From c587740215262e6dbbcfff6f5f71ec19de186b63 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Thu, 16 May 2024 12:22:14 +0200
Subject: [PATCH] Reimplemented neighbour-finding functions
This used to be done by Agents.jl, is now done natively
---
src/nature/macros.jl | 25 +++---
src/nature/nature.jl | 19 ++++-
src/nature/populations.jl | 118 ++++++++++++++++-------------
src/nature/species/wolpertinger.jl | 12 +--
src/world/landscape.jl | 5 +-
5 files changed, 105 insertions(+), 74 deletions(-)
diff --git a/src/nature/macros.jl b/src/nature/macros.jl
index c4be686..5d6dcd6 100644
--- a/src/nature/macros.jl
+++ b/src/nature/macros.jl
@@ -77,7 +77,6 @@ Set the parameters that are used to initialise this species' population.
For parameter options, see [`PopInitParams`](@ref).
"""
macro populate(species, params)
- println("Will register $(species).")
quote
# convert the macro body to a dict
Core.@__doc__ fun = function() # metaprogramming is great - this is a fun fun function ;-)
@@ -232,17 +231,6 @@ macro migrate(arrival)
:(migrate!($(esc(:self)), $(esc(:model)), $(esc(arrival))))
end
-"""
- @neighbours(radius)
-
-Return an iterator over all animals in the given radius around this animal, excluding itself.
-This can only be used nested within [`@phase`](@ref).
-"""
-macro neighbours(radius)
- #TODO enable filtering by species
- :(nearby_animals($(esc(:self)), $(esc(:model)), $(esc(radius))))
-end
-
"""
@habitat
@@ -356,13 +344,24 @@ macro randompixel(args...)
end
"""
- @countanimals(species="", radius=0)
+ @neighbours(radius=0)
+
+Return an iterator over all conspecific animals in the given radius around this animal,
+excluding itself. This can only be used nested within [`@phase`](@ref).
+"""
+macro neighbours(args...)
+ :(neighbours($(esc(:self)), $(esc(:model)); $(map(esc, args)...)))
+end
+
+"""
+ @countanimals(radius=0, species="")
Count the number of animals of the given species in this location.
This is a utility wrapper that can only be used nested within
[`@phase`](@ref) or [`@habitat`](@ref).
"""
macro countanimals(args...)
+ #XXX do I want/need this?
:(countanimals($(esc(:pos)), $(esc(:model)); $(map(esc, args)...)))
end
diff --git a/src/nature/nature.jl b/src/nature/nature.jl
index b1aeb9e..11975b6 100644
--- a/src/nature/nature.jl
+++ b/src/nature/nature.jl
@@ -33,7 +33,24 @@ abstract type Animal <: ModelAgent end
Return the species name of this animal as a string.
"""
function speciesof(a::Animal)
- string(typeof(a))
+ # strip out the module name if necessary (`Persefone.<species>`)
+ spstrings = split(string(typeof(a)), ".")
+ length(spstrings) == 1 ? spstrings[1] : spstrings[2]
+end
+
+"""
+ speciestype(animal)
+
+Return the Type of this species.
+"""
+function speciestype(species::String)
+ # get the species Type from its namestring by looking in the module namespace
+ speciestype = nothing
+ for name in names(Persefone, all=true)
+ string(name) == species && (speciestype = getfield(Persefone, name))
+ end
+ isnothing(speciestype) && @error("Species $species is not defined.")
+ speciestype
end
"""
diff --git a/src/nature/populations.jl b/src/nature/populations.jl
index 75a80c0..e7a8818 100644
--- a/src/nature/populations.jl
+++ b/src/nature/populations.jl
@@ -41,25 +41,25 @@ using [`@populate`](@ref).
asexual::Bool = false
end
+"""
+ populationparameters(type)
+
+A function that returns a [`PopInitParams`](@ref) object for the given species type.
+Parametric methods for each species are defined with [`@populate`](@ref). This is the
+catch-all method, which throws an error if no species-specific function is defined.
+"""
populationparameters(t::Type) = @error("No population parameters defined for $(t), use @populate.")
"""
- initpopulation!(species, model)
+ initpopulation!(speciesname, model)
Initialise the population of the given species, based on the parameters stored
in [`PopInitParams`](@ref). Define these using [`@populate`](@ref).
"""
-function initpopulation!(species::String, model::SimulationModel)
- # get the species Type from its namestring
- speciestype = nothing
- for name in names(Persefone, all=true)
- string(name) == species && (speciestype = getfield(Persefone, name))
- end
- isnothing(speciestype) && @error "Species $species is not defined."
