Fixed bug in makieplots

Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.9.3"
 manifest_format = "2.0"
-project_hash = "ce171af7d57f8fcad6d5ea123349f467345ec803"
+project_hash = "ba06f527c3b60c5d5c4950e08943bcf1017cc1e3"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]

Project.toml

 name = "Persefone"
 uuid = "039acd1d-2a07-4b33-b082-83a1ff0fd136"
 authors = ["Daniel Vedder <daniel.vedder@idiv.de>"]
-version = "0.2.0"
+version = "0.3.0"
 
 [deps]
 Agents = "46ada45e-f475-11e8-01d0-f70cc89e6671"
@@ -18,12 +18,14 @@ ImageMagick = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 LoggingExtras = "e6f89c97-d47a-5376-807f-9c37f3926c36"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+TiffImages = "731e570b-9d59-4bfa-96dc-6df516fadf69"
 
 [compat]
 Agents = ">= 5.6"

docs/persefonejl_logo_v3_icon.svg

@@ -8,10 +8,10 @@
    version="1.1"
    id="svg8"
    inkscape:version="1.3 (1:1.3+202307231459+0e150ed6c4)"
-   sodipodi:docname="persefonejl_logo_v3.svg"
+   sodipodi:docname="persefonejl_logo_v3_icon.svg"
    inkscape:export-filename="persefonejl_logo_v3.png"
-   inkscape:export-xdpi="300"
-   inkscape:export-ydpi="300"
+   inkscape:export-xdpi="40.639999"
+   inkscape:export-ydpi="40.639999"
    xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
    xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
    xmlns:xlink="http://www.w3.org/1999/xlink"

src/Persefone.jl

@@ -16,6 +16,7 @@ module Persefone
 using
     Agents,
     ArgParse,
+    CairoMakie, #XXX this is a very big dependency :-(
     CSV,
     Dates,
     DataFrames,
@@ -26,7 +27,7 @@ using
     GeoArrays, #XXX this is a big dependency - can we get rid of it?
     Logging,
     LoggingExtras,
-    CairoMakie, #XXX this is a very big dependency :-(
+    #PrecompileTools, #TODO
     Random,
     Serialization,
     StableRNGs,
@@ -114,4 +115,8 @@ include("nature/species/wyvern.jl")
 
 include("core/simulation.jl") #this must be last
 
+#XXX precompile?
+# https://julialang.org/blog/2021/01/precompile_tutorial/
+# https://julialang.github.io/PrecompileTools.jl/stable/
+
 end

src/analysis/makieplots.jl

@@ -4,30 +4,33 @@
 ###
 
 """
-    visualisemap(model, date)
+    visualisemap(model, date, landcovermap)
 
-Draw the model's land cover map and plot all individuals as points on it at the
-specified date. If no date is passed, use the last date for which data are available.
+Draw the model's land cover map and plot all individuals as points on it at
+the specified date. If no date is passed, use the last date for which data
+are available. Optionally, you can pass a landcover map image (this is needed
+to reduce the frequency of disk I/O for Persefone Desktop).
 Returns a Makie figure object.
 """
-function visualisemap(model::AgentBasedModel, date::Union{Date,Nothing}=nothing)
-    # extract the data from the model and load the map
-    inds = model.datatables["individuals"]
-    isnothing(date) && (date = inds.Date[end])
-    landcover = load(@param(world.landcovermap))
-    # draw the map
+function visualisemap(model::AgentBasedModel,date=nothing,landcover=nothing)
+    # load and plot the map
+    isnothing(landcover) && (landcover = load(@param(world.landcovermap)))
     f = Figure()
     ax = Axis(f[1,1])
     hidedecorations!(ax)
     image!(f[1,1], rotr90(landcover))
     ax.aspect = DataAspect()
-    # plot individuals
+    # check if there are individuals and plot them
+    inds = model.datatables["individuals"]
+    iszero(size(inds)[1]) && return f
+    isnothing(date) && (date = inds.Date[end])
     for s in unique(inds.Species)
-        points = @select!(@subset(inds, :Species .== s, :Date .== date), :X, :Y)
+        points = @select!(@subset(inds, :Species .== s, :Date .== date),
+                          :X, :Y)
         # The origin in Makie is in the bottom-left rather than in the top-left as
         # on the model map, so we have to invert the Y coordinates
         @transform!(points, :Y = size(model.landscape)[2] .- :Y)
-        scatter!(f[1,1], Matrix{Float32}(points), markersize=10)
+        scatter!(f[1,1], Matrix{Float32}(points), markersize=8)
     end
     f
 end