added DownloadCreditsCommand some updates

laravel_app/app/Console/Commands/DownloadCreditsCommand.php

@@ -0,0 +1,91 @@
+<?php
+
+namespace App\Console\Commands;
+
+use Illuminate\Console\Command;
+use Illuminate\Support\Facades\Storage;
+
+class DownloadCreditsCommand extends Command
+{
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'app:download-credits-command';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Command description';
+
+    private $processingUnits = [];
+
+    private $totalSum = 0;
+    private $totalCount = 0;
+    private $allValues = [];
+    private $stdDev = 0;
+    private $overallAvg;
+
+    /**
+     * Execute the console command.
+     */
+    public function handle()
+    {
+        $path = 'Bagamoyo_trial/single_images/';
+        $datesDir = Storage::directories($path);
+
+        $this->extractData($datesDir);
+//        dd($this->processingUnits);
+        $this->calculateStatistics();
+
+        // Output the statistics
+        $this->info('Total sum: '.$this->totalSum);
+        $this->info('Total count: '.$this->totalCount);
+        $this->info('Overall average: '.$this->overallAvg);
+        $this->info('Standard deviation: '.$this->stdDev);
+    }
+
+    private function extractProcessingUnitsFromFile($filePath)
+    {
+        $data = json_decode(Storage::get($filePath), true);
+        $responseHeaders = $data['response']['headers'];
+        $processingUnits = $responseHeaders['x-processingunits-spent'];
+        return $processingUnits;
+    }
+
+    private function calculateStatistics()
+    {
+        foreach ($this->processingUnits as $date => $values) {
+            $processingUnitsPerDate = array_sum($values);
+            $this->totalSum += $processingUnitsPerDate;
+            $this->totalCount++;
+            $this->allValues[$date] = $processingUnitsPerDate;
+        }
+
+        $this->overallAvg = $this->totalSum / $this->totalCount;
+        $variance = array_reduce($this->allValues, function ($carry, $item) {
+                return $carry + pow($item - $this->overallAvg, 2);
+            }, 0) / $this->totalCount;
+
+        $this->stdDev = sqrt($variance);
+    }
+
+    private function extractData(array $datesDir): void
+    {
+        foreach ($datesDir as $dateDir) {
+            $date = basename($dateDir);
+            $subdirectories = Storage::directories($dateDir);
+            $this->processingUnits[$date] = [];
+
+            foreach ($subdirectories as $subdirectory) {
+                $requestPath = $subdirectory.'/request.json';
+                if (Storage::fileExists($requestPath)) {
+                    $this->processingUnits[$date][] = $this->extractProcessingUnitsFromFile($requestPath);
+                }
+            }
+        }
+    }
+}

r_app/interpolate_growth_model.R

@@ -26,7 +26,7 @@ if (file.exists(file_path)) {
         group_by(field, sub_field) %>%
         summarise(across(everything(), ~ first(na.omit(.))), .groups = "drop")
 }
-
+head(pivot_stats2)
    #%>% drop_na(pivot_quadrant)
 
 # gather data into long format for easier calculation and visualisation
@@ -61,20 +61,23 @@ extract_CI_data <- function(field_names, harvesting_data, field_CI_data, season)
     return(data.frame())
   }
   
+  
   # Create a linear interpolation function for the CI data
   ApproxFun <- approxfun(x = filtered_field_CI_data$Date, y = filtered_field_CI_data$value)
   Dates <- seq.Date(ymd(min(filtered_field_CI_data$Date)), ymd(max(filtered_field_CI_data$Date)), by = 1)
   LinearFit <- ApproxFun(Dates)
   # Combine interpolated data with the original CI data
+
   CI <- data.frame(Date = Dates, FitData = LinearFit) %>%
-    left_join(., filtered_field_CI_data, by = "Date") %>%
+    left_join(., filtered_field_CI_data, by = "Date")  %>%
     filter(Date > filtered_harvesting_data$season_start & Date < filtered_harvesting_data$season_end)
   
   # If CI is empty after filtering, return an empty dataframe
   if (nrow(CI) == 0) {
+    message ('CI empty after filtering')
     return(data.frame())
   }
-
+  
   # Add additional columns if data exists
   CI <- CI %>%
     mutate(DOY = seq(1, n(), 1),
@@ -85,7 +88,7 @@ extract_CI_data <- function(field_names, harvesting_data, field_CI_data, season)
   return(CI)
 }
 
-
+message(harvesting_data)
 
 CI_all <- map_df(years, function(yr) {
   # yr = 2021
@@ -96,11 +99,13 @@ CI_all <- map_df(years, function(yr) {
     filter(year == yr) %>%
     filter(!is.na(season_start)) %>%
     pull(sub_field)
+  
 
   # Filter sub_fields to only include those with value data in pivot_stats_long
   valid_sub_fields <- sub_fields %>%
     keep(~ any(pivot_stats_long$sub_field == .x))
-  # Extract data for each valid field
+  
+    # Extract data for each valid field
   map(valid_sub_fields, ~ extract_CI_data(.x, harvesting_data = harvesting_data, field_CI_data = pivot_stats_long, season = yr)) %>%
     list_rbind()
 })
@@ -112,9 +117,7 @@ CI_all <- map_df(years, function(yr) {
             mutate(CI_per_day = FitData - lag(FitData), cumulative_CI = cumsum(FitData))
 # }
 
-message('CI_all cumulative')
 
-message('show head')
 
 saveRDS(CI_all, here(cumulative_CI_vals_dir,"All_pivots_Cumulative_CI_quadrant_year_v2.rds"))
 message('rds saved')

r_app/parameters_project.R

@@ -29,9 +29,10 @@ dir.create(here(daily_vrt), showWarnings = FALSE)
 dir.create(merged_final,showWarnings = FALSE)
 dir.create(harvest_dir,showWarnings = FALSE)
 
-field_boundaries_sf <- st_read(here(data_dir, "pivot.geojson"))
+field_boundaries_sf <- st_read(here(data_dir, "pivot.geojson"), crs = 4326)
 
 names(field_boundaries_sf) <- c("field", "sub_field", "geometry")
+
 field_boundaries <- field_boundaries_sf %>% terra::vect()
 
 harvesting_data <- read_excel(here(data_dir, "harvest.xlsx")) %>%

update_RDS.sh

@@ -1,8 +1,8 @@
 #!/bin/bash
 
 end_date=$(date +'%Y-%m-%d')
-offset=7
-project_dir="chemba"
+offset=28
+project_dir="Bagamoyo_trial"
 
 # Parse command line arguments
 for arg in "$@"; do
@@ -29,7 +29,7 @@ echo "offset: $offset"
 
 # Check if required arguments are set
 if [ -z "$end_date" ] || [ -z "$project_dir" ] || [ -z "$offset" ]; then
-    echo "Missing arguments. Use: update_RDS.sh --end_date=2024-01-01 --offset=7 --project_dir=chemba"
+    echo "Missing arguments. Use: update_RDS.sh --end_date=2024-01-01 --offset=28 --project_dir=Bagamoyo_trial"
     exit 1
 fi