scripts/spectral_analysis.py

#!/usr/bin/env python3
"""
Spectral analysis of Prisma / Circuit Transformer checkpoints.

Computes SVD spectra of weight matrices and (optionally) activation covariances,
revealing how the model organizes information geometrically.

Analyses:
  1. Weight spectra     — singular value distributions per matrix
  2. Effective rank     — how many dimensions carry real signal
  3. Power-law fit      — Martin & Mahoney alpha exponent (training quality)
  4. MP bound           — Marchenko-Pastur separation of signal vs noise
  5. Mirror comparison  — expand vs compress activation spectra (Prisma-specific)
  6. Embedding alignment— spectral similarity between embed and final hidden states
  7. Layer-wise summary — effective rank progression through the network (the lens)

Usage:
    # Weight-only analysis (no data needed)
    python -m circuits.scripts.spectral_analysis --checkpoint path/to/checkpoint.pt

    # Full analysis with activation spectra (needs data)
    python -m circuits.scripts.spectral_analysis --checkpoint path/to/checkpoint.pt \
        --data hf:HuggingFaceFW/fineweb-edu:sample-10BT:train --num-samples 512

    # Compare two checkpoints
    python -m circuits.scripts.spectral_analysis \
        --checkpoint path/to/prisma.pt --checkpoint-b path/to/standard.pt

    # Compare against HuggingFace model
    python -m circuits.scripts.spectral_analysis \
        --checkpoint path/to/prisma.pt --hf-model gpt2-medium
"""

import argparse
import json
import sys
import os
from pathlib import Path
from collections import defaultdict

import numpy as np
import torch
import torch.nn as nn
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec


# ---------------------------------------------------------------------------
# Model loading
# ---------------------------------------------------------------------------

def load_prisma_model(checkpoint_path: str, device: str = "cpu"):
    """Load a Prisma/Circuit checkpoint, return (model, config_dict, model_type)."""
    sys.path.insert(0, str(Path(__file__).resolve().parents[2]))
    from circuits.config import CircuitConfig
    from circuits.model import CircuitTransformer
    from circuits.mirrored import MirroredConfig, MirroredTransformer

    ckpt = torch.load(checkpoint_path, map_location="cpu", weights_only=False)
    model_type = ckpt.get("model_type", "standard")
    config_dict = ckpt.get("config", {})

    if model_type == "mirrored":
        if config_dict.get("dual_gate_middle"):
            config_dict.pop("dual_gate_middle")
        config = MirroredConfig.from_dict(config_dict)
        model = MirroredTransformer(config)
    else:
        config = CircuitConfig.from_dict(config_dict)
        model = CircuitTransformer(config)

    state_dict = ckpt["model"]
    if any(k.startswith("_orig_mod.") for k in state_dict):
        state_dict = {k.removeprefix("_orig_mod."): v for k, v in state_dict.items()}
    model.load_state_dict(state_dict, strict=False)
    model.to(device).eval()

    return model, config_dict, model_type


def load_hf_model(model_name: str, device: str = "cpu"):
    """Load a HuggingFace causal LM."""
    from transformers import AutoModelForCausalLM
    model = AutoModelForCausalLM.from_pretrained(model_name, torch_dtype=torch.float32)
    model.to(device).eval()
    return model


# ---------------------------------------------------------------------------
# SVD utilities
# ---------------------------------------------------------------------------

def compute_singular_values(weight: torch.Tensor) -> np.ndarray:
    """Compute singular values of a 2D weight matrix."""
    w = weight.detach().float().cpu()
    if w.ndim != 2:
        return None
    sv = torch.linalg.svdvals(w).numpy()
    return sv


def effective_rank(sv: np.ndarray) -> float:
    """Entropy-based effective rank (Roy & Vetterli, 2007).

    erank = exp(H(p)) where p_i = sigma_i / sum(sigma)
    and H is Shannon entropy. Ranges from 1 (rank-1) to min(m,n) (full rank).
    """
    sv = sv[sv > 1e-10]
    if len(sv) == 0:
        return 0.0
    p = sv / sv.sum()
    entropy = -(p * np.log(p)).sum()
    return float(np.exp(entropy))


def stable_rank(sv: np.ndarray) -> float:
    """Stable rank = ||W||_F^2 / ||W||_2^2 = sum(sigma^2) / max(sigma)^2."""
    if len(sv) == 0 or sv[0] < 1e-10:
        return 0.0
    return float((sv ** 2).sum() / (sv[0] ** 2))


def marchenko_pastur_bound(m: int, n: int, sv: np.ndarray) -> float:
    """Estimate Marchenko-Pastur upper edge.

    For a random matrix with variance sigma^2, the MP upper bound is
    sigma * (1 + sqrt(m/n))^2  (assuming m >= n).
    We estimate sigma from the bulk of singular values.
    """
    gamma = max(m, n) / min(m, n)
    # Estimate noise level from bottom half of spectrum
    bottom_half = sv[len(sv) // 2:]
    if len(bottom_half) == 0:
        return sv[-1] if len(sv) > 0 else 0.0
    sigma_est = float(np.median(bottom_half)) / np.sqrt(max(m, n))
    mp_upper = sigma_est * (1.0 + np.sqrt(gamma)) ** 2 * np.sqrt(min(m, n))
    return mp_upper


def fit_power_law(sv: np.ndarray, fit_fraction: float = 0.8) -> tuple[float, float]:
    """Fit power law to singular value distribution tail.

