feat: Remove unused asset library removal function

* 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refactor: Clean up AGENTS.md and remove outdated test files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

README.md

@@ -38,11 +38,6 @@ If you want to cite this work, you can cite it from Zenodo:
 
 [![DOI](https://zenodo.org/badge/786623459.svg)](https://zenodo.org/badge/latestdoi/786623459)
 
-## Known Limitations
-
--   Only one cutter supported in EEVEE render
--   Shader fail to work when convert to mesh.
--   Section surface cannot be generated when convert to mesh (will be supported soon)
 
 ## Roadmap
 

docs/index.en.md

@@ -49,15 +49,8 @@ Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any
 
 ![eevee](https://omoolab.github.io/BioxelNodes/latest/assets/eevee.gif)
 
-👍 EEVEE NEXT is absolutely AWESOME! Bioxel Nodes is fully support EEVEE NEXT now! However, there are some limitations:
+👍 EEVEE NEXT is absolutely AWESOME! Bioxel Nodes is fully support EEVEE NEXT now! 
 
-1. Only one cutter supported.
-2. EEVEE result is not that great as Cycles does.
-
-## Known Limitations
-
--   Only works with Cycles CPU , Cycles GPU (OptiX), EEVEE
--   Section surface cannot be generated when convert to mesh (will be supported soon)
 
 ## Roadmap
 

docs/index.md

@@ -49,15 +49,7 @@ Bioxel Nodes 是一款用于科学体数据可视化的 Blender 插件。它利
 
 ![eevee](https://omoolab.github.io/BioxelNodes/latest/assets/eevee.gif)
 
-EEVEE NEXT 太棒了！Bioxel Nodes 现在全面支持 EEVEE NEXT！但仍有以下限制：
+EEVEE NEXT 太棒了！Bioxel Nodes 现在全面支持 EEVEE NEXT！
-
-1. 仅支持一个切割器
-2. EEVEE 渲染效果不如 Cycles
-
-## 已知限制
-
-- 仅支持 Cycles CPU、Cycles GPU (OptiX)、EEVEE
-- 转换为网格时无法生成剖面（即将支持）
 
 ## 路线图
 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "bioxelnodes"
-version = "2.0.1"
+version = "2.0.4"
 description = ""
 authors = [{ name = "MaNan", email = "icrdr2010@outlook.com" }]
 requires-python = ">=3.11.0,<3.12.dev0"
@@ -18,7 +18,7 @@ dependencies = [
 
 [dependency-groups]
 dev = [
-    "bpy>=4.2.0,<5",
+    "bpy==5.0.0",
     "pytest>=8.3.2,<9",
     "pytest-dependency>=0.6.0,<0.7",
     "pytest-cov>=5.0.0,<6",

src/bioxelnodes/__init__.py

@@ -9,6 +9,8 @@ from . import menus
 
 auto_load.init()
 
+CLI_COMMAND_NAME = "bioxelnodes_import_worker"
+
 
 def register():
     pcoll = previews.new()
@@ -41,9 +43,11 @@ def register():
 
     auto_load.register()
     menus.add()
+    register_cli_commands()
 
 
 def unregister():
+    unregister_cli_commands()
     menus.remove()
     auto_load.unregister()
 
@@ -56,3 +60,21 @@ def unregister():
     for pcoll in PREVIEW_COLLECTIONS.values():
         previews.remove(pcoll)
     PREVIEW_COLLECTIONS.clear()
+
+
+def import_worker_cli(args):
+    from .operators import io_worker
+
+    return io_worker.main(args)
+
+
+def register_cli_commands():
+    unregister_cli_commands()
+    bpy.utils.register_cli_command(CLI_COMMAND_NAME, import_worker_cli)
+
+
+def unregister_cli_commands():
+    try:
+        bpy.utils.unregister_cli_command(CLI_COMMAND_NAME)
+    except Exception:
+        pass

src/bioxelnodes/asset_library.py

@@ -1,10 +1,20 @@
 import bpy
 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_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():
@@ -19,6 +29,26 @@ def _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():
     lib_path = _normalized_path(_asset_library_path())
 
