From 65c8ac67cd0c3684369b76c771b89badbef41a08 Mon Sep 17 00:00:00 2001 From: "Edgar P. Burkhart" Date: Fri, 8 Apr 2022 11:11:13 +0200 Subject: [PATCH] Updated mat file conversion: layered, layered vectors... --- swash/processing/mat_npz.py | 58 ++++----------- swash/processing/read_mat.py | 138 +++++++++++++++++++++++++++++++++++ 2 files changed, 152 insertions(+), 44 deletions(-) create mode 100644 swash/processing/read_mat.py diff --git a/swash/processing/mat_npz.py b/swash/processing/mat_npz.py index 0d4b6bc..4fb3865 100644 --- a/swash/processing/mat_npz.py +++ b/swash/processing/mat_npz.py @@ -9,6 +9,8 @@ from multiprocessing.pool import ThreadPool import numpy as np import scipy.io as sio +from .read_mat import ReadSwash + parser = argparse.ArgumentParser(description="Convert swash output to numpy") parser.add_argument("-v", "--verbose", action="count", default=0) parser.add_argument("-c", "--config", default="config.ini") @@ -26,48 +28,16 @@ inp = pathlib.Path(config.get("post", "inp")) inp.mkdir(parents=True, exist_ok=True) log.info(f"Reading swash output from '{sws_out}'") -raw_tsec = sio.loadmat(sws_out.joinpath("tsec.mat")) -i = np.fromiter( - (k[5:] for k in raw_tsec.keys() if re.compile(r"^Tsec_").match(k)), dtype="U10" -) -t = np.fromiter((raw_tsec[f"Tsec_{k}"][0, 0] * 10**3 for k in i), dtype=np.uintc) -np.save(inp.joinpath("t"), t) -del raw_tsec -raw_xp = sio.loadmat(sws_out.joinpath("xp.mat"), variable_names="Xp") -x = raw_xp["Xp"][0] -np.save(inp.joinpath("x"), x) -del raw_xp -raw_botl = sio.loadmat(sws_out.joinpath("botl.mat"), variable_names="Botlev") -botl = raw_botl["Botlev"][0] -np.save(inp.joinpath("botl"), botl) -del raw_botl, botl - -raw_watl = sio.loadmat(sws_out.joinpath("watl.mat")) -watl = np.asarray( - [raw_watl[i0][0] for i0 in np.char.add("Watlev_", i)], dtype=np.single -) -np.save(inp.joinpath("watl"), watl) -del raw_watl, watl - -raw_vel = sio.loadmat(sws_out.joinpath("vel.mat")) -vel_x = np.asarray([raw_vel[i0][0] for i0 in np.char.add("vel_x_", i)], dtype=np.single) -np.save(inp.joinpath("vel_x"), vel_x) -del raw_vel, vel_x - -raw_zk = sio.loadmat(sws_out.joinpath("zk.mat")) -n_zk = (len(raw_zk.keys()) - 3) // t.size -zk = np.asarray( - [ - raw_zk[i0][0] - for i0 in np.char.add( - np.char.replace("zki_", "i", np.arange(n_zk).astype("U1"), count=1)[ - None, : - ], - i[:, None], - ).reshape(-1) - ], - dtype=np.single, -).reshape((t.size, n_zk, x.size)) -np.save(inp.joinpath("zk"), zk) -del raw_zk, zk +swr = ReadSwash(sws_out, inp) +swr.save("t") +swr.save("x") +swr.save("c", "botl", "Botlev") +swr.save("s", "watl", "Watlev") +swr.save("s", "press", "Press") +swr.save("v", "vel", "vel") +swr.save("sk", "zk", "zk") +swr.save("sk", "nhprsk", "Nprs_k") +swr.save("sk", "pressk", "Pres_k") +swr.save("sk", "vz", "w") +swr.save("vk", "velk", "vel_k") diff --git a/swash/processing/read_mat.py b/swash/processing/read_mat.py new file mode 100644 index 0000000..9180c2d --- /dev/null +++ b/swash/processing/read_mat.py @@ -0,0 +1,138 @@ +import logging +import subprocess +import tempfile + +import