From e801bcdc3aa3e3f39b521d0e0e11d3b3a6e83482 Mon Sep 17 00:00:00 2001
From: Michael Crawford <mscrawfor@gmail.com>
Date: Wed, 11 Sep 2024 17:31:20 +0200
Subject: [PATCH] Added convertToNetCDF output script

---
 CHANGELOG.md                           |  1 +
 scripts/output/extra/convertToNetCDF.R | 43 ++++++++++++++++++++++++++
 2 files changed, 44 insertions(+)
 create mode 100644 scripts/output/extra/convertToNetCDF.R

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d0015d3fd..e856625b7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,6 +18,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 
 ### added
+- **scripts** added output script converting all grid-level .mz files to .nc (netCDF)
 - **scripts** added output report `EU_report.R` that uses `EU_report.Rmd`
 - **scripts** added out of bounds check as output script
 - **70_livestock** added realization `fbask_jan16_sticky`
diff --git a/scripts/output/extra/convertToNetCDF.R b/scripts/output/extra/convertToNetCDF.R
new file mode 100644
index 000000000..99d9dffec
--- /dev/null
+++ b/scripts/output/extra/convertToNetCDF.R
@@ -0,0 +1,43 @@
+# |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+# |  authors, and contributors see CITATION.cff file. This file is part
+# |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
+# |  AGPL-3.0, you are granted additional permissions described in the
+# |  MAgPIE License Exception, version 1.0 (see LICENSE file).
+# |  Contact: magpie@pik-potsdam.de
+
+# --------------------------------------------------------------
+# description: Convert all .mz files to NetCDF (.nc) for a magpie directory
+# comparison script: FALSE
+# ---------------------------------------------------------------
+
+# Version 1.00 - Michael Crawford
+# 1.00: first working version
+
+library(gms)
+library(magclass)
+
+############################# BASIC CONFIGURATION #######################################
+if (!exists("source_include")) {
+
+    title       <- NULL
+    outputdir   <- NULL
+
+    # Define arguments that can be read from command line
+    readArgs("outputdir", "title")
+
+}
+#########################################################################################
+
+message("Converting all .mz outputs to .nc for output directory: ", outputdir)
+
+mzFiles <- list.files(path = outputdir, pattern = "0\\.5(_share)?\\.mz$", full.names = TRUE)
+
+lapply(X = mzFiles, FUN = function(x) {
+    tryCatch({
+        magObj <- magclass::read.magpie(x)
+        newName <- sub("\\.[^.]+$", "", x)
+        write.magpie(x = magObj, file_name = paste0(newName, ".nc"), file_folder = outputdir, append = FALSE)
+    }, error = function(e) {
+        message("Error processing file: ", x, " - ", e$message)
+    })
+})
\ No newline at end of file