wip
This commit is contained in:
Martin Folkerts
parent
915284ba04
commit
1f194c5670
29
interpolate_growth_model.sh
Executable file
29
interpolate_growth_model.sh
Executable file
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@ -0,0 +1,29 @@
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#!/bin/bash
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project_dir="chemba"
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# Parse command line arguments
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for arg in "$@"; do
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case $arg in
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--project_dir=*)
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project_dir="${arg#*=}"
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;;
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*)
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echo "Unknown option: $arg"
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exit 1
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;;
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esac
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shift
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done
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# Check if required arguments are set
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if [ -z "$project_dir" ]; then
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echo "Missing argument project_dir. Use: interpolate_growth_model.sh --project_dir=chemba"
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exit 1
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fi
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echo interpolate_growth_model.R $project_dir
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cd ../r_app
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Rscript interpolate_growth_model.R $project_dir
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@ -56,6 +56,7 @@ harvest_dir <- here(data_dir, "HarvestData")
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source("parameters_project.R")
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source("parameters_project.R")
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source("ci_extraction_utils.R")
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source("ci_extraction_utils.R")
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source("mosaic_creation_utils.R")
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dir.create(here(laravel_storage_dir))
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dir.create(here(laravel_storage_dir))
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dir.create(here(data_dir))
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dir.create(here(data_dir))
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@ -86,7 +87,60 @@ print(dates)
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# flatten_chr()
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# flatten_chr()
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# head(filtered_files)
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# head(filtered_files)
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raster_files <- list.files(planet_tif_folder,full.names = T, pattern = ".tif")
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filtered_files <- map(dates$days_filter, ~ raster_files[grepl(pattern = .x, x = raster_files)]) %>%
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compact() %>%
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flatten_chr()
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# filtered_files <- raster_files #for first CI extraction
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# create_mask_and_crop <- function(file, field_boundaries) {
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# message("starting ", file)
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# CI <- rast(file)
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# # names(CI) <- c("green","nir")
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# message("raster loaded")
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#
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# CI <- CI[[2]]/CI[[1]]-1
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# # CI <- CI$nir/CI$green-1
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# message("CI calculated")
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# CI <- terra::crop(CI, field_boundaries, mask = TRUE) #%>% CI_func()
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#
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# new_file <- here(merged_final, paste0(tools::file_path_sans_ext(basename(file)), ".tif"))
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# writeRaster(CI, new_file, overwrite = TRUE)
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#
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# vrt_file <- here(daily_vrt, paste0(tools::file_path_sans_ext(basename(file)), ".vrt"))
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# terra::vrt(new_file, vrt_file, overwrite = TRUE)
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#
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# return(CI)
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# }
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vrt_list <- list()
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# for (file in raster_files) {
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# v_crop <- create_mask_and_crop(file, field_boundaries)
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# message(file, " processed")
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# gc()
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# }
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for (file in filtered_files) {
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v_crop <- create_mask_and_crop(file, field_boundaries)
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emtpy_or_full <- global(v_crop, "notNA")
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vrt_file <- here(daily_vrt, paste0(tools::file_path_sans_ext(basename(file)), ".vrt"))
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if(emtpy_or_full[1,] > 10000){
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vrt_list[vrt_file] <- vrt_file
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}else{
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file.remove(vrt_file)
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}
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message(file, " processed")
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gc()
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}
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# Extracting CI
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# Extracting CI
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@ -129,7 +183,6 @@ print("combined_CI_data.rds exists, adding the latest image data to the table.")
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filtered_files <- map(dates$days_filter, ~ raster_files_NEW[grepl(pattern = .x, x = raster_files_NEW)]) %>%
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filtered_files <- map(dates$days_filter, ~ raster_files_NEW[grepl(pattern = .x, x = raster_files_NEW)]) %>%
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compact() %>%
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compact() %>%
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flatten_chr()
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flatten_chr()
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walk(filtered_files, extract_rasters_daily, field_geojson= field_boundaries, quadrants = TRUE, daily_CI_vals_dir)
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walk(filtered_files, extract_rasters_daily, field_geojson= field_boundaries, quadrants = TRUE, daily_CI_vals_dir)
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extracted_values <- list.files(daily_CI_vals_dir, full.names = TRUE)
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extracted_values <- list.files(daily_CI_vals_dir, full.names = TRUE)
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@ -140,103 +193,11 @@ extracted_values <- map(dates$days_filter, ~ extracted_values[grepl(pattern = .x
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pivot_stats <- extracted_values %>%
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pivot_stats <- extracted_values %>%
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map(readRDS) %>% list_rbind() %>%
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map(readRDS) %>% list_rbind() %>%
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group_by(sub_field) %>%
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group_by(sub_field)
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summarise(across(everything(), ~ first(na.omit(.))))
