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adding fixed locations to SFDP - update #52

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75f99be
adding capability to specify fixed SFDP positions
claytonpbarrows Aug 19, 2022
489c4a7
cleanup
claytonpbarrows Aug 19, 2022
2f2e826
scaling against fixed positions
claytonpbarrows Aug 26, 2022
675af4a
reverting
claytonpbarrows Sep 2, 2022
43f732a
interface improvements
claytonpbarrows Sep 3, 2022
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78 changes: 62 additions & 16 deletions src/sfdp.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -24,27 +24,60 @@ the nodes.
positions will be truncated or filled up with random values between [-1,1] in every coordinate.

- `seed=1`: Seed for random initial positions.
- `pin=Dict{Int,Bool}()` : Anchors positions of nodes to initial position
"""
@addcall struct SFDP{Dim,Ptype,T<:AbstractFloat} <: IterativeLayout{Dim,Ptype}
tol::T
C::T
K::T
iterations::Int
initialpos::Vector{Point{Dim,Ptype}}
initialpos::Dict{Int, Point{Dim,Ptype}}
seed::UInt
pin::Dict{Int, Bool}
function SFDP(tol::T, C::T, K::T, iterations::Int, initialpos::Dict, seed::UInt, pin::Dict) where T<:AbstractFloat
for (ix, p) in pin
if !haskey(initialpos, ix) && p
@warn "No coordinate provided for pinned position $ix"
end
end
dim = get_pt_dim(initialpos)
ptype = get_pt_ptype(initialpos)
new{dim, ptype, typeof(tol)}(tol, C, K, iterations, initialpos, seed, pin)
end
end

# TODO: check SFDP default parameters
function SFDP(; dim=2, Ptype=Float64, tol=1.0, C=0.2, K=1.0, iterations=100, initialpos=Point{dim,Ptype}[],
seed=1)
if !isempty(initialpos)
initialpos = Point.(initialpos)
Ptype = eltype(eltype(initialpos))
# TODO fix initial pos if list has points of multiple types
Ptype == Any && error("Please provide list of Point{N,T} with same T")
dim = length(eltype(initialpos))
end
return SFDP{dim,Ptype,typeof(tol)}(tol, C, K, iterations, initialpos, seed)
function SFDP(; dim=2, Ptype=Float64, tol=1.0, C=0.2, K=1.0, iterations=100, initialpos=Dict{Int, Point{dim,Ptype}}(),
seed::UInt=UInt(1), pin = Dict{Int, Bool}())
return SFDP(tol, C, K, iterations, initialpos, seed, pin)
end

function SFDP(tol::T, C::T, K::T, iterations::Int, initialpos::Vector, seed::UInt, pin) where T<:AbstractFloat
initialpos = Dict(zip(1:length(initialpos), Point.(initialpos)))
# TODO fix initial pos if list has points of multiple types
return SFDP(tol, C, K, iterations, initialpos, seed, pin)
end

function SFDP(tol::T, C::T, K::T, iterations::Int, initialpos::Dict{Int, <:Point}, seed::UInt, pin::Vector{Bool}) where T<:AbstractFloat
dim = get_pt_dim(initialpos)
fixed = Dict(zip(1:length(pin), pin))
return SFDP(tol, C, K, iterations, initialpos, seed, fixed)
end

function get_pt_ptype(ip::Dict{Int, <:Point})
ptype = eltype(eltype(values(ip)))
ptype == Any && error("Please provide list of Point{N,T} with same T")
return ptype
end

function get_pt_dim(ip::Vector)
dims = length.(ip)
length(unique(dims)) != 1 && error("Please provide list of Point{N,T} with same N")
return first(dims)
end

function get_pt_dim(ip::Dict{Int, <:Point})
return typeof(ip).parameters[2].parameters[1] #based on type of point
end

function Base.iterate(iter::LayoutIterator{SFDP{Dim,Ptype,T}}) where {Dim,Ptype,T}
Expand All @@ -54,12 +87,23 @@ function Base.iterate(iter::LayoutIterator{SFDP{Dim,Ptype,T}}) where {Dim,Ptype,
rng = MersenneTwister(algo.seed)
startpos = Vector{Point{Dim,Ptype}}(undef, N)
# take the first
for i in 1:min(N, M)
startpos[i] = algo.initialpos[i]
for (i, p) in algo.initialpos
startpos[i] = p
end

