From 1350bbfb3671b8dfe84f73b348bbf46bc0aabf6f Mon Sep 17 00:00:00 2001 From: Nan <7956213+icrdr@users.noreply.github.com> Date: Sat, 15 Aug 2026 17:53:20 +0800 Subject: [PATCH] 5.0 (#65) * feat: Add Bioxel asset catalog and layer management functionality - Introduced a new asset catalog definition file for Blender to manage Bioxel assets. - Implemented layer caching and snapshot functionality in `layer.py`, allowing for VDB file generation and low-resolution snapshots. - Created node management functions in `node.py` for handling Bioxel nodes within Blender's Geometry Node Editor. - Added an operator to extract mesh data from selected nodes in `structure.py`. - Developed UI panels in `panels.py` for layer management, including import options and layer library display. * Add unit tests for bioxel module and documentation - Created README.md for test instructions and categories. - Implemented comprehensive unit tests for the Data, Layer, and utility functions in the bioxel module. - Added tests for reading NRRD and DICOM formats, data properties, and edge cases. - Included tests for real data files to ensure functionality with actual datasets. * feat: Update .gitattributes and .gitignore for improved asset management and ignore patterns chore: Add app.json and omoolab.css for Obsidian integration refactor: Clean up AGENTS.md and remove outdated test files * feat: Update .gitignore to include scipy_ndimage directory * feat: Update release workflow and manifest for improved dependency management and layer handling * feat: Update .gitignore and add binary files for scipy_ndimage across multiple platforms * feat: Add OPSX commands for archiving, exploring, and proposing changes * feat: Refactor asset library management and update manifest for improved organization * feat: Downgrade h5py version to 3.14.0 in requirements and manifest * feat: Update Help operator and panel labels to use English terminology * Translate documentation to Chinese, add support format details, and enhance styling with new fonts. Update mkdocs configuration for multilingual support and improve package dependencies. * feat: Remove default version setting from extra configuration in mkdocs.yml * fix: Update documentation links to point to the correct URLs for Chinese and English versions * Add documentation for basic usage, supported formats, and performance tips - Created English and Chinese documentation for basic usage of the add-on, including data download, import, extraction, and rendering steps. - Added support format documentation listing compatible file types for the add-on. - Included links to open databases for volumetric data. - Provided performance improvement tips for voxel reconstruction and rendering, including settings for low-resolution previews and balanced rendering configurations. * Add OpenSpec skills for change management and exploration - Implement openspec-apply-change skill for applying tasks from OpenSpec changes. - Create openspec-archive-change skill for archiving completed changes. - Introduce openspec-explore skill for exploring ideas and clarifying requirements. - Add openspec-propose skill for proposing new changes with generated artifacts. - Migrate source command skills: source-command-opsx-apply, source-command-opsx-archive, source-command-opsx-explore, and source-command-opsx-propose for improved command handling. * feat: Update version to 2.0.1, refactor asset library handling, and enhance layer import process * fix: downgrade scipy version to 1.16.3 in build.py and pyproject.toml * Remove deprecated modules and functions from bioxel package - Deleted _ni_support.py, _utils.py, and dtype.py as they contained unused or redundant functions. - Removed the resize function and related utilities from _warps.py to streamline image processing. - Cleaned up the skimage module by removing unnecessary imports and functions. * feat: Add SKIP_MODULE_NAMES to exclude specific modules during import and refactor io_worker import logic * refactor: Remove known limitations section from documentation for EEVEE NEXT support * feat: Implement CLI command registration for bioxelnodes_import_worker and refactor io_worker for improved module handling * chore: Update version to 2.0.2 in project files and dependencies * feat: Enhance volumetric data parsing by adding progress updates and refactoring worker processes * feat: Enhance asset library management with status checks and error handling * feat: Update version to 2.0.3 and adjust dependencies in project files * feat: Remove unused asset library removal function * feat: Expand documentation with project overview, build instructions, and architecture details --- AGENTS.md | 73 +++++++++++++++++++++++++++ pyproject.toml | 2 +- src/bioxelnodes/__init__.py | 2 - src/bioxelnodes/blender_manifest.toml | 2 +- uv.lock | 2 +- 5 files changed, 76 insertions(+), 5 deletions(-) diff --git a/AGENTS.md b/AGENTS.md index 870aad8..d03f5ba 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -1,3 +1,63 @@ +# Bioxel Nodes + +## 项目概览 + +Bioxel Nodes 是一个基于 Blender 的科学体数据可视化插件，利用 Blender 自带的 Geometry Nodes 与 Cycles（同时支持 EEVEE NEXT）处理并渲染体数据。 + +- 支持格式：`.dcm`、`.tif`/`.tiff`、`.nii`/`.nii.gz`、`.nrrd`、`.ome.tiff`、`.mrc`、`.h5` 等，完整列表见 `src/bioxelnodes/bioxel/data.py` 的 `SUPPORT_EXTS` +- 支持 4D 体数据（多帧 / 多通道 / 时间序列） +- v2.0.x 仅支持 Blender 5.0+ +- 核心依赖：SimpleITK、pyometiff、mrcfile、h5py、numpy、scipy、transforms3d、matplotlib + +## 构建、测试与开发命令 + +- 环境：Python 3.11，依赖由 uv 管理（`uv.lock`） +- `uv sync` 安装 / 同步依赖 +- `uv run pytest` 运行测试（当前暂无测试用例） +- `uv run mkdocs serve` 本地预览文档；`uv run mkdocs build` 构建到 `site/` +- `uv run mike deploy -p` 发布版本化文档 +- `uv run build.py 3.11` 下载第三方 wheel 并更新 `src/bioxelnodes/blender_manifest.toml`，`platform` 取 `windows-x64` / `linux-x64` / `macos-arm64` / `macos-x64` +- `python pack.py [output.zip]` 将 `src/bioxelnodes` 打包为 zip +- 发布：推送 `v*` 标签触发 `.github/workflows/release.yml`，产物命名 `BioxelNodes...zip` + +## 架构 + +```text +src/bioxelnodes/ 插件包根目录 +├── __init__.py 入口：register/unregister、CLI 命令与 WindowManager 属性 +├── auto_load.py 自动发现并按拓扑排序注册 bpy 类 +├── constants.py 常量（节点库路径等） +├── preferences.py AddonPreferences（缓存目录） +├── props.py PropertyGroup / UIList / 属性更新回调 +├── menus.py 菜单与右键菜单 +├── panels.py 面板 +├── asset_library.py "O Bioxel" 资产库管理 +├── node.py 节点组加载与添加 +├── layer.py VDB 缓存、快照、图层元数据（text datablock JSON） +├── utils.py 通用工具（进度、对象查找、驱动等） +├── exceptions.py 向后兼容占位（自定义异常已改用内置异常） +├── blender_manifest.toml Blender 扩展清单 +├── assets/O_Bioxel/ 节点库 .blend 与资产目录 +├── wheels/ 随扩展分发的第三方 wheel +├── bioxel/ 核心数据模型（不依赖 Blender） +│ ├── data.py Data 类与解析（read / read_meta） +│ ├── parse.py 解析函数（parse_volumetric_data 等） +│ ├── layer.py Layer：TXYZC 顺序 ndarray + affine 变换 +│ ├── container.py Container：name + layers +│ └── io.py HDF5 读写 Container +└── operators/ Operator 实现 + ├── io.py 导入 / 导出算子，启动后台导入进程 + ├── io_worker.py 后台 CLI 导入 worker（bioxelnodes_import_worker） + ├── layer.py 图层管理算子 + ├── node.py AddNode + ├── structure.py ExtractMesh + └── misc.py 杂项算子 +``` + +数据流：导入时主进程通过 `operators/io.py` 启动一个后台 Blender 子进程（`blender --background --command bioxelnodes_import_worker`），由 `io_worker.py` 解析数据、生成 `Layer`，写为 VDB 缓存，并通过 JSON 文件（`progress.json` / `result.json` / `cancel`）回传进度与结果，避免阻塞 UI。 + +仓库根目录另有 `docs/`（mkdocs-material 文档，中英双语）、`openspec/`（spec-driven 变更流程）、`.agents/`（技能定义）。 + ## 总规范 - 说明性内容（例如提交说明、文档、注释、mermaid），以中文为主，专有名词、约定俗称可用英文 @@ -17,3 +77,16 @@ - 使用的依赖越少越好 - 选用简单直接的方式实现 - 代码、执行方式改变，调整已有的文档、计划，而非新建 + +## Shell 规范 + +- 优先使用、提供 Git Bash 执行所有 Shell 命令 +- Windows 路径在 Bash 命令中优先使用正斜杠形式 + +## Blender 开发规范 + +- 插件、资产库压缩包名用大驼峰，如果需要，用`b45`来表示适用blender版本。比如`OmooLab.v0.1.0.b45.zip` +- Operator、Menu、Panel、AddonPreferences... Class 用大驼峰命名，不加任何前缀。Operator 动宾结构，比如`RenderImage`。Menu、Panel 以它们本身为后缀，比如`RenderPanel` +- 根据项目名提炼项目缩写，作为 bl_idname 和 自定义 Property 的前缀以区分其他功能和属性，以`Omoo`为例 + - bl_idname 用下划线小写命名，Operator 的 bl_idname 以`omoo.*`为前缀，比如`omoo.render_panel`；Menu 的以`OMOO_MT_*`为前缀；Panel 的以`OMOO_PT_*`为前缀。比如`OMOO_PT_render_panel` + - 自定义 Property 用下划线小写命名，以`omoo_*`为前缀。比如`omoo_progress_factor` \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 0a90d37..e723dc2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "bioxelnodes" -version = "2.0.3" +version = "2.0.4" description = "" authors = [{ name = "MaNan", email = "icrdr2010@outlook.com" }] requires-python = ">=3.11.0,<3.12.dev0" diff --git a/src/bioxelnodes/__init__.py b/src/bioxelnodes/__init__.py index fe7a9b8..01735ff 100644 --- a/src/bioxelnodes/__init__.py +++ b/src/bioxelnodes/__init__.py @@ -2,7 +2,6 @@ import bpy import bpy.utils.previews as previews from .constants import PREVIEW_COLLECTIONS -from .asset_library import remove_bioxel_asset_library_if_exists from .props import _bioxel_layer_items, _update_layer_gallery, _update_snapshot_z from . import auto_load @@ -48,7 +47,6 @@ def register(): def unregister(): - remove_bioxel_asset_library_if_exists() unregister_cli_commands() menus.remove() auto_load.unregister() diff --git a/src/bioxelnodes/blender_manifest.toml b/src/bioxelnodes/blender_manifest.toml index 8755deb..8137d07 100644 --- a/src/bioxelnodes/blender_manifest.toml +++ b/src/bioxelnodes/blender_manifest.toml @@ -1,7 +1,7 @@ schema_version = "1.0.0" id = "bioxelnodes" -version = "2.0.3" +version = "2.0.4" name = "Bioxel Nodes" tagline = "For scientific volumetric data visualization in Blender" maintainer = "Nan " diff --git a/uv.lock b/uv.lock index 7d4e276..be61a35 100644 --- a/uv.lock +++ b/uv.lock @@ -25,7 +25,7 @@ wheels = [ [[package]] name = "bioxelnodes" -version = "2.0.3" +version = "2.0.4" source = { editable = "." } dependencies = [ { name = "h5py" },