Notebooks for AGU 2025 sims

3_rowcrop/01_ERA5_nc_to_clim.R

@@ -0,0 +1,93 @@
+#!/usr/bin/env Rscript
+
+# Converts ERA5 meteorology data from PEcAn's standard netCDF format
+# to Sipnet `clim` driver files.
+
+# This is basically a thin wrapper around `met2model.SIPNET()`.
+# Only the filenames are specific to ERA5 by assuming each file is named
+# "ERA5.<ens_id>.<year>nc" with ens_id between 1 and 10.
+
+## --------- runtime values: change for your system and simulation ---------
+
+options <- list(
+  optparse::make_option("--site_era5_path",
+    default = "data_raw/ERA5_nc",
+    help = paste(
+      "Path to your existing ERA5 data in PEcAn CF format, organized as",
+      "single-site, single-year netcdfs in subdirectories per ensemble member.",
+      "Files should be named",
+      "'<site_era5_path>/ERA5_<siteid>_<ensid>/ERA5.<ensid>.<year>.nc'"
+    )
+  ),
+  optparse::make_option("--site_sipnet_met_path",
+    default = "data/ERA5_SIPNET",
+    help = paste(
+      "Output path:",
+      "single-site, multi-year Sipnet clim files, one per ensemble member.",
+      "Files will be named",
+      "<site_sipnet_met_path>/<siteid>/ERA5.<ensid>.<start>.<end>.clim"
+    )
+  ),
+  optparse::make_option("--site_info_file",
+    default = "site_info.csv",
+    help = "CSV file with one row per location. Only the `id` column is used",
+  ),
+  optparse::make_option("--start_date",
+    default = "2016-01-01",
+    help = "Date to begin clim file",
+  ),
+  optparse::make_option("--end_date",
+    default = "2023-12-31",
+    help = "Date to end clim file",
+  ),
+  optparse::make_option("--n_cores",
+    default = 1L,
+    help = "number of CPUs to use in parallel",
+  ),
+  optparse::make_option("--parallel_strategy",
+    default = "multisession",
+    help = "Strategy for parallel conversion, passed to future::plan()",
+  )
+) |>
+  # Show default values in help message
+  purrr::modify(\(x) {
+    x@help <- paste(x@help, "[default: %default]")
+    x
+  })
+
+args <- optparse::OptionParser(option_list = options) |>
+  optparse::parse_args()
+
+
+# ----------- end system-specific ---------------------------------
+
+
+future::plan(args$parallel_strategy, workers = args$n_cores)
+
+site_info <- read.csv(args$site_info_file)
+site_info$start_date <- args$start_date
+site_info$end_date <- args$end_date
+
+
+file_info <- site_info |>
+  dplyr::rename(site_id = id) |>
+  dplyr::cross_join(data.frame(ens_id = 1:10))
+
+if (!dir.exists(args$site_sipnet_met_path)) {
+  dir.create(args$site_sipnet_met_path, recursive = TRUE)
+}
+furrr::future_pwalk(
+  file_info,
+  function(site_id, start_date, end_date, ens_id, ...) {
+    PEcAn.SIPNET::met2model.SIPNET(
+      in.path = file.path(
+        args$site_era5_path,
+        paste("ERA5", site_id, ens_id, sep = "_")
+      ),
+      start_date = args$start_date,
+      end_date = args$end_date,
+      in.prefix = paste0("ERA5.", ens_id),
+      outfolder = file.path(args$site_sipnet_met_path, site_id)
+    )
+  }
+)