GRN/grn_ccfm/src/data/scgpt_cache.py

"""
ScGPT feature caches — Load pre-extracted scGPT features from HDF5.

ScGPTFeatureCache: per-cell encoder features (for feature_mode="encoder").
ScGPTAttnDeltaCache: per-cell attn@gene_emb features (for feature_mode="attention_delta").
    Stores raw per-cell features; computes delta (tgt - src) at lookup time.
"""

import h5py
import numpy as np
import torch


class ScGPTFeatureCache:
    """
    Loads pre-extracted per-gene scGPT features from HDF5 and provides
    batch lookup by cell name and gene indices.

    HDF5 layout:
        /features    (N, G_full, scgpt_dim) float16
        /norm_mean   (scgpt_dim,) float32
        /norm_var    (scgpt_dim,) float32
        /cell_names  (N,) string
    """

    def __init__(self, h5_path: str, target_std: float = 1.0):
        self.h5_path = h5_path
        self.target_std = target_std

        self.h5 = h5py.File(h5_path, "r")
        self.features = self.h5["features"]  # lazy dataset, shape (N, G, D)
        self.norm_mean = torch.from_numpy(self.h5["norm_mean"][:]).float()  # (D,)
        self.norm_var = torch.from_numpy(self.h5["norm_var"][:]).float()    # (D,)

        # Build cell_name -> row index mapping
        cell_names = self.h5["cell_names"].asstr()[:]
        self.name_to_idx = {name: i for i, name in enumerate(cell_names)}

    def lookup(self, cell_names, gene_indices, device=None) -> torch.Tensor:
        """
        Retrieve pre-extracted features for a batch.

        Args:
            cell_names: list of str, cell identifiers from batch
            gene_indices: (G_sub,) tensor, gene subset indices
            device: target torch device

        Returns:
            (B, G_sub, D) tensor, normalized features
        """
        # Map cell names to HDF5 row indices
        row_indices = np.array([self.name_to_idx[n] for n in cell_names])

        # h5py fancy indexing requires sorted, unique indices
        unique_indices, inverse = np.unique(row_indices, return_inverse=True)
        raw = self.features[unique_indices.tolist()]  # (U, G_full, D) as numpy

        # Map back to original batch order (handles duplicates)
        raw = raw[inverse]

        # Select gene subset
        gene_idx_np = gene_indices.cpu().numpy()
        raw = raw[:, gene_idx_np, :]      # (B, G_sub, D)

        z = torch.from_numpy(raw.astype(np.float32))

        # Normalize: (x - mean) / sqrt(var) * target_std
        eps = 1e-6
        z = (z - self.norm_mean) / (self.norm_var.sqrt() + eps)
        z = z * self.target_std

        if device is not None:
            z = z.to(device)

        return z

    def close(self):
        self.h5.close()

    def __del__(self):
        try:
            self.h5.close()
        except Exception:
            pass


class ScGPTAttnDeltaCache:
    """
    Attention-delta cache: stores per-cell attn@gene_emb features.
    At lookup time, computes delta = tgt_raw - src_raw, selects gene subset, normalizes.

    HDF5 layout (same as ScGPTFeatureCache):
        /features    (N, G_full, scgpt_dim) float16 — raw features per cell
        /norm_mean   (scgpt_dim,) float32 — mean of delta features
        /norm_var    (scgpt_dim,) float32 — var of delta features
        /cell_names  (N,) string
    """

    def __init__(self, h5_path: str, target_std: float = 1.0):
        self.h5_path = h5_path
        self.target_std = target_std

        self.h5 = h5py.File(h5_path, "r")
        self.features = self.h5["features"]  # lazy dataset, shape (N, G_full, D)
        self.norm_mean = torch.from_numpy(self.h5["norm_mean"][:]).float()  # (D,)
        self.norm_var = torch.from_numpy(self.h5["norm_var"][:]).float()    # (D,)

        # Build cell_name -> row index mapping
        cell_names = self.h5["cell_names"].asstr()[:]
        self.name_to_idx = {name: i for i, name in enumerate(cell_names)}

    def _lookup_raw(self, cell_names) -> np.ndarray:
        """Retrieve raw features for a batch of cells. Returns (B, G_full, D) numpy fp16."""
        row_indices = np.array([self.name_to_idx[n] for n in cell_names])

        # h5py fancy indexing requires sorted, unique indices
        unique_indices, inverse = np.unique(row_indices, return_inverse=True)
        raw = self.features[unique_indices.tolist()]  # (U, G_full, D)
        raw = raw[inverse]  # (B, G_full, D)
        return raw

    def lookup_delta(self, src_cell_names, tgt_cell_names, gene_indices, device=None):
        """
        Compute normalized attention delta for (src, tgt) cell pairs.

        Args:
            src_cell_names: list of str, control cell identifiers
            tgt_cell_names: list of str, perturbation cell identifiers
            gene_indices: (G_sub,) tensor, gene subset indices
            device: target torch device

        Returns:
            (B, G_sub, D) tensor, normalized delta features
        """
        src_raw = self._lookup_raw(src_cell_names)  # (B, G_full, D) fp16
        tgt_raw = self._lookup_raw(tgt_cell_names)  # (B, G_full, D) fp16

        # Delta in float32
        delta = tgt_raw.astype(np.float32) - src_raw.astype(np.float32)

        # Select gene subset
        gene_idx_np = gene_indices.cpu().numpy()
        delta = delta[:, gene_idx_np, :]  # (B, G_sub, D)

        z = torch.from_numpy(delta)

        # Normalize: (x - mean) / sqrt(var) * target_std
        eps = 1e-6
        z = (z - self.norm_mean) / (self.norm_var.sqrt() + eps)
        z = z * self.target_std

        if device is not None:
            z = z.to(device)

        return z

    def close(self):
        self.h5.close()

    def __del__(self):
        try:
            self.h5.close()
        except Exception:
            pass