spatial-memory-mcp 1.6.1__py3-none-any.whl

spatial_memory/core/spatial_ops.py

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+"""Core spatial algorithms for memory navigation and exploration."""
+
+from __future__ import annotations
+
+import logging
+from collections.abc import Sequence
+from dataclasses import dataclass, field
+from typing import TypeVar
+
+import numpy as np
+from numpy.typing import NDArray
+
+logger = logging.getLogger(__name__)
+
+T = TypeVar("T")
+Vector = NDArray[np.float32]
+
+
+# =============================================================================
+# Vector Operations
+# =============================================================================
+
+
+def normalize(v: Vector) -> Vector:
+    """
+    Normalize a vector to unit length.
+
+    Args:
+        v: Input vector to normalize.
+
+    Returns:
+        Unit vector in same direction as v, or zero vector if input norm is negligible.
+    """
+    norm = np.linalg.norm(v)
+    if norm < 1e-10:
+        return np.zeros_like(v)
+    return v / norm
+
+
+def normalize_batch(vectors: Vector, copy: bool = True) -> Vector:
+    """
+    Normalize multiple vectors efficiently.
+
+    Args:
+        vectors: 2D array of shape (n_vectors, n_dimensions).
+        copy: If True, creates a copy before modifying. If False, modifies in place.
+
+    Returns:
+        Array of unit vectors with same shape as input.
+    """
+    if copy:
+        vectors = vectors.copy()
+    norms = np.linalg.norm(vectors, axis=1, keepdims=True)
+    norms = np.maximum(norms, 1e-10)
+    vectors /= norms
+    return vectors
+
+
+# =============================================================================
+# SLERP (Spherical Linear Interpolation)
+# =============================================================================
+
+
+def slerp(v0: Vector, v1: Vector, t: float) -> Vector:
+    """
+    Spherical linear interpolation between two unit vectors.
+
+    SLERP produces a constant-speed path along the great circle connecting two
+    points on the unit sphere. This is more geometrically correct than linear
+    interpolation for normalized embedding vectors.
+
+    Handles edge cases:
+    - Parallel vectors (omega ~ 0): Falls back to linear interpolation
+    - Antipodal vectors (omega ~ pi): Chooses arbitrary perpendicular path
+
+    Args:
+        v0: Starting unit vector.
+        v1: Ending unit vector.
+        t: Interpolation parameter in [0, 1].
+
+    Returns:
+        Interpolated unit vector at parameter t.
+
+    Example:
+        >>> v0 = np.array([1.0, 0.0, 0.0], dtype=np.float32)
+        >>> v1 = np.array([0.0, 1.0, 0.0], dtype=np.float32)
+        >>> mid = slerp(v0, v1, 0.5)
+        >>> np.linalg.norm(mid)  # Always unit length
+        1.0
+    """
+    # Work in float64 for numerical stability
+    v0 = normalize(v0.astype(np.float64))
+    v1 = normalize(v1.astype(np.float64))
+
+    # Compute dot product, clamp to [-1, 1] for numerical stability
+    dot = np.clip(np.dot(v0, v1), -1.0, 1.0)
+
+    # Handle nearly parallel vectors (dot ~ 1.0)
+    # Linear interpolation is a good approximation when angle is very small
+    if dot > 0.9995:
+        result = v0 + t * (v1 - v0)
+        return normalize(result.astype(np.float32))
+
+    # Handle nearly antipodal vectors (dot ~ -1.0)
+    # Choose an arbitrary perpendicular path
+    if dot < -0.9995:
+        perp = _find_perpendicular(v0)
+        half_angle = np.pi * t
+        result = v0 * np.cos(half_angle) + perp * np.sin(half_angle)
+        return result.astype(np.float32)
+
+    # Standard SLERP formula
+    omega = np.arccos(dot)
+    sin_omega = np.sin(omega)
+    s0 = np.sin((1.0 - t) * omega) / sin_omega
+    s1 = np.sin(t * omega) / sin_omega
+
+    return (s0 * v0 + s1 * v1).astype(np.float32)
+
+
+def _find_perpendicular(v: Vector) -> Vector:
+    """
+    Find a unit vector perpendicular to v.
+
+    Uses the approach of creating a vector from the standard basis that differs
+    most from v, then applying Gram-Schmidt orthogonalization.
+
+    Args:
+        v: Input unit vector.
+
+    Returns:
+        A unit vector orthogonal to v.
