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"""
NetCDF4 file IO
"""
from netCDF4 import Dataset
from pathlib import Path
import typing as T
import numpy as np
from datetime import datetime
from .utils import datetime2ymd_hourdec
LSP = 7
def get_simsize(path: Path) -> T.Tuple[int, ...]:
"""
get simulation size
"""
path = Path(path).expanduser().resolve()
with Dataset(path, "r") as f:
if "lxs" in f.variables:
lxs = f["lxs"][:]
elif "lx" in f.variables:
lxs = f["lx"][:]
elif "lx1" in f.variables:
if f["lx1"].ndim > 0:
lxs = (f["lx1"][:].squeeze()[()], f["lx2"][:].squeeze()[()], f["lx3"][:].squeeze()[()])
else:
lxs = (f["lx1"][()], f["lx2"][()], f["lx3"][()])
else:
raise KeyError(f"could not find 'lxs', 'lx' or 'lx1' in {path.as_posix()}")
return lxs.data
def readgrid(fn: Path) -> T.Dict[str, np.ndarray]:
raise NotImplementedError("TODO: NetCDF4 simgrid.nc")
def write_grid(p: T.Dict[str, T.Any], xg: T.Dict[str, T.Any]):
""" writes grid to disk
Parameters
----------
p: dict
simulation parameters
xg: dict
grid values
"""
(p["out_dir"] / "inputs").mkdir(parents=True, exist_ok=True)
fn = p["out_dir"] / "inputs/simsize.nc"
print("write_grid:", fn)
with Dataset(fn, "w") as f:
f.createDimension("length", len(xg["lx"]))
g = f.createVariable("lx", np.int32, ("length",))
g[:] = xg["lx"]
fn = p["out_dir"] / "inputs/simgrid.nc"
print("write_grid:", fn)
Ng = 4 # number of ghost cells
with Dataset(fn, "w") as f:
f.createDimension("x1ghost", xg["lx"][0] + Ng)
f.createDimension("x1d", xg["lx"][0] + Ng - 1)
f.createDimension("x1i", xg["lx"][0] + 1)
f.createDimension("x1", xg["lx"][0])
f.createDimension("x2ghost", xg["lx"][1] + Ng)
f.createDimension("x2d", xg["lx"][1] + Ng - 1)
f.createDimension("x2i", xg["lx"][1] + 1)
f.createDimension("x2", xg["lx"][1])
f.createDimension("x3ghost", xg["lx"][2] + Ng)
f.createDimension("x3d", xg["lx"][2] + Ng - 1)
f.createDimension("x3i", xg["lx"][2] + 1)
f.createDimension("x3", xg["lx"][2])
f.createDimension("ecef", 3)
for i in (1, 2, 3):
_write_var(f, f"x{i}", (f"x{i}ghost",), xg[f"x{i}"])
_write_var(f, f"x{i}i", (f"x{i}i",), xg[f"x{i}i"])
_write_var(f, f"dx{i}b", (f"x{i}d",), xg[f"dx{i}b"])
_write_var(f, f"dx{i}h", (f"x{i}",), xg[f"dx{i}h"])
_write_var(f, f"h{i}", ("x1ghost", "x2ghost", "x3ghost"), xg[f"h{i}"])
_write_var(f, f"h{i}x1i", ("x1i", "x2", "x3"), xg[f"h{i}x1i"])
_write_var(f, f"h{i}x2i", ("x1", "x2i", "x3"), xg[f"h{i}x2i"])
_write_var(f, f"h{i}x3i", ("x1", "x2", "x3i"), xg[f"h{i}x3i"])
_write_var(f, f"gx{i}", ("x1", "x2", "x3"), xg[f"gx{i}"])
_write_var(f, f"e{i}", ("x1", "x2", "x3", "ecef"), xg[f"e{i}"])
for k in ("alt", "glat", "glon", "Bmag", "nullpts", "r", "theta", "phi", "x", "y", "z"):
_write_var(f, k, ("x1", "x2", "x3"), xg[k])
for k in ("er", "etheta", "ephi"):
_write_var(f, k, ("x1", "x2", "x3", "ecef"), xg[k])
_write_var(f, "I", ("x2", "x3"), xg["I"])
def _write_var(f, name: str, dims: tuple, value: np.ndarray):
g = f.createVariable(name, np.float32, dims, zlib=True, complevel=1, shuffle=True, fletcher32=True, fill_value=np.nan)
g[:] = value
def write_state(time: datetime, ns: np.ndarray, vs: np.ndarray, Ts: np.ndarray, out_dir: Path):
"""
WRITE STATE VARIABLE DATA.
