From 49f84fc04d58ccf4dea843d26990a7754cf0d722 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Thu, 3 Aug 2023 20:56:00 +0200
Subject: [PATCH] Wrote code to read in crop data files
---
src/crop/crops.jl | 158 ++++++++++++++++++++++++++------------------
src/parameters.toml | 6 +-
2 files changed, 99 insertions(+), 65 deletions(-)
diff --git a/src/crop/crops.jl b/src/crop/crops.jl
index 036cb1f..7f51beb 100644
--- a/src/crop/crops.jl
+++ b/src/crop/crops.jl
@@ -3,85 +3,117 @@
### This file is responsible for managing the crop growth modules.
###
-@enum GrowthPhase janfirst sow marchfirst harvest1 harvest2 vegphase
+#TODO write tests for input functions
+#TODO write actual growth function
"""
- CropType
+ GrowthPhase
-The type struct for all crops. Currently follows the crop
-growth model as implemented in ALMaSS.
+ALMaSS crop growth curves are split into five phases, triggered by
+seasonal dates or agricultural events.
"""
-@kwdef struct CropType
- name::String
- sowdate::Date
- harvestdate::Date
- mingrowthtemp::Float64
- inflectionpoints::Dict{GrowthPhase,Vector{Float64}}
- slopes::Dict{GrowthPhase,Vector{Float64}}
- #issowable::Union{Function,Bool}=true
+@enum GrowthPhase janfirst sow marchfirst harvest1 harvest2
+
+"""
+ CropCurveParams
+
+The values in this struct define one crop growth curve.
+"""
+struct CropCurveParams
+ 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
-let croptypes = Dict{String,CropType}()
- global function registercrop(ct::CropType)
- croptypes[ct.name] = ct
- end
+"""
+ CropType
- global function getcrop(name::String)
- croptypes[name]
- end
+The type struct for all crops. Currently follows the crop growth model as
+implemented in ALMaSS.
+"""
+struct CropType
+ 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
"""
- @dday(datestring)
+ Base.tryparse(type, str)
-A utility macro to make it quicker to create dates in the
-format "21 August".
+Extend `tryparse` to allow parsing GrowthPhase values.
+(Needed to read in the CSV parameter file.)
"""
-macro dday(date::String)
- :(Date($(date), dateformat"d U"))
+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
-let croplist = Dict{String,CropType}()
-
- global function newcrop(;kwargs...)
- crop = CropType(;kwargs...)
- croplist[crop.name] = crop
- end
+"""
+ buildgrowthcurve(data)
- global function cropdefinition(name)
- croplist[name]
+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
-#
-# XXX It would be nicer to be able to define crops with a macro
-# (like @species), but since macros are so tricky to get right,
-# I'll leave that for later.
-#
-# """
-# @crop
-#
-# A macro to create and register a new crop type. Pass a list
-# of keyword arguments to instantiate each field of the
-# [`CropType`](@ref) struct.
-# """
-# macro crop(;kwargs...) # macros don't take kwargs
-# quote
-# registercrop(CropType($(esc(kwargs))))
-# end
-# end
-#
-# @crop "winter wheat" begin
-# minsowdate = @dday("1 November")
-# maxsowdate = @dday("31 November")
-# growthparameter = 1.0
-# issowable = true
-# end
-
-newcrop(name="winter wheat",
- sowdate = @dday("1 November"),
- harvestdate = @dday("1 July"),
- mingrowthtemp = 5.0,
- growthparameter = 1.0,
- issowable = true)
+"""
+ 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, cropgrowthfile::String)
+ @debug "Reading crop parameters"
+ cropdata = CSV.File(generalcropfile, missingstring="NA", dateformat="d U",
+ types=[String,Date,Date,Date,Date,Float64])
+ growthdata = CSV.File(cropgrowthfile, missingstring="NA",
+ types=[Int,String,String,GrowthPhase,String,
+ Float64,Float64,Float64,Float64])
+ croptypes = Vector{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"))
+ append!(croptypes, [CropType(crop.name, crop.minsowdate, crop.maxsowdate,
+ crop.minharvestdate, crop.maxharvestdate,
+ crop.mingrowthtemp, highnuts, lownuts)])
+ end
+ croptypes
+end
diff --git a/src/parameters.toml b/src/parameters.toml
index 172575d..6b26cac 100644
--- a/src/parameters.toml
+++ b/src/parameters.toml
@@ -30,8 +30,10 @@ farmmodel = "FieldManager" # which version of the farm model to use (not yet imp
targetspecies = ["Wolpertinger", "Wyvern"] # list of target species to simulate
popoutfreq = "daily" # output frequency population-level data, daily/monthly/yearly/end/never
indoutfreq = "end" # output frequency individual-level data, daily/monthly/yearly/end/never
-insectmodel = ["season", "habitat", "pesticides"] # which factors affect insect growth ("weather" is not yet implemented)
+insectmodel = ["season", "habitat", "pesticides", "weather"] # factors affecting insect growth
[crop]
-cropmodel = "linear" # crop growth model to use, "linear" or "aquacrop" (not yet implemented)
+cropmodel = "almass" # crop growth model to use, "almass" or "aquacrop"
+cropfile = "data/crop_data_general.csv" # file with general crop parameters
+cropgrowthfile = "data/almass_crop_growth_curves.csv" # file with crop growth parameters
--
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