    Returns (alpha, r_squared). alpha < 2 = heavy-tailed (well-trained).
    """
    sv = sv[sv > 1e-10]
    if len(sv) < 10:
        return 0.0, 0.0
    # Fit to the top `fit_fraction` of the spectrum (exclude noise floor)
    n_fit = max(10, int(len(sv) * fit_fraction))
    sv_fit = sv[:n_fit]

    log_rank = np.log(np.arange(1, n_fit + 1))
    log_sv = np.log(sv_fit)

    # Linear regression in log-log space: log(sv) = -alpha * log(rank) + c
    coeffs = np.polyfit(log_rank, log_sv, 1)
    alpha = -coeffs[0]

    # R-squared
    predicted = np.polyval(coeffs, log_rank)
    ss_res = ((log_sv - predicted) ** 2).sum()
    ss_tot = ((log_sv - log_sv.mean()) ** 2).sum()
    r_sq = 1.0 - ss_res / ss_tot if ss_tot > 0 else 0.0

    return float(alpha), float(r_sq)


# ---------------------------------------------------------------------------
# Weight spectrum analysis
# ---------------------------------------------------------------------------

def analyze_weight_spectra(model: nn.Module, model_label: str = "model") -> dict:
    """Compute SVD spectra for all 2D weight matrices."""
    results = {}
    for name, param in model.named_parameters():
        if param.ndim != 2:
            continue
        sv = compute_singular_values(param)
        if sv is None:
            continue
        m, n = param.shape
        mp_bound = marchenko_pastur_bound(m, n, sv)
        n_above_mp = int((sv > mp_bound).sum())
        alpha, r_sq = fit_power_law(sv)

        results[name] = {
            "shape": (m, n),
            "singular_values": sv,
            "effective_rank": effective_rank(sv),
            "stable_rank": stable_rank(sv),
            "spectral_norm": float(sv[0]),
            "frobenius_norm": float(np.sqrt((sv ** 2).sum())),
            "mp_bound": mp_bound,
            "n_above_mp": n_above_mp,
            "n_total": len(sv),
            "signal_ratio": n_above_mp / len(sv) if len(sv) > 0 else 0,
            "alpha": alpha,
            "alpha_r2": r_sq,
            "condition_number": float(sv[0] / sv[-1]) if sv[-1] > 1e-10 else float("inf"),
        }
    return results


# ---------------------------------------------------------------------------
# Activation spectrum analysis
# ---------------------------------------------------------------------------

def collect_activations(model, input_ids: torch.Tensor,
                        word_positions: torch.Tensor = None,
                        model_type: str = "standard") -> dict[str, torch.Tensor]:
    """Run a forward pass and collect intermediate activations via hooks."""
    activations = {}
    hooks = []

    def make_hook(name):
        def hook_fn(module, input, output):
            if isinstance(output, tuple):
                out = output[0]
            else:
                out = output
            # Store mean over batch and sequence for covariance
            activations[name] = out.detach().float().cpu()
        return hook_fn

    # Register hooks based on model type
    if model_type == "mirrored":
        # Expand phase
        for i, block in enumerate(model.mirror_blocks):
            hooks.append(block.register_forward_hook(make_hook(f"expand_{i}")))
        # Middle
        for i, block in enumerate(model.middle_blocks):
            hooks.append(block.register_forward_hook(make_hook(f"middle_{i}")))
        # Compress — mirror blocks are reused in reverse, so we hook the FFN output
        # We'll collect compress activations differently via a custom forward
    else:
        for i, block in enumerate(model.layers):
            hooks.append(block.register_forward_hook(make_hook(f"layer_{i}")))

    # Also hook the embedding output
    hooks.append(model.embed.register_forward_hook(make_hook("embedding")))

    with torch.no_grad():
        kwargs = {}
        if word_positions is not None:
            kwargs["word_positions"] = word_positions
        model(input_ids, **kwargs)

    for h in hooks:
        h.remove()

    return activations


def collect_mirrored_activations(model, input_ids: torch.Tensor,
                                  word_positions: torch.Tensor = None) -> dict[str, torch.Tensor]:
    """Collect activations from a MirroredTransformer, separating expand and compress phases.

