field-scale-dataset-preview / view_preview.py
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Initial release: single-family preview of subsurfacegen/field-scale-dataset.
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#!/usr/bin/env python
"""Field-Scale Dataset Preview — NeurIPS-ready viewer for the 4-file sample.
Renders five publication-quality figures matching the manuscript's intro
figure style. Pure NumPy + Matplotlib + h5py + hdf5plugin.
Usage:
pip install huggingface_hub h5py hdf5plugin numpy matplotlib scipy
huggingface-cli download subsurfacegen/field-scale-dataset-preview \\
--repo-type=dataset --local-dir=./preview_data
python view_preview.py --plot all --input-dir ./preview_data --output-dir ./figs
Individual:
python view_preview.py --plot cube # 3D cutaway render of the volume
python view_preview.py --plot orthogonal # 3 orthogonal slices w/ crosshairs
python view_preview.py --plot slice # 2D slice w/ source + streamer
python view_preview.py --plot wavefield # Wavefield panels w/ velocity bg
python view_preview.py --plot gather # Shot gather panels (Left/Middle/Right)
"""
from __future__ import annotations
import argparse
import sys
from pathlib import Path
# Optional: register HDF5 compression filters used by wavefield + gather files.
try:
import hdf5plugin # noqa: F401
except ImportError:
print("WARNING: hdf5plugin not installed; wavefield + gather reads may fail. "
"Install via: pip install hdf5plugin", flush=True)
import h5py
import matplotlib
matplotlib.use("Agg")
import matplotlib.colors as mcolors
import matplotlib.pyplot as plt
import numpy as np
from mpl_toolkits.mplot3d import Axes3D # noqa: F401 (registers projection)
# ---------------- Paper-figure constants ----------------
# Match render_shot_gather_clean / render_wavefield_panel_clean conventions.
GATHER_SOURCE_INDICES = (8, 32, 56) # paper: SG_SOURCE_INDICES
GATHER_POSITION_NAMES = ("Left", "Middle", "Right")
GATHER_SOURCE_COLORS = ("#B87100", "#004A77", "#A00000") # bronze/navy/burgundy
# Wavefield time panels (more than the paper's 3 to show fuller progression)
WAVEFIELD_FRAMES = [
("0.20 s", 14), # Start (paper)
("1.00 s", 71),
("1.96 s", 140), # Middle (paper)
("3.00 s", 214),
("4.00 s", 285),
("5.00 s", 357), # End (paper)
]
# 3D orthogonal-slices configuration: which inline + crossline + depth slice
INLINE_INDEX = 507 # the inline that the 2D slice was extracted at
CROSSLINE_INDEX = 500 # mid-y by convention
DEPTH_INDEX_FRAC = 0.5 # mid-depth
# Velocity colormap (paper convention: TwoSlopeNorm + seismic)
VEL_VMIN, VEL_VCENTER, VEL_VMAX = 1500.0, 2300.0, 4500.0
# 3D-cube cutaway render config (matches cutaway_3d_d619_batch.py)
CUBE_VEL_VCENTER = 3100.0
CUBE_DEPTH_RANGE = (80, 619)
CUBE_CROSSLINE_RANGE = (150, 1000)
CUBE_INLINE_RANGE = (150, 1000)
CUBE_VIEW_ELEV = 20
CUBE_VIEW_AZIM = -115
CUBE_MAX_FACE_DIM = 350
DX_KM = 0.010
# NeurIPS-ready typography (apply globally so every figure is consistent)
plt.rcParams.update({
"font.size": 14,
"axes.titlesize": 16,
"axes.labelsize": 14,
"xtick.labelsize": 12,
"ytick.labelsize": 12,
"legend.fontsize": 12,
"figure.titlesize": 18,
"axes.titleweight": "bold",
"figure.titleweight": "bold",
"axes.linewidth": 1.4,
"xtick.major.width": 1.2,
"ytick.major.width": 1.2,
"xtick.major.size": 5,
"ytick.major.size": 5,
"lines.linewidth": 1.6,
"savefig.bbox": "tight",
"savefig.dpi": 150,
})
# ---------------- helpers ----------------
def _vel_norm() -> mcolors.TwoSlopeNorm:
return mcolors.TwoSlopeNorm(vmin=VEL_VMIN, vcenter=VEL_VCENTER, vmax=VEL_VMAX)
def _wf_alpha_cmap() -> mcolors.ListedColormap:
"""Seismic with alpha proportional to |v|; tiny values become transparent."""
