From 6efa6b6b05b53403887db69144ac5ac789ac2988 Mon Sep 17 00:00:00 2001
From: Timon <timon@resiliencebv.com>
Date: Tue, 3 Feb 2026 14:56:04 +0100
Subject: [PATCH] "wip"

---
 r_app/10_create_per_field_tiffs.R | 8 ++++++++
 r_app/run_full_pipeline.R         | 4 ++--
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/r_app/10_create_per_field_tiffs.R b/r_app/10_create_per_field_tiffs.R
index 56fd5f9..5d88573 100644
--- a/r_app/10_create_per_field_tiffs.R
+++ b/r_app/10_create_per_field_tiffs.R
@@ -79,6 +79,14 @@ load_field_boundaries <- function(geojson_path) {
     }
   }
   
+  # FIX: Validate and repair geometries (handles duplicate vertices, degenerate edges, etc)
+  invalid_count <- sum(!st_is_valid(fields))
+  if (invalid_count > 0) {
+    smartcane_log(paste("WARNING: Found", invalid_count, "invalid geometry/geometries - attempting repair"))
+    fields <- st_make_valid(fields)
+    smartcane_log(paste("Repaired invalid geometries using st_make_valid()"))
+  }
+  
   smartcane_log(paste("Loaded", nrow(fields), "field(s)"))
   return(fields)
 }
diff --git a/r_app/run_full_pipeline.R b/r_app/run_full_pipeline.R
index 4a06d14..d3d1e33 100644
--- a/r_app/run_full_pipeline.R
+++ b/r_app/run_full_pipeline.R
@@ -30,8 +30,8 @@
 # ==============================================================================
 
 # *** EDIT THESE VARIABLES ***
-end_date <- as.Date("2026-01-07") # or specify: as.Date("2026-01-27") , Sys.Date()
-project_dir <- "aura" # project name: "esa", "aura", "angata", "chemba"
+end_date <- Sys.Date() # or specify: as.Date("2026-01-27") , Sys.Date()
+project_dir <- "angata" # project name: "esa", "aura", "angata", "chemba"
 data_source <- "merged_tif" # Standard data source directory
 force_rerun <- FALSE # Set to TRUE to force all scripts to run even if outputs exist
 # ***************************