scripts/paper_figures.py

#!/usr/bin/env python3
"""
Paper-ready validation figures: clean + noisy data on the same axes.

Open symbols = Case A (ideal conditions)
Filled symbols = Case B (degraded, SNR ~8)
DNS reference = solid black line with 95% CI band

Produces:
  1. fig_mean_velocity.png    — U+ vs y+
  2. fig_stresses.png         — 1x3 subplots (uu+, vv+, -uv+)
  3. fig_combined_stresses.png — all stresses on one axis
"""

import numpy as np
import scipy.io as sio
from scipy.interpolate import interp1d
import matplotlib.pyplot as plt
import matplotlib as mpl
from pathlib import Path

# ── Publication font setup: match LaTeX body text ─────────────────────────────
mpl.rcParams.update({
    'font.family': 'serif',
    'font.serif': ['CMU Serif', 'Computer Modern Roman', 'DejaVu Serif'],
    'mathtext.fontset': 'cm',
    'axes.unicode_minus': False,
    'text.usetex': False,
    'axes.labelsize': 11,
    'axes.titlesize': 11,
    'legend.fontsize': 9,
    'xtick.labelsize': 10,
    'ytick.labelsize': 10,
    'lines.linewidth': 1.5,
    'figure.dpi': 600,
    'savefig.dpi': 600,
    'savefig.bbox': 'tight',
    'savefig.pad_inches': 0.05,
})

# ── Okabe-Ito colourblind-safe palette ────────────────────────────────────────
COLORS = {
    'Instantaneous': '#0072B2',
    'Ensemble':      '#D55E00',
    'Stereo':        '#009E73',
}
MARKERS = {
    'Instantaneous': 'o',
    'Ensemble':      's',
    'Stereo':        '^',
}
DNS_COLOR = 'k'


# =============================================================================
# Data loading (reuse from benchmark_comparison)
# =============================================================================

def _load_gt(gt_dir):
    from benchmark_comparison import load_wall_units, load_ground_truth
    gt_dir = Path(gt_dir)
    for name in ('wall_units.mat', 'diagnostics.mat', 'direct_stats.mat'):
        p = gt_dir / name
        if p.exists():
            wu = load_wall_units(p)
            break
    for name in ('profiles.mat', 'ensemble_statistics_full.mat', 'direct_stats.mat'):
        p = gt_dir / name
        if p.exists():
            gt = load_ground_truth(p, wall_units_path=gt_dir / 'direct_stats.mat')
            break
    gt_plus = {
        'y_plus': gt['y_plus'], 'U_plus': gt['U_plus'],
        'uu_plus': gt['uu_plus'], 'vv_plus': gt['vv_plus'], 'uv_plus': gt['uv_plus'],
    }
    for key in ('uu_plus_ci_lo', 'uu_plus_ci_hi', 'vv_plus_ci_lo', 'vv_plus_ci_hi',
                'uv_plus_ci_lo', 'uv_plus_ci_hi', 'U_plus_ci_lo', 'U_plus_ci_hi'):
        if key in gt:
            gt_plus[key] = gt[key]
    return gt_plus, wu


def _load_inst(stats_path, run_idx, wu, y_offset):
    from benchmark_comparison import (
        load_piv_statistics, compute_piv_profiles, convert_to_wall_units)
    piv = load_piv_statistics(Path(stats_path), run_idx=run_idx)
    prof = compute_piv_profiles(piv, x_exclude_vectors=4)
    plus = convert_to_wall_units(prof, wu, y_offset_mm=-prof['y_mm'].min())
    plus['y_plus'] = plus['y_plus'] + 1.0 + y_offset
    return plus


def _load_ens(ens_path, coords_path, run_idx, wu, y_offset):
    from benchmark_comparison import (
        load_ensemble_statistics, compute_piv_profiles, convert_to_wall_units)
    piv = load_ensemble_statistics(Path(ens_path), Path(coords_path), run_idx=run_idx)
    prof = compute_piv_profiles(piv, x_exclude_vectors=4)
    plus = convert_to_wall_units(prof, wu, y_offset_mm=-prof['y_mm'].min())
    plus['y_plus'] = plus['y_plus'] + 1.0 + y_offset
    return plus