    This manually runs the forward pass to capture compress-phase activations
    from the reversed mirror blocks.
    """
    import math

    activations = {}

    with torch.no_grad():
        # Embed
        x = model.embed(input_ids)
        if model.embed_proj is not None:
            import torch.nn.functional as F
            if model.embed_g3 is not None:
                g4 = F.silu(model.embed_g4(x))
                g3 = F.silu(model.embed_g3(x) * g4)
                x = model.embed_proj(x) * g3
            else:
                x = F.silu(model.embed_proj(x))
        x = x * model.embed_scale
        activations["embedding"] = x.detach().float().cpu()

        # Expand phase
        for i, block in enumerate(model.mirror_blocks):
            x, _ = block(x, word_positions=word_positions)
            activations[f"expand_{i}"] = x.detach().float().cpu()

        # Middle phase
        for i, block in enumerate(model.middle_blocks):
            x, _ = block(x, word_positions=word_positions)
            activations[f"middle_{i}"] = x.detach().float().cpu()

        # Compress phase (reversed)
        for i in reversed(range(len(model.mirror_blocks))):
            x, _ = model.mirror_blocks[i](x, word_positions=word_positions)
            compress_idx = len(model.mirror_blocks) - 1 - i
            activations[f"compress_{compress_idx}"] = x.detach().float().cpu()

        # Final norm
        x = model.norm(x)
        activations["final_norm"] = x.detach().float().cpu()

    return activations


def activation_spectrum(act: torch.Tensor, max_components: int = 256) -> dict:
    """Compute eigenspectrum of activation covariance.

    act: [B, T, D] — reshape to [B*T, D], compute covariance, eigendecompose.
    """
    # Flatten batch and sequence
    flat = act.reshape(-1, act.shape[-1])  # [N, D]
    N, D = flat.shape

    if N < 2:
        return None

    # Center
    flat = flat - flat.mean(dim=0, keepdim=True)

    # Compute covariance via SVD of the data matrix (more stable than cov matrix)
    n_components = min(max_components, D, N)
    try:
        U, S, Vh = torch.pca_lowrank(flat, q=n_components)
        eigenvalues = (S ** 2 / (N - 1)).numpy()
    except Exception:
        # Fallback: full covariance
        cov = (flat.T @ flat) / (N - 1)
        eigenvalues = torch.linalg.eigvalsh(cov).flip(0).numpy()
        eigenvalues = eigenvalues[:max_components]

    eigenvalues = eigenvalues[eigenvalues > 1e-10]

    return {
        "eigenvalues": eigenvalues,
        "effective_rank": effective_rank(np.sqrt(np.maximum(eigenvalues, 0))),
        "total_variance": float(eigenvalues.sum()),
        "top1_variance_ratio": float(eigenvalues[0] / eigenvalues.sum()) if len(eigenvalues) > 0 else 0,
        "top10_variance_ratio": float(eigenvalues[:10].sum() / eigenvalues.sum()) if len(eigenvalues) >= 10 else 0,
        "n_components": len(eigenvalues),
    }


# ---------------------------------------------------------------------------
# Plotting
# ---------------------------------------------------------------------------

def plot_weight_spectra(results: dict, output_dir: Path, model_label: str = "model",
                        results_b: dict = None, model_b_label: str = "model_b"):
    """Plot singular value distributions for all weight matrices."""
    # Group by layer/component type
    groups = defaultdict(list)
    for name, data in results.items():
        # Identify the component type
        if "attn" in name and ("q_proj" in name or "wq" in name):
            groups["attention_Q"].append((name, data))
        elif "attn" in name and ("k_proj" in name or "wk" in name):
            groups["attention_K"].append((name, data))
        elif "attn" in name and ("v_proj" in name or "wv" in name):
            groups["attention_V"].append((name, data))
        elif "attn" in name and ("o_proj" in name or "wo" in name):
            groups["attention_O"].append((name, data))
        elif "w1" in name or "up_proj" in name:
            groups["ffn_W1"].append((name, data))
        elif "w2" in name or "down_proj" in name:
            groups["ffn_W2"].append((name, data))
        elif "w3" in name or "gate_proj" in name:
            groups["ffn_gate_W3"].append((name, data))
        elif "w4" in name:
            groups["ffn_gate_W4"].append((name, data))
        elif "embed" in name or "wte" in name:
            groups["embedding"].append((name, data))
        elif "lm_head" in name:
            groups["lm_head"].append((name, data))
        else:
            groups["other"].append((name, data))

    # Plot each group
    for group_name, items in groups.items():
        if not items:
            continue

        fig, axes = plt.subplots(1, 2, figsize=(14, 5))
        fig.suptitle(f"{model_label} — {group_name} weight spectra", fontsize=13)

        ax_linear, ax_log = axes

        cmap = plt.cm.viridis(np.linspace(0.1, 0.9, len(items)))
        for idx, (name, data) in enumerate(items):
            sv = data["singular_values"]
            short_name = name.split(".")[-2] + "." + name.split(".")[-1] if "." in name else name
            ax_linear.plot(sv, color=cmap[idx], alpha=0.7, linewidth=0.8, label=short_name)
            ax_log.loglog(np.arange(1, len(sv) + 1), sv, color=cmap[idx], alpha=0.7,
                         linewidth=0.8, label=short_name)
            # MP bound
            ax_linear.axhline(data["mp_bound"], color=cmap[idx], linestyle=":", alpha=0.3)

        ax_linear.set_xlabel("Rank")
        ax_linear.set_ylabel("Singular value")
        ax_linear.set_title("Linear scale")
        ax_linear.legend(fontsize=6, ncol=2)

        ax_log.set_xlabel("Rank")
        ax_log.set_ylabel("Singular value")
        ax_log.set_title("Log-log scale (power law)")
        ax_log.legend(fontsize=6, ncol=2)

