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SWATMINT0.2.R
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# Add NSE and Observed for cases with observed flow
#
if (!require("pacman")) install.packages("pacman")
pacman::p_load(SWATmodel,RSQLite,argparse,stringi,stringr,rgdal,ggplot2,rgeos,rnoaa,moments,sf,readr,tools,
diffobj,png,grid,gridExtra,ncdfgeom,purrr,raster)
source("./MINTSWATcalib.R")
source("./SWAToutput.R")
source("https://r-forge.r-project.org/scm/viewvc.php/*checkout*/pkg/EcoHydRology/R/get_grdc_gage.R?root=ecohydrology")
source("https://raw.githubusercontent.com/cran/sampSurf/master/R/spCircle.R")
setwd("~")
basedir=getwd()
outbasedir=paste0(basedir,"/MINTSWATmodel_output")
inbasedir=paste0(basedir,"/MINTSWATmodel_input")
dir.create(outbasedir)
dir.create(inbasedir)
setwd(inbasedir)
Sys.setenv(R_USER_CACHE_DIR=inbasedir)
# If a parameter change scenario, we use --swatscen
parser <- ArgumentParser()
parser$add_argument("-p","--swatparam", action="append", metavar="param:val[:regex_file]",
help = "Add in SWAT parameters that need to be modified")
parser$add_argument("-s","--swatscen", metavar="calib01",
help = "Scenario folder name, 'calib' for calibration, 'scen' for scenario")
parser$add_argument("-d","--swatiniturl", metavar="url to ArcSWAT init or GRDC format dataset",
help = "Scenario folder name")
# Examples:
# geojson example
exampleargs=c("-d https://data.mint.isi.edu/files/files/geojson/guder.json")
# GRDC Calibration example
exampleargs=c("-s calib01","-p deiter:10","-p rch:3","-d https://portal.grdc.bafg.de/grdcdownload/external/7ce24ffd-3c99-407f-84e8-bd4a99417c06/2022-07-08_00-05.zip")
# ArcSWAT example
#exampleargs=c("-d https://raw.githubusercontent.com/vtdrfuka/MINTSWATmodel/main/tb_s2.zip")
#
args <- parser$parse_args()
if(is.null(args$swatiniturl)){
args <- parser$parse_args(c(exampleargs))
}
print(paste0("This run's args: ",args))
dlfilename=basename(args$swatiniturl)
dlurl=trimws(args$swatiniturl)
paramloc=grep("deiter",args$swatparam)
if(length(paramloc)>0){
deiter=as.numeric(strsplit(args$swatparam[paramloc],split = ":")[[1]][2])
}else{
deiter=200
}
paramloc=grep("rch",args$swatparam)
if(length(paramloc)>0){
rch=as.numeric(strsplit(args$swatparam[paramloc],split = ":")[[1]][2])
}else{
rch=3
}
# *** download
dlfiletype=file_ext(dlfilename)
if(dlfiletype=="json"){
print("geojson single run")
download.file(dlurl,paste0("data.",dlfiletype))
swatrun="basic"
} else {
print("different")
dlfiletype="zip"
download.file(dlurl,paste0("data.",dlfiletype))
if(grepl("Q_Day",unzip("data.zip", list=T)[1])){
swatrun="GRDC"
}
}
if(swatrun=="GRDC"){
print("GRDC Format Uninitialized")
dir.create("GRDCstns")
setwd("GRDCstns")
currentdir=getwd()
unzip("../data.zip")
tryCatch({
stationbasins_shp=readOGR("stationbasins.geojson")
}, error=function(e){cat("ERROR :",conditionMessage(e), "\n")})
for(grdcfilename in list.files(pattern = "_Q_Day")){
print(grdcfilename)
setwd(currentdir)
flowgage=get_grdc_gage(lfilename = grdcfilename)
if(is.null(flowgage)){print("Not enough Gage Info");next()}
basinid=strsplit(grdcfilename,"_")[[1]][1]
basinname=basinid
if(is.character(flowgage)){next()}
GRDC_mindate=min(flowgage$flowdata$mdate)
GRDC_maxdate=max(flowgage$flowdata$mdate)
# Depends on: rnoaa, lubridate::month,ggplot2
declat=flowgage$declat
declon=flowgage$declon
proj4_ll = "+proj=longlat"
proj4_utm = paste0("+proj=utm +zone=", trunc((180+declon)/6+1), " +datum=WGS84 +units=m +no_defs")
crs_ll=CRS(proj4_ll)
crs_utm=CRS(proj4_utm)