def _load_stereo(stats_path, run_idx, wu, y_offset, trim_top=10):
    from benchmark_comparison import convert_to_wall_units
    stats = sio.loadmat(str(stats_path), squeeze_me=True, struct_as_record=False)
    piv_s = stats['piv_result'][run_idx]
    coords_s = stats['coordinates'][run_idx]
    x, y = coords_s.x, coords_s.y
    valid_cols = np.any(~np.isnan(y), axis=0)
    col_indices = np.where(valid_cols)[0]
    mid_col = col_indices[len(col_indices) // 2]
    y_unique = y[:, mid_col]
    valid_rows = ~np.isnan(y_unique)
    y_unique = y_unique[valid_rows]
    if trim_top > 0:
        if y_unique[0] > y_unique[-1]:
            y_unique = y_unique[trim_top:]
            vi = np.where(valid_rows)[0][trim_top:]
        else:
            y_unique = y_unique[:-trim_top]
            vi = np.where(valid_rows)[0][:-trim_top]
        tm = np.zeros(valid_rows.shape, dtype=bool)
        tm[vi] = True
        valid_rows = tm
    xs = col_indices[0] + 4
    xe = col_indices[-1] - 3
    x_mask = np.zeros(x.shape[1], dtype=bool)
    x_mask[xs:xe] = True
    prof = {
        'y_mm': y_unique,
        'U': np.nanmean(piv_s.ux[valid_rows][:, x_mask] * 1000, axis=1),
        'V': np.nanmean(piv_s.uy[valid_rows][:, x_mask] * 1000, axis=1),
        'uu': np.nanmean(piv_s.uu[valid_rows][:, x_mask] * 1e6, axis=1),
        'vv': np.nanmean(piv_s.vv[valid_rows][:, x_mask] * 1e6, axis=1),
        'uv': np.nanmean(piv_s.uv[valid_rows][:, x_mask] * 1e6, axis=1),
    }
    plus = convert_to_wall_units(prof, wu, y_offset_mm=-prof['y_mm'].min())
    plus['y_plus'] = plus['y_plus'] + 1.0 + y_offset
    return plus


def _trim(plus, n=1):
    """Remove n near-wall points."""
    if n <= 0:
        return plus
    yp = plus['y_plus']
    if yp[0] > yp[-1]:
        sl = slice(None, -n)
    else:
        sl = slice(n, None)
    return {k: (v[sl] if isinstance(v, np.ndarray) and len(v) > n else v)
            for k, v in plus.items()}


# =============================================================================
# Plotting helpers
# =============================================================================

def _ci_band(ax, yp, lo, hi, sign=1):
    if sign == -1:
        lo, hi = hi, lo
    ax.fill_between(yp, sign * lo, sign * hi,
                    color=DNS_COLOR, alpha=0.10, linewidth=0)


def _plot_method(ax, yp, vals, method, filled=True, label=None, ms=3.5, alpha=0.7):
    """Plot a single method series — filled or open markers."""
    color = COLORS[method]
    marker = MARKERS[method]
    if filled:
        ax.plot(yp, vals, color=color, marker=marker, markersize=ms,
                alpha=alpha, linestyle='none', label=label, zorder=5)
    else:
        ax.plot(yp, vals, marker=marker, markersize=ms, alpha=alpha,
                linestyle='none', label=label, zorder=4,
                markerfacecolor='none', markeredgecolor=color, markeredgewidth=0.8)


# =============================================================================
# Figure 1: Mean velocity
# =============================================================================

def plot_velocity(gt_plus, clean, noisy, wu, output_dir):
    Re_tau = wu['Re_tau']
    fig, ax = plt.subplots(figsize=(7, 5))

    # DNS + CI
    if 'U_plus_ci_lo' in gt_plus:
        _ci_band(ax, gt_plus['y_plus'], gt_plus['U_plus_ci_lo'], gt_plus['U_plus_ci_hi'])
    ax.semilogx(gt_plus['y_plus'], gt_plus['U_plus'], color=DNS_COLOR,
                linewidth=2, label='DNS', zorder=10)

    # Clean (open)
    for method, plus in clean.items():
        _plot_method(ax, plus['y_plus'], plus['U_plus'], method, filled=False,
                     label=f'{method} — Case A')

