Something went wrong on our end
-
Marco Matthies authoredMarco Matthies authored
Code owners
Assign users and groups as approvers for specific file changes. Learn more.
almass.jl 10.51 KiB
### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe.
###
### This file is responsible for managing the crop growth modules.
###
#TODO write tests for input functions
module ALMaSS
using Persefone:
AbstractFarmPlot,
EventType,
SimulationModel,
fertiliser,
initfields_fill_with!,
maxtemp,
mintemp
import Persefone: stepagent!
using Dates: Date, month, monthday
using CSV: CSV
"""
GrowthPhase
ALMaSS crop growth curves are split into five phases, triggered by
seasonal dates or agricultural events.
"""
@enum GrowthPhase janfirst sow marchfirst harvest1 harvest2
"""
CropCurveParams
The values in this struct define one crop growth curve.
"""
struct CropCurveParams
#TODO add Unitful
curveID::Int
highnutrients::Bool
GDD::Dict{GrowthPhase,Vector{Float64}}
LAItotal::Dict{GrowthPhase,Vector{Float64}}
LAIgreen::Dict{GrowthPhase,Vector{Float64}}
height::Dict{GrowthPhase,Vector{Float64}}
end
"""
CropType
The type struct for all crops. Currently follows the crop growth model as
implemented in ALMaSS.
"""
struct CropType
#TODO make this into an abstract type and create subtypes for different
# crop submodels (#70)
name::String
minsowdate::Union{Missing,Date}
maxsowdate::Union{Missing,Date}
minharvestdate::Union{Missing,Date}
maxharvestdate::Union{Missing,Date}
mingrowthtemp::Union{Missing,Float64}
highnutrientgrowth::Union{Missing,CropCurveParams}
lownutrientgrowth::Union{Missing,CropCurveParams}
#issowable::Union{Function,Bool}
end
"""
Base.tryparse(type, str)
Extend `tryparse` to allow parsing GrowthPhase values.
(Needed to read in the CSV parameter file.)
"""
function Base.tryparse(type::Type{GrowthPhase}, str::String)
str == "janfirst" ? janfirst :
str == "sow" ? sow :
str == "marchfirst" ? marchfirst :
str == "harvest1" ? harvest1 :
str == "harvest2" ? harvest2 :
nothing
end
"""
buildgrowthcurve(data)
Convert a list of rows from the crop growth data into a CropCurveParams object.
"""
function buildgrowthcurve(data::Vector{CSV.Row})
isempty(data) && return missing
GDD = Dict(janfirst=>Vector{Float64}(), sow=>Vector{Float64}(),
marchfirst=>Vector{Float64}(), harvest1=>Vector{Float64}(),
harvest2=>Vector{Float64}())
LAItotal = Dict(janfirst=>Vector{Float64}(), sow=>Vector{Float64}(),
marchfirst=>Vector{Float64}(), harvest1=>Vector{Float64}(),
harvest2=>Vector{Float64}())
LAIgreen = Dict(janfirst=>Vector{Float64}(), sow=>Vector{Float64}(),
marchfirst=>Vector{Float64}(), harvest1=>Vector{Float64}(),
harvest2=>Vector{Float64}())
height = Dict(janfirst=>Vector{Float64}(), sow=>Vector{Float64}(),
marchfirst=>Vector{Float64}(), harvest1=>Vector{Float64}(),
harvest2=>Vector{Float64}())
for e in data
append!(GDD[e.growth_phase], e.GDD)
append!(LAItotal[e.growth_phase], e.LAI_total)
append!(LAIgreen[e.growth_phase], e.LAI_green)
append!(height[e.growth_phase], e.height)
end
CropCurveParams(data[1].curve_id, data[1].nutrient_status=="high",
GDD, LAItotal, LAIgreen, height)
end
"""
readcropparameters(generalcropfile, cropgrowthfile)
Parse a CSV file containing the required parameter values for each crop
(as produced from the original ALMaSS file by `convert_almass_data.py`).
"""
function readcropparameters(generalcropfile::String, growthfile::String)
@debug "Reading crop parameters"
cropdata = CSV.File(generalcropfile, missingstring="NA", dateformat="d U",
types=[String,Date,Date,Date,Date,Float64])
growthdata = CSV.File(growthfile, missingstring="NA",
types=[Int,String,String,GrowthPhase,String,
Float64,Float64,Float64,Float64])
croptypes = Dict{String,CropType}()
for crop in cropdata
cropgrowthdata = growthdata |> filter(x -> !ismissing(x.crop_name) &&
x.crop_name == crop.name)
highnuts = buildgrowthcurve(cropgrowthdata |>
filter(x -> x.nutrient_status=="high"))
lownuts = buildgrowthcurve(cropgrowthdata |>
filter(x -> x.nutrient_status=="low"))
croptypes[crop.name] = CropType(crop.name, crop.minsowdate, crop.maxsowdate,
crop.minharvestdate, crop.maxharvestdate,
crop.mingrowthtemp, highnuts, lownuts)
end
croptypes
end
#XXX not sure whether it makes sense to have this as an agent type,
# or perhaps better a grid property?
"""
FarmPlot
This represents one field, i.e. a collection of pixels with the same management.
This is the spatial unit with which the crop growth model and the farm model work.