+    """
+    # Find the component with smallest absolute value
+    min_idx = np.argmin(np.abs(v))
+
+    # Create a basis vector that differs most from v
+    basis = np.zeros_like(v)
+    basis[min_idx] = 1.0
+
+    # Gram-Schmidt: subtract projection of basis onto v
+    perp = basis - np.dot(v, basis) * v
+    return normalize(perp)
+
+
+def slerp_path(
+    v0: Vector,
+    v1: Vector,
+    steps: int,
+    include_endpoints: bool = True,
+) -> list[Vector]:
+    """
+    Generate N interpolation steps between two vectors using SLERP.
+
+    Creates a path of evenly-spaced points along the great circle connecting
+    two embedding vectors. Useful for exploring the semantic space between
+    two memories.
+
+    Args:
+        v0: Starting vector.
+        v1: Ending vector.
+        steps: Number of vectors to generate.
+        include_endpoints: If True, path starts at v0 and ends at v1.
+            If False, generates intermediate points only.
+
+    Returns:
+        List of interpolated unit vectors.
+
+    Raises:
+        ValueError: If steps < 1.
+
+    Example:
+        >>> v0 = np.array([1.0, 0.0, 0.0], dtype=np.float32)
+        >>> v1 = np.array([0.0, 1.0, 0.0], dtype=np.float32)
+        >>> path = slerp_path(v0, v1, steps=5)
+        >>> len(path)
+        5
+    """
+    if steps < 1:
+        raise ValueError("steps must be at least 1")
+
+    vectors: list[Vector] = []
+
+    if include_endpoints:
+        for i in range(steps):
+            t = i / (steps - 1) if steps > 1 else 0.0
+            vectors.append(slerp(v0, v1, t))
+    else:
+        for i in range(steps):
+            t = (i + 1) / (steps + 1)
+            vectors.append(slerp(v0, v1, t))
+
+    return vectors
+
+
+# =============================================================================
+# Temperature-based Selection (for Wander)
+# =============================================================================
+
+
+def softmax_with_temperature(
+    scores: NDArray[np.float64],
+    temperature: float = 1.0,
+) -> NDArray[np.float64]:
+    """
+    Compute softmax probabilities with temperature scaling.
+
+    Temperature controls the randomness of the resulting distribution:
+    - T -> 0: Deterministic (all probability mass on highest score)
+    - T = 1: Standard softmax
+    - T -> inf: Uniform random selection
+
+    Uses numerically stable computation by shifting scores before exponentiation.
+
+    Args:
+        scores: Array of raw scores (higher = better).
+        temperature: Temperature parameter (must be >= 0).
+
+    Returns:
+        Probability distribution over scores (sums to 1).
+
+    Raises:
+        ValueError: If temperature is negative.
+
+    Example:
+        >>> scores = np.array([0.9, 0.7, 0.3])
+        >>> probs = softmax_with_temperature(scores, temperature=1.0)
+        >>> np.sum(probs)  # Always sums to 1
+        1.0
+    """
+    if temperature < 0:
+        raise ValueError("Temperature must be non-negative")
+
+    scores = np.asarray(scores, dtype=np.float64)
+
+    if len(scores) == 0:
+        return np.array([], dtype=np.float64)
+
+    if len(scores) == 1:
+        return np.array([1.0], dtype=np.float64)
+
+    # Handle temperature = 0 (greedy/deterministic selection)
+    if temperature < 1e-10:
+        result = np.zeros_like(scores)
+        result[np.argmax(scores)] = 1.0
+        return result
+
+    # Scale scores by temperature
+    scaled = scores / temperature
+
+    # Subtract max for numerical stability (prevents overflow in exp)
+    scaled_shifted = scaled - np.max(scaled)
+    exp_scores = np.exp(scaled_shifted)
+
+    return exp_scores / np.sum(exp_scores)
+
+
+def temperature_select(
+    items: Sequence[T],
+    scores: NDArray[np.float64],
+    temperature: float = 1.0,
+    rng: np.random.Generator | None = None,
+) -> T:
+    """
+    Select an item using temperature-scaled softmax probabilities.
+
+    Combines softmax_with_temperature with random selection. Lower temperatures
+    favor higher-scored items, while higher temperatures approach uniform random.
+
+    Args:
+        items: Sequence of items to choose from.
+        scores: Score for each item (higher = more likely to be selected).
+        temperature: Controls randomness (0.1=focused, 2.0=random).
+        rng: Optional numpy random generator for reproducibility.
+
+    Returns:
+        Selected item from the sequence.
+
+    Raises:
+        ValueError: If items and scores have different lengths.
+
+    Example:
+        >>> items = ["a", "b", "c"]
+        >>> scores = np.array([0.9, 0.7, 0.3])
+        >>> # Low temperature: almost always picks "a"
+        >>> temperature_select(items, scores, temperature=0.1)
+        'a'
+    """
+    if len(items) != len(scores):
+        raise ValueError("items and scores must have same length")
+
+    if rng is None:
+        rng = np.random.default_rng()
+
+    probabilities = softmax_with_temperature(scores, temperature)
+    idx = rng.choice(len(items), p=probabilities)
+    return items[idx]
+
+
+# =============================================================================
+# HDBSCAN Clustering (for Regions)
+# =============================================================================
+
+
+@dataclass
+class ClusterInfo:
+    """
+    Information about a discovered cluster.