        plt.tight_layout()
        fig.savefig(output_dir / f"weight_spectra_{group_name}.png", dpi=150)
        plt.close(fig)


def plot_effective_rank_progression(results: dict, output_dir: Path,
                                    model_label: str = "model",
                                    results_b: dict = None,
                                    model_b_label: str = "model_b"):
    """Plot effective rank per layer — the biconcave lens in eigenvalues."""
    # Extract layer-ordered FFN W1 effective ranks (the main signal path)
    layer_data = []
    for name, data in sorted(results.items()):
        if "w1" in name or "up_proj" in name:
            # Extract layer index
            parts = name.split(".")
            layer_label = name
            for p in parts:
                if p.isdigit():
                    layer_label = p
                    break
            layer_data.append((name, data["effective_rank"], data["stable_rank"],
                             data["alpha"], data["signal_ratio"], layer_label))

    if not layer_data:
        return

    fig, axes = plt.subplots(2, 2, figsize=(14, 10))
    fig.suptitle(f"{model_label} — Layer-wise spectral properties (FFN W1)", fontsize=13)

    names = [d[0] for d in layer_data]
    x = range(len(layer_data))
    short_labels = [d[5] for d in layer_data]

    # Effective rank
    axes[0, 0].bar(x, [d[1] for d in layer_data], color="steelblue", alpha=0.8)
    axes[0, 0].set_ylabel("Effective rank")
    axes[0, 0].set_title("Effective rank (entropy-based)")
    axes[0, 0].set_xticks(x)
    axes[0, 0].set_xticklabels(short_labels, rotation=45, fontsize=7)

    # Stable rank
    axes[0, 1].bar(x, [d[2] for d in layer_data], color="coral", alpha=0.8)
    axes[0, 1].set_ylabel("Stable rank")
    axes[0, 1].set_title("Stable rank (Frobenius/spectral)")
    axes[0, 1].set_xticks(x)
    axes[0, 1].set_xticklabels(short_labels, rotation=45, fontsize=7)

    # Power-law alpha
    axes[1, 0].bar(x, [d[3] for d in layer_data], color="mediumpurple", alpha=0.8)
    axes[1, 0].set_ylabel("Alpha")
    axes[1, 0].set_title("Power-law exponent (lower = heavier tail = more structure)")
    axes[1, 0].axhline(2.0, color="red", linestyle="--", alpha=0.5, label="alpha=2 boundary")
    axes[1, 0].legend(fontsize=8)
    axes[1, 0].set_xticks(x)
    axes[1, 0].set_xticklabels(short_labels, rotation=45, fontsize=7)

    # Signal ratio (above MP)
    axes[1, 1].bar(x, [d[4] for d in layer_data], color="seagreen", alpha=0.8)
    axes[1, 1].set_ylabel("Signal ratio")
    axes[1, 1].set_title("Fraction of singular values above MP bound")
    axes[1, 1].set_xticks(x)
    axes[1, 1].set_xticklabels(short_labels, rotation=45, fontsize=7)

    plt.tight_layout()
    fig.savefig(output_dir / "layer_progression.png", dpi=150)
    plt.close(fig)


def plot_activation_spectra(act_spectra: dict, output_dir: Path,
                            model_label: str = "model"):
    """Plot activation eigenspectra across layers."""
    if not act_spectra:
        return

    # Sort layers in processing order
    order_keys = {"embedding": -1, "final_norm": 999}
    def sort_key(name):
        if name in order_keys:
            return order_keys[name]
        parts = name.split("_")
        phase = parts[0]
        idx = int(parts[1]) if len(parts) > 1 and parts[1].isdigit() else 0
        phase_offset = {"expand": 0, "middle": 100, "compress": 200, "layer": 0}
        return phase_offset.get(phase, 300) + idx

    sorted_names = sorted(act_spectra.keys(), key=sort_key)

    # -- Eigenvalue distributions --
    fig, axes = plt.subplots(1, 2, figsize=(14, 6))
    fig.suptitle(f"{model_label} — Activation eigenspectra", fontsize=13)

    cmap = plt.cm.coolwarm(np.linspace(0, 1, len(sorted_names)))
    for idx, name in enumerate(sorted_names):
        data = act_spectra[name]
        ev = data["eigenvalues"]
        axes[0].semilogy(ev / ev.sum(), color=cmap[idx], alpha=0.7, linewidth=1.0, label=name)
        axes[1].plot(np.cumsum(ev) / ev.sum(), color=cmap[idx], alpha=0.7, linewidth=1.0, label=name)

    axes[0].set_xlabel("Component")
    axes[0].set_ylabel("Normalized eigenvalue (log)")
    axes[0].set_title("Eigenvalue distribution")
    axes[0].legend(fontsize=6, ncol=2)

    axes[1].set_xlabel("Component")
    axes[1].set_ylabel("Cumulative variance explained")
    axes[1].set_title("Variance concentration")
    axes[1].axhline(0.9, color="gray", linestyle="--", alpha=0.4, label="90%")
    axes[1].legend(fontsize=6, ncol=2)

    plt.tight_layout()
    fig.savefig(output_dir / "activation_spectra.png", dpi=150)
    plt.close(fig)

