iomgaa
c582fe426f
- build.yaml 加必填字段 ceus_run（CEUS 运行目录或 null）。 - 不为 null 时按视频号找结果；在 failed.csv 里或缺结果目录的整例跳过，记 C15；关键帧图沿用 C14 检查。 - 资料库超声一路加 keyframes/<槽位>.png（去附加数据重编码）和 tic.json（白名单逐字段构造： 四条曲线的拟合成败与 R²、灌注指标、紫圈曲线是否可用、7 个槽位的定位与视频时间或原因）。 - manifest 的 CEUS 来源写运行号；泄露扫描已覆盖 tic.json，补命中测试。 - 真实构建等配准改完、全量 CEUS 运行之后再做。 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
321 lines
14 KiB
Python
321 lines
14 KiB
Python
"""`scripts/ceus_quant.py`：逐例循环、failed.csv、输出布局、分割缓存。
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假交付包两例：第 1 例是能过质量门的合成分屏造影视频（造影在右半，绿框是病灶的空心描边），第 2 例
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同样的画面但没有绿框。分割换成计数的假函数（monkeypatch 脚本里引用的 `segment_video`），交出病灶
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方块挪到左半局部坐标的掩码，不调显卡。
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手算的预期（视频 400×200、10 fps、40 秒，推注时间 X = 5 秒，同 test_ceus_pipeline）：
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- 第 2 例两半都没有绿框 → 第 2 步失败，进 failed.csv，没有输出目录，也不调分割；
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- 第 1 例 F1 在视频第 20 − 5 = 15 秒，有关键帧图；F2 在第 55 秒，超出视频，未定位，没有图。
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"""
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import csv
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import importlib.util
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import json
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from collections.abc import Callable, Mapping, Sequence
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from datetime import datetime
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from pathlib import Path
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from types import ModuleType
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from typing import Any
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import cv2
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import numpy as np
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import numpy.typing as npt
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import pytest
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import yaml
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from cadx.answers import read_aliases
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from cadx.build import run_build
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from cadx.ceus import ANCHOR_SLOTS, LognormalParameters, evaluate_lognormal
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from cadx.library import list_aliases, read_ultrasound
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from conftest import CEUS_YAML
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from fake_delivery import REPO_ROOT, make_delivery, write_config
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_SCRIPT = Path(__file__).resolve().parents[1] / "scripts" / "ceus_quant.py"
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_WIDTH, _HEIGHT, _SPLIT = 400, 200, 200
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_FPS, _FRAMES = 10.0, 400
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_LESION = (250, 60, 369, 159) # 整帧坐标 x1, y1, x2, y2（含端点）
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_CYST = (290, 95, 320, 125)
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_BOLUS = LognormalParameters(area=1300.0, mu=2.4, sigma=0.45, arrival_offset_s=4.0, baseline=40.0)
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def _load_script() -> ModuleType:
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spec = importlib.util.spec_from_file_location("ceus_quant", _SCRIPT)
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assert spec is not None and spec.loader is not None
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module = importlib.util.module_from_spec(spec)
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spec.loader.exec_module(module)
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return module
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def _write_video(path: Path, green_box: bool) -> None:
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rng = np.random.default_rng(3)
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intensity = evaluate_lognormal(np.arange(_FRAMES) / _FPS, _BOLUS)
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writer = cv2.VideoWriter(str(path), cv2.VideoWriter.fourcc(*"mp4v"), _FPS, (_WIDTH, _HEIGHT))
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x1, y1, x2, y2 = _LESION
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for index in range(_FRAMES):
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frame = np.zeros((_HEIGHT, _WIDTH, 3), dtype=np.uint8)
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frame[:, :_SPLIT] = 120
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frame[:, _SPLIT + 1 :] = 30
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lesion = np.clip(
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intensity[index] + rng.normal(0.0, 6.0, (y2 - y1 + 1, x2 - x1 + 1)), 0, 255
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)
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frame[y1 : y2 + 1, x1 : x2 + 1] = lesion.astype(np.uint8)[:, :, None]
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cx1, cy1, cx2, cy2 = _CYST
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frame[cy1 : cy2 + 1, cx1 : cx2 + 1] = 10
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if green_box:
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cv2.rectangle(frame, (x1, y1), (x2, y2), (0, 255, 0), thickness=3)
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writer.write(frame)
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writer.release()
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def _config_dict(tmp_path: Path, delivery_dir: Path) -> dict[str, Any]:
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document: dict[str, Any] = yaml.safe_load(CEUS_YAML.read_text(encoding="utf-8"))
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document["paths"] = {
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"delivery_dir": str(delivery_dir),
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"runs_root": str(tmp_path / "runs"),
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"work_root": str(tmp_path / "work"),
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}
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checkpoint = tmp_path / "fake_checkpoint.pt"
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checkpoint.write_bytes(b"fake weights")
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document["segment"].update(
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{"medsam2_dir": str(tmp_path / "MedSAM2"), "checkpoint": str(checkpoint), "device": "cpu"}
