"""ELYRION III: declared four-state photochemical selection model.

All examples are mathematical simulations, not measured photoresist parameters.
States are A=eligible, B=marked, X=rejected within a pass, C=committed.
Arrays of occupancies have shape (4, n_points); columns conserve one material unit.
"""
from __future__ import annotations

from math import e, pi
import numpy as np
from scipy.optimize import brentq
from scipy.sparse import bmat, diags, lil_matrix
from scipy.sparse.linalg import expm_multiply

A, B, X, C = range(4)


def transition(source: int, target: int, action: float) -> np.ndarray:
    """Exact finite-action first-order source -> target stochastic matrix."""
    if source not in range(4) or target not in range(4) or source == target:
        raise ValueError("Two different state indices in 0..3 are required.")
    if not np.isfinite(action) or action < 0:
        raise ValueError("Action must be finite and nonnegative.")
    out = np.eye(4)
    stay = np.exp(-action)
    out[source, source] = stay
    out[target, source] = -np.expm1(-action)
    return out


def ideal_filter() -> np.ndarray:
    """Ideal limit A->X, B->A, X->X, C->C; finite-time exactness is NOT assumed."""
    out = np.zeros((4, 4))
    out[X, A] = out[A, B] = out[X, X] = out[C, C] = 1.0
    return out


def finite_filter(h_reject: float, h_reset: float) -> np.ndarray:
    """Reject unmarked A first, then reset protected B. Order is essential."""
    return transition(B, A, h_reset) @ transition(A, X, h_reject)


def ideal_commit(probability: float) -> np.ndarray:
    """Commit a fraction of A; reinitialize uncommitted X/B; preserve C."""
    if not np.isfinite(probability) or not 0 <= probability <= 1:
        raise ValueError("Commit probability must lie in [0,1].")
    out = np.zeros((4, 4))
    out[A, A], out[C, A] = 1.0 - probability, probability
    out[A, B] = out[A, X] = out[C, C] = 1.0
    return out


def mark(state: np.ndarray, action: float, fringe: np.ndarray) -> np.ndarray:
    """Patterned first-order A->B exposure; other states are optically inert."""
    state = np.asarray(state, dtype=float)
    fringe = np.asarray(fringe, dtype=float)
    if state.ndim != 2 or state.shape[0] != 4 or fringe.shape != (state.shape[1],):
        raise ValueError("Expected state (4,n) and fringe (n,).")
    if action < 0 or not np.isfinite(action) or np.any(fringe < 0):
        raise ValueError("Nonnegative finite action and nonnegative fringes required.")
    out = state.copy()
    moved = -np.expm1(-action * fringe) * state[A]
    out[A] -= moved
    out[B] += moved
    return out


def run_pass(fringes: np.ndarray, actions: np.ndarray,
             committed: float = 0.0, filter_action: float | None = None) -> np.ndarray:
    """One pass, with no commit at its end. Return all four state fields."""
    fringes = np.asarray(fringes, dtype=float)
    actions = np.asarray(actions, dtype=float)
    if fringes.ndim != 2 or actions.shape != (fringes.shape[0],):
        raise ValueError("Fringes must have shape (n_gates,n_points).")
    if not 0 <= committed <= 1:
        raise ValueError("Committed fraction must lie in [0,1].")
    state = np.zeros((4, fringes.shape[1]))
    state[A], state[C] = 1.0 - committed, committed
    filt = ideal_filter() if filter_action is None else finite_filter(filter_action, filter_action)
    for g, action in zip(fringes, actions):
        state = filt @ mark(state, float(action), g)
    return state


def fringes(m: int, theta: np.ndarray, phases: np.ndarray | None = None,
            floor: float = 0.0) -> np.ndarray:
    if not isinstance(m, (int, np.integer)) or m < 1 or floor < 0:
        raise ValueError("m>=1 and a nonnegative floor are required.")
    theta = np.asarray(theta, dtype=float).reshape(-1)
    if phases is None:
        phases = 2 * pi * np.arange(m) / m
    phases = np.asarray(phases, dtype=float)
    if phases.shape != (m,):
        raise ValueError("Exactly m phases required.")
    # Numerically nonnegative version of 1-cos(theta-phase).
    return 2 * np.sin((theta[None, :] - phases[:, None]) / 2)**2 + floor