    # -- Effective rank progression (the lens shape) --
    fig, ax = plt.subplots(figsize=(12, 5))
    fig.suptitle(f"{model_label} — Activation effective rank progression", fontsize=13)

    eranks = [act_spectra[n]["effective_rank"] for n in sorted_names]
    colors = []
    for name in sorted_names:
        if "expand" in name:
            colors.append("steelblue")
        elif "middle" in name:
            colors.append("goldenrod")
        elif "compress" in name:
            colors.append("coral")
        else:
            colors.append("gray")

    ax.bar(range(len(sorted_names)), eranks, color=colors, alpha=0.8)
    ax.set_xticks(range(len(sorted_names)))
    ax.set_xticklabels(sorted_names, rotation=45, ha="right", fontsize=8)
    ax.set_ylabel("Effective rank")
    ax.set_title("Expand (blue) → Middle (gold) → Compress (coral)")

    plt.tight_layout()
    fig.savefig(output_dir / "activation_rank_progression.png", dpi=150)
    plt.close(fig)


def plot_mirror_comparison(act_spectra: dict, output_dir: Path,
                           model_label: str = "model"):
    """Compare expand vs compress activation spectra for each mirror pair."""
    expand_layers = sorted([n for n in act_spectra if n.startswith("expand_")])
    compress_layers = sorted([n for n in act_spectra if n.startswith("compress_")])

    if not expand_layers or not compress_layers:
        return

    n_pairs = min(len(expand_layers), len(compress_layers))
    fig, axes = plt.subplots(1, n_pairs, figsize=(4 * n_pairs, 4), squeeze=False)
    fig.suptitle(f"{model_label} — Mirror pair activation spectra (expand vs compress)", fontsize=13)

    for i in range(n_pairs):
        ax = axes[0, i]
        exp_ev = act_spectra[expand_layers[i]]["eigenvalues"]
        comp_ev = act_spectra[compress_layers[i]]["eigenvalues"]

        n_plot = min(len(exp_ev), len(comp_ev), 100)
        ax.semilogy(exp_ev[:n_plot] / exp_ev.sum(), color="steelblue", alpha=0.8,
                    linewidth=1.5, label="expand")
        ax.semilogy(comp_ev[:n_plot] / comp_ev.sum(), color="coral", alpha=0.8,
                    linewidth=1.5, label="compress")

        exp_er = act_spectra[expand_layers[i]]["effective_rank"]
        comp_er = act_spectra[compress_layers[i]]["effective_rank"]
        ax.set_title(f"Pair {i}\nerank: {exp_er:.0f} / {comp_er:.0f}", fontsize=10)
        ax.set_xlabel("Component")
        if i == 0:
            ax.set_ylabel("Normalized eigenvalue")
        ax.legend(fontsize=8)

    plt.tight_layout()
    fig.savefig(output_dir / "mirror_pair_comparison.png", dpi=150)
    plt.close(fig)


def plot_gate_spectra(results: dict, output_dir: Path, model_label: str = "model"):
    """Compare W3 vs W4 gate weight spectra (G2LU inner vs outer gate)."""
    w3_items = [(n, d) for n, d in sorted(results.items()) if "w3" in n and "ffn" in n]
    w4_items = [(n, d) for n, d in sorted(results.items()) if "w4" in n and "ffn" in n]

    if not w3_items or not w4_items:
        return

    n_pairs = min(len(w3_items), len(w4_items))
    fig, axes = plt.subplots(2, 1, figsize=(12, 8))
    fig.suptitle(f"{model_label} — G2LU gate spectra (W3 outer vs W4 inner)", fontsize=13)

    # Overlay all W3 vs W4
    cmap_w3 = plt.cm.Blues(np.linspace(0.3, 0.9, n_pairs))
    cmap_w4 = plt.cm.Reds(np.linspace(0.3, 0.9, n_pairs))

    for i in range(n_pairs):
        sv3 = w3_items[i][1]["singular_values"]
        sv4 = w4_items[i][1]["singular_values"]
        axes[0].semilogy(sv3, color=cmap_w3[i], alpha=0.6, linewidth=0.8, label=f"W3 pair {i}")
        axes[0].semilogy(sv4, color=cmap_w4[i], alpha=0.6, linewidth=0.8, label=f"W4 pair {i}")

    axes[0].set_xlabel("Rank")
    axes[0].set_ylabel("Singular value (log)")
    axes[0].set_title("Gate weight spectra")
    axes[0].legend(fontsize=6, ncol=4)

