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Support for vertex and hyperedge values #12

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Feb 8, 2019
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Support for vertex and hyperedge values #12

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713f523
Support for vertex and hyperedge values
pszufe Feb 7, 2019
be94895
Update src/hypergraph.jl
bkamins Feb 7, 2019
1ff7acc
update meta
pszufe Feb 8, 2019
b4fad6b
update meta docs
pszufe Feb 8, 2019
5f35ddc
update meta indent
pszufe Feb 8, 2019
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11 changes: 8 additions & 3 deletions docs/src/reference.md
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Expand Up @@ -18,8 +18,13 @@ Hypergraph
Manipulating vertices and hyperedges
------------------------------------
```@docs
add_hyperedge!(::Hypergraph{T};::Dict{Int,T}) where T <: Real
add_vertex!(::Hypergraph{T};::Dict{Int,T}) where T <: Real

add_hyperedge!(::Hypergraph{T, V, E}; ::Dict{Int,T}, ::Union{UndefInitializer, E}) where {T <: Real, V, E}
add_vertex!(::Hypergraph{T, V, E};::Dict{Int,T},::Union{UndefInitializer,V}) where {T <: Real, V, E}
set_vertex_value!(::Hypergraph{T, V, E}, ::V, ::Int) where {T <: Real, V, E}
get_vertex_value(::Hypergraph{T, V, E}, ::Int) where {T <: Real, V, E}
set_hyperedge_value!(::Hypergraph{T, V, E}, ::E, ::Int) where {T <: Real, V, E}
get_hyperedge_value(::Hypergraph{T, V, E}, ::Int) where {T <: Real, V, E}
```

Hypergraph array getters and setters
Expand All @@ -33,7 +38,7 @@ h

# output

2×3 Hypergraph{Int64}:
2×3 Hypergraph{Int64,Nothing,Nothing}:
nothing 5 5
nothing nothing nothing
```
Expand Down
2 changes: 2 additions & 0 deletions src/SimpleHypergraphs.jl
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Expand Up @@ -4,6 +4,8 @@ using LightGraphs

export Hypergraph, getvertices, gethyperedges, hg_load, hg_save
export add_vertex!, add_hyperedge!
export set_vertex_value!, get_vertex_value
export set_hyperedge_value!, get_hyperedge_value
export BipartiteView, shortest_path
export TwoSectionView

Expand Down
115 changes: 100 additions & 15 deletions src/hypergraph.jl
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Expand Up @@ -14,35 +14,61 @@ A hypergraph storing information about vertices and hyperedges.
**Constructors**

Hypergraph{T}(n,k) where {T<:Real}
Hypergraph{T,V}(n, k) where {T<:Real, V}
Hypergraph{T,V,E}(n, k) where {T<:Real, V, E}

Construct a hypergraph with a given number of vertices and hyperedges.
Optionally, values of type `V` can be stored at vertices and values of type `E`
can be stored at hyperedges.

Hypergraph(m::AbstractMatrix{T}) where {T<:Real}
Hypergraph(m::AbstractMatrix{Union{T, Nothing}}) where {T<:Real}
Hypergraph{V}(m::AbstractMatrix{Union{T, Nothing}}) where {T<:Real, V}
Hypergraph{V, E}(m::AbstractMatrix{Union{T, Nothing}}) where {T<:Real, V, E}

Construct a hypergraph using its matrix representation.
In the matrix representation rows are vertices and columns are hyperedges.
Optionally, values of type `V` can be stored at vertices and values of type `E`
can be stored at hyperedges.

**Arguments**

* `T` : type of values stored in the hypergraph
* `T` : type of weight values stored in the hypergraph
* `V` : type of values stored in the vertices of the hypergraph
* `E` : type of values stored in the edges of the hypergraph
* `n` : number of vertices
* `k` : number of hyperedges
* `m` : a matrix representation rows are vertices and columns are hyperedges

"""
struct Hypergraph{T} <: AbstractMatrix{Union{T, Nothing}}
struct Hypergraph{T,V,E} <: AbstractMatrix{Union{T, Nothing}}
v2he::Vector{Dict{Int,T}}
he2v::Vector{Dict{Int,T}}
Hypergraph{T}(n, k) where {T<:Real} =
new([Dict{Int,T}() for i in 1:n], [Dict{Int,T}() for i in 1:k])
vs::Vector{V}
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hes::Vector{E}
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Hypergraph{T,V,E}(n, k) where {T<:Real, V, E} =
new{T,V,E}([Dict{Int,T}() for i in 1:n], [Dict{Int,T}() for i in 1:k],Vector{V}(undef,n),Vector{E}(undef,k))
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end

function Hypergraph(m::AbstractMatrix{T}) where {T<:Real}
h = Hypergraph{T}(size(m)...)