def comb_profile(m: int, action: float | np.ndarray, theta: np.ndarray,
                 phases: np.ndarray | None = None, floor: float = 0.0) -> np.ndarray:
    g = fringes(m, theta, phases, floor)
    a = np.broadcast_to(np.asarray(action, dtype=float), (m,))
    if np.any(a < 0) or not np.all(np.isfinite(a)):
        raise ValueError("Actions must be finite and nonnegative.")
    return np.prod(-np.expm1(-a[:, None] * g), axis=0)


def log_midpoint_yield(m: int, action: float) -> float:
    if m < 2 or action <= 0:
        return -np.inf
    # Pair symmetric distances to avoid loss near 2*pi at large m.
    d = 2 * np.sin(pi * (2 * np.arange(m//2) + 1) / (2*m))**2
    result = 2*np.log(-np.expm1(-action*d)).sum()
    if m % 2:
        result += np.log(-np.expm1(-2*action))
    return float(result)


def optimal_action(m: int, target: float) -> float:
    """Unique per-gate action attaining all m prescribed midpoint yields."""
    if m < 2 or not 0 < target < 1:
        raise ValueError("m>=2 and 0<target<1 are required.")
    hi = float(m*m)
    while log_midpoint_yield(m, hi) < np.log(target):
        hi *= 2
    return float(brentq(lambda u: log_midpoint_yield(m, u)-np.log(target),
                        1e-14, hi, xtol=1e-12, rtol=1e-13))


def limit_product_bounds(c: float, terms: int = 12) -> tuple[float, float]:
    """Analytic truncation bounds evaluated in floating point (not interval arithmetic).

    Actual P_inf is between P_R*exp(-tail_log_bound) and P_R.
    Floating output is descriptive; the manuscript proves the exact inequalities.
    """
    if c <= 0 or terms < 1:
        raise ValueError("c>0, terms>=1 are required.")
    aa = c * pi*pi / 2
    r = np.arange(terms)
    upper = float(np.exp(2*np.log(-np.expm1(-aa*(2*r+1)**2)).sum()))
    qr = float(np.exp(-aa*(2*terms+1)**2))
    ratio = float(np.exp(-8*aa*(terms+1)))
    tail_log = 2*qr/((1-qr)*(1-ratio))
    return upper*np.exp(-tail_log), upper


def cubic_constant(target: float) -> float:
    if not 0 < target < 1:
        raise ValueError("0<target<1 required.")
    return float(brentq(lambda c: limit_product_bounds(c, 32)[1]-target,
                        1e-5, 20.0, xtol=1e-14))


def repeated_commits(survival: np.ndarray, coefficient: float, scale: float
                     ) -> tuple[np.ndarray, int, float]:
    """Log remaining fraction from finite full commits plus one partial commit.

    Commit weights sum to coefficient/scale. Collapse repetition algebraically;
    report the actual number of passes rather than treating them as free.
    """
    if coefficient < 0 or scale <= 0:
        raise ValueError("coefficient>=0 and scale>0 required.")
    survival = np.asarray(survival, dtype=float)
    if np.any(survival < 0) or np.any(survival >= 1):
        raise ValueError("0<=survival<1 required for finite logarithms.")
    x = coefficient/scale
    whole = int(np.floor(x))
    fractional = float(x-whole)
    logs = whole*np.log1p(-survival) + np.log1p(-fractional*survival)
    return logs, whole + int(fractional > 0), fractional