+
+    Represents a semantic region in the memory space discovered by HDBSCAN
+    clustering. Contains metadata about the cluster including its size,
+    central tendency, and sample members.
+
+    Attributes:
+        cluster_id: Unique identifier for this cluster (-1 indicates noise).
+        size: Number of memories in this cluster.
+        centroid: Mean vector of all memories in the cluster (normalized).
+        centroid_memory_id: ID of the memory closest to the centroid.
+        sample_memory_ids: IDs of representative sample memories.
+        coherence: Average pairwise similarity within the cluster (0-1).
+        keywords: Extracted topic keywords for this cluster.
+    """
+
+    cluster_id: int
+    size: int
+    centroid: Vector
+    centroid_memory_id: str
+    sample_memory_ids: list[str]
+    coherence: float
+    keywords: list[str] = field(default_factory=list)
+
+
+def configure_hdbscan(
+    n_samples: int,
+    min_cluster_size: int | None = None,
+    min_samples: int | None = None,
+) -> dict:
+    """
+    Configure HDBSCAN parameters based on dataset characteristics.
+
+    Provides sensible defaults for HDBSCAN clustering on embedding vectors.
+    The min_cluster_size is computed adaptively based on dataset size if not
+    provided explicitly.
+
+    Args:
+        n_samples: Number of samples in the dataset.
+        min_cluster_size: Minimum number of points to form a cluster.
+            If None, computed as sqrt(n_samples)/2, clamped to [3, 50].
+        min_samples: Minimum samples in neighborhood for core point.
+            If None, set to min_cluster_size // 2.
+
+    Returns:
+        Dictionary of HDBSCAN parameters ready to use with hdbscan.HDBSCAN().
+
+    Example:
+        >>> params = configure_hdbscan(1000)
+        >>> params["min_cluster_size"]
+        15
+        >>> import hdbscan  # doctest: +SKIP
+        >>> clusterer = hdbscan.HDBSCAN(**params)  # doctest: +SKIP
+    """
+    if min_cluster_size is None:
+        # Adaptive min_cluster_size based on dataset size
+        min_cluster_size = max(3, int(np.sqrt(n_samples) / 2))
+        min_cluster_size = min(min_cluster_size, 50)
+
+    if min_samples is None:
+        min_samples = max(2, min_cluster_size // 2)
+
+    return {
+        "min_cluster_size": min_cluster_size,
+        "min_samples": min_samples,
+        "metric": "euclidean",  # Use with normalized vectors for cosine distance
+        "cluster_selection_method": "eom",  # Excess of Mass for varied cluster sizes
+        "core_dist_n_jobs": -1,  # Use all available cores
+    }
+
+
+# =============================================================================
+# UMAP Projection (for Visualize)
+# =============================================================================
+
+
+def configure_umap(
+    n_samples: int,
+    n_components: int = 2,
+    n_neighbors: int = 15,
+    min_dist: float = 0.1,
+    random_state: int = 42,
+) -> dict:
+    """
+    Configure UMAP parameters for memory visualization.
+
+    Provides sensible defaults for projecting high-dimensional embedding
+    vectors to 2D or 3D for visualization. Parameters are adjusted based
+    on the number of samples.
+
+    Args:
+        n_samples: Number of samples to project.
+        n_components: Target dimensionality (2 for 2D, 3 for 3D visualization).
+        n_neighbors: Size of local neighborhood for manifold approximation.
+            Larger values capture more global structure.
+        min_dist: Minimum distance between points in embedded space.
+            Smaller values create tighter clusters.
+        random_state: Random seed for reproducibility.
+
+    Returns:
+        Dictionary of UMAP parameters ready to use with umap.UMAP().
+
+    Example:
+        >>> params = configure_umap(500, n_components=2)
+        >>> params["n_neighbors"]
+        15
+        >>> import umap  # doctest: +SKIP
+        >>> reducer = umap.UMAP(**params)  # doctest: +SKIP
+    """
+    return {
+        "n_components": n_components,
+        # n_neighbors cannot exceed n_samples - 1
+        "n_neighbors": min(n_neighbors, n_samples - 1),
+        "min_dist": min_dist,
+        "metric": "cosine",  # Natural metric for embeddings
+        "random_state": random_state,
+        # Enable low memory mode for large datasets
+        "low_memory": n_samples > 5000,
+    }