Merge pull request #376 from Circuitscape/RA/network_adv

network: check if nodes start from zero

src/io.jl

@@ -8,7 +8,7 @@ end
 function IncludeExcludePairs(V)
     IncludeExcludePairs(:undef, V[], Matrix{V}(undef,0,0))
 end
-Base.isempty(x::IncludeExcludePairs) = isempty(x.include_pairs)
+Base.isempty(t::IncludeExcludePairs) = t.mode == :undef
 
 struct NetworkData{T,V} <: Data
     coords::Tuple{Vector{V},Vector{V},Vector{T}}
@@ -66,17 +66,24 @@ function load_graph(V, gpath::String, ::Type{T}) where {T}
 			j[iter] = g[iter,2] + 1
 		end
 	end
-    i,j,v
+    i,j,v, min_node==0
 end
 
-read_focal_points(V, path::String) = V.(vec(readdlm(path)) .+ 1)
+function read_focal_points(V, path::String) 
+	ret = try 
+			vec(readdlm(path, V)) 
+		catch
+			vec(V.(readdlm(path)))
+		end
+	minimum(ret) == 0 && (ret .+= 1)
+	ret
+end
 
-function read_point_strengths(T, path::String, inc = true)
-    a = readdlm(path, T)
-    if inc
-        @. a[:,1] = a[:,1] + 1
-    end
-    a
+function read_point_strengths(T, path::String, starts_from_zero) 
+	str = readdlm(path, T)
+	starts_from_zero = minimum(str[:,1]) == 0 || starts_from_zero 
+	starts_from_zero && (str[:,1] .+= 1)
+	str
 end
 
 function read_cellmap(habitat_file::String, is_res::Bool, ::Type{T}) where {T}
@@ -370,7 +377,8 @@ function get_network_data(T, V, cfg)::NetworkData{T,V}
 
     is_pairwise = cfg["scenario"] in PAIRWISE
 
-    i,j,v = load_graph(V, hab_file, T)
+    i,j,v,starts_from_zero = load_graph(V, hab_file, T)
+
     if hab_is_res
         v = 1 ./ v
     end
@@ -382,14 +390,14 @@ function get_network_data(T, V, cfg)::NetworkData{T,V}
     end
 
     if !is_pairwise
-        source_map = read_point_strengths(T, source_file)
-        ground_map = read_point_strengths(T, ground_file)
+		source_list = read_point_strengths(T, source_file, starts_from_zero)
+		ground_list = read_point_strengths(T, ground_file, starts_from_zero)
     else
-        source_map = Matrix{T}(undef,0,0)
-        ground_map = Matrix{T}(undef,0,0)
+        source_list = Matrix{T}(undef,0,0)
+        ground_list = Matrix{T}(undef,0,0)
     end
 
-    NetworkData((i,j,v), fp, source_map, ground_map)
+    NetworkData((i,j,v), fp, source_list, ground_list)
 end
 
 function load_raster_data(T, V, cfg)::RasterData{T,V}
@@ -469,7 +477,7 @@ function load_raster_data(T, V, cfg)::RasterData{T,V}
 
     # Variable source strengths
     if use_var_source
-        strengths = read_point_strengths(T, var_source_file)
+        strengths = read_point_strengths(T, var_source_file, false)
     else
         strengths = Matrix{T}(undef, 0,0)
     end

src/network/advanced.jl

@@ -31,6 +31,8 @@ function compute_advanced_data(data::NetworkData{T,V},
     A = A + A'
 
     cc = connected_components(SimpleWeightedGraph(A))
+	c = size(A,1)
+	csinfo("Graph has $c nodes and $(length(cc)) connected components", cfg["suppress_messages"] in TRUELIST)
 
     t = @elapsed G = laplacian(A)
     csinfo("Time taken to construct graph laplacian = $t", cfg["suppress_messages"] in TRUELIST)

src/network/pairwise.jl

@@ -47,6 +47,8 @@ function compute_graph_data(data::NetworkData{T,V}, cfg)::GraphProblem{T,V} wher
     A = A + A'
 
     cc = connected_components(SimpleWeightedGraph(A))
+	c = size(A,1)
+	csinfo("Graph has $c nodes and $(length(cc)) connected components", cfg["suppress_messages"] in TRUELIST)
 
     t = @elapsed G = laplacian(A)
     csinfo("Time taken to construct graph laplacian = $t", cfg["suppress_messages"] in TRUELIST)

src/raster/onetoall.jl

@@ -33,7 +33,6 @@ function onetoall_kernel(data::RasterData{T,V}, flags, cfg)::Matrix{T} where {T,
         points_unique = included_pairs.point_ids
         prune_points!(points_rc, included_pairs.point_ids)
         if use_variable_strengths
-            strengths[:,1] .-= 1
             strengths = prune_strengths(strengths, included_pairs.point_ids)
         end
     end

src/raster/pairwise.jl

@@ -235,7 +235,6 @@ function compute_graph_data_no_polygons(data::RasterData{T,V},
                 hbmeta, cellmap, cum, solver)
 
 end
-Base.isempty(t::IncludeExcludePairs) = t.mode == :undef
 
 function generate_exclude_pairs(points_rc, included_pairs::IncludeExcludePairs{V}) where V
 

src/utils.jl

@@ -328,7 +328,7 @@ function runtests(f = compute)
 
         @testset "Raster One to All" begin
             # Raster one to all test
-            for i in 1:13
+			for i in 1:13
                 @info("Testing oneToAllVerify$i")
                 r = f("input/raster/one_to_all/$i/oneToAllVerify$(i).ini")
                 x = readdlm("output_verify/oneToAllVerify$(i)_resistances.out")