NOTE THAT WE don't write ANY OF THE ELECTRODYNAMIC
VARIABLES SINCE THEY ARE NOT NEEDED TO START THINGS
UP IN THE FORTRAN CODE.
INPUT ARRAYS SHOULD BE TRIMMED TO THE CORRECT SIZE
I.E. THEY SHOULD NOT INCLUDE GHOST CELLS
"""
fn = out_dir / "inputs/initial_conditions.nc"
print("write_state:", fn)
with Dataset(fn, "w") as f:
f.createDimension("ymd", 3)
g = f.createVariable("ymd", np.int32, "ymd")
g[:] = [time.year, time.month, time.day]
g = f.createVariable("UTsec", np.float32)
g[:] = time.hour * 3600 + time.minute * 60 + time.second + time.microsecond / 1e6
f.createDimension("species", 7)
f.createDimension("x1", ns.shape[1])
f.createDimension("x2", ns.shape[2])
f.createDimension("x3", ns.shape[3])
_write_var(f, "ns", ("species", "x1", "x2", "x3"), ns)
_write_var(f, "vsx1", ("species", "x1", "x2", "x3"), vs)
_write_var(f, "Ts", ("species", "x1", "x2", "x3"), Ts)
def write_Efield(p: T.Dict[str, T.Any], E: T.Dict[str, np.ndarray]):
"""
write Efield to disk
TODO: verify dimensions vs. data vs. Fortran order
"""
outdir = E["Efield_outdir"]
print("write E-field data to", outdir)
with Dataset(outdir / "simsize.nc", "w") as f:
for k in ("llon", "llat"):
g = f.createVariable(k, np.int32)
g[:] = E[k]
with Dataset(outdir / "simgrid.nc", "w") as f:
f.createDimension("lon", E["mlon"].size)
f.createDimension("lat", E["mlat"].size)
_write_var(f, "mlon", ("lon",), E["mlon"])
_write_var(f, "mlat", ("lat",), E["mlat"])
for i, t in enumerate(E["time"]):
fn = outdir / (datetime2ymd_hourdec(t) + ".nc")
# FOR EACH FRAME WRITE A BC TYPE AND THEN OUTPUT BACKGROUND AND BCs
with Dataset(fn, "w") as f:
f.createDimension("lon", E["mlon"].size)
f.createDimension("lat", E["mlat"].size)
g = f.createVariable("flagdirich", np.int32)
g[:] = p["flagdirich"]
f.createDimension("ymd", 3)
g = f.createVariable("ymd", np.int32, "ymd")
g[:] = [t.year, t.month, t.day]
g = f.createVariable("UTsec", np.float32)
g[:] = t.hour * 3600 + t.minute * 60 + t.second + t.microsecond / 1e6
for k in ("Exit", "Eyit", "Vminx1it", "Vmaxx1it"):
_write_var(f, k, ("lon", "lat"), E[k][i, :, :])
for k in ("Vminx2ist", "Vmaxx2ist"):
_write_var(f, k, ("lat",), E[k][i, :])
for k in ("Vminx3ist", "Vmaxx3ist"):
_write_var(f, k, ("lon",), E[k][i, :])
def write_precip(precip: T.Dict[str, np.ndarray]):
"""
write precipitation to disk
TODO: verify dimensions vs. data vs. Fortran order
"""
outdir = precip["precip_outdir"]
print("write precipitation data to", outdir)
with Dataset(outdir / "simsize.nc", "w") as f:
for k in ("llon", "llat"):
g = f.createVariable(k, np.int32)
g[:] = precip[k]
with Dataset(outdir / "simgrid.nc", "w") as f:
f.createDimension("lon", precip["mlon"].size)
f.createDimension("lat", precip["mlat"].size)
_write_var(f, "mlon", ("lon",), precip["mlon"])
_write_var(f, "mlat", ("lat",), precip["mlat"])
for i, t in enumerate(precip["time"]):
fn = outdir / (datetime2ymd_hourdec(t) + ".nc")
with Dataset(fn, "w") as f:
f.createDimension("lon", precip["mlon"].size)
f.createDimension("lat", precip["mlat"].size)
for k in ("Q", "E0"):
_write_var(f, f"/{k}p", ("lon", "lat"), precip[k][i, :, :])