Merge pull request #4 from Circuitscape/vl/dev

LightGraphs interface fixes, add more tests

Author: vlandau

src/graph_interface.jl

@@ -5,10 +5,9 @@ import LightGraphs:
     inneighbors, outneighbors, is_directed, add_edge!
 
 import SimpleWeightedGraphs:
-    add_edge!, get_weight
+    add_edge!, get_weight, add_vertex!, vertices
 
-import Base:
-    eltype, zero
+import Base: zero
 
 ### LightGraphs interface
 nv(g::AbstractSpatialGraph) = nv(g.graph)
@@ -22,8 +21,31 @@ has_vertex(g::AbstractSpatialGraph, v) = has_vertex(g.graph, v)
 inneighbors(g::AbstractSpatialGraph, v) = inneighbors(g.graph, v)
 outneighbors(g::AbstractSpatialGraph, v) = outneighbors(g.graph, v)
 is_directed(g::AbstractSpatialGraph) = is_directed(g.graph)
-zero(g::AbstractSpatialGraph) = zero(g.graph)
+function Base.zero(g::AbstractRasterGraph)
+    if g.graph isa SimpleGraph
+        SimpleRasterGraph(
+            zero(typeof(g.graph)),
+            g.vertex_raster
+        )
+    elseif g.graph isa SimpleDiGraph
+        SimpleRasterDiGraph(
+            zero(typeof(g.graph)),
+            g.vertex_raster
+        )
+    elseif g.graph isa SimpleWeightedGraph
+        WeightedRasterGraph(
+            SimpleWeightedGraph{eltype(g.graph), weighttype(g.graph)}(),
+            g.vertex_raster
+        )
+    elseif g.graph isa SimpleWeightedDiGraph
+        WeightedRasterDiGraph(
+            SimpleWeightedDiGraph{eltype(g.graph), weighttype(g.graph)}(),
+            g.vertex_raster
+        )
+    end
+end
 add_edge!(g::AbstractSpatialGraph, a::Integer, b::Integer, c::Number) = add_edge!(g.graph, a, b, c)
+add_vertex!(g::AbstractSpatialGraph) = add_vertex!(g.graph)
 
 ### SimpleWeightedGraphs
 get_weight(g::WeightedRasterGraph, a::Integer, b::Integer) = get_weight(g.graph, a, b)

src/rastergraphs.jl

@@ -396,7 +396,16 @@ function make_raster_graph(
 
     sources = Vector{Int64}()
     destinations = Vector{Int64}()
-    weighted && (node_weights = Vector{Float64}())
+
+    weighted && (weight_type = eltype(raster))
+
+    if weighted && (weight_type <: Integer)
+        @info ("weight_raster eltype is $(weight_type). " *
+               "Promoting to Float64.")
+        weight_type = Float64
+    end
+
+    weighted && (node_weights = Vector{weight_type}())
 
     # Add the edges
     # Only need to do neighbors down or to the right for undirected graphs

test/lg_interface.jl

@@ -0,0 +1,34 @@
+using SpatialGraphs, Test, GeoData, LightGraphs, SimpleWeightedGraphs
+## This script tests methods for the LightGraph interface that aren't already 
+## used in other tests
+
+A_array = Array{Float32}(undef, (3, 4, 1))
+A_array[:,:,:] = [1, 3, 2, 0.5, 10, 8, 5, -9999, 3, 1, 2, 6]
+x = X(1:4)
+y = Y(1:3)
+band = Band(1:1)
+
+weight_raster = GeoArray(A_array, (y, x, band), missingval = -9999)
+rasgraph = weightedrastergraph(weight_raster)
+
+@test nv(rasgraph) == maximum(rasgraph.vertex_raster)
+num_edge = ne(rasgraph)
+@test vertices(rasgraph) == 1:maximum(rasgraph.vertex_raster)
+@test eltype(rasgraph) == Int # Should always be Int64 (or int32 on 32-bit)
+@test edgetype(rasgraph) == SimpleWeightedEdge{eltype(rasgraph), eltype(A_array)}
+
+for i in 1:maximum(rasgraph.vertex_raster)
+    @test has_vertex(rasgraph, i)
+end
+
+# In undirected graph incoming neighbors should equal outgoing
+@test inneighbors(rasgraph, 1) == outneighbors(rasgraph, 1)
+
+empty = zero(rasgraph)
+
+add_vertices!(empty, maximum(rasgraph.vertex_raster))
+add_edge!(empty, 1, 4, Float32(0.5))
+
+@test nv(empty) == maximum(rasgraph.vertex_raster)
+@test has_edge(empty, 1, 4)
+@test get_weight(empty, 1, 4) == Float32(0.5)

