From eb75861de83966f7c09f55b0b97f87cf1cf2af44 Mon Sep 17 00:00:00 2001 From: Emma Mendelsohn Date: Tue, 24 Oct 2023 17:11:27 -0400 Subject: [PATCH] calculate anomalies for NDVI - partial run --- R/calculate_ndvi_anomalies.R | 83 ++++ R/calculate_ndvi_historical_means.R | 6 +- _targets.R | 21 +- _targets/meta/meta | 744 ++++++++++++++-------------- data/ndvi_anomalies/.gitkeep | 0 5 files changed, 474 insertions(+), 380 deletions(-) create mode 100644 R/calculate_ndvi_anomalies.R create mode 100644 data/ndvi_anomalies/.gitkeep diff --git a/R/calculate_ndvi_anomalies.R b/R/calculate_ndvi_anomalies.R new file mode 100644 index 0000000..924408c --- /dev/null +++ b/R/calculate_ndvi_anomalies.R @@ -0,0 +1,83 @@ +#' .. content for \description{} (no empty lines) .. +#' +#' .. content for \details{} .. +#' +#' @title +#' @param ndvi_date_lookup +#' @param ndvi_historical_means +#' @param ndvi_anomalies_directory +#' @param model_dates +#' @param model_dates_selected +#' @param lag_intervals +#' @param overwrite +#' @return +#' @author Emma Mendelsohn +#' @export +calculate_ndvi_anomalies <- function(ndvi_date_lookup, ndvi_historical_means, + ndvi_anomalies_directory, model_dates, + model_dates_selected, lag_intervals, + overwrite = FALSE) { + + # Set filename + date_selected <- model_dates_selected + save_filename <- glue::glue("ndvi_anomaly_{date_selected}.gz.parquet") + message(paste0("Calculating NDVI anomalies for ", date_selected)) + + # Check if file already exists + existing_files <- list.files(ndvi_anomalies_directory) + if(save_filename %in% existing_files & !overwrite) { + message("file already exists, skipping download") + return(file.path(ndvi_anomalies_directory, save_filename)) + } + + # Get historical means for DOY + doy <- model_dates |> filter(date == date_selected) |> pull(day_of_year) + doy_frmt <- str_pad(doy,width = 3, side = "left", pad = "0") + historical_means <- read_parquet(ndvi_historical_means[str_detect(ndvi_historical_means, doy_frmt)]) |> + select(-day_of_year) + + # Get the lagged anomalies for selected dates, mapping over the lag intervals + row_select <- which(model_dates$date == date_selected) + + lag_intervals_start <- c(1 , 1+lag_intervals[-length(lag_intervals)]) + lag_intervals_end <- lag_intervals + + anomalies <- map2(lag_intervals_start, lag_intervals_end, function(start, end){ + + lag_dates <- model_dates |> slice((row_select - start):(row_select - end)) + + # get files and weights for the calculations + weights <- ndvi_date_lookup |> + mutate(lag_date = map(lookup_dates, ~. %in% lag_dates$date)) |> + mutate(weight = unlist(map(lag_date, sum))) |> + filter(weight > 0) |> + select(start_date, filename, weight) + + ndvi_dataset <- open_dataset(weights$filename) + + # Lag: calculate mean by pixel for the preceding x days + lagged_means <- ndvi_dataset |> + left_join(weights |> select(-filename)) |> + group_by(x, y) |> + summarize(lag_ndvi_mean = sum(ndvi * weight)/ sum(weight)) |> + ungroup() + + # Join in historical means to calculate anomalies raw and scaled + full_join(lagged_means, historical_means, by = c("x", "y")) |> + mutate(!!paste0("anomaly_ndvi_", end) := lag_ndvi_mean - historical_ndvi_mean, + !!paste0("anomaly_ndvi_scaled_", end) := (lag_ndvi_mean - historical_ndvi_mean)/historical_ndvi_sd) |> + select(-starts_with("lag"), -starts_with("historical")) + }) |> + reduce(left_join, by = c("x", "y")) |> + mutate(date = date_selected) |> + relocate(date) + + # Save as parquet + write_parquet(anomalies, here::here(ndvi_anomalies_directory, save_filename), compression = "gzip", compression_level = 5) + + return(file.path(ndvi_anomalies_directory, save_filename)) + + + + } + \ No newline at end of file diff --git a/R/calculate_ndvi_historical_means.R b/R/calculate_ndvi_historical_means.R index 77179dc..f609aa7 100644 --- a/R/calculate_ndvi_historical_means.R +++ b/R/calculate_ndvi_historical_means.R @@ -13,11 +13,7 @@ #' @return #' @author Emma Mendelsohn #' @export -calculate_ndvi_historical_means <- function(sentinel_ndvi_transformed, - sentinel_ndvi_transformed_directory, - modis_ndvi_transformed, - modis_ndvi_transformed_directory, - ndvi_historical_means_directory, +calculate_ndvi_historical_means <- function(ndvi_historical_means_directory, ndvi_date_lookup, days_of_year, overwrite = FALSE) { diff --git a/_targets.R b/_targets.R index b0dd38e..f939c1a 100644 --- a/_targets.R +++ b/_targets.R @@ -345,11 +345,7 @@ data_targets <- tar_plan( tar_target(ndvi_historical_means_directory, create_data_directory(directory_path = "data/ndvi_historical_means")), - tar_target(ndvi_historical_means, calculate_ndvi_historical_means(sentinel_ndvi_transformed, - sentinel_ndvi_transformed_directory, - modis_ndvi_transformed, - modis_ndvi_transformed_directory, - ndvi_historical_means_directory, + tar_target(ndvi_historical_means, calculate_ndvi_historical_means(ndvi_historical_means_directory, ndvi_date_lookup, days_of_year, overwrite = FALSE), @@ -357,6 +353,21 @@ data_targets <- tar_plan( format = "file", repository = "local"), + tar_target(ndvi_anomalies_directory, + create_data_directory(directory_path = "data/ndvi_anomalies")), + + tar_target(ndvi_anomalies, calculate_ndvi_anomalies(ndvi_date_lookup, + ndvi_historical_means, + ndvi_anomalies_directory, + model_dates, + model_dates_selected, + lag_intervals, + overwrite = FALSE), + pattern = head(model_dates_selected, 1), + format = "file", + repository = "local"), + + ) diff --git a/_targets/meta/meta b/_targets/meta/meta index 7e7b294..d2d4fc1 100644 --- a/_targets/meta/meta +++ b/_targets/meta/meta @@ -1,10 +1,11 @@ name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iteration|parent|children|seconds|warnings|error -.Random.seed|object|334ea9f1939ec074||||||||||||||| +.Random.seed|object|f9c0e6023780fec0||||||||||||||| all_targets|function|2dda5afbd1f92385||||||||||||||| aws_bucket|object|d9cf2c5ff7cc1be4||||||||||||||| aws_s3_upload_single_type|function|6d277b68ccbb67a2||||||||||||||| cache_aws_branched_target|function|6e2abfa4969de1bf||||||||||||||| -calculate_ndvi_historical_means|function|cea1d2e00390da25||||||||||||||| +calculate_ndvi_anomalies|function|6db15a3294a84787||||||||||||||| +calculate_ndvi_historical_means|function|a02a324eed41f50b||||||||||||||| calculate_weather_anomalies|function|57719f2f7340a5c0||||||||||||||| calculate_weather_historical_means|function|0d0788e09fb997a7||||||||||||||| continent_bounding_box|stem|cd4a4ddaa46d634a|bc00ded6218f3e10|d25ebcbef292030f|-1551480776|bucket=open-rvfcast-data*region=NULL*key=_targets/continent_bounding_box*endpoint=TlVMTA*version=|t19517.6854396s||650|qs|aws|vector|||0.001|| @@ -23,7 +24,7 @@ create_nasa_weather_dataset|function|7eb26dcea55b80b9||||||||||||||| create_ndvi_date_lookup|function|acddeddb4382e68c||||||||||||||| create_raster_template_plot|function|db738156a3247831||||||||||||||| create_sentinel_ndvi_dataset|function|201d4eaf8c87d0c3||||||||||||||| -data_targets|object|01a82e3d194707ec||||||||||||||| +data_targets|object|a08c7f7c5cba992d||||||||||||||| days_of_year|stem|e2673220ee124699|1e42c49f9959f217|787f005495551c49|-84662016|bucket=open-rvfcast-data*region=NULL*key=_targets/days_of_year*endpoint=TlVMTA*version=|t19642.833473024s||1502|qs|aws|vector|||0.001|| define_bounding_boxes|function|e614caacc0592e73||||||||||||||| define_country_regions|function|54808365a1bb460e||||||||||||||| @@ -4925,375 +4926,378 @@ nasa_weather_transformed_upload_aws_s3_f2170ca9|branch|8995e900f77f46ba|edddc7c5 nasa_weather_upload_aws_s3|stem|56ed36a5d19b0f00|5fbdf70412d0d976|d4569a69851ef960|-1238055393|bucket=open-rvfcast-data*region=NULL*key=_targets/nasa_weather_upload_aws_s3*endpoint=TlVMTA*version=|t19520.8369269456s||19108|qs|aws|vector|||168.689|| 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