Hypergraph{T,V}(n, k) where {T<:Real, V} = Hypergraph{T,V,Nothing}(n, k)
Hypergraph{T}(n, k) where {T<:Real} = Hypergraph{T,Nothing,Nothing}(n, k)


function Hypergraph{V, E}(m::AbstractMatrix{Union{T, Nothing}}) where {T<:Real, V, E}
n, k = size(m)
h = Hypergraph{T, V, E}(n,k)
h .= m
h
end

function Hypergraph{V}(m::AbstractMatrix{Union{T, Nothing}}) where {T<:Real, V}
Hypergraph{V, Nothing}(m)
end

function Hypergraph(m::AbstractMatrix{Union{T, Nothing}}) where {T<:Real}
Hypergraph{Nothing, Nothing}(m)
end


"""
Base.size(h::Hypergraph)

Expand Down Expand Up @@ -72,8 +98,8 @@ Removes a vertex from a given hyperedge for a hypergraph `h` and a given vertex-
"""
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so maybe add a comment that trying to remove a vertex from a hyperedge when it is not present is not an error, earlier we wanted it to throw an error.

@inline function Base.setindex!(h::Hypergraph, ::Nothing, idx::Vararg{Int,2})
@boundscheck checkbounds(h, idx...)
pop!(h.v2he[idx[1]], idx[2])
pop!(h.he2v[idx[2]], idx[1])
pop!(h.v2he[idx[1]], idx[2], nothing)
pop!(h.he2v[idx[2]], idx[1], nothing)
h
end

Expand Down Expand Up @@ -108,41 +134,100 @@ Returns hyperedges for a given vertex `v_id` in a hypergraph `h`.
@inline gethyperedges(h::Hypergraph, v_id::Int) = h.v2he[v_id]

"""
add_vertex!(h::Hypergraph{T};hyperedges::Dict{Int,T} = Dict{Int,T}()) where T <: Real
add_vertex!(h::Hypergraph{T, V, E}; hyperedges::Dict{Int,T} = Dict{Int,T}(), vertex_val::Union{UndefInitializer, V} = undef) where {T <: Real, V, E}

Adds a vertex to a given hypergraph `h`. Optionally, the vertex can be added
to existing hyperedges. The `hyperedges` parameter presents a dictionary
of hyperedge identifiers and values stored at the hyperedges
of hyperedge identifiers and values stored at the hyperedges.
Additionally, a value can be stored with the vertex using the `vertex_val` parameter.
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"""
function add_vertex!(h::Hypergraph{T};hyperedges::Dict{Int,T} = Dict{Int,T}()) where T <: Real
function add_vertex!(h::Hypergraph{T, V, E}; hyperedges::Dict{Int,T} = Dict{Int,T}(), vertex_val::Union{UndefInitializer, V} = undef) where {T <: Real, V, E}
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@boundscheck (checkbounds(h,1,k) for k in keys(hyperedges))
push!(h.v2he,hyperedges)
ix = length(h.v2he)
for k in keys(hyperedges)
h[ix,k]=hyperedges[k]
end
if vertex_val == undef
resize!(h.vs, length(h.vs)+1)
else
push!(h.vs, vertex_val)
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end
ix
end

"""
add_hyperedge!(h::Hypergraph{T};vertices::Dict{Int,T} = Dict{Int,T}()) where T <: Real
add_hyperedge!(h::Hypergraph{T, V, E}; vertices::Dict{Int,T} = Dict{Int,T}(), hyperedge_val::Union{UndefInitializer, E}=undef) where {T <: Real, V, E}
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Adds a hyperedge to a given hypergraph `h`. Optionally, existing vertices can be added
to the created hyperedge. The paramater `vertices` represents a dictionary
of vertex identifiers and values stored at the hyperedges
of vertex identifiers and values stored at the hyperedges.
Additionally, a value can be stored with the hyperedge using the `hyperedge_val` parameter.

"""
function add_hyperedge!(h::Hypergraph{T};vertices::Dict{Int,T} = Dict{Int,T}()) where T <: Real
function add_hyperedge!(h::Hypergraph{T, V, E}; vertices::Dict{Int,T} = Dict{Int,T}(), hyperedge_val::Union{UndefInitializer, E}=undef) where {T <: Real, V, E}
@boundscheck (checkbounds(h,k,1) for k in keys(vertices))
push!(h.he2v,vertices)
ix = length(h.he2v)
for k in keys(vertices)
h[k,ix]=vertices[k]
end
if hyperedge_val == undef
resize!(h.hes, length(h.hes)+1)
else
push!(h.hes, hyperedge_val)
end
ix
end

"""
set_vertex_value!(h::Hypergraph{T, V, E}, new_value::V, id::Int) where {T <: Real, V, E}

Sets a new value `new_value` for the vertex `id` in the hypegraph `h`.