    # Effective rank comparison
    er_w3 = [w3_items[i][1]["effective_rank"] for i in range(n_pairs)]
    er_w4 = [w4_items[i][1]["effective_rank"] for i in range(n_pairs)]
    x = np.arange(n_pairs)
    axes[1].bar(x - 0.15, er_w3, 0.3, color="steelblue", alpha=0.8, label="W3 (outer gate)")
    axes[1].bar(x + 0.15, er_w4, 0.3, color="coral", alpha=0.8, label="W4 (inner gate)")
    axes[1].set_xlabel("Mirror pair")
    axes[1].set_ylabel("Effective rank")
    axes[1].set_title("Gate effective rank by pair")
    axes[1].set_xticks(x)
    axes[1].legend()

    plt.tight_layout()
    fig.savefig(output_dir / "gate_spectra.png", dpi=150)
    plt.close(fig)


def plot_embedding_alignment(results: dict, act_spectra: dict, output_dir: Path,
                              model_label: str = "model"):
    """Compare embedding weight spectrum with final layer activation spectrum."""
    embed_data = None
    for name, data in results.items():
        if "embed" in name.lower() and "proj" not in name.lower() and "g3" not in name.lower() and "g4" not in name.lower():
            embed_data = data
            break

    final_act = act_spectra.get("final_norm") or act_spectra.get("compress_0")
    if embed_data is None or final_act is None:
        return

    fig, axes = plt.subplots(1, 2, figsize=(12, 5))
    fig.suptitle(f"{model_label} — Embedding vs final activation spectra", fontsize=13)

    # Normalized comparison
    sv_embed = embed_data["singular_values"]
    ev_final = final_act["eigenvalues"]
    sv_embed_norm = sv_embed / sv_embed.sum()
    ev_final_norm = ev_final / ev_final.sum()

    n_plot = min(len(sv_embed_norm), len(ev_final_norm), 200)
    axes[0].semilogy(sv_embed_norm[:n_plot], color="steelblue", linewidth=1.5,
                     label=f"Embedding (erank={embed_data['effective_rank']:.0f})")
    axes[0].semilogy(ev_final_norm[:n_plot], color="coral", linewidth=1.5,
                     label=f"Final act (erank={final_act['effective_rank']:.0f})")
    axes[0].set_xlabel("Component")
    axes[0].set_ylabel("Normalized value (log)")
    axes[0].set_title("Spectral shape comparison")
    axes[0].legend()

    # Cumulative variance
    axes[1].plot(np.cumsum(sv_embed_norm[:n_plot]), color="steelblue", linewidth=1.5, label="Embedding")
    axes[1].plot(np.cumsum(ev_final_norm[:n_plot]), color="coral", linewidth=1.5, label="Final activation")
    axes[1].set_xlabel("Component")
    axes[1].set_ylabel("Cumulative fraction")
    axes[1].set_title("Variance concentration")
    axes[1].axhline(0.9, color="gray", linestyle="--", alpha=0.4)
    axes[1].legend()

    plt.tight_layout()
    fig.savefig(output_dir / "embedding_alignment.png", dpi=150)
    plt.close(fig)


def plot_comparison(results_a: dict, results_b: dict,
                    label_a: str, label_b: str,
                    output_dir: Path):
    """Side-by-side comparison of two models' spectral properties."""
    # Collect effective ranks for FFN W1 / up_proj
    def extract_ffn_ranks(results):
        ranks = []
        for name, data in sorted(results.items()):
            if ("w1" in name or "up_proj" in name or "c_fc" in name
                    or "dense_h_to_4h" in name) and "embed" not in name:
                ranks.append((name, data["effective_rank"], data["stable_rank"], data["alpha"]))
        return ranks

    ranks_a = extract_ffn_ranks(results_a)
    ranks_b = extract_ffn_ranks(results_b)

    if not ranks_a or not ranks_b:
        return

    fig, axes = plt.subplots(1, 3, figsize=(18, 5))
    fig.suptitle(f"Comparison: {label_a} vs {label_b}", fontsize=13)

    n = min(len(ranks_a), len(ranks_b))
    x = np.arange(n)

    for ax_idx, (metric_idx, ylabel, title) in enumerate([
        (1, "Effective rank", "Effective rank per layer"),
        (2, "Stable rank", "Stable rank per layer"),
        (3, "Alpha", "Power-law alpha per layer"),
    ]):
        vals_a = [ranks_a[i][metric_idx] for i in range(n)]
        vals_b = [ranks_b[i][metric_idx] for i in range(n)]
        axes[ax_idx].bar(x - 0.15, vals_a, 0.3, color="steelblue", alpha=0.8, label=label_a)
        axes[ax_idx].bar(x + 0.15, vals_b, 0.3, color="coral", alpha=0.8, label=label_b)
        axes[ax_idx].set_xlabel("Layer")
        axes[ax_idx].set_ylabel(ylabel)
        axes[ax_idx].set_title(title)
        axes[ax_idx].legend(fontsize=8)

    plt.tight_layout()
    fig.savefig(output_dir / "comparison.png", dpi=150)
    plt.close(fig)


# ---------------------------------------------------------------------------
# Summary report
# ---------------------------------------------------------------------------

def print_summary(results: dict, model_label: str, act_spectra: dict = None):
    """Print a concise text summary of spectral analysis."""
    print(f"\n{'='*70}")
    print(f"  Spectral Analysis: {model_label}")
    print(f"{'='*70}")