basin_area=flowgage$area
# Building 3 basin Feature for NetCDF based on basin shape if available
# or a virtual circular basins on area and outlet.
if(exists("stationbasins_shp")&&any(stationbasins_shp@data$grdc_no==basinid)){
subs1_shp=subset(stationbasins_shp,grdc_no==basinid)
proj4_utm = paste0("+proj=utm +zone=", trunc((180+gCentroid(subs1_shp)$x)/6+1), " +datum=WGS84 +units=m +no_defs")
proj4_ll = "+proj=longlat"
crs_ll=CRS(proj4_ll)
crs_utm=CRS(proj4_utm)
subs1_shp_utm=spTransform(subs1_shp,crs_utm)
initsizeguess=-sqrt(gArea(subs1_shp_utm))/6
f <- function (x,a) {(gArea(subs1_shp_utm)*a-
gArea(gBuffer(subs1_shp_utm,width=x)))^2}
hru3scale <- optimize(f, c(initsizeguess, 0), tol = 0.0001,a=1/3)$minimum
hru2scale <- optimize(f, c(initsizeguess, 0), tol = 0.0001,a=2/3)$minimum
hru3_utm=gBuffer(subs1_shp_utm,width=hru3scale)
hru2_utm=gBuffer(subs1_shp_utm,width=hru2scale)
gArea(hru2_utm)/gArea(subs1_shp_utm)
gArea(hru3_utm)/gArea(subs1_shp_utm)
hru1_utm=gDifference(subs1_shp_utm,hru2_utm)
hru2_utm=gDifference(hru2_utm,hru3_utm)
combined_hrus=list(c(hru1_utm,hru2_utm,hru3_utm))
list(combined_hrus, makeUniqueIDs = T) %>%
flatten() %>%
do.call(rbind, .)
subs1_shp_utm <- do.call(bind, combined_hrus)
subs1_shp_ll=spTransform(subs1_shp_utm,crs_ll)
} else{
latlon <- cbind(declon,declat)
gagepoint_ll <- SpatialPoints(latlon)
proj4string(gagepoint_ll)=proj4_ll
gagepoint_utm=spTransform(gagepoint_ll,crs_utm)
hru1_utm=spCircle(sqrt(basin_area*1000^2/pi), spUnits = crs_utm,
centerPoint = c(x = gagepoint_utm@coords[1], y = gagepoint_utm@coords[2]),
nptsPerimeter = 30,spID = 1)$spCircle
hru2_utm=spCircle(sqrt(basin_area*2/3*1000^2/pi), spUnits = crs_utm,
centerPoint = c(x = gagepoint_utm@coords[1], y = gagepoint_utm@coords[2]),
nptsPerimeter = 30,spID = 1 )$spCircle
hru3_utm=spCircle(sqrt(basin_area/3*1000^2/pi), spUnits = crs_utm,
centerPoint = c(x = gagepoint_utm@coords[1], y = gagepoint_utm@coords[2]),
nptsPerimeter = 30,spID = 1 )$spCircle
hru1_utm=gDifference(hru1_utm,hru2_utm)
hru2_utm=gDifference(hru2_utm,hru3_utm)
combined_hrus=list(c(hru1_utm,hru2_utm,hru3_utm))
list(combined_hrus, makeUniqueIDs = T) %>%
flatten() %>%
do.call(rbind, .)
subs1_shp_utm <- do.call(bind, combined_hrus)
proj4string(subs1_shp_utm)=proj4_utm
subs1_shp_ll=spTransform(subs1_shp_utm,crs_ll)
}
if(exists("stationbasins_shp")&&length(try(which(stationbasins_shp$grdc_no==as.numeric(flowgage$id))))>0){
basinloc=which(stationbasins_shp$grdc_no==as.numeric(flowgage$id))
basin=stationbasins_shp[basinloc,]
basinutm=spTransform(basin,CRS(proj4_utm))
wxlat=gCentroid(basin)$y
wxlon=gCentroid(basin)$x
} else {
wxlat=declat
wxlon=declon
}
stradius=20;minstns=30
station_data=ghcnd_stations()
while(stradius<2000){
print(paste0("Looking for WX Stations within: ",stradius,"km"))
junk=meteo_distance(
station_data=station_data,
lat=wxlat, long=wxlon,
units = "deg",
radius = stradius,
limit = NULL
)
if(length(unique(junk$id))>minstns){break()}
stradius=stradius*1.2
}
basinoutdir=paste0(outbasedir,"/",basinid);dir.create(basinoutdir)
dir.create(basinoutdir,recursive = T)
setwd(basinoutdir)
WXData=FillMissWX(wxlat,wxlon,date_min = "1979-01-01",date_max = "2022-01-01", StnRadius = stradius,method = "IDW",alfa = 2)
GRDC_mindate=min(WXData$date)
GRDC_maxdate=max(WXData$date)
AllDays=data.frame(date=seq(GRDC_mindate, by = "day", length.out = GRDC_maxdate-GRDC_mindate))
WXData=merge(AllDays,WXData,all=T)
WXData$PRECIP=WXData$P
WXData$PRECIP[is.na(WXData$PRECIP)]=-99
WXData$TMX=WXData$MaxTemp
WXData$TMX[is.na(WXData$TMX)]=-99
WXData$TMN=WXData$MinTemp
WXData$TMN[is.na(WXData$TMN)]=-99
WXData$DATE=WXData$date
build_swat_basic(dirname=basinoutdir, iyr=min(year(WXData$DATE),na.rm=T), ###***basin name!
