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Merge pull request #3161 from DongchenZ/develop
Update SDA_runner script.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,39 +1,93 @@ | ||
| #query_pfts | ||
| setwd("/projectnb/dietzelab/dongchen/All_NEON_SDA") | ||
| settings <- PEcAn.settings::read.settings("test_NEON2.xml") | ||
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| #prepare obs | ||
| load("Obs_2012_2021/obs_cov.Rdata") | ||
| load("Obs_2012_2021/obs_mean.Rdata") | ||
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| library(dplyr) | ||
| library(xts) | ||
| library(PEcAn.all) | ||
| library(purrr) | ||
| library(furrr) | ||
| library(lubridate) | ||
| library(nimble) | ||
| library(ncdf4) | ||
| library(PEcAnAssimSequential) | ||
| library(dplyr) | ||
| library(sp) | ||
| library(raster) | ||
| library(zoo) | ||
| library(ggplot2) | ||
| library(mnormt) | ||
| library(sjmisc) | ||
| library(stringr) | ||
| library(doParallel) | ||
| library(doSNOW) | ||
| library(Kendall) | ||
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| setwd("/projectnb/dietzelab/dongchen/All_NEON_SDA/NEON42/SDA") | ||
| settings_dir <- "/projectnb/dietzelab/dongchen/All_NEON_SDA/NEON42/IC/pecan.xml" | ||
| settings <- PEcAn.settings::read.settings(settings_dir) | ||
| #prepare samples | ||
| get.parameter.samples(settings, ens.sample.method = settings$ensemble$samplingspace$parameters$method) | ||
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| # PEcAn.uncertainty::get.parameter.samples(settings, ens.sample.method = settings$ensemble$samplingspace$parameters$method) | ||
| #prepare settings | ||
| new.settings <- PEcAn.settings::prepare.settings(settings) | ||
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| #debug on sda.enkf_Multisite.R | ||
| settings <- new.settings | ||
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| #run sda main function | ||
| sda.enkf.multisite(settings, | ||
| obs.mean, | ||
| obs.cov, | ||
| Q = NULL, | ||
| restart = FALSE, | ||
| forceRun = TRUE, | ||
| keepNC = TRUE, | ||
| control=list(trace = TRUE, | ||
| FF = FALSE, | ||
| interactivePlot = FALSE, | ||
| TimeseriesPlot = FALSE, | ||
| BiasPlot = FALSE, | ||
| plot.title = NULL, | ||
| facet.plots = FALSE, | ||
| debug = FALSE, | ||
| pause = FALSE, | ||
| Profiling = FALSE, | ||
| OutlierDetection=FALSE)) | ||
| settings <- PEcAn.settings::prepare.settings(settings) | ||
| All_obs_prep <- settings$state.data.assimilation$Obs_Prep | ||
| folder_prefix <- c("AGB", "LAI", "SMP", "SoilC") | ||
| comb <- combn(4, 3) | ||
| for (i in 1:4) { | ||
| settings$state.data.assimilation$Obs_Prep <- All_obs_prep[c(comb[,i], 5:8)] | ||
| folder_name <- paste0(folder_prefix[comb[,i]], collapse = '_') | ||
| #prep obs | ||
| obs <- PEcAnAssimSequential::SDA_OBS_Assembler(settings = settings) | ||
| #prepare obs | ||
| load("/projectnb/dietzelab/dongchen/All_NEON_SDA/test_OBS/Rdata/obs.mean.Rdata") | ||
| load("/projectnb/dietzelab/dongchen/All_NEON_SDA/test_OBS/Rdata/obs.cov.Rdata") | ||
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| for (i in 1:length(obs.mean)) { | ||
| if(is.null(obs.mean[[i]][[1]])){ | ||
| next | ||
| } | ||
| for (j in 1:length(obs.mean[[i]])) { | ||
| obs.mean[[i]][[j]][which(obs.mean[[i]][[j]]==0)] <- 0.01 | ||
| if(length(obs.cov[[i]][[j]]) > 1){ | ||
| diag(obs.cov[[i]][[j]])[which(diag(obs.cov[[i]][[j]]==0))] <- 1 | ||
| }else{ | ||
| if(obs.cov[[i]][[j]] == 0){ | ||
| obs.cov[[i]][[j]] <- 1 | ||
| } | ||
| } | ||
| } | ||
| } | ||
| load("/projectnb/dietzelab/dongchen/All_NEON_SDA/NEON42/SDA_ALL/enkf.Rdata") | ||
| PEcAn.utils::sendmail("[email protected]", "[email protected]", "SDA progress report", paste("Started working on", folder_name)) | ||
| if(is.character(try(PEcAnAssimSequential::sda.enkf.multisite(settings = settings, | ||
| obs.mean = obs.mean, | ||
| obs.cov = obs.cov, | ||
| Q = NULL, | ||
| restart = FALSE, | ||
| forceRun = TRUE, | ||
| keepNC = TRUE, | ||
| pre_enkf_params = enkf.params, | ||
| control=list(trace = TRUE, | ||
| FF = FALSE, | ||
| interactivePlot = FALSE, | ||
| TimeseriesPlot = F, | ||
| BiasPlot = FALSE, | ||
| plot.title = NULL, | ||
| facet.plots = FALSE, | ||
| debug = FALSE, | ||
| pause = FALSE, | ||
| Profiling = FALSE, | ||
| OutlierDetection=FALSE)), silent = T))){ | ||
| PEcAn.utils::sendmail("[email protected]", "[email protected]", "SDA running error", "Error") | ||
| break | ||
| }else{ | ||
| PEcAn.utils::sendmail("[email protected]", "[email protected]", "SDA progress report", paste0(folder_name, " has been completed!")) | ||
| } | ||
| file.rename('/projectnb/dietzelab/dongchen/All_NEON_SDA/NEON42/SDA', | ||
| file.path('/projectnb/dietzelab/dongchen/All_NEON_SDA/NEON42', | ||
| paste0("SDA_", folder_name))) | ||
| dir.create('/projectnb/dietzelab/dongchen/All_NEON_SDA/NEON42/SDA') | ||
| dir.create('/projectnb/dietzelab/dongchen/All_NEON_SDA/NEON42/SDA/out') | ||
| dir.create('/projectnb/dietzelab/dongchen/All_NEON_SDA/NEON42/SDA/run') | ||
| file.copy(file.path('/projectnb/dietzelab/dongchen/All_NEON_SDA/NEON42', | ||
| paste0("SDA_", folder_name), | ||
| "samples.Rdata"), | ||
| file.path('/projectnb/dietzelab/dongchen/All_NEON_SDA/NEON42/SDA', | ||
| "samples.Rdata")) | ||
| } |