# Utils for ci extraction
date_list <- function(end_date, offset){
  offset <- as.numeric(offset) - 1
  end_date <- as.Date(end_date)
  start_date <- end_date - lubridate::days(offset)
  
  week <- week(start_date)
  year <- year(start_date)
  days_filter <- seq(from = start_date, to = end_date, by = "day")
  
  return(list("week" = week, "year" = year, "days_filter" = days_filter))
}

create_mask_and_crop <- function(file, field_boundaries, merged_final_dir) {
  message("starting ", file)
  loaded_raster <- rast(file)
  names(loaded_raster) <- c("Red", "Green", "Blue", "NIR")
  message("raster loaded")
  
  CI <- loaded_raster$NIR / loaded_raster$Green - 1
  
  loaded_raster$CI <- CI
  message("CI calculated")
  loaded_raster <- terra::crop(loaded_raster, field_boundaries, mask = TRUE) #%>% CI_func()
  
  loaded_raster[loaded_raster == 0] <- NA
  new_file <- here(merged_final_dir, paste0(tools::file_path_sans_ext(basename(file)), ".tif"))
  writeRaster(loaded_raster, new_file, overwrite = TRUE)
  
  vrt_file <- here(daily_vrt, paste0(tools::file_path_sans_ext(basename(file)), ".vrt"))
  terra::vrt(new_file, vrt_file, overwrite = TRUE)
  
  return(loaded_raster)
}

date_extract <- function(file_path) {
  str_extract(file_path, "\\d{4}-\\d{2}-\\d{2}")
}

extract_rasters_daily <- function(file, field_geojson, quadrants = TRUE, save_dir) {
  field_geojson <- sf::st_as_sf(field_geojson)
  x <- rast(file[1])
  date <- date_extract(file)
  
  pivot_stats <- cbind(field_geojson, mean_CI = round(exactextractr::exact_extract(x$CI, field_geojson, fun = "mean"), 2)) %>%
    st_drop_geometry() %>% rename("{date}" := mean_CI)
  
  save_suffix <- if (quadrants){"quadrant"} else {"whole_field"}
  save_path <- here(save_dir, paste0("extracted_", date, "_", save_suffix, ".rds"))
  
  saveRDS(pivot_stats, save_path)
}