"""
mutable struct FarmPlot <: AbstractFarmPlot
#TODO add Unitful
const id::Int64
pixels::Vector{Tuple{Int64, Int64}}
croptype::ALMaSS.CropType
phase::ALMaSS.GrowthPhase
growingdegreedays::Float64
height::Float64
LAItotal::Float64
LAIgreen::Float64
#biomass::Float64 #XXX I need to figure out how to calculate this
events::Vector{EventType}
end
"""
initfields!(model)
Initialise the model with its farm plots.
"""
function initfields!(model::SimulationModel)
initfields_fill_with!(model) do model, x, y
month(model.date) < 3 ? phase = ALMaSS.janfirst : phase = ALMaSS.marchfirst
FarmPlot(length(model.farmplots) + 1,
[(x,y)],
model.crops["natural grass"],
phase,
0.0, 0.0, 0.0, 0.0, Vector{EventType}())
end
end
"""
stepagent!(farmplot, model)
Update a farm plot by one day.
"""
function stepagent!(farmplot::FarmPlot, model::SimulationModel)
# update growing degree days
# if no crop-specific base temperature is given, default to 5°C
# (https://www.eea.europa.eu/publications/europes-changing-climate-hazards-1/heat-and-cold/heat-and-cold-2014-mean)
basetemp = farmplot.croptype.mingrowthtemp
ismissing(basetemp) && (basetemp = 5.0)
gdd = (maxtemp(model)+mintemp(model))/2 - basetemp
gdd > 0 && (farmplot.growingdegreedays += gdd)
# update the phase on key dates
monthday(model.date) == (1,1) && (farmplot.phase = ALMaSS.janfirst)
monthday(model.date) == (3,1) && (farmplot.phase = ALMaSS.marchfirst)
# update crop growth
growcrop!(farmplot, model)
end
## CROP MANAGEMENT AND GROWTH FUNCTIONS
"""
sow!(cropname, farmplot, model)
Sow the specified crop on this farmplot.
"""
function sow!(cropname::String, farmplot::FarmPlot, model::SimulationModel)
createevent!(model, farmplot.pixels, sowing)
farmplot.croptype = model.crops[cropname]
farmplot.phase = ALMaSS.sow
#XXX test if the crop is sowable?
end
"""
harvest!(farmplot, model)
Harvest the crop on this farmplot.
"""
function harvest!(farmplot::FarmPlot, model::SimulationModel)
createevent!(model, farmplot.pixels, harvesting)
farmplot.phase in [ALMaSS.harvest1, ALMaSS.harvest2] ?
farmplot.phase = ALMaSS.harvest2 :
farmplot.phase = ALMaSS.harvest1
# height & LAI will be automatically adjusted by the growth function
#TODO calculate and return yield
end
#TODO fertilise!()
#TODO spray!()
#TODO till!()
"""
growcrop!(farmplot, model)
Apply the relevant crop growth model to update the plants on this farm plot.
Currently only supports the ALMaSS crop growth model by Topping et al.
"""
function growcrop!(farmplot::FarmPlot, model::SimulationModel)
fertiliser in farmplot.events ?
curve = farmplot.croptype.lownutrientgrowth :
curve = farmplot.croptype.highnutrientgrowth
points = curve.GDD[farmplot.phase]
for p in 1:length(points)
if points[p] == 99999
return # the marker that there is no further growth this phase
elseif points[p] == -1 # the marker to set all variables to specified values
farmplot.height = curve.height[farmplot.phase][p]
farmplot.LAItotal = curve.LAItotal[farmplot.phase][p]
farmplot.LAIgreen = curve.LAIgreen[farmplot.phase][p]
return
else
gdd = farmplot.growingdegreedays
# figure out which is the correct slope value to use for growth
if p == length(points) || gdd < points[p+1]
farmplot.height += curve.height[farmplot.phase][p]
farmplot.LAItotal += curve.LAItotal[farmplot.phase][p]
farmplot.LAIgreen += curve.LAIgreen[farmplot.phase][p]
return
end
#XXX To be precise, we ought to figure out if one or more inflection
# points have been passed between yesterday and today, and calculate the
# growth exactly up to the inflection point with the old slope, and onward
# with the new slope. Not doing so will introduce a small amount of error,
# although I think this is acceptable.
end
end
end
## UTILITY FUNCTIONS
"""
averagefieldsize(model)
Calculate the average field size in hectares for the model landscape.
"""
function averagefieldsize(model::SimulationModel)
conversionfactor = 100 #our pixels are currently 10x10m, so 100 pixels per hectare
sizes::Vector{Float64} = []
for fp in model.farmplots
push!(sizes, size(fp.pixels)[1]/conversionfactor)
end
round(sum(sizes)/size(sizes)[1], digits=2)
end
"""
croptype(model, position)
Return the crop at this position, or nothing if there is no crop here (utility wrapper).
"""
function croptype(pos::Tuple{Int64,Int64}, model::SimulationModel)
ismissing(model.landscape[pos...].fieldid) ? nothing :
model.farmplots[model.landscape[pos...].fieldid].croptype
end
"""
cropname(model, position)
Return the name of the crop at this position, or an empty string if there is no crop here
(utility wrapper).
"""
function cropname(pos::Tuple{Int64,Int64}, model::SimulationModel)
field = model.landscape[pos...].fieldid
ismissing(field) ? "" : model.farmplots[field].croptype.name
end
"""
cropheight(model, position)
Return the height of the crop at this position, or nothing if there is no crop here
(utility wrapper).
"""
function cropheight(pos::Tuple{Int64,Int64}, model::SimulationModel)
ismissing(model.landscape[pos...].fieldid) ? nothing :
model.farmplots[model.landscape[pos...].fieldid].height
end
end # module ALMaSS