Merge pull request #187 from Circuitscape/RA/out

Fix 181 once and for all

src/out.jl

@@ -89,7 +89,7 @@ function write_cur_maps(name, output, component_data, finitegrounds, flags, cfg)
 end
 
 function write_currents(node_curr_arr, branch_curr_arr, name, cfg)
-   pref = split(cfg["output_file"], '.')[1]
+   pref = split(cfg["output_file"], ".out")[1]
    writedlm("$(pref)_node_currents$(name).txt", node_curr_arr, '\t')
    writedlm("$(pref)_branch_currents$(name).txt", branch_curr_arr, '\t')
 end
@@ -347,7 +347,7 @@ function write_aagrid(cmap, name, cfg, hbmeta, cellmap;
                         voltage = false, cum = false, max = false,
                         log_transform = false, set_null_to_nodata = false)
 
-    pref = split(cfg["output_file"], '.')[1]
+    pref = split(cfg["output_file"], ".out")[1]
 
     if log_transform
         map!(x -> x > 0 ? log10(x) : float(hbmeta.nodata), cmap, cmap)
@@ -414,7 +414,7 @@ function write_voltages(output, name, voltages::Vector{T}, cc) where {T}
     volt_arr[:,1] = cc
     volt_arr[:,2] = voltages
 
-    pref = split(output, '.')[1]
+    pref = split(output, ".out")[1]
     writedlm("$(pref)_voltages$(name).txt", volt_arr)
 
 end
@@ -453,7 +453,7 @@ function accum_currents!(base, newcurr, cfg, G, voltages, finitegrounds, nodemap
 end
 
 function save_resistances(r, cfg)
-    pref = split(cfg["output_file"], '.')[1]
+    pref = split(cfg["output_file"], ".out")[1]
     filename = "$(pref)_resistances.out"
     filename_3col = "$(pref)_resistances_3columns.out"
     rcol = compute_3col(r)

src/utils.jl

@@ -134,7 +134,7 @@ function accumulate_current_maps(path, f)
     base = basename(path)
 
     # If base file has a dot
-    name = split(base, '.')[1]
+    name = split(base, ".out")[1]
 
     cmap_list = readdir(dir) |>
                     x -> filter(y -> startswith(y, "$(name)_"), x) |>
@@ -332,7 +332,7 @@ function runtests(f = compute)
     end
     end
 
-    @testset "Raster ALl to One" begin
+    @testset "Raster All to One" begin
     # Raster all to one test
     for i in 1:12
         @info("Testing allToOneVerify$i")

test/input/raster/extra.one/1/cellmap.asc

@@ -0,0 +1,16 @@
+ncols         10									
+nrows         10									
+xllcorner     1									
+yllcorner     1									
+cellsize      1									
+NODATA_value  -9999									
+1	2	3	4	5	6	7	8	9	10
+2	-9999	-9999	1	1	2	1	1	1	1
+3	2	1	1	-9999	2	1	1	1	1
+4	2	1	1	1	2	-9999	-9999	1	2
+5	2	1	1	1	2	-9999	-9999	1	3
+-9999	-9999	-9999	-9999	7	2	-9999	-9999	1	4
+7	-9999	2	-9999	1	2	-9999	-9999	1	5
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999
+9	-9999	2	-9999	1	2	-9999	-9999	1	7
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999

test/input/raster/extra.one/1/oneToAllVerify1.ini

@@ -0,0 +1,59 @@
+[Options for advanced mode]
+ground_file_is_resistances = False
+source_file = (Browse for a current source file)
+remove_src_or_gnd = keepall
+ground_file = (Browse for a ground point file)
+use_unit_currents = False
+use_direct_grounds = False
+
+[Calculation options]
+low_memory_mode = False
+solver = cg+amg
+print_timings = False
+
+[Options for pairwise and one-to-all and all-to-one modes]
+included_pairs_file = None
+use_included_pairs = False
+point_file = input/raster/one_to_all/1/points.asc
+
+[Output options]
+write_cum_cur_map_only = False
+log_transform_maps = False
+output_file = output/oneToAllVerify1.out
+write_max_cur_maps = False
+write_volt_maps = True
+set_null_currents_to_nodata = False
+set_null_voltages_to_nodata = False
+compress_grids = False
+write_cur_maps = True
+
+[Short circuit regions (aka polygons)]
+use_polygons = True
+polygon_file = input/raster/one_to_all/1/polygons.asc
+
+[Connection scheme for raster habitat data]
+connect_four_neighbors_only = True
+connect_using_avg_resistances = True
+
+[Habitat raster or graph]
+habitat_file = input/raster/one_to_all/1/cellmap.asc
+habitat_map_is_resistances = True
+
+[Options for one-to-all and all-to-one modes]
+use_variable_source_strengths = False
+variable_source_file = None
+
+[Version]
+version = unknown
+
+[Mask file]
+use_mask = False
+mask_file = None
+
+[Circuitscape mode]
+data_type = raster
+scenario = one-to-all
+
+parallelize = True
+max_parallel = 2
+

test/input/raster/extra.one/1/points.asc

@@ -0,0 +1,16 @@
+ncols         10									
+nrows         10									
+xllcorner     1									
+yllcorner     1									
+cellsize      1									
+NODATA_value  -9999									
+1	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	2
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	4
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	9	-9999
+-9999	-9999	-9999	-9999	-9999	8	-9999	-9	-9999	5
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	6
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999
+51	-9999	11	-9999	-9999	-9999	-9999	3	-9999	-9999

test/input/raster/extra.one/1/polygons.asc

@@ -0,0 +1,16 @@
+ncols         10									
+nrows         10									
+xllcorner     1									
+yllcorner     1									
+cellsize      1									
+NODATA_value  -9999									
+-9999	-9999	-9999	6	6	6	-9999	-9999	-9999	-9999
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	1
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	1
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	1
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	1
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999
+-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999	-9999

test/internal.jl

@@ -159,11 +159,15 @@ SIZE_3 =
 
  @test model_problem(3) == SIZE_3
 
- # Issue 151
- # Issue 151
- try
-     Circuitscape.read_point_map(Int32, "samples.txt",
-                                 Circuitscape.RasterMeta(50, 50, 0.0, 0.0, 0.5, -9999.0, 2))
- catch e
-     @test e == "At least one focal node location falls outside of habitat map"
- end
+# Issue 151
+# Issue 151
+try
+    Circuitscape.read_point_map(Int32, "samples.txt",
+                                Circuitscape.RasterMeta(50, 50, 0.0, 0.0, 0.5, -9999.0, 2))
+catch e
+    @test e == "At least one focal node location falls outside of habitat map"
+end
+
+# Users with dots in their names - issue #181
+# Just check that this does not break
+compute("input/raster/extra.one/1/oneToAllVerify1.ini")