2 Commits
v2.0.2 ... main

Author SHA1 Message Date
Nan
1350bbfb36 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refactor: Clean up AGENTS.md and remove outdated test files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
2026-08-15 17:53:20 +08:00
Nan
d216bdf138 Keep asset library cleanup on unregister (#64)
* 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
2026-07-09 12:40:25 +08:00
9 changed files with 198 additions and 31 deletions

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@@ -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 <version> -p` 发布版本化文档
- `uv run build.py <platform> 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 <platform> [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.<version>.<platform>.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 ## 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 - 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 - 使用的依赖越少越好
- 选用简单直接的方式实现 - 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 - 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`

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@@ -1,6 +1,6 @@
[project] [project]
name = "bioxelnodes" name = "bioxelnodes"
version = "2.0.2" version = "2.0.4"
description = "" description = ""
authors = [{ name = "MaNan", email = "icrdr2010@outlook.com" }] authors = [{ name = "MaNan", email = "icrdr2010@outlook.com" }]
requires-python = ">=3.11.0,<3.12.dev0" requires-python = ">=3.11.0,<3.12.dev0"
@@ -18,7 +18,7 @@ dependencies = [
[dependency-groups] [dependency-groups]
dev = [ dev = [
"bpy>=4.2.0,<5", "bpy==5.0.0",
"pytest>=8.3.2,<9", "pytest>=8.3.2,<9",
"pytest-dependency>=0.6.0,<0.7", "pytest-dependency>=0.6.0,<0.7",
"pytest-cov>=5.0.0,<6", "pytest-cov>=5.0.0,<6",

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@@ -1,10 +1,20 @@
import bpy import bpy
from pathlib import Path from pathlib import Path
from .constants import NODE_LIB_DIRPATH from .constants import LATEST_NODE_LIB_PATH, NODE_LIB_DIRPATH, NODE_LIB_FILENAME
ASSET_LIBRARY_NAME = "O Bioxel" ASSET_LIBRARY_NAME = "O Bioxel"
ASSET_LIBRARY_READY = "READY"
ASSET_LIBRARY_OUTDATED = "OUTDATED"
ASSET_LIBRARY_MISSING = "MISSING"
STATUS_MESSAGES = {
"missing": "O Bioxel asset library is not installed.",
"missing_blend": "O Bioxel node library file is missing.",
"outdated": "O Bioxel node library needs update.",
"ready": "O Bioxel asset library is ready.",
}
def _asset_library_path(): def _asset_library_path():
@@ -19,6 +29,26 @@ def _asset_libraries():
return bpy.context.preferences.filepaths.asset_libraries return bpy.context.preferences.filepaths.asset_libraries
def _find_bioxel_asset_library():
lib_path = _normalized_path(_asset_library_path())
named_lib = None
for lib in _asset_libraries():
try:
if _normalized_path(lib.path) == lib_path:
return lib
if lib.name == ASSET_LIBRARY_NAME:
named_lib = lib
except Exception:
continue
return named_lib
def _node_lib_path_for_library(lib):
return _normalized_path(lib.path) / NODE_LIB_FILENAME
def get_bioxel_asset_library(): def get_bioxel_asset_library():
lib_path = _normalized_path(_asset_library_path()) lib_path = _normalized_path(_asset_library_path())
@@ -32,16 +62,47 @@ def get_bioxel_asset_library():
return None return None
def get_bioxel_asset_library_status():
lib = _find_bioxel_asset_library()
lib_path = _normalized_path(_asset_library_path())
if lib is None:
return {"code": ASSET_LIBRARY_MISSING, "reason": "missing",
"message": STATUS_MESSAGES["missing"]}
try:
installed_lib_path = _normalized_path(lib.path)
except Exception:
return {"code": ASSET_LIBRARY_MISSING, "reason": "missing",
"message": STATUS_MESSAGES["missing"]}
if not _node_lib_path_for_library(lib).is_file():
return {"code": ASSET_LIBRARY_MISSING, "reason": "missing_blend",
"message": STATUS_MESSAGES["missing_blend"]}
if installed_lib_path != lib_path:
return {"code": ASSET_LIBRARY_OUTDATED, "reason": "outdated",
"message": STATUS_MESSAGES["outdated"]}
return {"code": ASSET_LIBRARY_READY, "reason": "ready",
"message": STATUS_MESSAGES["ready"]}
def has_bioxel_asset_library(): def has_bioxel_asset_library():
return get_bioxel_asset_library() is not None return get_bioxel_asset_library_status()["code"] in {
ASSET_LIBRARY_READY,
ASSET_LIBRARY_OUTDATED,
}
def add_bioxel_asset_library(): def add_bioxel_asset_library():
if not NODE_LIB_DIRPATH.exists(): if not NODE_LIB_DIRPATH.exists():
raise FileNotFoundError(f"Node library path does not exist: {NODE_LIB_DIRPATH}") raise FileNotFoundError(f"Node library path does not exist: {NODE_LIB_DIRPATH}")
if not LATEST_NODE_LIB_PATH.is_file():
raise FileNotFoundError(f"Node library file does not exist: {LATEST_NODE_LIB_PATH}")
prefs = _asset_libraries() prefs = _asset_libraries()
lib = get_bioxel_asset_library() lib = _find_bioxel_asset_library()
if lib is None: if lib is None:
for item in prefs: for item in prefs:

