Export outputdata() and other small changes

Project.toml

 name = "Persefone"
 uuid = "039acd1d-2a07-4b33-b082-83a1ff0fd136"
 authors = ["Daniel Vedder <daniel.vedder@idiv.de>"]
-version = "0.3.3"
+version = "0.3.4"
 
 [deps]
 Agents = "46ada45e-f475-11e8-01d0-f70cc89e6671"

src/Persefone.jl

@@ -79,6 +79,7 @@ export
     stepsimulation!,
     createevent!,
     finalise!,
+    outputdata,
     visualisemap,
     populationtrends,
     visualiseoutput,

src/analysis/makieplots.jl

@@ -14,11 +14,12 @@ Returns a Makie figure object.
 """
 function visualisemap(model::AgentBasedModel,date=nothing,landcover=nothing)
     # load and plot the map
-    isnothing(landcover) && (landcover = load(@param(world.landcovermap)))
+    # Note: if the landcover map is supplied, it needs to be rotr90'ed
+    isnothing(landcover) && (landcover = rotr90(load(@param(world.landcovermap))))
     f = Figure()
     ax = Axis(f[1,1])
     hidedecorations!(ax)
-    image!(f[1,1], rotr90(landcover))
+    image!(f[1,1], landcover)
     ax.aspect = DataAspect()
     # check if there are individuals and plot them
     inds = model.datatables["individuals"]

src/core/input.jl

@@ -180,6 +180,10 @@ end
 Deserialise a model object that was previously saved with `[savemodelobject](@ref)`.
 """
 function loadmodelobject(fullfilename::String)
+    if !isfile(fullfilename)
+        @warn "File $(fullfilename) does not exist. Loading failed."
+        return
+    end
     object = deserialize(fullfilename)
     # Do basic integrity checks
     if !(typeof(object) <: Dict && typeof(object["model"]) <: AgentBasedModel)

src/core/output.jl

@@ -172,12 +172,13 @@ function newdataoutput!(model::AgentBasedModel, name::String, header::Vector{Str
 end
 
 """
-    outputdata(model)
+    outputdata(model, force=false)
  
 Cycle through all registered data outputs and activate them according to their
-configured frequency.
+configured frequency. If `force` is `true`, activate all outputs regardless
+of their configuration.
 """
-function outputdata(model::AgentBasedModel)
+function outputdata(model::AgentBasedModel, force=false)
     #XXX enable output every X days, or weekly?
     #XXX all output functions except for "end" are run on the first update
     # -> should they all be run on the last update, too?
@@ -185,9 +186,9 @@ function outputdata(model::AgentBasedModel)
     isnextmonth = d -> (day(d) == day(startdate))
     isnextyear = d -> (month(d) == month(startdate) && day(d) == day(startdate))
     for output in model.dataoutputs
-        (output.frequency == "never") && continue
+        (!force && output.frequency == "never") && continue
         # check if this output should be activated today
-        if (output.frequency == "daily") ||
+        if force || (output.frequency == "daily") ||
             (output.frequency == "monthly" && isnextmonth(model.date)) ||
             (output.frequency == "yearly" && isnextyear(model.date)) ||
             (output.frequency == "end" && model.date == @param(core.enddate))
@@ -236,7 +237,8 @@ function savemodelobject(model::AgentBasedModel, filename::String)
     object = Dict("model"=>model,
                   "modelversion"=>pkgversion(Persefone),
                   "juliaversion"=>VERSION)
-    filename = joinpath(@param(core.outdir), filename*".dat")
+    !endswith(filename, ".dat") && (filename *= ".dat")
+    filename = joinpath(@param(core.outdir), filename)
     serialize(filename, object)
     @debug "Saved model object to $(filename)."
 end

src/core/simulation.jl

@@ -62,9 +62,6 @@ function initmodel(settings::Dict{String, Any})
     createdatadir(settings["core.outdir"], settings["core.overwrite"])
     logger = modellogger(settings["core.loglevel"], settings["core.outdir"])
     with_logger(logger) do
-        events = Vector{FarmEvent}()
-        dataoutputs = Vector{DataOutput}()
-        datatables = Dict{String, DataFrame}()
         landscape = initlandscape(settings["world.landcovermap"],
                                   settings["world.farmfieldsmap"])
         weather = initweather(settings["world.weatherfile"],
@@ -79,16 +76,16 @@ function initmodel(settings::Dict{String, Any})
                                       :landscape=>landscape,
                                       :weather=>weather,
                                       :crops=>crops,
-                                      :dataoutputs=>dataoutputs,
-                                      :datatables=>datatables,
-                                      :events=>events)
-        model = AgentBasedModel(Union{Farmer,Animal,FarmPlot}, space, properties=properties,
+                                      :dataoutputs=>Vector{DataOutput}(),
+                                      :datatables=>Dict{String, DataFrame}(),
+                                      :events=>Vector{FarmEvent}())
+        model = AgentBasedModel(Union{Farmer,Animal,FarmPlot},
+                                space, properties=properties,
                                 rng=StableRNG(settings["core.seed"]), warn=false)
         saveinputfiles(model)
         initfields!(model)
         initfarms!(model)
         initnature!(model)
-        #outputdata(model) #XXX record data before run starts?
         model
     end
 end