"""
function set_vertex_value!(h::Hypergraph{T, V, E}, new_value::V, id::Int) where {T <: Real, V, E}
@boundscheck checkbounds(h.vs, id)
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h.vs[id] = new_value
h.vs
end

"""
get_vertex_value(h::Hypergraph{T, V, E}, id::Int) where {T <: Real, V, E}

Returns a value stored at the vertex `id` in the hypergraph `h`.

"""
function get_vertex_value(h::Hypergraph{T, V, E}, id::Int) where {T <: Real, V, E}
@boundscheck checkbounds(h.vs, id)
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h.vs[id]
end

"""
set_hyperedge_value!(h::Hypergraph{T, V, E}, new_value::E, id::Int) where {T <: Real, V, E}

Sets a new value `new_value` for the hyperedge `id` in the hypegraph `h`.

"""
function set_hyperedge_value!(h::Hypergraph{T, V, E}, new_value::E, id::Int) where {T <: Real, V, E}
@boundscheck checkbounds(h.hes, id)
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h.hes[id] = new_value
h.hes
end

"""
get_hyperedge_value(h::Hypergraph{T, V, E}, id::Int) where {T <: Real, V, E}

Returns a value stored at the hyperedge `id` in the hypergraph `h`.

"""
function get_hyperedge_value(h::Hypergraph{T, V, E}, id::Int) where {T <: Real, V, E}
@boundscheck checkbounds(h.hes, id)
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h.hes[id]
end


# TODO needs remove_vertex!(h::Hypergraph{T}, v_id::Int)

# TODO needs add_hyperedge!(h::Hypergraph{T}, he_id::Int)
Expand Down
136 changes: 82 additions & 54 deletions test/runtests.jl
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@@ -1,19 +1,6 @@
using Test, SimpleHypergraphs
import LightGraphs

h = hg_load("data/test1.hgf", Int)
@test size(h) == (4, 4)
m = Matrix(h)
@test m == h
@test h == [1 nothing 4 nothing
2 3 nothing nothing
nothing nothing 5 nothing
nothing nothing 6 nothing]
mktemp("data") do path, _
println(path)
hg_save(path, h)
@test read(path, String) == replace(read("data/test1.hgf", String), "\r\n" => "\n")
end

h1 = Hypergraph{Float64}(5,4)
h1[1:3,1] .= 1.5
Expand All @@ -23,63 +10,104 @@ h1[4,3:4] .= 4.5
h1[5,4] = 5.5
h1[5,2] = 6.5

h2 = Hypergraph{Float64}(0,0)
for i in 1:4 add_vertex!(h2) end
add_hyperedge!(h2;vertices=Dict(1:3 .=> 1.5))
add_hyperedge!(h2)
add_vertex!(h2;hyperedges=Dict(2=>6.5))
add_hyperedge!(h2;vertices=Dict(2 => 3.5, 4 => 4.5))
add_hyperedge!(h2;vertices=Dict(3:5 .=> (2.5,4.5,5.5)))
@test h1 == h2

@testset "SimpleHypergraphs Hypergraph " begin

h = hg_load("data/test1.hgf", Int)
@test size(h) == (4, 4)
m = Matrix(h)
@test m == h
@test h == [1 nothing 4 nothing
2 3 nothing nothing
nothing nothing 5 nothing
nothing nothing 6 nothing]
mktemp("data") do path, _
println(path)
hg_save(path, h)
@test read(path, String) == replace(read("data/test1.hgf", String), "\r\n" => "\n")
end

b = BipartiteView(h1)
h2 = Hypergraph{Float64}(0,0)
for i in 1:4 add_vertex!(h2) end
add_hyperedge!(h2;vertices=Dict(1:3 .=> 1.5))
add_hyperedge!(h2)
add_vertex!(h2;hyperedges=Dict(2=>6.5))
add_hyperedge!(h2;vertices=Dict(2 => 3.5, 4 => 4.5))
add_hyperedge!(h2;vertices=Dict(3:5 .=> (2.5,4.5,5.5)))
@test h1 == h2
m = Matrix(h1)
@test m == Matrix(h2)
@test h1 == Hypergraph(m)
@test h1 == Hypergraph{Nothing}(m)
@test h1 == Hypergraph{Nothing, Nothing}(m)
@test getindex(h1,3,1) == 1.5

@test sum(LightGraphs.adjacency_matrix(LightGraphs.SimpleGraph(b))) == 18
h3 = Hypergraph{Float64,String,Nothing}(1,1)
