一些小修改

GPUMD/Umap/umap_make.py

@@ -0,0 +1,76 @@
+from pathlib import Path
+import numpy as np
+import matplotlib
+matplotlib.use("Agg")  # 仅保存图片，不弹窗
+import matplotlib.pyplot as plt
+from umap import UMAP
+
+def umap_dir_to_pngs(dir_path: str) -> None:
+    """
+    对目录内每个 .npy 文件执行 UMAP(30D->2D) 并保存散点图。
+    - 输入 .npy 期望形状为 (n_samples, 30) 或 (30, n_samples)
+    - 输出图片保存在同目录，命名为 <原文件名>_umap.png
+    """
+    p = Path(dir_path)
+    if not p.is_dir():
+        raise ValueError(f"{dir_path!r} 不是有效文件夹")
+
+    files = sorted(p.glob("*.npy"))
+    if not files:
+        print(f"目录 {p} 中未找到 .npy 文件")
+        return
+
+    for f in files:
+        try:
+            data = np.load(f)
+            if data.ndim == 2:
+                if data.shape[1] == 30:
+                    X = data
+                elif data.shape[0] == 30:
+                    X = data.T
+                else:
+                    print(f"[跳过] {f.name}: shape={data.shape}, 未检测到 30 维特征")
+                    continue
+            else:
+                print(f"[跳过] {f.name}: 期望二维数组，实际 shape={data.shape}")
+                continue
+
+            # 清理非数值行
+            mask = np.isfinite(X).all(axis=1)
+            if not np.all(mask):
+                X = X[mask]
+                print(f"[提示] {f.name}: 移除了含 NaN/Inf 的样本行")
+
+            n_samples = X.shape[0]
+            if n_samples < 3:
+                print(f"[跳过] {f.name}: 样本数过少(n={n_samples})，无法稳定降维")
+                continue
+
+            # 确保 n_neighbors 合法
+            n_neighbors = min(15, max(2, n_samples - 1))
+            reducer = UMAP(
+                n_components=2,
+                n_neighbors=n_neighbors,
+                min_dist=0.1,
+                metric="euclidean",
+                random_state=42,
+            )
+            emb = reducer.fit_transform(X)
+
+            fig, ax = plt.subplots(figsize=(6, 5), dpi=150)
+            ax.scatter(emb[:, 0], emb[:, 1], s=6, c="#1f77b4", alpha=0.8, edgecolors="none")
+            ax.set_title(f"{f.name} • UMAP (n={len(X)}, nn={n_neighbors})", fontsize=10)
+            ax.set_xlabel("UMAP-1")
+            ax.set_ylabel("UMAP-2")
+            ax.grid(True, linestyle="--", linewidth=0.3, alpha=0.5)
+            fig.tight_layout()
+
+            out_png = f.with_suffix("").as_posix() + "_umap.png"
+            fig.savefig(out_png)
+            plt.close(fig)
+            print(f"[完成] {f.name} -> {out_png}")
+        except Exception as e:
+            print(f"[错误] 处理 {f.name} 失败: {e}")
+
+if __name__=="__main__":
+    umap_dir_to_pngs("data")