From 868e34777ed294533edf9168a6a2a0ade9a020f4 Mon Sep 17 00:00:00 2001
From: "Edgar P. Burkhart" <git@edgarpierre.fr>
Date: Fri, 4 Mar 2022 10:21:02 +0100
Subject: [PATCH] Changed swash reading procedure to read time and space data
 from output

---
 swash/processing/read_swash.py | 57 +++++++++++++++++++++++++---------
 swash/processing/sws_npz.py    | 34 ++++++++++----------
 2 files changed, 59 insertions(+), 32 deletions(-)

diff --git a/swash/processing/read_swash.py b/swash/processing/read_swash.py
index 62ddf5f..9287e30 100644
--- a/swash/processing/read_swash.py
+++ b/swash/processing/read_swash.py
@@ -1,28 +1,55 @@
 import numpy as np
 
 
-def read_nohead(path):
-    with open(path) as file:
-        return file.read()
+class ReadSwash:
+    def __init__(self):
+        self._n_x = None
+        self._n_t = None
+        self._t = None
+        self._x = None
+        self._data = None
 
+    @classmethod
+    def read_nohead(cls, path):
+        with open(path) as file:
+            return np.asarray(file.read().split(), dtype=np.float64)
 
-def read_reshape(path, shape):
-    return np.asarray(read_nohead(path).split(), dtype=np.float64).reshape(
-        shape
-    )
+    def read_time(self, path):
+        self._t = np.unique(self.read_nohead(path))
+        self._n_t = self._t.size
 
+    def read_x(self, path):
+        self._x = np.unique(self.read_nohead(path))
+        self._n_x = self._x.size
 
-def read_nohead_scalar(path, n):
-    return read_reshape(path, (-1, n))
+    def read_scalar(self, path):
+        self._data[path.stem] = self.read_nohead(path).reshape(
+            (self._n_t, self._n_x)
+        )
 
+    def read_vector(self, path):
+        self._data[path.stem] = self.read_nohead(path).reshape(
+            (self._n_t, 2, self._n_x)
+        )
 
-def read_nohead_k(path, n, k):
-    return read_reshape(path, (-1, n, k))
+    def read_scalar_lay(self, path):
+        self._data[path.stem] = self.read_nohead(path).reshape(
+            (self._n_t, -1, self._n_x)
+        )
 
+    def read_vector_lay(self, path):
+        self._data[path.stem] = self.read_nohead(path).reshape(
+            (self._n_t, 2, -1, self._n_x)
+        )
 
-def read_nohead_vect(path, n):
-    return read_reshape(path, (-1, 2, n))
+    @property
+    def t(self):
+        return self._t
 
+    @property
+    def x(self):
+        return self._x
 
-def read_nohead_vect_k(path, n):
-    return read_reshape(path, (-1, 2, n, k))
+    @property
+    def data(self):
+        return self._data
diff --git a/swash/processing/sws_npz.py b/swash/processing/sws_npz.py
index 1274732..077b045 100644
--- a/swash/processing/sws_npz.py
+++ b/swash/processing/sws_npz.py
@@ -1,12 +1,11 @@
 import argparse
 import configparser
-import pathlib
 import logging
+import pathlib
 
 import pandas as pd
 
-from .read_swash import *
-
+from .read_swash import ReadSwash
 
 parser = argparse.ArgumentParser(description="Convert swash output to numpy")
 parser.add_argument("-v", "--verbose", action="count", default=0)
@@ -19,25 +18,26 @@ log.info("Starting sws -> npz converter")
 config = configparser.ConfigParser()
 config.read("config.ini")
 
-data_out = pathlib.Path(config.get("data", "out"))
 sws_out = pathlib.Path(config.get("swash", "out"))
 inp = pathlib.Path(config.get("post", "inp"))
 
-log.info(f"Reading bathymetry from '{data_out}'")
-bathy = pd.read_hdf(data_out.joinpath("bathy.h5"), "bathy")
-n_x = bathy.index.size
-
 log.info(f"Reading swash output from '{sws_out}'")
-botl = read_nohead_scalar(sws_out.joinpath("botl.dat"), n_x)
-dep = np.maximum(0, read_nohead_scalar(sws_out.joinpath("dep.dat"), n_x))
-vel = read_nohead_vect(sws_out.joinpath("vel.dat"), n_x)
+rsws = ReadSwash()
+rsws.read_time(sws_out.joinpath("tsec.dat"))
+rsws.read_x(sws_out.joinpath("xp.dat"))
 
-dt = config.getfloat("post", "dt")
-n_t = botl.shape[0]
-t = np.arange(0, n_t * dt, dt)
+rsws.read_scalar(sws_out.joinpath("dep.dat"))
+rsws.read_scalar(sws_out.joinpath("botl.dat"))
+rsws.read_scalar(sws_out.joinpath("watl.dat"))
+rsws.read_scalar(sws_out.joinpath("press.dat"))
+rsws.read_vector(sws_out.joinpath("disch.dat"))
+rsws.read_scalar(sws_out.joinpath("ustar.dat"))
+rsws.read_vector(sws_out.joinpath("vel.dat"))
+rsws.read_scalar_lay(sws_out.joinpath("vz.dat"))
+rsws.read_vector_lay(sws_out.joinpath("velk.dat"))
+rsws.read_scalar_lay(sws_out.joinpath("zk.dat"))
+rsws.read_scalar(sws_out.joinpath("brkp.dat"))
 
 log.info(f"Writing npz file in '{inp}'")
 inp.mkdir(exist_ok=True)
-np.savez_compressed(
-    inp.joinpath("sws"), x=bathy.index, t=t, botl=botl[0, :], dep=dep, vel=vel
-)
+np.savez_compressed(inp.joinpath("sws"), t=rsws.t, x=rsws.x, *rsws.data)