From 331c21913440affe342767b602a0f2671edeb722 Mon Sep 17 00:00:00 2001
From: Nikolay Koldunov <koldunovn@gmail.com>
Date: Thu, 29 Feb 2024 21:04:58 +0100
Subject: [PATCH] Add missing_value option to save_data function

---
 src/fint/fint.py  | 13 +++++++++++++
 test/Taskfile.yml |  9 +++++++++
 2 files changed, 22 insertions(+)

diff --git a/src/fint/fint.py b/src/fint/fint.py
index 64c8a55..5008f72 100644
--- a/src/fint/fint.py
+++ b/src/fint/fint.py
@@ -443,6 +443,7 @@ def save_data(
     lon,
     lat,
     out_path,
+    missing_value=None,
 ):
     """
     Saves the interpolated data to a NetCDF file.
@@ -477,6 +478,10 @@ def save_data(
     else:
         out_time = np.atleast_1d(data.time.data[timesteps])
 
+    if missing_value is not None:
+        interpolated3d = np.where(np.isnan(interpolated3d), missing_value, interpolated3d)
+
+
     out1 = xr.Dataset(
         {variable_name: (["time", "depth", "lat", "lon"], interpolated3d)},
         coords={
@@ -678,6 +683,12 @@ def fint(args=None):
               Valid units are 'D' (days), 'h' (hours), 'm' (minutes), 's' (seconds). \
               To substract timedelta, put argument in quotes, and prepend ' -', so SPACE and then -, e.g. ' -10D'.",
     )
+    parser.add_argument(
+        "--missing_value",
+        default=None,
+        type=float,
+        help="Missing value for the output file. Default is None.",
+    )
 
     args = parser.parse_args()
 
@@ -1065,6 +1076,7 @@ def fint(args=None):
             lon,
             lat,
             out_path,
+            missing_value=args.missing_value,
         )
         if args.rotate:
             save_data(
@@ -1079,6 +1091,7 @@ def fint(args=None):
                 lon,
                 lat,
                 out_path2,
+                missing_value=args.missing_value,
             )
 
 
diff --git a/test/Taskfile.yml b/test/Taskfile.yml
index 910f17b..4f50513 100644
--- a/test/Taskfile.yml
+++ b/test/Taskfile.yml
@@ -23,6 +23,7 @@ tasks:
       - task: 3d_nodes_interfaces
       - task: 2d_elements
       - task: timedelta
+      - task: missing_value
       - task: cleanup
 
   download_test_data:
@@ -153,6 +154,14 @@ tasks:
      - fint ${FILE} ${MESH} ${INFL} -t 0:10 --timedelta '1h'
      - fint ${FILE} ${MESH} ${INFL} -t 0:10 --timedelta ' -1h'
 
+  missing_value:
+    deps:
+      - download_test_data
+    env:
+      FILE: "./test/data/ssh.fesom.1948.nc" 
+    cmds:
+      - fint ${FILE} ${MESH} ${INFL} -t 0:3 --missing_value -9999
+
   cleanup:
     cmds:
       - python -c "import os; [os.remove(f) for f in os.listdir() if f.endswith('.nc')]"