Initial commit: Speckle-Scanner 3D pipeline with setup README
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"""
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Pipeline runner for ZNCC stereo disparity.
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Resolves all paths from the project folder structure and drives
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stereo_disparity_main.py for each scan in a session (or all sessions in a date).
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Output layout per scan:
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<processing_dir>/<project>/<date>/<session>/<scan>/
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02_rect_images/ <- input (must exist)
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04_zncc_disp_map/ <- disparity.npy + Disparity_map_colorbar.png (always)
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+ vertical shift & correlation maps (troubleshooting only)
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06_zncc_pcl/ <- Point_cloud.ply + .txt (troubleshooting only)
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Q matrix is read from:
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<processing_dir>/<project>/<date>/<session>/params_link/lc-rc_Q.cvstore
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"""
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import sys
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import argparse
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import subprocess
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from pathlib import Path
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# Resolve config.py relative to ~/Speckle-Scanner regardless of CWD
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sys.path.insert(0, str(Path.home() / "Speckle-Scanner"))
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import config # noqa: E402
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SCRIPT = Path(__file__).parent / "stereo_disparity_main.py"
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def build_cmd(rect_dir, q_file, disp_out, pcl_out, zncc_args, troubleshooting):
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cmd = [
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sys.executable, str(SCRIPT),
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"--left_dir", str(rect_dir),
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"--right_dir", str(rect_dir),
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"--left_prefix", "lc_",
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"--right_prefix", "rc_",
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"--q_file", str(q_file),
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"--disp_output_dir", str(disp_out),
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"--pcl_output_dir", str(pcl_out),
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]
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if troubleshooting:
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cmd.append("--troubleshooting")
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# Forward ZNCC tuning params
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for key, val in zncc_args.items():
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if val is not None:
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cmd += [f"--{key}", str(val)]
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return cmd
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def run_scan(project, date, session, scan, zncc_args, troubleshooting):
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rect_dir = config.PROCESSING_DIR / project / date / session / scan / "02_rect_images"
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q_file = config.get_params_link_dir(project, date, session) / "lc-rc_Q.cvstore"
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disp_out = config.get_processing_step_dir(project, date, session, scan, "04_zncc_disp_map")
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pcl_out = config.get_processing_step_dir(project, date, session, scan, "06_zncc_pcl")
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if not rect_dir.exists():
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print(f"[SKIP] {session}/{scan}: 02_rect_images not found at {rect_dir}")
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return False
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if not q_file.exists():
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print(f"[SKIP] {session}/{scan}: Q matrix not found at {q_file}")
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return False
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mode = "troubleshooting" if troubleshooting else "disparity-only"
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print(f"\n{'='*60}")
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print(f"[SCAN] {session}/{scan} [{mode}]")
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print(f" rect : {rect_dir}")
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print(f" Q : {q_file}")
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print(f" disp : {disp_out}")
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if troubleshooting:
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print(f" pcl : {pcl_out}")
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print(f"{'='*60}")
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cmd = build_cmd(rect_dir, q_file, disp_out, pcl_out, zncc_args, troubleshooting)
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result = subprocess.run(cmd)
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if result.returncode != 0:
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print(f"[FAIL] {session}/{scan} exited with code {result.returncode}")
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return False
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print(f"[DONE] {session}/{scan}")
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return True
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def run_session(project, date, session, scan_arg, zncc_args, troubleshooting):
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if scan_arg:
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scans = [scan_arg]
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else:
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scans = config.list_scan_dirs(project, date, session)
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if not scans:
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print(f"[WARN] No scan folders found in {project}/{date}/{session}")
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return [], []
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print(f"\n Session {session}: {len(scans)} scan(s) found")
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failed = []
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for scan in scans:
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ok = run_scan(project, date, session, scan, zncc_args, troubleshooting)
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if not ok:
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failed.append(f"{session}/{scan}")
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return scans, failed
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def main():
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parser = argparse.ArgumentParser(
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description="ZNCC disparity pipeline runner — resolves paths from project structure"
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)
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# Project location
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parser.add_argument("--project", required=True, help="Project name (e.g. Olsen_wings)")
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parser.add_argument("--date", required=True, help="Date string (e.g. 2026-05-12)")
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parser.add_argument("--session", default=None, help="Session name (e.g. session1); omit to process ALL sessions on that date")
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parser.add_argument("--scan", default=None, help="Single scan to process (e.g. Scan000001); omit to process all scans in the session")
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# Output mode
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parser.add_argument("--troubleshooting", action="store_true",
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help="Save all outputs (vertical shift map, correlation map, point cloud PLY/TXT); "
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"by default only disparity map (npy + png) is saved")
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# ZNCC tuning — all optional, forwarded to stereo_disparity_main.py
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parser.add_argument(
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"--num_images",
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type=int,
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default=None,
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help="Stereo pairs per scan. Default: all matched pairs. "
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"If fewer than available, uses the last N (highest timestamps).",
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)
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parser.add_argument("--window_size", type=int, default=None)
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parser.add_argument("--H_neg_range", type=int, default=None)
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parser.add_argument("--H_pos_range", type=int, default=None)
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parser.add_argument("--v_neg_range", type=int, default=None)
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parser.add_argument("--v_pos_range", type=int, default=None)
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parser.add_argument("--zncc_threshold", type=float, default=None)
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parser.add_argument("--noise_filter", type=str, default=None, choices=["median", "open3d"])
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parser.add_argument("--interpolation", type=str, default=None)
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parser.add_argument("--noise_remove", type=str, default=None)
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parser.add_argument("--method", type=str, default=None, choices=["parabolic", "gaussian", "equiangular"])
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args = parser.parse_args()
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zncc_args = {
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"num_images": args.num_images,
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"window_size": args.window_size,
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"H_neg_range": args.H_neg_range,
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"H_pos_range": args.H_pos_range,
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"v_neg_range": args.v_neg_range,
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"v_pos_range": args.v_pos_range,
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"zncc_threshold": args.zncc_threshold,
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"noise_filter": args.noise_filter,
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"interpolation": args.interpolation,
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"noise_remove": args.noise_remove,
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"method": args.method,
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}
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# Determine sessions to process
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if args.session:
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sessions = [args.session]
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else:
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sessions = config.list_session_dirs(args.project, args.date)
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if not sessions:
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print(f"No session folders found under {args.project}/{args.date}")
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sys.exit(1)
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print(f"Found {len(sessions)} session(s): {sessions}")
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total_scans = 0
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all_failed = []
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for session in sessions:
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scans, failed = run_session(
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args.project, args.date, session,
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args.scan, zncc_args, args.troubleshooting
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)
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total_scans += len(scans)
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all_failed.extend(failed)
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print(f"\n{'='*60}")
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print(f"Finished: {total_scans - len(all_failed)}/{total_scans} scans succeeded.")
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if all_failed:
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print(f"Failed: {all_failed}")
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sys.exit(1)
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if __name__ == "__main__":
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main()
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