Merge pull request #108 from Circuitscape/compute

Write config file and UI integration

src/Circuitscape.jl

@@ -6,9 +6,9 @@ using IterativeSolvers
 using Memento
 using GZip
 
+include("consts.jl")
 include("config.jl")
 include("logging.jl")
-include("consts.jl")
 include("utils.jl")
 include("io.jl")
 include("out.jl")

src/config.jl

@@ -69,3 +69,70 @@ function init_config()
 
     a
 end
+
+function update!(cfg, new)
+    for (key,val) in new
+        cfg[key] = val
+    end
+end
+
+function write_config(cfg)
+    open(cfg["output_file"], "w") do f
+        write(f, """
+        [Circuitscape Mode]
+        data_type = $(cfg["data_type"])
+        scenario = $(cfg["scenario"])
+
+        [Version]
+        version = 5.0.0
+
+        [Habitat raster or graph]
+        habitat_file = $(cfg["habitat_file"])
+        habitat_map_is_resistances = $(cfg["habitat_map_is_resistances"])
+
+        [Connection Scheme for raster habitat data]
+        connect_four_neighbors_only = $(cfg["connect_four_neighbors_only"] in TRUELIST)
+        connect_using_avg_resistances = $(cfg["connect_using_avg_resistances"] in TRUELIST)
+
+        [Short circuit regions (aka polygons)]
+        use_polygons = $(cfg["use_polygons"] in TRUELIST)
+        polygon_file = $(cfg["use_polygons"])
+
+        [Options for advanced mode]
+        ground_file_is_resistances = $(cfg["ground_file_is_resistances"] in TRUELIST)
+        source_file = $(cfg["source_file"])
+        remove_src_or_gnd = $(cfg["remove_src_or_gnd"])
+        ground_file = $(cfg["ground_file"])
+        use_unit_currents = $(cfg["use_unit_currents"] in TRUELIST)
+        use_direct_grounds = $(cfg["use_direct_grounds"] in TRUELIST)
+
+        [Mask file]
+        use_mask = $(cfg["use_mask"] in TRUELIST)
+        mask_file = $(cfg["mask_file"])
+
+        [Options for one-to-all and all-to-one modes]
+        use_variable_source_strengths = $(cfg["use_variable_source_strengths"] in TRUELIST)
+        variable_source_file = $(cfg["variable_source_file"])
+
+        [Options for pairwise and one-to-all and all-to-one modes]
+        included_pairs_file = $(cfg["included_pairs_file"])
+        use_included_pairs = $(cfg["use_included_pairs"] in TRUELIST)
+        point_file = $(cfg["point_file"])
+
+        [Calculation options]
+        solver = cg+amg
+
+        [Output options]
+        write_cum_cur_map_only = $(cfg["write_cum_cur_map_only"] in TRUELIST)
+        log_transform_maps = $(cfg["log_transform_maps"] in TRUELIST)
+        output_file = $(cfg["output_file"])
+        write_max_cur_maps = $(cfg["write_max_cur_maps"] in TRUELIST)
+        write_volt_maps = $(cfg["write_volt_maps"] in TRUELIST)
+        set_null_currents_to_nodata = $(cfg["set_null_currents_to_nodata"] in TRUELIST)
+        set_null_voltages_to_nodata = $(cfg["set_null_voltages_to_nodata"] in TRUELIST)
+        compress_grids = $(cfg["compress_grids"] in TRUELIST)
+        write_cur_maps = $(cfg["write_cur_maps"] in TRUELIST)
+        """)
+    end
+end
+

src/consts.jl

@@ -16,7 +16,7 @@ const AAGRID = 2
 const TXTLIST = 3
 const PAIRS_AAGRID = 4
 const PAIRS_LIST = 5
-const truelist = ["True", "true"]
+const TRUELIST = ["True", "true"]
 
 # Constants for logging
 const NONE = ["NONE", "None", "none"]
@@ -26,4 +26,4 @@ const WARNING = ["WARNING", "WARN", "warning", "warn", "Warning", "Warn"]
 const CRITICAL = ["CRITICAL", "critical", "Critical"]
 
 # Constant for index type
-const INT = Int32
+const INT = Int32

src/io.jl

@@ -311,7 +311,7 @@ end
 
 function get_network_data(T, cfg)::NetworkData{T,INT}
 
-    hab_is_res = cfg["habitat_map_is_resistances"] in truelist
+    hab_is_res = cfg["habitat_map_is_resistances"] in TRUELIST
     hab_file = cfg["habitat_file"]
     fp_file = cfg["point_file"]
     source_file = cfg["source_file"]
@@ -345,33 +345,33 @@ function load_raster_data(T, cfg)::RasData{T,INT}
 
     # Habitat file
     hab_file = cfg["habitat_file"]
-    hab_is_res = cfg["habitat_map_is_resistances"] in truelist
+    hab_is_res = cfg["habitat_map_is_resistances"] in TRUELIST
 
