Add reconstruct.py

reconstruct.py

@@ -0,0 +1,119 @@
+"""Reconstruct: beamform one rotation frame of the eSAF rotational 3D US dataset.
+
+Loads a zea .hdf5 acquisition (raw RF channel data, one normal plane-wave
+transmit per rotation frame), reads the acquisition parameters, and runs the
+delay-and-sum beamforming pipeline configured in pipeline.yaml. The resulting
+B-mode image is saved as a PNG, together with a plot of the per-frame probe
+rotation angle (this dataset's special data: the linear array rotates 180
+degrees about its axial axis, 1 degree per frame) so downstream users know how
+to interpret the frame axis.
+
+Usage:
+    python reconstruct.py
+    python reconstruct.py --input data/acq_0016_point_d130_r4.hdf5
+    python reconstruct.py --frame-index 45
+"""
+
+import os
+
+# Default to the jax backend so the script runs without exporting KERAS_BACKEND.
+os.environ.setdefault("KERAS_BACKEND", "jax")
+os.environ.setdefault("MPLBACKEND", "Agg")
+
+import argparse
+from pathlib import Path
+
+import matplotlib.pyplot as plt
+import numpy as np
+import zea
+from zea import Config, File, Pipeline
+
+HERE = Path(__file__).parent
+DEFAULT_INPUT = HERE / "data" / "acq_0008_point_d60_r4.hdf5"
+DEFAULT_OUTPUT = HERE / "outputs" / "reconstruct_example.png"
+CONFIG = HERE / "pipeline.yaml"
+
+
+def main():
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument("--input", type=Path, default=DEFAULT_INPUT)
+    parser.add_argument("--output", type=Path, default=DEFAULT_OUTPUT)
+    parser.add_argument(
+        "--frame-index",
+        type=int,
+        default=None,
+        help="rotation frame to beamform (default: frame closest to 90 deg, "
+        "where an off-axis target lies in the imaging plane)",
+    )
+    args = parser.parse_args()
+
+    if not args.input.exists():
+        raise FileNotFoundError(f"{args.input} not found.")
+
+    zea.init_device()
+
+    # Load the whole processing chain + parameters from pipeline.yaml
+    config = Config.from_path(str(CONFIG))
+
+    # Load file: acquisition parameters (with config overrides), one raw RF frame,
+    # and this dataset's special data — the probe rotation angle per frame.
+    with File(str(args.input)) as f:
+        parameters = f.load_parameters(**config.parameters)
+        rotation_angles_deg = np.asarray(
+            {c.name: c for c in f.custom}["rotation_angles_deg"].data
+        ).ravel()
+        n_frames = f.data.raw_data.shape[0]
+        frame = args.frame_index
+        if frame is None:  # default: frame where the probe has rotated ~90 deg
+            frame = int(np.argmin(np.abs(rotation_angles_deg - 90.0)))
+        raw = f.data.raw_data[frame : frame + 1]  # (1, n_tx, n_ax, n_el, 1) — RF
+
+    print(f"raw_data frame : {raw.shape} ({n_frames} frames in file)")
+
+    # Build and run the beamforming pipeline defined in pipeline.yaml
+    pipeline = Pipeline.from_config(config)
+    inputs = pipeline.prepare_parameters(parameters)
+    outputs = pipeline(data=raw, **inputs)
+
+    recon = np.array(outputs["data"])  # (1, grid_z, grid_x), log-compressed dB
+    image = zea.display.to_8bit(
+        recon[0], dynamic_range=parameters.dynamic_range, pillow=False
+    )
+
+    # B-mode + rotation-angle plot (how to interpret the frame axis)
+    zea.visualize.set_mpl_style()
+    fig, axes = plt.subplots(
+        1, 2, figsize=(11, 5), gridspec_kw={"width_ratios": [1, 1.3]}
+    )
+
+    mm = plt.FuncFormatter(lambda v, _: f"{v * 1e3:.0f}")
+    axes[0].imshow(image, extent=parameters.extent_imshow, cmap="gray", aspect="equal")
+    axes[0].xaxis.set_major_formatter(mm)
+    axes[0].yaxis.set_major_formatter(mm)
+    axes[0].set(
+        title=f"B-mode frame {frame} @ {rotation_angles_deg[frame]:.0f} deg",
+        xlabel="Lateral [mm]",
+        ylabel="Depth [mm]",
+    )
+
+    axes[1].plot(np.arange(n_frames), rotation_angles_deg, color="tab:blue")
+    axes[1].axvline(frame, color="tab:red", linewidth=1.2, label="beamformed frame")
+    axes[1].set(
+        title="Probe rotation angle per frame\n(array rotates about its axial axis)",
+        xlabel="Frame index",
+        ylabel="Rotation angle [deg]",
+    )
+    axes[1].grid(True, color="0.85", linewidth=0.8)
+    axes[1].legend(loc="upper left", fontsize=8, frameon=False)
+
+    fig.suptitle(f"OpenH-RF eSAF rotational 3D US — {args.input.name}", y=0.98)
+    plt.tight_layout()
+    args.output.parent.mkdir(parents=True, exist_ok=True)
+    plt.savefig(str(args.output), bbox_inches="tight", dpi=150)
+
+    print(f"Reconstructed  : {recon.shape}")
+    print(f"Saved          : {args.output}")
+
+
+if __name__ == "__main__":
+    main()