From e157a17d69bdae31982372d9963f981bfb283bf6 Mon Sep 17 00:00:00 2001 From: Flash Date: Sun, 27 Jul 2025 17:57:58 +0800 Subject: [PATCH] Sync --- .gitattributes | 2 + embryo-backend/Data/CS11.glb | 3 + embryo-backend/Data/CS12.glb | 3 + embryo-backend/Data/CS13.glb | 3 + embryo-backend/Data/CS14.glb | 3 + embryo-backend/Data/CS15.glb | 3 + embryo-backend/Data/CS16.glb | 3 + embryo-backend/Data/CS17.glb | 3 + embryo-backend/Data/CS18.glb | 3 + embryo-backend/Data/CS19.glb | 3 + embryo-backend/Data/CS20.glb | 3 + embryo-backend/Data/CS21.glb | 3 + embryo-backend/Data/CS22.glb | 3 + embryo-backend/Data/CS23.glb | 3 + embryo-backend/Data/FakeEmbryo.py | 2 +- embryo-backend/Data/GetGeneName.py | 30 + .../Data/gencode.v48.annotation.gtf.gz | 3 + embryo-backend/Data/glbTrans.py | 173 + .../Data/human_protein_coding_genes.txt | 20068 ++++++++++++++++ 19 files changed, 20316 insertions(+), 1 deletion(-) create mode 100644 embryo-backend/Data/CS11.glb create mode 100644 embryo-backend/Data/CS12.glb create mode 100644 embryo-backend/Data/CS13.glb create mode 100644 embryo-backend/Data/CS14.glb create mode 100644 embryo-backend/Data/CS15.glb create mode 100644 embryo-backend/Data/CS16.glb create mode 100644 embryo-backend/Data/CS17.glb create mode 100644 embryo-backend/Data/CS18.glb create mode 100644 embryo-backend/Data/CS19.glb create mode 100644 embryo-backend/Data/CS20.glb create mode 100644 embryo-backend/Data/CS21.glb create mode 100644 embryo-backend/Data/CS22.glb create mode 100644 embryo-backend/Data/CS23.glb create mode 100644 embryo-backend/Data/GetGeneName.py create mode 100644 embryo-backend/Data/gencode.v48.annotation.gtf.gz create mode 100644 embryo-backend/Data/glbTrans.py create mode 100644 embryo-backend/Data/human_protein_coding_genes.txt diff --git a/.gitattributes b/.gitattributes index b1893d9..6534d4f 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1,3 @@ *.h5ad filter=lfs diff=lfs merge=lfs -text +*.glb filter=lfs diff=lfs merge=lfs -text +*.gz filter=lfs diff=lfs merge=lfs -text diff --git a/embryo-backend/Data/CS11.glb b/embryo-backend/Data/CS11.glb new file mode 100644 index 0000000..8258b15 --- /dev/null +++ b/embryo-backend/Data/CS11.glb @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8a81f760af79003f4f8059537850c3959cfa57cbcb6f9a0d2a8772c2652c69c8 +size 17591576 diff --git a/embryo-backend/Data/CS12.glb b/embryo-backend/Data/CS12.glb new file mode 100644 index 0000000..6feef4f --- /dev/null +++ b/embryo-backend/Data/CS12.glb @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a32afaecfd9986e096bc37d45f5f2a8ce02dfe35e4f7b44413e1bc8fbe28d89f +size 4990340 diff --git a/embryo-backend/Data/CS13.glb b/embryo-backend/Data/CS13.glb new file mode 100644 index 0000000..fff5e81 --- /dev/null +++ b/embryo-backend/Data/CS13.glb @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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sha256:cfeea0c96c60789ba9e8dfedf65aacc9dc1e7e88b514cc6ac7f56797fc65e4cf +size 18982200 diff --git a/embryo-backend/Data/CS23.glb b/embryo-backend/Data/CS23.glb new file mode 100644 index 0000000..64d0032 --- /dev/null +++ b/embryo-backend/Data/CS23.glb @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9de04d8fe8b054146bffe34fa6131cffda902dc83a2b2c4024dd583084e7d48a +size 12627176 diff --git a/embryo-backend/Data/FakeEmbryo.py b/embryo-backend/Data/FakeEmbryo.py index dbf8410..0aaa749 100644 --- a/embryo-backend/Data/FakeEmbryo.py +++ b/embryo-backend/Data/FakeEmbryo.py @@ -6,7 +6,7 @@ import os np.random.seed(42) # 参数配置 -stages = [("CS7", 500), ("CS7.5", 750), ("CS8", 1000), ("CS9", 1500)] +stages = [("CS7", 500), ("CS8", 1000), ("CS9", 1500)] genes = ["SOX2", "NANOG", "T", "POU5F1", "OTX2", "ZIC2", "FOXA2", "LEFTY1"] layers = { "Ectoderm": 1.0, # 外层 diff --git a/embryo-backend/Data/GetGeneName.py b/embryo-backend/Data/GetGeneName.py new file mode 100644 index 0000000..5e922a9 --- /dev/null +++ b/embryo-backend/Data/GetGeneName.py @@ -0,0 +1,30 @@ +import gzip +import re +import os + +# ==== 参数 ==== +gtf_file = "gencode.v48.annotation.gtf.gz" # 你的 GTF 文件 +output_file = "human_protein_coding_genes.txt" +script_dir = os.path.dirname(os.path.realpath(__file__)) +genes = set() + +# ==== 解析 GTF ==== +with gzip.open(f"{script_dir}/{gtf_file}", "rt") as f: + for line in f: + if line.startswith("#"): + continue + parts = line.split("\t") + if len(parts) > 2 and parts[2] == "gene": + # 仅保留 gene_type=protein_coding 的行 + if 'gene_type "protein_coding"' in line or 'gene_biotype "protein_coding"' in line: + m = re.search(r'gene_name "([^"]+)"', line) + if m: + genes.add(m.group(1)) + +# ==== 保存到文件 ==== +genes_sorted = sorted(genes) +with open(f"{script_dir}/{output_file}", "w") as f: + for g in genes_sorted: + f.write(g + "\n") + +print(f"✅ 已提取 {len(genes_sorted)} 个蛋白编码基因 → {output_file}") diff --git a/embryo-backend/Data/gencode.v48.annotation.gtf.gz b/embryo-backend/Data/gencode.v48.annotation.gtf.gz new file mode 100644 index 0000000..107d00c --- /dev/null +++ b/embryo-backend/Data/gencode.v48.annotation.gtf.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:37a298c2b57e41988cfe12667134106523c69c24a1807347679d19e88aa1f4a9 +size 58971717 diff --git a/embryo-backend/Data/glbTrans.py b/embryo-backend/Data/glbTrans.py new file mode 100644 index 0000000..386ef8f --- /dev/null +++ b/embryo-backend/Data/glbTrans.py @@ -0,0 +1,173 @@ +import os +import trimesh +import pandas as pd +import numpy as np +import anndata as ad +from collections import defaultdict + +# ==== 参数 ==== +script_dir = os.path.dirname(os.path.realpath(__file__)) +glb_files = [f"CS{i}.glb" for i in range(11,24,1)] +N_total = 30000 +use_surface_sampling = False +n_genes = 1000 +n_markers_per_label = 10 + +# ==== 读取真实基因名 ==== +gene_list_file = os.path.join(script_dir, "human_protein_coding_genes.txt") +assert os.path.exists(gene_list_file), f"❌ 缺少基因名文件 {gene_list_file}" +all_gene_names = pd.read_csv(gene_list_file, header=None)[0].tolist() +gene_names = all_gene_names[:n_genes] + +# ==== 真实 marker 基因 ==== +true_markers = { + "Ectoderm": ["SOX2", "PAX6", "NES", "TUBB3", "OTX2"], + "Mesoderm": ["TBXT", "MESP1", "HAND1", "GATA4", "PDGFRA"], + "Endoderm": ["SOX17", "FOXA2", "GATA6", "CXCR4", "HNF1B"], + "Notochord": ["SHH", "NOG", "CHRD", "FOXA2", "Brachyury"], + "NeuralTube": ["OLIG2", "NKX6-1", "HOXB4", "PAX3", "SNAI2"] +} + +# ==== 采样函数 ==== +def sample_mesh(mesh, label, n_samples): + if use_surface_sampling: + points, face_idx = trimesh.sample.sample_surface(mesh, n_samples) + if hasattr(mesh.visual, "vertex_colors") and len(mesh.visual.vertex_colors) == len(mesh.vertices): + face_colors = mesh.visual.vertex_colors[mesh.faces] + colors = face_colors.mean(axis=1)[face_idx, :3] + else: + mat_color = np.array([200, 200, 200]) + colors = np.tile(mat_color, (n_samples, 1)) + else: + verts = mesh.vertices + if len(verts) > n_samples: + idx = np.random.choice(len(verts), n_samples, replace=False) + verts = verts[idx] + else: + idx = np.arange(len(verts)) + if hasattr(mesh.visual, "vertex_colors") and len(mesh.visual.vertex_colors) == len(mesh.vertices): + colors = mesh.visual.vertex_colors[idx, :3] + else: + mat_color = np.array([200, 200, 200]) + colors = np.tile(mat_color, (len(verts), 1)) + points = verts + labels = np.array([label] * len(points)) + return points, colors, labels + +# ==== Step 1: 计算全局最大边长 ==== +all_bounds = [] +for glb_name in glb_files: + glb_path = os.path.join(script_dir, glb_name) + if not os.path.exists(glb_path): + continue + scene = trimesh.load(glb_path) + if isinstance(scene, trimesh.Scene): + for geom in scene.geometry.values(): + all_bounds.append(geom.bounds) # (min,max) + else: + all_bounds.append(scene.bounds) + +all_bounds = np.array(all_bounds) +global_min = np.min(all_bounds[:,0,:], axis=0) +global_max = np.max(all_bounds[:,1,:], axis=0) +global_size = np.max(global_max - global_min) +print(f"🌍 统一缩放基准: global_size={global_size}") + +# ==== Step 2: 处理单个 GLB ==== +def process_glb(glb_path, sample_name): + scene = trimesh.load(glb_path) + all_points, all_colors, all_labels = [], [], [] + + if isinstance(scene, trimesh.Scene): + total_points = sum(len(g.vertices) for g in scene.geometry.values()) + for name, geom in scene.geometry.items(): + ratio = len(geom.vertices) / total_points + n_samples = max(1, int(N_total * ratio)) + p, c, l = sample_mesh(geom, name, n_samples) + all_points.append(p) + all_colors.append(c) + all_labels.append(l) + else: + p, c, l = sample_mesh(scene, "mesh", N_total) + all_points.append(p) + all_colors.append(c) + all_labels.append(l) + + points = np.vstack(all_points) + colors = np.vstack(all_colors) + labels = np.concatenate(all_labels) + + if len(points) > N_total: + idx = np.random.choice(len(points), N_total, replace=False) + points, colors, labels = points[idx], colors[idx], labels[idx] + + # ✅ 平移到中心点 + center = points.mean(axis=0) + points_centered = points - center + + # ✅ 统一缩放（保持原始比例） + points_scaled = points_centered / global_size + + # ✅ 如需修正坐标系方向，可启用以下行（示例：交换Y和Z） + # points_scaled = points_scaled[:, [0, 2, 1]] + # points_scaled[:, 1] *= -1 + + df = pd.DataFrame(points_scaled, columns=["x","y","z"]) + df["r"], df["g"], df["b"] = colors[:,0], colors[:,1], colors[:,2] + df["label"] = labels + + csv_file = os.path.join(script_dir, f"{sample_name}_point_cloud_30000_centered_scaled.csv") + df.to_csv(csv_file, index=False) + print(f"✅ 已导出 {csv_file} (中心化 & 统一大小, 保持比例)") + return df + +# ==== Step 3: 生成 h5ad ==== +def create_h5ad(df, sample_name): + points = df[['x','y','z']].to_numpy() + cell_types = df['label'].to_numpy() + unique_labels = sorted(set(cell_types)) + + marker_genes = {} + all_marker_set = set() + for ct in unique_labels: + valid_markers = [g for g in true_markers.get(ct, []) if g in gene_names] + while len(valid_markers) < n_markers_per_label: + g = np.random.choice(gene_names) + if g not in valid_markers: + valid_markers.append(g) + marker_genes[ct] = valid_markers + all_marker_set.update(valid_markers) + + np.random.seed(42) + expr_matrix = np.random.poisson(lam=1.0, size=(len(df), len(gene_names))).astype(np.float32) + for ct in unique_labels: + cell_idx = np.where(cell_types == ct)[0] + marker_idx = [gene_names.index(g) for g in marker_genes[ct]] + expr_matrix[np.ix_(cell_idx, marker_idx)] += np.random.poisson(lam=5.0, size=(len(cell_idx), len(marker_idx))) + + obs = pd.DataFrame(index=[f"{sample_name}_cell{i}" for i in range(len(df))]) + obs["cell_type"] = cell_types + var = pd.DataFrame(index=gene_names) + var["is_marker"] = ["yes" if g in all_marker_set else "no" for g in gene_names] + + adata = ad.AnnData(X=expr_matrix, obs=obs, var=var) + adata.obsm["spatial"] = points + + output_h5ad = os.path.join(script_dir, f"{sample_name}.h5ad") + adata.write(output_h5ad) + + with open(os.path.join(script_dir, f"{sample_name}_marker_genes.txt"), "w") as f: + for ct, genes in marker_genes.items(): + f.write(f"{ct} : {', '.join(genes)}\n") + + print(f"✅ 已生成 {output_h5ad} ({len(df)} cells × {len(gene_names)} genes)") + +# ==== Step 4: 批量运行 ==== +for glb_name in glb_files: + glb_path = os.path.join(script_dir, glb_name) + if os.path.exists(glb_path): + sample_name = os.path.splitext(glb_name)[0] + df = process_glb(glb_path, sample_name) + create_h5ad(df, sample_name) + else: + print(f"⚠️ 未找到 {glb_name}，跳过") diff --git a/embryo-backend/Data/human_protein_coding_genes.txt b/embryo-backend/Data/human_protein_coding_genes.txt new file mode 100644 index 0000000..3bed174 --- /dev/null +++ b/embryo-backend/Data/human_protein_coding_genes.txt @@ -0,0 +1,20068 @@ +A1BG +A1CF +A2M +A2ML1 +A3GALT2 +A4GALT +A4GNT +AAAS +AACS +AADAC +AADACL2 +AADACL3 +AADACL4 +AADAT +AAGAB +AAK1 +AAMDC +AAMP +AANAT +AAR2 +AARD +AARS1 +AARS2 +AARSD1 +AASDH +AASDHPPT +AASS +AATF +AATK +ABAT +ABCA1 +ABCA10 +ABCA12 +ABCA13 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