def hazard_example(action: float, n: int = 24) -> dict:
    """Exact finite 3D hazard target with three positive first-harmonic products."""
    if not 0 < action < 0.5:
        raise ValueError("0<action<1/2 required.")
    x = 2*pi*np.arange(n)/n
    mesh = np.meshgrid(x, x, x, indexing='ij')
    shifts = [(0., 0., 0.), (2.0, 0.7, 4.0), (4.6, 3.4, 1.2)]
    weights = [0.15, 0.10, 0.07]
    ideal_h = np.zeros((n, n, n))
    log_remaining = np.zeros_like(ideal_h)
    passes = 0
    qmax = 0.0
    for shift, w in zip(shifts, weights):
        gs = [1 + np.cos(mesh[j]-shift[j]) for j in range(3)]
        pp = np.prod(gs, axis=0)
        qs = np.prod([-np.expm1(-action*g) for g in gs], axis=0)
        ideal_h += w*pp
        logs, count, _ = repeated_commits(qs, w, action**3)
        log_remaining += logs
        passes += count
        qmax = max(qmax, float(qs.max()))
    target = -np.expm1(-ideal_h)
    written = -np.expm1(log_remaining)
    # Jensen gives product gate >= a^m exp(-m*a) product fringe for 0<=g<=2.
    relative = (1-np.exp(-3*action)) + qmax/(2*(1-qmax))
    grid_bound = relative*float(ideal_h.max())
    # Whole-domain bounds, not maxima inferred from a finite spatial grid.
    global_qmax = float((-np.expm1(-2*action))**3)
    global_hmax = 8*sum(weights)
    global_relative = (1-np.exp(-3*action)) + global_qmax/(2*(1-global_qmax))
    bound = global_relative*global_hmax
    return dict(target=target, written=written, error=float(abs(target-written).max()),
                hazard_error=float(abs(-log_remaining-ideal_h).max()), bound=bound,
                grid_bound=grid_bound,
                passes=passes, factor_gates=3*passes,
                primitive_ideal_maps=7*passes, # 3 marks + 3 filters + 1 commit/reinitialize
                mark_action=3*action*passes, action=action)


def diffusion_comb(m: int, action: float, diffusion: float, n: int | None = None,
                   floor: float = 0.0, rate: float = 1.0) -> dict:
    """Finite-difference semigroup simulation of actual finite-duration marking.

    Continuum theta-space generator is D_theta*d²/dtheta²; rate is sigma*P.
    Filters are ideal instantaneous operations here. No splitting during marking.
    Grid-dependent dark bound uses the exact discrete first-mode eigenvalue.
    """
    if m < 2 or action <= 0 or diffusion < 0 or floor < 0 or rate <= 0:
        raise ValueError("Invalid kinetic parameters.")
    n = n or 64*m
    if n % (2*m) != 0:
        raise ValueError("Grid size must be divisible by 2*m.")
    theta = 2*pi*np.arange(n)/n
    h = 2*pi/n
    lap = lil_matrix((n, n), dtype=float)
    for i in range(n):
        lap[i, i] = -2/h**2
        lap[i, (i-1)%n] = lap[i, (i+1)%n] = 1/h**2
    dd = diffusion*lap.tocsr()
    zero = diags(np.zeros(n), format='csr')
    s = np.ones(n)
    tau = action/rate
    for j in range(m):
        r = rate*(2*np.sin((theta-2*pi*j/m)/2)**2 + floor)
        rr = diags(r, format='csr')
        generator = bmat([[dd-rr, zero], [rr, dd]], format='csr')
        # A and B diffuse with the same D. B is the retained population after filtering.
        state = expm_multiply(tau*generator, np.concatenate([s, np.zeros(n)]))
        s = state[n:]
    dark_idx = np.arange(m)*(n//m)
    bright_idx = dark_idx + n//(2*m)
    lam = 4*diffusion*np.sin(h/2)**2 / h**2
    bounds = []
    for j in range(m):
        if lam == 0:
            avg_decay = 1.0
        else:
            avg_decay = np.exp(-lam*(m-j-1)*tau)*(-np.expm1(-lam*tau))/(lam*tau)
        exponent = action*(floor + max(0.0, 1-avg_decay))
        bounds.append(-np.expm1(-exponent))
    return dict(theta=theta, survival=s, dark=s[dark_idx], bright=s[bright_idx],
                bounds=np.asarray(bounds), time=m*tau, discrete_lambda=lam,
                diffusion=diffusion, action=action, m=m, n=n)


def diffusion_bright_bound(m: int, action: float, diffusion: float,
                           total_time: float, tube: float) -> float:
    """Continuum Brownian-tube sufficient bright lower bound, in theta units."""
    if not 0 < tube < pi:
        raise ValueError("0<tube<pi required.")
    theta = pi/m
    phase = 2*pi*np.arange(m)/m
    dist = abs((theta-phase+pi) % (2*pi)-pi)
    g_lower = 2*np.sin(np.maximum(0., dist-tube/m)/2)**2
    conditional = float(np.prod(-np.expm1(-action*g_lower)))
    if diffusion*total_time == 0:
        return conditional
    probability = max(0., 1-4*np.exp(-tube*tube/(4*diffusion*total_time*m*m)))
    return probability*conditional