iomgaa
150eb5f6ae
- ceus 迁入 polygons、dark_region、reference_region、tic_fitting、tic、anchor_frames、 perfusion_metrics、trajectory、tic_curves、tic_plot、overlay，旧测试照搬（改 import 与配置读取）。 - 对外两段接口：prepare_segmentation（第 1–2 步）与 quantify_case（第 4–9 步）。 - 第 3 条：删掉 D1 取医生标注时刻的模式，D1 只从拟合曲线算。 - 第 4 条：F1/F2 取视频第 20−X、60−X 秒（X 为视频第 0 秒时已推注的秒数），落在视频外记未定位。 - 绿框融合权重、紫圈颜色阈值照搬；关键帧容差窗口的出处写进 ceus.yaml 注释。 - segment：同一进程调用 MedSAM2，设置写进 ceus.yaml 的 segment 段，全部必填；gpu 测试真跑通过。 - 依赖加 scipy、matplotlib、medsam2（可编辑安装，不编译 CUDA 扩展）；uv 只解析 linux x86_64。 - 导入契约：只有 segment 引用 torch、sam2；segment 不引用其他 cadx 模块。 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
155 lines
5.5 KiB
TOML
155 lines
5.5 KiB
TOML
[project]
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name = "cadx"
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version = "0.0.0"
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description = "胰腺囊性肿瘤多模态会诊诊断的研究代码"
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requires-python = ">=3.12"
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dependencies = [
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"matplotlib>=3.11.2",
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"medsam2",
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"numpy>=2.5.4",
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"opencv-python-headless>=5.0.0.93",
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"openpyxl>=3.1.5",
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"pillow>=12.3.0",
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"pydantic>=2.14.1",
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"pyyaml>=6.0.3",
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"scipy>=1.18.1",
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]
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[dependency-groups]
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dev = [
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"ruff>=0.6",
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"pyright>=1.1.380",
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"pytest>=8.3",
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"import-linter>=2.1",
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"pre-commit>=4.0",
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"types-pyyaml>=6.0.12.20260906",
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"types-openpyxl>=3.1.5.20260827",
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]
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[tool.uv]
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# 只在本机和远程服务器（都是 Linux x86_64）上跑；只为这一种平台解析依赖，
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# 免得 torch 的各平台 CUDA 轮子都要下载一遍。
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environments = ["sys_platform == 'linux' and platform_machine == 'x86_64'"]
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[tool.uv.sources]
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medsam2 = { path = "reference/MedSAM2", editable = true }
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[build-system]
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requires = ["hatchling>=1.26"]
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build-backend = "hatchling.build"
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[tool.hatch.build.targets.wheel]
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packages = ["src/cadx"]
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[tool.ruff]
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line-length = 100
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target-version = "py312"
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src = ["src", "tests", "scripts"]
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extend-exclude = ["research-wiki", "reference", "reference-pdf", "runs", "data"]
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[tool.ruff.lint]
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select = ["E", "W", "F", "I", "UP", "B", "BLE", "S", "SIM", "RUF"]
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# 允许注释和文档字符串里的中文全角标点。
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ignore = ["RUF001", "RUF002", "RUF003"]
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[tool.ruff.lint.per-file-ignores]
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"tests/**" = ["S101"]
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[tool.pyright]
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include = ["src", "tests", "scripts"]
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pythonVersion = "3.12"
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typeCheckingMode = "strict"
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venvPath = "."
