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Code source de axqua.core.selafin
"""Minimal, self-contained SELAFIN (Serafin) writer for TELEMAC geometry files.
Single-precision, big-endian, Fortran-record layout following the de-facto
reference implementation (pputils ``ppSELAFIN``). Vectorized with numpy so it
scales to large meshes. We only need to *write* a 2D geometry file (one frame
holding the BOTTOM variable), which TELEMAC reads as the GEOMETRY FILE.
A SELAFIN record is ``<int32 nbytes><payload><int32 nbytes>`` (the integers are
Fortran unformatted record markers), everything big-endian.
"""
from __future__ import annotations
import logging
from pathlib import Path
from typing import Sequence
import numpy as np
log = logging.getLogger("axqua")
_I4 = np.dtype(">i4")
_F4 = np.dtype(">f4")
_F8 = np.dtype(">f8")
def _record(payload: bytes) -> bytes:
marker = np.array(len(payload), dtype=_I4).tobytes()
return marker + payload + marker
def _read_record(f) -> bytes | None:
"""Read one Fortran unformatted record; return its payload (None at EOF)."""
head = f.read(4)
if len(head) < 4:
return None
n = int(np.frombuffer(head, dtype=_I4)[0])
payload = f.read(n)
f.read(4) # trailing record marker
return payload
[docs]
def read_slf(path: str | Path, *, frame: int = -1) -> dict:
"""Read a SERAFIN/SELAFIN file (our writer's output or a TELEMAC result).
Returns a dict with ``x``, ``y`` (NPOIN floats), ``ikle`` (NELEM×NDP, 0-based),
``ipobo``, ``var_names`` (list[str]), ``nplan``, the selected frame ``time`` and
its per-variable node arrays in ``values``. *frame* indexes the time steps
(default ``-1`` = last; a steady run's final state). Single- and double-precision
SERAFIN are both handled.
**3D results** (``nplan > 1``, e.g. a TELEMAC-3D ``r3d.slf``) are unrolled rather
than left flat: SERAFIN stores a 3D field plane by plane over the same 2D mesh, so
``x``/``y`` are cut back to the ``npoin2`` plan nodes and every variable comes back
shaped ``(nplan, npoin2)``. A 2D file is unchanged - ``nplan == 1`` and values stay
``(NPOIN,)`` - so nothing that reads a 2D result has to know this exists.
``ikle`` is left exactly as written (prisms, 6 nodes, indexing the flat 3D node
numbering). Callers that need plan connectivity should use a 2D file; the 3D path
exists to read *fields*, and axqua samples those on a KD-tree over ``x``/``y``.
"""
path = Path(path)
with open(path, "rb") as f:
title = _read_record(f)
fdtype = np.dtype(">f8") if title[72:80].strip() == b"SERAFIND" else _F4
nbv = np.frombuffer(_read_record(f), dtype=_I4)
nbv1, nbv2 = int(nbv[0]), int(nbv[1])
var_names = [
_read_record(f)[:16].decode("ascii", "replace").strip()
for _ in range(nbv1 + nbv2)
]
iparam = np.frombuffer(_read_record(f), dtype=_I4)
if iparam.size >= 10 and iparam[9] == 1:
_read_record(f) # DATE record
dims = np.frombuffer(_read_record(f), dtype=_I4)
nelem, npoin, ndp = int(dims[0]), int(dims[1]), int(dims[2])