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@@ -1,7 +1,7 @@
schema_version = "1.0.0" schema_version = "1.0.0"
id = "bioxelnodes" id = "bioxelnodes"
version = "2.0.2" version = "2.0.4"
name = "Bioxel Nodes" name = "Bioxel Nodes"
tagline = "For scientific volumetric data visualization in Blender" tagline = "For scientific volumetric data visualization in Blender"
maintainer = "Nan <icrdr2010@outlook.com>" maintainer = "Nan <icrdr2010@outlook.com>"

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@@ -89,7 +89,7 @@ def start_worker_process(owner, command: str, payload: dict):
write_worker_json(config_path, config) write_worker_json(config_path, config)
write_worker_json( write_worker_json(
progress_path, progress_path,
{"factor": 0.0, "text": "Starting background Blender..."}, {"factor": 0.0, "text": "Starting..."},
) )
print(f"Starting Bioxel worker with addon module: {addon_name}") print(f"Starting Bioxel worker with addon module: {addon_name}")

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@@ -3,6 +3,7 @@ import shutil
import bpy import bpy
from ..asset_library import ASSET_LIBRARY_MISSING, get_bioxel_asset_library_status
from ..node import add_bioxel_node, get_layer_nodes, get_main_node_group from ..node import add_bioxel_node, get_layer_nodes, get_main_node_group
from ..utils import refresh_bioxel_panels from ..utils import refresh_bioxel_panels
from ..layer import get_layer_caches, set_layer_caches from ..layer import get_layer_caches, set_layer_caches
@@ -91,6 +92,11 @@ class AddLayerNode(bpy.types.Operator):
cache_id: bpy.props.StringProperty() # type: ignore # 图层ID cache_id: bpy.props.StringProperty() # type: ignore # 图层ID
def execute(self, context): def execute(self, context):
status = get_bioxel_asset_library_status()
if status["code"] == ASSET_LIBRARY_MISSING:
self.report({"ERROR"}, status["message"])
return {"CANCELLED"}
# 获取图层数据 # 获取图层数据
caches = get_layer_caches() caches = get_layer_caches()