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combined_CI_data <- readRDS(here(cumulative_CI_vals_dir,"combined_CI_data.rds")) #%>% drop_na(pivot_quadrant)
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combined_CI_data <- readRDS(here(cumulative_CI_vals_dir,"combined_CI_data.rds")) #%>% drop_na(pivot_quadrant)
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pivot_stats2 <- bind_rows(pivot_stats, combined_CI_data)
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pivot_stats2 <- bind_rows(pivot_stats, combined_CI_data)
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# pivot_stats2 <- combined_CI_data
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# pivot_stats2 <- combined_CI_data
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print("All CI values extracted from latest 7 images.")
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print("All CI values extracted from latest image.")
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saveRDS(combined_CI_data, here(cumulative_CI_vals_dir,"combined_CI_data.rds")) #used to save the rest of the data into one file
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saveRDS(pivot_stats2, here(cumulative_CI_vals_dir,"combined_CI_data.rds")) #used to save the rest of the data into one file
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# gather data into long format for easier calculation and visualisation
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pivot_stats_long <- pivot_stats2 %>%
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tidyr::gather("Date", value, -field, -sub_field ) %>%
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mutate(Date = right(Date, 8),
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Date = lubridate::ymd(Date)
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) %>%
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drop_na(c("value","Date")) %>%
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mutate(value = as.numeric(value))%>%
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filter_all(all_vars(!is.infinite(.))) %>%
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# rename(field = pivot_quadrant,
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# sub_field = field) %>%
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unique()
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# #2021
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# pivot_select_model_Data_2021 <- harvesting_data %>% filter(Year == 2021) %>% pull(field)
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#
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# pivot_select_model_Data_2022 <- harvesting_data %>% filter(Year == 2022) %>% pull(field)
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# pivot_select_model_Data_2023 <- harvesting_data %>% filter(year == 2023) %>% filter(!is.na(season_start)) %>% pull(sub_field)
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pivot_select_model_Data_2024 <- harvesting_data %>% filter(year == 2024)%>% filter(!is.na(season_start)) %>% pull(sub_field)
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# pivots_dates_Data_2022 <- pivots_dates0 %>% filter(!is.na(season_end_2022))
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# pivot_select_model_Data_2022 <- unique(pivots_dates_Data_2022$pivot_quadrant )
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#
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# pivots_dates_Data_2023 <- pivots_dates0 %>% filter(!is.na(season_start_2023))
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# pivot_select_model_Data_2023 <- unique(pivots_dates_Data_2023$pivot_quadrant)
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#
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# pivots_dates_Data_2024 <- pivots_dates0 %>% filter(!is.na(season_start_2024))
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# pivot_select_model_Data_2024 <- unique(pivots_dates_Data_2024$pivot_quadrant)
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extract_CI_data <- function(field_names, harvesting_data, field_CI_data, season) { # nolint: line_length_linter.
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# field_names = "AG1D06P"
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# field_names = "1.13A"
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# harvesting_data = harvesting_data
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# field_CI_data = pivot_stats_long
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# season= 2023
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filtered_harvesting_data <- harvesting_data %>%
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na.omit() %>%
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filter(year == season, sub_field %in% field_names)
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filtered_field_CI_data <- field_CI_data %>%
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filter(sub_field %in% field_names)
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# CI <- map_df(field_names, ~ {
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ApproxFun <- approxfun(x = filtered_field_CI_data$Date, y = filtered_field_CI_data$value)
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Dates <- seq.Date(ymd(min(filtered_field_CI_data$Date)), ymd(max(filtered_field_CI_data$Date)), by = 1)
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LinearFit <- ApproxFun(Dates)
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CI <- data.frame(Date = Dates, FitData = LinearFit) %>%
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left_join(., filtered_field_CI_data, by = "Date") %>%
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filter(Date > filtered_harvesting_data$season_start & Date < filtered_harvesting_data$season_end) %>%
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mutate(DOY = seq(1, n(), 1),
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model = paste0("Data", season, " : ", field_names),
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season = season,
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sub_field = field_names)
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# }) #%>%
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#{if (length(field_names) > 0) message("Done!")}
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return(CI)
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}
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## Extracting the correct CI values
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# Data_2021 <- map(pivot_select_model_Data_2021, ~ extract_CI_data(.x, harvesting_data = harvesting_data, field_CI_data = pivot_stats_long, season = 2021)) %>% list_rbind() # nolint: line_length_linter.
