一些小修改
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161
GPUMD/Umap/umap_make_2.py
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161
GPUMD/Umap/umap_make_2.py
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from pathlib import Path
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import numpy as np
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import matplotlib
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matplotlib.use("Agg")
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import matplotlib.pyplot as plt
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try:
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from umap import UMAP
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except Exception:
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from umap.umap_ import UMAP
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def umap_dir_shared_coords(
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dir_path: str,
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*,
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metric: str = "cosine",
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n_neighbors: int = 15,
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min_dist: float = 0.0,
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spread: float = 1.2,
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standardize: bool = False,
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context: bool = True,
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make_joint: bool = True,
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init: str = "random", # 关键：禁用谱初始化，避免告警；也可用 "pca"
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jitter: float = 0.0, # 可选：拟合前加微弱噪声，如 1e-6
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random_state: int = 42
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) -> None:
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"""
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在同一 UMAP 坐标系中为目录内每个 .npy 文件生成 2D 图。
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- 每个 .npy 形状为 (n_samples, 30) 或 (30, n_samples)
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- 统一坐标轴范围；各自输出 *_umap_shared.png，另可输出总览图
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"""
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p = Path(dir_path)
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if not p.is_dir():
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raise ValueError(f"{dir_path!r} 不是有效文件夹")
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files = sorted(p.glob("*.npy"))
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if not files:
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print(f"目录 {p} 中未找到 .npy 文件")
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return
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X_list, paths, counts = [], [], []
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for f in files:
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try:
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data = np.load(f)
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if data.ndim != 2:
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print(f"[跳过] {f.name}: 期望二维数组，实际 shape={data.shape}")
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continue
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if data.shape[1] == 30:
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X = data
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elif data.shape[0] == 30:
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X = data.T
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else:
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print(f"[跳过] {f.name}: shape={data.shape}, 未检测到 30 维特征")
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continue
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mask = np.isfinite(X).all(axis=1)
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if not np.all(mask):
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X = X[mask]
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print(f"[提示] {f.name}: 移除了含 NaN/Inf 的样本行")
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if X.shape[0] < 3:
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print(f"[跳过] {f.name}: 样本数过少(n={X.shape[0]})")
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continue
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X_list.append(X)
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paths.append(f)
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counts.append(X.shape[0])
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except Exception as e:
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print(f"[错误] 读取 {f.name} 失败: {e}")
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if not X_list:
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print("未找到可用的数据文件")
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return
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X_all = np.vstack(X_list)
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if standardize:
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mean = X_all.mean(axis=0)
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std = X_all.std(axis=0)
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std[std == 0] = 1.0
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X_all = (X_all - mean) / std
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if jitter and jitter > 0:
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rng = np.random.default_rng(random_state)
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X_all = X_all + rng.normal(scale=jitter, size=X_all.shape)
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reducer = UMAP(
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n_components=2,
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n_neighbors=int(max(2, n_neighbors)),
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min_dist=float(min_dist),
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spread=float(spread),
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metric=metric,
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init=init, # 关键改动：避免谱初始化告警
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random_state=random_state,
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)
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Z_all = reducer.fit_transform(X_all)
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x_min, x_max = float(Z_all[:, 0].min()), float(Z_all[:, 0].max())
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y_min, y_max = float(Z_all[:, 1].min()), float(Z_all[:, 1].max())
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pad_x = 0.05 * (x_max - x_min) if x_max > x_min else 1.0
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pad_y = 0.05 * (y_max - y_min) if y_max > y_min else 1.0
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base_colors = [
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"#1f77b4","#ff7f0e","#2ca02c","#d62728","#9467bd",
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"#8c564b","#e377c2","#7f7f7f","#bcbd22","#17becf"
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]
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start = 0
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for i, (f, n) in enumerate(zip(paths, counts)):
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Zi = Z_all[start:start + n]
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start += n
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fig, ax = plt.subplots(figsize=(6, 5), dpi=150)
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if context:
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ax.scatter(Z_all[:, 0], Z_all[:, 1], s=5, c="#cccccc",
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alpha=0.35, edgecolors="none", label="All")
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ax.scatter(Zi[:, 0], Zi[:, 1], s=10,
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c=base_colors[i % len(base_colors)],
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alpha=0.9, edgecolors="none", label=f.name)
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ax.set_title(
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f"{f.name} • UMAP(shared) (nn={n_neighbors}, min={min_dist}, metric={metric}, init={init})",
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fontsize=9
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)
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ax.set_xlabel("UMAP-1")
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ax.set_ylabel("UMAP-2")
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ax.set_xlim(x_min - pad_x, x_max + pad_x)
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ax.set_ylim(y_min - pad_y, y_max + pad_y)
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ax.grid(True, linestyle="--", linewidth=0.3, alpha=0.5)
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if context:
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ax.legend(loc="best", fontsize=8, frameon=False)
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fig.tight_layout()
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out_png = f.with_suffix("").as_posix() + "_umap_shared.png"
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fig.savefig(out_png)
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plt.close(fig)
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print(f"[完成] {f.name} -> {out_png}")
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if make_joint:
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start = 0
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fig, ax = plt.subplots(figsize=(7, 6), dpi=150)
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for i, (f, n) in enumerate(zip(paths, counts)):
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Zi = Z_all[start:start + n]; start += n
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ax.scatter(Zi[:, 0], Zi[:, 1], s=8,
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c=base_colors[i % len(base_colors)],
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alpha=0.85, edgecolors="none", label=f.name)
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ax.set_title(f"UMAP(shared) overview (metric={metric}, nn={n_neighbors}, min={min_dist}, init={init})",
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fontsize=10)
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ax.set_xlabel("UMAP-1"); ax.set_ylabel("UMAP-2")
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ax.set_xlim(x_min - pad_x, x_max + pad_x)
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ax.set_ylim(y_min - pad_y, y_max + pad_y)
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ax.grid(True, linestyle="--", linewidth=0.3, alpha=0.5)
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ax.legend(loc="best", fontsize=8, frameon=False, ncol=1)
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fig.tight_layout()
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out_png = Path(dir_path) / "umap_shared_overview.png"
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fig.savefig(out_png.as_posix())
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plt.close(fig)
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print(f"[完成] 总览 -> {out_png}")
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if __name__=="__main__":
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umap_dir_shared_coords("data")
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