From 26eb0dd512a3fb1b585f099fb6bac9c672ac776a Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Tue, 10 Oct 2023 16:42:18 +0200
Subject: [PATCH] Small bug fixes.
This closes #47
---
src/Persefone.jl | 5 ++---
src/analysis/makieplots.jl | 5 +++--
src/core/input.jl | 12 ++++++++----
3 files changed, 13 insertions(+), 9 deletions(-)
diff --git a/src/Persefone.jl b/src/Persefone.jl
index a3550f2..be4ebff 100644
--- a/src/Persefone.jl
+++ b/src/Persefone.jl
@@ -22,10 +22,11 @@ using
DataFramesMeta,
Distributed,
FileIO,
+ #FIXME an upstream update broke GeoArrays for TableTransforms > 1.15.0
GeoArrays, #XXX this is a big dependency - can we get rid of it?
Logging,
LoggingExtras,
- CairoMakie,
+ CairoMakie, #XXX this is a very big dependency :-(
Random,
Serialization,
StableRNGs,
@@ -34,13 +35,11 @@ using
## Packages that may be useful later on:
# MacroTools, http://fluxml.ai/MacroTools.jl/stable/utilities/
# Debugger, https://github.com/JuliaDebug/Debugger.jl
-# Makie, https://docs.makie.org/stable/
# PackageCompiler, https://julialang.github.io/PackageCompiler.jl/stable/
# SpatialEcology, https://github.com/EcoJulia/SpatialEcology.jl
# OmniScape, https://circuitscape.org/
# PlantSimEngine, https://virtualplantlab.github.io/PlantSimEngine.jl/stable/
# Overseer, https://juliapackages.com/p/overseer -> ECS
-# QML, https://juliapackages.com/p/qml
## define exported functions and variables
export
diff --git a/src/analysis/makieplots.jl b/src/analysis/makieplots.jl
index 691c7f9..463a0f6 100644
--- a/src/analysis/makieplots.jl
+++ b/src/analysis/makieplots.jl
@@ -22,10 +22,11 @@ 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)
+ # 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)
end
f
diff --git a/src/core/input.jl b/src/core/input.jl
index 7d3ccf7..16b377c 100644
--- a/src/core/input.jl
+++ b/src/core/input.jl
@@ -13,6 +13,9 @@ const PARAMFILE = joinpath(pkgdir(Persefone), "src/parameters.toml")
## (DO NOT CHANGE THIS VALUE! Instead, specify simulation-specific configuration files
## by using the "--configfile" commandline argument, or when invoking simulate().)
+#XXX do I need to use absolute paths for all input files in case working dir is changed?
+# (can be done with `joinpath(dirname(@__FILE__), <filename>)` )
+
"""
@param(domainparam)
@@ -174,12 +177,11 @@ end
"""
loadmodelobject(fullfilename)
-Serialise a model object and save it to file for later reference.
-Includes the current model and Julia versions for compatibility checking.
+Deserialise a model object that was previously saved with `[savemodelobject](@ref)`.
"""
function loadmodelobject(fullfilename::String)
object = deserialize(fullfilename)
-
+ # Do basic integrity checks
if !(typeof(object) <: Dict && typeof(object["model"]) <: AgentBasedModel)
@warn "This file does not contain a model object. Loading failed."
return
@@ -189,6 +191,8 @@ function loadmodelobject(fullfilename::String)
@warn "This model object was saved with a different version of Persefone or Julia. It may be incompatible."
end
model = object["model"]
- model.logger = modellogger(@param(core.loglevel), @param(core.outdir)) #reset logger
+ # Reset the logger
+ !isdir(@param(core.outdir)) && mkpath(@param(core.outdir))
+ model.logger = modellogger(@param(core.loglevel), @param(core.outdir))
model
end
--
GitLab