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)
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return document
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def _write_config(tmp_path: Path, document: dict[str, Any], name: str) -> Path:
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path = tmp_path / name
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path.write_text(yaml.safe_dump(document, allow_unicode=True), encoding="utf-8")
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return path
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class _CountingSegment:
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"""假分割：每帧都是病灶方块挪到左半局部坐标后的位置（略往里收 3 像素）。"""
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def __init__(self) -> None:
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self.calls = 0
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def __call__(
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self,
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frames: Sequence[npt.NDArray[np.uint8]],
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prompt_masks: Mapping[int, npt.NDArray[np.bool_]],
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cfg: object,
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) -> npt.NDArray[np.bool_]:
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self.calls += 1
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height, width = frames[0].shape[:2]
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masks = np.zeros((len(frames), height, width), dtype=bool)
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x1, y1, x2, y2 = _LESION
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masks[:, y1 + 3 : y2 - 2, x1 - _SPLIT + 3 : x2 - _SPLIT - 2] = True
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return masks
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@pytest.fixture
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def setup(
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tmp_path: Path, monkeypatch: pytest.MonkeyPatch
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) -> tuple[ModuleType, _CountingSegment, dict[str, Any], Callable[[str], None]]:
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"""写假交付包（两例真视频），载入脚本并换掉分割、MedSAM2 提交号和运行号。"""
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delivery_dir = make_delivery(2).write(tmp_path / "delivery")
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_write_video(delivery_dir / "CEUS_agent" / "001" / "U001_roi2.mp4", green_box=True)
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_write_video(delivery_dir / "CEUS_agent" / "002" / "U002_roi2.mp4", green_box=False)
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module = _load_script()
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segment = _CountingSegment()
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monkeypatch.setattr(module, "segment_video", segment)
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run_ids: list[str] = []
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def fake_commit(medsam2_dir: Path) -> str:
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return "c" * 40
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def fake_run_id(now: object, git: object) -> str:
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return run_ids[-1]
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monkeypatch.setattr(module, "medsam2_commit", fake_commit)
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monkeypatch.setattr(module, "make_build_id", fake_run_id)
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return module, segment, _config_dict(tmp_path, delivery_dir), run_ids.append
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def test_run_writes_outputs_and_failed_case(
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tmp_path: Path,
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setup: tuple[ModuleType, _CountingSegment, dict[str, Any], Callable[[str], None]],
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capsys: pytest.CaptureFixture[str],
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) -> None:
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module, segment, document, next_run_id = setup
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next_run_id("run-a")
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module.main(["--config", str(_write_config(tmp_path, document, "ceus.yaml"))])
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run_dir = tmp_path / "runs" / "run-a"
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assert sorted(p.name for p in (tmp_path / "runs").iterdir()) == ["run-a"]
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with (run_dir / "failed.csv").open(encoding="utf-8", newline="") as handle:
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rows = list(csv.reader(handle))
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assert rows[0] == ["video_id", "step", "reason"]
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assert [row[:2] for row in rows[1:]] == [["U002", "2"]]
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assert "都没有" in rows[1][2]
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assert not (run_dir / "U002").exists()
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assert segment.calls == 1
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case_dir = run_dir / "U001"
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for name in ("trajectory.npz", "tic_curves.npz", "summary.json", "tic.png", "overlay.mp4"):
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assert (case_dir / name).stat().st_size > 0, name
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summary = json.loads((case_dir / "summary.json").read_text(encoding="utf-8"))
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assert summary["video_id"] == "U001"
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assert summary["injection_offset_s"] == 5.0
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assert list(summary["anchor_frames"]) == list(ANCHOR_SLOTS)
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assert summary["perfusion_metrics"]["roi_perf"] is not None
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assert "pan_detected_fraction" in summary
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assert summary["anchor_frames"]["F2"]["status"] == "not_covered"
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located = {s for s, a in summary["anchor_frames"].items() if a["frame_index"] is not None}
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assert "F1" in located and "F2" not in located