base = matplotlib.colormaps["seismic"](np.linspace(0, 1, 256))
t = np.linspace(-1.0, 1.0, 256)
alphas = np.clip(np.abs(t) * 1.6, 0.0, 1.0)
alphas[np.abs(t) < 0.04] = 0.0
base[:, 3] = alphas
return mcolors.ListedColormap(base, name="seismic_alpha")
def _load_h5_dataset(path: Path, key: str) -> tuple[np.ndarray, dict]:
with h5py.File(path, "r") as f:
ds = f[key]
data = ds[...]
attrs = {}
for k, v in ds.attrs.items():
attrs[k] = v.decode() if isinstance(v, bytes) else v
for k, v in f.attrs.items():
attrs[f"root.{k}"] = v.decode() if isinstance(v, bytes) else v
return data, attrs
def _save(fig, output_dir: Path, name: str):
output_dir.mkdir(parents=True, exist_ok=True)
out = output_dir / name
fig.savefig(out, dpi=150)
plt.close(fig)
print(f" wrote {out}")
def _block_mean(arr: np.ndarray, max_dim: int) -> np.ndarray:
h, w = arr.shape
bh = max(1, int(np.ceil(h / max_dim)))
bw = max(1, int(np.ceil(w / max_dim)))
if bh == 1 and bw == 1:
return arr.astype(np.float32, copy=False)
h2 = (h // bh) * bh
w2 = (w // bw) * bw
return (arr[:h2, :w2].astype(np.float32, copy=False)
.reshape(h2 // bh, bh, w2 // bw, bw).mean(axis=(1, 3)))
# ---------------- 3D cube cutaway (paper render_cube style) ----------------
def plot_3d_cube_cutaway(input_dir: Path, output_dir: Path):
p = input_dir / "models/gom_d619/gom_151_sos.h5"
print(f"Loading 3D volume for cutaway: {p}")
with h5py.File(p, "r") as fh:
vol = np.asarray(fh["velocity"][...], dtype=np.float32)
nz, ny, nx = vol.shape
print(f" shape (nz, ny, nx) = ({nz}, {ny}, {nx})")
norm = mcolors.TwoSlopeNorm(vmin=VEL_VMIN, vcenter=CUBE_VEL_VCENTER, vmax=VEL_VMAX)
cmap = plt.get_cmap("seismic")
# Take the cutaway sub-volume (top + 2 sides shaved per paper config)
z0, z1 = CUBE_DEPTH_RANGE
y0, y1 = CUBE_CROSSLINE_RANGE
x0, x1 = CUBE_INLINE_RANGE
raw_faces = {
"top": vol[z0, y0:y1, x0:x1],
"bottom": vol[z1 - 1, y0:y1, x0:x1],
"left": vol[z0:z1, y0:y1, x0],
"right": vol[z0:z1, y0:y1, x1 - 1],
"front": vol[z0:z1, y0, x0:x1],
"back": vol[z0:z1, y1 - 1, x0:x1],
}
faces = {k: _block_mean(v, CUBE_MAX_FACE_DIM) for k, v in raw_faces.items()}
del vol
x_km_lim = (x0 * DX_KM, (x1 - 1) * DX_KM)
y_km_lim = (y0 * DX_KM, (y1 - 1) * DX_KM)
z_km_lim = (z0 * DX_KM, (z1 - 1) * DX_KM)
def coords(face_shape, a_lim, b_lim):
nh, nw = face_shape
aa = np.linspace(a_lim[0], a_lim[1], nh)
bb = np.linspace(b_lim[0], b_lim[1], nw)
A, B = np.meshgrid(aa, bb, indexing="ij")
return A, B
fig = plt.figure(figsize=(10, 9))
ax = fig.add_subplot(111, projection="3d")
ax.set_facecolor("white")
surf_kw = dict(shade=False, rstride=1, cstride=1, linewidth=0,
antialiased=False, rasterized=True)
Y, X = coords(faces["top"].shape, y_km_lim, x_km_lim)