# NPLAN lives in IPARAM(7) - index 6 - and that is where TELEMAC-3D actually
# writes it: a real r3d.slf carries iparam[6] = 5 while the dims record's
# fourth slot stays 1, so reading dims[3] (the intuitive place, and what the
# format description suggests) silently reports every 3D result as 2D.
nplan = int(iparam[6]) if iparam.size > 6 and iparam[6] > 1 else 1
if nplan == 1 and dims.size > 3 and dims[3] > 1:
nplan = int(dims[3])
if nplan > 1 and npoin % nplan:
log.warning("%s: NPOIN %d is not divisible by NPLAN %d; reading it as 2D",
path.name, npoin, nplan)
nplan = 1
ikle = np.frombuffer(_read_record(f), dtype=_I4).reshape(nelem, ndp) - 1
ipobo = np.frombuffer(_read_record(f), dtype=_I4).copy()
x = np.frombuffer(_read_record(f), dtype=fdtype).astype(float)
y = np.frombuffer(_read_record(f), dtype=fdtype).astype(float)
times: list[float] = []
frames: list[dict[str, np.ndarray]] = []
while True:
t_rec = _read_record(f)
if t_rec is None:
break
times.append(float(np.frombuffer(t_rec, dtype=fdtype)[0]))
frames.append({
name: np.frombuffer(_read_record(f), dtype=fdtype).astype(float)
for name in var_names
})
if not frames:
raise ValueError(f"{path.name}: no time frames in SELAFIN file")
values = frames[frame]
if nplan > 1:
npoin2 = x.size // nplan
x, y = x[:npoin2], y[:npoin2]
ipobo = ipobo[:npoin2]
values = {name: v.reshape(nplan, npoin2) for name, v in values.items()}
return {
"x": x, "y": y, "ikle": ikle, "ipobo": ipobo, "var_names": var_names,
"nplan": nplan, "time": times[frame], "values": values,
"n_times": len(frames),
}
def _write_selafin(
path: Path,
x: np.ndarray,
y: np.ndarray,
ikle: np.ndarray,
ipobo: np.ndarray,
variables: list[tuple[str, str, np.ndarray]],
*,
title: str,
date: Sequence[int],
double_precision: bool,
) -> Path:
"""Write a single-frame (t=0) 2D triangular-mesh SELAFIN.
*variables* is an ordered list of ``(name, unit, values)`` written as the
file's node variables; their ``values`` must each be length NPOIN.
"""
x = np.asarray(x, dtype=float)
y = np.asarray(y, dtype=float)
ikle = np.asarray(ikle, dtype=np.int64)
ipobo = np.asarray(ipobo, dtype=np.int64)
npoin = x.size
nelem = ikle.shape[0]
ndp = ikle.shape[1]
if ndp != 3:
raise ValueError(f"only triangular meshes supported (NDP=3), got {ndp}")
if y.size != npoin or ipobo.size != npoin:
raise ValueError("x, y and ipobo must all have length NPOIN")
for name, _, values in variables:
if np.asarray(values).size != npoin:
raise ValueError(f"{name} length {np.asarray(values).size} != NPOIN={npoin}")
nbv1 = len(variables)
# IPARAM: index 9 == 1 -> a DATE record follows; index 6 == 0 -> 2D.
iparam = np.zeros(10, dtype=_I4)
iparam[0] = 1
iparam[9] = 1
fdtype = _F8 if double_precision else _F4
tag = b"SERAFIND" if double_precision else b"SERAFIN "
with open(path, "wb") as f:
# 1) title (72) + precision tag (8) = 80-byte record
f.write(_record(f"{title:<72}".encode("ascii") + tag))
# 2) NBV1, NBV2
f.write(_record(np.array([nbv1, 0], dtype=_I4).tobytes()))
# 3) one 32-byte record per variable: name(16) + unit(16)
for name, unit, _ in variables:
f.write(_record(f"{name:<16}{unit:<16}".encode("ascii")))
# 4) IPARAM (10 int)
f.write(_record(iparam.tobytes()))
# 5) DATE (6 int)
f.write(_record(np.array(date, dtype=_I4).tobytes()))
# 6) NELEM, NPOIN, NDP, NPLAN(=1)
f.write(_record(np.array([nelem, npoin, ndp, 1], dtype=_I4).tobytes()))
# 7) IKLE connectivity (row-major, 1-based)
f.write(_record(ikle.astype(_I4).tobytes()))
# 8) IPOBO
f.write(_record(ipobo.astype(_I4).tobytes()))
# 9) X, 10) Y
f.write(_record(x.astype(fdtype).tobytes()))
f.write(_record(y.astype(fdtype).tobytes()))
# 11) one time frame: t=0 then each variable's NPOIN values
f.write(_record(np.array([0.0], dtype=fdtype).tobytes()))
for _, _, values in variables:
f.write(_record(np.asarray(values, dtype=float).astype(fdtype).tobytes()))
return path
[docs]
def write_geometry(
path: str | Path,
x: np.ndarray,
y: np.ndarray,
ikle: np.ndarray,
ipobo: np.ndarray,
bottom: np.ndarray,
*,
friction_id: np.ndarray | None = None,
roughness: np.ndarray | None = None,
title: str = "axqua geometry",
date: Sequence[int] = (2026, 1, 1, 0, 0, 0),
double_precision: bool = True,
) -> Path:
"""Write a 2D triangular-mesh geometry SELAFIN.
Always writes the BOTTOM variable. If *friction_id* is given it is written as
``FRIC_ID`` (per node), which TELEMAC reads to map nodes to friction zones in
the FRICTION DATA FILE (no separate ZONES FILE needed). If *roughness* is
given it is written as ``BOTTOM FRICTION`` (per node, m) - the per-node
roughness value (e.g. a Nikuradse k_s) that HydroBayesCal later adjusts.
