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Fix medical diagnosis data setup paths #16

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Merged
ShuhaoZhangTony merged 1 commit into from
Apr 19, 2026
Merged

Fix medical diagnosis data setup paths #16

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3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -150,3 +150,6 @@ ehthumbs.db
Desktop.ini
$RECYCLE.BIN/
apps/src/sage/apps/medical_diagnosis/data/processed/*
apps/src/sage/apps/medical_diagnosis/data/test_results/*
apps/src/sage/apps/medical_diagnosis/data/medical/lumbar-spine-mri/cache/*
apps/src/sage/apps/medical_diagnosis/data/medical/lumbar-spine-mri/dataset_info.txt
10 changes: 8 additions & 2 deletions .vscode/settings.json
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@@ -1,5 +1,11 @@
{
"python-envs.defaultEnvManager": "ms-python.python:conda",
"python-envs.defaultPackageManager": "ms-python.python:conda",
"python-envs.pythonProjects": []
}
"python-envs.pythonProjects": [
{
"path": ".",
"envManager": "ms-python.python:conda",
"packageManager": "ms-python.python:conda"
}
]
}
2 changes: 1 addition & 1 deletion apps/src/sage/apps/medical_diagnosis/agents/diagnostic_agent.py
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Expand Up @@ -59,7 +59,7 @@ def _load_config(self, config_path: str | None) -> dict:
},
"services": {
"sagellm": {"enabled": True, "gpu_memory_utilization": 0.9},
"embedding": {"method": "hf", "cache_enabled": True},
"embedding": {"method": "hash", "cache_enabled": True},
"vector_db": {"collection_name": "lumbar_spine_cases", "top_k": 5},
},
}
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2 changes: 1 addition & 1 deletion apps/src/sage/apps/medical_diagnosis/config/agent_config.yaml
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Expand Up @@ -28,7 +28,7 @@ services:

# Embedding服务配置
embedding:
method: hf
method: hash
cache_enabled: true
normalize: true
batch_size: 32
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5 changes: 4 additions & 1 deletion apps/src/sage/apps/medical_diagnosis/run_diagnosis.py
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Expand Up @@ -16,6 +16,9 @@
from sage.apps.medical_diagnosis.agents import DiagnosticAgent


DEFAULT_CONFIG_PATH = Path(__file__).parent / "config" / "agent_config.yaml"


def check_and_setup_data(auto_setup: bool = False):
"""检查数据是否存在，如果不存在则自动下载和准备"""
# 获取当前脚本所在目录
Expand Down Expand Up @@ -120,7 +123,7 @@ def parse_args():
"--config",
"-c",
type=str,
default="examples/medical_diagnosis/config/agent_config.yaml",
default=str(DEFAULT_CONFIG_PATH),
help="配置文件路径",
)

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9 changes: 4 additions & 5 deletions apps/src/sage/apps/medical_diagnosis/scripts/prepare_data.py
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Expand Up @@ -15,9 +15,8 @@
# Note: This script assumes sage-apps package is installed
# Install with: cd sage-apps && pip install -e .

# 查找项目根目录
_current_file = Path(__file__).resolve()
project_root = _current_file.parent.parent.parent.parent.parent.parent # 到 sage-examples 根目录
# 当前 medical_diagnosis 应用目录
APP_DIR = Path(__file__).resolve().parent.parent


# 疾病类别映射 (模拟)
Expand Down Expand Up @@ -123,8 +122,8 @@ def generate_mock_report(label: int, patient_info: dict) -> str:
def prepare_dataset():
"""准备数据集"""

dataset_path = project_root / "data" / "medical" / "lumbar-spine-mri" / "cache"
output_dir = project_root / "examples" / "medical_diagnosis" / "data" / "processed"
dataset_path = APP_DIR / "data" / "medical" / "lumbar-spine-mri" / "cache"
output_dir = APP_DIR / "data" / "processed"
output_dir.mkdir(parents=True, exist_ok=True)

Copilot AI Apr 18, 2026

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prepare_dataset() now loads from APP_DIR/data/medical/.../cache, but there’s no explicit existence check before load_from_disk(...). When the dataset isn’t present (or was downloaded to a different working directory), this will raise a stack trace that’s not very actionable. Consider checking dataset_path.exists() and raising a FileNotFoundError with a message pointing to the expected location and the setup script to run.