ax.plot_surface(X, Y, np.full_like(X, z_km_lim[0]),
facecolors=cmap(norm(faces["top"])), **surf_kw)
Y, X = coords(faces["bottom"].shape, y_km_lim, x_km_lim)
ax.plot_surface(X, Y, np.full_like(X, z_km_lim[1]),
facecolors=cmap(norm(faces["bottom"])), **surf_kw)
Z2, Y2 = coords(faces["left"].shape, z_km_lim, y_km_lim)
ax.plot_surface(np.full_like(Y2, x_km_lim[0]), Y2, Z2,
facecolors=cmap(norm(faces["left"])), **surf_kw)
Z2, Y2 = coords(faces["right"].shape, z_km_lim, y_km_lim)
ax.plot_surface(np.full_like(Y2, x_km_lim[1]), Y2, Z2,
facecolors=cmap(norm(faces["right"])), **surf_kw)
Z3, X3 = coords(faces["front"].shape, z_km_lim, x_km_lim)
ax.plot_surface(X3, np.full_like(X3, y_km_lim[0]), Z3,
facecolors=cmap(norm(faces["front"])), **surf_kw)
Z3, X3 = coords(faces["back"].shape, z_km_lim, x_km_lim)
ax.plot_surface(X3, np.full_like(X3, y_km_lim[1]), Z3,
facecolors=cmap(norm(faces["back"])), **surf_kw)
ax.set_xlim(*x_km_lim); ax.set_ylim(*y_km_lim); ax.set_zlim(*z_km_lim)
ax.invert_zaxis()
ax.set_box_aspect((1, 1, 1))
ax.view_init(elev=CUBE_VIEW_ELEV, azim=CUBE_VIEW_AZIM)
ax.set_xticks([]); ax.set_yticks([]); ax.set_zticks([])
for pane in (ax.xaxis.pane, ax.yaxis.pane, ax.zaxis.pane):
pane.set_facecolor((1, 1, 1, 0)); pane.set_edgecolor((1, 1, 1, 0))
ax.set_title("3D SOS-smoothed velocity volume (cutaway)\n"
"gom_151_sos.h5 — Gulf of Mexico realization",
pad=18)
# Manual colorbar
sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
sm.set_array([])
cbar = fig.colorbar(sm, ax=ax, shrink=0.55, pad=0.05, aspect=20)
cbar.set_label("velocity (m/s)", fontsize=14)
cbar.ax.tick_params(labelsize=12)
_save(fig, output_dir, "model_3d_cube_cutaway.png")
# ---------------- 3D orthogonal slices with crosshairs ----------------
def plot_3d_orthogonal_slices(input_dir: Path, output_dir: Path):
p = input_dir / "models/gom_d619/gom_151_sos.h5"
print(f"Loading 3D volume: {p}")
vol, _ = _load_h5_dataset(p, "velocity")
nz, ny, nx = vol.shape
mid_z = int(round(nz * DEPTH_INDEX_FRAC))
print(f" shape (nz, ny, nx) = ({nz}, {ny}, {nx})")
print(f" inline_idx={INLINE_INDEX}, crossline_idx={CROSSLINE_INDEX}, depth_idx={mid_z}")
norm = _vel_norm()
crosshair_kw = dict(color="red", linestyle="--", linewidth=2.0,
alpha=0.95, dashes=(4, 3))
fig, axes = plt.subplots(1, 3, figsize=(20, 6.5),
gridspec_kw={"wspace": 0.25})
# Panel 1: inline slice (depth × x). Crossline + depth slices appear as crosshair.
inline = vol[:, INLINE_INDEX, :]
im = axes[0].imshow(inline, aspect="auto", cmap="seismic", norm=norm,
extent=[0, nx, nz, 0], interpolation="lanczos")
axes[0].set_title(f"Inline {INLINE_INDEX}\n(the 2D slice file)")
axes[0].set_xlabel("crossline x (sample)")
axes[0].set_ylabel("depth (sample)")
