From ef2e23ab15d36d871517331cf6ae108da9ae5074 Mon Sep 17 00:00:00 2001
From: "Edgar P. Burkhart" <git@edgarpierre.fr>
Date: Mon, 7 Mar 2022 11:10:01 +0100
Subject: [PATCH 1/4] Fixed sws_ola conversion

---
 olaflow/processing/sws_ola.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/olaflow/processing/sws_ola.py b/olaflow/processing/sws_ola.py
index f0083e2..0eb4ddb 100644
--- a/olaflow/processing/sws_ola.py
+++ b/olaflow/processing/sws_ola.py
@@ -32,6 +32,8 @@ of_x, of_y, of_z = mesh = readof.readmesh(str(olaflow_root))
 
 watl = interpolate.interp1d(x, sws["watl"][680])
 
+alpha_water = np.where(of_z < watl(of_x), "1", "0")
+
 with open(olaflow_root.joinpath("0", "alpha.water"), "r") as aw_file:
     aw_raw = aw_file.read()
 
@@ -39,7 +41,7 @@ with open(olaflow_root.joinpath("0", "alpha.water"), "w") as aw_file:
     aw_file.write(
         re.sub(
             r"(?<=\(\n).*?(?=\n\))",
-            "\n".join(map(str, alpha_water)),
+            "\n".join(alpha_water),
             aw_raw,
             count=1,
             flags=re.S,

From 62af6a03ed6ebbc7645d1da45ded79e04a9fc559 Mon Sep 17 00:00:00 2001
From: "Edgar P. Burkhart" <git@edgarpierre.fr>
Date: Mon, 7 Mar 2022 11:19:37 +0100
Subject: [PATCH 2/4] Added OFModel class to write fields

---
 olaflow/processing/olaflow.py | 21 +++++++++++++++++++++
 olaflow/processing/sws_ola.py | 19 +++++--------------
 2 files changed, 26 insertions(+), 14 deletions(-)
 create mode 100644 olaflow/processing/olaflow.py

diff --git a/olaflow/processing/olaflow.py b/olaflow/processing/olaflow.py
new file mode 100644
index 0000000..9556a84
--- /dev/null
+++ b/olaflow/processing/olaflow.py
@@ -0,0 +1,21 @@
+import re
+
+
+class OFModel:
+    def __init__(self, root):
+        self._root = root
+
+    def write_field(self, field, values):
+        with open(self._root.joinpath("0", field), "r") as aw_file:
+            aw_raw = aw_file.read()
+
+        with open(self._root.joinpath("0", field), "w") as aw_file:
+            aw_file.write(
+                re.sub(
+                    r"(?<=\(\n).*?(?=\n\))",
+                    "\n".join(values.astype(str)),
+                    aw_raw,
+                    count=1,
+                    flags=re.S,
+                )
+            )
diff --git a/olaflow/processing/sws_ola.py b/olaflow/processing/sws_ola.py
index 0eb4ddb..97940ec 100644
--- a/olaflow/processing/sws_ola.py
+++ b/olaflow/processing/sws_ola.py
@@ -9,6 +9,8 @@ import numpy as np
 from fluidfoam import readof
 from scipy import interpolate
 
+from .olaflow import OFModel
+
 parser = argparse.ArgumentParser(
     description="Convert swash output to olaFlow input"
 )
@@ -32,18 +34,7 @@ of_x, of_y, of_z = mesh = readof.readmesh(str(olaflow_root))
 
 watl = interpolate.interp1d(x, sws["watl"][680])
 
-alpha_water = np.where(of_z < watl(of_x), "1", "0")
+alpha_water = np.where(of_z < watl(of_x), 1, 0)
 
-with open(olaflow_root.joinpath("0", "alpha.water"), "r") as aw_file:
-    aw_raw = aw_file.read()
-
-with open(olaflow_root.joinpath("0", "alpha.water"), "w") as aw_file:
-    aw_file.write(
-        re.sub(
-            r"(?<=\(\n).*?(?=\n\))",
-            "\n".join(alpha_water),
-            aw_raw,
-            count=1,
-            flags=re.S,
-        )
-    )
+model = OFModel(olaflow_root)
+model.write_field("alpha.water", alpha_water)

From 4869c982bb7c07fd7bd54d378e1ea4e4bb5756cc Mon Sep 17 00:00:00 2001
From: "Edgar P. Burkhart" <git@edgarpierre.fr>
Date: Mon, 7 Mar 2022 11:30:53 +0100
Subject: [PATCH 3/4] Moved fluidfoam to olaflow file

---
 olaflow/processing/olaflow.py | 17 +++++++++++++++++
 olaflow/processing/sws_ola.py |  8 +++-----
 2 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/olaflow/processing/olaflow.py b/olaflow/processing/olaflow.py
index 9556a84..520289b 100644
--- a/olaflow/processing/olaflow.py
+++ b/olaflow/processing/olaflow.py
@@ -1,10 +1,15 @@
 import re
 
+from fluidfoam import readof
+
 
 class OFModel:
     def __init__(self, root):
         self._root = root
 
+    def read_mesh(self):
+        self._x, self._y, self._z = readof.readmesh(str(self._root))
+
     def write_field(self, field, values):
         with open(self._root.joinpath("0", field), "r") as aw_file:
             aw_raw = aw_file.read()
@@ -19,3 +24,15 @@ class OFModel:
                     flags=re.S,
                 )
             )
+
+    @property
+    def x(self):
+        return self._x
+
+    @property
+    def y(self):
+        return self._y
+
+    @property
+    def z(self):
+        return self._z
diff --git a/olaflow/processing/sws_ola.py b/olaflow/processing/sws_ola.py
index 97940ec..7b416be 100644
--- a/olaflow/processing/sws_ola.py
+++ b/olaflow/processing/sws_ola.py
@@ -6,7 +6,6 @@ import re
 
 import matplotlib.pyplot as plt
 import numpy as np
-from fluidfoam import readof
 from scipy import interpolate
 
 from .olaflow import OFModel
@@ -30,11 +29,10 @@ sws = np.load(sws_out.joinpath("sws.npz"))
 x, t = sws["x"], sws["t"]
 
 olaflow_root = pathlib.Path(config.get("olaflow", "root"))
-of_x, of_y, of_z = mesh = readof.readmesh(str(olaflow_root))
+model = OFModel(olaflow_root)
+model.read_mesh()
 
 watl = interpolate.interp1d(x, sws["watl"][680])
+alpha_water = np.where(model.z < watl(model.x), 1, 0)
 
-alpha_water = np.where(of_z < watl(of_x), 1, 0)
-
-model = OFModel(olaflow_root)
 model.write_field("alpha.water", alpha_water)

From 434db6af7c19f0e1aeef77ed204293adda446c80 Mon Sep 17 00:00:00 2001
From: "Edgar P. Burkhart" <git@edgarpierre.fr>
Date: Mon, 7 Mar 2022 11:34:32 +0100
Subject: [PATCH 4/4] Removed unused imports

---
 olaflow/processing/sws_ola.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/olaflow/processing/sws_ola.py b/olaflow/processing/sws_ola.py
index 7b416be..578d92c 100644
--- a/olaflow/processing/sws_ola.py
+++ b/olaflow/processing/sws_ola.py
@@ -2,9 +2,7 @@ import argparse
 import configparser
 import logging
 import pathlib
-import re
 
-import matplotlib.pyplot as plt
 import numpy as np
 from scipy import interpolate