numpy as np +import scipy.io as sio + + +log = logging.getLogger("read_mat") + + +class ReadSwash: + def __init__(self, root, out): + self._root = root + self._out = out + self._n_x = None + self._n_t = None + self._i = None + self._t = None + self._x = None + + def read_raw(self, var, var_names=None): + res = sio.loadmat(self._root.joinpath(f"{var}.mat"), variable_names=var_names) + res.pop("__header__") + res.pop("__version__") + res.pop("__globals__") + return res + + def read_t(self): + raw_t = self.read_raw("tsec") + self._i = np.char.lstrip(np.fromiter(raw_t.keys(), dtype="U15"), "Tsec_") + self._t = np.fromiter( + (raw_t[k][0, 0] * 10**3 for k in np.char.add("Tsec_", self._i)), + dtype=np.uintc, + ) + self._n_t = self._t.size + return self.t + + def read_x(self): + self._x = self.read_const("xp", "Xp") + self._n_x = self._x.size + return self.x + + def read_scalar(self, var, var_name): + raw = self.read_raw(var) + return np.asarray( + [raw[i0][0] for i0 in np.char.add(f"{var_name}_", self._i)], dtype=np.single + ) + + def read_const(self, var, var_name): + raw = self.read_raw(var, var_name) + return raw[var_name][0] + + def read_vector(self, var, var_name): + raw = self.read_raw(var) + return ( + np.asarray( + [raw[i0][0] for i0 in np.char.add(f"{var_name}_x_", self._i)], + dtype=np.single, + ), + np.asarray( + [raw[i0][0] for i0 in np.char.add(f"{var_name}_y_", self._i)], + dtype=np.single, + ), + ) + + def read_scalar_lay(self, var, var_name): + raw = self.read_raw(var) + n = len(raw.keys()) // self._n_t + ra = (n,) if f"{var_name}0_{self._i[0]}" in raw.keys() else (1, n + 1) + return np.asarray( + [ + raw[i0][0] + for i0 in np.char.add( + np.char.replace(f"{var_name}[]_", "[]", np.arange(*ra).astype("U1"))[ + None, : + ], + self._i[:, None], + ).reshape(-1) + ], + dtype=np.single, + ).reshape((self._n_t, n, self._n_x)) + + def read_vector_lay(self, var, var_name): + raw = self.read_raw(var) + n = len(raw.keys()) // (self._n_t * 2) + ra = (n,) if f"{var_name}0_x_{self._i[0]}" in raw.keys() else (1, n + 1) + return ( + np.asarray( + [ + raw[i0][0] + for i0 in np.char.add( + np.char.replace( + f"{var_name}[]_x_", "[]", np.arange(*ra).astype("U1") + )[None, :], + self._i[:, None], + ).reshape(-1) + ], + dtype=np.single, + ).reshape((self._n_t, n, self._n_x)), + np.asarray( + [ + raw[i0][0] + for i0 in np.char.add( + np.char.replace( + f"{var_name}[]_y_", "[]", np.arange(*ra).astype("U1") + )[None, :], + self._i[:, None], + ).reshape(-1) + ], + dtype=np.single, + ).reshape((self._n_t, n, self._n_x)), + ) + + def save(self, t, var=None, var_name=None): + fct = { + "t": self.read_t, + "x": self.read_x, + "s": self.read_scalar, + "c": self.read_const, + "v": self.read_vector, + "sk": self.read_scalar_lay, + "vk": self.read_vector_lay, + } + if t in ("x", "t"): + log.info(f"Converting {t}") + np.save(self._out.joinpath(t), fct[t]()) + else: + log.info(f"Converting {var}") + np.save(self._out.joinpath(var), fct[t](var, var_name)) + + @property + def t(self): + return self._t + + @property + def x(self): + return self._x