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venv = ".venv"
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# medsam2 以 setuptools 的导入钩子方式可编辑安装，pyright 跟不过去，直接指给它源码目录。
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extraPaths = ["tests", "reference/MedSAM2"]
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[tool.pytest.ini_options]
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testpaths = ["tests"]
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# 测试辅助（假交付包生成器）放在 tests/ 下，按普通模块导入。
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pythonpath = ["tests"]
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addopts = "--strict-markers --import-mode=importlib"
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markers = [
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"live: 真实模型调用，花钱，需要 .env 里的密钥",
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"gpu: 需要 CUDA 显卡（MedSAM2 分割）",
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]
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# 导入边界。改契约先改 research-wiki/explanation/结构.md，再改这里；
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# 不靠 ignore_imports 让违规通过。规划中的契约见结构.md 第五部分，模块落地时随任务书加入。
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[tool.importlinter]
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root_packages = ["cadx"]
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include_external_packages = true
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[[tool.importlinter.contracts]]
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# design 0001：torch 与 MedSAM2 只许出现在分割模块。import-linter 不能写「除 segment 外的 cadx」
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# （只有 ignore_imports 能开例外），所以逐个列出其余模块；新模块落地时加进 source_modules。
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name = "cadx 里只有 segment 引用 torch、sam2"
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type = "forbidden"
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source_modules = [
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"cadx.delivery", "cadx.library", "cadx.answers", "cadx.runs", "cadx.build", "cadx.ceus",
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]
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forbidden_modules = ["torch", "sam2"]
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[[tool.importlinter.contracts]]
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# 结构.md 第三部分依赖表：segment 不引用其他 cadx 模块（它不认识分屏和绿框）。
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name = "segment 不引用其他 cadx 模块"
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type = "forbidden"
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source_modules = ["cadx.segment"]
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forbidden_modules = [
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"cadx.delivery", "cadx.library", "cadx.answers", "cadx.runs", "cadx.build",
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"cadx.ceus", "cadx.llm", "cadx.ledger", "cadx.consult", "cadx.evaluate", "cadx.verdicts",
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]
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[[tool.importlinter.contracts]]
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# 结构.md 第三部分依赖表：外部层与格式层的模块不依赖其他 cadx 模块。
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name = "delivery、library、answers、runs 互不依赖"
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type = "independence"
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modules = ["cadx.delivery", "cadx.library", "cadx.answers", "cadx.runs"]
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[[tool.importlinter.contracts]]
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# 同上，依赖表的另一半：它们也不引用上层和其余规划中的模块（独立契约只管它们之间）。
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name = "delivery、library、answers、runs 不引用其他 cadx 模块"
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type = "forbidden"
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source_modules = ["cadx.delivery", "cadx.library", "cadx.answers", "cadx.runs"]
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forbidden_modules = [
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"cadx.build", "cadx.ceus", "cadx.segment", "cadx.llm", "cadx.ledger",
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"cadx.consult", "cadx.evaluate", "cadx.verdicts",
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]
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[[tool.importlinter.contracts]]
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# 结构.md 第三部分依赖表：ceus 是纯计算，不引用其他 cadx 模块（含 segment，分割结果由脚本传进来）。
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name = "ceus 不引用其他 cadx 模块"
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type = "forbidden"
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source_modules = ["cadx.ceus"]
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forbidden_modules = [
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"cadx.delivery", "cadx.library", "cadx.answers", "cadx.runs", "cadx.build",
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"cadx.segment", "cadx.llm", "cadx.ledger", "cadx.consult", "cadx.evaluate", "cadx.verdicts",
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]
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[[tool.importlinter.contracts]]
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# 结构.md 第三部分依赖表：build 只依赖 delivery、library、answers、runs（ceus 落地时加入）。
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name = "build 只引用 delivery、library、answers、runs"
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type = "forbidden"
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source_modules = ["cadx.build"]
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forbidden_modules = [
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"cadx.ceus", "cadx.segment", "cadx.llm", "cadx.ledger",
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"cadx.consult", "cadx.evaluate", "cadx.verdicts",
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]
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allow_indirect_imports = true
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[[tool.importlinter.contracts]]
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# 结构.md 第五部分：交付包的 Excel 只有 delivery 碰。
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name = "只有 delivery 引用 openpyxl"
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type = "forbidden"
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source_modules = ["cadx.library", "cadx.answers", "cadx.runs", "cadx.build"]
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forbidden_modules = ["openpyxl"]
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allow_indirect_imports = true
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[[tool.importlinter.contracts]]
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# 结构.md 第五部分：写资料库的图片（去掉元数据）只有 library 碰。
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name = "只有 library 引用 PIL"
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type = "forbidden"
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source_modules = ["cadx.delivery", "cadx.answers", "cadx.runs", "cadx.build"]
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forbidden_modules = ["PIL"]
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allow_indirect_imports = true
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