@test add_vertex!(h3,vertex_val="test") == 2
@test set_vertex_value!(h3,"t",1) == ["t","test"]
@test get_vertex_value(h3,2) == "test"
@test get_hyperedge_value(h3,1) == nothing
@test_throws BoundsError get_hyperedge_value(h3,2)

@test sort(collect(LightGraphs.outneighbors(b,5))) == [7,9]
@test sort(collect(LightGraphs.outneighbors(b,1))) == [6]
@test sort(collect(LightGraphs.inneighbors(b,9))) == [3,4,5]
h4 = Hypergraph{Float64,Nothing,String}(1,1)
@test add_hyperedge!(h4,hyperedge_val="test") == 2
@test set_hyperedge_value!(h4,"t",1) == ["t","test"]
@test get_hyperedge_value(h4,2) == "test"
@test get_vertex_value(h4,1) == nothing
@test_throws BoundsError get_vertex_value(h4,2)
end;

@test Set(LightGraphs.vertices(b)) == Set(1:LightGraphs.nv(b))
@testset "SimpleHypergraphs BipartiteView " begin
b = BipartiteView(h1)

@test shortest_path(b,1,5) == [1,3,5]
@test LightGraphs.is_weakly_connected(b) == true
@test sum(LightGraphs.adjacency_matrix(LightGraphs.SimpleGraph(b))) == 18

@test SimpleHypergraphs.add_vertex!(h1) == 6
@test add_hyperedge!(h1) == 5
h1[5,5] = 1
h1[6,5] = 1
@test sort(collect(LightGraphs.outneighbors(b,5))) == [7,9]
@test sort(collect(LightGraphs.outneighbors(b,1))) == [6]
@test sort(collect(LightGraphs.inneighbors(b,9))) == [3,4,5]

@test shortest_path(b,1,6) == [1,3,5,6]
@test Set(LightGraphs.vertices(b)) == Set(1:LightGraphs.nv(b))

@test shortest_path(b,1,5) == [1,3,5]
@test LightGraphs.is_weakly_connected(b) == true

#TwoSectionView test
t = TwoSectionView(h1)
@test SimpleHypergraphs.add_vertex!(h1) == 6
@test add_hyperedge!(h1) == 5
h1[5,5] = 1
h1[6,5] = 1

@test LightGraphs.nv(t) == 6
@test LightGraphs.ne(t) == 8
@test shortest_path(b,1,6) == [1,3,5,6]

@test sort(LightGraphs.all_neighbors(t, 1)) == [2,3]
@test sort(LightGraphs.outneighbors(t, 5)) == [3,4,6]
@test sort(LightGraphs.inneighbors(t, 4)) == [2,3,5]
@inferred LightGraphs.all_neighbors(t, 1)
end;

@test LightGraphs.has_edge(t, 1, 2) == true
@test LightGraphs.has_edge(t, 1, 5) == false
@testset "SimpleHypergraphs TwoSectionView" begin

@test sum(LightGraphs.adjacency_matrix(LightGraphs.SimpleGraph(t))) == 16
@test shortest_path(t,1,5) == [1,3,5]
@test LightGraphs.is_weakly_connected(t) == true
t = TwoSectionView(h1)

@test SimpleHypergraphs.add_vertex!(h1) == 7
h1[7,5] = 1
@test LightGraphs.nv(t) == 6
@test LightGraphs.ne(t) == 8

@test shortest_path(t,1,6) == [1,3,5,6]
@test sort(LightGraphs.all_neighbors(t, 1)) == [2,3]
@test sort(LightGraphs.outneighbors(t, 5)) == [3,4,6]
@test sort(LightGraphs.inneighbors(t, 4)) == [2,3,5]
@inferred LightGraphs.all_neighbors(t, 1)

@test LightGraphs.nv(t) == 7
@test LightGraphs.ne(t) == 10
@test sort(LightGraphs.outneighbors(t, 5)) == [3,4,6,7]
@test LightGraphs.has_edge(t, 1, 2) == true
@test LightGraphs.has_edge(t, 1, 5) == false

@test sum(LightGraphs.adjacency_matrix(LightGraphs.SimpleGraph(t))) == 20
@test sum(LightGraphs.adjacency_matrix(LightGraphs.SimpleGraph(t))) == 16
@test shortest_path(t,1,5) == [1,3,5]
@test LightGraphs.is_weakly_connected(t) == true

@test SimpleHypergraphs.add_vertex!(h1) == 7
h1[7,5] = 1

@test shortest_path(t,1,6) == [1,3,5,6]

@test LightGraphs.nv(t) == 7
@test LightGraphs.ne(t) == 10
@test sort(LightGraphs.outneighbors(t, 5)) == [3,4,6,7]

@test sum(LightGraphs.adjacency_matrix(LightGraphs.SimpleGraph(t))) == 20

end;