Implement segmentation utilities: compute_threshold, regime_shading_intervals, extract_transition_events

Agent-Logs-Url: https://github.com/dfeen87/Cell-DNA-Dynamics/sessions/baae8a33-0554-4a39-863e-b24589f4ecda

Co-authored-by: dfeen87 <158860247+dfeen87@users.noreply.github.com>

Author: Copilot

src/stage5_regime_transitions/segmentation_utils.py

@@ -1 +1,352 @@
+"""
+Segmentation utilities – Stage 5 Regime-Transition Detection
+=============================================================
 
+Provides three helper utilities that support the manuscript's validation
+pipeline:
+
+1. :func:`compute_threshold` – empirically derive the critical threshold Φ_c
+   from an instability-magnitude series ΔΦ(t) (manuscript Section 5).
+
+2. :func:`regime_shading_intervals` – convert per-time-point regime labels into
+   contiguous (start, end, regime) intervals suitable for axis shading
+   (e.g. ``matplotlib.axes.Axes.axvspan``).
+
+3. :func:`extract_transition_events` – extract the ordered sequence of regime
+   transitions from the label array, annotated with the time index at which
+   each transition occurs.
+
+None of the functions assign biological meaning to the detected segments; they
+operate purely on the numerical ΔΦ(t) series and the discrete label array
+produced by :func:`~src.stage5_regime_transitions.detect_regimes.detect_regimes`.
+
+References
+----------
+Manuscript Section 5 (Regime Transition Structure):
+
+    "The threshold Φ_c is not assumed to be universal and must be determined
+     empirically for each system under study, for example through baseline
+     characterisation, surrogate analysis, or controlled perturbation
+     experiments."
+
+Manuscript Section 8.3 (Synthetic Validation Protocol):
+
+    "Baseline statistics (μ_X, σ_X) are computed over the stable regime
+     (t < 60 s)."
+"""
+
+from __future__ import annotations
+
+from typing import List, NamedTuple
+
+import numpy as np
+
+
+# ---------------------------------------------------------------------------
+# 1. Threshold computation
+# ---------------------------------------------------------------------------
+
+def compute_threshold(
+    delta_phi: np.ndarray,
+    method: str = "quantile",
+    *,
+    q: float = 0.90,
+    baseline_mask: np.ndarray | None = None,
+    n_sigma: float = 2.0,
+) -> float:
+    """Compute an empirical threshold Φ_c from the instability magnitude ΔΦ(t).
+
+    The threshold is *not* assumed to be universal (manuscript Section 5).
+    Two estimation strategies are supported:
+
+    ``"quantile"``
+        Φ_c = quantile(ΔΦ, q).  The quantile is computed over the full
+        supplied series unless a *baseline_mask* is provided, in which case
+        only the masked samples are used.  This matches the quantile-based
+        empirical characterisation described in Sections 5 and 6 of the
+        manuscript.
+
+    ``"baseline"``
+        Φ_c = μ_baseline + n_sigma · σ_baseline, where μ and σ are the mean
+        and standard deviation of ΔΦ(t) restricted to the stable baseline
+        window identified by *baseline_mask*.  This mirrors the baseline
+        normalisation defined in manuscript Eq. (27):
+
+            X_n(t) = ( X(t) − μ_X ) / σ_X,   X ∈ {E, I, C}
+
+        and the protocol in Section 8.3 which computes baseline statistics
+        "over the stable regime (t < 60 s)".
+
+    Parameters
+    ----------
+    delta_phi : array_like, shape (T,)
+        Instability magnitude ΔΦ(t) ≥ 0 as produced by
+        :func:`~src.stage5_regime_transitions.compute_delta_phi.compute_delta_phi`.
+    method : {"quantile", "baseline"}, default "quantile"
+        Threshold estimation strategy (see above).
+    q : float, default 0.90
+        Quantile level for the ``"quantile"`` method.  Must be in (0, 1].
+    baseline_mask : array_like of bool, shape (T,), optional
+        Boolean mask identifying the stable baseline samples.
+        - For ``"quantile"``: when provided, the quantile is computed only
+          over the masked (``True``) samples.
+        - For ``"baseline"``: required; raises ``ValueError`` if omitted.
+    n_sigma : float, default 2.0
+        Number of standard deviations above the baseline mean for the
+        ``"baseline"`` method.  Must be non-negative.
+
+    Returns
+    -------
+    threshold : float
+        Empirical threshold Φ_c ≥ 0.
+
+    Raises
+    ------
+    ValueError
+        If *delta_phi* is not 1-D, *method* is unrecognised, quantile