    # Group by component type
    components = defaultdict(list)
    for name, data in sorted(results.items()):
        if "w1" in name or "up_proj" in name:
            components["FFN W1 (up)"].append(data)
        elif "w2" in name or "down_proj" in name:
            components["FFN W2 (down)"].append(data)
        elif "w3" in name:
            components["FFN W3 (outer gate)"].append(data)
        elif "w4" in name:
            components["FFN W4 (inner gate)"].append(data)
        elif "embed" in name.lower() and "proj" not in name and "g3" not in name and "g4" not in name:
            components["Embedding"].append(data)

    print(f"\n{'Component':<25} {'Shape':>12} {'eRank':>8} {'sRank':>8} {'Alpha':>8} {'Sig%':>8} {'Cond#':>10}")
    print("-" * 85)
    for comp_name, items in components.items():
        for i, data in enumerate(items):
            label = f"{comp_name}" if len(items) == 1 else f"{comp_name}[{i}]"
            shape_str = f"{data['shape'][0]}x{data['shape'][1]}"
            cond = f"{data['condition_number']:.0f}" if data['condition_number'] < 1e6 else "inf"
            print(f"{label:<25} {shape_str:>12} {data['effective_rank']:>8.1f} "
                  f"{data['stable_rank']:>8.1f} {data['alpha']:>8.3f} "
                  f"{data['signal_ratio']*100:>7.1f}% {cond:>10}")

    # Aggregate stats
    all_alphas = [d["alpha"] for d in results.values() if d["alpha"] > 0]
    all_eranks = [d["effective_rank"] for d in results.values()]
    if all_alphas:
        print(f"\n  Mean alpha: {np.mean(all_alphas):.3f}  (< 2.0 = heavy-tailed = well-structured)")
        print(f"  Mean effective rank: {np.mean(all_eranks):.1f}")

    # Activation summary
    if act_spectra:
        print(f"\n  Activation spectra:")
        print(f"  {'Layer':<25} {'eRank':>8} {'Top1%':>8} {'Top10%':>8}")
        print("  " + "-" * 55)

        order_keys = {"embedding": -1, "final_norm": 999}
        def sort_key(name):
            if name in order_keys:
                return order_keys[name]
            parts = name.split("_")
            phase = parts[0]
            idx = int(parts[1]) if len(parts) > 1 and parts[1].isdigit() else 0
            phase_offset = {"expand": 0, "middle": 100, "compress": 200, "layer": 0}
            return phase_offset.get(phase, 300) + idx

        for name in sorted(act_spectra.keys(), key=sort_key):
            data = act_spectra[name]
            print(f"  {name:<25} {data['effective_rank']:>8.1f} "
                  f"{data['top1_variance_ratio']*100:>7.1f}% "
                  f"{data['top10_variance_ratio']*100:>7.1f}%")


def save_results_json(results: dict, act_spectra: dict, output_path: Path):
    """Save numerical results (no numpy arrays) to JSON."""
    out = {}
    for name, data in results.items():
        out[name] = {k: v for k, v in data.items() if k != "singular_values"}
        out[name]["top_10_sv"] = data["singular_values"][:10].tolist()

    if act_spectra:
        out["_activations"] = {}
        for name, data in act_spectra.items():
            out["_activations"][name] = {k: v for k, v in data.items() if k != "eigenvalues"}
            out["_activations"][name]["top_10_ev"] = data["eigenvalues"][:10].tolist()

    with open(output_path, "w") as f:
        json.dump(out, f, indent=2, default=str)


# ---------------------------------------------------------------------------
# Data loading (minimal — just enough tokens for activation analysis)
# ---------------------------------------------------------------------------

def load_sample_data(data_source: str, tokenizer_name: str, num_samples: int = 256,
                     context_length: int = 512, device: str = "cpu"):
    """Load a small batch of tokenized data for activation analysis."""
    sys.path.insert(0, str(Path(__file__).resolve().parents[2]))
    from circuits.data import get_tokenizer

    tokenizer = get_tokenizer(tokenizer_name)

    if data_source.startswith("hf:"):
        from datasets import load_dataset
        parts = data_source[3:].split(":")
        ds_name = parts[0]
        ds_config = parts[1] if len(parts) > 1 else None
        ds_split = parts[2] if len(parts) > 2 else "train"
        dataset = load_dataset(ds_name, ds_config, split=ds_split, streaming=True)
        texts = []
        for item in dataset:
            texts.append(item.get("text", ""))
            if len(texts) >= num_samples:
                break
    else:
        with open(data_source) as f:
            texts = [line.strip() for line in f if line.strip()][:num_samples]

    # Tokenize and create batches
    all_ids = []
    for text in texts:
        ids = tokenizer.encode(text)
        if len(ids) >= context_length:
            all_ids.append(ids[:context_length])
        elif len(ids) > 32:
            all_ids.append(ids + [tokenizer.eos_token_id] * (context_length - len(ids)))

    if not all_ids:
        return None, tokenizer

    input_ids = torch.tensor(all_ids[:num_samples], device=device)
    return input_ids, tokenizer