axes[0].axvline(CROSSLINE_INDEX, **crosshair_kw) # where crossline panel cuts
axes[0].axhline(mid_z, **crosshair_kw) # where depth panel cuts
# Panel 2: crossline slice (depth × y). Inline + depth slices as crosshair.
cross = vol[:, :, CROSSLINE_INDEX]
axes[1].imshow(cross, aspect="auto", cmap="seismic", norm=norm,
extent=[0, ny, nz, 0], interpolation="lanczos")
axes[1].set_title(f"Crossline at x={CROSSLINE_INDEX}")
axes[1].set_xlabel("inline y (sample)")
axes[1].set_ylabel("depth (sample)")
axes[1].axvline(INLINE_INDEX, **crosshair_kw) # where inline panel cuts
axes[1].axhline(mid_z, **crosshair_kw) # where depth panel cuts
# Panel 3: depth slice (y × x). Inline + crossline cuts as crosshair.
depth = vol[mid_z, :, :]
axes[2].imshow(depth, aspect="auto", cmap="seismic", norm=norm,
extent=[0, nx, ny, 0], interpolation="lanczos")
axes[2].set_title(f"Depth slice at z={mid_z}")
axes[2].set_xlabel("crossline x (sample)")
axes[2].set_ylabel("inline y (sample)")
axes[2].axhline(INLINE_INDEX, **crosshair_kw) # where inline panel cuts
axes[2].axvline(CROSSLINE_INDEX, **crosshair_kw) # where crossline panel cuts
# Colorbar with key above it explaining the dashed lines.
cbar_ax = fig.add_axes([0.92, 0.13, 0.013, 0.66])
cbar = fig.colorbar(im, cax=cbar_ax)
cbar.set_label("velocity (m/s)", fontsize=14)
cbar.ax.tick_params(labelsize=12)
# Compact key just above the colorbar
fig.text(0.926, 0.85,
"‒‒ red dashed:\nlocations of\nother 2 panels",
fontsize=11, color="red", weight="bold",
ha="left", va="bottom")
fig.suptitle("3D SOS volume — orthogonal slices through gom_151_sos.h5",
y=0.98)
_save(fig, output_dir, "model_3d_orthogonal_slices.png")
# ---------------- 2D slice with source + streamer geometry ----------------
def plot_2d_slice(input_dir: Path, output_dir: Path):
"""2D velocity slice with seismic cmap, streamer + source geometry overlay."""
p = input_dir / "slices/slice_gom_151_il_0507.h5"
print(f"Loading 2D slice: {p}")
sl, _ = _load_h5_dataset(p, "velocity")
nz, nx = sl.shape
print(f" shape (nz, nx) = ({nz}, {nx})")
# Physical extent (10 m grid spacing)
extent = (0.0, nx * 0.01, nz * 0.01, 0.0)
norm = _vel_norm()
fig, ax = plt.subplots(1, 1, figsize=(13, 5.8))
im = ax.imshow(sl, cmap="seismic", norm=norm,
extent=extent, aspect="auto", interpolation="lanczos")
ax.set_xlabel("horizontal x (km)")
ax.set_ylabel("depth z (km)")
ax.set_title("2D velocity slice — slice_gom_151_il_0507.h5 (inline 507 of gom_151)")
# Streamer (1000 receivers @ 10 m depth, 10 m horizontal spacing,
# standard 0.5 km edge margin per the simulation config).
rec_z_km = 0.01
rec_x_km = np.linspace(0.6, 9.4, 1000)
rec_x_show = rec_x_km[::25]
ax.scatter(rec_x_show, np.full_like(rec_x_show, rec_z_km),
marker="v", s=24, c="black", edgecolors="white",
linewidths=0.4, zorder=10, label="receivers (every 25th)")
# Source for the wavefield panel (paper figure)
ax.scatter([4.958], [rec_z_km], marker="*", s=460,
c="gold", edgecolors="black", linewidths=1.2,
zorder=11, label="wavefield source @ x=4.958 km")
ax.legend(loc="upper right", framealpha=0.92)
cbar = fig.colorbar(im, ax=ax, pad=0.01, shrink=0.95)
cbar.set_label("velocity (m/s)")
_save(fig, output_dir, "slice_2d_velocity.png")
# ---------------- Wavefield panels (paper render style) ----------------
def plot_wavefield(input_dir: Path, output_dir: Path,
frames: list[tuple[str, int]] = WAVEFIELD_FRAMES):
"""Wavefield time progression with the velocity model drawn behind."""