    # Noisy (filled)
    for method, plus in noisy.items():
        _plot_method(ax, plus['y_plus'], plus['U_plus'], method, filled=True,
                     label=f'{method} — Case B')

    ax.set_xlabel(r'$y^+$')
    ax.set_ylabel(r'$U^+$')
    ax.set_xlim(1, Re_tau)
    ax.set_ylim(0, 25)
    ax.grid(True, alpha=0.25, linewidth=0.5)
    ax.legend(loc='lower right', framealpha=0.9)

    fig.tight_layout()
    out = Path(output_dir)
    out.mkdir(parents=True, exist_ok=True)
    fig.savefig(out / 'fig_mean_velocity.png')
    fig.savefig(out / 'fig_mean_velocity.pdf')
    plt.close(fig)
    print(f'  Saved: {out / "fig_mean_velocity.png"}')


# =============================================================================
# Figure 2: Stresses — 1x3 subplots
# =============================================================================

def plot_stresses_subplots(gt_plus, clean, noisy, wu, output_dir):
    Re_tau = wu['Re_tau']
    has_ci = 'uu_plus_ci_lo' in gt_plus

    panels = [
        ('uu_plus', r"$\overline{u'u'}^+$", 1),
        ('vv_plus', r"$\overline{v'v'}^+$", 1),
        ('uv_plus', r"$-\overline{u'v'}^+$", -1),
    ]

    fig, axes = plt.subplots(1, 3, figsize=(7, 2.8))

    for ax, (var, ylabel, sign) in zip(axes, panels):
        # CI band
        ci_lo_key, ci_hi_key = f'{var}_ci_lo', f'{var}_ci_hi'
        if has_ci and ci_lo_key in gt_plus:
            _ci_band(ax, gt_plus['y_plus'], gt_plus[ci_lo_key], gt_plus[ci_hi_key], sign=sign)

        # DNS
        ax.plot(gt_plus['y_plus'], sign * gt_plus[var], color=DNS_COLOR,
                linewidth=1.8, label='DNS', zorder=10)

        # Clean (open)
        for method, plus in clean.items():
            _plot_method(ax, plus['y_plus'], sign * plus[var], method,
                         filled=False, label=f'{method} — A', ms=2.5, alpha=0.65)

        # Noisy (filled)
        for method, plus in noisy.items():
            _plot_method(ax, plus['y_plus'], sign * plus[var], method,
                         filled=True, label=f'{method} — B', ms=2.5, alpha=0.65)

        ax.set_xlabel(r'$y^+$')
        ax.set_ylabel(ylabel)
        ax.set_xscale('log')
        ax.set_xlim(1, Re_tau)
        ax.grid(True, alpha=0.25, linewidth=0.5)

    # Shared legend
    handles, labels = axes[0].get_legend_handles_labels()
    fig.legend(handles, labels, loc='upper center', ncol=4,
               bbox_to_anchor=(0.5, 1.05), framealpha=0.9, fontsize=8)

    fig.tight_layout()
    fig.subplots_adjust(top=0.82)
    out = Path(output_dir)
    out.mkdir(parents=True, exist_ok=True)
    fig.savefig(out / 'fig_stresses.png')
    fig.savefig(out / 'fig_stresses.pdf')
    plt.close(fig)
    print(f'  Saved: {out / "fig_stresses.png"}')


# =============================================================================
# Figure 3: Combined stresses — single axis
# =============================================================================

def plot_combined_stresses(gt_plus, clean, noisy, wu, output_dir):
    Re_tau = wu['Re_tau']
    has_ci = 'uu_plus_ci_lo' in gt_plus

    component_styles = {
        'uu_plus': {'ls': '-',  'tex': r"$\overline{u'u'}^+$",  'sign': 1},
        'vv_plus': {'ls': '--', 'tex': r"$\overline{v'v'}^+$",  'sign': 1},
        'uv_plus': {'ls': ':',  'tex': r"$-\overline{u'v'}^+$", 'sign': -1},
    }

    fig, ax = plt.subplots(figsize=(7, 5))

    # DNS reference lines + CI bands
    for var, csty in component_styles.items():
        sign = csty['sign']
        ci_lo, ci_hi = f'{var}_ci_lo', f'{var}_ci_hi'
        if has_ci and ci_lo in gt_plus:
            _ci_band(ax, gt_plus['y_plus'], gt_plus[ci_lo], gt_plus[ci_hi], sign=sign)
        ax.plot(gt_plus['y_plus'], sign * gt_plus[var],
                color=DNS_COLOR, linewidth=1.8, linestyle=csty['ls'], zorder=10)