test/runtests.jl

@@ -1,4 +1,8 @@
-using Test, SpatialGraphs
+using GeoData, LightGraphs, SimpleWeightedGraphs, SpatialGraphs, Test
+
+@testset "Simple Raster Graph Construction" begin
+    include("simplerastergraphs.jl")
+end
 
 @testset "Weighted Raster Graph Construction" begin
     include("weightedrastergraphs.jl")
@@ -10,4 +14,21 @@ end
 
 @testset "Weighted Raster DiGraph Construction" begin
     include("weightedrasterdigraphs.jl")
-end
+end
+
+@testset "LightGraphs Interface" begin
+    include("lg_interface.jl")
+end
+
+printstyled("Checking that Base.show works...\n", bold = true)
+
+A_array = Array{Float64}(undef, (3, 4, 1))
+A_array[:,:,:] = [1, 3, 2, 0.5, 10, 8, 5, -9999, 3, 1, 2, 6]
+x = X(1:4)
+y = Y(1:3)
+band = Band(1:1)
+
+weight_raster = GeoArray(A_array, (y, x, band), missingval = -9999)
+rasgraph = weightedrastergraph(weight_raster)
+show(rasgraph);print("\n")
+

test/simplerasterdigraphs.jl

@@ -1,7 +1,7 @@
 using GeoData, LightGraphs, SimpleWeightedGraphs, SpatialGraphs, Test
 
 condition_array = Array{Float64}(undef, (3, 4, 1))
-condition_array[:,:,:] = [1, 3, 5, 2, 4, 8, 5, -9999, 2, 3, 6, 7]
+condition_array[:,:,:] = [1, 0.5, 5, 2, 4, 8, 5, -9999, 2, 3, 6, 7]
 
 x = X(1:4)
 y = Y(1:3)
@@ -52,3 +52,6 @@ for i in 1:length(graph_edges)
     col_diff = abs(source_coords[2] - dest_coords[2])
     @test col_diff <= 1
 end
+
+@test is_directed(rasgraph)
+@test zero(rasgraph).vertex_raster == rasgraph.vertex_raster

test/simplerastergraphs.jl

@@ -0,0 +1,57 @@
+using GeoData, LightGraphs, SimpleWeightedGraphs, SpatialGraphs, Test
+
+array = Array{Int}(undef, (3, 4, 1))
+array[:,:,:] = [1, 1, 1, 1, 2, 2, 2, -9999, 2, 3, 3, 3]
+
+x = X(1:4)
+y = Y(1:3)
+band = Band(1:1)
+
+raster = GeoArray(array, (y, x, band), missingval = -9999)
+
+compare = ==
+rasgraph = simplerastergraph(
+    raster,
+    directed = false,
+    condition = compare
+)
+
+# no vertices in NoData pixels?
+@test (rasgraph.vertex_raster .== 0) == 
+        ((raster .== raster.missingval) .| 
+         isnan.(raster))
+
+# Is the number of of vertices correct, and is the range of values correct?
+@test sort(collect(rasgraph.vertex_raster[rasgraph.vertex_raster .!= 0])) == 
+        collect(1:sum(
+            (raster .!= raster.missingval) .& 
+                (!).(isnan.(raster))
+        ))
+
+graph_edges = collect(edges(rasgraph))
+
+# Test that the edges are correct and have proper weights
+for i in 1:length(graph_edges)
+    source_i = src(graph_edges[i])
+    dest_i = dst(graph_edges[i])
+
+    source_coords = findall(rasgraph.vertex_raster .== source_i)[1]
+    dest_coords = findall(rasgraph.vertex_raster .== dest_i)[1]
+
+    # Check that condition is met
+    @test compare(
+        raster[source_coords],
+        raster[dest_coords]
+    )
+
+    # Test that source row is within 1 step of dest row
+    row_diff = abs(source_coords[1] - dest_coords[1])
+    @test row_diff <= 1
+
+    # Test that source column is within 1 step of dest row
+    col_diff = abs(source_coords[2] - dest_coords[2])
+    @test col_diff <= 1
+end
+
+@test is_directed(rasgraph) == false
+@test zero(rasgraph).vertex_raster == rasgraph.vertex_raster

