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Improve cycle reconstruction performance #173

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merged 3 commits into from
Dec 19, 2024
Merged

Improve cycle reconstruction performance #173

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db1fc53
Improve perfomance of cycle reconstruction
mtsch Dec 19, 2024
6f6587a
update Project.toml
mtsch Dec 19, 2024
1a55b61
Update src/extra/cycles.jl
mtsch Dec 19, 2024
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2 changes: 1 addition & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "Ripserer"
uuid = "aa79e827-bd0b-42a8-9f10-2b302677a641"
authors = ["mtsch <[email protected]>"]
version = "0.16.12"
version = "0.16.13"

[deps]
Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
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24 changes: 15 additions & 9 deletions src/extra/cycles.jl
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Expand Up @@ -23,6 +23,10 @@ function OneSkeleton(
return OneSkeleton{T,F,S,typeof(weights)}(filtration, thresh, weights, removed)
end

function Graphs.SimpleGraph(g::OneSkeleton)
SimpleGraph(edges(g))
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end

_birth_or_value(σ::AbstractCell) = birth(σ)
_birth_or_value(σ) = σ
_in(σ::S, g::OneSkeleton{S}) where {S} = !isnothing(σ) && σ ≤ g.threshold && σ ∉ g.removed
Expand Down Expand Up @@ -97,19 +101,21 @@ end

Find the shortest cycle in `g` that has exactly one edge from `g.removed`.
"""
function _find_cycle(g, dists)
function _find_cycle(skeleton, dists)
# Idea:
# best_weight is the current best length of shortest cycle.
# best_path is the current best candidate for shortest cycle.
# best_simplex completes best_path to a cycle.
# We go through all edges in g.removed and find the shortest path through its
# We go through all edges in skeleton.removed and find the shortest path through its
# endpoints. The shortest among those is the shortest cycle.
graph = SimpleGraph(skeleton)

best_weight = missing
best_path = edgetype(g)[]
best_sx = first(g.removed)
for sx in g.removed
u, v = _linear.(Ref(g), sx)
path = a_star(g, u, v, dists, _heuristic(g.filtration, v, dists))
best_path = edgetype(skeleton)[]
best_sx = first(skeleton.removed)
for sx in skeleton.removed
u, v = _linear.(Ref(skeleton), sx)
path = a_star(graph, u, v, dists, _heuristic(skeleton.filtration, v, dists))
weight = _path_length(dists, path) + dists[u, v]
if !isempty(path) && isless(weight, best_weight)
best_weight = weight
Expand All @@ -123,8 +129,8 @@ function _find_cycle(g, dists)
result = [best_sx]
# Convert the type of best_path from `Edge`s to the simplex type of the filtration.
for e in best_path
u, v = _inv_linear.(Ref(g), (src(e), dst(e)))
push!(result, simplex(g.filtration, Val(1), (u, v)))
u, v = _inv_linear.(Ref(skeleton), (src(e), dst(e)))
push!(result, simplex(skeleton.filtration, Val(1), (u, v)))
end
return result
end
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