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# message('2021')
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# Data_2022 <- map(pivot_select_model_Data_2022, ~ extract_CI_data(.x, harvesting_data = harvesting_data, field_CI_data = pivot_stats_long, season = 2022)) %>% list_rbind()
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# message('2022')
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# Data_2023 <- map(pivot_select_model_Data_2023, ~ extract_CI_data(.x, harvesting_data = harvesting_data, field_CI_data = pivot_stats_long, season = 2023)) %>% list_rbind()
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# message('2023')
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Data_2024 <- map(pivot_select_model_Data_2024, ~ extract_CI_data(.x, harvesting_data = harvesting_data, field_CI_data = pivot_stats_long, season = 2024)) %>% list_rbind()
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message('2024')
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#CI_all <- rbind(Data_2023, Data_2024)
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CI_all <- Data_2024
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message('CI_all created')
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#CI_all <- Data_2023
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CI_all <- CI_all %>% group_by(model) %>% mutate(CI_per_day = FitData - lag(FitData),
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cumulative_CI = cumsum(FitData))
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message('CI_all cumulative')
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head(CI_all)
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message('show head')
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saveRDS(CI_all, here(cumulative_CI_vals_dir,"All_pivots_Cumulative_CI_quadrant_year_v2.rds"))
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message('rds saved')
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# nolint end
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141
r_app/interpolate_growth_model.R
Normal file
141
r_app/interpolate_growth_model.R
Normal file
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@ -0,0 +1,141 @@
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library(here)
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library(sf)
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library(terra)
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library(tidyverse)
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library(lubridate)
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library(exactextractr)
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library(readxl)
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# Vang alle command line argumenten op
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args <- commandArgs(trailingOnly = TRUE)
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# Converteer het tweede argument naar een string waarde
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project_dir <- as.character(args[1])
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# Controleer of data_dir een geldige waarde is
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if (!is.character(project_dir)) {
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project_dir <- "sony"
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}
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laravel_storage_dir <- here("laravel_app/storage/app", project_dir)
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#preparing directories
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planet_tif_folder <- here(laravel_storage_dir, "merged_tif")
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merged_final <- here(laravel_storage_dir, "merged_final_tif")
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new_project_question = FALSE
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planet_tif_folder <- here(laravel_storage_dir, "merged_tif")
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merged_final <- here(laravel_storage_dir, "merged_final_tif")
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data_dir <- here(laravel_storage_dir, "Data")
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extracted_CI_dir <- here(data_dir, "extracted_ci")
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daily_CI_vals_dir <- here(extracted_CI_dir, "daily_vals")
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cumulative_CI_vals_dir <- here(extracted_CI_dir, "cumulative_vals")
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weekly_CI_mosaic <- here(laravel_storage_dir, "weekly_mosaic")
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daily_vrt <- here(data_dir, "vrt")
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harvest_dir <- here(data_dir, "HarvestData")
