Enhance logging functionality and update report generation scripts

- Improved safe_log function to include timestamps and conditional logging
- Added diagnostic messages for field visualization processing
- Updated CI map rendering parameters for consistency
- Refined raster mapping functions in report_utils for clarity
- Added .png files to .gitignore

python_app/.gitignore

@@ -41,3 +41,6 @@ dist/
 *.swo
 *.swp
 
+*.png
+
+

r_app/00_common_utils.R

@@ -48,10 +48,30 @@
 # #' safe_log("Check input file", "WARNING")
 # #' safe_log("Failed to load data", "ERROR")
 # #'
-# safe_log <- function(message, level = "INFO") {
+safe_log <- function(message, level = "INFO") {
-#   prefix <- sprintf("[%s]", level)
+  # Build the full log message with timestamp
-#   cat(sprintf("%s %s\n", prefix, message))
+  timestamp <- format(Sys.time(), "%Y-%m-%d %H:%M:%S")
-# }
+  log_msg <- sprintf("[%s] [%s] %s", timestamp, level, message)
+  
+  # Only output to console if NOT rendering with knitr
+  if (!isTRUE(getOption('knitr.in.progress'))) {
+    cat(log_msg, "\n")
+  }
+  
+  # Always write to log file if available
+  if (exists("LOG_FILE", envir = .GlobalEnv)) {
+    log_file <- get("LOG_FILE", envir = .GlobalEnv)
+    if (!is.null(log_file) && nzchar(log_file)) {
+      tryCatch({
+        cat(log_msg, "\n", file = log_file, append = TRUE)
+      }, error = function(e) {
+        # Silently fail if log file can't be written
+      })
+    }
+  }
+  
+  invisible(log_msg)
+}
 
 # #' SmartCane Debug Logging (Conditional)
 # #'

r_app/90_CI_report_with_kpis_agronomic_support.Rmd

@@ -841,7 +841,7 @@ tryCatch({
 
 ### Chlorophyll Index (CI) Overview Map - Current Week
 
-```{r render_farm_ci_map, echo=FALSE, fig.height=5.5, fig.width=6.5, dpi=150, dev='png', message=FALSE, warning=FALSE}
+```{r render_farm_ci_map, echo=FALSE, message=FALSE, warning=FALSE, fig.height=5.5, fig.width=6.5, dpi=150, dev='png', message=FALSE, warning=FALSE}
 # Create farm-level chlorophyll index map with OpenStreetMap basemap
 tryCatch({
   if (!is.null(farm_ci_current_ll)) {
@@ -1075,15 +1075,39 @@ This section provides detailed, field-specific analyses including chlorophyll in
 
 ```{r generate_field_visualizations, eval=TRUE, fig.height=3.8, fig.width=6.5, dpi=150, dev='png', message=TRUE, echo=FALSE, warning=TRUE, include=TRUE, results='asis'}
 # Generate detailed visualizations for each field using purrr::walk
+# DIAGNOSTIC MODE - Remove this after debugging
+cat("\n## DIAGNOSTIC: Starting field visualization processing\n\n")
+
 tryCatch({
-  # Prepare merged field list and week/year info
+   # Check prerequisites
-  AllPivots_merged <- AllPivots0 %>% 
+   cat("- Fields to process:", nrow(AllPivots_merged), "\n")
+   cat("- Field names:", paste(AllPivots_merged$field, collapse = ", "), "\n")
+   cat("- Weekly mosaic directory:", weekly_CI_mosaic, "\n")
+   cat("- CI quadrant data available:", !is.null(CI_quadrant), "\n")
+   cat("- Harvesting data available:", !is.null(harvesting_data), "\n\n")
+  
+   # Check if ci_plot function exists
+   if (!exists("ci_plot")) {
+    cat("**ERROR: ci_plot() function not found!**\n\n")
+    stop("ci_plot function missing")
+   }
+  
+   if (!exists("cum_ci_plot")) {
+    cat("**ERROR: cum_ci_plot() function not found!**\n\n")
+    stop("cum_ci_plot function missing")
+   }
+  
+   cat("- ci_plot() function:", "FOUND", "\n")
+   cat("- cum_ci_plot() function:", "FOUND", "\n\n")
+
+   # Prepare merged field list and week/year info
+   AllPivots_merged <- AllPivots0 %>% 
     dplyr::filter(!is.na(field), !is.na(sub_field)) %>%
     dplyr::group_by(field) %>% 
     dplyr::summarise(.groups = 'drop')
   
-  # Helper to get week/year from a date
+   # Helper to get week/year from a date
-  get_week_year <- function(date) {
+   get_week_year <- function(date) {
     list(
       week = as.numeric(format(date, "%V")),
       year = as.numeric(format(date, "%G"))

r_app/report_utils.R

@@ -64,9 +64,10 @@ create_CI_map <- function(pivot_raster, pivot_shape, pivot_spans, show_legend =
   map <- tm_shape(pivot_raster, unit = "m")
   
   # Add raster with continuous spectrum (fixed scale 8-1 for consistent comparison, reversed)
-  map <- map + tm_raster(col.scale = tm_scale_continuous(values = palette,
+  map <- map + tm_raster("CI",
+                          col_scale = tm_scale_continuous(values = palette,
                                                        limits = c(1,8)),
-                          col.legend = tm_legend(title = "CI",
+                          col_legend = tm_legend(title = "CI",
                                                orientation = if(legend_is_portrait) "portrait" else "landscape", 
                                                show = show_legend,
                                                position = if(show_legend) tm_pos_out("left", "center") else c("left", "bottom"),
@@ -135,10 +136,11 @@ create_CI_diff_map <- function(pivot_raster, pivot_shape, pivot_spans, show_lege
   map <- tm_shape(pivot_raster, unit = "m")
   
   # Add raster with continuous spectrum (centered at 0 for difference maps, fixed scale, reversed)
-  map <- map + tm_raster(col.scale = tm_scale_continuous(values = palette,
+  map <- map + tm_raster("CI",
+                          col_scale = tm_scale_continuous(values = palette,
                                                        midpoint = 0,
                                                        limits = c(-3, 3)),
-                          col.legend = tm_legend(title = "CI diff.",
+                          col_legend = tm_legend(title = "CI diff.",
                                                orientation = if(legend_is_portrait) "portrait" else "landscape",
                                                show = show_legend,
                                                position = if(show_legend) tm_pos_out("right", "center") else c("left", "bottom"),