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keyframes = {p.stem for p in (case_dir / "keyframes").iterdir()}
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assert keyframes == located
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image = cv2.imread(str(case_dir / "keyframes" / "F1.png"))
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assert image is not None and image.shape == (_HEIGHT, _WIDTH, 3) # 整幅原始画面
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snapshot = run_dir / "snapshot"
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assert (snapshot / "ceus.yaml").read_bytes() == (tmp_path / "ceus.yaml").read_bytes()
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segment_record = json.loads((snapshot / "segment.json").read_text(encoding="utf-8"))
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assert segment_record["medsam2_commit"] == "c" * 40
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assert segment_record["cuda_peak_memory_bytes"] is None # device 是 cpu
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assert (snapshot / "snapshot.json").is_file()
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out = capsys.readouterr().out
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assert "成功：1" in out and "第 2 步 1" in out
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assert "U001" not in out and "U002" not in out
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def test_build_reads_real_run_layout(
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tmp_path: Path,
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setup: tuple[ModuleType, _CountingSegment, dict[str, Any], Callable[[str], None]],
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) -> None:
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"""build 读这个脚本真实写出的运行目录：第 1 例带 tic.json 和关键帧进库，第 2 例记 C15。"""
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module, _, document, next_run_id = setup
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next_run_id("run-a")
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module.main(["--config", str(_write_config(tmp_path, document, "ceus.yaml"))])
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run_dir = tmp_path / "runs" / "run-a"
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delivery_dir = Path(document["paths"]["delivery_dir"])
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build_dir = tmp_path / "build"
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build_dir.mkdir()
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result = run_build(
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write_config(build_dir, delivery_dir, 1, None, run_dir),
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REPO_ROOT,
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datetime(2026, 10, 16, 12, 0, 0).astimezone(),
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)
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assert [r.case_no for r in read_aliases(result.answers_dir)] == ["001"]
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assert result.skipped_by_check == {"C15": 1}
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(alias,) = list_aliases(result.library_dir)
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route = read_ultrasound(result.library_dir, alias)
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summary = json.loads((run_dir / "U001" / "summary.json").read_text(encoding="utf-8"))
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located = {s for s, a in summary["anchor_frames"].items() if a["status"] == "ok"}
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assert set(route.keyframes) == located
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assert route.tic is not None
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assert set(route.tic) == {"fits", "perfusion_metrics", "pan_curve_usable", "keyframes"}
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assert route.tic["keyframes"]["F1"]["video_time_s"] == pytest.approx(15.0, abs=0.1)
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assert route.tic["keyframes"]["F2"]["located"] is False
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def test_unreadable_video_fails_at_step_1_and_next_case_runs(
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tmp_path: Path,
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monkeypatch: pytest.MonkeyPatch,
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setup: tuple[ModuleType, _CountingSegment, dict[str, Any], Callable[[str], None]],
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) -> None:
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module, segment, document, next_run_id = setup
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# 第 1 例换成损坏的视频（cv2 打不开），第 2 例换成正常视频。
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videos = Path(document["paths"]["delivery_dir"]) / "CEUS_agent"
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(videos / "001" / "U001_roi2.mp4").write_bytes(b"not a real video")
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_write_video(videos / "002" / "U002_roi2.mp4", green_box=True)
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next_run_id("run-a")
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module.main(["--config", str(_write_config(tmp_path, document, "ceus.yaml"))])
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run_dir = tmp_path / "runs" / "run-a"
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with (run_dir / "failed.csv").open(encoding="utf-8", newline="") as handle:
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rows = list(csv.reader(handle))
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assert [row[:2] for row in rows[1:]] == [["U001", "1"]]
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assert "打不开" in rows[1][2]
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assert not (run_dir / "U001").exists()
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assert (run_dir / "U002" / "summary.json").is_file()
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assert segment.calls == 1
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def test_segment_cache_reused_and_keyed_on_step_1_3_params(
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tmp_path: Path,
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setup: tuple[ModuleType, _CountingSegment, dict[str, Any], Callable[[str], None]],
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) -> None:
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module, segment, document, next_run_id = setup
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config = _write_config(tmp_path, document, "ceus.yaml")