     # Polygons
-    use_polygons = cfg["use_polygons"] in truelist
+    use_polygons = cfg["use_polygons"] in TRUELIST
     polygon_file = cfg["polygon_file"]
 
     # Mask file
-    use_mask = cfg["use_mask"] in truelist 
+    use_mask = cfg["use_mask"] in TRUELIST 
     mask_file = cfg["mask_file"]
 
     # Point file
     point_file = cfg["point_file"]
 
     # Variable source strengths
-    use_var_source = cfg["use_variable_source_strengths"] in truelist 
+    use_var_source = cfg["use_variable_source_strengths"] in TRUELIST 
     var_source_file = cfg["variable_source_file"]
 
     # Included Pairs
-    use_inc_pairs = cfg["use_included_pairs"] in truelist 
+    use_inc_pairs = cfg["use_included_pairs"] in TRUELIST 
     inc_pairs_file = cfg["included_pairs_file"]
 
     # Advanced mode
     is_pairwise = cfg["scenario"] in PAIRWISE
     is_advanced = cfg["scenario"] in ADVANCED
     source_file = cfg["source_file"]
     ground_file = cfg["ground_file"]
-    ground_is_res = cfg["ground_file_is_resistances"] in truelist
+    ground_is_res = cfg["ground_file_is_resistances"] in TRUELIST
 
     csinfo("Reading maps")
 

src/logging.jl

@@ -1,8 +1,10 @@
 const fmt = "[{date} | {level} | {name}]: {msg}"
+const ui_interface = Ref{Function}((x,y) -> nothing)
+
 const logger = Memento.config("info", 
                         fmt = fmt)
-csinfo(msg) = info(logger, msg)
-cswarn(msg) = warn(logger, msg)
+csinfo(msg) = (info(logger, msg); ui_interface[](msg, :info))
+cswarn(msg) = (warn(logger, msg); ui_interace[](msg, :warn))
 
 function update_logging!(cfg)
 
@@ -20,4 +22,4 @@ function update_logging!(cfg)
         push!(logger, 
             DefaultHandler(log_file, DefaultFormatter(fmt)))
     end
-end
+end

src/network/pairwise.jl

@@ -53,19 +53,19 @@ function get_network_flags(cfg)
     is_advanced = cfg["scenario"] in ADVANCED
     is_alltoone = false
     is_onetoall = false
-    grnd_file_is_res = cfg["ground_file_is_resistances"] in truelist
+    grnd_file_is_res = cfg["ground_file_is_resistances"] in TRUELIST
     policy = Symbol(cfg["remove_src_or_gnd"])
     solver = cfg["solver"]
 
     # Output flags
-    write_volt_maps = cfg["write_volt_maps"] in truelist
-    write_cur_maps = cfg["write_cur_maps"] in truelist
-    write_cum_cur_maps_only = cfg["write_cum_cur_map_only"] in truelist
-    write_max_cur_maps = cfg["write_max_cur_maps"] in truelist
-    set_null_currents_to_nodata = cfg["set_null_currents_to_nodata"] in truelist
-    set_null_voltages_to_nodata = cfg["set_null_voltages_to_nodata"] in truelist
-    compress_grids = cfg["compress_grids"] in truelist
-    log_transform_maps = cfg["log_transform_maps"] in truelist
+    write_volt_maps = cfg["write_volt_maps"] in TRUELIST
+    write_cur_maps = cfg["write_cur_maps"] in TRUELIST
+    write_cum_cur_maps_only = cfg["write_cum_cur_map_only"] in TRUELIST
+    write_max_cur_maps = cfg["write_max_cur_maps"] in TRUELIST
+    set_null_currents_to_nodata = cfg["set_null_currents_to_nodata"] in TRUELIST
+    set_null_voltages_to_nodata = cfg["set_null_voltages_to_nodata"] in TRUELIST
+    compress_grids = cfg["compress_grids"] in TRUELIST
+    log_transform_maps = cfg["log_transform_maps"] in TRUELIST
 
     o = OutputFlags(write_volt_maps, write_cur_maps,
                     write_cum_cur_maps_only, write_max_cur_maps,

src/raster/pairwise.jl

@@ -38,11 +38,11 @@ function get_raster_flags(cfg)
     is_advanced = cfg["scenario"] in ADVANCED
     is_onetoall = cfg["scenario"] in ONETOALL
     is_alltoone = cfg["scenario"] in ALLTOONE
-    four_neighbors = cfg["connect_four_neighbors_only"] in truelist
-    avg_res = cfg["connect_using_avg_resistances"] in truelist
+    four_neighbors = cfg["connect_four_neighbors_only"] in TRUELIST
+    avg_res = cfg["connect_using_avg_resistances"] in TRUELIST
     solver = cfg["solver"]
     ground_file_is_resistances = 
-        cfg["ground_file_is_resistances"] in truelist
+        cfg["ground_file_is_resistances"] in TRUELIST
     policy = Symbol(cfg["remove_src_or_gnd"])
 