*double_precision* (default ``True``, the ``SERAFIND`` format) writes node
coordinates and variables as 8-byte reals. This is **required** for fine
meshes on real-world projected coordinates: a single-precision (R4) float has
a ~24-bit mantissa, so at UTM northings of ~5.3e6 m the representable spacing
(ULP) is ~0.5 m. Storing a sub-metre mesh single precision snaps neighboring
nodes onto identical coordinates, collapsing thin channel triangles into
coincident / collinear / inverted cells that make TELEMAC abort with
``GEOELT: ... NEGATIVE DETERMINANT``. Only set ``False`` for coarse meshes
where the coordinate granularity is comfortably below the cell size.
Parameters
----------
x, y : (NPOIN,) float arrays of node coordinates.
ikle : (NELEM, 3) int array of 1-based node indices per triangle.
ipobo : (NPOIN,) int array - boundary numbering (0 interior, k>0 on contour).
bottom : (NPOIN,) float array of bed elevations (m).
friction_id : optional (NPOIN,) int array of friction-zone ids per node.
roughness : optional (NPOIN,) float array of per-node roughness values.
"""
bottom = np.asarray(bottom, dtype=float)
variables = [("BOTTOM", "M", bottom)]
if friction_id is not None:
variables.append(("FRIC_ID", "", np.asarray(friction_id, dtype=float)))
if roughness is not None:
variables.append(("BOTTOM FRICTION", "M", np.asarray(roughness, dtype=float)))
return _write_selafin(Path(path), x, y, ikle, ipobo, variables,
title=title, date=date, double_precision=double_precision)
[docs]
def write_initial_state(
path: str | Path,
x: np.ndarray,
y: np.ndarray,
ikle: np.ndarray,
ipobo: np.ndarray,
depth: np.ndarray,
*,
velocity_u: np.ndarray | None = None,
velocity_v: np.ndarray | None = None,
title: str = "axqua initial conditions",
date: Sequence[int] = (2026, 1, 1, 0, 0, 0),
double_precision: bool = True,
) -> Path:
"""Write a hotstart SELAFIN holding VELOCITY U, VELOCITY V and WATER DEPTH.
TELEMAC reads this as the ``PREVIOUS COMPUTATION FILE`` (which alone triggers
the continuation since release 9.0) to initialize the flow field, matching
variables by name on the *same* mesh as the geometry. It pre-wets the domain
(e.g. the channel) to a given *depth* so the wetting front does not have to be
advanced from a dry bed - a large time saving for steady runs.
Parameters
----------
x, y, ikle, ipobo : the geometry of the mesh this state initializes (must
match the GEOMETRY FILE: same NPOIN/NELEM, node order and connectivity).
depth : (NPOIN,) float array of initial water depths (m).
velocity_u, velocity_v : optional (NPOIN,) initial velocity components (m/s);
default to zero (a still pre-wetted pond, the usual hotstart).
"""
depth = np.asarray(depth, dtype=float)
npoin = depth.size
u = np.zeros(npoin) if velocity_u is None else np.asarray(velocity_u, dtype=float)
v = np.zeros(npoin) if velocity_v is None else np.asarray(velocity_v, dtype=float)
variables = [
("VELOCITY U", "M/S", u),
("VELOCITY V", "M/S", v),
("WATER DEPTH", "M", depth),
]
return _write_selafin(Path(path), x, y, ikle, ipobo, variables,
title=title, date=date, double_precision=double_precision)
[docs]
class SelafinFile:
"""One frame at a time out of a SERAFIN file, however long the simulation was.
:func:`read_slf` reads every frame to return one, which is right for the last frame
of a steady run and wrong for walking through an unsteady one: a result of a few
hundred printouts on a fine mesh is gigabytes. A SERAFIN file has frames of one
fixed size after its header, so a frame is found by arithmetic and read alone.
``x``, ``y``, ``ikle`` (0-based) and ``ipobo`` are read once. ``var_names`` and
``var_units`` are the two halves of the 32 characters each variable is named with.
Arrays come back **flat**, in the numbering of the file: for a 3D result that is
plane after plane over the same plan mesh (``npoin2`` nodes each), which is also
how the prisms of ``ikle`` index them.