+        parameters are out of range, or the ``"baseline"`` method is called
+        without a valid *baseline_mask*.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from src.stage5_regime_transitions.segmentation_utils import compute_threshold
+    >>> rng = np.random.default_rng(0)
+    >>> delta_phi = np.abs(rng.normal(1.0, 0.5, 300))
+    >>> thr = compute_threshold(delta_phi, method="quantile", q=0.90)
+    >>> float(thr) >= 0
+    True
+    >>> mask = np.zeros(300, dtype=bool)
+    >>> mask[:60] = True  # first 60 samples are the stable baseline
+    >>> thr_b = compute_threshold(delta_phi, method="baseline", baseline_mask=mask, n_sigma=2.0)
+    >>> float(thr_b) >= 0
+    True
+    """
+    delta_phi = np.asarray(delta_phi, dtype=float)
+    if delta_phi.ndim != 1:
+        raise ValueError(
+            f"delta_phi must be a 1-D array; got shape {delta_phi.shape}."
+        )
+
+    if method == "quantile":
+        if not (0.0 < q <= 1.0):
+            raise ValueError(
+                f"q must be in (0, 1]; got q={q}."
+            )
+        samples = delta_phi
+        if baseline_mask is not None:
+            mask = np.asarray(baseline_mask, dtype=bool)
+            if mask.shape != delta_phi.shape:
+                raise ValueError(
+                    "baseline_mask must have the same shape as delta_phi; "
+                    f"got {mask.shape} vs {delta_phi.shape}."
+                )
+            samples = delta_phi[mask]
+            if samples.size == 0:
+                raise ValueError(
+                    "baseline_mask selects no samples; cannot compute quantile."
+                )
+        return float(np.quantile(samples, q))
+
+    elif method == "baseline":
+        if baseline_mask is None:
+            raise ValueError(
+                "baseline_mask is required for method='baseline'."
+            )
+        if n_sigma < 0.0:
+            raise ValueError(
+                f"n_sigma must be non-negative; got n_sigma={n_sigma}."
+            )
+        mask = np.asarray(baseline_mask, dtype=bool)
+        if mask.shape != delta_phi.shape:
+            raise ValueError(
+                "baseline_mask must have the same shape as delta_phi; "
+                f"got {mask.shape} vs {delta_phi.shape}."
+            )
+        baseline_samples = delta_phi[mask]
+        if baseline_samples.size == 0:
+            raise ValueError(
+                "baseline_mask selects no samples; cannot compute baseline statistics."
+            )
+        mu = float(np.mean(baseline_samples))
+        sigma = float(np.std(baseline_samples, ddof=0))
+        return mu + n_sigma * sigma
+
+    else:
+        raise ValueError(
+            f"Unknown method '{method}'. Supported methods: 'quantile', 'baseline'."
+        )
+
+
+# ---------------------------------------------------------------------------
+# 2. Regime shading intervals
+# ---------------------------------------------------------------------------
+
+class ShadingInterval(NamedTuple):
+    """A contiguous block of time steps assigned to the same regime.
+
+    Attributes
+    ----------
+    regime : str
+        Regime label (one of ``"stable"``, ``"pre-instability"``,
+        ``"instability"``, ``"recovery"``).
+    start : int
+        Index of the first time step in the interval (inclusive).
+    stop : int
+        Index one past the last time step in the interval (exclusive),
+        matching Python slice semantics.  The interval covers indices
+        ``[start, stop)``.
+    """
+
+    regime: str
+    start: int
+    stop: int
+
+
+def regime_shading_intervals(labels: np.ndarray) -> List[ShadingInterval]:
+    """Convert a per-time-point regime label array into contiguous intervals.
+
+    Groups consecutive identical labels into :class:`ShadingInterval` records
+    that can be passed directly to ``matplotlib.axes.Axes.axvspan`` (or any
+    interval-based shading routine) for visualization of regime boundaries in
+    the validation pipeline.
+
+    Parameters
+    ----------
+    labels : array_like, shape (T,), dtype str or object
+        Per-time-point regime strings as produced by
+        :func:`~src.stage5_regime_transitions.detect_regimes.detect_regimes`.
+        Each element must be one of ``"stable"``, ``"pre-instability"``,
+        ``"instability"``, or ``"recovery"``.
+
+    Returns
+    -------
+    intervals : list of :class:`ShadingInterval`
