Errors about boundary_polygons

[JuanruMaryGuo]

Hi, I'm using the Julia-1.7.0 on ubuntu and successfully ran the Baysor for the first few steps.

However, when I want to analyze the boundary using the following codes:

grid_step = 1.0
@time polygons = B.boundary_polygons(df_spatial, df_spatial.cell, grid_step=grid_step);
length(polygons)

I got:

MethodError: no method matching kruskal_mst(::SimpleWeightedGraph{Int64, Float64}) Closest candidates are: kruskal_mst(::AG) where {U, AG<:LightGraphs.AbstractGraph{U}} at ~/.julia/packages/SimpleTraits/l1ZsK/src/SimpleTraits.jl:338 kruskal_mst(::AG, ::AbstractMatrix{T}; kwargs...) where {T<:Real, U, AG<:LightGraphs.AbstractGraph{U}} at ~/.julia/packages/SimpleTraits/l1ZsK/src/SimpleTraits.jl:338 kruskal_mst(::Type{SimpleTraits.Not{LightGraphs.IsDirected{AG}}}, ::AG, ::AbstractMatrix{T}; minimize) where {T<:Real, U, AG<:LightGraphs.AbstractGraph{U}} at ~/.julia/packages/LightGraphs/IgJif/src/spanningtrees/kruskal.jl:12

Stacktrace: [1] border_mst(border_points::Vector{Vector{UInt32}}; min_edge_length::Float64, max_edge_length::Float64) @ Baysor ~/.julia/packages/Baysor/Kag1d/src/data_processing/boundary_estimation.jl:65 [2] border_mst(border_points::Vector{Vector{UInt32}}) @ Baysor ~/.julia/packages/Baysor/Kag1d/src/data_processing/boundary_estimation.jl:42 [3] _broadcast_getindex_evalf @ ./broadcast.jl:670 [inlined] [4] _broadcast_getindex @ ./broadcast.jl:643 [inlined] [5] getindex @ ./broadcast.jl:597 [inlined] [6] copy @ ./broadcast.jl:899 [inlined] [7] materialize @ ./broadcast.jl:860 [inlined] [8] extract_polygons_from_label_grid(grid_labels::Matrix{UInt32}; min_border_length::Int64, shape_method::Symbol, max_dev::Float64, exclude_labels::Vector{Int64}, offset::Vector{Float64}, grid_step::Float64) @ Baysor ~/.julia/packages/Baysor/Kag1d/src/data_processing/boundary_estimation.jl:231 [9] boundary_polygons(pos_data::Matrix{Float64}, cell_labels::Vector{Int64}; min_x::Nothing, max_x::Nothing, grid_step::Float64, min_border_length::Int64, shape_method::Symbol, max_dev::Float64, bandwidth::Float64, exclude_labels::Vector{Int64}, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Baysor ~/.julia/packages/Baysor/Kag1d/src/data_processing/boundary_estimation.jl:270 [10] #boundary_polygons#214 @ ~/.julia/packages/Baysor/Kag1d/src/data_processing/boundary_estimation.jl:248 [inlined] [11] top-level scope @ ./timing.jl:220 [inlined] [12] top-level scope @ ./In[89]:0 [13] eval @ ./boot.jl:373 [inlined] [14] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String) @ Base ./loading.jl:1196

Is that because I'm using the wrong versions of dependency packages?

Thank you in advance! :)

[JuanruMaryGuo]

Hi,

I read about the source codes and find out that this is caused by the conflicts among the current versions of Graph, LightGraphs, and SimpleWeightedGraphs.

The following is my codes for two specific functions:

    function find_longest_paths(g_inc::SimpleWeightedGraph{Int64, Float64})::Array{Vector{Int}, 1}
        
        mtx_after_simple = SimpleGraph(g_inc)
        edges = collect(Graphs.edges(mtx_after_simple))
    
        if length(edges) == 0
            return []
        end
    
    
        vert_counts = StatsBase.countmap(vcat(map(x -> [x.src, x.dst], edges)...));
        n_verts = maximum(keys(vert_counts));
        leafs = collect(keys(vert_counts))[collect(values(vert_counts)) .== 1];
    
        conn_comps = SimpleWeightedGraphs.connected_components(g_inc);
        longest_paths = Array{Int, 1}[]
        for vert_inds in conn_comps
            if size(vert_inds, 1) < 3
                continue
            end
    
            comp_leafs = intersect(vert_inds, leafs)
            max_dist, max_source, max_target = -1, -1, -1
            paths = []
            for src_id in comp_leafs
                paths = Graphs.dijkstra_shortest_paths(g_inc, src_id);
                cur_target = comp_leafs[findmax(paths.dists[comp_leafs])[2]];
                if isinf(paths.dists[cur_target])
                    @warn "Infinite distance for verteces $src_id and $cur_target"
                    continue
                end
    