- #XXX can we get rid of the Persefone.<species> in the speciestype?
- @debug "Initialising population of $species/$speciestype."
+function initpopulation!(speciesname::String, model::SimulationModel)
# get the PopInitParams and check for validity
- p = populationparameters(speciestype)
+ species = speciestype(speciesname)
+ p = populationparameters(species)
(p.popsize <= 0 && p.popdensity <= 0) && #XXX not sure what this would do
@warn("initpopulation() called with popsize and popdensity both <= 0")
(p.popsize > 0 && p.popdensity > 0) && #XXX not sure what this would do
@@ -74,18 +74,19 @@ function initpopulation!(species::String, model::SimulationModel)
if p.habitat((x,y), model) &&
(p.popdensity <= 0 || @chance(1/p.popdensity)) #XXX what if pd==0?
if p.pairs
- a1 = speciestype(length(model.animals)+1, male, (-1, -1), (x,y), p.phase)
- a2 = speciestype(length(model.animals)+1, female, (-1, -1), (x,y), p.phase)
+ a1 = species(length(model.animals)+1, male, (-1, -1), (x,y), p.phase)
+ a2 = species(length(model.animals)+1, female, (-1, -1), (x,y), p.phase)
create!(a1, model)
create!(a2, model)
- push!(model.animals, a1)
- push!(model.animals, a2)
+ push!(model.animals, a1, a2)
+ push!(model.landscape[x,y].animals, a1.id, a2.id)
n += 2
else
sex = p.asexual ? hermaphrodite : @rand([male, female])
- a = speciestype(length(model.animals)+1, sex, (-1, -1), (x,y), p.phase)
+ a = species(length(model.animals)+1, sex, (-1, -1), (x,y), p.phase)
create!(a, model)
push!(model.animals, a)
+ push!(model.landscape[x,y].animals, a.id)
n += 1
end
end
@@ -121,10 +122,9 @@ function reproduce!(animal::Animal, model::SimulationModel,
else
sex = @rand([male, female])
end
- #FIXME get birth phase
- child = typeof(animal)(length(model.animals)+1, sex,
- (animal.id, mate), animal.pos)
- initindividual(child, model)
+ bphase = populationparameters(typeof(animal)).phase
+ child = typeof(animal)(length(model.animals)+1, sex, (animal.id, mate), animal.pos, bphase)
+ create!(child, model)
push!(model.animals, child)
push!(animal.offspring, child.id)
mate > 0 && push!(models.animals[mate].offspring, child.id)
@@ -143,6 +143,7 @@ function kill!(animal::Animal, model::SimulationModel,
if @rand() < probability
postfix = isempty(cause) ? "." : " from $cause."
@debug "$(animalid(animal)) has died$(postfix)"
+ filter!(x -> x!=animal.id, model.landscape[animal.pos...].animals)
model.animals[animal.id] = nothing
return true
end
@@ -178,42 +179,59 @@ function isalive(animalid::Int64, model::SimulationModel)
end
"""
- nearby_animals(pos, model, radius)
+ nearby_ids(pos, model, radius)
-Return an iterator over all animals in the given radius around this position.
+Return a list of IDs of the animals within a given radius of the position.
"""
-function nearby_animals(pos::Tuple{Int64,Int64}, model::SimulationModel, radius::Int64)
- #FIXME remove agents.jl code
- #TODO enable filtering by species
- neighbours = (model[id] for id in nearby_ids(pos, model, radius))
- Iterators.filter(a -> typeof(a) == Animal, neighbours)
+function nearby_ids(pos::Tuple{Int64,Int64}, model::SimulationModel, radius::Int64)
+ ids = []
+ msize = size(model.landscape)
+ for x in (pos[1]-radius):(pos[1]+radius)
+ (x < 1 || x > msize[1]) && continue
+ for y in (pos[2]-radius):(pos[2]+radius)
+ (y < 1 || y > msize[2]) && continue
+ append!(ids, model.landscape[x,y].animals)
+ end
+ end
+ ids
end
+
"""
- nearby_animals(animal, model, radius)
+ nearby_animals(pos, model; radius= 0, species="")
-Return an iterator over all animals in the given radius around this animal, excluding itself.
+Return a list of animals in the given radius around this position, optionally filtering by species.