@@ -32,16 +62,47 @@ def get_bioxel_asset_library():
     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():
-    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():
     if not NODE_LIB_DIRPATH.exists():
         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()
-    lib = get_bioxel_asset_library()
+    lib = _find_bioxel_asset_library()
 
     if lib is None:
         for item in prefs:

src/bioxelnodes/blender_manifest.toml

@@ -1,7 +1,7 @@
 schema_version = "1.0.0"
 
 id = "bioxelnodes"
-version = "2.0.1"
+version = "2.0.4"
 name = "Bioxel Nodes"
 tagline = "For scientific volumetric data visualization in Blender"
 maintainer = "Nan <icrdr2010@outlook.com>"

src/bioxelnodes/operators/io.py

@@ -13,7 +13,7 @@ import SimpleITK as sitk
 from ..props import BIOXEL_Series
 from ..utils import get_layer_obj, wrapped_label
 
-from ..bioxel.parse import DICOM_EXTS, SUPPORT_EXTS, get_ext
+from ..bioxel.parse import DICOM_EXTS, SUPPORT_EXTS, get_ext, parse_volumetric_data
 
 from ..utils import get_cache_dir, progress_update, progress_bar
 from ..layer import get_layer_caches, set_layer_caches
@@ -61,6 +61,14 @@ def remove_progress_bar_safe():
         pass
 
 
+def get_addon_module_name():
+    package_name = __package__ or "bioxelnodes.operators"
+    suffix = ".operators"
+    if package_name.endswith(suffix):
+        return package_name[: -len(suffix)]
+    return package_name
+
+
 def start_worker_process(owner, command: str, payload: dict):
     job_dir = Path(tempfile.mkdtemp(prefix="bioxel_import_", dir=str(get_cache_dir())))
     config_path = job_dir / "config.json"
@@ -69,24 +77,29 @@ def start_worker_process(owner, command: str, payload: dict):
     cancel_path = job_dir / "cancel"
     log_path = job_dir / "worker.log"
 
+    addon_name = get_addon_module_name()
     config = {
         **payload,
         "command": command,
+        "addon_name": addon_name,
         "progress_path": str(progress_path),
         "result_path": str(result_path),
         "cancel_path": str(cancel_path),
     }
     write_worker_json(config_path, config)
-    write_worker_json(progress_path, {"factor": 0.0, "text": "Starting..."})
+    write_worker_json(
+        progress_path,
+        {"factor": 0.0, "text": "Starting..."},
+    )
 
-    worker_path = Path(__file__).with_name("io_worker.py")
+    print(f"Starting Bioxel worker with addon module: {addon_name}")
     cmd = [
         bpy.app.binary_path,
         "--background",
-        "--factory-startup",
+        "--addons",
-        "--python",
+        addon_name,
-        str(worker_path),
+        "--command",
-        "--",
+        "bioxelnodes_import_worker",
         str(config_path),
     ]
 
@@ -188,7 +201,6 @@ class ImportDataBase:
         context.window_manager.fileselect_add(self)
         return {"RUNNING_MODAL"}
 
-
 class ImportData(bpy.types.Operator, ImportDataBase):
     bl_idname = "bioxel.import_data"
     bl_label = "Import Data"
@@ -291,64 +303,26 @@ class ParseVolumetricData(bpy.types.Operator):
 
     def execute(self, context):
         print("Collecting Meta Data...")
-        self.is_cancelled = False
+        progress_update(context, 0.0, "Collecting Meta Data...")
-        self.has_error = None
-        self.meta = None
-        self.label_count = 0
-        self.dtype = None
 
-        start_worker_process(
+        def progress_callback(factor, text):
-            self,
+            progress_update(context, factor, text)
-            "read_meta",
-            {
-                "filepath": self.filepath,
-                "series_id": self.series_id,
-            },
-        )
 