# create bounds for random initial positions
if isempty(algo.initialpos)
startposbounds = (min = zero(Point{Dim, Ptype}), max = zero((Point{Dim, Ptype})) .+ one(Ptype))
else
startposbounds = (
min = Point{Dim, Ptype}([minimum((p[d] for p in values(algo.initialpos))) for d in 1:Dim]),
max = Point{Dim, Ptype}([maximum((p[d] for p in values(algo.initialpos))) for d in 1:Dim])
)
end

# fill the rest with random points
for i in (M + 1):N
startpos[i] = 2 .* rand(rng, Point{Dim,Ptype}) .- 1
for i in setdiff(1:N, keys(algo.initialpos))
startpos[i] = (startposbounds.max .- startposbounds.min) .* (2 .* rand(rng, Point{Dim,Ptype}) .- 1) .+ startposbounds.min
end
# iteratorstate: (#iter, energy, step, progress, old pos, stopflag)
return startpos, (1, typemax(T), one(T), 0, startpos, false)
Expand Down Expand Up @@ -93,7 +137,9 @@ function Base.iterate(iter::LayoutIterator{<:SFDP}, state)
((locs[j] .- locs[i]) / norm(locs[j] .- locs[i])))
end
end
locs[i] = locs[i] .+ step .* (force ./ norm(force))
if !get(algo.pin, i, false)
locs[i] = locs[i] .+ step .* (force ./ norm(force))
end
energy = energy + norm(force)^2
end
step, progress = update_step(step, energy, energy0, progress)
Expand Down
21 changes: 14 additions & 7 deletions test/runtests.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ using SparseArrays: sparse
using Test

function jagmesh()
jagmesh_path = joinpath(dirname(@__FILE__), "jagmesh1.mtx")
jagmesh_path = joinpath(pkgdir(NetworkLayout), "test", "jagmesh1.mtx")
array = round.(Int, open(readdlm, jagmesh_path))
row = array[:, 1]
col = array[:, 2]
Expand All @@ -29,6 +29,11 @@ jagmesh_adj = jagmesh()
ip = [Point2f(1, 2)]
algo = SFDP(; initialpos=ip)
@test algo isa SFDP{2,Float32}
ip = Dict(1=>Point(1.0,3.0))
algo = SFDP(; initialpos = ip)
@test algo isa SFDP{2, Float64}
p = [true, true]
algo = SFDP(; initialpos = ip, pin = p)
end

@testset "iterator size" begin
Expand All @@ -46,22 +51,24 @@ jagmesh_adj = jagmesh()

@testset "Testing Jagmesh1 graph" begin
println("SFDP Jagmesh1")
positions = @time SFDP(; dim=2, Ptype=Float32, tol=0.9, K=1, iterations=10)(jagmesh_adj)
positions = @time SFDP(; dim=2, Ptype=Float32, tol=0.9, K=1.0, iterations=10)(jagmesh_adj)
@test typeof(positions) == Vector{Point2f}
positions = @time SFDP(; dim=3, Ptype=Float32, tol=0.9, K=1, iterations=10)(jagmesh_adj)
positions = @time SFDP(; dim=3, Ptype=Float32, tol=0.9, K=1.0, iterations=10)(jagmesh_adj)
@test typeof(positions) == Vector{Point3f}
end

@testset "Testing wheel_graph" begin
println("SFDP Wheelgraph")
g = wheel_graph(10)
adj_matrix = adjacency_matrix(g)
positions = @time SFDP(; dim=2, Ptype=Float32, tol=0.1, K=1)(adj_matrix)
positions = @time SFDP(; dim=2, Ptype=Float32, tol=0.1, K=1.0)(adj_matrix)
@test typeof(positions) == Vector{Point2f}
@test positions == sfdp(adj_matrix; dim=2, Ptype=Float32, tol=0.1, K=1)
positions = @time SFDP(; dim=3, Ptype=Float32, tol=0.1, K=1)(adj_matrix)
@test positions == sfdp(adj_matrix; dim=2, Ptype=Float32, tol=0.1, K=1.0)
positions = @time SFDP(; dim=3, Ptype=Float32, tol=0.1, K=1.0)(adj_matrix)
@test typeof(positions) == Vector{Point3f}
@test positions == sfdp(adj_matrix; dim=3, Ptype=Float32, tol=0.1, K=1)
@test positions == sfdp(adj_matrix; dim=3, Ptype=Float32, tol=0.1, K=1.0)
ip = [Point2f(3.0, 1.0)]
@test ip[1] == sfdp(adj_matrix; dim=3, Ptype=Float32, tol=0.1, K=1.0, initialpos = ip, pin = [true])[1]
end
end

Expand Down