Refactor AmeriFlux CF coverage checks into reusable helper

modules/data.atmosphere/R/Ameriflux_met_ensemble.R

@@ -178,57 +178,14 @@ AmeriFlux_met_ensemble <- function(site_id,
         overwrite = overwrite
       )
 
-    # ERA5 fallback 
-    if (verbose) PEcAn.logger::logger.info("Checking data coverage for ERA5 fallback")
-    # check coverage of radiation variables (PAR and Rg) needed for metgapfill
-    nc <- ncdf4::nc_open(cf_results$file)
-    time_dim <- ncdf4::ncvar_get(nc, "time")
-    n_total <- length(time_dim)
-    # check shortwave radiation(Rg) coverage
-    has_rg <- "surface_downwelling_shortwave_flux_in_air" %in% names(nc$var)
-    rg_coverage <- 0
-    if (has_rg) {
-      rg_data <- ncdf4::ncvar_get(nc, "surface_downwelling_shortwave_flux_in_air")
-      rg_coverage <- sum(!is.na(rg_data)) / n_total
-    }
-    # check PAR coverage
-    has_par <- "surface_downwelling_photosynthetic_photon_flux_in_air" %in% names(nc$var)
-    par_coverage <- 0
-    if (has_par) {
-      par_data <- ncdf4::ncvar_get(nc, "surface_downwelling_photosynthetic_photon_flux_in_air")
-      par_coverage <- sum(!is.na(par_data)) / n_total
-    }
-    # check soil moisture coverage since this is not filled by metgapfill
-    has_swc <- "volume_fraction_of_condensed_water_in_soil" %in% names(nc$var)
-    swc_coverage <- 0
-    if (has_swc) {
-      swc_data <- ncdf4::ncvar_get(nc, "volume_fraction_of_condensed_water_in_soil")
-      swc_coverage <- sum(!is.na(swc_data)) / n_total
-    }
-    ncdf4::nc_close(nc)
-
-    if(verbose) {
-      PEcAn.logger::logger.info(paste("Shortwave radiation (Rg) coverage:", round(rg_coverage * 100, 1), "%"))
-      PEcAn.logger::logger.info(paste("PAR coverage:", round(par_coverage * 100, 1), "%"))
-      PEcAn.logger::logger.info(paste("Soil moisture coverage:", round(swc_coverage * 100, 1), "%"))
-    }
-
-    fill_vars <- c()
-    # if BOTH PAR and Rg have insufficient coverage
-    if ((!has_rg || rg_coverage < threshold) && 
-        (!has_par || par_coverage < threshold)) {
-      fill_vars <- c(fill_vars, "surface_solar_radiation_downwards")
-      if(verbose) {
-        PEcAn.logger::logger.info("Adding shortwave radiation to ERA5 fallback (insufficient PAR and Rg coverage)")
-      }
-    }
-    # if variable exists but has ANY missing values
-    if (has_swc && swc_coverage < 1.0) {
-      fill_vars <- c(fill_vars, "volumetric_soil_water_layer_1")
-      if(verbose) {
-        PEcAn.logger::logger.info("Adding soil moisture to ERA5 fallback (missing data detected)")
-      }
-    }
+    coverage_results <- check_met_coverage_for_fallback(
+      cf_file = cf_results$file,
+      threshold = threshold,
+      verbose = verbose
+    )
+
+    fill_vars <- coverage_results$fill_vars
+
     if (length(fill_vars) > 0) {
       start_year <- lubridate::year(as.Date(start_date))
       end_year <- lubridate::year(as.Date(end_date))

modules/data.atmosphere/R/check_met_coverage_for_fallback.R

@@ -0,0 +1,80 @@
+#' Check AmeriFlux CF coverage for ERA5 fallback
+#'
+#' Determines whether radiation and/or soil moisture require ERA5 fallback
+#' based on variable presence and data coverage.
+#'
+#' @param cf_file character. Path to CF-compliant NetCDF file
+#' @param threshold numeric. Coverage threshold (0–1) for radiation fallback
+#' @param verbose logical. Emit logger messages
+#'
+#' @return list with:
+#' \itemize{
+#'   \item fill_vars: ERA5 variables to request
+#'   \item coverage: named list of coverage fractions
+#' }
+#'
+#' @noRd
+check_met_coverage_for_fallback <- function(cf_file,
+                                            threshold = 0.5,
+                                            verbose = FALSE) {
+
+  if (verbose) {
+    PEcAn.logger::logger.info("Checking data coverage for ERA5 fallback")
+  }
+
+  nc <- ncdf4::nc_open(cf_file)
+  on.exit(ncdf4::nc_close(nc), add = TRUE)
+
+  time_vals <- ncdf4::ncvar_get(nc, "time")
+  n_total <- length(time_vals)
+
+  # ---- Radiation (Rg)
+  has_rg <- "surface_downwelling_shortwave_flux_in_air" %in% names(nc$var)
+  rg_coverage <- 0
+  if (has_rg) {
+    rg_data <- ncdf4::ncvar_get(nc, "surface_downwelling_shortwave_flux_in_air")
+    rg_coverage <- sum(!is.na(rg_data)) / n_total
+  }
+
+  # ---- PAR
+  has_par <- "surface_downwelling_photosynthetic_photon_flux_in_air" %in% names(nc$var)
+  par_coverage <- 0
+  if (has_par) {
+    par_data <- ncdf4::ncvar_get(nc, "surface_downwelling_photosynthetic_photon_flux_in_air")
+    par_coverage <- sum(!is.na(par_data)) / n_total
+  }
+
+  # ---- Soil moisture
+  has_swc <- "volume_fraction_of_condensed_water_in_soil" %in% names(nc$var)
+  swc_coverage <- 0
+  if (has_swc) {
+    swc_data <- ncdf4::ncvar_get(nc, "volume_fraction_of_condensed_water_in_soil")
+    swc_coverage <- sum(!is.na(swc_data)) / n_total
+  }
+
+  if (verbose) {
+    PEcAn.logger::logger.info(paste("Rg coverage:", round(rg_coverage * 100, 1), "%"))
+    PEcAn.logger::logger.info(paste("PAR coverage:", round(par_coverage * 100, 1), "%"))
+    PEcAn.logger::logger.info(paste("Soil moisture coverage:", round(swc_coverage * 100, 1), "%"))
+  }
+
+  fill_vars <- character(0)
+
+  if ((!has_rg || rg_coverage < threshold) &&
+      (!has_par || par_coverage < threshold)) {
+    fill_vars <- c(fill_vars, "surface_solar_radiation_downwards")
+  }
+
+  if (has_swc && swc_coverage < 1.0) {
+    fill_vars <- c(fill_vars, "volumetric_soil_water_layer_1")
+  }
+
+  list(
+    fill_vars = fill_vars,
+    coverage = list(
+      rg = rg_coverage,
+      par = par_coverage,
+      swc = swc_coverage
+    )
+  )
+}