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5.0 (#63)

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* 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refactor: Clean up AGENTS.md and remove outdated test files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
This commit is contained in:
Nan
2026-07-09 00:50:34 +08:00
committed by GitHub
parent e9ea4c5248
commit 1ced263441
6 changed files with 92 additions and 100 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
pyproject.toml
View File

@@ -1,6 +1,6 @@
[project]
name = "bioxelnodes"
version = "2.0.1"
version = "2.0.2"
description = ""
authors = [{ name = "MaNan", email = "icrdr2010@outlook.com" }]
requires-python = ">=3.11.0,<3.12.dev0"

22
src/bioxelnodes/__init__.py
View File

@@ -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

2
src/bioxelnodes/blender_manifest.toml
View File

@@ -1,7 +1,7 @@
schema_version = "1.0.0"
id = "bioxelnodes"
version = "2.0.1"
version = "2.0.2"
name = "Bioxel Nodes"
tagline = "For scientific volumetric data visualization in Blender"
maintainer = "Nan <icrdr2010@outlook.com>"

96
src/bioxelnodes/operators/io.py
View File

@@ -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 background Blender..."},
)
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",
"--python",
str(worker_path),
"--",
"--addons",
addon_name,
"--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
self.has_error = None
self.meta = None
self.label_count = 0
self.dtype = None
progress_update(context, 0.0, "Collecting Meta Data...")
start_worker_process(
self,
"read_meta",
{
"filepath": self.filepath,
"series_id": self.series_id,
},
def progress_callback(factor, text):
progress_update(context, factor, text)
try:
series_id = self.series_id if self.series_id != "empty" else ""
data, meta = parse_volumetric_data(
data_file=self.filepath,
series_id=series_id,
progress_callback=progress_callback,
)
except Exception as e:
raise e
self._timer = context.window_manager.event_timer_add(
time_step=0.1, window=context.window
)
bpy.types.STATUSBAR_HT_header.append(progress_bar)
context.window_manager.modal_handler_add(self)
return {"RUNNING_MODAL"}
def modal(self, context, event):
if event.type == "ESC":
cancel_worker_process(self, context)
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()
self.meta = meta
self.label_count = int(np.max(data))
self.dtype = data.dtype
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}")

42
src/bioxelnodes/operators/io_worker.py
View File

@@ -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():
config_path = Path(sys.argv[-1])
def main(args):
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(),
},
)
if __name__ == "__main__":
main()
return 0

28
uv.lock generated
View File

@@ -25,7 +25,7 @@ wheels = [
[[package]]
name = "bioxelnodes"
version = "2.0.0"
version = "2.0.2"
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" },
]
@@ -949,23 +949,23 @@ wheels = [
[[package]]
name = "scipy"
version = "1.17.1"
version = "1.16.3"
source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "numpy" },
]
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