"""
-function nearby_animals(animal::Animal, model::SimulationModel, radius::Int64)
- #FIXME remove agents.jl code
- #TODO enable filtering by species
- neighbours = (model[id] for id in nearby_ids(animal.pos, model, radius))
- Iterators.filter(a -> typeof(a) == Animal && a.id != animal.id, neighbours)
+function nearby_animals(pos::Tuple{Int64,Int64}, model::SimulationModel;
+ radius::Int64=0, species="")
+ neighbours = nearby_ids(pos, model, radius)
+ isempty(neighbours) && return neighbours
+ if species == ""
+ model.animals[neighbours]
+ else
+ filter(x -> speciesof(x) == species, model.animals[neighbours])
+ end
end
"""
- countanimals(pos, model; species="", radius=0)
+ neighbours(animal, model; radius=0)
+
+Return a list of conspecific animals in the given radius around this animal, excluding itself.
+"""
+function neighbours(animal::Animal, model::SimulationModel; radius::Int64=0)
+ filter(a -> a.id != animal.id,
+ nearby_animals(animal.pos, model, radius=radius, species=speciesof(animal)))
+end
+
+"""
+ countanimals(pos, model; radius= 0, species="")
Count the number of animals in this location (optionally supplying a species name and radius).
"""
function countanimals(pos::Tuple{Int64,Int64}, model::SimulationModel;
- species::String="", radius::Int64=0)
- n = 0 #FIXME fix nearby_animals
- #XXX can we ignore capitalisation in the spelling of `species`?
- for a in nearby_animals(pos, model, radius)
- (species == "" || a.traits["name"] == species) && (n += 1)
- end
- return n
+ radius::Int64=0, species="")
+ #XXX do I want/need this?
+ length(nearby_animals(pos, model, radius=radius, species=species))
end
"""
@@ -233,18 +251,14 @@ end
move!(animal, model, position)
Move the animal to the given position, making sure that this is in-bounds.
-Return true if successful, return false and leave the animal where it is if
-the position is out of bounds.
+If the position is out of bounds, the animal stops at the map edge.
"""
function move!(animal::Animal, model::SimulationModel, position::Tuple{Int64,Int64})
- width, height = size(model.landscape)
- if position[1] < 0 || position[2] < 0 || position[1] > width || position[2] > height
- #XXX should this be a warning? or just pass silently?
- @debug "$(animalid(animal)) tried to move out of bounds to $position."
- return false
- end
- animal.pos = position
- return true
+ #XXX should this function give some sort of warning (e.g. return false)
+ # if the original position is not reachable?
+ filter!(x -> x != animal.id, model.landscape[animal.pos...].animals)
+ animal.pos = safebounds(position, model)
+ push!(model.landscape[animal.pos...].animals, animal.id)
end
"""
diff --git a/src/nature/species/wolpertinger.jl b/src/nature/species/wolpertinger.jl
index 20dabb5..02ea9c4 100644
--- a/src/nature/species/wolpertinger.jl
+++ b/src/nature/species/wolpertinger.jl
@@ -19,7 +19,7 @@ end
"""
Wolpertingers are rather stupid creatures, all they do is move around randomly
-and occasionally reproduce by spontaneous parthogenesis...
+and occasionally reproduce by spontaneous parthenogenesis...
"""
@phase Wolpertinger lifephase begin
for i in 1:@rand(1:self.maxspeed)
@@ -27,11 +27,10 @@ and occasionally reproduce by spontaneous parthogenesis...
#walk!(animal, direction, model; ifempty=false)
end
- #FIXME need to fix countanimals() and reproduce() first
- # if @rand() < self.fecundity &&
- # @countanimals(species="Wolpertinger") < self.crowding
- # @reproduce()
- # end
+ if @rand() < self.fecundity &&
+ @countanimals(species="Wolpertinger") < self.crowding
+ @reproduce()
+ end
@kill self.mortality
end
@@ -48,6 +47,7 @@ end
Population densities of the endangered Wolpertinger are down to 1 animal per 10km².
"""
@populate Wolpertinger begin
+ asexual = true
phase = lifephase
popdensity = 100000 #XXX use Unitful.jl for conversion?
end
diff --git a/src/world/landscape.jl b/src/world/landscape.jl
index 9beb16d..bd9af0f 100644
--- a/src/world/landscape.jl
+++ b/src/world/landscape.jl
@@ -9,6 +9,7 @@
"The types of landscape event that can be simulated"
@enum EventType tillage sowing fertiliser pesticide harvesting
+#XXX rename to Management or similar?
"""
Pixel
@@ -21,7 +22,7 @@ mutable struct Pixel
landcover::LandCover
fieldid::Union{Missing,Int64}
events::Vector{EventType}
- #TODO add list of animal IDs
+ animals::Vector{Int64}
end
"""
@@ -60,7 +61,7 @@ function initlandscape(landcovermap::String, farmfieldsmap::String)
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}())
+ landscape[x,y] = Pixel(lcv, ff, Vector{Symbol}(), [])
end
end
return landscape
--
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