From 6c00c57b376abd7d184014f9c8a9f589a8d840ba Mon Sep 17 00:00:00 2001
From: Timon <timon.weitkamp@hotmail.com>
Date: Mon, 4 Mar 2024 17:12:20 +0100
Subject: [PATCH] changed CI extract to extract all sat images if parameter
 new_project_question is set to TRUE, to add when new project start

---
 r_app/2_CI_data_prep.R | 24 ++++++++++++++++--------
 r_app/r_app.Rproj      | 13 -------------
 2 files changed, 16 insertions(+), 21 deletions(-)
 delete mode 100644 r_app/r_app.Rproj

diff --git a/r_app/2_CI_data_prep.R b/r_app/2_CI_data_prep.R
index 4769518..fa32198 100644
--- a/r_app/2_CI_data_prep.R
+++ b/r_app/2_CI_data_prep.R
@@ -29,22 +29,23 @@ if (is.na(weeks_ago)) {
 }
 
 # 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
-planet_tif_folder <- here(laravel_storage_dir, "chemba/merged_tif")
-merged_final <- here(laravel_storage_dir, "chemba/merged_final_tif")
+project = "chemba"
+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")
 daily_CI_vals_dir <- here(extracted_CI_dir, "daily_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")
 harvest_dir <-  here(data_dir, "HarvestData")
 
+dir.create(here(data_dir))
 dir.create(here(extracted_CI_dir))
 dir.create(here(daily_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")
   
 }else{
-  message("No cloud free images available")
-  x <-  rast(vrt_list[1]) %>% setValues(NA)
+  message("No cloud free images available, all images combined")
+
+  rsrc <- sprc(vrt_list)
+  x <- mosaic(rsrc, fun = "max")
+  # x <-  rast(vrt_list[1]) %>% setValues(NA)
   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 <- st_read(here(data_dir, "pivot_20210625.geojson")) %>% dplyr::select(pivot, pivot_quadrant)   %>% group_by(pivot) %>% summarise() %>% vect()
 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")
 filtered_files  <- map(dates$days_filter, ~ raster_files_NEW[grepl(pattern = .x, x = raster_files_NEW)]) %>%
   compact() %>%
diff --git a/r_app/r_app.Rproj b/r_app/r_app.Rproj
deleted file mode 100644
index 8e3c2eb..0000000
--- a/r_app/r_app.Rproj
+++ /dev/null
@@ -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