From 515037efeccd0dac5a2bba60f186ec18ec2d64e6 Mon Sep 17 00:00:00 2001
From: Geet George <g.george@tudelft.nl>
Date: Mon, 13 Nov 2023 17:18:39 +0100
Subject: [PATCH 1/3] add L2 placeholder steps

---
 src/halodrops/pipeline.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/src/halodrops/pipeline.py b/src/halodrops/pipeline.py
index a233eaa..bc9e5a1 100644
--- a/src/halodrops/pipeline.py
+++ b/src/halodrops/pipeline.py
@@ -296,4 +296,18 @@ def run_pipeline(pipeline: dict, config: configparser.ConfigParser):
         ],
         "output": "sondes",
     },
+    "create_L2": {
+        "intake": "sondes",
+        "apply": iterate_Sonde_method_over_dict_of_Sondes_objects,
+        "functions": [],
+        "output": "sondes",
+        "comment": "This steps creates the L2 files after the QC (user says how QC flags are used to go from L1 to L2) and then saves these as L2 NC datasets.",
+    },
+    "read_and_process_L2": {
+        "intake": "sondes",
+        "apply": iterate_Sonde_method_over_dict_of_Sondes_objects,
+        "functions": [],
+        "output": "sondes",
+        "comment": "This step reads from the saved L2 files and prepares individual sonde datasets before they can be concatenated to create L3.",
+    },
 }

From a52991ee459180deabef57fd994601b9faf550b6 Mon Sep 17 00:00:00 2001
From: Geet George <g.george@tudelft.nl>
Date: Tue, 14 Nov 2023 17:26:18 +0100
Subject: [PATCH 2/3] add placeholder fns and pipeline steps from L2 to L4

---
 src/halodrops/pipeline.py | 54 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)

diff --git a/src/halodrops/pipeline.py b/src/halodrops/pipeline.py
index bc9e5a1..708a830 100644
--- a/src/halodrops/pipeline.py
+++ b/src/halodrops/pipeline.py
@@ -202,6 +202,23 @@ def iterate_Sonde_method_over_dict_of_Sondes_objects(
     return my_dict
 
 
+def sondes_to_gridded(sondes: dict) -> xr.Dataset:
+    pass
+
+
+def iterate_method_over_dataset(dataset: xr.Dataset, functions: list) -> xr.Dataset:
+    pass
+
+
+def gridded_to_pattern(
+    gridded: xr.Dataset, config: configparser.ConfigParser
+) -> xr.Dataset:
+    """
+    The flight-phase segmentation file must be provided via the config file.
+    """
+    pass
+
+
 def run_substep(
     previous_substep_output, substep: dict, config: configparser.ConfigParser
 ):
@@ -310,4 +327,41 @@ def run_pipeline(pipeline: dict, config: configparser.ConfigParser):
         "output": "sondes",
         "comment": "This step reads from the saved L2 files and prepares individual sonde datasets before they can be concatenated to create L3.",
     },
+    "concatenate_L2": {
+        "intake": "sondes",
+        "apply": sondes_to_gridded,
+        "output": "gridded",
+        "comment": "This step concatenates the individual sonde datasets to create the L3 dataset and saves it as an NC file.",
+    },
+    "create_L3": {
+        "intake": "gridded",
+        "apply": iterate_method_over_dataset,
+        "functions": [],
+        "output": "gridded",
+        "comment": "This step creates the L3 dataset after adding additional products.",
+    },
+    "create_patterns": {
+        "intake": "gridded",
+        "apply": gridded_to_pattern,
+        "output": "pattern",
+        "comment": "This step creates a dataset with the pattern-wide variables by creating the pattern with the flight-phase segmentation file.",
+    },
+    "create_L4": {
+        "intake": "pattern",
+        "apply": iterate_method_over_dataset,
+        "functions": [],
+        "output": "pattern",
+        "comment": "This step creates the L4 dataset after adding additional products and saves the L4 dataset.",
+    },
+    "quicklooks": {
+        "intake": ["sondes", "gridded", "pattern"],
+        "apply": [
+            iterate_Sonde_method_over_dict_of_Sondes_objects,
+            iterate_method_over_dataset,
+            iterate_method_over_dataset,
+        ],
+        "functions": [[], [], []],
+        "output": "plots",
+        "comment": "This step creates quicklooks from the L3 & L4 dataset.",
+    },
 }

From 1a5e2f4d2a32327d8d3492e8272508549903dad2 Mon Sep 17 00:00:00 2001
From: Geet George <g.george@tudelft.nl>
Date: Tue, 14 Nov 2023 17:33:24 +0100
Subject: [PATCH 3/3] import xarray

---
 src/halodrops/pipeline.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/halodrops/pipeline.py b/src/halodrops/pipeline.py
index 708a830..97f5975 100644
--- a/src/halodrops/pipeline.py
+++ b/src/halodrops/pipeline.py
@@ -2,6 +2,7 @@
 from .sonde import Sonde
 import configparser
 import inspect
+import xarray as xr
 
 
 def get_mandatory_args(function):