-        self._timer = context.window_manager.event_timer_add(
+        try:
-            time_step=0.1, window=context.window
+            series_id = self.series_id if self.series_id != "empty" else ""
-        )
+            data, meta = parse_volumetric_data(
-        bpy.types.STATUSBAR_HT_header.append(progress_bar)
+                data_file=self.filepath,
-        context.window_manager.modal_handler_add(self)
+                series_id=series_id,
-        return {"RUNNING_MODAL"}
+                progress_callback=progress_callback,
+            )
+        except Exception as e:
+            raise e
 
-    def modal(self, context, event):
+        self.meta = meta
-        if event.type == "ESC":
+        self.label_count = int(np.max(data))
-            cancel_worker_process(self, context)
+        self.dtype = data.dtype
-            return {"PASS_THROUGH"}
-
-        if event.type != "TIMER":
-            return {"PASS_THROUGH"}
-
-        bpy.context.workspace.status_text_set_internal(None)
-        update_worker_progress(self, context)
-
-        if self.process.poll() is None:
-            return {"PASS_THROUGH"}
-
-        context.window_manager.event_timer_remove(self._timer)
-        remove_progress_bar_safe()
         progress_update(context, 1.0)
 
-        result = read_worker_json(self.result_path)
-        if self.is_cancelled or (result and result.get("cancelled")):
-            self.report({"WARNING"}, "Canncelled by user.")
-            return {"CANCELLED"}
-
-        if not result:
-            self.report({"ERROR"}, f"Import worker failed. See log: {self.log_path}")
-            return {"CANCELLED"}
-
-        if not result.get("ok"):
-            print(result.get("traceback", ""))
-            self.report({"ERROR"}, result.get("error", "Import worker failed."))
-            return {"CANCELLED"}
-
-        self.meta = result["meta"]
-        self.label_count = int(result["label_count"])
-        self.dtype = np.dtype(result["dtype"])
-
         for key, value in self.meta.items():
             print(f"{key}: {value}")
 

src/bioxelnodes/operators/io_worker.py

@@ -1,24 +1,7 @@
 import json
-import sys
 import traceback
 from pathlib import Path
 
-import numpy as np
-import transforms3d
-
-if __package__:
-    from ..bioxel.layer import Layer
-    from ..bioxel.parse import parse_volumetric_data
-    from ..layer import save_layers_to_cache
-else:
-    PACKAGE_PARENT = Path(__file__).resolve().parents[2]
-    if str(PACKAGE_PARENT) not in sys.path:
-        sys.path.insert(0, str(PACKAGE_PARENT))
-
-    from bioxelnodes.bioxel.layer import Layer
-    from bioxelnodes.bioxel.parse import parse_volumetric_data
-    from bioxelnodes.layer import save_layers_to_cache
-
 
 def get_layer_shape(bioxel_size: float, orig_shape: tuple, orig_spacing: tuple):
     shape = (
@@ -72,6 +55,10 @@ def progress_callback_factory(progress_path: Path, cancel_path: Path, layer_name
 
 
 def read_meta(config, progress_path: Path, cancel_path: Path):
+    import numpy as np
+
+    from ..bioxel.parse import parse_volumetric_data
+
     progress_callback = make_progress_writer(progress_path, cancel_path)
     series_id = config["series_id"] if config["series_id"] != "empty" else ""
     data, meta = parse_volumetric_data(
@@ -94,6 +81,13 @@ def read_meta(config, progress_path: Path, cancel_path: Path):
 
 
 def build_layers(config, progress_path: Path, cancel_path: Path):
+    import numpy as np
+    import transforms3d
+
+    from ..bioxel.layer import Layer
+    from ..bioxel.parse import parse_volumetric_data
+    from ..layer import save_layers_to_cache
+
     write_json(progress_path, {"factor": 0.0, "text": "Parsing Volumetirc Data..."})
     progress_callback = make_progress_writer(progress_path, cancel_path, scale=0.2)
     data, meta = parse_volumetric_data(
@@ -229,14 +223,19 @@ def build_layers(config, progress_path: Path, cancel_path: Path):
     return {"cache_infos": cache_infos, "added_ids": [item["id"] for item in cache_infos]}
 