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source("parameters_project.R")
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source("ci_extraction_utils.R")
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pivot_stats2 <- readRDS(here(cumulative_CI_vals_dir,"combined_CI_data.rds")) %>%
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ungroup() %>%
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group_by(field, sub_field) %>%
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summarise(across(everything(), ~ first(na.omit(.))), .groups = "drop")
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#%>% drop_na(pivot_quadrant)
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# gather data into long format for easier calculation and visualisation
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pivot_stats_long <- pivot_stats2 %>%
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tidyr::gather("Date", value, -field, -sub_field ) %>%
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mutate(Date = right(Date, 8),
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Date = lubridate::ymd(Date)
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) %>%
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drop_na(c("value","Date")) %>%
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mutate(value = as.numeric(value))%>%
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filter_all(all_vars(!is.infinite(.))) %>%
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# rename(field = pivot_quadrant,
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# sub_field = field) %>%
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unique()
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# #2021
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# pivot_select_model_Data_2021 <- harvesting_data %>% filter(Year == 2021) %>% pull(field)
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#
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# pivot_select_model_Data_2022 <- harvesting_data %>% filter(Year == 2022) %>% pull(field)
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# pivot_select_model_Data_2023 <- harvesting_data %>% filter(year == 2023) %>% filter(!is.na(season_start)) %>% pull(sub_field)
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pivot_select_model_Data_2024 <- harvesting_data %>% filter(year == 2024)%>% filter(!is.na(season_start)) %>% pull(sub_field)
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# pivots_dates_Data_2022 <- pivots_dates0 %>% filter(!is.na(season_end_2022))
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# pivot_select_model_Data_2022 <- unique(pivots_dates_Data_2022$pivot_quadrant )
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#
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# pivots_dates_Data_2023 <- pivots_dates0 %>% filter(!is.na(season_start_2023))
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# pivot_select_model_Data_2023 <- unique(pivots_dates_Data_2023$pivot_quadrant)
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#
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# pivots_dates_Data_2024 <- pivots_dates0 %>% filter(!is.na(season_start_2024))
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# pivot_select_model_Data_2024 <- unique(pivots_dates_Data_2024$pivot_quadrant)
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extract_CI_data <- function(field_names, harvesting_data, field_CI_data, season) {
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# field_names = "4042902"
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# field_names = "1.13A"
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# harvesting_data = harvesting_data
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# field_CI_data = pivot_stats_long
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# season= 2024
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filtered_harvesting_data <- harvesting_data %>%
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na.omit() %>%
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filter(year == season, sub_field %in% field_names)
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filtered_field_CI_data <- field_CI_data %>%
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filter(sub_field %in% field_names)
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# CI <- map_df(field_names, ~ {
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ApproxFun <- approxfun(x = filtered_field_CI_data$Date, y = filtered_field_CI_data$value)
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Dates <- seq.Date(ymd(min(filtered_field_CI_data$Date)), ymd(max(filtered_field_CI_data$Date)), by = 1)
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LinearFit <- ApproxFun(Dates)
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CI <- data.frame(Date = Dates, FitData = LinearFit) %>%
