From 22268d3439f0e76ce7ed564f2aaa5a772257930c Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Fri, 6 Oct 2023 14:56:29 +0200
Subject: [PATCH] Activated Makie plotting
Compile time still increased to 50s (from 15s), but at the moment I
can just about live with that.
---
Manifest.toml | 14 +++++++++++++-
Project.toml | 1 +
src/Persefone.jl | 10 +++++-----
src/analysis/makieplots.jl | 11 ++++++++---
src/core/output.jl | 30 +++++++++++++++---------------
src/core/simulation.jl | 2 +-
src/nature/ecologicaldata.jl | 4 ++--
src/world/landscape.jl | 14 +++++++-------
8 files changed, 52 insertions(+), 34 deletions(-)
diff --git a/Manifest.toml b/Manifest.toml
index 72340ca..77e1ea9 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -2,7 +2,7 @@
julia_version = "1.9.3"
manifest_format = "2.0"
-project_hash = "37a066281d4eb014f2c662ec23deb18c4d89d4e2"
+project_hash = "ce171af7d57f8fcad6d5ea123349f467345ec803"
[[deps.AbstractFFTs]]
deps = ["LinearAlgebra"]
@@ -165,6 +165,12 @@ git-tree-sha1 = "4435559dc39793d53a9e3d278e185e920b4619ef"
uuid = "0e736298-9ec6-45e8-9647-e4fc86a2fe38"
version = "0.2.8"
+[[deps.BinaryProvider]]
+deps = ["Libdl", "Logging", "SHA"]
+git-tree-sha1 = "ecdec412a9abc8db54c0efc5548c64dfce072058"
+uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
+version = "0.5.10"
+
[[deps.BitFlags]]
git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d"
uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
@@ -822,6 +828,12 @@ git-tree-sha1 = "bca20b2f5d00c4fbc192c3212da8fa79f4688009"
uuid = "82e4d734-157c-48bb-816b-45c225c6df19"
version = "0.6.7"
+[[deps.ImageMagick]]
+deps = ["BinaryProvider", "FileIO", "ImageCore", "InteractiveUtils", "Libdl", "Pkg", "Random"]
+git-tree-sha1 = "54dfa264804aefc44630c96619474e683a522d78"
+uuid = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
+version = "0.7.9"
+
[[deps.ImageMetadata]]
deps = ["AxisArrays", "ImageAxes", "ImageBase", "ImageCore"]
git-tree-sha1 = "355e2b974f2e3212a75dfb60519de21361ad3cb7"
diff --git a/Project.toml b/Project.toml
index 463fe12..d98f001 100644
--- a/Project.toml
+++ b/Project.toml
@@ -14,6 +14,7 @@ Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
GeoArrays = "2fb1d81b-e6a0-5fc5-82e6-8e06903437ab"
+ImageMagick = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
LoggingExtras = "e6f89c97-d47a-5376-807f-9c37f3926c36"
Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
diff --git a/src/Persefone.jl b/src/Persefone.jl
index 165f399..a3550f2 100644
--- a/src/Persefone.jl
+++ b/src/Persefone.jl
@@ -25,7 +25,7 @@ using
GeoArrays, #XXX this is a big dependency - can we get rid of it?
Logging,
LoggingExtras,
- #CairoMakie,
+ CairoMakie,
Random,
Serialization,
StableRNGs,
@@ -80,9 +80,9 @@ export
stepsimulation!,
createevent!,
finalise!,
- #visualisemap,
- #populationtrends,
- #visualiseoutput,
+ visualisemap,
+ populationtrends,
+ visualiseoutput,
savemodelobject,
loadmodelobject
@@ -90,7 +90,7 @@ export
## b references something from file a, it must be included later)
include("core/input.jl")
include("core/output.jl")
-#include("analysis/makieplots.jl")
+include("analysis/makieplots.jl")
include("world/landscape.jl")
include("world/weather.jl")
diff --git a/src/analysis/makieplots.jl b/src/analysis/makieplots.jl
index 00e871d..3422917 100644
--- a/src/analysis/makieplots.jl
+++ b/src/analysis/makieplots.jl
@@ -22,6 +22,8 @@ function visualisemap(model::AgentBasedModel, date::Union{Date,Nothing}=nothing)
image!(f[1,1], rotr90(landcover))
ax.aspect = DataAspect()
# plot individuals
+ #FIXME this function displays the individuals in a different location than the
+ # R script does - somewhere, I'm confusing coordinates...
for s in unique(inds.Species)
points = @select!(@subset(inds, :Species .== s, :Date .== date), :X, :Y)
scatter!(f[1,1], Matrix{Float32}(points), markersize=10)
@@ -38,8 +40,11 @@ Returns a Makie figure object.