"""
def __init__(self, path: str | Path) -> None:
self.path = Path(path)
with open(self.path, "rb") as f:
title = _read_record(f)
if title is None or len(title) < 72:
raise ValueError(f"{self.path.name} is not a SERAFIN file")
self.title = title[:72].decode("ascii", "replace").strip()
self.double = title[72:80].strip() == b"SERAFIND"
self.dtype = _F8 if self.double else _F4
nbv = np.frombuffer(_read_record(f), dtype=_I4)
count = int(nbv[0]) + int(nbv[1])
names = [_read_record(f) for _ in range(count)]
self.var_names = [n[:16].decode("ascii", "replace").strip() for n in names]
self.var_units = [n[16:32].decode("ascii", "replace").strip() for n in names]
iparam = np.frombuffer(_read_record(f), dtype=_I4)
self.date: tuple[int, ...] | None = None
if iparam.size >= 10 and iparam[9] == 1:
self.date = tuple(int(v) for v in
np.frombuffer(_read_record(f), dtype=_I4))
dims = np.frombuffer(_read_record(f), dtype=_I4)
self.nelem, self.npoin, self.ndp = int(dims[0]), int(dims[1]), int(dims[2])
# NPLAN is IPARAM(7); see read_slf for why not the dimensions record.
nplan = int(iparam[6]) if iparam.size > 6 and iparam[6] > 1 else 1
if nplan == 1 and dims.size > 3 and dims[3] > 1:
nplan = int(dims[3])
if nplan > 1 and self.npoin % nplan:
nplan = 1
self.nplan = nplan
self.ikle = np.frombuffer(_read_record(f), dtype=_I4).reshape(
self.nelem, self.ndp) - 1
self.ipobo = np.frombuffer(_read_record(f), dtype=_I4).copy()
self.x = np.frombuffer(_read_record(f), dtype=self.dtype).astype(float)
self.y = np.frombuffer(_read_record(f), dtype=self.dtype).astype(float)
self._start = f.tell()
item = self.dtype.itemsize
self._time_size = 4 + item + 4
self._var_size = 4 + self.npoin * item + 4
self._frame_size = self._time_size + len(self.var_names) * self._var_size
self.n_frames = max(0, (self.path.stat().st_size - self._start)
// self._frame_size)
self.times = [self._time(i) for i in range(self.n_frames)]
@property
def npoin2(self) -> int:
"""Nodes of the plan mesh; all of them in a 2D file."""
return self.npoin // self.nplan
def __len__(self) -> int:
return self.n_frames
def _time(self, index: int) -> float:
with open(self.path, "rb") as f:
f.seek(self._start + index * self._frame_size + 4)
return float(np.frombuffer(f.read(self.dtype.itemsize), dtype=self.dtype)[0])
[docs]
def frame(self, index: int, names: Sequence[str] | None = None
) -> dict[str, np.ndarray]:
"""The variables of one printout, as flat arrays in the file's precision.
*names* limits what is read. A negative *index* counts from the end.
"""
if index < 0:
index += self.n_frames
if not 0 <= index < self.n_frames:
raise IndexError(f"{self.path.name} has {self.n_frames} frames, "
f"not one with index {index}")
wanted = list(self.var_names) if names is None else list(names)
out: dict[str, np.ndarray] = {}
base = self._start + index * self._frame_size + self._time_size
with open(self.path, "rb") as f:
for position, name in enumerate(self.var_names):
if name not in wanted:
continue
f.seek(base + position * self._var_size + 4)
out[name] = np.fromfile(f, dtype=self.dtype, count=self.npoin)
return out
[docs]
def extract_hotstart(results: str | Path, out: str | Path, *, frame: int = -1,
title: str = "axqua hotstart") -> Path:
"""Write a one-frame ``PREVIOUS COMPUTATION FILE`` from a multi-frame result.
A steady run's result carries every printout - hundreds of frames of eight
variables - but a continuation only reads the *last* frame's VELOCITY U,
VELOCITY V and WATER DEPTH. Handing the full file to a fleet of calibration
runs makes every one of them copy hundreds of megabytes into its temporary work
directory for the sake of a few, so extract the frame once instead: on the KB15
case this turns a 2.3 GB seed into ~11 MB with no change in what TELEMAC reads.
The mesh is carried over from *results*, so the output matches the same
GEOMETRY FILE. Depth is taken directly when the result carries WATER DEPTH,
else derived as FREE SURFACE - BOTTOM.
"""
r = read_slf(Path(results), frame=frame)
values = r["values"]
if "WATER DEPTH" in values:
depth = np.asarray(values["WATER DEPTH"], dtype=float)
elif "FREE SURFACE" in values and "BOTTOM" in values:
depth = (np.asarray(values["FREE SURFACE"], dtype=float)
- np.asarray(values["BOTTOM"], dtype=float))
else:
raise ValueError(
f"{Path(results).name} has neither WATER DEPTH nor FREE SURFACE+BOTTOM "
f"(has {sorted(values)}) - cannot build a hotstart from it")
return write_initial_state(
Path(out), r["x"], r["y"], r["ikle"], r["ipobo"], np.maximum(depth, 0.0),
velocity_u=values.get("VELOCITY U"), velocity_v=values.get("VELOCITY V"),
title=title)