+        Ordered list of non-overlapping contiguous regime intervals that
+        together cover the full index range ``[0, T)``.  The list is ordered
+        by increasing *start* index.
+
+    Raises
+    ------
+    ValueError
+        If *labels* is not a 1-D array or is empty.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from src.stage5_regime_transitions.segmentation_utils import regime_shading_intervals
+    >>> labels = np.array(
+    ...     ["stable"] * 4 + ["pre-instability"] * 3 + ["instability"] * 2
+    ... )
+    >>> intervals = regime_shading_intervals(labels)
+    >>> [(iv.regime, iv.start, iv.stop) for iv in intervals]
+    [('stable', 0, 4), ('pre-instability', 4, 7), ('instability', 7, 9)]
+    """
+    labels = np.asarray(labels, dtype=object)
+    if labels.ndim != 1:
+        raise ValueError(
+            f"labels must be a 1-D array; got shape {labels.shape}."
+        )
+    if labels.size == 0:
+        raise ValueError("labels array must not be empty.")
+
+    intervals: List[ShadingInterval] = []
+    current_regime = labels[0]
+    block_start = 0
+
+    for i in range(1, len(labels)):
+        if labels[i] != current_regime:
+            intervals.append(ShadingInterval(str(current_regime), block_start, i))
+            current_regime = labels[i]
+            block_start = i
+
+    # Close the final block.
+    intervals.append(ShadingInterval(str(current_regime), block_start, len(labels)))
+
+    return intervals
+
+
+# ---------------------------------------------------------------------------
+# 3. Transition event extraction
+# ---------------------------------------------------------------------------
+
+class TransitionEvent(NamedTuple):
+    """A single regime-transition event.
+
+    Attributes
+    ----------
+    from_regime : str
+        Regime label at time step ``index - 1``.
+    to_regime : str
+        Regime label at time step ``index`` (the first step of the new regime).
+    index : int
+        Time-step index at which the transition occurs, i.e. the first index
+        that belongs to the new regime.
+    """
+
+    from_regime: str
+    to_regime: str
+    index: int
+
+
+def extract_transition_events(labels: np.ndarray) -> List[TransitionEvent]:
+    """Extract regime-transition events from a per-time-point label array.
+
+    A transition event is recorded whenever adjacent time steps carry
+    different regime labels.  The returned list contains one
+    :class:`TransitionEvent` per detected boundary, ordered by increasing
+    *index*.
+
+    This function supports the manuscript's validation pipeline (Section 5
+    and 8.3) by providing a discrete, ordered representation of when the
+    instability magnitude ΔΦ(t) crosses regime boundaries—enabling
+    quantitative evaluation of detection lead times, false-positive rates,
+    and regime-ordering statistics (manuscript Table 3).
+
+    Parameters
+    ----------
+    labels : array_like, shape (T,), dtype str or object
+        Per-time-point regime strings as produced by
+        :func:`~src.stage5_regime_transitions.detect_regimes.detect_regimes`.
+
+    Returns
+    -------
+    events : list of :class:`TransitionEvent`
+        Ordered list of transition events.  Empty if *labels* contains only
+        a single regime throughout.
+
+    Raises
+    ------
+    ValueError
+        If *labels* is not a 1-D array or is empty.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from src.stage5_regime_transitions.segmentation_utils import extract_transition_events
+    >>> labels = np.array(
+    ...     ["stable"] * 4 + ["pre-instability"] * 3 + ["instability"] * 2
+    ... )
+    >>> events = extract_transition_events(labels)
+    >>> [(e.from_regime, e.to_regime, e.index) for e in events]
+    [('stable', 'pre-instability', 4), ('pre-instability', 'instability', 7)]
+    """
+    labels = np.asarray(labels, dtype=object)
+    if labels.ndim != 1:
+        raise ValueError(
+            f"labels must be a 1-D array; got shape {labels.shape}."
+        )
+    if labels.size == 0:
+        raise ValueError("labels array must not be empty.")
+
+    events: List[TransitionEvent] = []
+    for i in range(1, len(labels)):
+        if labels[i] != labels[i - 1]:
+            events.append(
+                TransitionEvent(
+                    from_regime=str(labels[i - 1]),
+                    to_regime=str(labels[i]),
+                    index=i,
+                )
+            )
+    return events