nbyr=(max(year(WXData$DATE),na.rm=T)-min(year(WXData$DATE),na.rm=T)),
wsarea=basin_area, elev=mean(WXData$prcpElevation,na.rm=T),
declat=declat, declon=declon, hist_wx=WXData)
build_wgn_file(metdata_df=WXData,declat=declat,declon=declon)
if(!is.null(args$swatscen) &&
substr(trimws(args$swatscen),1,5)=="calib"){
MINTSWATcalib()
}
runSWAT2012()
SWAToutput()
}
}
if(dlfiletype=="json"){
basinname=strsplit(basename(args$swatiniturl),split = "\\.")[[1]][1]
basinoutdir=paste0(outbasedir,"/",basinname);dir.create(basinoutdir)
basin=readOGR("data.json")
declat=gCentroid(basin)$y
declon=gCentroid(basin)$x
proj4_utm = paste0("+proj=utm +zone=", trunc((180+declon)/6+1), " +datum=WGS84 +units=m +no_defs")
proj4_ll = "+proj=longlat"
crs_ll=CRS(proj4_ll)
crs_utm=CRS(proj4_utm)
basinutm=spTransform(basin,CRS(proj4_utm))
basin_area=gArea(basinutm)/10^6
# Replace with conversion of geojson
latlon <- cbind(declon,declat)
gagepoint_ll <- SpatialPoints(latlon)
proj4string(gagepoint_ll)=proj4_ll
gagepoint_utm=spTransform(gagepoint_ll,crs_utm)
hru1_utm=spCircle(sqrt(basin_area*1000^2/pi), spUnits = crs_utm,
centerPoint = c(x = gagepoint_utm@coords[1], y = gagepoint_utm@coords[2]),
nptsPerimeter = 30,spID = 1)$spCircle
hru2_utm=spCircle(sqrt(basin_area*2/3*1000^2/pi), spUnits = crs_utm,
centerPoint = c(x = gagepoint_utm@coords[1], y = gagepoint_utm@coords[2]),
nptsPerimeter = 30,spID = 1 )$spCircle
hru3_utm=spCircle(sqrt(basin_area/3*1000^2/pi), spUnits = crs_utm,
centerPoint = c(x = gagepoint_utm@coords[1], y = gagepoint_utm@coords[2]),
nptsPerimeter = 30,spID = 1 )$spCircle
hru1_utm=gDifference(hru1_utm,hru2_utm)
hru2_utm=gDifference(hru2_utm,hru3_utm)
combined_hrus=list(c(hru1_utm,hru2_utm,hru3_utm))
list(combined_hrus, makeUniqueIDs = T) %>%
flatten() %>%
do.call(rbind, .)
subs1_shp_utm <- do.call(bind, combined_hrus)
proj4string(subs1_shp_utm)=proj4_utm
subs1_shp_ll=spTransform(subs1_shp_utm,crs_ll)
# End replace with GeoJSON conversion
stradius=20;minstns=30
station_data=ghcnd_stations()
while(stradius<2000){
print(stradius)
junk=meteo_distance(
station_data=station_data,
lat=gCentroid(basin)$y, long=gCentroid(basin)$x,
units = "deg",
radius = stradius,
limit = NULL
)
if(length(unique(junk$id))>minstns){break()}
stradius=stradius*1.2
}
setwd(basinoutdir)
WXData=FillMissWX(gCentroid(basin)$y,gCentroid(basin)$x,date_min = "1979-01-01",date_max = "2022-01-01", StnRadius = stradius,method = "IDW",alfa = 2)
GRDC_mindate=min(WXData$date)
GRDC_maxdate=max(WXData$date)
AllDays=data.frame(date=seq(GRDC_mindate, by = "day", length.out = GRDC_maxdate-GRDC_mindate))
WXData=merge(AllDays,WXData,all=T)
WXData$PRECIP=WXData$P
WXData$PRECIP[is.na(WXData$PRECIP)]=-99
WXData$TMX=WXData$MaxTemp
WXData$TMX[is.na(WXData$TMX)]=-99
WXData$TMN=WXData$MinTemp
WXData$TMN[is.na(WXData$TMN)]=-99
WXData$DATE=WXData$date
build_swat_basic(dirname=basinoutdir, iyr=min(year(WXData$DATE),na.rm=T),
nbyr=(max(year(WXData$DATE),na.rm=T)-min(year(WXData$DATE),na.rm=T)),
wsarea=basin_area, elev=mean(WXData$prcpElevation,na.rm=T),
declat=declat, declon=declon, hist_wx=WXData)
build_wgn_file(metdata_df=WXData,declat=declat,declon=declon)
runSWAT2012()
SWAToutput()
}
setwd(outbasedir)
unlink(list.files(pattern = "output.*",recursive = TRUE))
unlink(list.files(pattern = "*.out",recursive = TRUE))
unlink(list.files(pattern = "pcp1.pcp",recursive = TRUE))
unlink(list.files(pattern = "tmp1.tmp",recursive = TRUE))
quit()