1:length(StepInds)-1], [StepInds[end]+1:ymaxind])

function GetFirstStepInd(R::MultistartResults, ymaxind::Int=FindLastIndSafe(R); StepTol::Real=0.01)
(@assert 1 ≤ ymaxind ≤ length(R) && StepTol > 0); F=-R.FinalObjectives
FirstStepInd = findfirst(i->isfinite(F[i+1]) && abs(F[i+1]-F[i]) > StepTol, 1:ymaxind-1)
isnothing(FirstStepInd) ? ymaxind : FirstStepInd
Expand Down Expand Up @@ -249,7 +252,7 @@ RecipesBase.@recipe function f(R::MultistartResults, ::Union{Val{:ParameterPlot}
ymaxind = (Q=findlast(x->isfinite(x) && abs(x-Fin[1]) < MaxValue, Fin); isnothing(Q) ? length(Fin) : Q)
@assert StepTol > 0
StepInds = GetStepInds(R, ymaxind; StepTol=StepTol)
AllSteps = vcat([1:StepInds[1]], [StepInds[i]:StepInds[i+1] for i in 1:length(StepInds)-1], [StepInds[end]:ymaxind])
AllSteps = GetStepRanges(R, ymaxind, StepInds)
Steps = @view AllSteps[1:min(Nsteps, length(AllSteps))]
dfs = [(DoBiLog ? BiLog : identity)(reduce(vcat, R.FinalPoints[step])) for step in Steps]
Xvals = 1.0:Spacer*length(dfs):Spacer*length(dfs)*length(pnames) |> collect
Expand All @@ -275,3 +278,28 @@ RecipesBase.@recipe function f(R::MultistartResults, ::Union{Val{:ParameterPlot}
end
end
end

"""
DistanceMatrixWithinStep(DM::AbstractDataModel, R::MultistartResults, Ind::Int; logarithmic::Bool=true, plot::Bool=true, kwargs...)
Returns matrix of mutual distances between optima in step `Ind` with respect to Fisher Metric of first entry in step.
"""
function DistanceMatrixWithinStep(DM::AbstractDataModel, R::MultistartResults, Ind::Int; logarithmic::Bool=true, plot::Bool=true, kwargs...)
ymaxind = FindLastIndSafe(R); StepInds = GetStepInds(R, ymaxind); Steps = GetStepRanges(R, ymaxind, StepInds)
@assert 1 ≤ Ind ≤ length(Steps)
F = FisherMetric(DM, R.FinalPoints[Steps[Ind][1]]) # get first point in ProfileDomain
Dists = [sqrt(InnerProduct(F, R.FinalPoints[i] - R.FinalPoints[j])) for i in Steps[Ind], j in Steps[Ind]]
plot && display(RecipesBase.plot((logarithmic ? log1p : identity).(Dists + Diagonal(fill(NaN, size(Dists,1)))); st=:heatmap, clims=(0, Inf), margin=2Plots.mm, kwargs...))
Dists
end

"""
DistanceMatrixBetweenSteps(DM::AbstractDataModel, R::MultistartResults; logarithmic::Bool=true, plot::Bool=true, kwargs...)
Returns matrix of mutual distances between first optima in steps with respect to Fisher Metric of best optimum.
"""
function DistanceMatrixBetweenSteps(DM::AbstractDataModel, R::MultistartResults; logarithmic::Bool=true, plot::Bool=true, kwargs...)
ymaxind = FindLastIndSafe(R); StepInds = GetStepInds(R, ymaxind); Steps = GetStepRanges(R, ymaxind, StepInds)
F = FisherMetric(DM, R.FinalPoints[1])
Dists = [sqrt(InnerProduct(F, R.FinalPoints[Steps[i][1]] - R.FinalPoints[Steps[j][1]])) for i in eachindex(Steps), j in eachindex(Steps)]
plot && display(RecipesBase.plot((logarithmic ? log1p : identity).(Dists + Diagonal(fill(NaN, size(Dists,1)))); st=:heatmap, clims=(0, Inf), margin=2Plots.mm, kwargs...))
Dists
end

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Registration pull request created: JuliaRegistries/General/119809

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Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v1.16.0 -m "<description of version>" d8d1eddaf672af01f130e597437b2a98de0e50ad
git push origin v1.16.0

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