     # Output Flags

src/run.jl

@@ -14,6 +14,7 @@ Inputs:
 function compute(path::String)
     cfg = parse_config(path)
     update_logging!(cfg)
+    write_config(cfg)
     T = cfg["precision"] in SINGLE ? Float32 : Float64
     csinfo("Precision used: $(cfg["precision"])")
     t = @elapsed r = _compute(T, cfg)
@@ -41,4 +42,15 @@ function _compute(T, cfg)
             network_advanced(T, cfg)
         end
     end
-end
+end
+
+function compute(dict)
+    cfg = init_config()
+    update!(cfg, dict)
+    update_logging!(cfg)
+    T = cfg["precision"] in SINGLE ? Float32 : Float64
+    csinfo("Precision used: $(cfg["precision"])")
+    t = @elapsed r = _compute(T, cfg)
+    csinfo("Time taken to complete job = $t")
+    r
+end

src/utils.jl

@@ -85,14 +85,14 @@ end
 function get_output_flags(cfg)
 
     # Output flags
-    write_volt_maps = cfg["write_volt_maps"] in truelist
-    write_cur_maps = cfg["write_cur_maps"] in truelist
-    write_cum_cur_maps_only = cfg["write_cum_cur_map_only"] in truelist
-    write_max_cur_maps = cfg["write_max_cur_maps"] in truelist
-    set_null_currents_to_nodata = cfg["set_null_currents_to_nodata"] in truelist
-    set_null_voltages_to_nodata = cfg["set_null_voltages_to_nodata"] in truelist
-    compress_grids = cfg["compress_grids"] in truelist
-    log_transform_maps = cfg["log_transform_maps"] in truelist
+    write_volt_maps = cfg["write_volt_maps"] in TRUELIST
+    write_cur_maps = cfg["write_cur_maps"] in TRUELIST
+    write_cum_cur_maps_only = cfg["write_cum_cur_map_only"] in TRUELIST
+    write_max_cur_maps = cfg["write_max_cur_maps"] in TRUELIST
+    set_null_currents_to_nodata = cfg["set_null_currents_to_nodata"] in TRUELIST
+    set_null_voltages_to_nodata = cfg["set_null_voltages_to_nodata"] in TRUELIST
+    compress_grids = cfg["compress_grids"] in TRUELIST
+    log_transform_maps = cfg["log_transform_maps"] in TRUELIST
 
     o = OutputFlags(write_volt_maps, write_cur_maps,
                     write_cum_cur_maps_only, write_max_cur_maps,

test/compare_output.jl

@@ -3,6 +3,7 @@ function compare_all_output(str)
     gen_list, list_to_comp = generate_lists(str)
 
     for f in gen_list
+        !contains(f, "_") && continue
         contains(f, "resistances") && continue
 
         info("Testing $f")

test/input/raster/all_to_one/1/allToOneVerify1.ini

@@ -19,7 +19,7 @@ point_file = input/raster/one_to_all/1/points.asc
 [Output options]
 write_cum_cur_map_only = False
 log_transform_maps = False
-output_file = circuitscape/verify/output/oneToAllVerify1.out
+output_file = output/allToOneVerify1.out
 write_max_cur_maps = False
 write_volt_maps = False
 set_null_currents_to_nodata = False

test/input/raster/all_to_one/10/allToOneVerify10.ini

@@ -19,7 +19,7 @@ point_file = input/raster/one_to_all/10/points_polys7.asc
 [Output options]
 write_cum_cur_map_only = False
 log_transform_maps = False
-output_file = circuitscape/verify/output/oneToAllVerify10.out
+output_file = output/allToOneVerify10.out
 write_max_cur_maps = False
 write_volt_maps = False
 set_null_currents_to_nodata = False

test/input/raster/all_to_one/11/allToOneVerify11.ini

@@ -19,7 +19,7 @@ point_file = input/raster/one_to_all/11/points_polys7.asc
 [Output options]
 write_cum_cur_map_only = False
 log_transform_maps = False
-output_file = circuitscape/verify/output/oneToAllVerify11.out
+output_file = output/allToOneVerify11.out
 write_max_cur_maps = False
 write_volt_maps = False
 set_null_currents_to_nodata = False

test/input/raster/all_to_one/12/allToOneVerify12.ini

@@ -19,7 +19,7 @@ point_file = input/raster/one_to_all/12/points.asc
 [Output options]
 write_cum_cur_map_only = False
 log_transform_maps = False
-output_file = circuitscape/verify/output/oneToAllVerify12.out
+output_file = output/allToOneVerify12.out
 write_max_cur_maps = False
 write_volt_maps = False
 set_null_currents_to_nodata = False