                if paths.dists[cur_target] > max_dist
                    max_dist = paths.dists[cur_target]
                    max_target = cur_target
                    max_source = src_id
                end
            end
    
            if max_source < 0 | max_target < 0
                @warn "Source/target vertex id is 0"
                continue
            end
    
            cur_target = max_target
            path = Int[cur_target]
            paths = Graphs.dijkstra_shortest_paths(g_inc, max_source);
            if isinf(paths.dists[max_target])
                @warn "Infinite distance for verteces $src_id and $cur_target"
                continue
            end
            while cur_target != max_source
                cur_target = paths.parents[cur_target]
                push!(path, cur_target)
                if size(path, 1) > 2 * paths.dists[max_target]
                    @warn "Can't build path"
                    break
                end
            end
            push!(longest_paths, path)
        end
    
        return longest_paths
    end
    
    
    function border_mst(border_points::Array{<:Vector{<:Real},1}; min_edge_length::Float64=0.1, max_edge_length::Float64=1.5)
        leafsize = min(size(border_points, 1), 10) # Some performance feature?
        tree = KDTree(Matrix{Float64}(hcat(border_points...)), leafsize=leafsize);
        src_verts, dst_verts, weights = Int[], Int[], Float64[]
        edges = Set{Tuple{Int, Int}}()
    
        n_neighbs = min(length(border_points), 5)
        for (i, p) in enumerate(border_points)
            inds, dists = knn(tree, p, n_neighbs, true) # 5 to get border for sure
            filt_mask = (dists .> min_edge_length) .& (dists .< max_edge_length)
    
            for (ind, dist) in zip(inds[filt_mask], dists[filt_mask])
                edge = sort([i, ind])
                edge = (edge...,)
                if !(edge in edges)
                    push!(src_verts, edge[1])
                    push!(dst_verts, edge[2])
                    push!(weights, dist)
                    push!(edges, edge)
                end
            end
        end
    
        adj_mtx = sparse(src_verts, dst_verts, weights, size(border_points, 1), size(border_points, 1));
        edges_after = SimpleWeightedGraphs.kruskal_mst(SimpleWeightedGraph(adj_mtx + adj_mtx'));
        mtx_after_a = SimpleWeightedGraph(Int(sqrt(length(adj_mtx))));
        for i in edges_after
            add_edge!(mtx_after_a,i.src,i.dst,i.weight);
        end
        return mtx_after_a;
    end
    

Here are my versions for all the packages: [cc9f9468] Baysor v0.5.1 https://github.com/kharchenkolab/Baysor.git#master [336ed68f] CSV v0.10.1 [13f3f980] CairoMakie v0.7.0 [5ae59095] Colors v0.12.8 [a93c6f00] DataFrames v1.3.1 [1313f7d8] DataFramesMeta v0.10.0 [31c24e10] Distributions v0.25.40 [7a1cc6ca] FFTW v1.4.5 [86223c79] Graphs v1.5.1 [7073ff75] IJulia v1.23.2 [787d08f9] ImageMorphology v0.3.0 [916415d5] Images v0.25.1 [4138dd39] JLD v0.12.5 [033835bb] JLD2 v0.4.17 [682c06a0] JSON v0.21.2 [5ab0869b] KernelDensity v0.6.3 [093fc24a] LightGraphs v1.3.5 [23992714] MAT v0.10.2 [ee78f7c6] Makie v0.16.1 [6f286f6a] MultivariateStats v0.8.0 [b8a86587] NearestNeighbors v0.4.9 [ccf2f8ad] PlotThemes v2.0.1 [91a5bcdd] Plots v1.25.6 [92933f4c] ProgressMeter v1.7.1 [438e738f] PyCall v1.93.0 https://github.com/JuliaPy/PyCall.jl.git#master [d330b81b] PyPlot v2.10.0 [55797a34] SimpleGraphs v0.7.15 [47aef6b3] SimpleWeightedGraphs v1.2.1 [90137ffa] StaticArrays v1.3.2 [2913bbd2] StatsBase v0.33.14 [c4f8c510] UMAP v0.1.9 https://github.com/dillondaudert/UMAP.jl.git#master

and I'm running on Julia 1.7.0 (2021-11-30) for Ubuntu.

Hope this would help

[VPetukhov]

Thanks for the input, @JuanruMaryGuo ! Indeed, LightGraphs.jl were archived and now should be replaced with Graphs.jl. So I did that in the dev (https://github.com/kharchenkolab/Baysor/commit/ada8a77b4cdf0b91b5fefd2cd25ed987b695ed30) and now it seems to work. I also fixed some dependencies, so hopefully there will be fewer problems in the future.