 
-def main():
+def main(args):
-    config_path = Path(sys.argv[-1])
+    if not args:
+        print("Usage: blender --command bioxelnodes_import_worker <config_path>")
+        return 2
+
+    config_path = Path(args[0])
     config = json.loads(config_path.read_text(encoding="utf-8"))
     progress_path = Path(config["progress_path"])
     result_path = Path(config["result_path"])
     cancel_path = Path(config["cancel_path"])
 
     try:
+        write_json(progress_path, {"factor": 0.0, "text": "Loading import modules..."})
         if config["command"] == "read_meta":
             result = read_meta(config, progress_path, cancel_path)
         elif config["command"] == "import_layers":
@@ -257,7 +256,4 @@ def main():
                 "traceback": traceback.format_exc(),
             },
         )
-
+    return 0
-
-if __name__ == "__main__":
-    main()

src/bioxelnodes/operators/layer.py

@@ -3,6 +3,7 @@ import shutil
 
 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 ..utils import refresh_bioxel_panels
 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
 
     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
         caches = get_layer_caches()
 

src/bioxelnodes/operators/misc.py

@@ -5,7 +5,12 @@ import bpy
 from pathlib import Path
 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 ..utils import (
     get_all_layer_objs,
@@ -138,8 +143,17 @@ class AddAssetLibrary(bpy.types.Operator):
                 if area.type == "NODE_EDITOR":
                     area.tag_redraw()
 
-        self.report({"INFO"}, "O Bioxel asset library is ready.")
+        status = get_bioxel_asset_library_status()
-        return {"FINISHED"}
+        if status["code"] == ASSET_LIBRARY_READY:
+            self.report({"INFO"}, status["message"])
+            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

src/bioxelnodes/panels.py

@@ -1,7 +1,12 @@
 from pathlib import Path
 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 .utils import load_icon
 from .layer import get_layer_caches
@@ -78,13 +83,23 @@ class HeaderPanel(bpy.types.Panel, BioxelPanelBase):
 
     def draw(self, context):
         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(
                 AddAssetLibrary.bl_idname,
                 text="Add Nodes Library",
                 icon="ASSET_MANAGER",
             )
+            layout.label(text=status["message"], icon="INFO")
             return
 
         layout.operator(

uv.lock

@@ -25,7 +25,7 @@ wheels = [
 
 [[package]]
 name = "bioxelnodes"
-version = "2.0.0"
+version = "2.0.4"
 source = { editable = "." }
 dependencies = [
     { name = "h5py" },
@@ -60,7 +60,7 @@ requires-dist = [
     { name = "matplotlib", specifier = "==3.10.7" },
     { name = "mrcfile", specifier = "==1.5.1" },
     { name = "pyometiff", specifier = "==1.0.0" },
-    { name = "scipy", specifier = "==1.17.1" },
+    { name = "scipy", specifier = "==1.16.3" },
     { name = "simpleitk", specifier = "==2.3.1" },
     { name = "transforms3d", specifier = "==0.4.2" },
 ]
@@ -68,7 +68,7 @@ requires-dist = [
 [package.metadata.requires-dev]
 dev = [
     { 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 = "mkdocs", specifier = ">=1.6.0,<2" },
     { name = "mkdocs-click", specifier = ">=0.9.0" },
@@ -84,7 +84,7 @@ dev = [
 
 [[package]]
 name = "bpy"
-version = "4.2.0"
+version = "5.0.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "cython" },
@@ -93,10 +93,10 @@ dependencies = [
     { name = "zstandard" },
 ]
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/ea/5a/d085d433ad26687d7ba5be235c57679780a3b41316cd7ece1ee65694ebad/bpy-4.2.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:e6e8857c9f483d42f5388642601080ad3e7488970cbc9e59efeedf4a8c26c90b", size = 207901162, upload-time = "2024-07-25T09:03:05.781Z" },
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