Merge pull request #374 from Circuitscape/RA/polyinclude

add include pairs logic when polygons in point files

src/io.jl

@@ -8,6 +8,7 @@ end
 function IncludeExcludePairs(V)
     IncludeExcludePairs(:undef, V[], Matrix{V}(undef,0,0))
 end
+Base.isempty(x::IncludeExcludePairs) = isempty(x.include_pairs)
 
 struct NetworkData{T,V} <: Data
     coords::Tuple{Vector{V},Vector{V},Vector{T}}

src/raster/pairwise.jl

@@ -81,13 +81,17 @@ function _pt_file_polygons_path(rasterdata::RasterData{T,V},
         # construct new graph
         # solve for two points
     # end
+
 
     # Data
     gmap = rasterdata.cellmap
     polymap = rasterdata.polymap
     points_rc = rasterdata.points_rc
     avg_res = flags.avg_res
     four_neighbors = flags.four_neighbors
+	included_pairs = rasterdata.included_pairs
+	exclude_pairs = isempty(included_pairs) ? Vector{Tuple{V,V}}() : 
+						generate_exclude_pairs(points_rc, included_pairs)
 
     # Cumulative maps
     cum = initialize_cum_maps(gmap, flags.outputflags.write_max_cur_maps)
@@ -105,6 +109,9 @@ function _pt_file_polygons_path(rasterdata::RasterData{T,V},
             pt2 = pts[j]
             csinfo("Solving pair $k of $n", cfg["suppress_messages"] in TRUELIST)
             k += 1
+			if (pt1,pt2) in exclude_pairs || (pt2, pt1) in exclude_pairs 
+				continue
+			end
             graphdata = compute_graph_data_polygons(rasterdata, flags, pt1, pt2, cum, cfg)
             pairwise_resistance = single_ground_all_pairs(graphdata, flags, cfg, false)
             resistances[i,j] = resistances[j,i] = pairwise_resistance[2,3]