test/input/raster/all_to_one/2/allToOneVerify2.ini

@@ -19,7 +19,7 @@ point_file = input/raster/one_to_all/2/points.asc
 [Output options]
 write_cum_cur_map_only = False
 log_transform_maps = False
-output_file = circuitscape/verify/output/oneToAllVerify2.out
+output_file = output/allToOneVerify2.out
 write_max_cur_maps = False
 write_volt_maps = False
 set_null_currents_to_nodata = False

test/input/raster/all_to_one/3/allToOneVerify3.ini

@@ -19,7 +19,7 @@ point_file = input/raster/one_to_all/3/points.asc
 [Output options]
 write_cum_cur_map_only = False
 log_transform_maps = False
-output_file = circuitscape/verify/output/oneToAllVerify3.out
+output_file = output/allToOneVerify3.out
 write_max_cur_maps = False
 write_volt_maps = False
 set_null_currents_to_nodata = False

test/input/raster/all_to_one/4/allToOneVerify4.ini

@@ -19,7 +19,7 @@ point_file = input/raster/one_to_all/4/points.asc
 [Output options]
 write_cum_cur_map_only = False
 log_transform_maps = False
-output_file = circuitscape/verify/output/oneToAllVerify4.out
+output_file = output/allToOneVerify4.out
 write_max_cur_maps = False
 write_volt_maps = False
 set_null_currents_to_nodata = False

test/input/raster/all_to_one/5/allToOneVerify5.ini

@@ -19,7 +19,7 @@ point_file = input/raster/one_to_all/5/points5x5_polys.txt
 [Output options]
 write_cum_cur_map_only = False
 log_transform_maps = False
-output_file = circuitscape/verify/output/oneToAllVerify5.out
+output_file = output/allToOneVerify5.out
 write_max_cur_maps = False
 write_volt_maps = False
 set_null_currents_to_nodata = False

test/input/raster/all_to_one/6/allToOneVerify6.ini

@@ -19,7 +19,7 @@ point_file = input/raster/one_to_all/6/points5x5_polys.txt
 [Output options]
 write_cum_cur_map_only = False
 log_transform_maps = False
-output_file = circuitscape/verify/output/oneToAllVerify6.out
+output_file = output/allToOneVerify6.out
 write_max_cur_maps = False
 write_volt_maps = False
 set_null_currents_to_nodata = False

test/input/raster/all_to_one/7/allToOneVerify7.ini

@@ -19,7 +19,7 @@ point_file = input/raster/one_to_all/7/points5x5.txt
 [Output options]
 write_cum_cur_map_only = False
 log_transform_maps = False
-output_file = circuitscape/verify/output/oneToAllVerify7.out
+output_file = output/allToOneVerify7.out
 write_max_cur_maps = False
 write_volt_maps = False
 set_null_currents_to_nodata = False

test/input/raster/all_to_one/8/allToOneVerify8.ini

@@ -19,7 +19,7 @@ point_file = input/raster/one_to_all/8/points5x5_polys.asc
 [Output options]
 write_cum_cur_map_only = False
 log_transform_maps = False
-output_file = circuitscape/verify/output/oneToAllVerify8.out
+output_file = output/allToOneVerify8.out
 write_max_cur_maps = False
 write_volt_maps = False
 set_null_currents_to_nodata = False

test/input/raster/all_to_one/9/allToOneVerify9.ini

@@ -19,7 +19,7 @@ point_file = input/raster/one_to_all/9/points5x5_polys.asc
 [Output options]
 write_cum_cur_map_only = False
 log_transform_maps = False
-output_file = circuitscape/verify/output/oneToAllVerify9.out
+output_file = output/allToOneVerify9.out
 write_max_cur_maps = False
 write_volt_maps = False
 set_null_currents_to_nodata = False

test/input/raster/one_to_all/12/oneToAllVerify12.ini

@@ -19,7 +19,7 @@ point_file = input/raster/one_to_all/12/points.asc
 [Output options]
 write_cum_cur_map_only = False
 log_transform_maps = False
-output_file = circuitscape/verify/output/oneToAllVerify12.out
+output_file = output/oneToAllVerify12.out
 write_max_cur_maps = False
 write_volt_maps = False
 set_null_currents_to_nodata = False

test/input/raster/one_to_all/13/oneToAllVerify13.ini

@@ -19,7 +19,7 @@ point_file = input/raster/one_to_all/13/points.asc
 [Output options]
 write_cum_cur_map_only = False
 log_transform_maps = False
-output_file = circuitscape/verify/output/oneToAllVerify13.out
+output_file = output/oneToAllVerify13.out
 write_max_cur_maps = False
 write_volt_maps = False
 set_null_currents_to_nodata = False