    # Clean (open) — all components
    for method, plus in clean.items():
        for var, csty in component_styles.items():
            _plot_method(ax, plus['y_plus'], csty['sign'] * plus[var], method,
                         filled=False, ms=2.5, alpha=0.55)

    # Noisy (filled) — all components
    for method, plus in noisy.items():
        for var, csty in component_styles.items():
            _plot_method(ax, plus['y_plus'], csty['sign'] * plus[var], method,
                         filled=True, ms=2.5, alpha=0.55)

    # ── Two-part legend ──────────────────────────────────────────────────
    # Part 1: method + condition
    method_handles = [
        plt.Line2D([], [], color=DNS_COLOR, linewidth=1.8, linestyle='-', label='DNS')
    ]
    for method in list(clean.keys()) + [m for m in noisy if m not in clean]:
        c = COLORS[method]
        m = MARKERS[method]
        # Open (Case A)
        method_handles.append(
            plt.Line2D([], [], color=c, marker=m, markersize=5, linestyle='none',
                       markerfacecolor='none', markeredgecolor=c, markeredgewidth=0.8,
                       label=f'{method} — Case A'))
        # Filled (Case B)
        method_handles.append(
            plt.Line2D([], [], color=c, marker=m, markersize=5, linestyle='none',
                       label=f'{method} — Case B'))

    # Part 2: component line styles
    comp_handles = []
    for var, csty in component_styles.items():
        comp_handles.append(
            plt.Line2D([], [], color='gray', linewidth=1.5,
                       linestyle=csty['ls'], label=csty['tex']))

    leg1 = ax.legend(handles=method_handles, loc='upper right',
                     framealpha=0.9, title='Method')
    ax.add_artist(leg1)
    ax.legend(handles=comp_handles, loc='upper left',
              framealpha=0.9, title='Component')

    ax.set_xlabel(r'$y^+$')
    ax.set_ylabel(r'Stress$^+$')
    ax.set_xscale('log')
    ax.set_xlim(1, Re_tau)
    ax.grid(True, alpha=0.25, linewidth=0.5)

    fig.tight_layout()
    out = Path(output_dir)
    out.mkdir(parents=True, exist_ok=True)
    fig.savefig(out / 'fig_combined_stresses.png')
    fig.savefig(out / 'fig_combined_stresses.pdf')
    plt.close(fig)
    print(f'  Saved: {out / "fig_combined_stresses.png"}')


# =============================================================================
# Main
# =============================================================================

if __name__ == '__main__':
    import argparse
    parser = argparse.ArgumentParser(
        description='Generate combined clean+noisy paper figures. '
                    'All path arguments accept either the Case A (clean) or Case B (noisy) '
                    'variant; if only noisy paths are supplied, only Case B is plotted.')
    parser.add_argument('--output-dir', '-o', type=str, required=True,
                        help='Output directory for generated figures')

    # Ground truth (required — at least one of the two must be provided)
    parser.add_argument('--gt-clean-dir', type=str, default=None,
                        help='Directory containing direct_stats.mat for Case A (clean / 85k particles)')
    parser.add_argument('--gt-noisy-dir', type=str, default=None,
                        help='Directory containing direct_stats.mat for Case B (noisy / 22k particles)')

    # Case A (clean) PIV results
    parser.add_argument('--inst-clean-stats', type=str, default=None,
                        help='Path to instantaneous mean_stats.mat for Case A')
    parser.add_argument('--ens-clean-dir', type=str, default=None,
                        help='Directory containing ensemble_result.mat + coordinates.mat for Case A')
    parser.add_argument('--stereo-clean-stats', type=str, default=None,
                        help='Path to stereo mean_stats.mat for Case A')

    # Case B (noisy) PIV results
    parser.add_argument('--inst-noisy-stats', type=str, default=None,
                        help='Path to instantaneous mean_stats.mat for Case B')
    parser.add_argument('--ens-noisy-dir', type=str, default=None,
                        help='Directory containing ensemble_result.mat + coordinates.mat for Case B')
    parser.add_argument('--stereo-noisy-stats', type=str, default=None,
                        help='Path to stereo mean_stats.mat for Case B')

    args = parser.parse_args()
    output_dir = Path(args.output_dir)

    if not args.gt_clean_dir and not args.gt_noisy_dir:
        parser.error('At least one of --gt-clean-dir / --gt-noisy-dir must be provided')