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next_run_id("run-a")
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module.main(["--config", str(config)])
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assert segment.calls == 1
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cache = tmp_path / "work" / "segment_cache"
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assert [p.name.endswith(".partial") for p in cache.iterdir()] == [False]
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next_run_id("run-b")
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module.main(["--config", str(config)])
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assert segment.calls == 1 # 同样的输入，读缓存
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# 同一进程里第二次跑（cv2 的随机数已被第一次推进过）结果也逐位相同：quantify_case 每例重设种子。
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first = json.loads((tmp_path / "runs/run-a/U001/summary.json").read_text(encoding="utf-8"))
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second = json.loads((tmp_path / "runs/run-b/U001/summary.json").read_text(encoding="utf-8"))
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assert first == second
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# 改设备不改结果，不重算；改第 1 步的参数，键变了，重新分割。
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document["segment"]["device"] = "cuda:0"
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document["segment"]["offload_state_to_cpu"] = True
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next_run_id("run-c")
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module.main(["--config", str(_write_config(tmp_path, document, "device.yaml"))])
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assert segment.calls == 1
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document["ceus"]["views"]["split_sample_frames"] = 20
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next_run_id("run-d")
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module.main(["--config", str(_write_config(tmp_path, document, "views.yaml"))])
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assert segment.calls == 2
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assert len(list(cache.iterdir())) == 2
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def test_existing_run_directory_is_not_overwritten(
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tmp_path: Path,
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setup: tuple[ModuleType, _CountingSegment, dict[str, Any], Callable[[str], None]],
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) -> None:
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module, _, document, next_run_id = setup
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config = _write_config(tmp_path, document, "ceus.yaml")
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next_run_id("run-a")
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module.main(["--config", str(config)])
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before = sorted(str(p) for p in (tmp_path / "runs").rglob("*"))
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with pytest.raises(FileExistsError, match="运行目录已存在"):
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module.main(["--config", str(config)])
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assert sorted(str(p) for p in (tmp_path / "runs").rglob("*")) == before
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def _key(module: ModuleType, document: dict[str, Any]) -> str:
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config = module.QuantConfig.model_validate(document)
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return module.segment_cache_key("v" * 64, config, "w" * 64, "c" * 40)
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@pytest.mark.parametrize(
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("section", "path", "value", "changes"),
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[
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("ceus", ("views", "split_search_band"), [0.3, 0.7], True),
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("ceus", ("prompt_source", "min_area"), 9000, True),
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("ceus", ("keyframes", "iou_threshold"), 0.9, True),
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("segment", ("sam2_config",), "configs/other.yaml", True),
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("segment", ("checkpoint",), "models/other.pt", True),
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("segment", ("device",), "cuda:1", False),
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("segment", ("offload_video_to_cpu",), True, False),
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("ceus", ("smoothing", "temporal_window"), 9, False), # 第 4 步
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("ceus", ("tic_analysis", "fitting", "minimum_r2"), 0.5, False), # 第 7 步
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],
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)
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def test_cache_key_covers_exactly_step_1_3_params(
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tmp_path: Path,
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section: str,
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path: tuple[str, ...],
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value: object,
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changes: bool,
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) -> None:
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module = _load_script()
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document = _config_dict(tmp_path, tmp_path)
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base = _key(module, document)
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node = document[section]
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for name in path[:-1]:
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node = node[name]
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node[path[-1]] = value
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assert (_key(module, document) != base) is changes
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assert _key(module, document) == _key(module, document) # 同输入同键
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other = module.QuantConfig.model_validate(document)
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assert module.segment_cache_key("x" * 64, other, "w" * 64, "c" * 40) != _key(module, document)
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