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left_join(., filtered_field_CI_data, by = "Date") %>%
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filter(Date > filtered_harvesting_data$season_start & Date < filtered_harvesting_data$season_end) %>%
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mutate(DOY = seq(1, n(), 1),
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model = paste0("Data", season, " : ", field_names),
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|
season = season,
|
||||||
|
sub_field = field_names)
|
||||||
|
# }) #%>%
|
||||||
|
|
||||||
|
return(CI)
|
||||||
|
}
|
||||||
|
|
||||||
|
## Extracting the correct CI values
|
||||||
|
# Data_2021 <- map(pivot_select_model_Data_2021, ~ extract_CI_data(.x, harvesting_data = harvesting_data, field_CI_data = pivot_stats_long, season = 2021)) %>% list_rbind()
|
||||||
|
# message('2021')
|
||||||
|
# Data_2022 <- map(pivot_select_model_Data_2022, ~ extract_CI_data(.x, harvesting_data = harvesting_data, field_CI_data = pivot_stats_long, season = 2022)) %>% list_rbind()
|
||||||
|
# message('2022')
|
||||||
|
# Data_2023 <- map(pivot_select_model_Data_2023, ~ extract_CI_data(.x, harvesting_data = harvesting_data, field_CI_data = pivot_stats_long, season = 2023)) %>% list_rbind()
|
||||||
|
# message('2023')
|
||||||
|
Data_2024 <- map(pivot_select_model_Data_2024, ~ extract_CI_data(.x, harvesting_data = harvesting_data, field_CI_data = pivot_stats_long, season = 2024)) %>% list_rbind()
|
||||||
|
message('2024')
|
||||||
|
|
||||||
|
|
||||||
|
#CI_all <- rbind(Data_2023, Data_2024)
|
||||||
|
CI_all <- Data_2024
|
||||||
|
message('CI_all created')
|
||||||
|
#CI_all <- Data_2023
|
||||||
|
|
||||||
|
CI_all <- CI_all %>% group_by(model) %>% mutate(CI_per_day = FitData - lag(FitData),
|
||||||
|
cumulative_CI = cumsum(FitData))
|
||||||
|
message('CI_all cumulative')
|
||||||
|
|
||||||
|
head(CI_all)
|
||||||
|
message('show head')
|
||||||
|
|
||||||
|
saveRDS(CI_all, here(cumulative_CI_vals_dir,"All_pivots_Cumulative_CI_quadrant_year_v2.rds"))
|
||||||
|
message('rds saved')
|
||||||
|
|
||||||
|
|
@ -87,64 +87,10 @@ print(dates)
|
||||||
#load pivot geojson
|
#load pivot geojson
|
||||||
# pivot_sf_q <- st_read(here(data_dir, "pivot.geojson")) %>% dplyr::select(pivot, pivot_quadrant) %>% vect()
|
# pivot_sf_q <- st_read(here(data_dir, "pivot.geojson")) %>% dplyr::select(pivot, pivot_quadrant) %>% vect()
|
||||||
|
|
||||||
raster_files <- list.files(planet_tif_folder,full.names = T, pattern = ".tif")
|
vrt_files <- list.files(here(daily_vrt),full.names = T)
|
||||||
|
vrt_list <- map(dates$days_filter, ~ vrt_files[grepl(pattern = .x, x = vrt_files)]) %>%
|
||||||
filtered_files <- map(dates$days_filter, ~ raster_files[grepl(pattern = .x, x = raster_files)]) %>%
|
|
||||||
compact() %>%
|
compact() %>%
|
||||||
flatten_chr()
|
flatten_chr()
|
||||||
head(filtered_files)
|
|
||||||
|
|
||||||
# filtered_files <- raster_files #for first CI extraction
|
|
||||||
|
|
||||||
# create_mask_and_crop <- function(file, field_boundaries) {
|
|
||||||
# message("starting ", file)
|
|
||||||
# CI <- rast(file)
|
|
||||||
# # names(CI) <- c("green","nir")
|
|
||||||
# message("raster loaded")
|
|
||||||
#
|
|
||||||
# CI <- CI[[2]]/CI[[1]]-1
|
|
||||||
# # CI <- CI$nir/CI$green-1
|
|
||||||
# message("CI calculated")
|
|
||||||
# CI <- terra::crop(CI, field_boundaries, mask = TRUE) #%>% CI_func()
|
|
||||||
#
|
|
||||||
# new_file <- here(merged_final, paste0(tools::file_path_sans_ext(basename(file)), ".tif"))
|
|
||||||
# writeRaster(CI, 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(CI)
|
|
||||||
# }
|
|
||||||
|
|
||||||
|
|
||||||
vrt_list <- list()
|
|
||||||
|
|
||||||
# for (file in raster_files) {
|
|
||||||
# v_crop <- create_mask_and_crop(file, field_boundaries)
|
|
||||||
# message(file, " processed")
|
|
||||||
# gc()
|
|
||||||
# }
|
|
||||||
|
|
||||||
for (file in filtered_files) {
|
|
||||||
v_crop <- create_mask_and_crop(file, field_boundaries)
|
|
||||||
emtpy_or_full <- global(v_crop, "notNA")
|
|
||||||
|
|
||||||
vrt_file <- here(daily_vrt, paste0(tools::file_path_sans_ext(basename(file)), ".vrt"))
|
|
||||||
|
|
||||||
if(emtpy_or_full[1,] > 10000){
|
|
||||||
vrt_list[vrt_file] <- vrt_file
|
|
||||||
|
|
||||||
}else{
|
|
||||||
file.remove(vrt_file)
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
message(file, " processed")
|
|
||||||
gc()
|
|
||||||
}
|
|
||||||
|
|
||||||
# list_global <- list_global %>% flatten_chr()
|
|
||||||
vrt_list <- vrt_list %>% flatten_chr()
|
|
||||||
|
|
||||||
total_pix_area <- rast(vrt_list[1]) %>% terra::subset(1) %>% setValues(1) %>%
|
total_pix_area <- rast(vrt_list[1]) %>% terra::subset(1) %>% setValues(1) %>%
|
||||||
crop(field_boundaries, mask = TRUE) %>%
|
crop(field_boundaries, mask = TRUE) %>%
|
||||||
|
|
|
||||||
Loading…
Reference in a new issue