Merge pull request #421 from Circuitscape/RA/source_and_ground

Support flags: use_unit_currents and use_direct_grounds

src/io.jl

@@ -248,10 +248,12 @@ end
 
 
 function read_source_and_ground_maps(T, V, source_file, ground_file, habitatmeta,
-                                        is_res)
+                                        is_res, cfg)
 
     ground_map = Matrix{T}(undef,0,0)
     source_map = Matrix{T}(undef,0,0)
+	use_unit_currents = cfg["use_unit_currents"] in TRUELIST
+	use_direct_grounds = cfg["use_direct_grounds"] in TRUELIST
 
     f = endswith(ground_file, "gz") ? GZip.open(ground_file, "r") : open(ground_file, "r")
     filetype = _guess_file_type(ground_file, f)
@@ -276,9 +278,10 @@ function read_source_and_ground_maps(T, V, source_file, ground_file, habitatmeta
     if filetype == FILE_TYPE_AAGRID || filetype == FILE_TYPE_GEOTIFF
         source_map = read_polymap(T, source_file, habitatmeta)
         source_map = map(T, source_map)
+		source_map[findall(isequal(-9999), source_map)] .= 0
     elseif filetype == FILE_TYPE_TXTLIST
         rc = _txt_list_reader(source_file, T, habitatmeta)
-        source_map = -9999 * ones(T, habitatmeta.nrows, habitatmeta.ncols)
+        source_map = zeros(T, habitatmeta.nrows, habitatmeta.ncols)
 		for (x,y,v) in zip(rc[:,2], rc[:,3], rc[:,1])
 			source_map[V(x), V(y)] = v
 		end
@@ -296,6 +299,14 @@ function read_source_and_ground_maps(T, V, source_file, ground_file, habitatmeta
         ground_map[ind] .= 0
     end
 
+	# use_unit_currents & use_direct_grounds
+	if use_unit_currents
+		source_map[findall(!iszero, source_map)] .= 1
+	end
+	if use_direct_grounds
+		ground_map[findall(!iszero, ground_map)] .= Inf
+	end
+
     source_map, ground_map
 end
 
@@ -467,7 +478,7 @@ function load_raster_data(T, V, cfg)::RasterData{T,V}
     if is_advanced
         source_map, ground_map =
         read_source_and_ground_maps(T, V, source_file, ground_file,
-                                    hbmeta, ground_is_res)
+                                    hbmeta, ground_is_res, cfg)
     else
         source_map, ground_map = Matrix{T}(undef,0,0), Matrix{T}(undef,0,0)
     end

test/input/raster/advanced/7/TestArea1_SourcePoints25.txt

@@ -0,0 +1,25 @@
+1	631110.108	3400879.813
+2	631110.108	3398906.798
+3	631110.108	3396933.784
+4	631110.108	3394960.769
+5	631110.108	3392987.754
+6	631110.108	3391014.740
+7	629703.647	3390448.186
+8	627730.632	3390448.185
+9	625757.617	3390448.185
+10	623784.603	3390448.185
+11	621811.588	3390448.184
+12	619838.573	3390448.184
+13	617865.559	3390448.184
+14	616879.054	3391434.693
+15	616879.054	3393407.708
+16	616879.054	3395380.723
+17	616879.054	3397353.737
+18	616879.054	3399326.752
+19	617299.005	3400879.815
+20	619272.020	3400879.815
+21	621245.035	3400879.815
+22	623218.049	3400879.814
+23	625191.064	3400879.814
+24	627164.079	3400879.814
+25	629137.093	3400879.813

test/input/raster/advanced/7/mgVerify7.ini

@@ -0,0 +1,64 @@
+[Options for advanced mode]
+ground_file_is_resistances = False
+remove_src_or_gnd = keepall
+ground_file = input/raster/advanced/7/TestArea1_GroundNodes_raster.asc
+use_unit_currents = True
+source_file = input/raster/advanced/7/TestArea1_SourcePoints25.txt
+use_direct_grounds = False
+
+[Mask file]
+
+
+[Calculation options]
+low_memory_mode = False
+parallelize = False
+solver = cg+amg
+print_timings = True
+preemptive_memory_release = False
+print_rusages = False
+max_parallel = 30
+
+[Short circuit regions (aka polygons)]
+
+
+[Options for one-to-all and all-to-one modes]
+
+
+[Output options]
+set_null_currents_to_nodata = False
+set_focal_node_currents_to_zero = False
+set_null_voltages_to_nodata = False
+compress_grids = True
+write_cur_maps = True
+write_volt_maps = False
+output_file = output/mgVerify7.out
+write_cum_cur_map_only = True
+log_transform_maps = False
+write_max_cur_maps = True
+
+[Version]
+version = 5
+
+[Options for reclassification of habitat data]
+
+
+[Logging Options]
+log_level = INFO
+log_file = output/mgVerify7.log
+profiler_log_file = output/mgVerify7_rusages.log
+screenprint_log = False
+
+[Options for pairwise and one-to-all and all-to-one modes]
+
+
+[Connection scheme for raster habitat data]
+connect_using_avg_resistances = True
+connect_four_neighbors_only = False
+
+[Habitat raster or graph]
+habitat_map_is_resistances = True
+habitat_file = input/raster/advanced/7/resistance_TestArea1.asc
+
+[Circuitscape mode]
+data_type = raster
+scenario = advanced