From f816c25865bfe5d4101b1aaa21f90cf26586ea51 Mon Sep 17 00:00:00 2001
From: "Edgar P. Burkhart" <git@edgarpierre.fr>
Date: Wed, 2 Mar 2022 12:21:48 +0100
Subject: [PATCH] Pre-processing

---
 swash/config.ini          |  2 +-
 swash/processing/bathy.py | 35 +++++++++++++++++++++++++++++------
 2 files changed, 30 insertions(+), 7 deletions(-)

diff --git a/swash/config.ini b/swash/config.ini
index 31a9864..3a14e2c 100644
--- a/swash/config.ini
+++ b/swash/config.ini
@@ -1,5 +1,5 @@
 [proc]
-plot=True
+#plot=True
 
 [data]
 root=data
diff --git a/swash/processing/bathy.py b/swash/processing/bathy.py
index a17a0ef..1574817 100644
--- a/swash/processing/bathy.py
+++ b/swash/processing/bathy.py
@@ -1,4 +1,5 @@
 import pathlib
+import argparse
 import configparser
 import logging
 import sys
@@ -12,7 +13,11 @@ except ImportError:
     plt = None
 
 
-logging.basicConfig(level="INFO")
+parser = argparse.ArgumentParser(description="Pre-process bathymetry")
+parser.add_argument("-v", "--verbose", action="count", default=0)
+args = parser.parse_args()
+
+logging.basicConfig(level=max((10, 20 - 10 * args.verbose)))
 log = logging.getLogger("bathy")
 
 log.info("Starting bathymetry pre-processing")
@@ -25,6 +30,8 @@ log.info(f"Reading input data from '{root}'")
 bathy_hires = np.loadtxt(root.joinpath(config.get("data", "hires")))
 bathy_lores = np.loadtxt(root.joinpath(config.get("data", "bathy")))
 hstru = np.loadtxt(root.joinpath(config.get("data", "hstru")))
+poro = np.loadtxt(root.joinpath(config.get("data", "poro")))
+psize = np.loadtxt(root.joinpath(config.get("data", "psize")))
 
 log.info("Generating grid")
 x_hires = np.arange(-0.5 * bathy_hires.size, 0, 0.5)
@@ -37,19 +44,33 @@ bathy_lores_pd = pd.Series(bathy_lores.copy(), index=x_lores)
 
 bathy = pd.DataFrame(
     index=bathy_lores_pd.index.union(bathy_hires_pd.index),
-    columns=("z", "hstru"),
+    columns=("z", "hstru", "poro", "psize"),
+    data=0,
 )
 bathy.z[bathy_lores_pd.index] = bathy_lores_pd
 bathy.z[bathy_hires_pd.index] = bathy_hires_pd
 
-bathy.hstru = 0
-bathy.loc[x_hstru, "hstru"] = hstru
+bathy.loc[x_hstru, ("hstru", "poro", "psize")] = np.array(
+    (hstru, poro, psize)
+).T
+
+bathy = bathy.reindex(bathy_lores_pd.index)
+log.debug(f"Bathymetry:\n{bathy}")
+log.info(
+    f"xmin: {bathy.index.min()}, "
+    f"xmax: {bathy.index.max()}, "
+    f"n: {bathy.index.size}"
+)
 
 if config.has_section("out"):
-    log.info("Writing output data")
     out = pathlib.Path(config.get("out", "root"))
+    log.info(f"Writing output data to '{out}'")
     np.savetxt(out.joinpath("bathy.dat"), bathy.z, newline=" ")
     np.savetxt(out.joinpath("hstru.dat"), bathy.hstru, newline=" ")
+    np.savetxt(out.joinpath("poro.dat"), bathy.poro, newline=" ")
+    np.savetxt(out.joinpath("psize.dat"), bathy.psize, newline=" ")
+
+    bathy.to_hdf(out.joinpath("bathy.h5"), "bathy", mode="w")
 
 if config.getboolean("proc", "plot", fallback=False):
     if plt is None:
@@ -62,7 +83,9 @@ if config.getboolean("proc", "plot", fallback=False):
     ax.plot(x_hires, bathy_hires, label="High-res")
     ax.plot(x_lores, bathy_lores, label="Low-res")
     ax.plot(bathy.index, bathy.z, ls="-.", c="k", label="Combined")
-    ax.plot(bathy.index, bathy.hstru, label="H stru")
+    ax.plot(bathy.index, bathy.hstru, label="Hstru")
+    ax.plot(bathy.index, bathy.poro, label="Poro")
+    ax.plot(bathy.index, bathy.psize, label="Psize")
 
     ax.grid()
     ax.legend()