    # Ground truth: prefer clean (85k particles, tighter CI) for reference axes
    gt_dir_primary = args.gt_clean_dir or args.gt_noisy_dir
    gt_plus, wu = _load_gt(Path(gt_dir_primary))
    print(f"DNS: Re_tau={wu['Re_tau']:.0f}")

    # ── Case A (clean) ───────────────────────────────────────────────────
    clean = {}
    if args.inst_clean_stats or args.ens_clean_dir or args.stereo_clean_stats:
        print("\nLoading Case A (ideal)...")
        if args.inst_clean_stats:
            inst_clean = _trim(_load_inst(
                Path(args.inst_clean_stats), run_idx=3, wu=wu, y_offset=3.0))
            print(f"  Instantaneous 16x16: y+={inst_clean['y_plus'].min():.1f}-{inst_clean['y_plus'].max():.1f}")
            clean['Instantaneous'] = inst_clean
        if args.ens_clean_dir:
            ens_dir = Path(args.ens_clean_dir)
            ens_clean = _load_ens(
                ens_dir / 'ensemble_result.mat',
                ens_dir / 'coordinates.mat',
                run_idx=3, wu=wu, y_offset=0.8)
            print(f"  Ensemble 8x16:       y+={ens_clean['y_plus'].min():.1f}-{ens_clean['y_plus'].max():.1f}")
            clean['Ensemble'] = ens_clean
        if args.stereo_clean_stats:
            stereo_clean = _trim(_load_stereo(
                Path(args.stereo_clean_stats), run_idx=3, wu=wu, y_offset=0.8))
            print(f"  Stereo 16x16:        y+={stereo_clean['y_plus'].min():.1f}-{stereo_clean['y_plus'].max():.1f}")
            clean['Stereo'] = stereo_clean

    # ── Case B (noisy) ───────────────────────────────────────────────────
    noisy = {}
    if args.inst_noisy_stats or args.ens_noisy_dir or args.stereo_noisy_stats:
        print("\nLoading Case B (degraded, SNR ~8)...")
        wu_n = wu  # fallback to clean wu
        if args.gt_noisy_dir:
            _, wu_n = _load_gt(Path(args.gt_noisy_dir))
        if args.inst_noisy_stats:
            inst_noisy = _trim(_load_inst(
                Path(args.inst_noisy_stats), run_idx=2, wu=wu_n, y_offset=3.0))
            print(f"  Instantaneous 32x32: y+={inst_noisy['y_plus'].min():.1f}-{inst_noisy['y_plus'].max():.1f}")
            noisy['Instantaneous'] = inst_noisy
        if args.ens_noisy_dir:
            ens_dir_n = Path(args.ens_noisy_dir)
            ens_noisy = _load_ens(
                ens_dir_n / 'ensemble_result.mat',
                ens_dir_n / 'coordinates.mat',
                run_idx=3, wu=wu_n, y_offset=1.0)
            print(f"  Ensemble 8x16:       y+={ens_noisy['y_plus'].min():.1f}-{ens_noisy['y_plus'].max():.1f}")
            noisy['Ensemble'] = ens_noisy
        if args.stereo_noisy_stats:
            stereo_noisy = _trim(_load_stereo(
                Path(args.stereo_noisy_stats), run_idx=2, wu=wu_n, y_offset=0.8))
            print(f"  Stereo 32x32:        y+={stereo_noisy['y_plus'].min():.1f}-{stereo_noisy['y_plus'].max():.1f}")
            noisy['Stereo'] = stereo_noisy

    if not clean and not noisy:
        parser.error('At least one PIV result path must be provided (--*-clean-* or --*-noisy-*)')

    # ── Generate figures ─────────────────────────────────────────────────
    print("\nGenerating figures...")
    plot_velocity(gt_plus, clean, noisy, wu, output_dir)
    plot_stresses_subplots(gt_plus, clean, noisy, wu, output_dir)
    plot_combined_stresses(gt_plus, clean, noisy, wu, output_dir)
    print("Done.")