Closed nraynaud closed 2 years ago
The restriction on the metrics for KDTree
is of algorithmic type and has nothing to do with the given implementation here. But BallTree
and BruteTree
should work with pretty much any metric from Distances.jl.
Thank you for your answer, I re-read the code and I agree that it should work. I had read too fast the time prior, you made a special case for some metrics in the hypersphere, but there is another code path.
when I change runtest.jl to run the BallTree with the SqEuclidean metric, I get an error:
using NearestNeighbors
using StaticArrays
using Test
using LinearAlgebra
using Distances: Distances, Metric, evaluate, PeriodicEuclidean, SqEuclidean # CHANGED HERE
struct CustomMetric1 <: Metric end
Distances.evaluate(::CustomMetric1, a::AbstractVector, b::AbstractVector) = maximum(abs.(a .- b))
function NearestNeighbors.interpolate(::CustomMetric1,
a::V,
b::V,
x,
d,
ab) where {V <: AbstractVector}
idx = (abs.(b .- a) .>= d - x)
c = copy(Array(a))
c[idx] = (1 - x / d) * a[idx] + (x / d) * b[idx]
return c, true
end
struct CustomMetric2 <: Metric end
Distances.evaluate(::CustomMetric2, a::AbstractVector, b::AbstractVector) = norm(a - b) / (norm(a) + norm(b))
# TODO: Cityblock()
const metrics = [SqEuclidean()] # CHANGED HERE
const fullmetrics = metrics # CHANGED HERE
const trees = [BallTree] # CHANGED HERE
const trees_with_brute = trees # CHANGED HERE
include("test_knn.jl")
include("test_inrange.jl")
include("test_monkey.jl")
include("test_datafreetree.jl")
@testset "periodic euclidean" begin
pred = PeriodicEuclidean([Inf, 2.5])
l = [0.0 0.0; 0.0 2.5]
S = BallTree(l, pred)
@test inrange(S,[0.0,0.0], 1e-2, true) == [1, 2]
end
error message:
tree type: Error During Test at /Users/nraynaud/.julia/dev/NearestNeighbors/test/test_knn.jl:7
Got exception outside of a @test
MethodError: no method matching BallTree(::Matrix{Float64}, ::SqEuclidean; leafsize=2)
Closest candidates are:
BallTree(::AbstractVecOrMat{T}) where T<:AbstractFloat at ~/.julia/packages/NearestNeighbors/VZzTb/src/ball_tree.jl:84 got unsupported keyword argument "leafsize"
BallTree(::AbstractVecOrMat{T}, ::M; leafsize, storedata, reorder, reorderbuffer) where {T<:AbstractFloat, M<:Metric} at ~/.julia/packages/NearestNeighbors/VZzTb/src/ball_tree.jl:84
Stacktrace:
[1] (::var"#test#1"{SqEuclidean, UnionAll})(data::Matrix{Float64})
@ Main ~/.julia/dev/NearestNeighbors/test/test_knn.jl:9
[2] macro expansion
@ ~/.julia/dev/NearestNeighbors/test/test_knn.jl:64 [inlined]
is that expected?
Edit: for context I'm new to julia, so I may completely misread the situation.
Sorry, now I was too quick. From the error message, we learn that BallTree
requires a Metric
, most likely because it assumes validity of the triangle inequality to build the ball tree. As for the kdtree, yet another, additional assumption is required ("Minkowski metric").
I don't think there is oversight here, this package is very carefully written. It may just be that there is sparse documentation with regard to the underlying assumptions, but I haven't looked at docs and code for a while.
I see, I was under the impression that everything the euclidean distance did could be done by the square euclidean distance. I was under the impression that the square root function being monotonous meant that it wouldn't mess with distance comparisons.
Thank you for your time.
Hi, I'm a little bit out of my element in maths, but I think sqeuclidean distances should work as well as euclidean for those data structures. Is there a reason it's not supported?
Broadening a bit the question, the Distances.jl package has defined some types for the various mathematical predicates that can be expected from the various metrics it exposes, is there a reason not to use one of those types to limit what's accessible to BallTree and KDTree?
thank you for your nice library.