function populationtrends(model::AgentBasedModel)
pops = model.datatables["populations"]
f = Figure()
- for s in unique(inds.Species)
- points = @select!(@subset(pops, :Species .== s), :X, :Y)
- lines!(f[1,1], Matrix{Float32}(points), markersize=10)
+ ax = Axis(f[1,1])
+ for s in unique(pops.Species)
+ points = @select!(@subset(pops, :Species .== s), :Abundance)
+ lines!(f[1,1], Vector{Float32}(points.Abundance))
end
+ #TODO prettify, add legend & labels
+ f
end
diff --git a/src/core/output.jl b/src/core/output.jl
index 0ce93ea..f9366bb 100644
--- a/src/core/output.jl
+++ b/src/core/output.jl
@@ -208,21 +208,21 @@ function outputdata(model::AgentBasedModel)
end
end
-# """
-# visualiseoutput(model)
-
-# Cycle through all data outputs and call their respective plot functions,
-# saving each figure as a PDF.
-# """
-# function visualiseoutput(model::AgentBasedModel)
-# #TODO write tests
-# @debug "Visualising output."
-# for output in model.dataoutputs
-# isnothing(output.plotfunction) && continue
-# figure = output.plotfunction(model)
-# save(joinpath(@param(core.outdir), output.name*".pdf"), figure)
-# end
-# end
+"""
+ visualiseoutput(model)
+
+Cycle through all data outputs and call their respective plot functions,
+saving each figure as a PDF.
+"""
+function visualiseoutput(model::AgentBasedModel)
+ #TODO write tests
+ @debug "Visualising output."
+ for output in model.dataoutputs
+ isnothing(output.plotfunction) && continue
+ figure = output.plotfunction(model)
+ save(joinpath(@param(core.outdir), output.name*".pdf"), figure)
+ end
+end
"""
savemodelobject(model, filename)
diff --git a/src/core/simulation.jl b/src/core/simulation.jl
index 21bff1a..51dfdbf 100644
--- a/src/core/simulation.jl
+++ b/src/core/simulation.jl
@@ -152,7 +152,7 @@ function finalise!(model::AgentBasedModel)
with_logger(model.logger) do
@info "Simulated $(model.date-@param(core.startdate))."
@info "Simulation run completed at $(Dates.now()),\nwrote output to $(@param(core.outdir))."
- #visualiseoutput(model) #TODO
+ visualiseoutput(model)
model
end
end
diff --git a/src/nature/ecologicaldata.jl b/src/nature/ecologicaldata.jl
index 5f65954..99bb68d 100644
--- a/src/nature/ecologicaldata.jl
+++ b/src/nature/ecologicaldata.jl
@@ -14,9 +14,9 @@ Create output files for each data group collected by the nature model.
"""
function initecologicaldata(model::AgentBasedModel)
newdataoutput!(model, "populations", ["Date", "Species", "Abundance"],
- savepopulationdata, @param(nature.popoutfreq), visualisemap)
+ savepopulationdata, @param(nature.popoutfreq), populationtrends)
newdataoutput!(model, "individuals", ["Date","ID","X","Y","Species","Sex","Age"],
- saveindividualdata, @param(nature.indoutfreq), populationtrends)
+ saveindividualdata, @param(nature.indoutfreq), visualisemap)
end
"""
diff --git a/src/world/landscape.jl b/src/world/landscape.jl
index d97a91c..4d8e283 100644
--- a/src/world/landscape.jl
+++ b/src/world/landscape.jl
@@ -46,19 +46,19 @@ function initlandscape(landcovermap::String, farmfieldsmap::String)
#TODO replace errors with exception
!(isfile(landcovermap)) && Base.error("Landcover map $(landcovermap) doesn't exist.")
!(isfile(farmfieldsmap)) && Base.error("Field map $(farmfieldsmap) doesn't exist.")
- landcover = GeoArrays.read(landcovermap)
- farmfields = GeoArrays.read(farmfieldsmap)
+ #XXX can I read the files in using FileIO, to avoid the GeoArrays dependency?
+ # read in TIFFs, replacing missing values with 0
+ landcover = coalesce(GeoArrays.read(landcovermap), 0)
+ farmfields = coalesce(GeoArrays.read(farmfieldsmap), 0)
(size(landcover) != size(farmfields)) && Base.error("Input map sizes don't match.")
width, height = size(landcover)[1:2]
landscape = Matrix{Pixel}(undef, width, height)
for x in 1:width
for y in 1:height
# convert the numeric landcover value to LandCover, then create the Pixel object
- lc = landcover[x,y][1]
- (ismissing(lc)) && (lc = 0)
- lcv = LandCover(Int(lc/10))
- ff = farmfields[x,y][1]
- !(ismissing(ff)) && (ff = Int64(ff))
+ lcv = LandCover(Int(landcover[x,y][1]/10))
+ ff = Int64(farmfields[x,y][1])
+ (iszero(ff)) && (ff = missing)
landscape[x,y] = Pixel(lcv, ff, Vector{Symbol}())
end
end
--
GitLab