p = input_dir / "wavefields/5s/3-6Hz/wavefield_gom_151_il_0507_srchorizontal4.958km.h5"
print(f"Loading wavefield: {p}")
wf, _ = _load_h5_dataset(p, "wavefield")
print(f" wavefield shape (nt, _, _) = {wf.shape}")
# Background velocity slice (loaded for the underlay)
vp = input_dir / "slices/slice_gom_151_il_0507.h5"
vel, _ = _load_h5_dataset(vp, "velocity")
print(f" velocity background shape (nz, nx) = {vel.shape}")
extent = (0.0, 10.0, 6.19, 0.0)
src_x_km = 4.958
wf_cmap = _wf_alpha_cmap()
n = len(frames)
ncols = 3
nrows = int(np.ceil(n / ncols))
fig, axes = plt.subplots(nrows, ncols, figsize=(6.5 * ncols, 4.8 * nrows),
gridspec_kw={"wspace": 0.18, "hspace": 0.30})
axes = np.atleast_2d(axes).flatten()
for idx, (label, frame_idx) in enumerate(frames):
ax = axes[idx]
frame_idx = max(0, min(frame_idx, wf.shape[0] - 1))
# Wavefield is stored (nt, nx, nz) where nx=1000, nz=619 (devito
# convention). Transpose to (nz, nx) so it aligns with the velocity
# slice (nz=619, nx=1000) when overlaid on the same physical extent.
wf_frame = wf[frame_idx].T
# Underlay velocity model in gray, alpha 0.40
ax.imshow(vel, cmap="gray", alpha=0.40, extent=extent,
aspect="auto", interpolation="nearest",
vmin=float(vel.min()), vmax=float(vel.max()))
# Wavefield with seismic-alpha cmap (transparent near 0)
clip = float(np.percentile(np.abs(wf_frame), 99.5))
if clip <= 0:
clip = float(np.abs(wf_frame).max() + 1e-12)
ax.imshow(wf_frame, cmap=wf_cmap,
norm=mcolors.Normalize(-clip, clip),
extent=extent, aspect="auto", interpolation="nearest")
# Source marker
ax.scatter([src_x_km], [0.0], marker="*", s=320, c="gold",
edgecolors="black", linewidths=1.2, zorder=10)
ax.set_xlim(0, 10); ax.set_ylim(6.19, 0)
ax.set_xlabel("horizontal x (km)")
ax.set_ylabel("depth z (km)")
ax.set_title(f"t = {label}", fontsize=15)
for j in range(n, len(axes)):
axes[j].set_visible(False)
fig.suptitle("Wavefield time progression — 3-6 Hz, source @ x=4.958 km\n"
"(velocity model in grayscale; wavefield amplitude in red/blue)",
y=1.00, fontsize=17)
_save(fig, output_dir, "wavefield_time_progression.png")
# ---------------- Shot gather (paper render style) ----------------
def plot_shot_gather(input_dir: Path, output_dir: Path,
source_indices=GATHER_SOURCE_INDICES,
position_names=GATHER_POSITION_NAMES,
source_colors=GATHER_SOURCE_COLORS):
"""1x4 layout: velocity model with color-coded source positions (left)
+ 3 shot-gather panels (Left/Middle/Right matching paper figure)."""
p_gather = input_dir / "shot_gathers/8s/3-25Hz/shot_gather_cube_gom_151_il_0507.h5"
p_slice = input_dir / "slices/slice_gom_151_il_0507.h5"
print(f"Loading shot-gather cube: {p_gather}")
cube, gather_attrs = _load_h5_dataset(p_gather, "shot_gather_cube")
n_src, nt, n_rec = cube.shape
print(f" shape (n_src, nt, n_rec) = ({n_src}, {nt}, {n_rec})")
print(f"Loading velocity slice for geometry panel: {p_slice}")
vel, _ = _load_h5_dataset(p_slice, "velocity")
# Source x-positions in km from the gather cube's flat attr (length 64).
src_x_all = np.asarray(gather_attrs.get("source_horizontal_km", []), dtype=float)
if src_x_all.size != n_src:
# Fall back: linear sample if attr missing/wrong length
src_x_all = np.linspace(0.6, 9.4, n_src)
rec_z_km = float(gather_attrs.get("receiver_depth_km", 0.01))