Suggested change
if not dataset_path.exists() or not dataset_path.is_dir():
raise FileNotFoundError(
"未找到医疗数据集缓存目录。\n"
f"预期位置: {dataset_path}\n"
"请先运行 medical_diagnosis 应用的数据下载/初始化脚本，"
"确保数据集已下载到上述目录后，再重新执行本脚本。"
)

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print("=" * 80)
Expand Down
13 changes: 7 additions & 6 deletions apps/src/sage/apps/medical_diagnosis/setup_data.sh
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Expand Up @@ -6,6 +6,7 @@ set -e
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
PROJECT_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
DATA_DIR="$SCRIPT_DIR/data/processed"
PYTHON_BIN="${PYTHON_BIN:-python}"

Copilot AI Apr 18, 2026

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PYTHON_BIN is introduced to avoid drifting to another environment, but the early “dataset already exists” stats block still uses a hard-coded python3 -c (above). For consistency and to ensure the same interpreter is always used, switch that invocation to use $PYTHON_BIN as well.

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Copilot AI Apr 18, 2026

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setup_data.sh calls download_lumbar_dataset.py, which writes to a relative Path("data/..."), but this script never cds to $SCRIPT_DIR. If a user runs setup_data.sh from another working directory, the dataset will be downloaded to the wrong location and prepare_data.py (which reads under the app dir) won’t find it. Consider cd "$SCRIPT_DIR" early in the script (or invoke the Python scripts with an explicit working directory) to make paths robust.

Suggested change
# 确保后续 Python 脚本中的相对路径始终相对于当前应用目录解析
cd "$SCRIPT_DIR" || {
echo "❌ 无法切换到脚本目录: $SCRIPT_DIR"
exit 1
}

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echo "=========================================="
echo "医疗诊断数据集自动设置"
Expand Down Expand Up @@ -40,7 +41,7 @@ echo ""

# 1. 安装必要的依赖
echo "1️⃣ 检查Python依赖..."
pip install -q huggingface_hub datasets pillow scikit-learn || {
"$PYTHON_BIN" -m pip install -q huggingface_hub datasets pillow scikit-learn || {
echo "❌ 依赖安装失败"
exit 1
}
Expand All @@ -49,7 +50,7 @@ echo " ✓ 依赖已安装"
# 2. 下载数据集
echo ""
echo "2️⃣ 下载腰椎MRI数据集..."
python3 "$PROJECT_ROOT/scripts/download_lumbar_dataset.py" || {
"$PYTHON_BIN" "$SCRIPT_DIR/scripts/download_lumbar_dataset.py" || {
echo "❌ 数据集下载失败"
exit 1
}
Expand All @@ -58,7 +59,7 @@ echo " ✓ 数据集下载完成"
# 3. 预处理数据
echo ""
echo "3️⃣ 预处理数据集..."
python3 "$SCRIPT_DIR/scripts/prepare_data.py" || {
"$PYTHON_BIN" "$SCRIPT_DIR/scripts/prepare_data.py" || {
echo "❌ 数据预处理失败"
exit 1
}
Expand All @@ -71,7 +72,7 @@ if [ -f "$DATA_DIR/train_index.json" ] && [ -f "$DATA_DIR/test_index.json" ]; th
echo " ✓ 数据集验证成功"

# 显示统计信息
python3 -c "
"$PYTHON_BIN" -c "
import json
with open('$DATA_DIR/stats.json', 'r') as f:
stats = json.load(f)
Expand All @@ -93,6 +94,6 @@ echo ""
echo "✅ 数据集设置完成！"
echo ""
echo "可以开始使用:"
echo " python examples/medical_diagnosis/test_diagnosis.py --mode single"
echo " python examples/medical_diagnosis/run_diagnosis.py --interactive"
echo " python apps/tests/medical_diagnosis/test_diagnosis.py --mode single"
echo " python examples/run_medical_diagnosis.py --interactive"
Comment on lines +97 to +98

Copilot AI Apr 18, 2026

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The post-setup usage hint suggests running a pytest test file directly (python apps/tests/medical_diagnosis/test_diagnosis.py ...). That file calls pytest.skip(...) and relies on pytest markers, which can behave unexpectedly when executed as a standalone script. Consider updating the message to a python -m pytest ... invocation (and/or keep the example entrypoint python examples/run_medical_diagnosis.py --interactive).

Suggested change
echo " python apps/tests/medical_diagnosis/test_diagnosis.py --mode single"
echo " python examples/run_medical_diagnosis.py --interactive"
echo " $PYTHON_BIN -m pytest apps/tests/medical_diagnosis/test_diagnosis.py"
echo " $PYTHON_BIN examples/run_medical_diagnosis.py --interactive"

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echo ""
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