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changed CI extract to extract all sat images if parameter new_project_question is set to TRUE, to add when new project start

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Timon 2024-03-04 17:12:20 +01:00
parent 86f4a49d30
commit 6c00c57b37
2 changed files with 16 additions and 21 deletions
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24
r_app/2_CI_data_prep.R
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@ -29,22 +29,23 @@ if (is.na(weeks_ago)) {
} }
# laravel_storage_dir <- here("../laravel_app/storage/app") # laravel_storage_dir <- here("../laravel_app/storage/app")
here("C:/Users/timon/Resilience BV/4020 SCane ESA DEMO - Documenten/General/4020 SCDEMO Team/4020 TechnicalData/WP2/smartcane") laravel_storage_dir <- here("laravel_app","storage","app")
laravel_storage_dir <- here("laravel_app/storage/app")
#preparing directories #preparing directories
planet_tif_folder <- here(laravel_storage_dir, "chemba/merged_tif") project = "chemba"
merged_final <- here(laravel_storage_dir, "chemba/merged_final_tif") planet_tif_folder <- here(laravel_storage_dir, project, "merged_tif")
merged_final <- here(laravel_storage_dir, project,"merged_final_tif")
data_dir <- here(laravel_storage_dir, "Data") data_dir <- here(laravel_storage_dir, project,"Data")
extracted_CI_dir <- here(data_dir, "extracted_ci") extracted_CI_dir <- here(data_dir, "extracted_ci")
daily_CI_vals_dir <- here(extracted_CI_dir, "daily_vals") daily_CI_vals_dir <- here(extracted_CI_dir, "daily_vals")
cumulative_CI_vals_dir <- here(extracted_CI_dir, "cumulative_vals") cumulative_CI_vals_dir <- here(extracted_CI_dir, "cumulative_vals")
weekly_CI_mosaic <- here(laravel_storage_dir, "chemba/weekly_mosaic") weekly_CI_mosaic <- here(laravel_storage_dir, project,"weekly_mosaic")
daily_vrt <- here(data_dir, "vrt") daily_vrt <- here(data_dir, "vrt")
harvest_dir <- here(data_dir, "HarvestData") harvest_dir <- here(data_dir, "HarvestData")
dir.create(here(data_dir))
dir.create(here(extracted_CI_dir)) dir.create(here(extracted_CI_dir))
dir.create(here(daily_CI_vals_dir)) dir.create(here(daily_CI_vals_dir))
dir.create(here(cumulative_CI_vals_dir)) dir.create(here(cumulative_CI_vals_dir))
@ -221,8 +222,11 @@ if(sum(missing_pixels_count$thres_5perc)>1){
names(x) <- c("CI") names(x) <- c("CI")
}else{ }else{
message("No cloud free images available") message("No cloud free images available, all images combined")
x <- rast(vrt_list[1]) %>% setValues(NA)
rsrc <- sprc(vrt_list)
x <- mosaic(rsrc, fun = "max")
# x <- rast(vrt_list[1]) %>% setValues(NA)
names(x) <- c("CI") names(x) <- c("CI")
} }
@ -253,6 +257,10 @@ extract_rasters_daily <- function(file, field_geojson, quadrants = TRUE, save_di
# pivot_sf_q <- st_read(here("..", "Data", "pivot_20210625.geojson")) %>% dplyr::select(pivot, pivot_quadrant) %>% vect() # pivot_sf_q <- st_read(here("..", "Data", "pivot_20210625.geojson")) %>% dplyr::select(pivot, pivot_quadrant) %>% vect()
pivot_sf <- st_read(here(data_dir, "pivot_20210625.geojson")) %>% dplyr::select(pivot, pivot_quadrant) %>% group_by(pivot) %>% summarise() %>% vect() pivot_sf <- st_read(here(data_dir, "pivot_20210625.geojson")) %>% dplyr::select(pivot, pivot_quadrant) %>% group_by(pivot) %>% summarise() %>% vect()
message("pivot loaded") message("pivot loaded")
if (!file.exists(here(cumulative_CI_vals_dir,"combined_CI_data.rds"))) {
print("combined_CI_data.rds does not exist. Running this part of the script...")
}
raster_files_NEW <- list.files(merged_final,full.names = T, pattern = ".tif") raster_files_NEW <- list.files(merged_final,full.names = T, pattern = ".tif")
filtered_files <- map(dates$days_filter, ~ raster_files_NEW[grepl(pattern = .x, x = raster_files_NEW)]) %>% filtered_files <- map(dates$days_filter, ~ raster_files_NEW[grepl(pattern = .x, x = raster_files_NEW)]) %>%
compact() %>% compact() %>%

13
r_app/r_app.Rproj
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@ -1,13 +0,0 @@
Version: 1.0
RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default
EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8
RnwWeave: Sweave
LaTeX: pdfLaTeX