# ---------------------------------------------------------------------------
# Main
# ---------------------------------------------------------------------------

def main():
    parser = argparse.ArgumentParser(description="Spectral analysis of Prisma checkpoints")
    parser.add_argument("--checkpoint", type=str, required=True, help="Path to Prisma/Circuit checkpoint")
    parser.add_argument("--checkpoint-b", type=str, default=None, help="Second checkpoint for comparison")
    parser.add_argument("--hf-model", type=str, default=None, help="HuggingFace model name for comparison")
    parser.add_argument("--data", type=str, default=None,
                        help="Data source for activation analysis (hf:dataset:config:split or path)")
    parser.add_argument("--num-samples", type=int, default=256, help="Number of samples for activation analysis")
    parser.add_argument("--context-length", type=int, default=512, help="Context length for activation analysis")
    parser.add_argument("--output-dir", type=str, default=None, help="Output directory (default: auto)")
    parser.add_argument("--gpu", type=int, default=0, help="GPU index")
    parser.add_argument("--no-activations", action="store_true", help="Skip activation analysis even if data provided")
    args = parser.parse_args()

    device = f"cuda:{args.gpu}" if torch.cuda.is_available() else "cpu"
    print(f"Device: {device}")

    # Output directory
    if args.output_dir:
        output_dir = Path(args.output_dir)
    else:
        ckpt_name = Path(args.checkpoint).parent.name
        output_dir = Path("circuits/scripts/spectral_output") / ckpt_name
    output_dir.mkdir(parents=True, exist_ok=True)
    print(f"Output: {output_dir}")

    # ── Load model A ──
    print(f"\nLoading: {args.checkpoint}")
    model_a, config_a, model_type_a = load_prisma_model(args.checkpoint, device)
    label_a = Path(args.checkpoint).parent.name
    print(f"  Type: {model_type_a}")
    n_params = sum(p.numel() for p in model_a.parameters())
    print(f"  Parameters: {n_params:,}")

    # ── Weight spectra (A) ──
    print("\nAnalyzing weight spectra...")
    weight_results_a = analyze_weight_spectra(model_a, label_a)
    print(f"  Analyzed {len(weight_results_a)} weight matrices")

    # ── Activation spectra (A) ──
    act_spectra_a = None
    if args.data and not args.no_activations:
        tokenizer_name = torch.load(args.checkpoint, map_location="cpu",
                                     weights_only=False).get("tokenizer_name", "gpt2")
        print(f"\nLoading data for activation analysis ({args.num_samples} samples)...")
        input_ids, tokenizer = load_sample_data(
            args.data, tokenizer_name, args.num_samples, args.context_length, device
        )
        if input_ids is not None:
            print(f"  Data shape: {input_ids.shape}")

            # Compute word positions if needed
            word_positions = None
            word_rope_dims = config_a.get("word_rope_dims", 0)
            if word_rope_dims > 0:
                from circuits.layers import build_word_start_table, compute_word_positions
                word_start_table = build_word_start_table(tokenizer, len(tokenizer)).to(device)
                word_positions = compute_word_positions(input_ids, word_start_table)

            print("  Collecting activations...")
            if model_type_a == "mirrored":
                raw_acts = collect_mirrored_activations(model_a, input_ids, word_positions)
            else:
                raw_acts = collect_activations(model_a, input_ids, word_positions, model_type_a)

            print(f"  Computing activation spectra ({len(raw_acts)} layers)...")
            act_spectra_a = {}
            for name, act in raw_acts.items():
                spec = activation_spectrum(act)
                if spec is not None:
                    act_spectra_a[name] = spec

    # ── Model B (optional comparison) ──
    weight_results_b = None
    label_b = None
    if args.checkpoint_b:
        print(f"\nLoading comparison: {args.checkpoint_b}")
        model_b, config_b, model_type_b = load_prisma_model(args.checkpoint_b, device)
        label_b = Path(args.checkpoint_b).parent.name
        weight_results_b = analyze_weight_spectra(model_b, label_b)
        del model_b
    elif args.hf_model:
        print(f"\nLoading HF model: {args.hf_model}")
        model_b = load_hf_model(args.hf_model, device)
        label_b = args.hf_model
        weight_results_b = analyze_weight_spectra(model_b, label_b)
        del model_b

    if device.startswith("cuda"):
        torch.cuda.empty_cache()

    # ── Plots ──
    print("\nGenerating plots...")
    plot_weight_spectra(weight_results_a, output_dir, label_a)
    plot_effective_rank_progression(weight_results_a, output_dir, label_a)
    plot_gate_spectra(weight_results_a, output_dir, label_a)

    if act_spectra_a:
        plot_activation_spectra(act_spectra_a, output_dir, label_a)
        plot_mirror_comparison(act_spectra_a, output_dir, label_a)
        plot_embedding_alignment(weight_results_a, act_spectra_a, output_dir, label_a)

    if weight_results_b and label_b:
        plot_comparison(weight_results_a, weight_results_b, label_a, label_b, output_dir)
        # Also print summary for B
        print_summary(weight_results_b, label_b)

    # ── Summary ──
    print_summary(weight_results_a, label_a, act_spectra_a)

    # ── Save ──
    save_results_json(weight_results_a, act_spectra_a, output_dir / "results.json")
    if weight_results_b:
        save_results_json(weight_results_b, None, output_dir / "results_b.json")

    print(f"\nAll outputs saved to: {output_dir}")
    print(f"  Plots: {len(list(output_dir.glob('*.png')))} PNG files")
    print(f"  Data:  results.json")


if __name__ == "__main__":
    main()