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@@ -5,7 +5,12 @@ import bpy
from pathlib import Path from pathlib import Path
import shutil import shutil
from ..asset_library import add_bioxel_asset_library from ..asset_library import (
ASSET_LIBRARY_OUTDATED,
ASSET_LIBRARY_READY,
add_bioxel_asset_library,
get_bioxel_asset_library_status,
)
from ..constants import LATEST_NODE_LIB_PATH from ..constants import LATEST_NODE_LIB_PATH
from ..utils import ( from ..utils import (
get_all_layer_objs, get_all_layer_objs,
@@ -138,9 +143,18 @@ class AddAssetLibrary(bpy.types.Operator):
if area.type == "NODE_EDITOR": if area.type == "NODE_EDITOR":
area.tag_redraw() area.tag_redraw()
self.report({"INFO"}, "O Bioxel asset library is ready.") status = get_bioxel_asset_library_status()
if status["code"] == ASSET_LIBRARY_READY:
self.report({"INFO"}, status["message"])
return {"FINISHED"} return {"FINISHED"}
if status["code"] == ASSET_LIBRARY_OUTDATED:
self.report({"WARNING"}, status["message"])
return {"FINISHED"}
self.report({"ERROR"}, status["message"])
return {"CANCELLED"}
# 定义虚无化切换操作 # 定义虚无化切换操作
class TogglePhantom(bpy.types.Operator): class TogglePhantom(bpy.types.Operator):

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@@ -1,7 +1,12 @@
from pathlib import Path from pathlib import Path
import bpy import bpy
from .asset_library import has_bioxel_asset_library from .asset_library import (
ASSET_LIBRARY_OUTDATED,
ASSET_LIBRARY_READY,
get_bioxel_asset_library_status,
has_bioxel_asset_library,
)
from .node import get_layer_nodes, get_main_node_group from .node import get_layer_nodes, get_main_node_group
from .utils import load_icon from .utils import load_icon
from .layer import get_layer_caches from .layer import get_layer_caches
@@ -78,13 +83,23 @@ class HeaderPanel(bpy.types.Panel, BioxelPanelBase):
def draw(self, context): def draw(self, context):
layout = self.layout layout = self.layout
status = get_bioxel_asset_library_status()
if not has_bioxel_asset_library(): if status["code"] == ASSET_LIBRARY_OUTDATED:
layout.operator(
AddAssetLibrary.bl_idname,
text="Update Nodes Library",
icon="ASSET_MANAGER",
)
layout.label(text=status["message"], icon="INFO")
elif status["code"] != ASSET_LIBRARY_READY:
layout.operator( layout.operator(
AddAssetLibrary.bl_idname, AddAssetLibrary.bl_idname,
text="Add Nodes Library", text="Add Nodes Library",
icon="ASSET_MANAGER", icon="ASSET_MANAGER",
) )
layout.label(text=status["message"], icon="INFO")
return return
layout.operator( layout.operator(

36
uv.lock generated
View File

@@ -25,7 +25,7 @@ wheels = [
[[package]] [[package]]
name = "bioxelnodes" name = "bioxelnodes"
version = "2.0.2" version = "2.0.4"
source = { editable = "." } source = { editable = "." }
dependencies = [ dependencies = [
{ name = "h5py" }, { name = "h5py" },
@@ -68,7 +68,7 @@ requires-dist = [
[package.metadata.requires-dev] [package.metadata.requires-dev]
dev = [ dev = [
{ name = "autopep8", specifier = ">=2.3.1,<3" }, { name = "autopep8", specifier = ">=2.3.1,<3" },
{ name = "bpy", specifier = ">=4.2.0,<5" }, { name = "bpy", specifier = "==5.0.0" },
{ name = "mike", specifier = ">=2.1.2,<3" }, { name = "mike", specifier = ">=2.1.2,<3" },
{ name = "mkdocs", specifier = ">=1.6.0,<2" }, { name = "mkdocs", specifier = ">=1.6.0,<2" },
{ name = "mkdocs-click", specifier = ">=0.9.0" }, { name = "mkdocs-click", specifier = ">=0.9.0" },
@@ -84,7 +84,7 @@ dev = [
[[package]] [[package]]
name = "bpy" name = "bpy"
version = "4.2.0" version = "5.0.0"
source = { registry = "https://pypi.org/simple" } source = { registry = "https://pypi.org/simple" }
dependencies = [ dependencies = [
{ name = "cython" }, { name = "cython" },
@@ -93,10 +93,10 @@ dependencies = [
{ name = "zstandard" }, { name = "zstandard" },
] ]
wheels = [ wheels = [
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