delta_t_stored = 14e-3
total_s = nt * delta_t_stored
# 1 x 4 grid: velocity panel (wider so it stays roughly square)
# then three gather panels.
fig, axes = plt.subplots(
1, 4,
figsize=(26, 6.8),
gridspec_kw={"width_ratios": [1.55, 1.0, 1.0, 1.0], "wspace": 0.22},
)
# ----- Panel 0: velocity model with source positions overlay -----
ax0 = axes[0]
extent_vel = (0.0, 10.0, 6.19, 0.0)
ax0.imshow(vel, cmap="seismic", norm=_vel_norm(),
extent=extent_vel, aspect="auto", interpolation="lanczos")
# Streamer (1000 receivers @ 10 m depth, every 25th shown)
rec_x_all = np.linspace(0.6, 9.4, 1000)
rec_x_show = rec_x_all[::25]
ax0.scatter(rec_x_show, np.full_like(rec_x_show, rec_z_km),
marker="v", s=22, c="black", edgecolors="white",
linewidths=0.4, zorder=10, label="receivers (every 25th)")
# Highlight the 3 chosen sources at their actual horizontal_km
for sidx, color, name in zip(source_indices, source_colors, position_names):
sx = float(src_x_all[sidx])
ax0.scatter([sx], [rec_z_km], marker="*", s=520,
c=color, edgecolors="black", linewidths=1.4, zorder=11,
label=f"{name} (idx {sidx}, x={sx:.2f} km)")
ax0.set_xlim(0, 10); ax0.set_ylim(6.19, 0)
ax0.set_xlabel("horizontal x (km)")
ax0.set_ylabel("depth z (km)")
ax0.set_title("Source positions on the velocity model", fontsize=15)
ax0.legend(loc="lower right", framealpha=0.92, fontsize=10)
# ----- Panels 1-3: gathers -----
clip = float(np.percentile(np.abs(cube), 97.0))
if clip <= 0:
clip = float(np.abs(cube).max() + 1e-12)
for ax, sidx, label, color in zip(axes[1:], source_indices,
position_names, source_colors):
sidx = max(0, min(sidx, n_src - 1))
gather = cube[sidx]
ax.imshow(gather, cmap="seismic", vmin=-clip, vmax=clip,
aspect="auto", interpolation="lanczos",
extent=[0, n_rec, total_s, 0])
ax.set_xlabel("receiver index")
ax.set_ylabel("time (s)")
for s in ax.spines.values():
s.set_color(color); s.set_linewidth(2.4)
ax.set_title(f"{label} (source idx {sidx})",
color=color, fontweight="bold", fontsize=15)
fig.suptitle("Shot-gather panels — 3-25 Hz, 64-source cube "
"(velocity model on left shows the 3 source positions; matches manuscript intro figure)",
y=1.02, fontsize=17)
_save(fig, output_dir, "shot_gather_panels.png")
# ---------------- main ----------------
def main():
ap = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
ap.add_argument("--input-dir", type=Path, default=Path("./preview_data"),
help="Dir holding the 4 h5 files. Default: ./preview_data")
ap.add_argument("--output-dir", type=Path, default=Path("./figs"),
help="Where to save PNGs. Default: ./figs")
ap.add_argument("--plot",
choices=("cube", "orthogonal", "slice", "wavefield", "gather", "all"),
default="all", help="Which figure to render. Default: all")
args = ap.parse_args()
if not args.input_dir.exists():
sys.exit(f"--input-dir does not exist: {args.input_dir}")
plots = ("cube", "orthogonal", "slice", "wavefield", "gather") \
if args.plot == "all" else (args.plot,)
for p in plots:
if p == "cube": plot_3d_cube_cutaway(args.input_dir, args.output_dir)
elif p == "orthogonal": plot_3d_orthogonal_slices(args.input_dir, args.output_dir)
elif p == "slice": plot_2d_slice(args.input_dir, args.output_dir)
elif p == "wavefield": plot_wavefield(args.input_dir, args.output_dir)
elif p == "gather": plot_shot_gather(args.input_dir, args.output_dir)
print(f"\nDone. PNGs in {args.output_dir}/")
if __name__ == "__main__":
main()