99 lines
3.0 KiB
Python
99 lines
3.0 KiB
Python
from flask import Flask, request, jsonify
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from flask_cors import CORS
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import anndata as ad
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import os
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app = Flask(__name__)
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CORS(app)
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# 存放所有 h5ad 文件的目录
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DATA_DIR = os.path.join(os.path.dirname(__file__), "Data")
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# 缓存已加载的 AnnData 对象，避免重复加载
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loaded_data = {}
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def load_adata(stage):
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if stage not in loaded_data:
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filepath = os.path.join(DATA_DIR, f"{stage}.h5ad")
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if not os.path.exists(filepath):
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return None
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loaded_data[stage] = ad.read_h5ad(filepath)
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return loaded_data[stage]
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@app.route("/api/genes")
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def list_genes():
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stage = request.args.get("stage")
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adata = load_adata(stage)
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if not adata:
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return jsonify({"error": f"Stage '{stage}' not found"}), 404
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return jsonify(list(adata.var_names))
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@app.route("/api/gene_expression")
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def get_gene_expression():
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gene = request.args.get("gene")
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stage = request.args.get("stage")
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adata = load_adata(stage)
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if not adata:
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return jsonify({"error": f"Stage '{stage}' not found"}), 404
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if gene not in adata.var_names:
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return jsonify({"error": f"Gene '{gene}' not found in {stage}"}), 404
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# 读取表达值
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expr = adata[:, gene].X
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expr = expr.toarray().flatten() if hasattr(expr, "toarray") else expr.flatten()
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# 读取三维坐标
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if "spatial" in adata.obsm:
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coords = adata.obsm["spatial"]
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elif all(k in adata.obs for k in ("x", "y", "z")):
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coords = adata.obs[["x", "y", "z"]].values
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else:
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return jsonify({"error": "No spatial coordinates found"}), 500
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result = [
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{"x": float(x), "y": float(y), "z": float(z), "value": float(v)}
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for (x, y, z), v in zip(coords, expr)
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]
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return jsonify({"gene": gene, "expression": result})
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@app.route("/api/cell")
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def get_cell_types():
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stage = request.args.get("stage")
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adata = load_adata(stage)
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if not adata:
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return jsonify({"error": f"Stage '{stage}' not found"}), 404
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# 查找细胞类型列，按常见的列名优先级查找
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cell_type_columns = ['cell_type', 'celltype', 'cluster', 'annotation', 'cell_types', 'clusters']
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cell_type_col = None
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for col in cell_type_columns:
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if col in adata.obs.columns:
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cell_type_col = col
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break
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if cell_type_col is None:
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return jsonify({"error": "No cell type information found"}), 404
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# 读取细胞类型
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cell_types = adata.obs[cell_type_col].values
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# 读取三维坐标
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if "spatial" in adata.obsm:
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coords = adata.obsm["spatial"]
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elif all(k in adata.obs for k in ("x", "y", "z")):
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coords = adata.obs[["x", "y", "z"]].values
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else:
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return jsonify({"error": "No spatial coordinates found"}), 500
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result = [
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{"x": float(x), "y": float(y), "z": float(z), "value": str(ct)}
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for (x, y, z), ct in zip(coords, cell_types)
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]
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return jsonify({"stage": stage, "cells": result})
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if __name__ == "__main__":
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app.run(debug=True)
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