test/weightedrasterdigraphs.jl

@@ -3,7 +3,7 @@ A_array = Array{Float64}(undef, (3, 4, 1))
 A_array[:,:,:] = [1, 3, 2, 0.5, 10, 8, 5, -9999, 3, 1, 2, 6]
 
 condition_array = Array{Float64}(undef, (3, 4, 1))
-condition_array[:,:,:] = [1, 3, 5, 2, 4, 8, 5, -9999, 2, 3, 6, 7]
+condition_array[:,:,:] = [1, 0.5, 5, 2, 4, 8, 5, -9999, 2, 3, 6, 7]
 
 x = X(1:4)
 y = Y(1:3)
@@ -68,3 +68,6 @@ for i in 1:length(graph_edges)
                                            weight_raster[dest_coords])
     end
 end
+
+@test is_directed(rasgraph)
+@test zero(rasgraph).vertex_raster == rasgraph.vertex_raster

test/weightedrastergraphs.jl

@@ -8,8 +8,11 @@ band = Band(1:1)
 
 weight_raster = GeoArray(A_array, (y, x, band), missingval = -9999)
 weight_raster2d = GeoArray(A_array[:, :, 1], (y, x), missingval = -9999)
-rasgraph2d = weightedrastergraph(weight_raster2d)
-rasgraph = weightedrastergraph(weight_raster)
+rasgraph2d = weightedrastergraph(
+    weight_raster2d,
+    connect_using_avg_weights = false
+)
+rasgraph = weightedrastergraph(weight_raster, connect_using_avg_weights = false)
 
 # Test that graphs are the same regardless of whether weight_raster has Band dim
 @test rasgraph2d.graph == rasgraph.graph
@@ -48,11 +51,44 @@ for i in 1:length(graph_edges)
     # Test that the weight is what it should be (assumes connect_using_avg_weights = true in graph construction)
     if (row_diff == 1 && col_diff == 1) # get diagonal average
         @test weight_i == 
-            SpatialGraphs.res_diagonal_avg(weight_raster[source_coords], 
+            SpatialGraphs.cond_diagonal_avg(weight_raster[source_coords], 
                                            weight_raster[dest_coords])
     else
         @test weight_i == 
-            SpatialGraphs.res_cardinal_avg(weight_raster[source_coords],
+            SpatialGraphs.cond_cardinal_avg(weight_raster[source_coords],
                                            weight_raster[dest_coords])
     end
 end
+
+# check that no edges exist that shouldn't
+vertex_raster = rasgraph.vertex_raster
+for src_row in 1:size(vertex_raster)[1]
+    for src_col in 1:size(vertex_raster)[2]
+        for dst_row in 1:size(vertex_raster)[1]
+            for dst_col in 1:size(vertex_raster)[2]
+                if ((vertex_raster[src_row, src_col] == 0) | 
+                        (vertex_raster[dst_row, dst_col] == 0))
+                    continue
+                elseif ((abs(src_row - dst_row) <= 1) &
+                        (abs(src_col - dst_col) <= 1)) & (
+                            (abs(src_row - dst_row) > 0) |
+                            (abs(src_col - dst_col) > 0))
+                    @test has_edge(
+                        rasgraph, 
+                        vertex_raster[src_row, src_col],
+                        vertex_raster[dst_row, dst_col]
+                    ) == true
+                else
+                    @test (has_edge(
+                        rasgraph, 
+                        vertex_raster[src_row, src_col],
+                        vertex_raster[dst_row, dst_col]
+                    ) == false)
+                end
+            end
+        end
+    end
+end
+
+@test is_directed(rasgraph) == false
+@test zero(rasgraph).vertex_raster == rasgraph.vertex_raster